New User Special Price Expires in

Let's log you in.

Sign in with Facebook


Don't have a StudySoup account? Create one here!


Create a StudySoup account

Be part of our community, it's free to join!

Sign up with Facebook


Create your account
By creating an account you agree to StudySoup's terms and conditions and privacy policy

Already have a StudySoup account? Login here

Semester Notes

by: Alyssa Rieger

Semester Notes 01:119:115

Alyssa Rieger
GPA 3.0
General Biology
Dr. D'Arville

Almost Ready


These notes were just uploaded, and will be ready to view shortly.

Purchase these notes here, or revisit this page.

Either way, we'll remind you when they're ready :)

Preview These Notes for FREE

Get a free preview of these Notes, just enter your email below.

Unlock Preview
Unlock Preview

Preview these materials now for free

Why put in your email? Get access to more of this material and other relevant free materials for your school

View Preview

About this Document

General Biology
Dr. D'Arville
75 ?




Popular in General Biology

Popular in Biology

This 109 page Bundle was uploaded by Alyssa Rieger on Tuesday February 17, 2015. The Bundle belongs to 01:119:115 at Rutgers University taught by Dr. D'Arville in Fall. Since its upload, it has received 227 views. For similar materials see General Biology in Biology at Rutgers University.

Similar to 01:119:115 at Rutgers


Reviews for Semester Notes


Report this Material


What is Karma?


Karma is the currency of StudySoup.

You can buy or earn more Karma at anytime and redeem it for class notes, study guides, flashcards, and more!

