BSC 121 Lecture Notes
BSC 121 Lecture Notes Bsc121
Popular in General Biology
Popular in Biological Sciences
This 111 page Bundle was uploaded by Amber bryant on Sunday September 20, 2015. The Bundle belongs to Bsc121 at Marshall University taught by Dr. Axel in Summer 2015. Since its upload, it has received 116 views. For similar materials see General Biology in Biological Sciences at Marshall University.
Reviews for BSC 121 Lecture Notes
Same time next week teach? Can't wait for next weeks notes!
-Ms. Raphaelle Sawayn
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: 09/20/15
1 2 3 4 5 6 7 Biology Notes Ch1 1 Cells are the simplest unit of life 2 3 4 5 6 7 Living organisms use energy Living organisms interact with their environment Living organisms maintains homeostasis Living organisms grow and develops The genetic material provides a blue print for reproduction DNA Organisms evolves over generations 8 All species related by evolutionary history 9 Structure determines function 10 New properties of life emerges from complex interactions 11 Biology is an experimental science 12 Biology affects our society Seven Ch cterislics of Life Cells and organization Energy use and metabolism Regulation and homeostasis Response to environmental changes Growth and development Reproduction Biological evolution diversity Figure 14 M cells and organization simplest unit of organization M energy use and metabolism photosynthesis M regulation and homeostasis stable internal conditions M growth and development characteristics Dolphin reproduction offspring genetics Anteater biological evolution everything evolves Living organisms interact with their environment Levels of Biological Organization 1 Atoms 6 Organism 2 Molecule 7 Population 3 Cells 8 Community 4 Tissues 9 Ecosphere 5 Organs 10 Biosphere 0 Four different tissues makes up the heart Unitv and Diversity of Life Unity all life displays a common set of characteristics 0 Diverse forms of life in diverse environments Themes Form fits the function and efficient forms of that function well are conserved gt Structure fits function 0 Trees function of branches is surface area to catch sunlight 0 Needs a lot of energy Evolutionary History 0 Helps us understand the structure and function of an organisms body 0 Involves modifications of characteristics in preexisting populations 0 Structures may be modified to serve new purposes Two Mechanisms of Evolutionary Change 1 Vertical with modification 0 Progression of changes in a lineage 0 New species evolve mutation 0 Natural selection takes advantage of beneficial mutations Mutations in chromosomes evolution 2 Horizontal Gene Transfer 0 Genetic exchange between different species 0 Relatively rare Genomes and Proteomes Genome the entire genetic makeup of an organism Evolutionary history and relatedness of all living organisms can be illuminated by genome analysis Genomics Technique used to analyze DNA sequences in genomes Viruses are one of the smallest genomes Proteomes complete compliment of proteins that a cell or organism can make The genome carries the information to make its proteome Proteomics Used to analyze the proteome of a single species Biotechnology Application Chrystal jellyfish is bioluminescent Makes green orescent protein GFP Gene for GFP is the jellyfish genome GFP only expressed as part of the protein GFP forms glowing spots Biologv as a Scientific Discinline Observation identification investigation explanation Scientific method is used to test hypothesis and theories Some scientists gathers information also Discoverv Based Science Collection and analysis of data Without the need for a preconceived hypothesis 0 Goal is to gather information 0 Often leads to hypothesis testing Hypothesis prediction and explanation that you have observed testable 0 Never 100 proven Hypothesis Testin2 Scientj c Method Observation Hypothesis TestingExperiment controlexperimental group Analyze data Acceptrej ect hypothesis Not significantly different then you reject the hypothesis 39M ePPr Theory 0 Broad explanation of major aspects of the natural world 0 Makes predictions 0 Never be proven true Two Kev Attributes of a Theory 1 Consistency With a vast amount of known data 2 Ability to make many correct predictions Class of Organisms Taxonomy grouping species common ancestry 1 Bacteria unicellular prokaryote 2 Archaea unicellular prokaryote 3 Eukaryote unicellular to multicellular 4 Kingdoms Protista fungi plantae and animalia Domain largest taxonomy group Species more specific Biology Notes Ch Biology 0 Based on the principles of chemistry and physics 0 All living organisms are a collection of atoms and molecules 0 All forms composed of matter 0 Anything that contains mass and occupies space Atoms Smallest units of matter that form all chemical substances Cannot be further broken down into other substances by ordinary chemical or physical means 0 Each specific type of atom is a chemical element Three Subatomic Particles 1 Protons positive found in the nucleus same number as electrons 2 Neutrons neutral found in the nucleus number can vary 3 Electrons negative found in orbitals same number as protons Entire atom has no net electric charge Electrons OCCuDV Shells 0 Scientists initially visualize an atom as a mini solar system 0 This is an oversimplified but convenient image 0 Electrons travel Within regions surrounding the nucleus shells in which the probability is high of finding that electron Atoms With progressively more electrons have electron shells that are at greater and greater distances from the center of the nucleus 0 1St Shell Holds up to 2 electrons 0 2nd Shell can hold up to 8 electrons Nitrogen Example 0 A nitrogen atom has seven protons and seven electrons 0 2 electrons fills the 1st shell 0 5 electrons fills the 2rld shell 0 Outer 2nd shell is not full 0 Electrons in the outer shell that are available to combine with other atoms are called the valence electrons Octet Rule Atoms are stable when their outer shell is full Periodic Table 0 Organized by atomic number 0 Rows correspond to number of electron shells 0 Columns from left to right indicates the numbers of electrons in the outer shell 0 Similarities of elements within a column occur because they have the same number of electrons in their outer shells and therefore they have similar chemical bonding properties Atomic Mass 0 Protons and neutrons are nearly equal in mass and both are more than 1800 times the mass of an electron 0 Most common form of carbon has six protons and six neutrons is assigned an atomic mass of exactly 12 O A hydrogen atom has an atomic mass of 1 indicating that is has 1 12 the mass of a carbon atom O A magnesium atom with an atomic mass of 24 has twice the mass of a carbon atom Isotopes 0 Multiple forms of an element that differ in the number of neutrons 0 12C contains 6 protons and 6 neutrons 0 14C contains 6 protons and 8 neutrons 0 Atomic masses are averages of the weights of different isotopes of an element Units Dalton 0 Unit of measurement for atomic mass 0 Also known as atomic mass unit amu 0 Carbon has an atomic mass of 12 Daltons 0 1 mole of any element contains the same number of atoms 6022 X 1023 0 Avogadro s number Hvdrogen Oxvgen Cgrbon and Nitrogen Typically make up about 95 of the atoms in living organisms 0 Hydrogen and oxygen occur primarily in water 0 Nitrogen is found in proteins 0 Carbon is in the building block of all living matter Mineral elements less than 1 Trace elements less than 001 0 Essential for normal growth and function Chemical Bonds and Molecules Molecule 0 2 or more atoms bonded together Molecular Formula 0 Contains chemical symbols of elements found in a molecule 0 Subscript indicates how many of each atom are present 3 Types of Bonds Covalent 0 Polar Covalent 0 Nonpolar Covalent Hydrogen Ionic Covalent Bonds Atoms share a pair of electrons Occurs between atoms whose outer electron shells are not full Covalent bonds are strong chemical bonds because the shared electrons behave as if they belong to each atom Can share 0 1 pair of electrons single bond HF 0 2 pairs of electrons double bond 00 0 3 pairs of electrons triple bond w Atoms are stable when their outer shell is full For many atoms the outer shell fills with 8 electrons One exception is hydrogen which fills its outer shell with 2 electrons Polar Covalent Bonds When two atoms with different electronegativities form a covalent bond the shared electrons are more likely to be in the outer shell of the atom of higher electronegativity rather than the atom of lower electronegativity Polar covalent bonds occur because the distribution of electrons around the atoms creates a polarity or difference in electric charge across the molecule Electronegativity Prosperity for an atom to attract electrons OxygengtNitrogengtCarbongtHydrogen Oxygen is the most electronegative Water p x Classic example of polar covalent bonds Electrons tend to be in the more electronegative oxygen atom rather than either of the less electronegative hydrogen atoms Molecule has a partial negative charge region and a partial positive charge region Nonnolgr Covalent Bonds Bonds between atoms with similar electronegativities Equal sharing of electrons Hydrogen Bonds Hydrogen atom from one polar molecule attracted to an electronegative atom Represented as dashed or dotted lines Collectively strong bond overall 0 Holds DNA strands together Individually weak bonds can form and break easily Ionic Bonds An ion is an atom or molecule that has gained or lost one or more electrons 0 Now has a net electric charge Cations net positive charge Anions net negative charge Ionic bonds occurs when a cation binds to an anion 3 Types of Bonds Covalent Strongest Bond Hydrogen Weakest Bond Ionic Intermediate Strength Properties of Water A solution is made up of O Solvent liquid 0 Solutes substances dissolved in solvent Aqueous solution water is a solvent Ions and molecules that contain polar covalent bonds will dissolve in water Hydrophilic waterloving O Readily dissolve in water 0 Molecules that contain ionic andor polar covalent bonds Hydrophobic waterfearing 0 Do not readily dissolve in water 0 Nonpolar molecules like hydrocarbon Amphipathic molecule 0 Have both polarionized and nonpolar regions 0 May from micelles in water Polar hydrophilic regions at the surface of the micelle Nonpolar hydrophobic ends are oriented toward the interior of the micelle m Concentration 0 Amount of solute dissolved in a unit volume of solution 0 1 gram of NaCl was dissolved in 1 liter of water 1 gL Molarity 0 Number of moles of a solute dissolved in 1 L of water 0 1 mole of a substance is the amount of the substance in grams equal to its atomic or molecular mass H20 in 3 States of Matter Solid Ice liquid water and gas water vapor Changes in state such as changes between the solid liquid and gas states of H20 involve an input or release of energy 0 Heat of vaporization high specific heat 0 Heat of fusion Water is extremely stable as a liquid Colligative Properties of Water Temperature at which a solution freezes in uenced by amounts of dissolved solutes Addition of solutes to water lowers its freezing point below 0 degrees Celsius and raises its boiling point about 100 degrees Celsius Some animals produce antifreeze molecules that dissolve in their body uids thereby lowering the freezing point of the uids and preventing their blood and cells from freezing in the extreme cold Not Just a Solvent Water has many important functions in living organisms 0 Participants in chemical reactions I Hydrolysis or dehydration condensation Provides force or support Removes toxic waste components Evaporative cooling Cohesionadhesionlubrication Surface tension OOOOO Acids and Bases Pure water has the ability to ionize to a very small extent into hydrogen ions H and hydroxide ions OH In pure water HOH 10quot7 M 10quot7 M 10A14 M Acids are molecules that release hydrogen ions in solution 0 A strong acid releases more H than a weak acid Bases lower the H Concentration 0 Some release OH 0 Others bind H E pH log 10 H Acidic solutions are pH 6 or below pH 7 is neutral Alkaline solutions are pH 8 or above The pH solution can affect O The shapes and functions of molecules 0 The rates of many chemical reactions 0 The ability of two molecules to bind to each other 0 The ability of ions or molecules to dissolve in water Buffers Organisms usually tolerate only small changes in pH Buffers help to keep a constant pH An acidbase buffer system can shift to generate or release H to adjust for changes in pH CO 2 H20 lt gt H2CO3 lt gt H HCO 3 1 2 3 4 Chapter 3 Biology Notes Organic Chemistry Organic molecules contain carbon Abundant in living organisms Macromolecules are large complex organic molecules m 0 Carbon has 4 electrons in its outer shell Needs 4 more electrons to fill the shell It can make up to 4 bonds 0 Usually single or double bonds 0 Molecules With nonpolar bonds like hydrocarbons are poorly water soluble O Molecules With polar bonds are more water soluble Functional Groups Groups of atoms With special chemical features that are functionally important Each type of functional group exhibits the same properties in all molecules in which it occurs Four Maior Types of Organic Macromolecules Carbohydrates Lipids Proteins Nucleic Acids mcromolecules Synthesis vs Degradation Condensation or dehydration reaction 0 Links monomers to form polymers Hydrolysis 0 Polymers broken down into monomers Carbohydrates Composed of carbon hydrogen and oxygen atoms 0 Most of the carbon atoms in a carbohydrate are linked to a hydrogen atom and a hydroxyl group Monosaccharide 0 Simplest sugars 0 Most common are 5 or 6 carbons O Pentose ribose deoxyribose 0 Hexose glucose C6 H12 06 0 Different ways to depict structures 0 Ring or linear Disaccharides 0 Carbohydrates composed of two monosaccharides 0 Joined by dehydration or condensation reaction 0 Glyosidic bond 0 Broken apart by hydrolysis 0 Examples sucrose maltose lactose Polvsacchgrides 0 Many monosaccharides linked together to form a long polymers 1000s of monomers 0 Examples 0 Energy storage starch glycogen 0 Structural role cellulose chitin Li ids 0 Composed predominantly of hydrogen and carbon atoms 0 Defining feature of lipids is that they are nonpolar and therefore very insoluble in water Fats 0 Also known as triglycerides or triacylglycerol 0 Formed by bonding glycerol to three fatty acids 0 Joined by condensation reaction 0 Broken apart by hydrolysis 0 Fatty acids 0 Saturated all carbons are linked by a single covalent bond I Tend to be at room temperature 0 Unsaturated contain one or more double bonds I Tend to be liquid at room temperature oils I Cis forms naturally I Trans formed by synthetic process disease link Phospholipids I Glycerol 2 fatty acids and a phosphate group 0 Amphipathic molecule 0 Phosphate region polar hydrophilic head 0 Fatty acid chain nonpolar hydrophobic tail Steroids 0 Four interconnected fused rings of carbon atoms 0 Usually not very water soluble 0 Cholesterol 0 Tiny differences in chemical structure can lead to profoundly different biological properties 0 Estrogen vs testosterone Proteins I Composed of carbon hydrogen oxygen nitrogen and small amounts of other elements notably sulfur 0 Amino acids are the monomers 0 Common structure With variable Rgroup O 20 amino acids 0 Sidechain determines structure and function 0 Joined by dehydration or condensation reaction 0 Peptide bond 0 Forms polypeptidesprotein 0 Broken apart by hydrolysis Protein Structure 0 Primary 0 Amino acid sequence 0 Determined by genes 0 Secondary 0 Chemical and physical interactions cause folding O Repeating patterns 0 A helices and B pleated sheets I Key determinants of a protein s characteristics 0 Random Coiled Regions I Not on helix or B pleated sheet I Shape is specific and important to function 0 Tertiary 0 Folding gives complex threedimensional shape 0 Final level of structure for single polypeptide chain 0 Quaternary 0 Made up of 2 or more polypeptides I Protein Subunits Individual polypeptides I Multimeric Proteins Proteins With multiple parts 4 Main Factors Promotin2 Protein Folding and Stability 1Hydrogen Bonds 2 Ionic Bonds 3 Hydrophobic Effects 4Disulfide Bridges ProteinProtein Interactions Many cellular processes involve steps in Which two or more different proteins interact With each other Specific binding at surface of each protein Mainly use 3 types of bonds 1 Hydrogen Bonds 2 Ionic Bonds 3 Hydrophobic Bonds Nucleic Acid Responsible for the storage expression and transmission of genetic information Two Classes 0 Deoxyribonucleic Acid DNA I Store genetic information encoded in the sequence of their monomer building blocks 0 Ribonucleic Acid RNA I Involved in decoding this information into instructions for linking together a specific