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by: Jercell Notetaker


Jercell Notetaker

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Biology notes
Dr. Wilson
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This 50 page Study Guide was uploaded by Jercell Notetaker on Sunday March 6, 2016. The Study Guide belongs to BIOL1081 at University of Cincinnati Blue Ash College taught by Dr. Wilson in Spring 2016. Since its upload, it has received 84 views. For similar materials see Biology in Biology at University of Cincinnati Blue Ash College.

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Date Created: 03/06/16
Jercell Respicio Bio • - - Aug 31 Monday - Canus Lupus (Wolf) Genus-Species - Canus Lupus Familiarus (Dog) - Applied Selective breeding (Took the ones who were friendly) • Started to look different because we selected for “puppy” like behavior • So we derived different colors and shapes • Different species cannot make fertile offspring - Bacteria, archaea, (prokaryotes) and eukarya - Prokaryotes: without a membrane bound nucleus • there are eukaryotes that are single celled - Ursidae family of bears • Genus ursus • Species ursus americanus - - Sept 3 Thursday reading notes - DNA is the universal genetic language - - - Sept. 3 Thursday Reading notes: Chapter 2 Chemical Context of Life - Key concepts • 2.1: Matter consists of elements in pure form and in combinations called compounds • 2.2: An element’s properties depend on the structure of its atoms • 2.3: The formation and function of molecules depend on chemical bonding between atoms • 2.4: Chemical reactions make and break chemical bonds • 2.5: Hydrogen bonding gives water properties that help make life possible on earth - 2.1 Matter consists of elements in pure form and in combinations called compounds • Organized matter has emergent properties - Ex:) metal Sodium and poisonous gas Chlorine form and edible compound Sodium chloride • Elements of life - about 20-25% of 92 elements are essential elements - O, C, H, N make up 96% of living matter - Ca, P, K, S are responsible for other 4% - Trace elements are elements required only in minute amounts Jercell Respicio Bio • • Ex) Fe is required for some living creatures, Iodine is important in vertebrae animals for hormone production in the thyroid gland • Some organisms are tolerant to chemicals that are otherwise harmful to other organisms - Ex) Sunflower plants are able to take up zinc, lead, and other heavy metals in concentrations that are harmful to other organisms - 2.1 Section Questions: • Are trace elements essential elements? - Yes although they are small amounts required, it is still essential for the functioning of an organism • Iron is a trace element that humans require in order for hemoglobin to carry oxygen into blood stream. What might be the effects for an iron deficiency? - Person will have lack of iron in their blood (anemia, caused by abnormal hemoglobin) - 2.2 Element’s Properties Depend on the Structure of its atoms • An atom is the smallest unit of matter that still retains properties of an element • An atom is broken down to even smaller units called Subatomic Particles - Proton - Neutron - Electron • The opposite charges of electrons and protons are the reason electrons remain in the vicinity of the nucleus • Radioactive Isotope: the nucleus decays spontaneously, giving off particles and energy - When a radioactive isotope gives leads to a change of protons it becomes a different element - Used in dating relics of past life - Used to trace and follow atoms through metabolism Atoms would use them as they would use the normal nonradioactive elements but • radioactive elements are easier to keep track off • Electrons - the further an electron is from the nucleus the more potential energy it contains Jercell Respicio Bio • - For an electron to move shells, it must lose or gain the same amount of potential energy as the shell below or above • light excites electrons and some jump to a higher shell • when they lose energy, the usually release it via heat • First shell cannot contain more than 2 electrons • Second shell holds 8 electrons • Electrons with the same number of valence electrons have similar properties - Ex:) fluorine and chlorine both have seven valence electrons and form compounds with sodium Electrons with completed valence electrons are non-reactive or inert • • Reactivity of an atom arise from the presence of one or more unpaired electrons in its valence shell • Atoms interact in a way that completes their valence shells • Chemical bonds - Covalent bonds: when atoms share their electrons Ex) two hydrogen atoms completing valence shells - two or more atoms joined together by a covalent bond constitutes a molecule - Valence : how many electrons required to complete valence shell, or, bonding capacity - 2.3 The Formation and Function of Molecules Depend on Chemical Reactions between atoms • Nonpolar Covalent Bond: two atoms of the same elements form a bond, it’s at a stand off • Polar Covalent Bond: When one atom is more electronegative than the atom and the electrons are shared unequally • Covalent Bonds are the strongest bonds • Weak bonds are advantageous - Two molecules can come together, respond to one another in some way and separate • Weak Bonds - Hydrogen Bonds - Vander Waals • accumulate in one area - Ex:) geckos tip of micro hairs and surface have so many bonds it supports its weight Jercell Respicio Bio • - Questions 2.3 1. Why does the structure H-C=C-H fail to make sense chemically? Because there can’t be a double bond on that side of Carbon if it’s already bonding with two Hydrogen atoms on either side 2. What holds the atoms together in a crystal of magnesium chloride? An ionic bond (metal then non-metal) 3. If you were a pharmaceutical worker why would it be important to know the 3-D shape of a molecule? Because the shape can react with different receptors in our body and can elicit different responses. Example, drugs that mimic endorphins. 2.4 Chemical reactions make and break bonds • Chemical Reactions: the making and breaking of chemical bonds leading to changes in the composition of matter. • All chemical reactions are reversible • The rate of the reaction depends on the concentration of the reactant molecules same with products since they’re reversible • Products and reactants finally reach a chemical equilibrium where they offset one another - Reactions are still happening they just have no net result on the products or reactants - Does NOT mean equal in concentration just stabilized in a certain ratio • Some reactants stop when it’s almost fully converted into a product Questions 2.4: 1. Which type of chemical reaction is formed faster in equilibrium, the formation of reactant to products or products to reactants? It depends on the concentration of either, if the concentration is high in the reactants it will most likely accelarate the rate in which it becomes a product but the product may reach and become the reactant depending on the amount of concentration; it may happen at a faster, slower, or the same rate 2. Write an equation that uses the products as reactants and vise versa. Add energy as another product. This is cellular respiration. Describe how this is related to breathing. C₆H₁₂O₆ + O₂ → CO₂ + H₂O + energy Sugar and Oxygen is converted to carbon dioxide, water, and energy Jercell Respicio Bio • 2.5 Hydrogen Bonding Gives Water Properties that Help Make Life Possible on Earth - Cohesion: water molecules adhering together - Adhesion: clinging of water molecules to other surfaces/substances - Surface Tension: measure of how difficult it is to stretch or break the surface of the liquid - Water has the ability to store a lot of heat • Water releases this heat when the air gets cold • Reason why coastal regions are so warm - A calorie of heat causes a relatively small change in the temperature of water much of the heat is used to disrupt hydrogen bonds before the water molecules can begin • moving faster • when the temperature of the water drops slightly, many hydrogen bonds reform giving of a lot of heat - Organisms are able to resist drastic changes of temperature Evaporative Cooling - Molecules that are moving fast enough can depart and enter the air as gas - Even in low temperatures the fastest molecules still enter the air - There is always some sort of evaporation happening - Heat of Vaporization is how much it takes for 1g of liquid to evaporate • It takes water 580 cal, a high number - Earths Surface • A lot of heat is consumed during the evaporative process of the surface of sea water - Heat required to break the bonds and make molecules fast enough to exit in the air • Then as moist air condenses a lot of heat is released as it rains - Bonds form again so heat is released • When the fastest molecules leave, then the average speed of kinetic energy (temp) lowers so the sea surface becomes cooler - Organism Level • Steam burns - When steam hits the skin it cools and becomes water, it then releases heat • When the sea becomes cooler because of evaporative cooling - This helps prevent marine life from over-heating Jercell Respicio Bio • • In plants, they evaporate water to prevent overheating Sweat evaporating has the same concept, it dissipates body heat • - In humid days, the water vapor in the air disrupts our bodies ability to evaporate sweat - Floating of Ice on Liquid water - Floating of Ice on water • Water in its solid form is less dense • When the molecules are moving too slow, nothing disrupts the hydrogen bonding so water becomes locked in a crystalline structure, the molecules an “arms length” away - Below 4C to 0C When Ice absorbs heat to be above 4C the molecules begin to move and the crystalline • structure begins to fall apart • Water reaches its greatest density right when ice melts then becomes less dense since the molecules move faster and faster - Water The Solvent of Life • Solute is what’s being dissolved • Solvent is what’s dissolving • Solution is the homogenous mixture Aqueous solution is one where water is the solvent • • Because of waters polarity (hydrogen are partially positive and oxygen negative) - Ions are attracted to each - Example • in NaCl the sodium cations are attracted to the negative oxygen ion and the Cl anions are attracted to hydrogen - This surrounds each ion separating them from the larger molecule • This is called a hydration shell A compound doesn’t have to be ionic for it to be dissolved • - Solute Concentration in Aqueous Solutions • Find Comp molec. mass (all amus added) • Make it g • Whatever that measurement represent one mole of molecules • Molarity is how many moles of a solute are in one L of water - Acids and Bases • Water combines with Carbon Dioxide to for Carbonic Acid Jercell Respicio Bio • •Yields a bicarbonate Ion and a hydrogen ion The more acidic, calcification of marine life can’t form, H+ ions bind with Co32- inhibiting calcification Chapter 3 Carbon Compounds and Life - A compound that contains Carbon is said to be an Organic Molecule - 3.1 Carbon Atoms can Form Diverse Molecules by bonding to four other atoms • Usually bonds with C,H,O,N,S,P Chemical Groups Most important to Life • Chemical groups can change the place of a hydrogen attach to the carbon skeleton • Just the shape of the molecule determines ints function - Ex) Estradiol and Testosterone • Chemical groups are called Functional Groups Except for Sulfuhdryl, they are hydrophilic which increases solubility of org. compounds in • water Jercell Respicio Bio • • Methyl group is not reactive - acts as a tag on molecules ATP: Important Source of Energy for Cell Proc. • Adenosine attached to three phosphate groups Jercell Respicio Bio • 3.1 Questions 1. How are gasoline and fat chemically similar? 1. Hydrocarbon linkages are non polar and don’t dissolve in water 2. What does the term amino acid signify about the structure of such a molecule? 1. It has an amine group and an extra H+ ion 3. What if suppose you had an organic molecule such as cytesine, and you chemically removed the -NH2 group and replaced it with -COOH. How would this change the chemical properties of the molecule? 1. This would no longer have an amine group Macromolecules are Polymers built from Monomers • Monomers are smaller molecules that when put together form chains Polymers are all these chains combined which are Macromolecules • • Dehydration Synthesis takes water from polymer chains and break them apart • Hyrolysis puts water back in places that need an- H and another- OH • In our digestive track, various enzymes (which speed up chem. reactions) attack polymer chains that we consume - Hydrolysis breaks them apart - Bloodstream takes up to cells - Cells then use dehydration synthesis to put them back together Jercell Respicio Bio • 3.3 Carbohydrates Serve as Fuel and Building Material • Carbohydrates include sugars and polymers of sugars • Monosaccharides Sugars • Sugars - Monosaccharides contain CH2O • Ex) glucose C₆H₁₂O₆ • Carbonyl group can either be at the end - Glucose • Or in the middle - Fructose • Polysaccharides are long polymer chains - Ex) starch for plants and glycogen for animals - Structural Polyssacharides • Plants have cellulose • Cellulose is a monomer of starch - Glycosidic linkage is upside down • Starch and glycogen are helical • Cellulose is straight - the beta form of glucose dictates this - Always straight and bond with other straight cellulose polymers parallel to it (-OH) - this is how cell walls are formed • We don’t have enzymes to digest cellulose that’s why we secrete plants the way they are in our fecal matter. • The