Date Created: 02/17/15
LECTURE TWO NOTES 0 Concept 21 The emergent properties of a compound 0 O 0 Metal sodium combines with the poisonous gas chlorine forming the edible compound sodium chloride Most of the body mass is made up of oxygen carbon hydrogen and nitrogen 963 Emergence H02 water hydrogen peroxide C H O sugars and fats H and N ammonia amine group as in amino acids Sugar and amine gucosamine insect skeleton NO NO biproduct in combustion and important cell signaling molecule vasodilator Concept 22 An elements properties depend on the structure of the atoms 0 O OO Atom smallest unit of matter that still has properties of an element Composed of Protons positive Electrons negative Neutrons neutral Neutrons and protons for the atomic nucleus Daltons measure neutron mass and proton mass Atomic mass and atomic number Atomic number number of protons in the nucleus Mass number number of protons and neutrons in the nucleus Atomic mass atoms total mass approximated by the mass number aka the atomic weight Elements and lsotopes lsotope an element that has the same number of protons and electrons but differs in it s neutron content 0 All isotopes have the same characteristics the same atomic number but different atomic masses Radioactive isotopes Decay by emitting alpha beta and gamma particles 0 Used in the medical eld 0 Alpha particles radium uranium decay to radon effects stop at skin level unless penetration lung cancer 0 Beta particles radioactive iodide emits beta particlescan t pass through skin treatment for thyroid cancer The chemical behavior of an atom is determined by the distribution of electrons in the atoms electron shell 0 Concept 23 Covalent Bonding 0 Number of electrons required to complete an atom s valence shell generally determines how many covalent bonds 0 Nonpolar covalent bonds electrons are shared equally atoms have the same electronegativity symmetrical 0 Polar covalent an atom is bonded to a more electronegative atom so the electrons aren t shared equally asymmetrical 0 Weak chemical bonds Most of the strong bonds are covalent but weak ionic hydrogen and Van Der Waals are also important Reinforce shapes of large molecules and help molecule adhere to each other lonic Bonding Attraction of oppositely charged atoms or ions Cation positive ion 0 Anion negative ion Hydrogen Bonding Made between the partial positive charge of hydrogen of water and the partial negative charge on the N in ammonia 0 Weak individually strong together Van Der Waals Weak but collectively strong Caused by attraction between electronrich regions of one molecule and the electron poor regions of another molecule Intermolecular forces that cause molecules to cohere to liquid and solid states of matter 0 Gecko sticking to the wall 0 Saturated fat is solid at room temperature 0 Molecular shape and function Shape is dictated by the bonds Biological molecules recognize and interact with each other with a speci ty based on molecular shape Similar shapes can have similar biological effects different endorphins can bind to similar receptors 0 Concept 24 Chemical Reactions Make and Break Chemical Bonds 0 Chemical reactions making and breaking chemical bonds Reactants starting molecules Products ending molecules All chemical reactions are reversible 0 Chemical equilibrium reached when the forward and reverse reactions are equal 0 Photosynthesis sun powers the carbon dioxide and water to change to glucose and oxygen Sugar is converted to other food molecules Oxygen is a biproduct 6C026H20 l C6H1206602 Concept 3132 Emergent Properties of water contribute to Earth s suitability as a support for life 1 Hydrogen Bonding a Transpiration evaporation cohesion adhesion surface tension b Hydrogen bonding enables cohesion that pulls water up against gravity l produces surface tension column of water hard to break c Surface tension allows resistance 2 Ability to moderate temperature a High speci c heat i Minimize large temperature uctuations on land and in water b High heat of vaporization i Water molecules resist evaporation hold heat longer harder to break the hydrogen bonds c Evaporative cooling i Gaseous molecules released reduces heat of surface sweating is a cooling process 3 Versatility as a solvent a Due to polarity water can act as the universal solvent and help dissolve and dissociate most compounds i Salts dissolve in water dissociating and forming a hydration shell 4 Three phases of water a Water vapor greenhouse gas that traps energy radiated from the planet l keeps it warm b Pure water essential to life as a solvent 0 c Ice forms at 0 C forms crystal lattices when it begins to freeze oats in water less dense LECTURE THREE Chapter 4 and 5 Organic compounds l carbon is covalently bonded to one another Concept 42 Hydrocarbon l carbon and hydrogennonpolar 0 When a carbon atom bonds to 4 other atoms l tetrahedral 0 Two carbons joined by a double bond all atoms in the same plane Methane CH2 Ethane C2H2 Ethene C2H4 ane l saturated ene l unsaturated Carbon sketches vary in 4 ways Length branchedunbranched double bonds arranged in rings 0 Pharmacological importance of enantiomers lbuprofen l painin ammation 0 Effective enantiomer sibuprofen inactive enantiomer ribuprofen Albuterol l asthma 0 Effective enantiomer ralbuterol inactive enantiomer salbuterol Concept 43 A few chemical groups are key to the functioning of molecules 0 Properties depend on the carbon skeleton and the molecular characteristics 0 Most important chemical groups Functional groups the components of organic molecules that are most commonly involved in chemical reactions 0 Number and arrangement of functional groups give each molecule it s unique properties Hydroxyl Group OH Alcohols Polar because of electrons spending more time near the electronegative oxygen atom Form hydrogen bonds with water molecules helping dissolve organic compounds such as sugars Carbonyl Ketones carbonyl group is within a carbon skeleton acetone OOOOOO Aldehydes carbonyl group is at the end of the carbon skeleton propanol Isomer molecules with the same molecular formula but different chemical structures Ketone and aldehyde are also found in sugars l give ketoses and aldoses Carboxyl Carboxylic acids aka organic acids Acts as an acid can donate an H ion because the covalent bond between oxygen and hydrogen is so polar 0 Found in cells in the ionized form with a charge of 1 and called a carboxylate ion Acetic acid and vinegar Amino o Amines Acts as a base can pick up an H ion from the surrounding solution water in living functions 0 Found in cells in the ionized form with a charge of 1 Sulfhydryl Thiois 0 Two sulfyhydryl groups can react forming a covalent bond 0 The quotcrosslinking helps stabilize structure 0 Cysteine groups in hair maintains the curliness or straightness l disulphide bonds curly hair Phosphates ATP Importance of energy for cellular processes 0 Adenosine Triphosphate primary energy transferring process in the cell 0 Consists of an organic molecule called adenosine attached to a string of three phosphate groups 0 Concept 51 Polymers and Macromolecules 0 Polymers Long chains of monomers Linked through condensation reactions Water molecule lost 0 Macromolecules Carbohydrates proteins and nucleic acid Large polymers Emergent properties not found in individual building blocks Broken down by hydrolysis reactions Water is consumed Concept 52 Carbohydrates o 1 C 2 H 1 O l ratio that exists naturally in ring form 0 Aldehyde sugar carbonyl group at the end of the C skeleton Glyceraldehyde o Ketone sugar carbonyl group within the C skeleton Dihydroxyacetone o Disaccharides Condensation dehydration two monosaccharides joined by glycosidic linkage for disaccharide enzymatically lose water Hydrolysis disaccharide is broken down enzymatically to produce two monomers require water 0 Polysaccharides Repeating units of simple sugars monomers Long chains or branched Storage polysaccharides Starch a14 glucose in plant amylopasts 0 Storage in plant roots Glycogen a14 glucose in animals more soluble than starch 0 Storage molecule in liver and muscle Cellulose B14 glucose in plant cells 0 Added to ber in foods since can t be metabolized o Cows use microbes to help metabolize cellulose to glucose 0 Modi ed and complex CHO Carbohydrate with amino group Nacetyl glucosamine Tough because of hydrogen bonding Eg insect exoskeleton Carbohydrates with protein units Glycoproteins eg cellular receptors extracellular glycocalyx Carbohydrates with lipids Glycolipids makers for cell surface recognition 0 Eg red blood cell antigens ABO Concept 53 Lipids are a broad group o Lipids a broad group of naturally occurring molecules Fats waxes steroids fatsoluble vitamins such as A D E and K phospholipids carotenoids Not considered polymers Main biological functions energy storage signaling molecules structural components of cell membranes 0 Fats a triacylglycerol Condensation reaction FA is added to glycerol at each hydroxyl group one molecule of water released Saturated fats maximum number of hydrogen atoms 0 Solid at room temperature 0 Van der Waals forces limit free motion Unsaturated fats one or more adjacent pairs of double bonds Chains are bent or kinked oleic acid linoleic acid 0 Liquid at room temperature 0 Fewer Van der Waals forces allow free motion 0 Hydrogenation makes them solid 0 Certain unsaturated fatty acids are not synthesized in the body 0 These must be supplied in the diet 0 Essential fatty acids omega3 fatty acids required for normal growth and protection against cardiovascular disease Trans Fatty Acids Partial hydrogenation H atoms on the same side of the double bonds become rearranged preventing bending Product is more solid at room temperature 0 Greater association with cardiovascular risk 0 Cell membrane phospholipid ln water hydrophilic heads interact with water hydrophobic tails form internal bilayer Amphipathic molecule exible and selfsealing o Steroids Carbon atoms arranged in 4 rings 3 contain 6 C s 4th contains 5 C s Cholesterol bile salts lipid hormones Hydrophobic small enough to diffuse across plasma membrane except cholesterol Hormones regulate l sodium in kidney reproduction stress response Concept 54 Proteins include a diverse group 0 Enzymatic Proteins selective acceleration of chemical reactions Digestive enzymes catalyze the hydrolysis of bonds in food molecules 0 Defensive Proteins protections against diseases Antibodies inactivate and help ght virus and bacteria 0 Storage Proteins storage of amino acids Casein the protein of milk is the major source of amino acids for baby mammals Plants have storage proteins in their seeds Ovalbumin is the protein of egg white used as an amino acid source for the developing embryo 0 Transport Proteins transport of substances Hemoglobin the ironcontaining protein of vertebrate blood transports oxygen from the lungs to other parts of the body Other proteins transport molecules across cell membranes 0 Hormonal Proteins coordination of an organisms activities lnsulin a hormone secreted by the pancreas causes other tissues to take up glucose thus regulating blood sugar concentration 0 Receptor Proteins response of cell to chemical stimuli Receptors built into the membrane of a nerve cell detect signaling molecules released by other nerve cells 0 Contractile and Motor Proteins movement Motor proteins are responsible for the undulations of cilia and agella Actin and myosin proteins are responsible for the contraction of muscles 0 Structural Proteins support Keratin is the protein of hair horns feathers and other skin appendages Insects and spiders use silk bers to make their cocoons and webs respectively Collagen and elastin proteins provide a brous framework in animal connective tissue 0 Figure 516 l 20 amino acids polar nonpolar electrically charged 0 Polypeptide backbone developed by condensation of amino acids via covalent bonds 0 Functional protein has one or more polypeptide bonds precisely twisted into a unique shape 0 Sequence of amino acids determines the 3D structure 0 Figure 520 Protein Structures Hbond every 4th CO NH grouping Primary structure Secondary structure l helixpleated sheet Tertiary structure l determined by interactions between R groups rather than backbone constituents Have hydrophobic interactions Van der Waals forces ionic bonds Quaternary structure l two or more polypeptide chains form one macromolecule Collagen is a brous protein with 3 polypeptides like a rope coiled Hemoglobin is a globular protein consisting of four polypeptides 0 Two alpha two beta 0 Figure 519 I biological activity genetic determinants Sicklecell hemoglobin exposed hydrophobic region Molecules crystallize into a ber capacity to carry oxygen is reduced 0 Resistance to malaria Carry valise and not glucose 0 Figure 521 Protein folding facilitated by molecular chaperones Misfolded proteins destroyed in proteasome high delity even small alteration sent to proteasome eg Cystic Fibrosis The chaperonin tells if the protein needs to be re folded if it is structurally not correct LECTURE ONE NOTES Bio is the study of life scienti cally o How does a cell develop into an organism o How does the human mind work 0 How do living things interact in communities CONCEPT 11 0 Theme 1 the study of life can be divided into different levels of organization biosphere ecosystems communities populations organisms etc Emergent Properties result from the arrangement and interaction of parts in a system functioning bike Reductionism reduction of complex systems to simpler components that are easier to study study of molecular structure Systems Biology constructs models for the dynamic behavior of whole biological systems and asks o How does a speci c drug affect the rest of the body 0 How does increasing C02 affect the biosphere o Fundamentally everything is made up of the same things 0 Theme 2 organisms interact with other organisms and the physical environment changes in the physical environment No organism lives in complete isolation 0 Theme 3 life requires energy transfer and transformation Energy ows through the ecosystem light l heat 0 Theme 4 form and function are directly correlated Leaf is thin and at l maximum capture of light Bird wings are adapted to ight Humming birds wings rotate in all directions l hover 0 Theme 5 cell is lowest level of organization Eukaryotic cell has membraneenclosed organelles and a nucleus usually the largest Prokaryotic cell usually simpler and smaller no nucleus or other membraneenclosed organelles 0 Theme 6 continuity of life is based on heritable information DNA Deoxyribonucleic acid l the substance of genes Chromosomes contain DNA Inherited by parents 0 Controls development and maintenance of organisms Cell division is basis of all reproduction growth and repair Genes transmit information from parents to offspring and encode into it for building proteins CONCEPT 13 Scienti c Method Uses both inductive and deductive reasoning Identify a problem and pose a question Collect background info Induce tentative info hypothesis Deducepredict outcome if hypothesis is true Test accuracy of predictions Draw conclusions 0 Deductive reasoning can t argue logical Take known facts and nd speci c relationships Arrive at a conclusion based on true facts 0 Inductive reasoning can be argued facts must be tested Takes speci c pieces of information and produces a generalized statement Must be tested l to test draw up a hypothesis 0 Hypothesis proposed explanation for an observation that can t be completely proved 0 Theory a hypothesis that has received a substantial amount of evidence accepted by the scienti c world 0 To prove a hypothesis use reliable and factual tests 0 Homer Simpson example SCIENTIFIC METHOD make observations ask a question form hypothesis prediction based on hypothesis test prediction use statistics to evaluate signi cance results support hypothesis results not supporting FP P FP NI V V repeat experiment to verify reexamine experiment and revise hypothesis LECTURE FOUR NOTES 0 Overview 0 Past organisms were very different from what they are now 0 Fossil record shows macroevolutionary changes over large time scales Emergence of terrestrial vertebrates through speciation events Impact of mass extinctions on biodiversity Origins of key adaptations such as ight in birds 0 Concept 251 Conditions on early Earth made the origin of life possible 0 0 Chemical and physical process on early Earth may have produced very simple cells through a sequence of 4 stages Abiotic synthesis of small organic molecules eg amino acids Joining of these small molecules into macromolecules eg proteins and nucleic acids Packaging of molecules into protocells Origin of selfreplicating molecules made inheritance possible Synthesis of organic compounds on early Earth Earth and solar system formed about 46 billion years ago Bombardment by rocks and ice 0 Atmosphere likely contained water vapor and chemicals released by volcanic eruptions In the 1920 s Oparin and Haldane hypothesized that the early atmosphere was a reducing environment Figure 252 Amino acid synthesis in a simulated volcanic eruption 1953 Stanley Miller and Harold Urey found abiotic synthesis of small organic molecules in a reducing atmosphere to be possible 0 First synthesized by volcanoes or deep sea vents RNA molecules spontaneously formed from simple molecules 0 Small organic molecules could polymerize when concentrated on hot sand clay or rock Figure 254 features of abiotically produced vesicles In water lipids and other organic molecules can spontaneously form vesicles with a lipid bilayer Protocells may have been uid billed vesicles with a membranelike structure able to absorb RNA and selfreplicating o Selfreplicating RNA and the dawn of natural selection First genetic material was probably RNA not DNA 0 Ribozymes catalyze many different reactions Ribozymes function within the ribosome as part of the large subunit ribosomes RNA to link amino acids during protein synthesis 0 Also present during RNA splicing and transfer 0 Natural selection would have acted to produce the most successful cells Early genetic material might have formed an RNA world Abiotic synthesis of small organic molecules 0 Formation of macromolecules Formation of metabolically active protocells with sequestered internal environment 0 Formation of selfreplicating molecules with enzymatic abilities 0 First unicellular organisms Concept 253 Key events in life s history include the origins of singlecelled and multicellular organisms and the colonization of land 0 Geological record divided into the Archean the Proterozoic and the Phanerozoic era Archean and Proterozoic era led up to colonization of land and the beginning of the Phanerozoic era Eon extremely long and unde ned period of time Phanerozoic l multicellular eukaryotic life forms 0 The Paleozoic The Mesozoic The Cenozoic 0 Figure 258 Geological clock Major boundaries between geological divisions o The rst singlecelled organisms Stromatolites oldest known fossils sedimentary materials built up on bacterial mats Photosynthesizing prokaryotes are sole inhabitants 3521 billion years ago 0 Most atmospheric oxygen was of biological origin Produced by oxygenic photosynthesis 27 billion years ago oxygen started accumulating rusting ironrich terrestrial rocks quotoxygen revolutionquot Some prokaryotic groups survived l capable of cellular respiration to harvest energy 0 Figure 259 Early rise in oxygen l produced by cyanobacteria Followed by an increase in oxygen from evolution of eukaryotic cells containing chloroplasts o The First Eukaryotes Oldest eukaryotic cell fossils date back 21 billion years First cells had a nuclear envelope mitochondria endoplasmic reticulum and a cytoskeleton 0 Evolution of the rst Eukaryotes Endosymbiont Theory proposes that mitochondria and plastids chloroplasts and related organelles were formerly small prokaryotes living within larger host cells endosymbionts The prokaryotic ancestors of mitochondria and plastids probably gained entrance into the host cell as a parasite or undigested prey Figure 2510 a hypothesis for the origin of eukaryotes through serial endosymbiosis Serial endosymbiosis suppose that mitochondria evolved before plastids chloroplasts through a sequence of endosymbiotic events 0 Key evidence supports and endosymbiotic origin from mitochondria and plastids Double membrane organelles with inner membranes similar to plasma membranes of prokaryotes enzymes and transport mechanisms Organelles divide split transcribe and translate their own circular DNA structurally similar to prokaryotes Their ribosomes are closer to prokaryotic than eukaryotic in characteristics 0 Including sensitivity to antibiotics like streptomycin o The earliest multicellular eukaryotes evolved Comparisons of DNA sequences date the common ancestor or multicellular eukaryotes to 18 billion years ago The Ediacaren organisms followed were larger more diverse and included softbodied animals living from 575535 million years ago 0 The Cambrian Explosion follows Fossils resembling animal phyla arose in the Cambrian period 535525 million years ago Provided the rst evidence of a predatorprey interaction 0 The Chinese fossils suggest that the Cambrian Explosion had a quotvery long fusequot DNA analysis suggest that many animal phyla diverged before the Cambrian explosion Fossils in China prove evidence 0 The Colonization of Land Fungi plants and animals began to colonize about 500 million years ago Vascular tissue in plants transports materials internally and appeared about 420 million years ago Plants and fungi today form mutually beneficial associations and likely colonized land together Arthropods and tetrapods were the most wide spread and diverse land animals Tetrapods evolved from a finned water organism around 665 million years ago 0 Evolution of Fish Diagram in book LECTU RE FIVE NOTES 0 Cellular Homeostasis o Homeostasis maintaining appropriate internal environment Plasma membrane separates and maintains internal conditions Allows exchange materials with outer environment Fundamental units of life 0 All organisms are made of cells 0 A cell is the simplest collection of matter that can be alive 0 The structure is correlated with the function 0 All cells are related by their descent from earlier cells 0 Concept 61 Tools in biochemistry can be used to study cells 0 Microscopy Visualize cells too small to see with the naked eye Light microscope passes through a specimen and through lenses Lenses bend the light image becomes magni ed 3 important parameters 0 Figure 63 Light Microscopy Magni cation ratio of image size to actual size Resolution measure of the clarity of the image or the minimum distance between two points Size and shape EM has a higher resolution than LM because electron beams have shorter wavelengths than visible light Bright eld unstained specimen light passes directly through the specimen image has little contrast Bright eld stained specimen stained with various dyes enhances contrast killing cells to dye Phasecontrast variations in density within the specimen are ampli ed to enhance contrast in unstained cells Di erentialinterferencecontrast image appears almost 3D Fluorescence the locations of speci c molecules in the cell can be revealed by labeling the molecules with uorescent dyes or antibodies about uv rays and emit light Superresolution light up individual uorescent molecules and record their position Deconvolution digitally removes out of focus light and reassigns it to it s source Confocal using a laser it eliminates out of focus light from a thick sample Electron Microscopy Scanning electron microscopy micrographs taken with a scanning electron microscope show a 3D image of the surface of the specimen 0 Transmission electron microscopy pro les a thin section of a specimen Figure 65 Cell Fractionation Sucrose density gradient ultracentrifugation membranes and organelles separate as bands in gradient above organelle density 0 Ultracentrifuge spins are 500000g to separate out cell fractions according to size Concept 62 Prokaryotic and Eukaryotic cells have different compartmentalization o Prokaryotic cells lack internal membrane organization Cell wall surrounds plasma membrane 0 Eukaryotic cells divide into compartments by internal membranes Provide separate small areas for special activities 0 Figure 65 Prokaryotic Cell Lacking a true nucleus and the other membrane enclosed organelles of the eukaryotic cell the prokaryotic cell is far simpler Includes bacteria and archea Proteins that are secreted are synthesized on ribosomes bound to cytoplasmic surface of the plasma membrane 0 Eukaryotic Cells DNA in the nucleus that is bounded by a membranous nuclear envelope Membrane bound organelles Cytoplasm in the region between the plasma membrane and nucleus Generally bigger than prokaryotic 0 General structure of a biological membrane is a double layer of phospholipids 0 Concept 63 Eukaryotic cell s nucleus 0 0 Cells genetic instructions are housed in the nucleus and carried out by ribosomes Nuclear envelope double membrane and pores lines with supporting nuclear lamina Mutations premature aging disease DNA and protein chromatin l long thin ber condensed as chromosomes in dividing cells 46 in humans mRNA produced from DNA and exported through pores to cytoplasm for protein synthesis Nucleolus no membrane produces rRNA combines with protein to produce ribosomes exported through pores to ER nuclear membranes or cytosol Concept 64 Endomembrane System 0 O quotA series of closed membranes wit eukaryotic cells that are either continuous or communicate with each other via vesicles which are formed at one surface and move to a second where they are incorporated Members of the system Endoplasmic Reticulum Golgi Apparatus Various vesicles Lysosomes and peroxisomes Plasma membrane Nuclear envelope Regulates protein traf c and performs metabolic functions in the cell 0 The cytoplasm Endoplasmic Reticulum Figure 611 O Smooth endoplasmic reticulum Calcium storage 0 Lipid biosynthesis including phospholipid for membrane synthesis Steroid metabolism increased in reproductive cells 0 ln liver increased for enzymatic breakdown of carcinogens toxins alcohol drugs Rough endoplasmic reticulum Membrane houses ribosomes for glycoprotein synthesis transported to Golgi Apparatus for modi cation and secretion Figure 612 The Golgi Apparatus shipping and receiving center Consists of attening membranous sacs called cisternae Functions modi es products of the ER manufactures and secretes glycolipid plantsmanufactures polysaccharides sorts and packages materials into transport vesicles 0 Other organelles Peroxisome Important during breakdown of long chains of fatty acids Proli c in WBC when it kills bacteria Zellweger syndrome autosomal recessive no functional peroxisomes o Accumulation of fatty acids and neuronal impairment decreased CNS myelin Vacuole In animal cells some protists rare in plants 0 Phagocytose contain enzymes pH 5 for wastedegradative processes Lack of enzymes eg Tay Sachs lipid accumulation neurodegenerative to brain 0 Endomembrane System does not include Mitochondria and Chloroplasts Mitochondria Proli c in highly active cells liver Lite of aerobic respiration production of ATP Produce proteins for apoptosis Mutation in mitochondrial DNA l somatic not inher ed o Damage to membranes l leak three radicals and mutations adult blindness Plastids Chromoplasts pigment synthesis storage Leukoplasts eg amyloplasts store starch Chloroplasts carry out photosynthesis 0 Figure 631 Emergence of Cellular Functions Eg phagocytosis macrophage recognizes and destroys bacteria because of emergent properties that result from coordinated activity of the different components in the whole cell LECTURE SIX NOTES 0 Concept 71 Fluid Mosaic Model Fig 7235 O 0 Figure 73 uid mosaic model suggests that the plasma membrane is a mosaic of protein molecules bobbing in a semi uid layer of phospholipids allowing lateral movement Phospholipid