sequence of amino acids to form polypeptide chain Monomer is a nucleotide 0 Made up of phosphate group a fivecarbon sugar either ribose or deoxyribose and a single or double ring of carbon and nitrogen atoms known as a base Monomers linked into polymer With a sugarphosphate backbone phosphodiesterase bond Biology Notes Chapter 4 Cell Theor 1All living organisms are composed of one or more cells 2 3 Cells are the smallest unit of life New cells come only from preexisting cells by cell division Cell Biology The study of individual cells and their interactions with each other Microscopy Magnification 0 Ratio between the size of an image produced by a microscope and its actual size Resolution 0 Ability to observe two adjacent objects as distinct from one another Contrast 0 How different one structure looks from another enhanced by dyes Two Groups of Microscopes based on Source of Illumination Light Microscope 0 Uses light for illumination 0 Resolution 02 pm Electron Microscope 0 Uses an electron beam 0 Resolution nm Life All life can be placed into 2 categories based on cell structure 1Prokaryotes 2Eukaryotes Typical Bacterial Cell Plasma Membrane barrier Cytoplasm contained inside plasma membrane Nucleoid region where genetic material found Ribosomes involved in protein synthesis Many structures are located outside the plasma membrane 0 Cell Wall support and protection 0 Gycocalyx traps water protection 39 Capsule may help invade immune system 0 Appendages pili attachment agella locomotion Eukaryotic Cells DNA housed inside the cell Eukaryotic cells exhibit compartmentalization Organelle membrane bound compartment with its own unique structure and function Shape size and organization of cells vary considerably among different species and even among different cell types of the same species Cytoskeleton Network of three different types of protein filaments Microtubu1es 0 Long hollow cylindrical structures 0 Dynamic instability Intermediate Filaments 0 Intermediate in size 0 Form twisted rope1ike structure Actin Filaments 0 Also known as microfilaments 0 Long thin fibers 0 Dynamic instability Motor Proteins Category of cellular proteins that use ATP as a source of energy to promote movement Three different kinds of movement 0 Motor protein moves the cargo from one location to another 0 Motor protein can remain in place and cause the filament to move 0 Motor protein attempting to move but is restricted in their movement exerts a force that causes the filaments to bend Flagella and Cilia Both Microtubules Flagella are usually longer than cilia and present singly or in pairs Cilia are often shorter than agella and tend to cover all or part of the surface of a cell Endomembrane Svstem Network of membranes enclosing the nucleus endoplasmic reticulum Golgi apparatus lysosomes and vacuoles Also includes plasma membrane May be directly connected to each other or pass materials via vesicles Nuclear Envelone Doublemembrane structure enclosing nucleus Outer membrane of the nuclear envelope is continuous with the endoplasmic reticulum membrane Nuclear pores provide passageways Materials within the nucleus are not part of the endomembrane system Nucleus Chromosomes O Composed of DNA and protein chromatin Nuclear Matrix 0 Filamentous network 0 Organizes chromosomes Ribosomes assembly occurs in the nucleolus Translation Process of protein synthesis Information within a gene is ultimately translated into the sequence of amino acids in a protein Ribosome site of synthesis Transfer RNA tRNA brings amino acids Messenger RNA mRNA information to make a protein Endonlgsmic Reticulum Network of membranes that form attened uidfilled tubules or cisternae ER membrane encloses a single compartment called ER lumen Rough endoplasmic reticulum rough ER 0 Studded with ribosomes O Involved in protein synthesis and sorting Smooth endoplasmic reticulum smooth ER 0 Lack ribosomes O Detoxification carbohydrate metabolism calcium balance synthesis and modification of lipids Golgi apparatus Also called the Golgi body Golgi complex or simply Golgi Stacked of attened membranebounded compartments Vesicles transport materials between stacks Three overlapping functions 0 Secretion processing and protein sorting Plasma Membrane Boundary between the cell and the extracellular environment Functions 0 Membrane transport in and out of cell 39 Selectively permeable 0 Cell signaling using receptors 0 Cell adhesion Lysosomes Contain acid hydrolases that perform hydrolysis Enzymes are biological molecules proteins that act as catalysts and perform many complex chemical reactions like dehydration or hydrolysis Many different types of hydrolases to break down proteins carbohydrates nucleic acids and lipids Autophagy 0 Recycling of wornout organelles through endocytosis Defects in lysosomes cause lysosomal storage diseases Vacuoles Functions of vacuoles are extremely varied and they differ among cell types and even environmental conditions Central vacuoles in plants for storage and support Contractile vacuoles in protists for expelling excess water Phagocytic vacuoles in protists and White blood cells for degradation Peroxisomes General function to catalyze certain reactions that break down molecules by removing hydrogen or adding oxygen Byproduct of reaction is H202 Catalase breaks down H202 into water and oxygen Semigutonomous Organelles Can grow and divide to reproduce themselves but they are not completely autonomous because they depend on other parts of the cell for their internal components Mitochondria and chloroplasts Mitochondria Primary role is to make ATP Outer and inner membrane 0 Intermembrane space and mitochondrial matrix Also involved in the synthesis modification and breakdown of several types of cellular molecules Contain their own DNA divide by binary fission Chloroplasts Photosynthesis 0 Capture light energy and use some of that energy to synthesize organic molecules such as glucose Found in nearly all species of plants and algae Outer and inner membrane With an intermembrane space and a thylakoid membrane Contain their own DNA divide by binary fission Biology Notes Chapter 5 Biological Membranes Framework of the membrane is the phospholipid bilayer Phospholipids are amphipathic molecules 0 Hydrophobic waterfearing region faces in O Hydrophobic waterloving region faces out Membranes also contain proteins and carbohydrates 0 Relative amount of each vary FluidMosaic Model Membrane is considered a mosaic of lipid protein and carbohydrate molecules Membrane exhibits properties that resemble a uid because lipids and proteins can move relative to each other Within the membrane Protein Bound to Membranes Integral or intrinsic membrane proteins 0 Transmembrane proteins l One or more regions that are physically embedded in the hydrophobic region of the phospholipid bilayer 0 Lipidanchored protein 39 Covalent attachment of a lipid to an amino acid side chain Within a protein Peripheral membrane or extrinsic proteins 0 Noncovalently bound to regions of integral membrane proteins that project out from the membrane or they are bound to the polar head groups of phospholipids Approximatelv 25 of All Genes Encode Membrane Proteins Membranes are important biologically and medically Computer programs can be used to predict the number of membrane proteins Estimated percentage of membrane proteins is substantial 2030 of all genes may encode membrane proteins This trend is found throughout all domains of life including archaea bacteria and eukaryotes Functions of many genes unknown study may provide better understanding and better treatments Membranes and Semi uid Fluidity individual molecules remain in close association yet have the ability to readily move Within the membrane Semi uid most lipids can rotate freely along their long axes and more laterally Within the membrane lea et Flip op of lipids from one lea et to the opposite lea et does not occur spontaneously 0 Flippase requires ATP to transport lipids from one lea et to another ctors Affectin2 Fluiditv Length of fatty acyl tails O Shorter acyl tails are less likely to interact Which makes the membrane more uid Presence of double bonds in the acyl tails 0 Double bond creates a kink in the fatty acyl tail making it more difficult for neighboring tails to interact and making the bilayer more uid Presence of cholesterol 0 Cholesterol tends to stabilize membranes 0 Effects depend on temperature Not All Integral Membrane Proteins Can Move Depending on the cell type 1070 of membrane proteins may be restricted in their movement Integral membrane proteins may be bound to components of the cytoskeleton Which restricts the proteins from moving laterally Also membrane proteins may be attached to molecules that are outside the cell such as the interconnected network of proteins that forms the extracellular matrix Synthesis of Membrane Components In eukaryotes cytosol and endomembrane system work together to synthesize most lipids Process occurs at cytosolic lea et of smooth ER Fatty acid building blocks made via enzymes in cytosol or taken into cells from food Transfer of Lipids to Other Membranes Lipids in ER membrane can diffuse laterally to nuclear envelope Transported via vesicles to Golgi lysosomes vacuoles or plasma membrane Lipid exchange proteins extract lipid from one membrane for insertion in another ER Membrane Except for proteins destined for semiautonomous organelles most transmembrane proteins directed to rough ER membrane Form the rough ER membrane proteins can be transferred via vesicles to other regions of the cell Gl cos lation Process of covalently attaching a carbohydrate to a membrane protein or lipid O Glycolipid carbohydrate to lipid O Glycoprotein carbohydrate to protein Can serve as recognition signals for other cellular proteins Often play a role in cell surface recognition Membrane TI E SDOI t Selectively permeable plasma membrane Structure ensures 0 Essential molecular enter 0 Metabolic intermediates remain 0 Waste products exit Wavs to Move Across Membranes Passive transport does not require an input of energy down or With gradient 0 Passive diffusion diffusion of a solute through a membrane Without transport protein 0 Facilitated diffusion diffusion of a solute through a membrane With the aid of a transport protein Active transport requires energy up or against gradient Cells Maintain Gradient Living cells maintain a relatively constant internal environment different from their external environment Transmembrane gradient 0 Concentration of a solute is higher on one side of a membrane than the other Ion electrochemical gradient 0 Both an electrical gradient and chemical gradient Tonicity Isotonic 0 Equal water and solute concentrations on either side of the membrane Hypertonic O Solute concentration is higher and water concentration lower on one side of the membrane Hypotonic O Solute concentration is lower and water concentration higher on one side of the membrane Osmosis Water diffuses through a membrane from one area with more water to an area with less water If the solutes cannot move water movement can make the cell shrink or swell as water leaves or enters the cell Osmotic pressure the tendency for water to move into any cell Animal cells must maintain a balance between extracellular and intracellular solute concentrations to maintain their size and shape Crenation shrinking in a hypertonic solution Lysis bursting in a hypotonic solution Transport Proteins Transmembrane proteins that provide a passageway for the movement of ions and hydrophilic molecules across membranes 2 classes based on manner of movement 0 Channels 0 Transporters Channels Form an open passageway for the direct diffusion of ions or molecules across the membrane Most are gated Transporters Also known as carriers Conformational change transports solute Principle pathway for the uptake of organic molecules such as sugars amino acids and nucleotides Transporter Types Uniporter 0 Single molecule or ion Symportercotransport O 2 or more ions or molecules transported in same direction Antiporter 2 or more ions or molecules transported in opposite directions Active Transport Movement of a solute across a membrane against its gradient from a region of low concentration to high concentration Energetically unfavorable and requires the input of energy Primary active transport uses a pump 0 Directly use energy to transport solute Secondary active transport 0 Use preexisting gradient to drive transport of solute ATPDriven Ion Pumps Generate Ion Electrochemical Gradients NaKATPase O Actively transport Na and K against their gradients by using the energy from ATP hydrolysis O 3 Na exported for 2 K imported into cell I Antiporter I Electrogenetic pump export 1 net positive charge ExocvtosisEndocvtosLs Transport larger molecules such as proteins and polysaccharides and even very large particles Exocytosis 0 Material inside the cell packaged into vesicles and excreted into the extracellular medium Endocytosis 0 Plasma membrane invaginates or folds inwards to form a vesicle that brings substances into the cell 0 Receptor mediated endocytosis Pinocytosis o Phagocytosis O Biology Notes Chapter 6 Energy 0 Ability to promote change or do work 0 2 forms 0 Kinetic associated with movement I Energy actively being used 0 Potential due to structure or location I Chemical energy energy in molecular bonds 39 Stored energy Conservation of Energy 0 Kinetic energy is the energy of motion 0 Potential energy is stored energy Is it energy that an object has because of its 0 Location like an electrochemical gradient or 0 Structure like ATP Types of Energy 0 Light kinetic 0 Heat kinetic 0 Mechanical kinetic 0 Chemical potential 0 Ion Gradient potential Units of Energy 0 A calorie is the amount of energy that can raise the temperature of one gram of water by 1 degree Celsius 0 Food Calories are kilocalories equal to 1000 calories ber Units of Energy 0 Joule 0 TNT equivalents lst atomic bomb 15 kilotons 0 Horsepower 0 Foodpound 0 Kilowatthour 0 BTU Two Laws of Thermodynamics 1First Law 0 Law of conservation of energy 0 Energy cannot be created or destroyed 0 Can be transformed from one type to another 2 Second Law 0 Transfer or transformation of energy from one form to another increases entropy or degree of disorder of a system Entropy 0 Every energy conversion releases some randomized disordered energy in the form of heat 0 Heat is a 0 Type of kinetic energy and 0 Product of all energy conversions Chemical Energy Chemical Energy 0 Arises from the arrangement of atoms and 0 Can be released by a chemical reaction 0 Chemical potential energy Cellular respiration 0 The energyreleasing chemical breakdown of fuel molecules and O The storage of that energy in a form the cell can use to perform work Humans convert about 34 of the energy in food to useful work such as the contraction of muscles About 66 of the energy released by the breakdown of fuel molecules generates body heat Change in Free Energy Determines Direction of 2 Biochemical Reaction Total energy Usable energy Unusable energy Energy transformations involved an increase in entropy Entropy a measure of the disorder that cannot be harnessed to do work Spontaneous Reactions Occur without input of additional energy Not necessary fast Key factor is the free energy change A gt BC Eg Glucose gt carbon dioxide plus water C6H1206 gt C02 H20 Total Energy Usable Energy Unusable Energy HGTS H enthalpy total energy G Gibbs free energy energy used to do work S entropy unusable energy T temperature GH TS Change in free energy determines direction of a biochemical reaction AG AH TAS Gibbs free energy Unusable energy Enthalpy Entropy 0 Exergonic 0 AG lt 0 or negative free energy change 0 Spontaneous 0 Endergonic 0 AG gt 0 or positive free energy change 0 Requires addition of free energy 0 Not spontaneous Hvdrolvsis of ATP 0 AG 73 kcalmole 0 Reaction favors formation of products 0 Energy liberated can drive a variety of cellular processes Cell Use ATP Hvdrolvsis 0 An endergonic reaction can be coupled to an exergonic reaction 0 Endergonic reaction Will be spontaneous if net free energy change for both processes is negative Glucose ATP gt glucosephosphate H20 AG 33 Kcalmole Endergonic ATP H20 gt ADP Pi AG 73 Kcalmole Exergonic Coupled Reaction Glucose ATP gt glucosephosphate ADP AG 40 Kcalmole Exergonic Enzymes A spontaneous reaction is not necessarily a fast reaction Catalyst agent that speeds up the rate of a chemical reaction without being consumed during the reaction Enzymes protein catalysts in living cells Activation Ener Initial input of energy to start reaction Allows molecules to get close enough to cause bond rearrangement Can now achieve transition state where bonds are stretched Lowering Activation Energy Straining bonds in reactants to make it