cellulose abrades the wall of the digestive track which stimulates mucus production providing easy passage for food to travel • Cows have protists and prokaryotes in digestive system that digest cellulose to form glucose • Same with termites Jercell Respicio Bio • • Bugs use chitin (structural polysaccharide) to from exoskeletons 3.4 Lipids are a diverse group of hydrophobic molecules • Not big enough to be considered macromolecules • Don’t include true polymers • Hydrocarbons • Hydrophobic • Fats, phospholipids, and steroids Fats • Glycerol and fatty acids - glycerol is an alcohol - fatty acid has a long carbon skeleton, end has a carboxyl • Triaglycerol: one glycerol with three fatty acids attached by esther linkages Saturated means that all carbons are single bonded so as many hydrogens can bond on • the chain - Ex) most human fats, butter and lard are solid at room temp, without kink they can solidify • Unsaturated means that there are double bonds, this forms a kink in the structure - Ex) fish oil, cod oil are unsaturated and are liquid at room temp • Fat stores twice as much energy as a polysaccharide • Plants can store large amount of molecules as form of starch because they’re stationary Jercell Respicio Bio • • Human need another source, which is fat Phospholipid • Important in cell membranes • Instead of three fatty acid chains it has a phosphate group so it has a negative charge • Form phospholipid bilayer, phosphate group is attracted to water Steroid • Lipids that have a carbon skeleton of four fused rings 3.5 Proteins Include a diversity of structures resulting in a wide range of functions • “Proteios” latin for primary or first • Functions in cells - Speed up chem reactions - Defense - Storage - Transport - Cellular comm - Movement - Structural Support • Enzymes are proteins that act as catalysts - Agents that speed up chemical reactions without being consumed by the reaction themselves • Vary in structure and function • Made of polymers called polypeptides • Protein consists of one or more polypeptide folded into a specific 3-D shape Amino Acid • Contains one amino group and one carboxyl group • Polypeptides and polymers constructed from same set of amino acids Jercell Respicio Bio • • Side chains (R groups) of Amino acid are acidic or basic (Hydrophilic) or hydrophobic depending on their chemical properties • End amine group (N-terminus) and end Carboxyl group (C-terminus) Protein Structure and Function • one or more polypeptide chains form a protein • Can be fibrous or globular proteins • Bonds within are determined by R groups Four groups • - Primary - Secondary • hydrogen bonds • Alpha Helix • Beta pleated sheet - Ex) spider web - Tertiary Hydrophobic interaction • - Quaternary • Collagen • Proteins that are formed from two or more polypeptide chains 
 Jercell Respicio Bio • 14 Sep. 2015 Lecture • Framework of biol. molecules Carbon binds mostly with - C,H,O,N,S,P • Forms us to 4 Covalent Bonds • Hydrocarbons: molecule consisting only of carbon and hydrogen - Non polar - Functional group add chemical properties - Macromolecules are polymers built from monomers • Polymer long molecule consisting of many similar building blocks • The small building block molecules are monomers • Three of the four classes of life organic molecules are polymers - Carbs - Proteins - Nucleic Acid • Lipids are most complex - Making and breaking polymers • Dehydration Synthesis - Formation of large molecules by removal of water - Monomers are joined to form polymers • Hydrolysis - Polymers broken down to monomers • addition of water - Carbohydrates • Molecules with a 1:2:1 ratio of Carbon, Hy, and Oxy • Empirical formula (Ch20) • C-H Bonds hold much energy - energy storage - Ex) sugars, starch, glucose - Monosaccharides • simplest carbohydrate • 6 carbon sugars are important • Glucose Jercell Respicio Bio • • Fructose is a structural isomer (put together differently that glucose) of glucose • Galactose is a stereoisomer of glucose (reflected) • Enzyme for each of these sugars that recognize six carbon skeleton Lecture Notes 25 Sep. 2015 • Defined group of molecules with one main chemical characteristic - insoluble in water • High proportion C-H bonds - Hydrophobic • Fats, oils, waxes, steroids • Fats - Triglycerides • Composed of one glycerol and 3 fatty acids - Fatty Acids • long chain of carbons attached with hydrogens (carbon skeleton) - Saturated-no double bonds between carbon atoms • Higher melting point • found in animal tissue - Unsaturated-one or more double bonds • Low melting