molecules arranged with cholesterol for optimum uidity interspersed by integral and peripheral proteins Cholesterol enables the plasma membrane in animals to stay more uid when cell temperatures drop prevents fracture of the bilayer Peripheral proteins bound to the surface of the membrane Integral proteins penetrate the hydrophobic core Proteins that span membrane l transmembrane proteins Hydrophobic regions of an integral protein one or more stretches of nonpolar amino acids often coiled into alpha helices 6 major functions of membrane proteins transport enzymatic activity signal transduction cellcell recognition intercellularjoining attachment to the cytoskeleton and extracellular matrix ECM Role of membrane carbs in cellcell recognition Recognize each other by binding to surface molecule often with carbs or the extracellular surface of the plasma membrane 0 Includes glycolipids and more commonly glycoproteins Carbs placed on the external side of the plasma membrane ECM vary between species and individuals 0 Natural killerT cells have Tcells receptors that put glycolipids on certain cells and aid in natural destruction Figure 78 glycoproteins on cell surfaces are important in cellcell recognition Figure 79 Synthesis of glycoproteins and glycolipids and orientation in the membrane cytoplasmic face differs from the extracellular face arising from the inside of the vesicle etc 0 Concept 72 Membrane structure results in selective permeability o A cell must exchange materials with it s surroundings 0 Plasma membranes selectively permeable Hydrophobic non polar l diffuse through lipid bHayer Large non polar and polar cannot cross easily 0 Transport proteins needed to facilitate 0 Concept 73 The diffusion of solutes across a synthetic membrane 0 Passive down the concentration gradient Figure 710 o Osmosis the passive diffusion of water across a selectively permeable membrane Water diffuses from high concentration to low concentration dilution making the concentrations equal 0 Figure 712 Tonicity is the ability of a surrounding solution to cause a cell to gain or lose water Hypotonic low concentration to high concentration Hypertonic high concentration to low concentration Depends on the concentration of the cell and surrounding solutions Adaptations made 0 Plant cell wall and contractile vacuole Animal cell and aquaporins 0 Large uncharged polar molecule and ions require membrane transport problems 0 Dissolving through easiest l hardest small hydrophobic molecules small uncharged polar molecules larger uncharged polar molecules ions 0 Facilitated Diffusion movement with concentration gradients provides intrinsic energy needed 0 Concept 74 0 Active Transport involve only carrier proteins and need potential andor metabolic energy 0 Figure 716 cotransport coupled transport by a membrane protein going against the gradient 0 Larger molecules cross the plasma membrane by endocytosis and exocytosis Exocytosis cell secretes molecules via transport vesicles budded from the Golgi Moved via microtubules to plasma membrane fusion allows secretion of contents Endocytosis cell takes in larger macromolecules by forming vesicles from the plasma membrane Endocytosis is a reversal of Exocytosis Three types of Endycytosis o Phagocytosis quotcellular eatingquot 0 Pinocytosis quotcellular drinkingquot 0 Receptor mediated endocytosis LECTURE SEVEN NOTES 0 Concept 81 An organism s metabolism transforms matter and energy 0 Metabolic pathway begins with a starting molecule and ends with a nal product Each step is catalyzed by a speci c enzyme Metabolism totality of an organism s chemical reaction arises from interactions between molecules within the cells Bioenergetics how organisms manage their energy sources Catabolic pathways releases energy by breaking down complex molecules into simple compounds Anabolic pathways consume energy to build complex molecules from simpler ones Energy capacity to cause change and can be converted from one form to another Kinetic Energy energy associated with motion 0 Heat Thermal l associated with random movement of atoms and molecules Potential Energy energy that matter possesses because of the construction of the molecule 0 Chemical energy Laws of Thermodynamics First Law of Thermodynamics Energy of the universe is constant and energy can be transferred and transformed but not created or destroyed 0 Chemical reactions in the brown bear will convert the potential energy in the sh into kinetic energy for running Second Law of Thermodynamics 0 During every energy transfer or transformation some energy is unusable ad is often lost as heat 0 Disorder develops around the bear as it runs due to the release of heat 0 Concept 82 The free energy change of a reaction tes whether the reaction occurs spontaneously O Spontaneous processes give off energy they can happen quickly or slowly and will increase the entropy disorder of the universe Always some energy in a system free energy is called G Change in free energy is AG Spontaneous processes represent a negative charge in free energy AG as energy is released 0 Figure 85 the relationship of free energy to stability work capacity and spontaneous change Bonds are broken releasing party 0 Exergonic and Endergonic Reactions in Metabolism Exergonic proceeds with a net release of free energy and it is spontaneous eg ATP hydrolysis Represents a AG Endergonic absorbs free energy from its surroundings and it is nonspontaneous Represents a AG Concept 83 ATP powers cellular work by coupling endergonic reactions to exergonic reactions 0 Bonds between phosphate groups of ATP s tail l hydrolysis 0 Energy released by ATP when terminal phosphate bond broken 0 Comes from the chemical change lower free energy 0 In the cell energy from the exergonic reaction of ATP hydrolysis can be used to drive and endergonic reaction via intermediate Concept 84 Enzymes speed up metabolic reactions by lowering energy barriers without affecting the free energy change AG for that reactions 0 Figure 814 Activation energy the initial energy needed to start a chemical reaction In the graph free energy is the same 0 Catalysis in the Enzyme s Active Site The substrate binds to the active site of the enzyme which then lowers the activation energy barrier and speeds up the reaction by Bonding to the substrate weakly Helping to orientate substrates correctly for reaction thus lowering activation energy Induced fir of a substrate causes change of shape of enzyme catalyzing the reaction Effects of Temperature and pH 0 Optimal conditions favor the most active shape for the enzyme molecule 0 Each enzyme has optimal temperature in which it can function 0 Each enzyme has an optimal pH in which it can function Cofactors non protein enzyme helpers that may be inorganic such as a metal in ionic form or organic o Coenzyme an organic cofactor o Niacin B Vitamin helps to make nicotinamide adenine dinucleotide NAD One of the coenzymes that carries electrons from Krebs cycle through electron transport Figure 818 Enzyme Inhibitors Competitive inhibitors bind to the active site of an enzyme competing with substrate Noncompetitive inhibitors bind to another part of an enzyme alloristic site causing the enzyme to change shape making the active site less available toxins and poisons 0 Evolution of Enzymes Enzymes are proteins encoded by genes Changes mutations in genes lead to changes in amino acid composition of an enzyme Altered amino acids in enzymes may alter their substrate speci city Alteration in optimal temperatures of pH Catalase gene mutations l diabetes meitus hype engon LECTURE EIGHT NOTES Overview 0 Life is work living cells require energy from outside sources 0 Carnivores vs herbivores Energy ows into an ecosystem as sunlight and leaves as heat Photosynthesis generates oxygen and organic molecules which are used in cellular respiration Cells use chemical energy stored in organic molecules Concept 91 Catabolic pathways yield energy by oxidizing organic fuels 0 Several processes are central to cellular respiration and related pathways Fermentation partial degradation of sugars Aerobic respiration release of energy with the presence of oxygen Anaerobic respiration release of energy without the presence of oxygen 0 Chemical reactions called redox oxidation reduction reactions lnvolve an electron transfer Some change the electron sharing in a chemical bond Reducing agent becomes oxidized Oxidizing agent becomes reduced 0 During cellular respiration the fuel is oxidized and the oxygenisreduced Stepwise energy harvest occurs via NAD and the Electron Transport Chain Electrons form organic compounds are transferred to NAD NAD l electron acceptor and oxidizing agent reduced 0 Synthesize ATP during electron transfer 0 Pair of H atoms removed from glucose oxidized dehydrogenase then delivers 2 electrons and one protein to coenzyme NAD forming NADH NAD acts as an electron shuttle 0 An overview of cellular respiration The process that generates most of the ATP is called oxidative phosphorylation because it is powered by redox reactions Oxidative phosphorylation accounts for about 90 of the ATP generated by cellular respiration o A smaller amount of ATP is formed in glycolysis and the citric acid cycle by substratelevel phosphorylation For each molecule of glucose degraded up to 32 molecules of ATP are formed Concept 92 Glycolysis harvest chemical energy by oxidizing glucose to pyruvate o Glycolysis quotsplitting of sugarquot breaks down glucose into two molecule of pyruvate Energy investment phase Energy payoff phase Concept 93 After pyruvate is oxidized the citric acid cycle completes the energyyielding oxidation of organic molecules 0 Reaction 1 occurs in the mitochondria must occur before the citric acid cycle 0 Reaction 2 l citric acid cycle 7 steps decompose citrate back to oxaloacetate making the process a cycle Acetyl group CoA joins Concept 94 Reaction 3 during oxidative phosphorylation chemiosmosis electron transport to ATP synthesis 0 Electrons transferred from NADH to electron transport chain 0 Proteins pump hydrogen to the intermembrane space 0 ATP synthase hydrogen moves back across the membrane Uses exergonic ow to drive phosphorylation of ATP 0 Pathway of Electron Transport Carriers including cytochromes alternate between reduced and oxidized states as the accept and donate electrons o Electrons move down chain and are nally passed to oxygen 0 Protonmotive force hydrogen gradient l measures the capacity to do work Figure 916 about 34 of energy in glucose molecule is transferred to ATP during cellular respiration LECTURE NINE NOTES Overview 0 Photosynthesis process that converts solar energy into chemical energy 0 Photoautotrophs producers of the biosphere using sunlight to produce organic molecules from Carbon Dioxide and other inorganic molecules 0 Almost all heterotrophs depend on photoautotrophs fro food and oxygen Concept 101 in chloroplasts photosynthesis converts light energy to the chemical energy of food 0 Stomata microscopic pores where Carbon Dioxide enters and Oxygen exits o Chloroplasts contain chlorophyll in membranes of stacked thylakoids which captures light energy 0 Mesophyll cells contain chloroplasts in the interior of the leaf 0 Photosynthesis The Splitting of Water ln chloroplasts water is split incorporating the electrons of hydrogen into sugar molecules and releasing oxygen as a byproduct 6C02 12H20 Light Energy C6H1206 6H20 o Photosynthesis is a Redox Process Reverses the direction of electron ow compared to respiration Water is oxidized oxygen is reduced 0 Two Stages of Photosynthesis Light Reactions photo 0 Split water release oxygen reduce NADP to NADPH generate ATP from ADP photophosphorylation Calvin Cycle synthesis 0 In the stroma or the uid between grana Forms sugar from C02 using ATP and NADPH and carbon xation Concept 102 The light reactions convert solar energy to the chemical energy of ATP and NADPH o Chlorophyll a is the main photosynthetic pigment o Chlorophyll b is a ller to broaden the spectrum 0 Carotenoids accessory pigments that hold extra light that could damage chlorophyll o Excitation of Chlorophyll by Light When a pigment absorbs light it goes from a ground state to an excited state unstable When excited electrons fall back to ground state photons are given off uorescence o The Photosystem sits in the Thylakoid Membrane Consists of reactioncenter complex surrounded by lightharvesting complexes Lightharvesting complex pigment molecules bound to proteins transfer energy of photons to reaction center Excited e from special chlorophyll a are transferred to primary electron acceptor 0 Two types of photosystems in the thylakoid membrane Photosystem ll PS II functions rst and absorbs wavelength of 680 nm Photosystem l PS l functions second and absorbs wavelength of 700 nm Some have PS I and not PS II 0 During light reactions there are two possible routes for electron ow cyclical and linear Cyclic electron ow is thought to have evolved before linear electron ow Cyclic electron ow uses only PS and produces ATP not NADPH No oxygen released Generates more ATP l satis es demands of Calvin Cycle Linear Electron Flow primary pathway and involves both PS and PS ll producing ATP and NADPH using light energy 0 Photosystem ll P680 is a strong oxidizing agent 1 A photon of light hits a pigment molecule boosting e to a higher level a Photon energy passed among other pigment molecules until it excites the 2 electrons in 2 x P680 2 E are transferred from P680 which become P680 and an electron acceptor 3 Water is split by enzymes a Two electrons two hydrogen and an oxygen atom are released b 2 hydrogen ions are released in to the thylakoid space c Oxygen atom combines with oxygen atom 02 byproduct 4 The photoexcited electrons from PSll are transferred to an electron transport chain between PS and PSl a Energy released by fall of electrons provides energy to pump hydrogen into the thylakoid space b Contributes to a proton gradient that drives chemiosmosis 5 A photon of light hits a pigment molecule boosting electrons to a higher level a Photon energy passed among other pigment molecules until it excites 2 electrons in P700 6 Photoexcited electrons are passed from PSI electron acceptor down electron transport chain to protein ferredoxin Fd 7 Two electrons are transferred from Fd to NADP via a reduction producing NADPH a No proton gradient produced no chemiosmosis Figure 1018 the light reactions and chemiosmosis the organization of the thylakoid membrane 0 ATP and NADPH are produced on the side facing the stroma o In Summary light reactions generates ATP and increase the potential energy of electrons by moving them from water to NADPH Comparison of Chemiosmosis in Chloroplasts and Mitochondria O O O Chloroplasts and mitochondria generate ATP by chemiosmosis but use different sources of energy Spatial organization of chemiosmosis differs between chloroplasts and mitochondria but also shows similarities Mitochondria Electron transfer chain pumps hydrogen to inter membrane space Drives ATP synthesis as hydrogen diffuse back into mitochondrial matrix Chloroplasts Electron transfer chain pumps protons into the thylakoid space Drives ATP synthesis as hydrogen diffuse back into the stroma Concept 103 The Calvin Cycle uses the chemical energy of ATP and HADPH to reduce Carbon Dioxide to sugar 0 O O The Calvin cycle the citric acid cycle regenerates it s starting material after molecules enter and leave the cycle The cycle builds sugar from smaller molecules by using ATP and the reducing power of electrons carried by NADPH Calvin Cycle has three phases Carbon enters the cycle as carbon dioxide and leaves a glyceraldehyde 3phosphate For net synthesis of 1 G3P the cycle must take place three times xing three molecules of Carbon Dioxide The light reactions sustain the Calvin Cycle by regenerating ATP and NADPH LECTURE TEN NOTES 0 Cells need to divide and replicate to make an organism grow 0 All cells of a eukaryotic zygote divide by mitosis 0 Concept 121 The function of cell division 0 Figure 122 Reproduction amoeba l single celled eukaryote dividing into two cells binary ssion each new cell individual organism Growth and development sand dollar embryo shortly after fertilized egg divided forming two cells Tissue renewal two dividing bone cells will give rise to new blood cells 0 Figure 123 Eukaryotic Cells Cell approaches division l chromatin condenses Chromosomes visible Each human cell has 46 chromosomes 3 billion base pairs Gametes are haploids used in meiosis o Chromatin DNA and protein in chromatids highly condensed at division 0 Concept 122 somatic cells and Germine cells divide by mitosis gure 126 0 Through embryogenesis all cells divide by mitosis Terminally differentiated cells permanent Go 0 Eg mature muscle liver parenchyma Others remain as stem cells capable of division when needed 0 Blood skin germline etc Human cells have cycles between 8 hours and 12 hours 0 lnterphase 115 h o M phase 5h 0 Figure 125 chromosome duplication and distribution during cell division Chromosomes divide l sister chromatids produced 0 lnterphase 115h First Gap Phase 61 5h 0 Prepare for sphase Synthesizes enzymes etc for DNA replication Synthesis phase S 45h DNA duplicates l sister chromatids produced 0 Histone and cyclin synthesis Second Gap Phase 62 2h 0 RNA protein synthesis continues Centrosomes and centrioles replicate Interphase chromosomes duplicate during sphase gure 124 0 Each homologous chromosome becomes a pair of sister chromatids DNA and protein Held together by centromere region cohesions o Kinetochore multiprotein complex at centromere region to which spindle microtubules bind o MPhase 5h in a 12 hr cycle Mitosis 62 ends mitosis begins Produces 2 nuclei identical to parent Phases 0 Prophase prometaphase metaphase anaphase telephase PPMAT Cytokinesis Cytoplasm divided 0 Two daughter cells produced 0 Mitotic spindle chromosomes centrioles gure 128 Mitotic Spindle prophase each centrosome contains 2 centrioles embedded in gamma tubulin One end of a microtubule becomes stabilized in each centrosome Other end goes through dynamic instability to form mitotic spindle Aster microtubules Kinetochore microtubules stabilize spindle lnterpolar microtubules guide chromosomes 0 Microtubules Tubulin heterodimers alpha beta assemble in linear proto laments Proto laments assemble into microtubules Microtubules grow and shrink During growth heterodimers are added to end during shrinkage heterodimers come off as intact subunits I dynamic instability o Prophase gure 127b Chromosomes become visible 0 Long chromatin bers begin to condense as compact mitotic chromosomes condensin Nuclear envelope disappears MS begins to form 0 Prometaphase gure 127c Nuclear envelope continues to fragment Spindle microtubules seek out chromosomes 0 Capture sister chromatids Chromosomes moved towards cells midplane o Metaphase 127d Chromosomes aligned at the center of the cell three types of microtubules are now visible 0 Polar aster kinetochore o Anaphase 127e Sister chromatids pulled apart Cohesions destroyed by enzyme seprase Kinetochore microtubules shorten and depolarize Pull chromatids towards opposite poles Spindle elongates Polar microtubules slide past each other Decreases overlap l pulls pores apart 0 Figure 129 anaphase Chromosomes walked along microtubule as it is depolymerized o Telephase 122f Chromosomes at poles and uncoil Start to decondense l ionic shifts Condensation breaks down Nuclear envelope reforms around chromosomes at poles Spindle disappears Nucleoli reorganize Cytokinesis begins 0 Cytokinesis gure 1210 Animal cells l actomyasin contractile ring attaches to plasma membrane around midline Constriction provides two identical daughter cells Plant cells l golgi produces vesicles containing cell plate materials Vesicles collect inside cell and deposit cell plate cell wall o 2 daughter cells result each producing own plasma membrane with own cell wall No cytokinesis multinucleate o Prokaryotic Binary Fission Simpler than mitosis DNA in bacterium is 1000th that of a eukaryote 0 Ring of DNA many times larger than cell Prokaryotes produce genetically identical progeny via binary ssion asexual reproduction Single parent produces offspring with identical traits LECTURE ELEVEN NOTES 0 Why meiosis 0 During development all cells germline and somatic divide by mitosis and remain 2n diploid 46 chromosomes 0 Puberty I germline cells produce the sex cells 0 Gamete cells must go from diploid to haploid so that when they meet with another they form two new 2n diploid organisms 0 Therefore each germ cell undergoes meiosis or reductive division 0 Concept 131 offspring acquire genes from parents by inheriting chromosomes 0 Asexual reproduction a single individual passes genes to it s offspring without any gametes figure 132 0 Clone a group of genetically identical individuals from the same parent 0 Sexual reproduction two parents give rise to offspring that have unique combinations of genes inherited by two parents 0 Sets of chromosomes in human cells I Human diploid somatic cells have 23 pairs of chromosomes 0 2 chromosomes in each pair are called homologous chromosomes homologs I Chromosomes in a homologous pair are the same length and shape carry genes with the same inherited characteristics I Karyotype shows homologous chromosomes 0 Concept 132 Fertilization and meiosis alternate in sexual cycles 0 A gamete contains a single set of chromosomes and is haploid n I Human haploid number23 n23 I 22 single autosomes and a single sex chromosome 0 Fertilization and meiosis figure 135 I At sexual maturity ovaries and testes produce diploid spermocytes and oocytes I reduced to haploid gametes I Gametes are the only type of cell in humans to divide using meiosis 0 Figure 136 compare cycles I Alterations of generations spores produce a diploid organism which produces gametes plants I No multicellular diploid stage zygotes 0 Concept 133 the stages of meiosis production of haploid chromosomes 0 Cell prepares in Interphase after chromosomes duplicate two divisions follow I Meiosis I recombination I replicated homologs pair up and then separate 0 Two haploid daughter cells I made up of two sister chromatids O O I Meiosis 11 reduction I sister chromatids separate The result is four haploid daughter cells with single chromosomes Figure 138 I how meiosis reduces chromosome number I Interphase prepares the cell as it does in mitosis Figure 138a Meiosis II recombination and separation I Prophase I duplicated homologous chromosomes pair and exchange segments nonsister exchange I Metaphase I chromosomes line up by homologous pairs I Anaphase I each pair of homologous chromosomes separate I Telephase I and Cytokinesis two haploid cells form each chromosome still consists of two sister chromatids Figure 139 bk Meiotic Synapsis I Prophase I homologous pairs of chromosomes form a tetrad 0 Human cell has 23 tetrads I 92 chromatids I Close association produces a synapsis and a synaptonemal complex or scaffold 0 Allows nonsister to cross over and recombination to occur I Nonsister chromatids pair up Crossing over figure 139 I At particular crossover points chiasmata enzymes help break and rejoin DNA molecules I allow recombination I Major checkpoints proper recombination of DNA correct formation of the synaptonemal complex 0 If not won t complete cycle Figure 138 Meiosis II separates sister chromatids and produces haploids I Prophase IIDMetaphase III Anaphase III Telephase II and Cytokinesis I During another round of cell diVision the sister chromatids separate I 4 haploid daughter cells produced containing unduplicated chromosomes Comparison of Mitosis vs Meiosis I Look at PowerPoint and table figure 139 in book Remember recombination for genetics LECTURE TWELVE NOTES Mendelian Genetics Start with the parental generation Took a plant with a green pod color and crossed them with a plant that had yellow color Cross pollenated to create the F1 generation lst felial generation All were green just like the green dominant parent plant Took the green F1 generation and selffertilized them and obtained the F2 offspring and found that of the generation was green and IA was yellow 0 Explanation called PARTICULATE INHERITANCE I Characters are determined by heritable factors genes that are passed from generation to generation I Each character is proposed by 2 factors I One of the factors from one of the parents is masking the factor from the second parten Mendel s Model 0 How to explain the 31 inheritance in F2 0 Need to understand differences in alleles O Allele alternative version of a gene 0 Each gene is on the same locus on homologous chromosome I Yet theses genes could vary slightly on their nucleotide sequence 0 For each character an organism inherits there are 2 copies of a gene alleles I Can be identical or different I If the alleles are different than the dominant allele will determine the phenotype what the organism looks like I The recessive allele is masked 0 Law of segregation I Two alleles for a heritable character are going to segregate during gamete formation and end up in different gametes 0000 0 Events that take place in meiosis I If the identical allele for particular character the allele present in all gametes I In different alleles 12 gametes get on allele and the other 12 are going to get the other allele I This process is going to account for the 3 to 1 ration observed in the F2 generation 0 EX GreenG dominant and yellowg recessive I Genotypes can either be 0 Homozygous I 2 identical alleles in a particular locus therefore the individual is going to be GG homozygous dominant green or gg homozygous recessive yellow 0 Heterozygous 0 2 different alleles in particular locus therefore the individual is going to be Gg showing green pod color because it has dominant G 0 Are NOT true breeding I All of the offspring Will NOT be identical I Fig 146 0 Monohybrid cross Genetic cross that follows the behavior of alleles at a single locus Parents that are heterozygous for a particular character This is how Mendel explained the inheritance of a single character specifically Law of Segregation Take true breeding parents meaning that they are homozygous at that particular locus Parents GG X gg Green yellow goes through meiosis all gametes G g LECTURE THIRTEEN NOTES Chromosomes Take a good look at Fig 152 because it goes over the lecture Chromosome theory of inheritance I Genes have specific loci on chromosomes I Chromosomes undergo segregation and independent assortment Thomas Morgan I Working during the early 20th century and he was an experimental embryologist I Significance of his work is that he provided evidence that chromosomes are the location of Mendel s heritable factors I Experimental organism Drosophila melanogaster 0 Fruit y 0 Very common experimental organism I Prolific breeders one mating will produce 100 s of offspring between one male and one female I Quickly new generation every 2 weeks I 4 pairs of chromosomes I 3 of which are autosomes I 1 pair is the sex chromosome I traits that were in fruit ies 0 wild type trait phenotype for a character that is most commonly observed in natural populations I red eyes 0 mutant phenotype alternative to the wild type I white eyes 0 notation to allow them to symbolize the alleles I for any given character eye color the gene is going to be given a symbol for the first mutant observed I ex allele for white eyes w I allele for red eyes w I behavior of genes alleles with behavior of chromosome pair I P generation red eyed females and mate them with white eyed males I F1 generation all offspring had red eyes 0 Based on this observation red eyes are dominant I F1 generation bred red eyed females to red eyed males I F2 generation found a 3 to 1 phenotypic ratio 0 Same as Mendel except for a little different all of the white eyed ies were males 0 Based on this he concluded that the eye color gene was located on the X chromosome and there is no corresponding locus on the Y chromosome