easier to achieve transition state Positioning reactants together to facilitate bonding Change local environment 0 Direct participation through very temporary bonding mher Enzyme Features Active site location where reaction takes place Substrate reactants that bind to active site Enzyme substrate complex formed when enzyme and substrate bind Substrate Binding Enzymes have a high affinity or high degree of specificity for a substrate Example of a lock and key for substrate and enzyme binding Induced fit interaction also involves conformational changes Enzyme Reactions Saturation plateau where nearly all active sites occupied by substrate 0 Vmax velocity of reaction near maximal rate Km substrate concentration at which velocity is half maximal value 0 Also called Michaelis constant 0 High Km enzyme needs higher substrate concentration 0 Inversely related to affinity between enzyme and substrate Inhibition Competitive inhibition 0 Molecule binds to active site 0 Inhibits ability of substrate to bind 0 Apparent Km increases more substrate needed Noncompetitive 0 Lowers Vmax without affecting Km 0 Inhibitor binds to allosteric site not active site mher Requirements for Enzymes Prosthetic groups small molecules permanently attached to the enzyme Cofactor usually inorganic ion that temporarily binds to enzyme Coenzyme organic molecules that participates in reaction but left unchanged afterward Enzvmes are Affected bv Environment Most enzymes function maximally in a narrow range of temperature and pH Outside of this narrow range enzyme function decreases Overview of Metabolism Chemical reactions occur in metabolic pathways Each step is coordinated by a specific enzyme Catabolic pathways 0 Result in breakdown and are exergonic Anabolic pathways O Promotes synthesis and are endergonic 0 Must be coupled to exergonic reaction Catabolic Reactions Breakdown of reactants Used to obtain energy for endergonic reactions 0 Energy stored in energy intermediates I ATP NADH Redox Oxidation 0 Removal of electrons Reduction 0 Addition of electrons Redox Reaction 0 Electron removed from one molecule is added to another AeB gtABe A 0 Has been oxidized 0 Electron removed B 0 Has been reduced 0 Electron added Energy Intermediates Electrons removed by oxidation are used to create energy intermediates like NADH NAD Nicotinamide adenine dinucleotide NADH O Oxidized to make ATP 0 Can donate electrons during synthesis reactions Anabolic Reactions Biosynthetic reactions Make larger macromolecules or smaller molecules not available from food Endergonic and are coupled to exergonic reactions usually ATP hydrolysis mnv Proteins Use ATP M Source of Energy Each ATP undergoes 10000 cycles of hydrolysis and resynthesizes every day Particular amino acid sequences in proteins function as ATPbinding sites Can predict whether a newly discovered protein uses ATP or not On average 20 of all proteins bind ATP Likely underestimated because there may be other types of ATPbinding sites Enormous importance of ATP as energy source Regulation of Metabolic Pathways 1 Gene Regulation 0 Turn on or off genes 2 Cellular Regulation 0Cellsignaling pathways like hormones Biochemical Regulation 0 Feedback inhibition product of pathway inhibits early steps to prevent 3 overaccumulation of product mlur t Biology Notes Ch7 Cellular Resniration Process by which living cells obtain energy from organic molecules Primary aim to make ATP and NADH Aerobic respiration uses oxygen 0 O2 consumed and C02 released Focus on glucose but other organic molecules also used Glucose Metabolism C6H1206 602 gt 6CO2 6H2O 4 Metabolic Pathways Glycolysis Breakdown oxidation of pyruvate to an acetyl group Citric acid cycle Oxidative phosphorylation Sime 1 lecolvsis Glycolysis can occur with or without oxygen Occurs in the cytoplasm Steps in glycolysis nearly identical in all living species 10 steps in 3 phases 1Energy investment 2 Cleavage 3 Energy liberation 3 Phases 10 Steps of lecolvsis 1 Energy Investment ATP Utilization 0 Steps 13 0 2 ATP hydrolyzed to create fructosel 6 bisphosphate 2 Cleavage 0 Steps 45 0 6 carbon molecule broken into two 3 carbon molecules of gyceraldehyde3 phosphate 3 Energy Liberation ATP Production 0 Steps 610 0 Two glyceraldehyde3phosphate molecules broken down into two pyruvate molecules producing 2 NADH and 4 ATP 0 Not yield in ATP of 2 Stage 2 Glycolysis Key control point involves the enzyme phosphofructokinase which catalyzes the third step in glycolysis which is believed to be the slowest When a cell has a sufficient amount of ATP feedback inhibition occurs At high concentrations ATP binds to an allosteric site in phosphofructokinase causing a conformal change that renders the enzyme functionally inactive If ATP binds to this enzyme its function is stimulated increasing the rate of glycolysis mac 3 Citric Acid Cvcle Krebs TCA Metabolic Cycle 0 Particular molecules enter while other leave involving a series of organic molecules regenerated with each cycle Acetyl is removed from Acetyl CoA and attached to oxaloacetate to form citrate or citric acid Series of steps releases 2C02 1 ATP 3 NADH and 1 FADH2 Oxaloacetate is regenerated to start the cycle again Stage 4 Oxidative Phosphorylation High energy electrons removed from NADH and FADH2 to make ATP Requires oxygen Oxidative process involves electron transport chain Phosphorylation of ADP occurs by ATP synthase ADP P04 gtATP NADH and FADH is made in the Krebs cycle Movement e is in the matrix and goes to H which is in the intermembrane space Oxidation ETC Electron transport chains ETC 0 Group of protein complexes and small organic molecules embedded in the inner mitochondrial membrane Can accept and donate electrons in a linear manner in a series of redox reactions Movement of electrons generates H electrochemical gradientprotonmotive force 0 Excess of positive charges outside of matrix Phosphorylation ATP Svnthase Lipid bilayer of inner mitochondrial membrane relatively impermeable to H Can pass through ATP synthase Harnesses free energy release to synthesize ATP from ADP Chemiosmosis chemical synthesis of ATP as a result of pushing H across a membrane NADH Oxidation and ATP Synthesis Oxidation of NADH results in electrochemical gradient used to synthesize ATP 3034 ATP molecules per glucose molecules broken down into C02 and H20 Electron TI E SDOI t System and Formation of ATP During glycolysis and the tricarboxylic acid cycle oxidation of organic molecules results in production of reduced coenzymes such as NADH mher Organic Molecules Focus on glucose but other carbohydrates proteins and fats also used for energy Enter into glycolysis or citric acid cycle at different points Utilizing the same pathways for breakdown increases efficiency Metabolism can also be used to make other molecules anabolismfermentation NAD transported back to cytoplasm No more NAD is made after 02 is depleted Fermentationmakes NAD Anaerobic Metabolism For environments that lack oxygen or during oxygen deficits 2 Strategies 0 Used substance other than 02 as final electron acceptor in electron transport chain 0 Produce ATP only Via substratelevel phosphorylation Fermentation Many organisms can only use 02 as final electron acceptor Make ATP Via glycolysis only Need to regenerate NAD to keep glycolysis running Muscle cells produce lactate Yeast make ethanol Produces far less ATP Secondary Metabolism Primary metabolism essential for cell structure and function catabolism and anabolism Secondary metabolism synthesis of secondary metabolites that are not necessary for cell structure and growth Secondary metabolites unique to a species or group Roles in defense attraction protection competition Chapter 8 Biology Notes Photosynthesis Energy Within light is captured and used to synthesize carbohydrates C02 H20 light energy C6H1206 02 H20 C02 is reduced H20 is oxidized Energy from light drives this endergonic reaction Trophs Heterotroph 0 Must eat food organic molecules from their last environment to sustain life Autotroph 0 Make organic molecules from inorganic sources I Chemoautotroph mainly Archaea can live off of rocks lava methane ammonia sulfur Photoautotroph Use light as a source of energy 0 Green plants algae cyanobacteria Chloroplast Organelles in plants and algae that carry out photosynthesis Chlorophyll green pigment Majority of photosynthesis occurs in leaves in mesophyll Stomata carbon dioxide enters and oxygen exits leaf 2 Stages of Photosvnthesis 0 Uses light energy Take place in thylakoid membranes 0 Calvin cycle 0 Occurs in stroma 0 Light Reactions 0 Produce ATP NADPH and 02 Uses ATP and NADPH to incorporate C02 into organic molecules Light Energy Type of electromagnetic radiation Travels as waves 0 Short to long wavelengths O Shorter wavelengths have more energy Photosynthetic pigments absorb some light energy and re ect others 0 Leaves are green because they re ect green wavelengths Absorption boosts electrons to higher energy levels Wavelength of light that a pigment absorbs depends on the amount of energy needed to boost an electron to a higher orbital After an electron absorbs energy it is an excited state and usually unstable Energy from excited electrons in pigments can be transferred to another molecule or captured Absorntjon vs Actin Spectrum Actin Spectrum 0 Rate of photosynthesis by chloroplasts at specific wavelengths Absorption Spectrum 0 Wavelengths that are absorbed by purified pigments Photosystems gLight Reaction Captured light energy can be transferred to other molecules to ultimately produce energy intermediates for Calvin cycle Thylakoid membranes of chloroplast contain 0 Photosystem I PS1 0 Photosystem II PSII Photosvstem 11 P811 0 2 Main Components 0 Lightharvesting complex or antenna complex I Directly absorbs photons I Energy transferred via resonance energy transfer 0 Reaction Center I P680 gtP680 I Relatively unstable I Transferred to primary electron acceptor I Removes electrons from water to replace oxidized P680 0 Oxidation of water yields oxygen gas 0 ATP synthesis 0 Chemiosmosic mechanisms 0 Driven by ow of H from thylakoid lumen into stroma via ATP synthase 0 H gradient generated by 0 T H in thylakoid lumen by splitting of water 0 T H by ETC pumping H into lumen O l H from formation of NADPH in stroma Calvin C cle 0 ATP and NADPH used to make carbohydrates 0 C02 incorporated into carbohydrates 0 Precursors to all organic molecules 0 Energy storage C02 Incorporation 0 Requires massive input of energy 0 For every 6 C02 incorporated 18 ATP and 12 NADPH used 0 Direct carbohydrate is glyceraldehyde3phosphate G3P O Glucose is not directly made but is made from G3P 3 Phases 1 Carbon Fixation 0 C02 incorporated in RuBP using rubisco 0 6 carbon intermediate splits into 2 3PG 2 Reduction and Carbohydrate Production 0 ATP is used to convert 3PG into 13bisphosphoglycerate O NADPH electrons reduce it to G3P 0 6 C02 gt 12 G3P 0 2 for carbohydrates 0 10 for regeneration of RuBP 3 Regeneration of RuBP O 10 G3P converted into 6 RuBP using 6 ATP Variations in Photosvnthesis 0 Certain environmental conditions can in uence both the way the Calvin cycle works 0 Light intensity 0 Temperature 0 Water availability CAM Plants 0 Some plants separate processes using time 0 Crassulacean Acid Metabolism 0 CAM plants open their stomata at night 0 C02 enters and is converted to malate OStomata close during the day to conserve water 0 Malate broken down into C02 to drive Calvin cycle during the day Chapter 9 Biology Notes Cell Communication 0 Cell communication is the process of cells detecting and responding to signals in the extracellular environment 0 Needed to coordinate cellular activities in a multicellular organism including cell death 0 Cell communication or cell signaling involves incoming and outgoing signals 0 Signals are agents that in uence the properties of cells 0 Signals affect the conformation of a receptor leading to a response in the cell Whv Do Cells Need to Resnond to Sign 1 Need to respond to a changing environment CelltoEnvironment communication 0 Adaptation or a cellular response is critical for survival 2 Cells need to communicate with each other 0 CelltoCell communication direct or indirect Signals Relaved Between Cells 1 Direct intercellular signaling 0 Cell junctions allow signaling molecules to pass from one cell to another 2 Contactdependent signaling 0 Some molecules are bound to the surface of cells and serve as signals to cell coming in contact With them 3 Autocrine signaling 0 Cells secrete signaling molecules that bind to their own cell surface or neighboring cells of the same type 4 Paracrine signaling 0 Signal does not affect cell secreting the signal but does in uence cells in close proximity synaptic signaling 5 Endocrine signaling 0 Signals hormones travel long distances and are usually longer lasting 3 Stages of Cell Signaling 1 Receptor Activation Signaling molecule binds to receptor 2 Signal Transduction Activated receptor stimulates sequence of changes signal transduction pathway 0 Signaling molecule binds to cell surface receptor 0 In most cases stimulates signal transduction pathways I Enzymelinked receptor 39 Gproteincoupled receptors 3 Cellular Response Several different responses 0 Alter activity of 1 or more enzymes 0 Alter structural protein function 0 Change gene expression transcription factor Li and Signaling molecule Binds noncovalently to receptor with high degree of specificity Binding and release between receptor and ligand relatively rapid Ligands alter receptor structure conformational change Once a ligand is released the receptor is no longer activated Cell Surface Receptors gFOUR Kinds 1 Enzymelinked receptors Found in all living species Extracellular domain binds signal Causes intracellular domain to become functional catalyst Most are protein kinases 2 Gprotein coupled receptors GPCR Found in all eukaryotes common in animals Activated receptor binds to G protein Releases GDP and binds GTP instead GTP causes G protein to disassociate A subunit and By dimer interact with other proteins in a signaling pathway 3 Ligandgated ion channels Plant and animal cells Ligand binding causes ion channels to open and ions to ow through the membrane 4 0 Animals signals between nerve and muscle cells or between 2 nerve cells Intercellular receptors 0 Some receptors are inside the cell 0 Estrogen example 0 Passes through membrane and binds to receptor in cytoplasmnucleus O Dimer of estrogen 0 receptor complexes binds to DNA I Transcription factors regulate transcription of specific genes Receptor Tyrosine Kinases Category of enzymelinked receptors found in animals Recognize various types of signaling molecules 0 Growth factor hormone that acts to stimulate cell growth or division Epidermal Growth Factor EGF O Stimulates epidermal cells to divide GProteinCoupled Receptors Signals binding to cell surface are first messenger Many signal transduction pathways lead to production of second messengers 0 Relay signals inside cells 0 Examples cAMP Ca2 Diacylglycerol and inositol triphosphate Signal Trz sductjon Vi cAMP Cyclic adenosine monophosphate Signal binding to GPCR activates G protein to bind GTP causing dissociation 0 subunit binds to adenylyl cyclase stimulating synthesis of cAMP One effect of cAMP is to activate protein kinase A PKA Activated catalytic PKA subunits phosphorylates specific cellular proteins When signaling molecules no longer produced eventually effects of PKA reversed cAMP Has 2 Advantages Signal amplification 0 Binding of signal to single receptor can cause the synthesis of many cAMP that activate PKA each PKA can phosphorylate many proteins Speed 0 In one experiment a substantial amount of CAMP was made within 20 seconds after addition of signal Signal Trz sductjon via Diacvlglvcerol and Inositol Triphosphate 0 Second way for an activated G protein to in uence signal transduction pathway 0Ot subunit can activate phospholipase C ODiacylglycerol DAG and inositol triphosphate 1P3 made from plasma membrane phospholipid 0Ca2 channels in ER open 0 Variety of effect of Ca2 on cell behavior Type of cellular response caused by a given signaling molecule depends in the type of cell responding to the signal Variation in response determined by types of proteins that each cell makes Epinephrine Example FightorFlight hormone Different effects throughout body Apoptosis Programmed cell death Cell shrinks and forms rounder shape 0 Due to destruction of nucleus and cytoskeleton Chapter 11 Biology Notes Genetic Material has Four Features 1 Information 2 Replication 3 Transmission 4 Variation Levels of DNA Structure 1 Nucleotides are the building blocks of DNA and RNA 2 A strand of DNA or RNA 3 Two stands form a double helix 4 In living cells DNA is associated with an array of different proteins to form chromosomes 5 A genome