point, plant origin - Trans Fats • Produced industrially - Triaclyglycerol • fats - Phospholipids • bilayer - Steroids • shape function Chapter 1: Introduction Evolution and Foundations of Biology Key Concepts: - 1.1 Studying diverse forms of life reveals common themes - 1.2 The Core Theme: Evolution accounts the unity and diversity of life Jercell Respicio Bio • - 1.3 Biological Inquiry entails forming and testing hypotheses based on observations of nature - Overview • Evolution - beach mice example 1.1 Studying Diverse forms of life reveals common themes Biosphere: consists of all life on earth and all places where life exists - Ecosystem: All living things in an area as well as all the non living things that interact with living things like soil water atmospheric gases and light. Ex) deciduous tree forest • Communities: All the organisms that live in an ecosystem. Ex) bacteria, trees, fungi, animal, plants (all the species) - Populations: individuals of a species that inhabit a specified area. Ex) White tailed deer • Organisms: Individual living things - Organs and Organ Systems: a team of organs that work together. Organs consists of multiple tissues - Tissues:a group of cells that work together Cells: fundamental unit of life • - Organelles: functional components of a cell - Molecules: chemical structure composed of two or more atoms • Reductionism - a way of simplifying things in biology • Emergent Properties - new things that arise as complexity increases • Systems Biology: analyzing how parts work together in a system - Ex) how can a drug that lowers blood pressure affect organ system. How does the increase of carbon dioxide alter ecosystems and entire biosphere? Structure and Function • Structure lets us know what it does and why it does that - Ex) Hummingbird’s wings lets it hover and long beak lets it collect nectar The Cell: An organism’s basic unit of structure and function • It can perform all required activities • All are enclosed by a membrane Jercell Respicio Bio • • Two cells - Prokaryotes: Without a nucleus • bacteria and archaea • generally smaller than eukaryoes • do not have a membrane bound nucleus or organelles - Eukaryotes: With a nucleus • all other forms of life • contains membrane enclosed organelles Theme: Life’s Processes Involve the Expression and Transmission of Genetic Information - Chromosomes contain genetic material in the form of DNA DNA Structure and Function • DNA is replicated and each cell gets a complete set of chromosomes • Chromosome contains a long strand of DNA that encodes for genes • DNA encodes for proteins which carry out cells work - Ex) certain enzyme protein required to assemble the cell membrane, while a human gene may denote production of anti-body • Gene Expression - RNA is used to encode for specific proteins - Called Gene expression Genomics: Large-Scale Analysis of DNA sequences • Genome is an entire library of genetic instruction of an organism • Reseatches use genomics, looking at whole sets of genes instead of one at a time • Bioinformatics allows researches to store large amounts of information. Theme: Life Requires Transfer and Transformation of Energy and Matter • energy flow chemical recycling • releases heat • Energy enters as light and leaves as heat (through) • Contrast chemical elements are recycled (within) - Ex) chemicals plant absorbs from air or soil incorporates in plants body then animal eats eat so energy flows then animal dies and chemicals returned to environment by decomposition. Chemicals are available for plant uptake again. Completing cycle. Jercell Respicio Bio • Theme: Organisms Interact with Other Organisms and the Physical environment Living things interact with its environment benefiting them • Evolution • descent with modification • common ancestor 1.2 Evolution accounts for unity and diversity of life • Diversity arises from evolutionary processes The Three Domains of Life Bacteria • • Archaea • Eukarya - Plantae - Fungi - Animalia • Classified by how the obtain food (fungi uses its surroundings) Charles Darwin’s Natural Selection Species arose from descendants different from them • • Descent with modification (duality of life’s diversity and unity) • Natural Selection is the mechanism for descent with modification 1.3 Biological inquiry entails forming and testing hypotheses based on observations of nature Making Observations • Hypothesis: tentative answer to a well framed question; explanation being tested\ • Rational Accounting for a set of observations and inductive reasoning Jercell