Female Fly Male Fly P XWXW P XW Y F1 generation XWXW I red eyed female XWY I red eyed males F2 generation 31 ratio fig 154 XWXW I red eyed females XWXW I red eyed females XWY I red eyed males XWY I White eyed males 0 Support of chromosome theory for inheritance O Says that specific gene is carried on a specific chromosome 0 Genes on sex chromosomes have a unique ratio Sex chromosomes 0 Autosomes NOT sex chromosomes 0 All the other chromosomes 0 Homomorphic same shape 0 Sex chromosome 0 One pair 0 Major sex determining genes 0 Act homologous during meiosis I During synapse I Crossing over 0 Do contain genes that are not involved in sex determination I Ex eye color in fruit ies O Sexlinked genes I genes that are passed down 0 Humans O Males heterogametic sex XY genotype I During meiosis I When male produces sperm the chromosomes split up and half the sperm get X chromosomes and half get Y chromosomes 0 Y chromosomes are important because it makes an indiVidual a male 0 Females homogametic sex XX genotype I During meiosis I When the female produces eggs all of them get the X chromosome 0 Female because of the lack of the Y chromosome Fig 156 all animals don t work the same as the XY male and XX female as in humans 0 ex In birds males are homogametic sex and females are the heterogametic sex Xlinked genes genes located specifically on the X chromosome X chromosomes 0 In most species they are larger and have a lot of genes on them as many genes as an autosome of similar size 0 Many of these genes loci are very important in the development of both sexes I Nothing to do With sex determination 0 Xlinked genes are inheritance is coupled to the X chromosomes I If you get the X chromosome you get the specific gene on the chromosomes 0 Xlinked traits controlled by genes on the X chromosome I Inheritance pattern as usual Inheritance in sex cells Mother XX and Father XY F1 generation XX XX XY XY 0 First take a look at the males I Only have one X chromosome I Every allele on that chromosome is going to be expressed depending on if it is dominant or recessive because there are no other factors I Everything gets expressed I Males are hemizygous for Xlinked alleles meaning they show all alleles on the X chromosome 0 Issue With red green color blindness fig 157 I What happens in the recessive allele Which is recessive I In females they can be homozygous dominant XNXn I color vision carrier of homozygous recessiveXnXn I red green color blind I In males they can be hemizygous dominant XN I color vision of hemizygous recessive Xn I redgreen color blind 0 Color blind male mates With carrier female I Male I XnY I Female I XNXn I F1 generation XNXn XnXn XNY XnY I 50 chance of being male 50 chance of being a female 25 chance of being a colorblind male 25 chance of being a colorblind female 0 Hemophilia 0 Xlinked recessive disorder 0 Father With hemophilia I Daughter Who also has hemophilia how did this happen 0 Xinactivation occurs in females 0 Means that in female one of the X chromosomes in every single one of her cells is going to be inactivated during embryotic development I One active X chromosome and one inactive X chromosome I Inactive chromosome barr body I At functional level females are hemizygous because only one of the X chromosomes is active I Barr body very easy to pick out in cell 0 Very dense structure I Stains very darkly 0 You ll find it in the inner side of the nuclear envelope I Active chromosome form of chromatin 0 Spread out thread like material 0 Looks like the autosomes 0 Inactivation I DNA and histone proteins have been modified I Modification involves DNA methylation means that methyl groups are added to the DNA nucleotide to inactive DNA I Random inactivation 0 The X chromosome inactive in one cell may not be the same chromosome in another cell 0 If the female is heterozygous XAXa 0 Some cells have the XA allele active and some have the Xa allele active 0 5050 split I in case of red green colorblindness I therefore she has color vision because enough of the dominant alleles are active and enough protein is made to make color vision 0 fig 158 0 tortoise shell cats calico I turns out that some of the genes for coat color are Xlinked I heterozygous female will have some cells that will show one color while another cell will show another color therefore the patchy coat color I mosaic pattern of gene expression Linked genes genes that are on the same chromosome 0 humans 0 20000 genes 0 23 pairs of homologous chromosomes 0 lots of genes on any particular chromosome 0 Linkage tendency for a group of genes that are on the same chromosome to be inherited together 0 Pair and separate during meiosis 0 Linked genes inherited together from generation to generation I Let genes A and B be UNLINKED 0 Means that they are independently assorted 0 On 2 different chromosomes 0 Unlinked dihybrid cross 0 Parent generation AABB X aabb O Gametes AB ab 0 F1 AaBb 0 F1 gametes AB aB Ab ab 0 Test cross I AaBb X aabb O Offspring IA AaBb IA Aabb IA aaBb IA aabb I important result for unlinked genes 0 Complete linkage O 2 genes are so close together on the same chromosome that they are inherited as a single unit 0 example genes B and D I completely linked I Parent generation BBDD X bbdd I Gametes BD X bd I F1 generation Bde I F1 gametes BD bd I because these genes are linked I Re ect the arrangement of alleles in the parental generation 0 Parental arrangements because they re ect the parent gametes 0 Determine if genes are linked by dihybrid test cross 0 Dihybrid because we re looking at alleles at 2 loci I Mate a heterozygous F1 with homozygous recessive individual 0 Parental generation Bde X bbdd O Gametes BD bd bd 0 F1 generation 12 Bde and 12 bbdd I 100 represents the parental generation 0 incomplete linkage 0 between unlinked and completely linked I look at some fruit y experiments 0 body color and Wings incompletely linked 0 body color gray Wild type black mutant 0 Alleles b b 0 Wings normal Wild type vestigial mutant 0 Alleles v V I Parental generation bbvv X bbvv 0 Gray normal crossed With black vestigial 0 F1 bbvv lgray nomal 0 Cross With a homozygous recessive individual Offspring 40 bbvv and 40 bbvv I parental genotype 10 bbvv and 10 bbvv I recombinants O Reasoning for this outcome is that linked genes recombined during crossing over during prophase 1 of meiosis I Non sister homologous chromosomes I Genes that are located far apart on a chromosome have a greater probability of being separated by an exchange of gene segments than genes that are close together I Some are linked and others unlinked 0 You can determine linkage by test cross results 0 Parental genotype recombinant genotype linkage 100 0 complete 50 50 unlinked 50gtXlt100 0gtXlt50 incomplete 0 Genetic recombination O 2 ways to get recombinant gametes one that is different from the parent I With unlinked genes 0 independent assortment I With linked genes 0 crossing over during prophase 1 of meiosis I gure 159 and 1510 LECTURE FOURTEEN NOTES DNA DNA genetic material 0 Chromosomes 0 DNA deoxyribose nucleic acid I 4 nucleotides 0 proteins I 20 amino acids 0 which are the genes I is it DNA or protein I Early research hypothesis is that genes are made of protein 0 Frederick Griffith 1928 0 Evidence to reject the protein hypothesis 0 His evidence supported the hypothesis that DNA is the genetic material 0 Used streptococcus pneumonia I Bacterium I Studied 2 different strains of this bacterium 0 Smooth or S strain because when it grew in agar petree dish it would form smooth shiny colonies O Polysaccharide capsule O Protects the cell from the host immune cells 0 S strain was the virulent strain and would kill th mice 0 Rough or R strain because it formed rough surface colonies O No capsule and destroyed by host immune cells 0 Avirulent strain and does not kill mice 0 His experiment 0 Took live S strain cells and injected them into mice and the mice died 0 He took live R strain cells and injected them into mice and the mice survived 0 He took heat killed S strain and injected them into mice and the mice survived 0 Live R strain heat killed S strain cells and injected into mice and the mice died I Recovered live S strain from dead mice 0 Realized that something in the heat killed S strain converted R strain into the virulent form 0 Transformation genetic change in whice properties of a strain of dead cells is conferred on a different strain of living cells 0 Figure 162 Avery Macleod and McCartney 1994 I Took S cells and lysed them broke them apart I Took cell contents and separated it into a variety of fractions 0 Lipids 0 Proteins O Polysaccharides 0 Nucleic acids I Took each one of the fractions and tested them for their transforming ability 0 Which one could transform the R strain into the S strain 0 The only thing that could transform it was the nucleic acids Hershey Chase 1952 I Used a T2 bacteriophage 0 Fig 163 0 Called page for short is a virus that infects bacterium cells 0 Consists of DNA core that is surrounded by a protein coat I Looks like a hexagon with a tail and legs with DNA in the hexagon center 0 During infection the virus enters the bacterial cell I Virus enters bacterial cell I Only part of the virus enters the cell I Once it is in the cell it reproduces and eventually the bacterial cell lyse and all the newly formed viruses are going to be released 0 Purpose of their eXperiments was to determine whether protein or DNA was the genetic material hereditary information I Able to trace the protein and the DNA through the cycle of the virus 0 Focused in on sulfur which is present in a lot of proteins specifically amino acids cysteine and methoionine and it is not present in DNA 0 Therefore they labeled one batch of the virus with radioactive S35 O Took a different batch of virus and focused in on phosphorous which is found extensively in nucleic acids not present in proteins I Labeled P32 0 Results of the eXperiment were that the viral progeny all contained P32 by NOT S35 I Therefore proving that DNA is the hereditary genetic material 0 Fig 164 What is the structure of DNA 0 Nucleotides basic building blocks of DNA 0 Each nucleotide contains a phosphate group a sugar deoxyribose and l of 4 nitrogenous bases I all one nucleotide 0 Where the 3C is on the sugar the new nucleotide will connect to one of the oxygen s on the phosphate group 0 Fig 165 0 3 nitrogenous bases 0 purines basic structure of 2 rings I 6 member ring connected to a 5C ring I adenine and guanine O pyrimidine I one 6C ring I cytosine and thymine 0 Evidence for structure of DNA 0 James Watson and Francis Crick 1953 O Rosalind Franklin 1951 1953 I X ray crystallographer I Studied X ray diffraction of DNA I Fig 166 I Method for determining the 3D structure of a molecule I Found that DNA was helical width of heliX distance between turns and nucleotide bases are staced O ErVin Chargatt I Studied the composition of DNA from many different organisms human horse mouse etc I Found that no matter what organism that he got the DNA from there were certain rules and patterns that he always consistently found I DeVised 2 rules 0 Total purines A and G total pyrimidines C and T 0 Amount of A always equals the amount of T and the amount of C always equals the amount of G 0 But AT doesn t equal CG 0 Scientific skills exercise page 316 in book that makes you calculate the base composition 0 Watson and Crick model of DNA structure 0 Explains how DNA can carry the genetic information and also how that information can be replicated 0 Features of the Watson Crick Model DNA is a double helix consisting of 2 strands of DNA that are wound around each other 0 One unduplicated chromosome consists of 2 strands of DNA 0 One chromosome during prophase O 2 sister chromatid with each sister chromatid composed of 2 strands DNA 0 4 strands DNA total 0 back to one duplicated chromosome 0 each strand has a sugar phosphate backbone upright portion of the ladder I the sugar and phosphate are connected by phosphodiester linkages I no variability 0 also has nitrogenous bases that point towards the center of the helix I attached to the backbone by covalent bonds I lots of variability possible I nitrogenous bases carry the genetic information in their sequence 0 Untwist the helix looks like a ladder the nitrogenous base from one side connects to a nitrogenous base from the other side to represent the rungs of the ladder I Held together by hydrogen bonds between the bases I Between A and T there are 2 hydrogen bonds I Between C and G there are 3 hydrogen bonds 0 Two strands run antiparallel I Opposite directions I Direction of a poly nucleotide O In backbone all the sugar is numbered as aforementioned in the picture added to show structure of a DNA molecule 0 Phosphate groups connects to 3 C of one sugar and the 5 C of the next sugar I 3 5 phosphodiester linkage O the opposite strand goes from 5 to 3 I 5 3 phosphodiester linkage 3 end has a free OH O 5 end has a free phosphate 0 0 g 167 I specific base pairing rules 0 purine will always pair with a pyrimidine 0 specific pairing at AT and CG 0 AT are complementary 2 hydrogen bonds 0 DG are complementaty 3 hydrogen bonds 0 Strands are complementary which means that if you know the sequence of one strand you automatically know the sequence of another strand 0 This complementarity provides the mechanism for DNA replication 0 Each strand serves as a template DNA Replication 0 Being semi conservation meaning that each new molecule of DNA 2 strands consists of one parental strand and one newly synthesized strand 0 Fig 1610 0 1st proposed by Watson and Crick and later confirmed by Meselson and Stahl 0 experiment in Fig 1611 0 process of semi conservative replication 0 initiation I Fig 1613 I Discusses the proteins that are involved in initiation DNA is twisted into a heliX and it needs to be unwound I Unwind 2 strands of double helix 0 3 requirements to unwind 0 DNA helicases enzymes that break h bonds between the bases cause the strands to separate from each other and causes the heliX to unwind ATP required 0 SSB proteins single strand binding prevent the reformation of double helix 0 Topoisomerases function to relieve the strain caused by unwinding by producing breaks in the backbone phosphodiester bond than rejoin after translation is complete I More relaxed formation prevents knots 0 Origin of replication I Fig 1612 I Location in a DNA molecule where replication is taking place 0 Where 2 strands are unwinding and where they separate 0 Look in eukaryotic chromosomes which are linear and along the length of one chromosomes there will be several origins Replication does not begin at ends I Each origin results in a bubble which has 2 replication forks O Replication fork I Both strands of the double heliX and being synthesized at the same time I Replication occurs in both directions 0 Elongation Nucleotide monomers added in orderly fashion I Fig 1614 Always occurs in the 5 to 3 direction Saying that the linkage of the 5 phosphate group of the next nucleotide subunit is to the 3 OH of sugar at the end of preO eXisting strand Nucleoside triphosphate actual monomers that are actually added that consists of a nucleoside base sugar attached to 3 phosphate groups I 2 of the phosphates are removed provides the energy to drive this elongation reaction I enzyme is DNA polymerases O O Bidirectional Opposite direction on the two strands enzymes that are able to read the DNA template use complementarity only synthesize this reaction In the 5 to 3 direction can only add a nucleotide to the 3 end of a growing molecule template is being read antiparallel 3 to 5 direction only add to an eXisting strand and in order to overcome this we use an RNA primer short piece of RNA 0 primer synthesized at the fork which is complementary to the SS DNA template at that location 0 primase enzyme does this A which is able to start the piece of RNA 0 does not require a free 3 end 0 Look at the origin of replication at a fork I Leading strand is always growing and being synthesized and growing toward the replication fork I Described as being smooth and continuous I Other strand is called the lagging strand and is being synthesized in short discontinuous segments Okazaki fragments Within okazaki fragment the direction of synthesis is away from the fork but the overall direction of lagging strand synthesis is towards the fork I Various fragments that are being produced are eventually joined together by DNA ligase Figure 161517 Brings DNA pieces together by covalent bonds Usually happens with no ERRORS But an error is a mutation which is a change in the DNA sequence Usually they are caught by the correction system The errors that slip through are changes that are passed to daughter molecules 0 Huge evolutionary significance 0 If the mutation is occurring in germ cells gametes than these mutations can be passed on the subsequent generations 0 Mutation is the source of variation on which natural selection operates during evolution LECTURE FIFTEEN NOTES Gene Expression Gene expression 0 Process by which DNA directs synthesis of proteins ampRNA Intro 0 History 0 Garrod 1902 I Studied inherited diseases particularly on people who are unable to make a particular enzyme I inborn errors of metabolism I Suggested that genes are responsible for phenotypes O Beadle and Tatum 1920 s I Neurospora crassa bread mold I Bombard this bread mold with Xrays I showed genetic changes that occurred I mutations I These mutations were nutritional and unable to produce particular enzymes I Figure 172 I One Gene One Enzyme Hypothesis genes dictate production of an enzyme I We now know that not all proteins are enzymes I One Gene One Polypeptide Protein Hypothesis 0 Eukaryotes O Nucleus I Where the enzymes are located 0 Cytoplasm I Ribosomes composed of RNA and proteins and their function is protein synthesis 0 RNA messenger 0 RNA 0 Ribonucleic Acid 0 DNA RNA Sugar Deoxyribose Ribose Bases ACGT ACGU Stranded Double Single 2 0 Ribose OH group at 2 prime 0 Uracil Base subsitutes for thymine pyrimidine lacks a methyl group complementary to adenine U A O 3 types I mRNA messenger encode and entire polypeptide I rRNA ribosomal structural part of a ribosome I tRNA transfer carries indiVidual amino acids to a ribosome during translation 0 Central Dogma of molecule biology 0 Proposed by Francis Crick 1956 0 Suggested that there is an unidirectional one way ow of genetic information I DNA used to produce RNA which is used to produce proteins I DNA I RNA I proteins 0 Transcription I The synthesis of RNA using information that is in the DNA I First arrow 0 Translation I The synthesis of a polypeptide done by a ribosome using the information that is in mRNA I Second arrow 0 Occurs in prokaryotes and eukaryotes 0 Figure 173 I Where do transcription and translation occur in prokaryotic and eukaryotic cells Genetic Code 0 Proteins 0 Amino acids 0 Linked together by peptide bonds 0 20 amino acids 0 Genetic Code 0 4 bases of mRNA encode amino acid sequence of protein 0 mRNA code language I Codon 0 Sequence of mRNA Comprised of 3 nucleotides Triplet Function code for a single amino acid Ex codon UCG codes for serine UUU codes for phenylalanine Nonoverlapping I UCGUUU I Possible to get 64 amino acids I Figure 174 I Unambiguous 0 A single triplet specifies only one amino acid 0 Degenerate 0 Most amino acids are specified by more than one triplet 0 EX tyrosine is coded for by UAU and UAC 0 If an amino acid has more than one codon then it is the last base that varies I wobbles 0 Figure 175 00000 I Start codon 0 AUG 0 Marks the beginning of protein synthesis for the ribosome 0 Codes for methionine always going to be the first amino acid in the polypeptide I Stop codons O UAA UAG UGA 0 Do NOT code for amino acids 0 Triggers the termination for protein synthesis 0 Reading frame 0 EX the red dog ate the bug I mutation I her edd oga tet he bug 0 Deleted the T in the and caused the mutation causes problems for the readings I Universal 0 Genetic code is universal 0 Used by all viruses prokaryotes and eukaryotes 0 Figure 176 Transcription I Synthesis of RNA that is complementary to DNA I 3 stages 0 Initiation I DNA is going to serve at the template for RNA synthesis I One strand is going to be transcribed template strand I Read in the 3 to 5 direction I Other strand is not going to be transcribed I Promoter 0 Specific DNA sequence on the transcribed strand at the beginning of the gene 3 end I the upstream location 0 Designates the starting site of transcription 0 Not transcribed 0 RNA Polymerase 0 Does not require a primer 0 It binds to the promoter and then unwinds the helix and begins transcription 0 It synthesizes RNA in the 5 to 3 direction 0 Elongation I Template strand read 3 to 5 direction I RNA polymerase 5 to 3 direction I Nucleotide triphosphate 2 phosphate groups removed I provides energy 0 Termination I Specific DNA sequence I Signals RNA polymerase to stop I Transcript comes off the DNA 0 Figure 177 0 Eukaryotes 0 Have to undergo posttranscriptional modification 0 PremRNA O Alteration of the ends of the premRNA I 5 end gets a 5 cap a modified guanine nucleotide I 3 end gets a poly a tail 50250 adenine nucleotides I Function export from nucleus 0 Protect mRNA from enzyme degradation 0 Help the ribosome attach to the mRNA 0 Figure 1710 0 RNA splicing I Pre mRNA I Exons 0 Expressed regions I Coding region that code for proteins 0 Transcribed from DNA 0 Translate I Introns 0 Intervening sequences 0 Transcribe I Not translated I noncoding regions I Must be removed before translation can occur 0 Removed by splicing I Splicing removes introns from pre mRNA I Spliceosome I Compromised of proteins and RNA 0 Bind the to intron Splice at the boundary between an exon and intron Intron degraded I Exons put together I mature mRNA I moves to cytoplasm I Figure 1711 and 1712 Translation 0 Synthesis of polypeptide form in RNA 0 Summary 0 Initiation mRNA binds to ribosome tRNA brings the first amino acids to ribosome O Elongation tRNA s continue to bring amino acids to ribosome Which then covalently links the amino acids together 0 Termination ribosome gets a stop message mRNA is released from the ribosome tRNA are released and the newly synthesized polypeptide is going to be released 0 Figure 1714 I tRNA 0 transcribed from DNA function bind to specific amino acids bring amino acids to mRNA on ribosome structure I single stranded I about 80 nucleotides I 3D structure I complementary base pairing by Hbonds with the molecule causing it to fold I unpaired bases form loops 000 I anticodon loop 0 3 bases 0 recognizes and binds to a codon in mRNA 0 AminoacyltRNA O 20 amino acids 0 covalently link the carboxyl group of amino acids to the 3 end of tRNA 0 ATP I AminoacyltRNA I able to bind to mRNA I Figure 1716 0 Ribosome O Comprised of I protein I rRNA transcribed from RNA catalytic function 0 2 parts I small subunit I large subunit 0 has 3 grooves or depressions in the order EPA 0 location where tRNA molecules attach 0 The A binding site I AminoacyltRNA delivering to next amino acid in sequence binds 0 The P binding site I tRNA holding growing polypeptides bind 0 The E binding site I Where the tRNA that delivered an amino acid to the growing chain is going to exit on ribosome 0 Enzyme complex bind mRNA and forms peptide bonds 0 Initiation O O O O 0 Figure 1718 Small unit I mRNA attaches I AUG 3 mRNA I tRNA methionine I 5 AUG mRNA Large subunit then attaches has 3 groups A P and E P binding site lines up With the tRNA Small subunit I mRNA I large subunit Translation initiation complex 0 Elongation O O 0 Series of repeated cycles Each cycle is going to add a single amino acid to the growing polypeptide chain 3step cycle I condon regocnition I peptide bond formation I translocation 0 Termination O 0 Stop signals UAG UAA UGA Release factor protein shaped like tRNA that binds directly to stop codon I adds water NOT amino acid LECTURE SIXTEEN NOTES AminoacyltRNA for next codon in chain binds to A site between anticodon and codon on mRNA 0 Ribozyme peptidyl transferase O Ribosomal RNA that functions as an enzyme that is not a protein 0 Catalyzes a peptide bond between the amino acids in the P and A sites I Covalent bond between the amino acid and the transfer RNA at the P site is going to be broken 0 Ribosome is going to translocate 0 Moves down one codon on the messenger RNA is the 5 to 3 direction 0 Next codon tells what amino acid is next in the sequence 0 Look at the 5 side of the P site is the growing peptide chain 0 Uncharged tRNA no amino acid moves from P to E and this will come of the E site and move into the cytosol to be used again 0 tRNA from the A site moves to the P site 0 next aminoacyltRNA moves into the A site I this keeps repeating until it hits a stop codon on the mRNA 0 GTP is the source of energy Termination Fig 1720 I Stop codon 0 Not recognized by any of the tRNA 0 UAG UAA UGA O Recognized by release factors I A site is open at this point and instead of a tRNA binding a release factor binds at the A site and it causes the release of the polypeptide from the P site I Release of mRNA I Release of last tRNA and recycled I Ribosomal subunit to dissociate 0 Finally made a full poly peptide Replication one DNA I 2 DNA molecules Transcription part of the DNA molecule I mRNA Translation start off with info on mRNA lpolypeptide proteins Gene Regulation 0 Kidney cell nerve cell brain cell 0 These three types of cells all contain the same DNA information in each nuclei 0 All cells have exact same genetic information yet they have different functions and shapes 0 This is because gene function is regulated Therefore only a certain subset of the cell is going to be expressed in each cell which gives the different types of cells 0 Genes vary on how they are expressed O Constitutive genes aka housekeeping genes do not function constantly or levels are adjusted up and down I Enzymes needed in cellular respiration 0 Most cells have some genes non housekeeping do not function constantly or levels are adjusted up and down 0 Bacterial gene regulation 0 Simpler than what happens in eukaryotes 0 Regulation mainly at the transcription level I DNA I RNA 0 Classic example is the Lac Operon I This type of gene regulation was found by Jacob and Maiod 1961 0 1st to demonstrate gene regulation 0 organism Escherichia coli E Coli I looked at lactose metabolism I E Coli 0 Normal inhabitant of the human intestine I Must be able to adjust to the chemical environment food that the host eats 0 EX If the host drinks milk than there is going to be lactose O E Colie must be able to digest lactose O In order to be able to use lactose O Lactose permease I Transmembrane carrier brings lactose into the bacteria cell I Also needs the enzyme beta galactosidase Bgal I Lactose I glucose and galactose I Galactoside transeactylase 0 Enzyme that plays a role in lactose metabolism 0 Grew bacterium in the lab under many conditions 0 Grew E Coli in or on medium with no lactose I All three proteins are present at very low levels 0 Now you grow on a medium with lactose I Synthesis of the three proteins begins 0 Terms I Induction turning on gene expression I Inducer compound that stimulates synthesis of an enzyme I Inducible enzyme coded for by an inducible gene 0 Produced in response to the inducer I 3 genes for lactose metabolism 0 these three genes lay next to each other in the chromosome 0 share the single promoter nucleotide sequence in the DNA Where the RNA polymerase is going to bind and being transcription 0 information is going to be transcribed into a single continuous RNA molecule 0 either all genes are on or all genes are off I all 3 or none 0 genes are all part of an operon O operon genetic structure found only in prokaryotes complex consisting of a group of structural genes that have related functions plus some closely related DNA sequences responsible for controlling the genes 0 operon consists of the promoter place Where RNA binds operator on DNA that acts as a switch