is the complete complement of an organism s genetic material DNA Monomer is Nucleotide 0 3 components 0 Phosphate group 0 Pentose sugar I Deoxyribose O Nitrogenous base I Purines 0 Adenine A 0 Guanine G I Pyrim idines I Cytosine C I Thymine T RNA 0 3 components 0 Phosphate group O Pentose sugar I Ribose O Nitrogenous base I Purines I Adenine A I Guanine G I Pyrim idines I Cytosine C 0 Uracil U Conventional numbering system Sugar carbons l to 5 Base attached to l Phosphate attached to 5 Strands Nucleotides covalently bonded Phosphodiester bond phosphate group links 2 sugars Phosphates and sugars from backbone Bases project from backbone Directionality 5 to 3 5 TAGC 3 ATGC or Chargoff s rule 0 A pairs with T O G pairs with C 0 Keeps width consistent 10 base pairs per turn 2 DNA strands are complementary O 5 GCGGATTT 3 O 3 CGCCTAAA 5 2 strands are antiparallel 0 One strand 5 to 3 O Other strand 3 to 5 DNA is 0 Double stranded O Helical SugarPhosphate backbone Bases on the inside Stabilized by hydrogen bonding Base pairs with specific pairing Spacefilling model shows grooves 0 Major groove I Where proteins bind and affect gene expression Minor groove 0 IO 390 IO 0 Semiconservgtive Replication During replication 2 parental strands separate and serve as template strands New nucleotides must obey the ATGC rule End result 2 new double helices with same base sequences as original DNA Replication Origin of replication provides an opening called a replication bubble that forms two replication forks DNA replication proceeds outward from forks Bacteria have single origin of replication Eukaryotes have multiple origins of replication DNA helicase 0 Binds to DNA and travels 5 to 3 using ATP to separate strand and move fork forward DNA topoisomerase O Singlestrand binding proteins Relieves additional coiling ahead of replication fork 0 Keep parental strands open to act as templates DNA polymerase 0Covalently links nucleotides ODeoxynucleoside triphosphate Deoxynucleoside triphosphate 0 Breaking covalent bond to release pyrophosphate 2 phosphate groups provides energy to connect adjacent nucleotides DNA Polvmerz 2 other enzymatic features 1DNA polymerase unable to begin DNA synthesis on a bare template strand 0 DNA primer will be removed and replaced with DNA later 2 DNA polymerase can only work 5 to 3 Leading and Lagging Strands In the leading strand 0 DNA synthesized as one long continuous molecule 0 DNA primase makes RNA primer 0 DNA polymerase attaches nucleotides in a 5 to 3 direction as it slides forward In the lagging strand 0 DNA synthesized 5 to 3 but as Okazaki fragments O Okazaki fragments at short RNA primer made by DNA primase at the end 5 end and then DNA laid down by DNA polymerase In both Strands 0 RNA primers will be removed by DNA polymerase and filled in with DNA 0 DNA ligase will join adjacent DNA fragments DNA Replication is Very Accurate 3 reasons 1Hydrogen bonding between A and T or G and C more stable than mismatches 2 Active site of DNA polymerase unlikely to form bonds if pairs mismatched 3 DNA polymerase removes mismatched pairs 0 Proofreading results in DNA polymerase backing up and digesting linkage O Other DNA repair enzyme Telomeres Series of short nucleotide sequences repeated at the ends of eukaryotic chromosomes Specialized form of DNA replication only in eukaryotes in the telomeres Telomere at 3 does not have a complementary strand and is calls a 3 overhang DNA polymerase cannot copy the tip of the DNA strand with a 3 end 0 No place for upstream primer to be made If this replication problem were not solved linear chromosomes would become progressively shorter Telomerase enzyme attaches many copies of DNA repeat sequence to the ends of chromosomes Progressive shortening of telomeres correlated with cellular senescences Telomerase function reduced as organism ages 99 of all types of human cancers have high levels of telomerase Eukarvotic Chromosomes Structure Typical eukaryotic chromosome may be hundreds of millions of base pairs long 0 Length would be 1 meter 0 Must fit in cell 10100um Chromosome 0 Discrete unit of genetic material Chromosomes composed of chromatin 0 DNA protein complex Different Levels of DNA Compaction 1 DNA wrapping 0 DNA wrapped around histones to form nucleosome 0 Shortens length of DNA molecule 7fold 2 30nm fiber 0 Current model suggests asymmetric 3D zigzag of nucleosomes 0 Shortens length another 7fold 0 Each chromosome located in discrete territory 0 Level of compaction of chromosomes not uniform O Heterochromatin tight 0 Euchromatin loose D 5 Chapter 12 Biology Notes Gene Expression Genes constitute the genetic material 0 Blueprint for organisms characteristics Structural genes code for polypeptides Polypeptide becomes a unit of function or protein Activities of proteins determine structure and function of cells Traits or characteristics of organism based on cellular activities Behaviors also genetically determined Transcription A gene is an organized unit of DNA sequences that enables a segment of DNA to be transcribed into RNA and ultimately results in the formation of a functional product Not all genes encode proteins Other genes code for 0 Transfer RNA tRNA translates mRNA into amino acids 0 Ribosomal RNA rRNA part of ribosomes Three Stages of Trz scrinti Initiation 0 Recognition step In bacteria sigma factor causes RNA polymerase to recognize promoter region Stage completed When DNA strands separated near promoter to form open complex Elongation RNA polymerase synthesizes RNA Template or coding strand used for RNA synthesis 0 Noncoding strand is not used 0 Uracil substituted for thymine Termination 0 RNA polymerase reaches termination sequence Causes it and newly made RNA transcript to dissociate from DNA irection of transcription and DNA strand used varies among genes In all cases synthesis of RNA transcript is 5 to 3 and DNA template strand reads 3 and Eukarvotjc Trz scrintion Basic features identical to prokaryotes However each step has more proteins 3 forms of RNA polymerase 0 RNA polymerase II transcribes mRNA 0 RNA polymerase I and III transcribes nonstructural genes for rRNA and tRNA RNA polymerase 11 requires 5 general transcription factors to initiate transcription RNA Processin2 Bacterial mRNAs can be translated into polypeptides as soon as they are made Eukaryotic mRNAs are made in a longer premRNA form that requires processing into mature mRNA Introns transcribed but not translated Exons coding sequence found in mature mRNA Splicing removal of introns and connection of exons Other modifications also occur addition of tails and caps mg Introns found in many eukaryotic genes 0 Most structural genes have 1 or more introns Spliceosome removes introns precisely O Composed of snRNPs small nuclear RNA Alternative splicing spicing can occur more than one way to produce different products rRNA and tRNA are selfsplicing O Ribozyme Additional RNA Processing in Eukarvotes Capping 0 Modified guanosine attached to 5 end 0 Needed for proper exit of mRNA from nucleus and binding to ribosome Poly A tail 0 100200 adenine nucleotides added to 3 end 0 Increases stability and lifespan in cytosol 0 Not encoded in gene sequence Translation Genetic code sequence of bases in an mRNA molecule Read in groups of three nucleotide bases or codons Most codons specify a particular amino acid 0 Also start and stop codons Degenerate more than one codon can specify that same amino acid 5 ribosomal binding site in bacterial mRNA Start codon is AUG Typical polypeptide is a few hundred amino acids in length l to 3 stop codons 0 Termination codons O UAA UAG or UGA Reading Frame Start codon defines reading frame 5 AUAAGGAGGUUACGgAUG 2CAGCAGGGCUUUACC 3 Met Gln Gln Gly Phe Thr Example of mutation addition of a U shifts the reading frame and changes the codons and amino acids specified 5 AUAAGGAGGUUACGgAUG 2UCACGAGGGCUUUAC 3 Met Ser Ala Gly Leu Tyr M Different tRNA molecules encoded by different genes tRNASer carries serine Common features 0 Cloverleaf structure 0 Anticodon O Acceptor stem for amino acid binding Aminoacvl tRNA Svnthetase Catalyzes the attachment of amino acids to tRNA 0 One for each of 20 different amino acids Reactions result in tRNA With amino acid attached or changed tRNA or aminoacyl tRNA Ability of aminoacyl tRNA synthetase to recognize appropriate tRNA has been called the second genetic code Ribosomes Prokaryotes have one kind Eukaryotes have distinct ribosomes in different cellular compartments 0 Focus on cytosolic ribosomes Composed of large and small subunits Structural differences between prokaryotes and eukaryotes exploited by antibiotics to inhibit bacterial ribosomes only Overall ribosomes shape determined by rRNA Discrete sites for tRNA binding and polypeptide synthesis P site peptidyl site A site aminoacyl site E site exit site 3 Stages of Translation 1 Initiation 0 mRNA first tRNA and ribosomal subunits assemble 2 Elongation 0 Synthesis from start codon to stop codon 3 Termination 0 Complex disassembles at stop codon releasing completed polypeptide 0 Bacteria 0 mRNA binds to small ribosomal subunit facilitated by ribosomal bind sequence 0 Start codon a few nucleotides downstream O Initiator tRNA recognizes start codon in mRNA 0 Large ribosomal subunit associates 0 At the end the initiator tRNA is in the P site 2 eukaryotic differences in initiation 0 Instead of a ribosomal binding sequence mRNAs have guanosine cap at 5 end Recognized by cap binding proteins 0 Position of start codon more variable I In many cases first AUG codon used as start codon Elongation Aminoacyl tRNA brings a new amino acid to the A site 0 Binding occurs due to codonanticodon recognition Elongation factors hydrolyze GTP to provide energy to bind tRNA to A site Peptidyl tRNA is in the P site 0 Aminoacyl tRNA is in the A site A peptide bond is formed between the amino acid at the A site and the growing polypeptide chain 0 The polypeptide is removed from the tRNA in the P site and transferred to the amino acid at the A site peptidyl transfer reaction 0 rRNA catalyzes peptide bond formation ribosome is an enzyme ribozyme Movement or translocation of the ribosome toward the 3 end of the mRNA by one codon 0 Shifts tRNAs at the P and A site to the E and P sites 0 The next codon is now at the A spot 0 Uncharged tRNA exits from E spot W When a stop codon is found in the A site translation ends 3 stop codons UAA UAG UGA Recognized by release factors Complete polypeptide attached to a tRNA in the P site and stop codon in the A site 1Re1ease factor binds to stop codon at the A site 2Cond between polypeptide and tRNA hydrolyzed to release polypeptide 3 Ribosomal subunits and release factors disassociate D 5 Chapter 12 Biology Notes Gene Expression Genes constitute the genetic material 0 Blueprint for organisms characteristics Structural genes code for polypeptides Polypeptide becomes a unit of function or protein Activities of proteins determine structure and function of cells Traits or characteristics of organism based on cellular activities Behaviors also genetically determined Transcription A gene is an organized unit of DNA sequences that enables a segment of DNA to be transcribed into RNA and ultimately results in the formation of a functional product Not all genes encode proteins Other genes code for 0 Transfer RNA tRNA translates mRNA into amino acids 0 Ribosomal RNA rRNA part of ribosomes Three Stages of Trz scrinti Initiation 0 Recognition step In bacteria sigma factor causes RNA polymerase to recognize promoter region Stage completed When DNA strands separated near promoter to form open complex Elongation RNA polymerase synthesizes RNA Template or coding strand used for RNA synthesis 0 Noncoding strand is not used 0 Uracil substituted for thymine Termination 0 RNA polymerase reaches termination sequence Causes it and newly made RNA transcript to dissociate from DNA irection of transcription and DNA strand used varies among genes In all cases synthesis of RNA transcript is 5 to 3 and DNA template strand reads 3 and Eukarvotjc Trz scrintion Basic features identical to prokaryotes However each step has more proteins 3 forms of RNA polymerase 0 RNA polymerase II transcribes mRNA 0 RNA polymerase I and III transcribes nonstructural genes for rRNA and tRNA RNA polymerase 11 requires 5 general transcription factors to initiate transcription RNA Processin2 Bacterial mRNAs can be translated into polypeptides as soon as they are made Eukaryotic mRNAs are made in a longer premRNA form that requires processing into mature mRNA Introns transcribed but not translated Exons coding sequence found in mature mRNA Splicing removal of introns and connection of exons Other modifications also occur addition of tails and caps mg Introns found in many eukaryotic genes 0 Most structural genes have 1 or more introns Spliceosome removes introns precisely O Composed of snRNPs small nuclear RNA Alternative splicing spicing can occur more than one way to produce different products rRNA and tRNA are selfsplicing O Ribozyme Additional RNA Processing in Eukarvotes Capping 0 Modified guanosine attached to 5 end 0 Needed for proper exit of mRNA from nucleus and binding to ribosome Poly A tail 0 100200 adenine nucleotides added to 3 end 0 Increases stability and lifespan in cytosol 0 Not encoded in gene sequence Translation Genetic code sequence of bases in an mRNA molecule Read in groups of three nucleotide bases or codons Most codons specify a particular amino acid 0 Also start and stop codons Degenerate more than one codon can specify that same amino acid 5 ribosomal binding site in bacterial mRNA Start codon is AUG Typical polypeptide is a few hundred amino acids in length l to 3 stop codons 0 Termination codons O UAA UAG or UGA Reading Frame Start codon defines reading frame 5 AUAAGGAGGUUACGgAUG 2CAGCAGGGCUUUACC 3 Met Gln Gln Gly Phe Thr Example of mutation addition of a U shifts the reading frame and changes the codons and amino acids specified 5 AUAAGGAGGUUACGgAUG 2UCACGAGGGCUUUAC 3 Met Ser Ala Gly Leu Tyr M Different tRNA molecules encoded by different genes tRNASer carries serine Common features 0 Cloverleaf structure 0 Anticodon O Acceptor stem for amino acid binding Aminoacvl tRNA Svnthetase Catalyzes the attachment of amino acids to tRNA 0 One for each of 20 different amino acids Reactions result in tRNA With amino acid attached or changed tRNA or aminoacyl tRNA Ability of aminoacyl tRNA synthetase to recognize appropriate tRNA has been called the second genetic code Ribosomes Prokaryotes have one kind Eukaryotes have distinct ribosomes in different cellular compartments 0 Focus on cytosolic ribosomes Composed of large and small subunits Structural differences between prokaryotes and eukaryotes exploited by antibiotics to inhibit bacterial ribosomes only Overall ribosomes shape determined by rRNA Discrete sites for tRNA binding and polypeptide synthesis P site peptidyl site A site aminoacyl site E site exit site 3 Stages of Translation 1 Initiation 0 mRNA first tRNA and ribosomal subunits assemble 2 Elongation 0 Synthesis from start codon to stop codon 3 Termination 0 Complex disassembles at stop codon releasing completed polypeptide 0 Bacteria 0 mRNA binds to small ribosomal subunit facilitated by ribosomal bind sequence 0 Start codon a few nucleotides downstream O Initiator tRNA recognizes start codon in mRNA 0 Large ribosomal subunit associates 0 At the end the initiator tRNA is in the P site 2 eukaryotic differences in initiation 0 Instead of a ribosomal binding sequence mRNAs have guanosine cap at 5 end Recognized by cap binding proteins 0 Position of start codon more variable I In many cases first AUG codon used as start codon Elongation Aminoacyl tRNA brings a new amino acid to the A site 0 Binding occurs due to codonanticodon recognition Elongation factors hydrolyze GTP to provide energy to bind tRNA to A site Peptidyl tRNA is in the P site 0 Aminoacyl tRNA is in the A site A peptide bond is formed between the amino acid at the A site and the growing polypeptide chain 0 The polypeptide is removed from the tRNA in the P site and transferred to the amino acid at the A site peptidyl transfer reaction 0 rRNA catalyzes peptide bond formation ribosome is an enzyme ribozyme Movement or translocation of the ribosome toward the 3 end of the mRNA by one codon 0 Shifts tRNAs at the P and A site to the E and P sites 0 The next codon is now at the A spot 0 Uncharged tRNA exits from E spot W When a stop codon is found in the A site translation ends 3 stop codons UAA UAG UGA Recognized by release factors Complete polypeptide attached to a tRNA in the P site and stop codon in the A site 1Re1ease factor binds to stop codon at the A site 2Cond between polypeptide and tRNA hydrolyzed to release polypeptide 3 Ribosomal subunits and release factors disassociate