and structural genes sequences that code for the protein 0 Promoter and operator function as binding sites on the DNA I NOT TRANSCRIBED 39 Structural genes are transcribed RNA polymerase reg ulatorgiI 1 holoenzyrn e gene oonsttutivel expression no transcription l nil lee repressor helixtum helixj 0 Plac promoter 0 O operator 0 lacZ beta gal 0 lacY permase operon repression 0 lacA Transacetylase Repressor Gene not a part of the operon and it s function is to code for the repressor protein 0 Pi promoter for the repressor gene 0 lacI repressor gene 0 I means inducibility Repressor Protein lactose repressor 0 Constitutive made all the time 0 Not being regulated at the transcriptional level 0 In absence of lactose DNA binding site on Lac operator 0 RNA polymerase binds to the operator therefore it blocks the transcription of the gene 0 Blue lego looking piece in the diagram is the repressor binding at the 0 site 0 If lactose if present 0 Small amount of lactose is going to enter the cell and converted to allolactose isomer of lactose same chemical structure with different shape 0 Allolactose goes and binds to the binding site on the repressor protein I Allosteric binding site I Deactivates the repressor so it can no longer block the transcription of the other genes I Allosteric regulation allolactose binds to allosteric binding site making it not bind to the operator 0 Allolactose inducer because it induces lac operongenes by inactivation repressor protein What is transcribed 0 One long mRNA which codes for all three genes 0 Each gene has it s own separate translation start and stop codons which is important because after translation we want to have 3 separate proteins 0 mRNA translated into 3 separate proteins 0 transcriptions and translations can occur simultaneously in prokaryotes but NOT in eukaryotes WHY 0 Eukaryotes have a nucleuse where transcription occurs where translation happens in the cytoplasm 0 Prokaryotes don t have a nucleus so it can immediately be used by ribosomes quick response 0 Fig 182 and 183 Iwalk you through tryptophan operon 0 Synthesis of RNA transcript I RNA polymerase binding and initiation of transcription 0 Start point where RNA synthesis begins 0 Transcription factors mediate the binding of RNA polymerase I Transcription initiation complex I Once promoter is attached and polymerase is bound the strands unwind 0 Elongation of the RNA strand I New RNA slowly peels away from the template DNA and double helix shape reforms I Transcription at a rate of 40 nucleotides per second 0 Termination of Transcription I Bacteria proceed through a terminator sequence 0 Polymerase detaches from DNA and releases transcript I Eukaryotes signal AAUAAA 1035 nucleotides down the proteins cut free from the polymerase I release premRNA 0 PremRNA goes through more processing Mechanisms of PostTranscriptional Regulation Fig 186 0 RNA processing 0 Alternative RNA splicing I Figure 1813 Alternative RNA splicing of troponin T gene 0 mRNA can have exon 3 or exon 4 0 mRNA degradation 0 Lifespan of mRNA I untranslated region UTR at the 3 0 Increase the time that mRNA can be active in the cytoplasm 0 Initiation of translation 0 Simultaneously activated in an egg following fertilization 0 Protein processing and degradation 0 Cleavage and the addition of chemical groups 0 Proteasomes degrade proteins l 0 29 l 3 CHAPTER TWENTY NOTES DNA Technology the main techniques for sequencing and manipulating DNA 0 Manipulation of organisms so they can produce products used for particular applications DNA Sequencing I using a machine 0 Understand the theory behind the process 0 Technique that allows us to know the sequence of nucleotides in a segment 0 Know the order of nucleotides so we can find out the genetic information 0 Synthesizes DNA indiVidually 0 DNA polymerase enzyme that adds nucleotides to the primer primase 0 Template strand strand of DNA that is going to be the basis for synthesis 0 What do you need for DNA sequencing 0 DNA polymerase 0 Primer 0 Template strand 0 Deoxyribonucleotides are replaced with dideoxyribonucleotides 0 Complementary base pairing is used at the start 0 Start with one strand of DNA I then synthesis goes up with nucleotides added one by one 0 Separate all of the strands that differ in one nucleotide 0 Moving through a tube and the detector figures out what the DNA is specific type 0 Machine figures out what order the nucleotides are in in the sequence Gel Electrophoresis 0 DNA fragment moves through a gel during electrophoresis 0 Size length 0 Charge 0 1 Mixture of DNA molecules of different sizes 0 2 Separate fragments by size 0 Can use this information for research Uses of DNA sequencing information 0 From the specimen tissue sample extract DNA I DNA sequencing identify specimen 0 Identify the specimen by determining the sequence of a specific gene and then comparing with the sequences of other organisms Methods in recombinant DNA technology 0 DNA Cloning tools from bacteria 0 Restriction enzymes specific enzyme in the nucleus that packs the DNA in specific places 0 Vector plasmids I Also bacteriophages transposons 0 Transformation 0 Multiple copies clones 0 DNA cloning steps 0 Extract plasmid DNA from bacteria 0 Cut the plasmid DNA I using restriction enzyme I End up With a plasmid With sticky ends I Use the same restriction enzyme for both the plasmid and the DNA fragment so you can fit the two together 0 Hydrogen bond the plasmid DNA to nonplasmid DNA fragments 0 Ligase I I Holds the DNA fragment to the plasmid I Forms the recombinant plasmid O Transform bacteria recombinant DNA molecule 0 Clones Using a restriction enzyme and DNA ligase to make recombinant DNA Fig 206 0 Restriction site little section of the DNA segment 0 Breaks in half with 2 separate sides not equal in length I Sticky ends on the ends of them 0 Restriction enzymes breaks sugarphosphate backbones 0 Ligase seals strands Amplifying DNA in vitro the Polymerase Chain Reaction PCR PCR directly make use of I Used for 0 To amplify a specific gene 0 To generate multiple copies of a DNA segment 0 Why is it important to generate multiple copies of a DNA segment 0 Applications Practical Applications of DNA technology 0 Genetic testing diagnosis and treatment of diseases I Us PCR With primers that target genes associated With genetic disorders I Amplified DNA product sequenced to reveal presence of disease causing mutations 0 Human Gene Therapy I Gene therapy introducing genes into af icted individuals for therapeutic purposes I Small number of disorders caused by single defective gene I Normal allele obtained from gene cloning introduced into all cells 0 EX Bone marrow I EX SCID severe combined immunodeficiency I Gene therapy using a retroviral vector 0 Insert RNA version of normal allele into retrovirus 0 Let retrovirus infect bone marrow cells that have been removed from the patient and cultured 0 Viral DNA carrying the normal allele inserts into the chromosome 0 Inject engineered cells into patient Pharmaceutical products I Pharmaceutical products that are proteins can be synthesized on a large scale I Protein production in cell cultures I clone the gene and introduce it into a plasmid plasmid is transferred into bacteria allowing it to grow I Protein production by Pharm animals Forensic evidence I Applications of DNA fingerprinting I the analysis of DNA fragments unique to an individual 0 Match the finger printing to the one from the crime scene I STR method of genetic profiling I All based on PCR polymerase chain reaction Environmental cleanup I Some genetically modified GM organisms can be used I To extract minerals from the environment I Do degrade potentially toxic waste minerals I Transforming organisms to handle the environment Agriculture genetically modified crops Transgenic Corn I resistant to drought I Genetically modified crops I GM plants are resistant to insect pests diseases heat cold herbicides salty or acidic soil drought 1 1113 HUMAN GENETICS NOTES Outline 0 Pedigree analysis 0 Recessively inherited disorders 0 Dominantly inherited disorders 0 Genetic testing 0 Alterations of chromosome number Pedigree Analysis 0 Many human traits follow Mendelian patterns of inheritance 0 Pedigree a family tree that describes the interrelationships of parents and children across generations 0 Inheritance patterns of particular traits 0 Fig 1415 I genetic map of a widow s peak dominant trait O From the phenotype we can figure out the genotype know which ones are homozygous dominant heterozygous or homozygous recessive 0 Have to be able to use this type of diagram as a summary of the information The Behavior of Recessive Alleles 0 Recessively inherited disorders show up only in individuals homozygous for the recessive allele 0 Albinism recessive condition lack of pigmentation in skin and hair 0 Fig 1416 punnett square for this trait with two heterozygous parents 0 Cystic Fibrosis O The cystic fibrosis allele results in defective chloride transport channels in plasma membranes leading to a buildup of chloride ions outside the cell 0 Sickle Cell Disease 0 The disease is caused by substitution of a single acid in hemoglobin O Heterozygous advantage against malaria 0 Fig 1723 I shows wild type hemoglobin vs sickle cell hemoglobin point mutation Dominantly Inherited Disorders 0 Achondroplasia 0 A form of dwarfism cause by a rare dominant allele 0 Fig 1418 I punnett square showing the probability of getting this disease with one heterozygous parent and one homozygous recessive parent 0 Huntington s Disease 0 The timing on onset of a disease significantly affects it s inheritance O Degenerative disease of the nervous system Testing a Fetus for Genetic Disorders Fig 1419 I Aminocentesis I Chorionic villus sampling CVS I Can only do these tests during the 12th14th weeks of pregnancy but look at test results during the 19th week need to process I Not the only techniques we have to predict genetic disorders I these are based of the karyotypes and the chromosomes Alterations of Chromosome Number or Structure Cause Genetic Disorders 0 Abnormal chromosome number 0 Aneuploidy abnormal number of chromosomes 0 Nondisjunction of homologous chromosomes in meiosis I O Nondisjunction of sister chromatids in meiosis II 0 Fig 1513 I nondisjunction steps and description I Alterations of chromosome structure 0 Causes I Errors in meiosis I Different chemicalphysical agents 0 Deletion removes a chromosomal segment I won t have genetic information that was in that specific gene 0 Duplication repeats a segment 0 Inversion reverses a segment within a chromosome most common during crossing over 0 Translocation moves a segment from one chromosome to a non homologous chromosome Human Disorders Due to Chromosomal Alterations I Aneuploidy in autosomes 0 Down Syndrome Trisomy 21 I Three copies of Trisomy 21 I Aneuploidy in sex chromosomes 0 X0 I Turner syndrome no Y chromosome I female sterile I no Barr bodies per cell 0 XXY I Klinefelter syndrome I male sterile I one Barr body per cell 0 Nondisjunction of sex chromosomes produces a variety of aneuploidy conditions In Lecture 0 Talked about the ow of genetic information I How the information travelled through the cycle and what happens during each step 1 1513 LECTURE NINETEEN NOTES Darwinian Evolution Outline of Lecture 0 Concept 12 core theme evolution accounts for the diversity and unity of life 0 Concept 221 Darwinian evolution and a challenge to traditional views that earth is inhabited by unchanged species 0 Concept 222 Darwin investigates natural selection and adaptation causing diversity of life 0 Concept 223 Several examples provide direct evidence of evolution Concept 12 The Core Theme Evolution accounts for the unity and diversity of life 0 Fig 112 Classifying life 0 Taxonomy is the branch of biology that names and classifies species into groups of increasing breadth 0 Domains followed by kingdoms are the broadest units of classification 0 Species are the smallest I a population that can interbreed 0 Domain I Kingdom I Phylum I Class I Order I Family I Genus I Species Three Domains of Life Fig 113 I Organisms are divided into three domains 0 Domain Bacteria Domain Archaea comprise of the prokaryotes I Prokaryotes are single celled and microscopic I Filamentous forms include cyanobacteria 0 Domain Eukarya I Plants which produce their own food by photosynthesis I Fungi which absorb nutrients I Animals which ingest their food Unity in the Diversity of Life Fig 114 0 A striking unity underlies the diversity of life 0 DNA is the universal genetic language common to all organisms 0 Everyone has genes but the differ within people and depending on heredity 0 Unity similarity is evident in many features of cell structure Charles Darwin and the Theory of Natural Selection 0 Charles Darwin published On the Origin of Species by Means of Natural Selection in 1859 0 Darwin made two main points 0 Species showed evidence of descent with modification from common ancestors 0 Via natural selection 0 People didn t accept this until after he was dead Darwin s Descent with Modification 0 Traits in individuals in population vary many are inheritable 0 More offspring are produced than survive competition is inevitable 0 Species generally suit adapt to their environment 0 Fig 118 I lightest colored beetles less likely to survive predation since easily seen darker grey beetles survive and thrive 0 Population with varied inherited traits I elimination of individuals with certain traits I reproduction of survivors I increasing frequency of traits that enhance survival and reproduction success Natural selection results in the adaptation of organisms to their environment Fig 119 0 For example bat wings are an example of adaptation 0 Unity same bones joints nerves etc as human arm foreleg of horse and ipper of a whale 0 Diversity mammalian forelimbs results from modification by natural selection operating over millions of generations Fig 120 Descent with modification adaptive radiation of finches on Galapagos Islands Concept 221 Darwinian revolution and a challenge to traditional views 0 Darwin s ideas were in uenced by the work of others and by his travels Jean Baptiste de Lamarck 17441829 0 His hypothesis nature is controlled by three biological laws 0 Environmental in uence physical chemical in the womb on organ development innate need to become more complex naturally 0 Use and disuse of parts parts of body used extensively get larger and stronger while others deteriorate e g stretching of the giraffe s neck intermediate giraffes O Inheritance of those modifications to the next generation 0 Experiments showed that traits acquired by usedisuse during an individual s life were not inherited Concept 222 Charles Darwin Origin of the Species by Natural Selection 1859 0 Developed the theory of evolution during voyage of HMS Beagle in 1831 0 Compared organism adaptations on arid Galapagos Islands with those on humid South American mainland new species arose from ancestral forms by gradual accumulation of adaptations to a different environment 0 The birds had to be able to swim of y in order to get anywhere Break Variation in Galapagos Finches 0 According to Darwin adaptations were essential to the understanding of evolution 0 Fig 226 I finch adaptations centered on natural selection where individuals with certain inherited traits survived and reproduced successfully in particular environments because of those traits Descent with Modification by Natural Selection 0 Darwin never used the word evolution in the first edition of The Origin of Species 0 The phrase descent with modification summarized Darwin s perception of the unity of life 0 That all organisms are related through descent from an ancestor that lived in the remote past I Descendants gradually accumulated diverse modifications specific to their way of life Fig 227 8 I Descent with Modifications and Branching Patterns of Evolutions 0 Darwin AD modern organisms living today Fig 227 0 Unlabeled branches were extinct Fig 227 0 Forks most recent ancestor of all lines of evolution branching from that point Fig 227 0 Seven lines of relatives are extinct therefore no living spp to fill morphological gap between elephants and hyraxesmanatees Fig 228 Artificial Selection 0 Darwin was particularly interested in artificial selection used by farmers allowing desired traits to be artificially bred O Cabbage broccoli kale Brussel sprouts etc distinct members but same species 0 Darwin reasoned that if artificial selection could provide beneficial traits in species in a short period of time that natural selection would do the same over successive generations Darwin s Theory of Evolution was based on 0 Observation 1 members of a population species often vary in their inherited traits Fig 2210 0 Observation 2 all species are capable of producing more offspring than the environment can support but many of these offspring fail to survive and reproduce Fig 2211 From these observations Darwin inferred 0 Inference 1 individuals whose inherited traits give them a higher probability of surviving and reproducing in a given environment tend to leave more offspring than other individuals 0 Natural selection increases the adaptation of organisms to their environment over time e g Fig 2212 camou age 0 Inference 2 This unequal ability of individuals to survive and reproduce will lead to the accumulation of favorable traits in the population over generations Concept 223 Several examples provide direct evidence of evolution 0 Example 1 Soapberry bugs feed most effectively when beak length matches seed depth in fruit 0 Removal of natural food source due to rarity leads to adaptation 0 Fig 2213 I in sorthern Florida balloon vine has larger fruit bugs have larger beaks in central Florida balloon vines are rare so bugs have adapted S aureus esh eating bacteria became resistant to methicillin in 1961 2 years after it was first widely used 0 Fig 2214 I Methicillin inhibits a protein used by bacteria in their cell walls 0 Methicillin resistant Staph aureus MSRA use different protein in their cell walls 0 When exposed to methicillin MRSA strains are more likely to survive and reproduce than nonresistant Saureus strains 0 Further resistance is being reported 0 Resistant forms exchanging genes producing further resistance Example 2 Comparative Anatomy and Homology in Animals Fig 2215 0 Evidence for evolution can also come from closely related species that share similar features yet often function differently O Similarity resulting from common ancestry is homology 0 These represent variations on a structural theme present in their common ancestor Vestigial structures served important functions in organism s common ancestor 0 Fig 2216 I at some point during embryonic development all vertebrates have a postanal tail as well a pharyngeal arches related to descent from a common ancestor 0 All pythons have remnants of hindlimb bones embedded in their bodes waling ancestors Genetic similarities in a wide range of organisms re ect shared evolutionary history 0 Fig 2217 homologies from nested patterns in evolutionary trees relationships among different groups 0 E g lungfishes and all tetrapods descended from ancestor l 0 Supported by anatomical and DNA sequence data A different cause of resemblance convergent evolution 0 Convergent evolution is the evolution of similar or analogous features in distantly related groups 0 analogous traits arise when groups independently adapt to similar environments for similar reasons e g competitive survival 0 often seen as mimicry eg when a nonpoisonous snake looks like a poisonous one to evade predators 0 does not provide information about ancestry 0 Fig 2218 I the ability to glide through the air evolved independently in distantly related species Example 3 Fossils can document extinction of species the origin of new groups and changes within groups over time 0 Fig 2220 I fossils document the reduction over time in the pelvis and hind limb bones of extinct cetacean ancestors mammalian order including whales dolphins and porpoises 0 While DNA sequencing data supports the hypothesis that cetaceans whales etc are most closely related to hippos Example 4 Biogeography 0 Study of the geographis distribution of living organisms and fossils 0 Geographical distribution range affects organism s evolution 0 From center of origin each species spreads until a physical environmental or biological barrier halts it 0 Darwin concluded species from neighboring continent migrated or were carried to the Galapagos islands PANGEA Continental Drift also contributed to evolution Fig 2516 0 At one time land masses were joined but as tectonic plates moved continents changed their relative positions 1 1813 MICROEVOLUTION Variation 0 Phenotypic variation observable differences in individuals 0 either or determined by a single gene locus O vary in gradations along continuum I Ex Height I people come in all sizes I In uence of 2 or more genes to show a single character I Result of genetic information 0 Genetic 0 Differences among individuals in geneDNA composition 0 Sources I Mutation I Alterations in chromosome structure 0 Rapid reproductive I Plants and animals very infrequent 0 Approximately one mutation in every 100000 genes per generation I Prokaryotes 0 Higher rate of mutation because of higher production rate reproduce every 20 minutes I More genetic variation I Viruses 0 Sexual reproduction I genetic variation I Unique allele combinations from parents Population I group of potentially interbreeding organisms of the same species living in the same area and the same time 0 Population genetics I study of genetic variability in populations and all environmental forces that act on population 0 Allele 0 One of the two or more alternative forms of a gene 0 Located at loci on chromosomes 0 Gene pool I all alleles of all of genes in population at any one time 0 Diploid sp I Each locus present twice E E 3 I Homozygous or heterozygous 0 Fixed allele I one where all individuals in the population gene pool are homozygous for the same allele 0 Allele frequency I proportion of a specific allele in a particular population I Each allele has a relative frequency I Ex Hamster population I coat color using 2 alleles 0 If 12 alleles code of black than 12 alleles are brown I Frequent for black allele brown allele 50 5 0 Allele frequencies over generations EX Plant look at ower color I Phenotype red or white dom recessive 0 red AA or Aa white aa Cross two heterozygotes Aa X Aa Gametes I A a A a I In parents total number of alleles 4 I In offspring total number of alleles 8 I Over generations the allele frequencies do not change EX 500 plants with red or white owers I Genotype frequency 0 320 AA 64 O 160 Aa 32 O 20 aa 4 I At this locus number of alleles in population 1000 500 plants X 2 alleles I What are allele frequencies o o A a I 320 AA 0 640 0 0 160 Aa I 160 160 I 120 aa 0 0 40 0 Total I 800 200 O freqA 80 8 0 freqa 20 2 I Allele frequency of A and a in the next generation 0 Give gametes their relative allele frequencies 0 Know 80 are A and 20 are a O O 8 A 0 2a 0 8A 0 64 AA 0 16Aa 0 2A 0 16 AA 0 04Aa I freqAA 64 I freqAa 32 I freqaa 4 0 In our offspring generation out allele frequencies 0 Genetic Equilibrium Gene frequencies and allele frequency do NOT change from generation to generation Not undergoing evolutionary change are the same as our parent generation I Fig 237 and 238 I 1908 Godfrey Hardy and Wilhelm Weinberg HardyWeinberg Principle HW If a population is larger than process of inheritance by itself it doesn t cause changes in allele frequency Explains why dominant alleles are not necessarily more common than recessive alleles Describes genetics of population that are not evolving seldom occurs in natural world Gives us a baseline to base observations of frequent allele changes in a population mean or what makes them change HW equilibrium 0 Population frequencies of alleles and genotypes will remain constant over generations 0 As long as population mates randomly and not acted upon by outside agents HW equation 0 Allow to calculate the allele and gene frequency under HW equilibrium O P frequency of dominant allele in population 0 Q frequency of recessive allele in population 0 pq1 o o p o q 0 p O pquot2 O pq 0 q 0 pq 0 qquot2 I probAA pquot2 I probAa 2pq I probaa qquot2 I total frequency needs to 1 pquot2 2pq qquot2 1 0 Use the equation to calculate the expected frequency of phenotypes if we know the gene frequency or gene frequency if we know the alleles 0 Ex Parent generation I FreqA 7 p I Freqa 3 q I 7quot2 273 3quot2 1 Allele frequency I not altered by the process of inheritance alone 0 Frequency in gene pool remain constant unless they are acted upon by outside agents I Changes in allele frequency microevolution O Microevolution I shifts in relative allele frequency over successive generations I Small changes 0 Macroevolution I large scare evolutionary events over long time spans make different species 0 HW Conditions 5 conditions must be met I Cannot be any mutations 0 Random mating I No natural selection 0 Large population size I No gene ow I Represents genetics of ideal population NOT in nature I Mutation I any heritable change in DNA 0 Permanent and unpredictable 0 Immediately changes the gene pool 0 NOT all mutations are passed on to next generation I Somatic cell body cell I Neutral silent mutation doesn t change protein structure or function I If very harmful individual dies 0 Little effect on allele frequencies if only one individual 0 Source of genetic variation in a population I Over time may lead to change in population 0 Non random mating 0 Random mating I each individual in a population has an equal change of mating With individual of opposite sex 0 Non random mating I no random mixing of alleles or gametes 0 Inbreeding I mating of closely related individuals genetically similar individuals I Organisms With limited ability probably close relation I Does not change allele frequencies but it does increase the frequency of homozygous phenotypes AA or aa 0 No natural selection I mechanisms of evolution 0 HW assumption all individuals have an equal probability to produce viable fertile offspring O Rarely ever met the assumption 0 Variation of population exists I some more likely to produce and survive than others I Their alleles are going to be passed on I Differential success is reproduction 0 Alters allele frequency in next generation 0 Adaptive evolution only agent of microevolution that is adaptive 0 Genetic Drift I production of random evolutionary changes in small breeding population 0 In small populations a change event can alter allele frequencies I Ex 10 plants I 5 red 5 White 0 Yummy to cow Who eats three red plants by chance I Leads to drastic change in allele frequency I Ex 1000 plants I 500 red 500 white I Cow eats three red plants I has a much lower affect on allele frequency 0 Most natural populations are large I Genetic drift usually has little effect I Fig 239 0 Bottleneck effect I Fig 2310 I Size of population is drastically reduced by some uctuation in the environment ood fire earthquake and only a very small part of the population is most likely going to have a different gene composition of original population Fig 2311 0 Founder effect I If a few individuals from a population colonize a new habitat I most of the new population will have a new phenotype compared to the original parent 0 Gene ow 0 Movement of alleles between populations 0 Effect of migration of one individual to a different population I Reduces differences in a population Natural Selection I mechanism of evolution 0 Acts on the phenotype do your physical traits make you good enough to survive 0 Changes allele frequency in ways that are going to increase adaptation 0 Phenotypic variation 0 Different alleles O Morphs contrasting phenotypes 0 Phenogenic control 0 Rare that allele at single locus controls phenotype 0 More common to have an interaction of alleles at several loci I