D 5 Chapter 12 Biology Notes Gene Expression Genes constitute the genetic material 0 Blueprint for organisms characteristics Structural genes code for polypeptides Polypeptide becomes a unit of function or protein Activities of proteins determine structure and function of cells Traits or characteristics of organism based on cellular activities Behaviors also genetically determined Transcription A gene is an organized unit of DNA sequences that enables a segment of DNA to be transcribed into RNA and ultimately results in the formation of a functional product Not all genes encode proteins Other genes code for 0 Transfer RNA tRNA translates mRNA into amino acids 0 Ribosomal RNA rRNA part of ribosomes Three Stages of Trz scrinti Initiation 0 Recognition step In bacteria sigma factor causes RNA polymerase to recognize promoter region Stage completed When DNA strands separated near promoter to form open complex Elongation RNA polymerase synthesizes RNA Template or coding strand used for RNA synthesis 0 Noncoding strand is not used 0 Uracil substituted for thymine Termination 0 RNA polymerase reaches termination sequence Causes it and newly made RNA transcript to dissociate from DNA irection of transcription and DNA strand used varies among genes In all cases synthesis of RNA transcript is 5 to 3 and DNA template strand reads 3 and Eukarvotjc Trz scrintion Basic features identical to prokaryotes However each step has more proteins 3 forms of RNA polymerase 0 RNA polymerase II transcribes mRNA 0 RNA polymerase I and III transcribes nonstructural genes for rRNA and tRNA RNA polymerase 11 requires 5 general transcription factors to initiate transcription RNA Processin2 Bacterial mRNAs can be translated into polypeptides as soon as they are made Eukaryotic mRNAs are made in a longer premRNA form that requires processing into mature mRNA Introns transcribed but not translated Exons coding sequence found in mature mRNA Splicing removal of introns and connection of exons Other modifications also occur addition of tails and caps mg Introns found in many eukaryotic genes 0 Most structural genes have 1 or more introns Spliceosome removes introns precisely O Composed of snRNPs small nuclear RNA Alternative splicing spicing can occur more than one way to produce different products rRNA and tRNA are selfsplicing O Ribozyme Additional RNA Processing in Eukarvotes Capping 0 Modified guanosine attached to 5 end 0 Needed for proper exit of mRNA from nucleus and binding to ribosome Poly A tail 0 100200 adenine nucleotides added to 3 end 0 Increases stability and lifespan in cytosol 0 Not encoded in gene sequence Translation Genetic code sequence of bases in an mRNA molecule Read in groups of three nucleotide bases or codons Most codons specify a particular amino acid 0 Also start and stop codons Degenerate more than one codon can specify that same amino acid 5 ribosomal binding site in bacterial mRNA Start codon is AUG Typical polypeptide is a few hundred amino acids in length l to 3 stop codons 0 Termination codons O UAA UAG or UGA Reading Frame Start codon defines reading frame 5 AUAAGGAGGUUACGgAUG 2CAGCAGGGCUUUACC 3 Met Gln Gln Gly Phe Thr Example of mutation addition of a U shifts the reading frame and changes the codons and amino acids specified 5 AUAAGGAGGUUACGgAUG 2UCACGAGGGCUUUAC 3 Met Ser Ala Gly Leu Tyr M Different tRNA molecules encoded by different genes tRNASer carries serine Common features 0 Cloverleaf structure 0 Anticodon O Acceptor stem for amino acid binding Aminoacvl tRNA Svnthetase Catalyzes the attachment of amino acids to tRNA 0 One for each of 20 different amino acids Reactions result in tRNA With amino acid attached or changed tRNA or aminoacyl tRNA Ability of aminoacyl tRNA synthetase to recognize appropriate tRNA has been called the second genetic code Ribosomes Prokaryotes have one kind Eukaryotes have distinct ribosomes in different cellular compartments 0 Focus on cytosolic ribosomes Composed of large and small subunits Structural differences between prokaryotes and eukaryotes exploited by antibiotics to inhibit bacterial ribosomes only Overall ribosomes shape determined by rRNA Discrete sites for tRNA binding and polypeptide synthesis P site peptidyl site A site aminoacyl site E site exit site 3 Stages of Translation 1 Initiation 0 mRNA first tRNA and ribosomal subunits assemble 2 Elongation 0 Synthesis from start codon to stop codon 3 Termination 0 Complex disassembles at stop codon releasing completed polypeptide 0 Bacteria 0 mRNA binds to small ribosomal subunit facilitated by ribosomal bind sequence 0 Start codon a few nucleotides downstream O Initiator tRNA recognizes start codon in mRNA 0 Large ribosomal subunit associates 0 At the end the initiator tRNA is in the P site 2 eukaryotic differences in initiation 0 Instead of a ribosomal binding sequence mRNAs have guanosine cap at 5 end Recognized by cap binding proteins 0 Position of start codon more variable I In many cases first AUG codon used as start codon Elongation Aminoacyl tRNA brings a new amino acid to the A site 0 Binding occurs due to codonanticodon recognition Elongation factors hydrolyze GTP to provide energy to bind tRNA to A site Peptidyl tRNA is in the P site 0 Aminoacyl tRNA is in the A site A peptide bond is formed between the amino acid at the A site and the growing polypeptide chain 0 The polypeptide is removed from the tRNA in the P site and transferred to the amino acid at the A site peptidyl transfer reaction 0 rRNA catalyzes peptide bond formation ribosome is an enzyme ribozyme Movement or translocation of the ribosome toward the 3 end of the mRNA by one codon 0 Shifts tRNAs at the P and A site to the E and P sites 0 The next codon is now at the A spot 0 Uncharged tRNA exits from E spot W When a stop codon is found in the A site translation ends 3 stop codons UAA UAG UGA Recognized by release factors Complete polypeptide attached to a tRNA in the P site and stop codon in the A site 1Re1ease factor binds to stop codon at the A site 2Cond between polypeptide and tRNA hydrolyzed to release polypeptide 3 Ribosomal subunits and release factors disassociate Chapter 13 Biology Notes Regulation of Gene Expression Gene regulation refers to the ability of cells to control their level of gene expression Majority of genes regulated so proteins produced at certain times and in specific amounts Constitutive genes are unregulated and have essentially constant levels of expression Overview Benefits of gene regulation 0 Conserve energy proteins produced only When needed 0 Ensures genes expressed in appropriate cell type and at the correct stage in development Gene Regulation Gan Occur at Different Points 0 Most commonly occurs at the level of transcription Eukaryotic Gene Bacterial Gene 0 Or control rate mRNA translated 0 Or regulated at protein or post translation level 0 Transcriptional regulation common 0 RNA processing 0 Translation 0 Posttranslation Gene Regulation in Prokarvotes Often used to respond to changes in the environment Escherichia coli and lactose example When lactose is not present E Coli does not make lactose permease lactose transporter and 5 galactosidase When lactose is available the proteins are made When lactose levels drop the proteins are no longer made Transcriptional Regulation in Bacteria Involves regulatory transcription factors Bind to DNA in the vicinity of a promoter and affect transcription of one or more nearby genes Repressors inhibit transcription 0 Negative control Activators increase the rate of transcription 0 Positive control Transcriptional regulation also involves small effector molecules like nutrients Binds to regulatory transcription factor and causes conformational change Determines Whether or not regulatory transcription factor can bind to DNA 2 domains in regulatory transcription factor that respond to small effector molecules 0 Site Where protein binds to DNA 0 Site for small effector molecule gm Operon in bacteria is a cluster of genes under transcriptional control of one promoter 0 Regulatory region called operator Transcribed into mRNA as polycistronic mRNA encodes more than one protein Allows regulation of a group of genes with a common function W In E Coli contains genes for lactose metabolism LacP promoter 3 genes encodes three polypeptides O LacZ Bgalactosidase O LacY lactose permease O LacA galactosidase transacetylase Near the lac promoter are 2 regulatory sites 0 LacO operator provides binding site for repressor protein CAP site activator protein binding site 0 Lacl gene codes for lac repressor O Considered a regulatory gene since its sole function is to regulate other gene s expression 0 Has its own promoter not part of lac Operon When lactose is absent 0 Lac repressor protein binds to nucleotides of lac operator site preventing RNA polymerase from transcribing lacZ LacY and LacA 0 RNA polymerase can bind but not move forward When lactose is present O Allolactose is a small effector moleculeis made from lactose a nutrient O 4 allolactose molecules binding to lac repressor prevents repressor from binding 0 Process called induction and lac operon is inducible Trp Operon In E Coli encodes enzymes required to make amino acid tryptophan Regulated by a repressor protein encoded by trpR gene Binding of repressor to trp operator site inhibits transcription When tryptophan levels low trp repressor cannot bind to operator site and operon genes transcribed When tryptophan levels are high tryptophan turns off the trp operon Tryptophan acts as a small effector molecule that activates a repressor Lac repressor binds to its operator in the absence of its small effector molecule allolactose receptor is inhibited O Inducible allolactose induces transcription 0 Genes turned off unless appropriate substances available effector represses the repressor Trp repressor binds to its operator only in the presence of its small effector molecule tryptophan repressor is activated 0 Repressible tryptophan represses transcription 0 When enough of product present genes are turned off to prevent overproduction Gene Regulation in Eukarvotes Produces different cell types in an organism by cell differentiation All of the organism s cells contain the same genome but expresses different proteomes 0 Different proteins 0 Different amounts of the same protein Develonmental Gene Regulation in Mammals Fetal human stage characterized by continued refinement of body parts and a large increase in size Example Gene regulation determines Which globin polypeptides are made to become functional hemoglobin Fetal hemoglobin has a higher affinity for oxygen than adult hemoglobin O Allows fetus to harvest oxygen from maternal blood Regulation of Transcription in Eukarvotes 0 Follow some of same principles found in prokaryotes O Activator and repressor proteins in uence ability of RNA polymerase to initiate transcription 0 Many regulated by small effector molecules 0 Many important differences 0 Genes always organize individually O No operons No polycistronic mRNAs 0 Regulation more intricate Eukaryotic Genes 0 3 Features found in most promoters 0 TATA box I 5 TATAAAA 3 I 25 base pairs upstream from transcriptional start site I Determines precise starting point for transcription 0 Transcriptional Start Site I Where transcription begins I With TATA box forms core promoter 0 By itself results in low level basal transcription 0 Regulatory or response elements I Recognized by regulatory proteins that control initiation of transcription I Enhancers and silencers Proteins Needed for Simple Basal Transcription RNA polymerase II Differential General Transcription factors Large protein complex called mediator Activators bind to enhancers Repressors bind to silencers Regulate rate of transcription of a gene Most do not bind directly to RNA polymerase II but to DNA sequences Gene Accessibilitv DNA is associated with proteins to form compact chromatin Chromatin packing affects gene expression Transcription is difficult or impossible in the tightly packed chromatin in the closed conformation Access to the DNA is allowed in the loosely packed open conformation Some activators diminish DNA compaction near a gene Recruit proteins to loosen DNA compaction O Histone acetyltransferase attaches acetyl groups to histone proteins so they don t bind DNA as tightly O ATPdependent chromatin remodeling enzymes also loosen DNA compaction Histone Code 0 Many different amino acids in the amino terminal tails of histone proteins subject to several types of covalent modification 0 Pattern of modifications on histone affects degree of chromatin compaction DNA Modi cation DNA methylase attaches methyl groups Common is some eukaryotes but not all In mammals 5 of DNA is methylated Usually inhibits transcription CG islands found near promoters in vertebrates and plants 0 Unmethylated CG islands are correlated with active genes 0 Repressed genes contain methylated CG islands Alternative Splicing of PremRNAs In eukaryotes a premRNA transcript is processed before it becomes a mature mRNA When a premRNA has multiple introns and exons splicing may occur in more than one way Alternative splicing causes mRNAs to contain different patterns of exons Allows same gene to make different proteins 0 At different stages of development 0 In different cell types 0 In response to a change in the environmental conditions Linear sequence of exons maintained in both alternates In most cases the alternative versions of a protein will have similar functions because much of their amino acid sequences will be identical to each other provide each protein With its own unique characteristics 0 Nevertheless alternative splicing produces differences in amino acid sequences that Will Advantage of alternative splicing is that two or more different polypeptides can be derived from a single gene thereby increasing the size of the proteome While minimizing the size of the genome Genomes and Proteomes Increase in biological complexity are correlated With greater sizes of genomes and proteomes Alternative splicing can increase the proteome size Without increasing the total number of genes 0 For organisms to become more complex as in higher plants and animals evolution has produced more complex proteomes 0 General trend is that less complex organisms tend to have fewer genes 0 Frequency of alternative splicing increases With increasing biological complexity Chapter 14 Biology Notes Mutation A heritable change in the genetic material Essential to the diversity of life 0 Source of variation for evolution BUT most mutations can just as easily be harmful than beneficial DNA repair systems reverse DNA damage Cancer is a disease caused by gene mutations Gene Mutations Alter the DNA Sequence Point mutation affects only a single base pair 2 basic alterations 1Change base sequence 2 Add or remove nucleotides Gene Mutations May Affect Amino Acid Seguence Silent mutation 0 Does not alter the amino acid sequence 0 Genetic code is degenerate Missense mutation 0 Changes a single amino acid in a polypeptide 0 May not alter function if substituted amino acid is similar in chemistry to original 0 Sicklecell disease is the result of a single amino acid substitution Nonsense mutation 0 Change from a normal codon to a stop or termination codon O Produces a truncated polypeptide Frameshift mutation 0 Addition or deletion of nucleotides that are not multiples of 3 0 Completely different amino acid sequence downstream from mutation Gene Mutations Outside of Coding Sequences A mutation may alter the sequence Within a promoter and affect the rate of transcription ie TATA mutated to TACA Mutations may occur in regulatory elements or operator sites 0 Mutation may alter DNA sequence of enhancersilencer so that activatorrepressor protein does not bind Spontaneous or Induced Mutations Spontaneous mutations result from abnormalities in biological processes Rates vary from species to species and from gene to gene Expected rate of background mutation approximately 1 point mutation for every genome each time it replicates 3 X 109bp Induced mutations are brought on by environmental agents Mutation rate higher than spontaneous mutation rate Mutagens are chemical or physical agents 0 Can alter DNA in various ways GermLine or Somatic Cell Mutations Exact time and location of a mutation is critical to severity of effect and to the ability to pass on the mutation Germ cells give rise to gametes 0 Can occur in a sperm or egg cell or in cell that gives rise to eggs and sperm Somatic cells are all other body cells 0 Can occur early or late in development I Genetic mosaic results from patches of mutated tissue Nucleotide Excision Repair NER Most common DNA repair system Region encompassing several nucleotides in the damaged strand is removed from the DNA Intact undamaged strand