Creates the expression of phenotype 0 Range of phenotypes find that most of the population is going to be in the median range of phenotype I Fewer individuals at the other extreme I Ex Height I standard bell curve showing normal distribution and no natural selection I 3 types of selection change in normal distribution Fig 2313 0 Stabilizing I favors intermediates variants by selecting against extreme phenotypes I Selects against variability I Stable environment I Ex Human birth weight O Directional I favors the variants of one extreme I EX Beak size finches O Disruptive I opposite extreme favored over intermediates I Variable environmental conditions l l 12 l 3 MACROEVOLUTION AND SPECIATION Microevolution varieties within a given population or species members interbreed small changes occur genetic variation but descendant is clearly same type as ancestor Macroevolution major evolutionary changes over time the origin of new types species from preciously existing but different ancestral types can t interbreed Concept 241 Biological Species Concept and Reproductive Isolation 0 A biological species where members interbreed in nature and produce fertile offspring emphasizing differences between species 0 Emphasizes reproductive barriers preventing interbreeding Fig 242a 0 But excludes hybrids gene ow that can result from interbreeding 0 And excludes asexual organisms Other definitions emphasize similarities between species 0 The morphological Species concept defines sexual and asexual species based on similarity of structural features 0 The ecological species concept view sexual and asexual species in terms of similarities in ecological niches 0 The phylogenic Species concept defines sexual and asexual species as the smallest group of individuals that share a common ancestor on a phylogenetic tree Reproductive isolating mechanisms prevent interbreeding amongst different species 0 Restriction of gene ow by preventing breeding between two different species whose geographies overlap O Prezygotic barriers prevent fertilization from taking place in the first place 0 Postzygotic barriers prevent gene ow after fertilization has taken place Prezygotic Barriers Fig 243 0 Habitat isolation closely related species breed in different habitats in same geographic area 0 Ex two species of garter snake live in same geographical area but one in water and one terrestrial 0 Temporal Isolation two species reproduce at different times of day season or year 0 Ex Easter spotted skunk and western spotted skunk geographies overlap but eastern mates in last winter western in late summer 0 Mechanical Isolation incompatible structures in reproductive organs of similar species 0 Ex Snail shells swirl in different directions so genital openings aren t aligned and mating can t be completed 0 Behavioral Isolation distinctive courtship behaviors prevent mating between different species 0 Ex Galapagos bluefooted boobie dance blue foot high step attracts female and distinguishable species 0 Gametic Isolation gametes from different species are incompatible because of molecular and chemical differences 0 Ex Surface of sea urchin egg has specific receptors that bind to specific antigens on surface of sperm of same species Postzygotic Barriers Fig 243 0 When fertilization occurs but postzygotic barriers help to prevent a fruitful union leads to reduced hybrid fertility 0 Union of gametes with different chromosome numbers normally results in faulty meiotic synapsis and segregation 0 Male donkey 62 female horse 64 mule 63 strong but usually infertile further fruitful unions are prevented 0 Reduced hybrid viability gene interaction occurs but leads to impaired hybrid development or survival 0 Ex Few salamander subspecies hybrids complete development or are very frail 0 Hybrid Breakdown first generation hybrids are fertile and viable but mating leads to feeble or sterile offspring 0 Ex Accumulation of certain recessive genes in rice leads to small and sterile next generations Concept 242 Evolution of a species 0 Method 1 formation of two species from a single species as subpopulations become reproductively isolated and gene pools diverge O Allopatric speciation occurs as a result of geographic isolation O Sympatric speciation occurs in populations living in the same geographic area 0 Method 2 if speciation process is incomplete diverging populations can come into contact 0 A zone of overlap exists where interbreeding can take place hybrid zone separate from the parental zone Allopatric Speciation 0 Evolution of new species from ancestral population occurs via geographic isolation preventing gene ow separate gene populations evolve independently via mutation natural selection genetic drift 0 Fig 246 I O predatory fish head of mosquito fish is streamlined tail is powerful allowing bursts of speed 0 predatory fishes mosquito fish have a different body shape favoring long steady swimming Experimental Evidence of Allopatric Speciation Fig 247 0 In control group all raised on starch no mating preference 0 In experiment group starch ies mostly mated and maltose ies mostly mated 0 Indicating that a reproductive barrier was starting to form between y populations as a result of food adaptations or courtship patterns Allopatric Speciation in Nature Fig 248 0 These Alpheus shrimp are just 2 of 15 pairs of sister species that arose as populations were divided by formation of the Isthmus of Panama Sympatric Speciation 0 Can occur in populations that live in the same geographic area due to polyploidy 0 Allopolyploid a species with multiple sets of chromosomes derived from different species 0 Tetraploids can produce fertile tetraploid offspring 0 Autopolyploidy the individual contains more that two chromosome sets derived from one species as a result of self fertilization and failure of cell division usually accompanied by reduced fertility Allopolyploidy 0 A new primrose Primula kewensis arose in 1898 as an allopolyploid derived from the hybridization of P oribunda 2n18 and P verticillata 2n18 0 Spontaneously formed fertile allopolyploid species produced a 2n36 viable species Sympatric Speciation can arise through sexual selection and habitat differentiation in animals 0 Sexual selection for mates of different colors has likely contributed to speciation in cichlid fish in Lake Victoria 0 Mate choice based on male breeding coloration is the main reproductive barrier that normally keeps the gene pools of pundamilia pundamilia and p nyererei separate 0 Sympatric speciation can also occur when subpopulations exploit different habitats 0 NA apple maggot ies occupying different types of fruit trees Concept 243 Hybrid zones reveal factors that cause reproductive isolation 0 Hybrid Zone a region in which members of different species can mate and produce hybrids Fig 2413 Formation of a hybrid zone and possible outcomes for hybrids over time 0 Reinforcement reproductive barriers mean hybrids cease to be formed over time because less fit 0 Fusion two species fuse due to weak reproductive barriers and somehow become a single species 0 Stability where hybrids continue to be formed and selected for Concept 244 Speciation can occur rapidly or slowly from changes in few or many genes 0 Many questions remain concerning how long it takes for new species to form or how many genes need to differ between species 0 Broad patterns in speciation can be studied using the fossil record morphological data or molecular data 0 The fossil record includes examples of species that appear suddenly persist essentially unchanged for some time and then apparently disappear Patterns in the Fossil Record 0 In a punctuated model new species change most as they branch from a parent species and then change very little for the rest of their existence 0 Whereas in a gradual model species diverge from one another more slowly and steadily over time Studying the Genetics of Speciation 0 A fundamental question of evolutionary biology persists How many genes change when a new species forms Depends on species in question 0 In Japanese Euhadra snails the direction of shell spiral affects mating and is controlled by a single gene change provides a mechanical barrier 0 Fig 2419 I but in monkey owers Mimulus two loci affect ower color and mutation at a single locus can in uence pollinator preference Multiple Speciation leads to Macroevolution 0 Macroevolution is the cumulative effect of a speciation and extinction events 0 Speciation may begin with differences as small as the color on a cichlid s back 0 Many differences accumulate 0 New groups of organisms differ greatly from their ancestors I Ex Whales from terrestrial mammals hox genes I One group may increase by producing many new species 0 Sweeping differences accumulate 1 11513 PHYLOGENY AND THE TREE OF LIFE Phylogeny the evolutionary history of a species or group of related species produced using systematics the collection of fossil molecular and genetic data to infer evolutionary relationships I Independent evolution from a common ancestor I produced plants and humansfungi Concept 261 Phylogenies show evolutionary relationships I In order to understand evolutionary relationships we must first provide and ordered division and naming of organisms taxonomy O In 18th century Carolus Linnaeus published system of taxonomy based on resemblances 0 Two key features twopart names for species binomial and hierarchical classification placement into increasingly inclusive categories I Binomial genus first letter is capitalized a unique epithet I E g Panthera genus that includes all close relatives I Entire species name is italicized e g Panthera pardus leopard I Related genera are placed in one family similar families in one order etc Hierarchical Classification I Linnaeus introduced a system for grouping species in increasingly broad categories 0 The taxonomic groups from broad to narrow are domain kingdom phylum class order family genus and species 0 A taxonomic unit at any level of hierarchy is called a taxon 0 Doesn t re ect evolutionary history all the time 0 Larger categories are often not comparable between lineages Linking Classification and Phylogeny I Systematics depicts evolutionary relationships in branching phylogenic trees 6 g carnivora Fig 264 I Each branch point represents the divergence of two species 0 1 most recent ancestor of the weasel Mustelidae and dog Canidae families O 2 most recent common ancestor of coyotes and gray wolves I Coyotes and gray wolves share and immediate common ancestor and are therefore sister taxa I Systematists interpret a phylogenic tree as recognizing groups that include a common ancestor and all its descendants Fig 265 0 A rooted tree is where a branch point within the tree farthest to the left represents the most recent common ancestor of all taxa in tree 6 g 1 O A basal taxon diverges early in the history of a group and originates near the common ancestor of the group e g Taxon G O A polytomy is a branch from which more than two groups emerge Concept 262 Phylogenies are inferred from morphological data 0 Phenotypic and genetic similarities due to shared ancestry are called homologies O Organisms with similar morphologies or DNA sequences are likely to be more closely related than organisms with different structures or sequences I Bat and bird wings are 0 Homologous as forelimbs common ancestor was a tetrapod but couldn t y 0 But analogous ight was a homoplastic derived feature as functional wings I Homology can be distinguished from analogy by comparing fossil evidence the degree of complexity and a common ancestor 0 The more complex two structures are the more likely they are derived from a common ancestor e g adult chimp and human skulls match Sorting Homology from Analogy 0 When constructing a phylogeny systematics needs to distinguish whether a similarity is the result of homology or analogy O Homology is similarity due to shared ancestry O Analogy homoplasy is similarity due to convergent evolution 0 Fig 267 two molelike individuals with similar features Ancestor did not have these features 0 Convergent evolution occurs when similar environmental pressures and natural selection produces similar analogous adaptations in organisms from different evolutionary lineages Evaluating Molecular Homologies 0 Molecular systematics uses computer programs and mathematical tools to analyze comparable DNA segments from different organisms O Analogous and homoplastic few but similar sequences are coincidental and share lt25 of their bases 0 Homologous and share gt25 of bases computer programming can identify when many common sequences interrupted by a deletion but still homologous Concept 263 Cladistics groups nested in larger clades group organisms by common descent 0 A monophyletic grouping clade consists of the ancestor species and all its descendants This is also a taxon 0 A paraphyletic grouping consists of an ancestral species and some but not all of the descendants 0 Includes the most recent common ancestor 0 A polyphyletic grouping consists of various species with different ancestors 0 Does not include the most recent common ancestor Shared Ancestral and Shared Derived Characteristics I In comparison with its ancestor an organism has both shared and different characteristics 0 A shared ancestral character is a character that originated in an ancestor of the taxon I All mammals have backbones I But doesn t distinguish mammals from other vertebrates as all vertebrates have backbones O A shared derived character is an evolutionary novelty unique to a particular clade I Hair is a character shared by all mammals but not ancestors I When it s derived it s not necessarily common in ancestors 0 All relative as a backbone could also be a shared derived characteristic to distinguish vertebrates from all other animals Constructing a Phylogenic Tree Using Derived Characters 0 Fig 2612 If we look at 5 groups of vertebrates that share a common ancestor for a set of derived characteristics ingroup I And then compare them to another group that shares evolutionary relatedness chordates but diverged before the ingroup members no vertebrate outgroup I A phylogenic tree of relatedness can be constructed 0 Character tables 0 A 0 indicates that a character is absent while a 1 shows a character is present 0 Phylogenic tree 0 Distribution of derived characteristics can provide insight into vertebrate phylogeny Phylogenetic Trees with Proportional Branch Lengths I In some trees length of branch can re ect number of genetic changes that have taken place in particular DNA sequence in lineage I Fig 2613 Tree compares sequences of homologs of a gene that plays role in development 0 Drosophila outgroup 0 Branch lengths genetic change in each lineage varying branch lengths indicates a particular gene has evolved at different rates in different lineages I Drosophila has incurred more genetic changes in that particular sequence than the mouse or the human In other trees branch length can represent chronological time and branching points determined from the fossil record 0 Fig 2614 tree draws on fossil data to place branch points in context of geological time 0 Possible to combine these two types of trees by labeling points with information about rates of genetic change Evidence that birds descended from theropods bipedal dinosaurs The best hypothesis for phylogenetic trees is the one that fits the most data morphological molecular and fossil Phylogenetic bracketing allows us to predict and infer features of an ancestor from features of its descendants Closest liVing relatives of birds are crocodiles Birds are crocodiles share numerous features 4 chambered hearts singing build nests care for eggs by brooding sitting out shrouding by body Both have common ancestor With dinosaur 1 1 1 9 1 3 ANIMAL BEHAVIOR Overview The how and why of animal activity 0 A behavior is the nervous system s response to a stimulus and is carried out by the muscular andor the hormonal system 0 Can be regarded as any action of an organism that changes its relationship to its environment innate andor learned I Fig 511 Fiddler crabs feed with their small claw and wave their large claw 39 Claw waving is used to repel other males and to attract females Concept 511 Discrete sensory inputs can stimulate both simple and complex behaviors 0 Niko Tinbergen identified four questions that should be asked about animal behavior 0 What stimulus and alterations in physiology change behavior 0 How does an animal s experience during growth and development in uence a response I 1 and 2 are proximate causations or how a behavior occurs or is modified How does a behavior aid survival and reproduction 0 What is a behavior s evolutionary history 39 3 and 4 are ultimate causations or why a behavior occurs in the context of natural selection Fixed Action Patterns 0 A xed action pattern is a sequence of unlearned innate behaviors triggered by an external cue known as a Sign stimulus O In male stickleback fish the stimulus for attack behavior is the red underside of an intruder Fig 512 0 0 Once initiated that pattern is then carried to completion Migration and Behavioral Rhythms 0 Environmental cues trigger movement in a particular direction e g migration Animals can orient themselves using 0 Position of North Star 0 Magnetoreceptors microscopic grains of magnetite FeO FeZO3 to detect the earth s magnetic field especially when stars are obscured by clouds e g migrating birds 0 Position of sun and circadian clock behavioral rhythms internal 24 hour clock that is an integral part of nervous system daylight and darkness Animal Signals and Communication 0 A signal an action that causes change in another animal s behavior 0 Communication transmission and reception of a signal 0 Forms of animal communication visual chemical tactile auditory e g honeybees and the dance language Fig 515 VIDEO I Honeybees show complex communication with symbolic language 0 A bee returning from the field performs a waggle dance to communicate information Stimulus Response Chain Fruit Fly Courtship Fig 514 0 Orienting male fruit y identifies female of same species and orient towards her 0 Chemical communication smells female s chemicals in the air 0 Visual communication sees female orients body towards her 0 Tapping male alerts female to his presence 0 Tactile communication taps female with foreleg 0 Chemical communication confirms female s identity chemical smell 0 Singing male produces courtship song species specific 0 Auditory communication extends and vibrates wing 0 If all three steps are successful the female will allow the male to copulate BINGO Chemical Signals include Pheromones 0 Many animals communicate through pheromones 0 A female moth can attract a male from several kilometers 0 A honeybee queen produces a pheromone that affects development and then behavior of female workers male drones 0 When a minnowcatfish is injured by a predator an alarm substance in the fish s skin disperses in the water inducing a fright response among fish in the area 0 Effective at very low concentrations Fig 516 Concept 512 Learning establishes specific links between experience and behavior 0 Innate behavior doesn t vary among individuals instinctual 0 Fixed action patterns courtship stimulusresponse chain and pheromone signaling are developmentally fixed in response to a genetic cue 0 Innate behaviors are those you develop on your own which do not need to be taught or learned You are in essence born with the propensity to display the behavior In the case of Identical Twins 0 In humans twin studies allow researchers to compare the relative in uences of genetics and environment on behavior 0 Identical twins raised apart can be compared to those raised in the same household 0 Twins are less likely to have the same IQ if they are raised in different families I The easiest explanation is that genes are not everything the environment is important too 0 Used to study schizophrenia anxiety disorders and alcoholism Learning is the modification of innate behavior based on specific experiences 0 Imprinting a rapid learning process by which a newborn or very young animal establishes a behavior pattern of recognition and attraction to another animal of its own kind or to a substitute or an object identified as the parent Fig 517 0 When baby geese spent the first few hours of their life with Lorenz they imprinted on him as their parent 0 Young whooping cranes can imprint on humans in crane suits who then lead crane migrations using ultra light aircraft Spatial Learning and Cognitive Maps I Spatial learning based on experience with the spatial structure of the environment 0 Niko Tinbergen showed how digger wasps use landmarks to find nest entrances Fig 518 I Nest surrounded by pinecones I Moving ring of pinecones but not the nest digger wasp continue to track pinecones missing nest Associative Learning animals associate one feature of their environment with another I Operant conditioning an animal learns to associate one of its behaviors with a reward or punishment reward for erging 0 It is also called trialanderror learning 0 Fig 519 a bluej ay having digested and vomited a monarch butter y has probably learned to avoid this species Classical Conditioning an arbitrary stimulus is associated with a conditioned response training I For example a dog that repeatedly hears a bell before being fed will salivate in anticipation at the bell s sound Pavlov s dog Cognition and Problem Serving I Cognition is the process of conscious reasoning or thinking that may include awareness reasoning recollection and judgment 0 Honeybees can distinguish same from different Fig 5110 I Bees trained in a color maze were rewarded for choosing the same color as the stimulus I Bees tested in a pattern maze if previously rewarded for choosing same color most often chose lines oriented the same way as the stimulus 0 Problem solving is the process of devising a strategy to overcome an obstacle 0 For example chimpanzees can stack boxes in order to reach suspended food Development of Learned Behaviors 0 The learned behaviors previous occurred in a short period of time but development of some behaviors takes longer 0 Song learning a whitecrowned sparrow listens and memorizes the some of its species during an early sensitive period 0 The bird then learns to sing the song during a second learning phase O The song crystallizes now as the final song that the sparrow will sing Social Learning is learning through observation of others forms the roots of culture 0 Young chimpanzees learn to crack palm nuts with stones by copying older chimpanzees Fig 5111 I Vervet monkeys learn to give and respond to distinct alarm calls Fig 5112 I Culture can alter the behavior and fitness of individuals 0 Defined by everything from language religion cuisine social habits music Concept 513 Selection for individual survival and reproductive success can explain most behaviors I Behaviors that enhance efficiency of feeding and finding food foraging are modified by natural selection genetic variation 0 In Drosophila melanogaster variation in gene for in uences the foraging behavior in larvae Fig 5113 I Larvae in highdensity populations with gene allele for s tend to forage farther for food less competition I Larvae in lowdensity populations with gene allele for r tend to benefit more from foraging closer to home Optimal foraging model views foraging behavior as a compromise between benefits of nutrition and costs of obtaining food I A crow will drop a whelk a mollusk from a height to break its shell and feed on the soft parts I The crow faces trade off between 0 Height from which it drops the whelk 0 The number of times it must drop the whelk O Predatorprey relationship I Minimizes cost predator energy and maximized benefits nutrition Mating Behavior and Mate Choice 0 Mating behavior includes seeking or attracting mates choosing among potential mates competing for mates and caring for offspring O In many species mating is promiscuous with no strong pairbonds or lasting relationships but 0 Fig 5114 in monogamy one male mates with one female I Males and females with monogamous mating systems have similar external morphologies I Male maximized reproductive success by staying with mate and caring for chicks I Paternal certainty Polygamous relationships individuals of one sex mates with several sexually dimorphic phenotypically different individuals of other sex I In polygyny one male mates with many females Fig 5114 0 Males more showy and larger than females 0 Male maximizes his reproductive success by seeking additional mates I In polyandry one female mates With many males Fig 5114 0 Females are often more showy then males 0 Fertility assurance and often production of offspring with better phenotypes and abilities Mating Choice by Females 0 Female choice is a form of intersexual competition 0 Females can drive sexual natural selection by choosing males With specific behaviors or features of anatomy I For example female stalkeyed ies choose males With relatively long eyestalks Fig 5116 I Female zebra finch chicks who imprint on ornamented fathers are more likely to select ornamented mates Fig 5117 Mate Choice by Males I Male competition for mates is a form of intrasexual selection that can reduce variation among males 0 Competition may involve agonistic behavior an often ritualized contest that determines Which competitor gains access to a mate Fig 5120 Concept 514 Genetic analyses and the concept of inclusive fitness provide a basis for studying the evolution of behavior I A master regulatory gene can control many behaviors O A single gene fru controls male fruit y courtship rituals I Mutation no courtship 0 Coastal Western Garter Snakes feed on banana slugs Fig 5123 inland populations do not I Differences in diet due to response to odor of slugs 0 Multiple gene systems referred to as quantitative trait loci QTL affect behavior in humans I Alcoholism schizophrenia 0 Male prairie voles pairbond With their mates and help care for young I Mutation in ADH they do not care for young Fig 5222 Altruism I Natural selection favors behaviors that maximized an individual s survival and reproduction 0 These behaviors are often selfish O BUT on occasion some animal behaviors reduce their individual fitness but increase the fitness of others 0 This kind of behavior is called altruism or sel essness I For example in naked mole rat populations Fig 5125 non reproductive individuals may sacrifice their lives protecting their reproductive queen and kings from predators Altruism can be explained for inclusive fitness 0 Inclusive fitness is the total effect an individual has on proliferating its genes by producing its own offspring and also helping close relatives produce offspring 0 Natural selection favors altruism by enhancing reproductive success of relatives this is called kin selection 0 Fig 5127 like most mammals female Belding ground squirrels settle close to their sit of birth males settle at distant sites 0 Most females in a group are closely related to each other 0 Most alarm calls are given by females aiding close relatives Reciprocal Altruism 0 Altruistic behavior toward unrelated individuals can be adaptive if the aided individual returns the favor in the future 0 This type of altruism is called reciprocal altruism I Reciprocal altruism is limited to species With stable social groups Where individuals meet repeatedly and cheaters Who didn t reciprocate are punished 1 12213 POPULATION ECOLOGY Concept 531 Dynamic biological processes in uence population density dispersion and demographics 0 Population ecology is the study of a population group of individuals of a single species living in the same general area in relation to their environment on density number of individuals per unit of area or volume dispersion age structure and population size 0 Population density is the result of an interplay between processes that add individuals to a population birth immigration and those that remove individuals death emigration Patterns of Dispersion 0 Environmental and social factors in uence the spacing of individuals in a population dispersion 0 Fig 5343 clumped dispersion individuals aggregate in patches I A clumped dispersion man by in uenced by resource availability food 0 A uniform dispersion is one in which individuals are evenly distributed Fig 534b 0 It may be in uenced by social interactions such as territoriality e g the defense of a bounded space against other individuals during nesting sometimes aggressive 0 A random dispersion the position of each individual is independent of other individuals 0 It occurs in the absence of strong attractions or repulsions Fig 534c when dandelion seeds are blown randomly and germinate Demographics 0 Demography study of vital statistics of a population and how they change over time especially birth and death 0 Utilizes a life table and agespecific summary of the survival pattern of a population 0 Made by following fate of cohort of individuals of same age 0 Tb1531 life table of Belding s ground squirrels 0 Provides data on proportions of males and females alive at each age 0 While death rate is fairly constant females have a greater life expectancy than males A survivorship curve is a way of representing the same data in a life table 0 Survivorship curves can be classified into three general types Fig 536 0 Type 1 low death rates during early and middle life and an increase in death rates among older age groups 0 Type II a constant death rate over the organisms life span 0 Type 111 high death rates for the young those that survive have a lower death rate Reproductive Rates 0 For species with sexual reproduction demographers concentrate on females 0 A reproductive table fertility schedule is agespecific 0 It describes reproductive patterns of population 0 Varies greatly by species I Reproduce at age lyr continue for about 10 years with peaks in terms of output around 4 years of age I Human reproductive life is longer but peaks are more random Concept 532 Exponential model describes population growth in an idealized unlimited environment 0 Change in population size births immigrants deaths emigrants 0 If immigration and emigration are ignored a population s growth rate equals birth rate minus death rate 0 The population growth rate can be expressed mathematically as 0 AN At BD 0 Where AN is change in population size At is time interval B of births D of deaths Fig 538 Population growth can be predicted by exponential model J shaped curve 0 2 populations with different t inst rates of growth all have access to abundant food and free to reproduce at their physiological capacity unrealistic 0 Blue population larger is accumulating more individuals at a quicker rate I More births and deaths 0 Red population smaller also continues to accumulate individuals but at a slower rate I JFE5 3 2mm 39quot 1510 um Ii Fig 539 nga increase due l IIil a 9 u 10100 a iPapwlatlon slze M I 3 a i 5 1i is Numberoiigenerations o quot ri g39 is growth rate at a particular moment in time Concept 533 The logistic model describes how a population grows more slowly as it nears carrying capacity 0 Exponential growth cannot be sustained for long in any population 0 A more realistic population model limits growth by incorporating carrying capacity 0 Carrying capacity K is the maximum population size the environment can support 0 Carrying capacity varies with the abundance of limiting resources 0 Per capita person rate of increase declines as carrying capacity is reached The logistic model of population growth produces a sigmoid Sshaped curve 0 Adds an expression that reduces per capita rate of increase as N approaches K Engn nlilaul 2 m l growth ung d1 i P imp Lila liv ai IE hi EPupu a i an grumh imagine Elfowing hereI The Logistic Model and Real Populations 0 Fig 53113 The growth of laboratory populations of paramecia fits a Sshaped curve 0 If these organisms are grown in a constant environment lacking predators and competitors and with limited resources sshaped curve occurs birth slows will decline if deaths increase 0 Fig 5311b Some populations like Daphnia can overshoot if before becoming a relatively stable density 0 Because when food becomes limiting females can use their own various other energy reserves to keep reproducing 0 Some populations uctuate greatly and make it difficult to define K O Show an Allee effect where individuals have a more difficult time surviving or reproducing if the population size is too small e g lacking protection 0 The logistic model fits few real populations but is useful for estimating possible growth 0 Conservations biologists use model to estimate critical size below which populations may become endangered an even extinct like the white rhinoceros Fig 5312 Concept 534 Life history traits are products of natural selection 0 An organism s life history comprises the traits that affect its schedule of reproduction and survival 0 The age at which reproduction begins 0 How often the organism reproduces 0 How many offspring are produced during each reproductive cycle 0 Life history traits are evolutionary outcomes re ected in the development physiology and behavior of an organism Evolution and Life History Diversity 0 Some species exhibit iteroparity or repeated reproduction like humans to produce offspring 0 Fig 5313 Other species like the Agave tree exhibit semelparity or bigbang reproduction after growing and accumulating nutrients for years tree sends up stalk of seeds then dies 0 Highly variable or unpredictable environments favor bigbang reproduction while dependable ones favor repeated births Tradeoffs and Life Histories 0 When organisms are semelparous bigbang finite resources may lead to trade offs between survival and reproduction 0 If young prone to die early or suffer high predation will produce many small offspring 0 Fig 5314 the lower survival rates of kestrels with larger broods indicates that caring for more offspring negatively affects the survival of the parents 1 12713 Community Ecology Overview Communities in Motion 0 A biological community is an assemblage of populations of various species living close enough for potential interaction Concept 541 Community interactions are classified by whether they help harm or have no effect on the species involved 0 Ecologists call relationships between species in a community interspecific interactions 0 Strong competition can lead to competitive exclusion sometimes the local elimination of a competing species Competitive Exclusion 0 Gause s competitive exclusion principle two species competing for the same limiting resources cannot coexist in the same location permanently e g Green and Brown Anoles unless 0 Special where the two are found together the Green Anoles are more common on the vegetation and higher up while the Brown Anoles tend to occupy the ground and the tree trunks 0 Temporal golden spiny mouse is active during the day common spiny at night 0 Leads to resource partitioning differentiation of ecological niches enabling similar species to coexist in a community A species use of biotic and abiotic resources is called the species ecological niche 0 A species fundamental niche niche potentially occupied by species 0 A species realized niche niche actually occupied by species 0 As a result of competition a species fundamental niche may be considerably reduced 0 For example the presence of one barnacle species limits the realized niche of another 0 Fig 543 interspecific competition by Balanus makes the realized niche of Chthamalus much smaller than it s fundamental niche Character Displacement 0 Character displacement is a tendency for characteristics to be more divergent in sympatric geographically overlapping populations of two species than in allopatric geographically separate populations of the same two species 0 Fig 544 an example is variation in beak size between populations of two species of Galapagos finches when sympatric adapting to differentsized seeds via natural selection Predation interaction 0 Fig 545 0 Cryptic coloration or camou age makes prey difficult to spot 0 Animals with effective chemical defense often exhibit bright warning coloration called aposematic coloration O In Batesian mimicry a palatable or harmless species mimics an unpalatable or harmful model 0 In Miillerian mimicry two or more unpalatable species resemble each other Herbivory 0 Herbivory interaction refers to an interaction in which an herbivore eats parts of plants of alga 0 Fig 547 It has led to evolution of plant mechanical and chemical defenses e g toxins spines thorns cinnamon aversion odor and strychnine neurotoxin from tropical vine Strychnos toxifera 0 And similarly adaptations by herbivores sense of smell specialized teeth etc Symbiosis Parasitism 0 In parasitism interaction the parasite derives nourishment from another organism its host which is harmed in the process 0 Parasites that live within body of host are called endoparasites e g tapeworm O Parasites that live on external surface of host are ectoparasites e g ticks and lice 0 Some parasites change behavior of host which increases parasites fitness eg ticks weaken moose 0 Many parasites have a complex life cycle involving a number of hosts e g blood ukes O Worm lays eggs in blood vessels human eggs reach bladder the urinefeces contaminate water through snail new worm enters new human host Symbiosis Mutualism 0 Mutualism interaction is an interspecific interaction that benefits both species 0 Obligate where one species cannot survive without the other 0 Microorganisms in termites and ruminants digest cellulose 0 Mycorrhizae and plant roots 0 Cutter ants VIDEO 0 Facultative where both species can survive alone ant plant 0 Fig 543 Pugnacious ants feed on tree nectar I Attack anything touching the tree remove fungal spores small herbivores and debris near Acacia Commensalism and Facilitation 0 Commensalism one species benefits and the other is neither harmed nor helped O Commensal interactions are hard to document in nature because any close association likely affects both species 0 Fig 549 cowbirds and egrets feed on insects in grasses around herbivores which are unaffected by their presence 0 Facilitation or 0 one species has positive effects on another without directintimate contact 0 Fig 5410 black rush increases number of plant species living in marsh middle zones I By making soil less salty reducing evaporation shading soil surface I Transporting 02 into lower reaches Concept 542 Diversity and tropic structure characterize biological communities 0 In general a few species in a community exert strong control on that community s structure Two fundamental features of community structure are feeding trophic structure and organism vary 0 Species richness is the number of different species 0 Relative abundance is the proportion each species representing all individuals 0 Fig 5410 both communities have the same species richness 4 but less relative abundance of A in community 2 but community 1 has greater species diversity variety Determining number and abundance of a species in a community is difficult especially for small organisms 0 Shannon diversity Feeding and Trophic Structure 0 Trophic Structure is the feeding relationship between organisms in a community 0 Food chains link trophic levels from producers to top carnivores Fig 5414 energy and nutrients pass through trophic levels of a community I Decomposers feed at all levels 0 Food webs link food chains together Fig 5415 a who eats who 0 A species can weave into the web at more than one trophic level e g an omnivore like a fox complicating the food web 0 Food webs can be simplified by grouping species with similar trophic relationships into broad functional groups e g the 100 phytoplankton at the base of web eg Fig 5415 I Fig 5416 or by isolating a portion of a community that interacts very little with the rest of the community 0 A partial food web or sea nettles Limits on food chain length 0 The energetic hypothesis suggests that chain length is limited by inefficient energy transfer along the chain 0 For example a producer level consisting of 100 kg of plant material can only support about 10 kg of herbivore biomass and 1 kg of carnivore biomass 0 Fig 5417 by varying amount of leaf litter food for communities like microorganisms and insects in tree holes 0 As expected holes with the most litter and primary food supply producer level supported the longest food chains Species with a large impact on community structure 0 Certain species have a very large impact on community structure 0 Dominant species are those that are most abundant or have the highest biomass and exert powerful control over the occurrence of distribution of other species I Most competitive in exploiting resources I Most successful at avoiding predators I Invasive species typically introduced to a new environment by humans often lack predators or disease 0 For example sugar maples have a major impact on shading and soil nutrient availability in eastern North America this affects the distribution of other plant species Keystone Species and Ecosystem Engineers 0 Keystone species exert strong control on a community by their ecological roles or niches but they are not necessarily abundant in a community 0 Field studies of sea stars illustrate their role as a keystone species in intertidal communities prey on sea urchins mussels and other shellfish that have no other natural predation 0 Fig 5418 removal of sea star from ecosystem 0 Means mussel population explodes uncontrollably dominance and domincnt urchin population annihilates coral reefs by eating the coral algae 0 Fruit baths pollinators Ecosystem Engineers 0 Ecosystem engineers or foundation species cause physical changes in the environment that affect community structure 0 Fig 5419 beaver dams can transform landscapes on a very large scale 0 By felling trees building dams and creating ponds beavers can transform the environment and habitat BottomUp and TopDown Controls 0 Bottomup model of community organization proposes unidirectional in uence from lower to higher trophic levels 0 mineral nutrients determines community structure including abundance of primary producers 0 Topdown model trophic cascade model proposes control comes from the trophic level above O Predators control herbivores which in turn control primary producers 0 Combination of topdown and bottom up models used to control pollution biomanipulation O Preventing algal blooms and excess plant growth eutrophication Concept 543 Disturbance in uences species diversity and composition 0 A disturbance is an event that changes a community removes organisms from it and alters resource availability e g a fire 0 A high level of disturbance is the result of a high intensity and high frequency of disturbance and would exclude many slowgrowing species storm fire 0 Low levels of disturbance would allow dominant species to exclude less competitive species farmland I Most communities are constantly changing after being buffered by disturbances nonequilibrium model 0 The intermediate disturbance hypothesis suggests that moderate levels of disturbance can foster greater diversity than either high of low levels of disturbance O Invertebrate richness peaked in streams with intermediate frequencyintensity of ooding 0 Ecological succession is the sequential process of community and ecosystem changes after a disturbance 0 Primary succession occurs where no soil exists as succession begins eg volcanic island lichens and moss Galapagos 0 Secondary succession begins in an area where soil remains after a disturbance e g forested land cleared for farming a fire 0 Earlyarriving species and laterarriving species may be linked in one of three processes 0 Early animals can facilitate appearance of later species y making the environment favorable 0 They may inhibit the establishment of later species 0 Or tolerate later species but have no impact on their establishment Fig 5423 I Primary Succession 0 Primary succession on Glacial Bay was seen as the result of changes induced by the vegetation itself as a result of the slow increase in soil nitrogen and lowering pH Fig 5421 I Secondary Succession 0 The large scale fire in Yellowstone National Park in 1988 demonstrated that communities can often respond very rapidly to a massive disturbance 0 Became an example of a nonequilibrium community and secondary succession O ie constantly changing after a disturbance which cleared an existing community Human Disturbance 0 Humans have the greatest impact on biological communities worldwide 0 Human disturbances to communities usually reduces species diversity 0 Fig 5424 eg disturbance of the ocean oor by trawling the sea oor of northwestern Australia before top and after bottom Concept 545 Pathogens alter community structure locally and globally 0 Ecological communities are universally affected by pathogens which include diseasecausing microorganisms viruses viroids ad prions mad cow disease CJ syndrome human mad cow disease 0 Pathogens can alter community structure quickly and extensively coral reef communities decimation by whiteband disease unknown pathogen 0 Human activities have facilitated the transportation of pathogens around the world at unprecedented rates Community Ecology and Zoonotic Diseases 0 Zoonotic pathogens are transferred from other animals to humans e g avian u spread to domesticated birds and then to humans 0 The transfer of pathogens can be direct or through an intermediate species called a vector ticks lice mosquitos malaria bubonic plague etc 0 Many of today s emerging human diseases are zoonotic 0 Fig 5428 recent studies identified two species of shrew as the primary hosts of the pathogen Borrelia for Lyme disease 0 For which a therapeutic can be produced 12613 Ecosystems and the Biosphere An ecosystem consists of all organisms living in a community as well as abiotic factors e g weather with which they interact 0 Regardless of an ecosystem s size its dynamics evolve two main processes energy ow and chemical cycling 0 Energy ows through ecosystems cannot be recycled whereas matter cycles within them 0 Ecosystems range from a microcosm such as an aquarium or desert spring Fig 552 to a large area such as a lake or forest Concept 551 Physical laws govern energy ow and chemical cycling in ecosystems 0 Ecologists study the transformations of energy and matter within ecosystems 0 The rst law of thermodynamics energy cannot be created or destroyed only transformed 0 Therefore energy enters an ecosystem as solar radiation is conserved and is lost from organisms as heat 0 The second law of thermodynamics every exchange of energy increases the entropy disorder of the universe 0 In an ecosystem energy conversions are not completely efficient and some energy is always lost as heat Conservation of Mass 0 Chemical elements are continually recycled within ecosystems 0 Most elements are not gained or lost on a global scale 0 Although gained by or lost from a particular ecosystem I In a forest ecosystem most nutrients enter as dust of solutes in rainwater leached from rocks or obtained via nitrogen fixation I Loss occurs as elements return to the atmosphere or are dispersed via water or wind 0 So ecosystems are open systems absorbing energy and mass and releasing heat and waste products Energy Mass and Trophic Levels in ecosystems 0 First trophic level contains mainly photoautotrophs some chemoautotrophs that build molecules using light energy 0 Heterotrophs depend on the biosynthetic output of autotrophs 0 Energy and nutrients pass from Fig 554 0 Primary producers autotrophs Primary consumers herbivores Secondary consumers carnivores Tertiary consumers carnivores that feed on other carnivores Fig 553 Detritivores obtain energy from detritus nonliving organic matter 0 Decomposition connects all trophic levels 0000 Concept 552 Energy and other limiting factors control primary production in ecosystems 0 In most ecosystems primary production is amount of light energy converted to chemical energy by photoautotrophs during a given time period 0 Extent of photosynthesis production dictates an ecosystem s energy budget 0 Amount of solar radiation reaching Earth s surface limits photosynthetic organisms Gross and Net Production 0 Total primary production is known as the ecosystem s gross primary production GPP all producer organic material or biomass 0 Net primary production NPP is GPP minus what is then used by primary producers for respiration Therefore NPP new producer biomass availability 0 Tropical rain forests contribute significantly to GPP and have a high NPP grasslands are similar 0 Estuaries and coral reefs cover only 1 10th of that covered by the rain forest but have a relatively high NPP in those areas 0 Marine ecosystems are relatively unproductive per unit area but contribute a lot to global net primary production because of their vast volume phytoplankton etc Fig 556 Net ecosystem production NEP measure of total biomass accumulation during a given period e g in the ocean Fig 557 0 NEP determines whether an ecosystem is gaining or losing carbon over times 0 The release of 02 detected by sensors placed on oats by a system is therefore an indication that it is producing and therefore also storing C02 Primary Production in Aquatic Ecosystems 0 In marine and freshwater ecosystems both light and nutrients control primary production 0 Depth of light penetration and nutrients affect primary production in the photic zone of an ocean or lake surface layer of the ocean that receives sunlight 0 But more than light and nutrients limit primary production in geographic regions of the ocean and in lakes A limiting nutrient is the element that must be added for production to increase in an area most often macronutrients nitrogen and phosphorous 0 Table 551 0 Experiments in the Sargasso Sea in the subtropical Atlantic Ocean showed that reduced micronutrient iron also limited primary production 0 Fig 558 0 Nutrient enrichment experiments confirm that nitrogen was limiting for phytoplankton growth off the shore of Long Island New York Upwelling areas where deep nutrientrich waters circulate to the ocean surface in parts of oceans contributes to regions of high primary production 0 The addition of large amounts of nutrients to lakes has a wide range of ecological impacts nutrient availability determines marine primary production 0 Largest areas of coastal upwelling include 0 Atlantic Ocean 0 Along equator 0 Coastal waters off Peru California and part of West Africa Eutrophication 0 In some areas sewage runoff has caused eutrophication of lakes the over enrichment of water by nutrients such as nitrogen and phosphorous promoting primary producer cyanobacteria blooms growth 0 Primary producers die detritovores decompose them and deplete waters 0 oxygen which can lead to loss of most fish species 0 In lakes phosphorous promotes cyanobacterial growth more often than nitrogen O Phosphatefree detergents to improve water quality 0 Water shows difference between mesotrophic moderately enriched upper basin and eutrophic water lower basin Primary Production in Terrestrial Ecosystems 0 In terrestrial ecosystems temperature and moisture affect primary production on a large scale 0 Fig 559 a global relationship exists between net primary production and mean annual precipitation for terrestrial ecosystems 0 Includes evapotranspiration water transpired by plants and evaporated from an landscape Nutrient limitations especially P and N2 reduce primary production and lead to adaptations 0 Many plants form mutualisms with mycorrhizal fungi these fungi supply plants with phosphorous and other limiting elements 0 Others like Rhizobia fix N2 for a plant 0 Roots have root hairs that increase surface area allow access to water allowing exchange of H in the plant for minerals in the soil Concept 553 Energy transfer between trophic levels is typically only about 10 efficient 0 Secondary production of an ecosystem is the amount of chemical energy in food converted to new biomass during a given period of time 0 Fig 5510 only 33 116th of the potential energy of the leaf is secondary production new biomass for secondary consumer 0 Production ef ciency is low since 67 are used up in respiration 0 Caterpillar 33Jassimilated 100 or 33 0 Birds are mammals 13 insects and microbes 40 0 Assimilated food total energy that can be used for growth reproduction Trophic efficiency is percentage of production transferred from one trophic level to next usually about 10 0 Fig 5511 A pyramid of net production represents the loss of energy with each transfer in a food chain 0 Progressive loss of energy severely limits the abundance of toplevel carnivores that an ecosystem can support 0 Can lead to extinction Concept 554 Biological and geochemical processes cycle nutrients and water in ecosystems Fig 5514 0 Liquid water primary physical phase in which water is used 0 Summary 0 Oceans contain 97 of biosphere s water 2 in glaciers polar ice caps and 1 in lakes rivers and groundwater 0 Water moves by processes of evaporation transpiration condensation into clouds precipitation and movement through surface and groundwater The Carbon Cycle carbonbased organic molecules are essential to all organisms 0 Summary 0 Photosynthetic organisms convert C02 to organic molecules Used by heterotrophs C02 is released back into atmosphere via respiration Carbon reservoirs I Burning fossil fuels soils and sediments aquatic organic matter I Dissolved in oceans I Plant and animal biomass I Sedimentary rocks limestone O Volcanoes also contribute C02 to the atmosphere The Nitrogen Cycle nitrogen is a component of amino acids proteins and nucleic acids 000 0 Summary 0 Main reservoir of nitrogen is atmospheric 78 N2 gas 0 For plants to uptake nitrogen must first be converted to NH4 ammonia I Via bacterial nitrogen fixation I decomposition of organic nitrogen to NH4 by ammonification bacteria 0 Then NH4 is decomposed to N03 nitrate by nitrification 0 N03 then taken up by plants 0 Denitrification converts N03 back to N2 released into the atmosphere The Phosphorous Cycle phosphorous is a major constituent of nucleic acids phospholipids and ATP 0 Summary 0 Phosphate P04quot3 is the most important inorganic form of phosphorous O The largest reservoirs are sedimentary rocks of marine origin weathering the oceans upwelling and organism decomposition 0 Actions return phosphate back to the soil or water 0 Phosphate binds With soil particles so recycling and movement is often localized Decomposition and Nutrient Cycling Rates 0 Detritivores decomposition rate of organic matter is controlled by temperature Fig 5515 moisture and nutrient availability 0 In a tropic rain forest warm decomposition is rapid I Most nutrients are tied up in trees and other living organisms I Very little organic material on the forest oor 0 In temperate forests opposite colder decomposition slower more organic material stays in soil Concept 555 Restoration ecologists help return degraded ecosystems to a more natural state I Given enough time biological communities can recover from many types of disturbances 0 Restoration ecology seeks to initiate or speed up the recovery of degraded ecosystems 0 Fig 5527 a gravel and clay mine site in New Jersey 0 A in 1991 before restoration 0 B in 2000 near completion of restoration Bioremediation 0 Biological argumentation uses organisms to add essential materials to a degraded ecosystem O Nitrogenfixing plants rhizobia and mycorrhizal fungi helping plants to access nutrients from soil 0 Bioremediation use of organisms to detoxify ecosystems O Organisms most often used prokaryotes fungi or plants I Lichens can take up metabolize and concentrate toxic molecules in tissues coloration can be used as a monitor of bioremediation nee 0 Fig 5518 shewanella oneidensis can metabolize uranium and other elements to insoluble forms that are less likely to leach into streams and groundwater