is used as a template for resynthesis of normal complementary strand Found in all eukaryotes and prokaryotes DNA Repair All living organisms must have the ability to repair changes that occur in DNA in order to minimize mutation Requires 0 DNA damage be detected 0 Repair of DNA damage NER and Human Genetic Disease NER systems were discovered in humans by the analysis of genetic diseases that affect DNA repair 0 Xeroderma pigmentosum XP Cockayne s syndrome CS others Photosensitivity is a common characteristic in these syndromes because of an inability to repair UVinduced lesions m Disease of multicellular organisms that is characterized by uncontrolled cell division 15 million Americans are diagnosed with cancer each year and over 05 million will die from the disease In about 10 of cancers a higher predisposition to develop the disease is an inherited trait Most cancers about 90 do not involve genetic changes that are passed from parent to offspring Carcino ens About 80 of all human cancers are related to exposure to carcinogens Agents that increase the likelihood of developing cancer Most carcinogens such as UV light and certain chemicals in cigarette smoke are mutagens that promote genetic changes in somatic cells DNA alterations can lead to effects on gene expression that ultimately affect cell division and thereby lead to cancer Cancers originate from a single cell Cell and its offspring mutate so cells grow abnormally Tumor an overgrowth of cells with no useful purpose Tumor may begin as benign or precancerous 0 Do not invade or spread Malignant Stage 0 Lost normal growth regulation 0 Invasive can invade healthy tissue 0 Metastatic can migrate to other parts of the body Left untreated malignant cells will cause the death of the organism Oncogenes a mutant gene the normill wild tvne gene isa promoncogene Cell division regulated by hormones called growth factors Bind to cell surface and initiate cascade leading to cell division which includes activating specific genes Mutations in genes producing cell growth signaling proteins can change them into oncogenes producing abnormally high level of activity in some proteins An oncogene may promote cancer by keeping the cell division signaling pathway in a permanent on position 0 In some cancers the amount of gene product is abnormally high O In others the gene produces a functionally hyperactive protein Ras Intracellular signaling protein 0 GTPase that hydrolyzes GTP to GDP 0 When GTP is bound Ras promotes cell division 0 Oncogenic mutations may decrease ability of Ras to hydrolyze GTP or exchange GDP for GTP faster 0 Both keeps signaling pathway on ProtoOncoaene Normal gene that if mutated can become an oncogene 4 common genetic changes 1Missense mutations e g Ras 2 Gene amplifications eg Myc 3 Chromosomal translocations e g BcrAbl 4Retroviral insertions And There is an additional generelated causing of cancer Cancer causing Viruses HPV hepatitis THESE ARE CURRENTLY DETECTED DURING TUMOR BIOPSIES Missense mutations 0 Chemical mutagens have been shown to cause missense mutations leading to cancer Gene amplifications 0 Abnormal increase in copy number results in too much of the encoded protein 0 Many human cancers are associated with the amplification of particular proto oncogenes Chromosomal translocations 0 Two different chromosomes break and the ends of the broken chromosomes fuse with each other incorrectly 0 Very specific types of chromosomal translocations have been identified in certain types of tumors 0 Chimeric genes are composed of two gene fragments fused together Retroviral insertions 0 Viral DNA may insert into a host chromosome in such a way that a Viral promoter and response elements are next to a protooncogene I May result in the overexpression of the protooncogene thereby promoting cancer 0 Alternatively a Virus may cause cancer because it carries an oncogene in the Viral genome TumorSuppressor Genes Normal role to prevent cancerous growth Proteins encoded by tumorsuppressor genes usually have one of two functions 1Proteins that maintain the integrity of the genome by monitoring andor repairing alterations in the genome 0 Checkpoint proteins check the integrity of the genome and prevent a cell from progressing past a certain point in the cell cycle 2 Proteins that are negative regulators or inhibitors of cell division 0 Their function is necessary to properly halt cell division otherwise cell division is abnormally accelerated P53 is a G1 checkpoint protein Expression of the p53 gene is induced when DNA is damaged Then a cell cannot progress from G1 to the S or synthesis phase of the cell cycle If DNA is repaired a cell may later proceed through the cell cycle Alternatively if the DNA damage is too severe the p53 protein will also activate other genes that promote programmed cell death or apoptosis Caspases function as proteases that digest selected cellular proteins causing the cell to break down It is beneficial for a multicellular organism to kill an occasional cell with cancer causing potential Loss of Tumor Suppressor Gene Function 3 common ways 0 Mutation occurs specifically within a tumorsuppressor gene to inactivate its function 0 Chromosome loss may contribute if the missing chromosome carries one or more tumorsuppressor genes 0 Abnormal methylation of CpG islands near promoter regions aner isa Series of Changes Cancer usually requires multiple genetic changes to the same cell Begin with a benign genetic alteration that over time and with additional mutations leads to malignancy Malignancy can continue to accumulate genetic changes that make it even more difficult to treat Chapter 15 Biology Notes m Reproduction of cells Highly regulated series of events 2 types in eukaryotes O Mitosis O Meiosis Eukarvotjc Chromosomes Cytogenetics field of genetics involving microscopic examination of chromosomes and cell division When cells get ready to divide the chromosomes compact enough to be seen With a light microscope Karyotype reveals number size and form of chromosomes in an actively divided cell Sets of Chromosomes Humans have 23 pairs of chromosomes or 46 total chromosomes 0 Autosomes 22 pairs in humans 0 Sex chromosomes 1 pair in humans I XX or XY Ploidy O Diploid or 2n humans have 23 pairs of chromosomes 0 Haploid or n gametes have 1 member of each pair of chromosomes or 23 total chromosomes Homologous In diploid species members of a pair of chromosomes are called homologues 0 They are homologous chromosomes Each homologue nearly identical in size and genetic composition 0 Both carry gene for eye color but one may have brown and the other blue Sex chromosomes are very different from each other X and Y differ in size and composition Cell C cle G1 first gap S synthesis of DNA G2 second gap M mitosis and cytokinesis Go substitute for G1 for cells postponing division or never dividing again Q Phase Cells accumulates molecular changes that cause progression through the cell cycle Passes restriction point Where cell is committed to enter S phase Chromosomes replicate during S phase forming sister chromatids S Phase Chromosomes replicate After replication 2 copies stay joined to each other and are called sister chromatids Human cell in G1 has 46 chromosomes 0 Same cell in G2 after S has 46 pairs of sister chromatids or 92 chromatids G2 0 Cell synthesizes proteins needed during mitosis and cytokinesis M phase mitosis 0 Divide one cell nucleus into two Cytokinesis 0 Division of cytoplasm follows in most cases Decision to Divide External factors 0 Environmental conditions 0 Signaling molecules Internal factors 0 Cell cycle control molecules 0 Checkpoints Checkpoint Proteins Cyclins or cyclin dependent kinases cdks responsible for advancing a cell through the phases of the cell cycle Amount of cyclins varies through cycle Kinases controlling cell cycle must bind to a cyclin to be active 3 critical regulatory points or checkpoints in eukaryotes 0 G1 checkpoint restriction point 0 G2 checkpoint O Metaphase checkpoint Checkpoint proteins act as sensors to determine if the cell is in proper condition to divide Cell cycle Will be delayed or until problems fixed or prevents division entirely Loss of checkpoint function can lead to mutation and cancer Mitotic Cell Division A cell divides to produce 2 new cells genetically identical to the original Original called mother new cells called daughters Involves mitosis and cytokinesis Can be asexual reproduction or for production and maintenance of multicellularity Preparation for Cell Division DNA replicated Sister chromatids 2 identical copies with associated proteins Tightly associated as centromere Serves as attachment site for kinetochore used in sorting chromosomes Mitotic Spindle Sorting process that ensures that each daughter cell will obtain the correct number and types of chromosomes Mitotic spindle is responsible for organizing and sorting the chromosomes during mitosis Composed of microtubules Interphase phase of the cell cycle during which the chromosomes are decondensed and found in the nucleus Mitosis 0 Prophase 0 Prometaphase O Metaphase 0 Anaphase 0 Telophase Cytokinesis 1 Bicked a Bizza for Me And Ihe Qat Prophase Chromosomes have already replicated to produce 12 chromatids joined as six pairs of sister chromatids Nuclear membrane dissociates into small vesicles Chromatids condense into highly compacted structure that are readily Visible by light microscopy Prometaphase 0 Nuclear envelop completely fragments 0 Mitotic spindle is fully formed during this phase 0 Centrosomes move apart and demarcate the two poles 0 Spindle fibers interact with sister chromatids 0 Two kinetochores on each pair of sister chromatids are attached to kinetochore microtubules from opposite poles Metaphase 0 Pairs of sister chromatids are aligned along a plane halfway between the poles called the metaphase plate 0 Organized into a single row 0 When this alignment is complete the cell is in metaphase Anaphase 0 Connections between the pairs of sister chromatids are broken 0 Each chromatid now an individual chromosome is linked to only one of the two poles by one or more kinetochore microtubules O Kinetochore microtubules shorten pulling the chromosomes toward the pole to which they are attached 0 Two poles move farther away from each other as overlapping polar microtubules lengthen and push against each other Telophase 0 Chromosomes have reached their respective poles and decondense 0 Nuclear membranes now reform to produce two separate nuclei Cytokinesis 0 In most cases mitosis is quickly followed by cytokinesis 0 Two nuclei are segregated into separate daughter cells 0 Process of cytokinesis is quite different in animals and plants 0 Animals cleavage furrow constricts like a drawstring to separate the cells 0 Plants cells plate forms a cell wall between the two daughter cells Meiosis Sexual reproduction requires a fertilization event in which two haploid gametes unite to create a diploid cell called a zygote Meiosis is the process by which haploid cells are produced from a cell that was originally diploid Like mitosis meiosis begins after a cell has progressed through the G1 S and G2 phases of the cell cycle 2 key differences 1Homologous pairs form a bivalent or tetrad 2 Crossing over Bivglent or Tetrad Homologous pairs of sister chromatids associate with each other lying side by side to form a bivalent or tetrad Process called synapsis Crossing Over Physical exchange between chromosome pieces of the crossing bivalent Increases the genetic variation of a species Chiasma arms of the chromosomes tend to separate but remain adhered at a crossover site Number of crossovers carefully controlled by cells Meiosis vs Mitosis Mitosis produces two diploid daughter cells that are genetically identical 0 6 chromosomes in 3 homologous pairs Meiosis produces four haploid daughter cells 0 Each daughter has a random mix of 3 chromosomes Chromosomes Geneticists have discovered that variations on chromosomes structure and number can have major effects on organisms 0 Several human diseases 0 Important in evolution of new species 0 Chromosome variation 0 On rare occasions structure or number of chromosomes changes so that individual is different from other members of same species abnormal 0 Normal for structure and number of chromosomes to vary between species Variation in Chromosomes 0 Chromosome composition Within a given species tends to remain relatively constant 0 Humans 2 sets of 23 chromosomes total of 46 0 Dog 2 sets of 39 total of 78 chromosomes 0 Fruit y 2 sets of 4 total of 8 chromosomes 0 Tomato 2 sets of 12 total of 24 chromosomes 0 Chromosomes identified by 0 Size 0 Location and centromere l Short arm is p long are is q short arms on top 0 Banding pattern I Giemsa stain gives G banding Chromosomgl Mutations 0 Deletions 0 Segment missing 0 Duplications 0 Section occurs 2 or more times in a row 0 Inversions 0 Changes in direction along a single chromosome 0 Translocations 0 One segment becomes attached to another chromosome 0 Simple or reciprocal Changes in Chromosome Number 0 Aneuploidy 0 Alteration number of particular chromosomes 0 Total number not an exact multiple of a set 0 Trisomic 0 Normal 2 copies of a chromosome plus a 3rd 0 2n1 0 Monosomic 0 Missing one of normal copies of a chromosome 0 2n1 Qused bv Nondisiunc Chromosomes do not sort properly during cell division During meiosis can produce gametes With too many or too few chromosomes Aneuploidy in all eukaryotic species usually has detrimental consequences Trisomic and monosomic individuals have an imbalance in the level of gene expression interfering with proper cell function Aneuploidv in Humans About 510 of all fertilized human eggs result in an embryo With an abnormality in chromosome number Approximately 50 of all spontaneous abortions are due to alterations in chromosome number Can survive some abnormalities 0 Trisomies or abnormalities in sex chromosome number Chapter 16 Biology Notes Gregor J ohann Mendel O Entered monastery and became a priest 0 Historic studies on pea plants 0 Paper ignored at the time 0 Independently rediscovered years later What Genetic Mechanisms Account for the Passing of Traits from Parents to Offspring O The blending hypothesis is the idea that genetic material from the two parents blends together like blue and yellow paint blend to make green Proved to NOT be accurate 0 The particulate hypothesis is the idea that parents pass on discrete heritable units genes Mendel s research supported the particulate hypothesis through his experiment with garden peas m insight Mendel s EX erimental ualitative A roach Advantages of pea plants for genetic study 0 There are many varieties with distinct heritable features or characters such as ower color character variants such as purple or white owers are called traits O Mating of plants can be controlled Each pea plant has spermproducing organs stamens and eggproducing organs stigma Crosspollination fertilization between different plants can be achieved by dusting one plant with pollen from another produces hybrids The Law of Segregation When Mendel crossed white and purple owered pea plants all of the F1 hybrids were purple When Mendel crossed the F1 hybrids many of the F2 plants had purple owers but some had white Mendel discovered a ratio of about three to one purple to white owers in the F2 generation Mendel reasoned that only the purple ower factor was affecting ower color in the F1 hybrids Mendel called the purple ower color a dominant trait and the white ower color a recessive trait Mendel observed the same pattern of inheritance in six other pea plant characters each represented by two traits When Mendel called a heritable factor is what we now call a gene Three Important Ideas Dominant and recessive traits 0 Dominant is displayed trait 0 Recessive trait is marked by dominant trait Genes and alleles 0 Particulate mechanism of inheritance 0 His unit factors are genes 0 Every individual has 2 genes for a character 0 Gene has two variant forms or alleles Segregation of alleles 0 Approximately 31 ratio Two copies of gene carried by an F1 plant segregated separate from each other so that each sperm or egg carries only one allele Mendel s Law of Segregation O 2 copies of a gene segregate from each other during the transmission from parent to offspring Genotype and Phenotvpe Genotype 0 Genetic composition of individual 0 TT homozygous dominant O tt homozygous recessive 0 Tt heterozygous Phenotype 0 Characteristics that are the result of gene expression TT and Tt are tall 0 0 tt is dwarf Punnett Sguare Step 1 Write down the genotypes of both parents 0 Male parent Tt 0 Female parent Tt Step 2 Write down the possible gametes that each parent can make 0 Male gametes T ort 0 Female gametes T ort Step 3 Create an empty Punnett Square Step 