Buy Material

Are you sure you want to buy this material for

75 Karma

Buy Material

BOOM! Enjoy Your Free Notes!

We've added these Notes to your profile, click here to view them now.


You're already Subscribed!

Looks like you've already subscribed to StudySoup, you won't need to purchase another subscription to get this material. To access this material simply click 'View Full Document'

Why people love StudySoup

Bentley McCaw University of Florida

"I was shooting for a perfect 4.0 GPA this semester. Having StudySoup as a study aid was critical to helping me achieve my goal...and I nailed it!"

Amaris Trozzo George Washington University

"I made $350 in just two days after posting my first study guide."

Steve Martinelli UC Los Angeles

"There's no way I would have passed my Organic Chemistry class this semester without the notes and study guides I got from StudySoup."


"Their 'Elite Notetakers' are making over $1,200/month in sales by creating high quality content that helps their classmates in a time of need."

Become an Elite Notetaker and start selling your notes online!

Refund Policy


All subscriptions to StudySoup are paid in full at the time of subscribing. To change your credit card information or to cancel your subscription, go to "Edit Settings". All credit card information will be available there. If you should decide to cancel your subscription, it will continue to be valid until the next payment period, as all payments for the current period were made in advance. For special circumstances, please email


StudySoup has more than 1 million course-specific study resources to help students study smarter. If you’re having trouble finding what you’re looking for, our customer support team can help you find what you need! Feel free to contact them here:

Recurring Subscriptions: If you have canceled your recurring subscription on the day of renewal and have not downloaded any documents, you may request a refund by submitting an email to

Satisfaction Guarantee: If you’re not satisfied with your subscription, you can contact us for further help. Contact must be made within 3 business days of your subscription purchase and your refund request will be subject for review.

Please Note: Refunds can never be provided more than 30 days after the initial purchase date regardless of your activity on the site.