4 Fill in the possible genotypes Step 5 Determine relative proportions of genotypes and phenotypes Testcross A dwarf pea plant must be tt A tall pea plant could be either TT or Tt Cross unknown individual to a homozygous recessive individual If some offspring are dwarf unknown individual must have been Tt If all offspring are tall the unknown individual was TT TwoFactor Cross Follow inheritance of 2 different traits Possible patterns 0 2 genes linked meaning on same chromosomes so that variants found together in parents are always inherited as a unit 0 2 genes are independent meaning on different chromosomes and randomly distributed Dihybrid offspring offspring are hybrids with respect to both traits Data for F2 hybrids consistent only with independent assortment Law of Independent Assortment 0 Alleles of different genes assort independently of each other during gamete formation means they are on different chromosomes Chromosome Theory of Inheritance Chromosomes are made of DNA which is the genetic material Genes are found within the DNA sequences of the chromosomes Chromosomes are replicated and passed from parent to offspring sexual reproduction They are also passed from cell to cell during the development of a multicellular organism The nucleus of a diploid cell contains two sets of pairs The maternal and paternal sets of homologous chromosomes are functionally equivalent each set carries a full complement of genes At meiosis one member of each chromosome pair segregates into one daughter nucleus and its homologue segregates into the other daughter nucleus During the formation of haploid cells the members of different chromosome pairs segregate independently of each other Gametes are haploid cells that combine to form a diploid cell during fertilization which each gamete transmitting one set of chromosomes to the offspring Chromosomes and Segregation Mendel s law of segregation can be explained by the pairing and segregation of homologous chromosomes during meiosis Locus physical location of a gene on a chromosome Chromosomes and Independent Assortment Law of independent assortment can also be explained by the behavior of chromosomes during meiosis Random alignment of chromosome pairs during meiosis I leads to the independent assortment of alleles found on different chromosomes Pedigree Analysis Inherited trait is analyzed over the course of a few generations in one family Cystic fibrosis CF example 0 Approximately 5 of Americans of European descent are heterozygous carriers of the recessive CF allele and phenotypically normal 0 Individuals who are homozygous exhibit disease symptoms Many of the alleles causing human genetic disease are recessive like CF Some are dominant like Huntington Disease autosomal dominant Sex Chromosomes Found in many but not all species With 2 sexes Several mechanisms for sex determination O XY system Males are XY and females XX 0 XO system Females are XX and males are X or XO 0 ZW system Makes is 22 and Females is ZW XLinked Traits In humans X chromosome is larger and carries more genes than the Y chromosome Genes found on the X but not the Y are Xlinked genes 0 Sex linked genes are found on one sex chromosome but not the other Males are hemizygous for Xlinked genes 0 Hemophilia A example Hemophilia A caused by recessive Xlinked gene Encodes defective clotting protein Mendelign Inheritance Inheritance pattern of genes that segregate and assort independently Simple Mendelian inheritance one trait is completely dominant over the other Xlinked inheritance pairs of dominant and recessive alleles found on the X chromosome In simple dominance the recessive allele does not affect the phenotype of the heterozygote A single copy of the dominant allele is sufficient to mask the recessive allele Purple pigment P 0 One P allele makes enough functional protein to provide a normal phenotype O In other cases the heterozygote may make more than 50 of the normal amount of protein upregulated Incomplete dominance O Heterozygote has intermediate phenotype 0 Neither allele is dominant 0 Pink fouro clocks 39 50 of normal protein not enough to give red color Role of Environment Norm of reaction effects of environmental variation on a phenotype Genetically identical plants grow to different heights in different temperatures Probability Chance that an event Will have a particular outcome Number of X on event occurs Total number of possible outcomes Selffertilization of a pea plant that was heterozygous for the height gene Tt Punnett square predicted that onefourth of the offspring would be dwarf In P 25 dwarf 1TT2Tt1tt i 4 Sal mm Accuracy of prediction depends on the number of events observed or sample size Random sampling error deviation between observed and expected outcome Larger samples have smaller sampling errors Humans have small families and observed data may be very different from expected outcome Product Rule Probability that two or more independent events will occur is equal to the product of their individual probabilities Two factor cross Each individual recessive trait has a 25 14 chance probability of occurring For two factor cross chance of an offspring exhibiting both recessive traits is 1 1 1 X 4 4 l6 Biology Notes Chapter 17 0 Many traits are in uenced by more than one gene Mendel studied strains that differed with regard to only one gene Gene interaction a single trait is controlled by 2 or more genes each of which has 2 alleles M and P Epistasis Alleles of one gene mask the function of the protein that is encoded by the alleles of another gene Often arise because 2 or more different proteins involved in a single cellular function Example 2 genes involved in a ower color 0 C requited for purple dominant to c white 0 P also required for purple dominant to p white 0 cc masks P or pp masks C producing white owers Types of Traits Discrete 0 Clearly defined phenotypic variants 0 Purple or white owers red or white eyes Quantitative 0 Majority of traits O Show continuous variation over a range of phenotypes Height skin color number of apples on a tree Polygenic several or many genes contribute to the outcome Environment also plays a role lteson and Punnett Showed Thpt Genes Do Not Always Assort Independently Independent assortment applied to genes on different chromosomes What happens when alleles of different genes are on the same chromosome Linkage when 2 genes are close on the same chromosomes they tend to be transmitted as a unit Linked genes do not follow the law of independent assortment Recombination s are the results of crossing over Genetic Mapping Genetic map shows linear arrangement of genes 0 Each gene has its own unique locus Genetic mapping allows us to estimate the relative distances between linked genes based on the likelihood that crossover will occur between them 0 Likelihood proportional to distance between genes Extrgnuclear Inheritance 0 Some genes are not found on the chromosomes in the cell nucleus 0 Mitochondria and chloroplasts contain their own genomes O Organelle genomes O Smaller than nuclear genome but important to phenotypes Chloroplast and Mitochondrigl Genomes are Relativelv Small But Contain Genes that Encode Important Proteins 0 Chloroplast and mitochondrial genomes composed of single circular DNA molecule 0 Mitochondrial genome of many mammals contains 37 genes 0 24 encoded tRNA needed for translation inside mitochondrion O 13 encode proteins for oxidative phosphorylation 0 Chloroplast genomes typically contain 110120 genes 0 Many encode proteins vital to photosynthesis 0 In most species of plants the egg cell provides most of the zygote s cytoplasm While the much smaller male gamete often provides little more than a nucleus 0 Chloroplasts are most often inherited via the egg 0 Most common transmission pattern in seed bearing plants 0 Biparental inheritance 0 Both the pollen and the egg contribute chloroplasts to the offspring 0 Paternal inheritance 0 Only the pollen contributes these organelles 0 Most types of pine trees Mitochondrial Genomes 0 Maternal inheritance is the most common pattern of mitochondrial transmission in eukaryotic species 0 Some species do exhibit biparental or paternal inheritance O Mutations in human mitochondrial genes can cause a variety of rare diseases 0 Usually affect organs and cells that require high levels of ATP QMPPP Biology Notes Chapter 18 Viral Genetics Viruses are nonliving particles with nucleic acid genomes that require the assistance of living cells to reproduce Viruses Small infectious particle that consists of nucleic acid enclosed in a protein coat Over 4000 different types Vary greatly in their characteristics including their host range structure and genome composition Differences Host Range 0 Number of species and cell types that can be infected Structural 0 All viruses have a capsid protein coat but it varies in shape and complexity 0 Some have viral envelope derived from host cell plasma membrane Genome 0 DNA vs RNA single stranded ss vs double stranded ds linear vs circular Elm Viruses are not alive 0 Not cells or composed of cells 0 Cannot carry out metabolism on their own Viral reproductive cycle can be quite different among types of viruses and one virus may have alternative cycles Basic Steps Attachment Entry Integration Synthesis of viral components Viral assembly Release Attachment and Entry 0 Attachment 0 Usually specific for one kind of cell due to binding to specific molecules on cell surface 0 Entry 0 Bacteriophages or phage injects only DNA into bacteria 0 HIV fuses with host membrane and the entire virus enters 0 One or several viral genes are expressed immediately 0 Virus may proceed to synthesis of viral components OR integrate into host chromosome Integration 0 Viral gene for integrase 0Integrase cuts host chromosomal DNA and inserts viral genome 0 Phage in bacterial DNA called prophage 0 May exercise later and proceed to synthesis 0 HIV is an RNA virus 0 Uses viral reverse transcriptase to make complementary DNA strand that Will be template for double stranded viral DNA 0 Integrates as a provirus Synthesis of Viral Components 0 Host cell enzymes such as DNA polymerase make many copies of the phage DNA and transcribe the genes Within these copies into mRNA 0 In the case of HIV the DNA provirus is not exercised from the host chromosome Instead it is transcribed in the nucleus to produce many copies of viral RNA 0 Translated to make viral proteins 0 Serve as genome for new viral particles Release 0Phages must lyse their host cell to escape 0Enveloped viruses bud from the host cell Qtencv in Bacterionhages 0 Some viruses can integrate their genomes into a host chromosome OProphage or provirus is inactive or latent 0 Most viral genes silenced Qtencv in Humgn Viruses 2 different ways 1HIV integrates into host genome and may remain dormant for long periods of time 2 Other viruses can exist as episomes genetic element that can replicate independently of chromosomal DNA but occasionally integrates into chromosomal DNA 0 Herpes simplex type HIV Reverse transcriptase lacks a proofreading function 0 Makes more errors and tends to create mutant strains of HIV 0 Makes it difficult to create vaccine Deoxynucleoside triphosphates 0 Breaking covalent bond to release pyrophosphate 2 phosphate groups provides energy to connect adjacent nucleotides Emerging Viruses are viruses that have suddenly come to the attention of science 0 Examples are swine u and avian u Avian Flu CDC 0 Infects birds 0 Responsible for 1918 Flu Pandemic 0 Infected 18 people in Hong Kong in 1997 and 0 Eventually spread to Europe and Africa infecting over 400 people and killing more than 240 of them Over 100 million birds have either 0 Died from the disease or 0 Been killed to prevent the spread of the infection If avian u mutates to a form that can easily spread between people the potential for a major human outbreak is significant New viruses can arise by 0 The mutation of existing viruses or O The spread of existing viruses to a new host species Prions Composed entirely of a single protein called prion so there is a gene that encodes the prion protein Disease causing conformation PrPSc Normal conformation PrPc Normal protein expressed at low levels on surface of nerve cells Prion PrPSc converts normal prion to abnormal conformation which will clump together and kill the neuron Several types of neurodegenerative diseases of human and livestock 0 Group of diseases called transmissible spongiform encephalopathesis TSE A Prion is a protein that can become misfolded This misfolded prion protein can then bind to and bend another molecule of prion causing this second prion also become misfolded leading to a cascade the spread of misfolded prion proteins This is infectious but is NOT a virus its a protein Prions are responsible for neurodegenerative disease called transmissible spongiform encephalopathies O Scrapie in sheep and goats 0 Mad cow disease 0 Chronic wasting disease in deer and elk and O CreutzfeldtJakob disease in humans Genetic Pronertjes of Bacteria Genes of bacteria are found in bacterial chromosomes Usually a single type of chromosome May have more than one copy of that chromosome Number of copies depends on the bacterial species and on growth conditions Typically 14 identical chromosomes Nucleoid region where tightly packed bacterial chromosome found Molecules of doublestranded DNA Usually circular Tend to be shorter Contains a few thousand unique genes Mostly structural genes Single origin or replication Plasmids 0 Small circular pieces of DNA that exist independently of the bacterial chromosome 0 Occur naturally in many strains of bacteria and in a few types of eukaryotic cells such as yeast 39 Own origin of replication that allows it to be replicated independently of the bacterial chromosome 0 Not usually necessary for survival but can provide growth advantages Biology Notes Chapter 19 Development Refers to a series of changes in the state of the cell tissue organ or organism Underlying process that gives rise to the structure and function of living organisms Developmental genetics aimed at understanding low gene expression controls this process General Themes Sperm and egg unite to produce a zygote That diploid cell divides and develops into the embryo Cells divide and begin to arrange themselves Each cell becomes determined destined to become a particular type Commitment to become a particular type of cell occurs long before a cell actually differentiates Model Organisms Fruit y Drosophila melanogaster 0 Advanced techniques for generating and analyzing mutants 0 Large enough for easy study but small enough to determine Where genes are expressed Pattern Formation Coordination of events leading to the formation of a body With a particular morphology Formation of an adult body 0 Animals I Dorsoventral anteroposterior and rightleft May also be segmented 0 Plants Rootshoot axis in a radial pattern Positional Information Each cell in the body must become the appropriate cell type based on its relative position At appropriate times during development each cell receives positional information that tells it Where to go and What to become Cell may respond by 0 Cell division cell migration cell differentiation or cell death apoptosis 2 main mechanisms used to communicate positional information 0 Morphogens 0 Cell adhesion Morphogens Give positional information and promote cellular changes Act in a concentration dependent manner With a critical threshold concentration Distributed asymmetrically O In the oocyte or egg precursor O In the embryo by secretion and transport I Induction cells govern fate of neighboring cells W Each animal cell makes its own cell adhesion molecules CAMs Positioning of a cell Within a multicellular organism is strongly in uenced by the combination of contacts it makes With other cells and With the extracellular matrix Hierarchv of Transcrintion Factors Four general phases for body formation 1Organize body along major axes 2 Organize into smaller regions organs legs 3 Cells organize to produce body parts 4 Cells themselves change morphologies and become differentiated Differential gene regulation certain genes expressed at specific phase of development in a particular cell type Parallel between phases and expression of specific transcription factors Animal Develonment Drosophila model Oocyte establishes pattern for adult 0 Elongated cell With positional information Key process is creation of segmented body plan 0 3 general areas head thorax and abdomen Larva free living 3 stages Pupa undergoes metamorphosis Adult Egg to adult in 10 days Mse 1 Pattern Develonment First phase is establishment of body axes Morphogens are distributed prior to fertilization Bicoid example morphogen O Mutation results in larva With 2 posterior ends 0 Nurse cells are located near anterior end of oocyte O Bicoid gene transcribed in nurse cells and mRNA transported into anterior end of oocyte l Maternal effect 0 Transcription factor that activates particular genes at specific times 0 Asymmetrical distribution means activated only in certain regions Phase 2 Segments Normal Drosophila embryo divided into 15 segments 0 3 head 3 thoracic and 9 abdominal 0 Each Will give rise to unique morphological features in adult 3 Classes of Segmentation Genes Gap genes Pairrule genes Segmentpolarity genes To create a segment in phase 2 a group of genes acts sequentially to govern the fate of given body region Maternal effect genes activate gap genes Gap gene and maternal effect gene products function as transcription factors to activate the pairrule genes Once the pairrule genes are activated their gene products then regulate the segment polarity genes Expression of a segmentpolarity gene corresponds to portions of segments in the adult y Phase 3 Segment Ch cteristics Each segment begins to develop its own unique characteristic Cell Fate Segment polarity genes regulate homeotic genes Mutations in homeotic genes alter cell fate 0 Bithorax is an example of homeotic mutation Bithorax gene complex 0 Normal Wings on 2rld thoracic segment and 2 halteres on 3rd thoracic segment Mutant 3rd segment has Wings so 2 sets of Wings and no halters Role of homeostatic genes determine identity of particular segments Mse 4 Cell Differentiation Emphasis shifts to cell differentiation Studied in mammalian cell culture lines Differential gene expression underlies cell differentiation Stem cell characteristics 0 Capacity to divide O Daughter cells can differentiate into 1 or more cell types lnt Develonment 2 key features of complex plant morphology O Rootshoot axis 0 Radial pattern Differs from animal development 0 No cell migration 0 No morphogens 0 An entirely new individual can be regenerated from somatic cells totipotent Similarities to animal development 0 Use differential gene expression 0 Use of transcription factors T 2 3 Chapter 20 Biology Notes Mg Recombinant DNA technology 0 Use of laboratory techniques to isolate and manipulate fragments of DNA Recombinant DNA contains DNA from two or more sources Once inside a host cell recombinant molecules are replicated to produce identical copies or clones Procedures that lead to many copies of a particular gene Why 0 Use copies of a gene for study or manipulation 0 To obtain large amounts of gene product mRNA or protein Gene Cloning Step 1 Vector DNA is a carrier for the DNA segment to be cloned When a vector is introduced into a living cell it can replicate making many copies Common vectors are plasmid and viral Also need the gene of interest from chromosomal DNA Gene Cloning Step 2 To insert chromosomal DNA into vector Cut DNA using restriction enzymes 0 Cut specific known DNA sequences called restriction sites 0 Most restriction sites palindromic 0 May produce sticky ends DNA ligase must be used to permanently link DNA DNA ligase is an enzyme that seals the bonds between restriction fragments Restriction enzyme cuts sugarphosphate backbones DNA fragments added from another molecule cut by same enzyme Base pairing occurs DNA ligase seals strands Gene Cloning Step 3 Goal is to have recombinant vector taken up by bacteria 0 Some will take up a single plasmid 0 Most cells fail to take up a plasmid at all Vector carries a selectable marker 0 Adding antibiotics selects for cells expressing antibiotic resistance gene ampR 0 Gene ampR codes for betalactamase that degrades ampicillin which normally kills bacteria Growth on ampicillin plates indicates that bacteria contain plasmid with the selectable marker 0 Electrophoresis Technique used to separate macromolecules on a gel 0 Can be used to separate DNA or proteins Can be used to separate molecules based on their charge sizelength and mass Polvmerase Chain Reaction gPCRz Allows us to amplify DNA make many copies 0 No vectors or host cells needed Ingredients 0 Primers that match sequences at each end of the DNA fragment dNTPs deoxynucleotide triphosphates O Taq polymerase a heat stable form of DNA polymerase called 0 DNA run through repeated cycles of denaturation annealing and synthesis 0 Thermocycler machine automates this process After 30 cycles of amplification a DNA sample will increase 230 fold In vitro fertilization and PGD A use for PCR in human reproduction PGD Preimplantation Genetic Diagnosis 0 Single cell removed from embryo 39 Genetic tests via PCR g place into petri dish to grow I Remaining embryo implanted into uterus Biotechnologv Technologies that involve the use of living organisms to benefit humans Use began about 12000 years ago with domestication of livestock More recently associated with molecular genetics Insulin In 1982 US FDA approved sale of human insulin made by recombinant bacteria Prior to 1982 insulin isolated from cattle 0 Some people developed allergies and had to use cadaver insulin Insulin composed of two polypeptides A and B O A and B coding sequence inserted into Ecoli 0 Purified A and B chain mixed to form functional protein Transgenics A transgenic organism carries genes introduced using molecular techniques such as gene cloning 0 Also called Genetically Modified Organisms GMOs Gene replacement cloned gene recombines with normal gene on a chromosome 0 Only 1 of 2 copies replaced creating hetrozygote O Heterozygotes can be crossed to yield homozygotes Gene knockout if cloned gene is a mutation that inactivates function homozygote will not have gene function Very useful for studying human disease 0 Used to create models to study disease 0 Used to test effect of therapies Transgenic Animals The goal is to w a function by adding a new gene protein to the animal s genome Examples 0 Growth hormone O Oncogenes 0 Transcription factors y protein can be expressed in a transgenic animal to determine the biological role of that protein Transgenic animals have been made from m species rats mice goats cows fish plants etc These are termed geneticallymodified organisms GMOs Molecular Pharming Production of medically important proteins in livestock mammary glands Certain proteins more likely to function when expressed in mammals O Posttranslational modification 0 Degraded or improperly folded in bacteria 0 High yield in cows Pharming Pharmaceuticals and Farming Using farm animals such as sheep goat or dairy cow to produce useful recombinant proteins in their milk Involves engineering a mammary glandspecific promoter in front of the DNA encoding the protein of interest then making a transgenic farm animal Trans2enic Plants GMO 0 Successful example of the use of transgenic plants has involved the introduction of genes from Bacillus thuringiensis Bt 0 Bacterium produces toxins that kill certain caterpillars and beetles and has been Widely used as an insecticide for several decades 0Bt varieties of plants produce the toxins themselves therefore are resistant to many caterpillars and beetles Mn 0 Human therapies using Gene Therapy almost GMA humans 0 First disease studied ADA deficiency SCID My 0 September 14 1990 0 Removed lymphocytes from girl 0 Treated With retroviral vector containing ADA gene 0 Returned cells to her bloodstream 0 Results suggest that this first gene therapy trial may offer benefit but Feature Investigation Hypothesis Infecting lymphocytes With a retrovirus containing the normal ADA gene Will correct the inherited deficiency of the mutated ADA gene in patients With ADA deficiency Key Materials A retrovirus With the normal ADA gene 1 Remove ADAdeficient lymphocytes from the patient With severe combined immunodeficiency disease SCID 2 Culture the cells in a laboratory 3 Infect the lymphocytes With a retrovirus that contains the normal ADA gene As described in Chapter 18 retroviruses insert their DNA into the host cell chromosome as part of their reproductive cycle 4 Infuse the ADAgenecorrected lymphocytes back into the SCID patient Cloning Animals Nuclear Transplantation 0 In nuclear transplantation the nucleus of an unfertilized egg or zygote is replaced With the nucleus of a differentiated cell OTermed Somatic Cell Nuclear Transfer W Cloning the adult animal greatly increases the chances of generating a new animal with the desired elite traits Scientists have worked on this since 1930 s Many hoaxes and formal cases of scientific fraud and misconducted The technology for this is termed somatic cell nuclear transfer SCNT This theory the offspring should be a copy of the adult donor The initial excitement was based on the promise of developing cloned animals that are exact genetic matches of the adult However problems have arisen not to mention the ethical storm that has erupted There are not geneticallymodified animals Cloning mammals To date about 22 species have been cloned e g sheep cats dogs cattle goats rabbits horse mice pigs monkey water buffalo SCNT Somatic Cell Nuclear Transfer NOTE So far every single cloned animal has been abnormal in one way or another Clone of the 77000 The Man boar that was champion at the 2000 Indiana State Fair Researchers create pigs that produce hearthealthy omega3 fatty acids usually found in fish Cloning Humans gReproductive Cloning Human nucleus into cow egg Interspecies embryo These somatic cells are able to initiate and promote development leading to interspecies embryos 26 M Stem cells are naturallyoccurring in many tissues and organs Experimentally stem cells can be derived from many sources including embryos fetuses amniotic uid umbilical cord adipose tissue bone marrow or peripheral blood Each source provides cells of various degrees of potency In theory ES cells are pluripotent while those from more mature sources are multipotent As a general rule adultderived stem cells are less potent than embryotic stem cells Stem cells hold tremendous potential as therapeutic agents to treat a number of diseases and disorders A stem cell under one set of conditions may differentiate into a muscle cell while that same cell under different conditions may differentiate into an endothelial cell In vitro fertilization to generate ES cells Using micromanipulators cells from the inner cell mass can be removed from the blastocyst and placed into a petri dish ES Cells Hone or ane The promise surrounding ES cells has been replaced with significant problems associated with their use There is a clear need for an alternative source of stem cells that hold the differentiation potential to be therapeutically useful Stem Cell Transplantation HSC hematopoietic stem cell RX is the easiest When marrow or bloodderived HSCs are intravenously delivered to a patient they simply homein to the marrow of the individual and grow thus reestablishing the marrow with health cells from the donor The challenge arises in regenerative medicine when brain spinal cord heart liver kidneys etc are the target for cell transplant Direct surgical transplantation must be performed The aim of stem cell research is to supply cells for the repair of damage or diseased organs 0 This is 99999999 BS 0 You can t grow organs in a laboratory It is possible to grow specific cell types derived from the same batch of stem cells using specific conditions These cells are used for RX Veteringrv Uses Stem cell RX autologous is now being performed on horses and dogs for joint repair The source is adipose tissue and the final desired cell types for RX are osteoblasts and chondrocytes Chapter 10 Biology Notes Multicellular Single organism composed of more than one cell Main benefit from the division of labor Larger genomes larger proteomes Additional proteins for 0 Cell communication 0 Arrangement and attachment of cells 0 Cell specialization Extracellular Matrix ECM Network of material secreted from the cells forming a complex meshwork outside of cells Major component of certain parts of plants and animals 0 Bone and cartilage of animals 0 Woody parts of plants Animal cells secrete ECM that helps to support and organize cells Maj or macromolecules are proteins and polysaccharides 0 Proteins form large fibers 0 Polysaccharides give a gellike character Important roles such as strength structural support organization and cell signaling Proteins of ECM Adhesive O Fibronectin and laminin O Adhere ECM components together and to the cell surface Structural O Collagen provides tensile strength I Main protein found in bone cartilage tendon skin Elastin provides elasticity Expands and returns to original shape 0 Collagens are a Family of Proteins that Give Animal Cells 3 Variety of ECM Properti At least 27 different types of collagen in humans Many different genes encode procollagen Collagens all have a common triple helix structure Similar yet distinct amino acid sequence affects structure and function of collagen fibers Differential gene regulation controls which types of collagens are made Wrinkling a symptom of decreasing collagen synthesis With age Polysaccharides in Animal ECM After proteins 2nd major component In vertebrates the most abundant are glycosaminoglycan s GAGs 0 Long unbranched polysaccharides with a repeating disaccharide unit 0 Highly negatively charge attracts positive ions and water GAGs and proteoglycans resist compression 0 Form gellike component Two GAG Examples 0 Chondroitin sulfate cartilage O Hyaluronic acid found in skin eyes joint uid Chitin important ECM in invertebrates O Exoskeleton Plant Cell Walls Protective cell wall outside the plasma membrane 0 Rigidity for mechanical support 0 Maintenance of cell shape 0 Direction of cell growth Usually stronger thicker and more rigid than ECM than in animals Cell Ilunctions Adhere cells to each other and to the ECM Animals cells have a more varied group of junctions In plants cellular organization is different because of the rigid cell wall Anchoring Junctions gAnimal Cell Attach cells to each other and to the ECM Rely on cell adhesion molecules CAM O Cadherin and integrin 4 Main categories 1 Adherins junctions 2 Desmosomes 3 Hemidesmosomes 4 Focal adhesions m CAMS that create celltocell junctions Ca2 dependent adhering molecule Extracellular domain of two cadherins each in adjacent cells bind to each other to promote celltocell adhesion Homodimer Inside the cell linker proteins connect cadherins to the cytoskeleton By expressing only certain types of cadherins each cell will only bind to other expressing same type Integrins Group of cellsurface receptor proteins 2nd type of CAMS Creates connections between cells and ECM Do not require Ca2 to function Extracellular domain to bind to ECM Intracellular domain for binding to cytoskeleton Tight Ilunctions in Animals Forms tight seal between adjacent cells Prevents uid in ECM from leaking between cells Tight junctions 0 Made by occluding and claudin O Bind to each to form tight seal 0 Not mechanically strong not bound to cytoskeleton Gap Ilunctions in Animals Small gap between plasma membranes of cells at junction Six connexin proteins in one cell align with six connexin proteins in an adjacent cell to form a connexon Connexon allows passage of ions and small molecules Allow adjacent cell to share metabolites and directly signal each other Middle Lgmellg in Plants Plants use additional component of ECM to form celltocell connections First layer to form when cells diViding Cement cell walls of adjacent cells together Middle lamella rich in pectins QMPPP O Ripening fruit secrete pectinases such that ripe fruit is less firm than unripe fruit Plasmodesmata in Plants Functionally similar to gap junctions Allow passage of ions and molecules between adjacent cells Different in that they are open channels where the cell membrane of one cell is continuous with adjacent cell membrane Desmotubule connects ER membrane of adjacent cells Tissue and Organs Tissue 0 Group of cells having similar structure or functions 0 Humans have over 200 different cell types that are grouped into a few general categories Organ 0 Collection of two or more tissues that perform a specific function or set of functions 4 General Types of Animal Tissue Epithelial tissue 0 Cells joined together forming continuous sheets to cover or line body surfaces Connective tissue Support body or connective tissues Nervous tissue 0 Receives generates and conducts electrical signals Muscle tissue 0 Generates force that facilitates movement 6 Basic Cell Processes to Form Tissues or Organs Cell division Cell growth Differentiation Migration Apoptosis Cell connections 3 Tvnes of Plant Tissue Dermal Tissue 0 Covering on various plant parts 2 Ground Tissue 0 Most of plant s body With variety of functions 3 Vascular Tissue 0 Form interconnected conducting vessels for water and nutrients
Are you sure you want to buy this material for
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'