Respicio Bio •   Chapter 4: A Tour of The Cell 4.1 Biologists use microscopes and the tools of biochemistry to study cells Microscopy • Developed the light microscope ( Antoni Leeuwenhoek) - Light Microscope-light passed through a specimen through lens which refracts the light in a way that magnifies specimen. • Three Parameters to light microscope - Magnification: ratio of an object’s image to it’s real size - Resolution: how clear the image is. Minimum distance two points can be separated and still be distinguished as separate points. • For Ex:) what seems like one star to the naked eye can be twin stars when looked at with a microscope - Contrast: distinguish brightness of certain ares of the specimen • Developed Electron Microscope - couldn’t use standard light microscopy to distinguish organelles - Instead of light, electron miscopies focus a beam of electrons onto the surface of a cell - Resolution is inversely related to the wavelength of the radiation a microscope uses for imaging - Electron beams have a super short wavelength - Modern Electron microscopes can achieve a resolution of about .002nm • Transmission Electron Microscope - Used to see internal structures of a cell - Aims electron beam through a thin section of the cell - Sections are stained with heavy metals so electrons are attracted to it Enhances density of a specific part • • Scanning Electron Microscope - Beam excites electrons on the surface and device translates pattern into a screen - Result is a 3-D image • Cytology: the study of cell structure Biochemistry: the study of the chemical processes of cells • Cell Fractionation Jercell Respicio Bio • • Broken up cells are placed in a tube that is spun around in a centrifuge This results in the largest cell’s components to settle in the bottom of the tube • • This process is repeated until there are multiple “pellets” on the bottom of tube consisting of cellular parts • EM revealed a lot of mitochondria in a cell and Fractionation revealed enzymes - Concluded that mitochondria is site for cellular respiration - Cytology and Biochem working together 4.2 Eukaryotic Cells Have Internal Membranes that Compartmentalize Their Functions Comparing Prokaryotic and Eukaryotic Cells • Eukaryotic Cells have a nucleus in which DNA is stored Prokaryotic Cell has a nucleoid in which DNA is located but not enclosed by a membrane • • Cytoplasm: - Both type have a cytoplasm - In cytosol, there are membrane bound structures suspended that carry out functions • Metabolic Requirements Dictate Size of the Cell - Plasma membrane allows for passages of very small things only - Surface area to volume ratio is important - As a cell increases size, volume grows more proportionately than S.A. - A small cell has a greater ratio of S.A. than volume As cells increase in volume, S.A. decreases which is bad because S.A. is needed to facilitate cellular metabolism Jercell Respicio Bio • • Things have to move faster in a cell so there has to be less volume thus creating a larger surface area so that things can get across more efficiently without having more dimensions to worry about - Fro Ex:) intestinal cells have microvilli which are projections that increase the surface area (more metabolic space) less volume to carry out functions Panoramic View of the Eukaryotic Cell • eukaryotes have membrane bound parts that carry out functions so a lot can be happening all at once • The membranes (plasma and organelle) are directly involved in the metabolic processes because many of them contain enzymes within the membrane • In the phospholipid bilayer (which many membrane bound organelles have), there are proteins embedded - each membrane have different arrangements of lipids and proteins that are specific for that cells function • for ex: mitchondria membrane have arragnements that are specific for cellular respiration 4.3 The Eukaryotic cell’s genetic instructions are housed in the nucleus and carried out by the ribosomes The Nucleus: Information Central • Nuclear envelope encloses the nucleus - Double membrane • Each membrane (inner and outer) have pores • Pore Complex lines each pore by regulating entry and exit of proteins, RNA’s as well as large complexes of macromolecules - Except for at the pores the membranes are lined with nuclear lamina which supports the shape of the nucleus by supporting the nuclear envelop • DNA is organized the nucleus in formations called Chromosomes - There are proteins that help coil the DNA - Complex of DNA and proteins that make chromosomes are chromatin - Chromatin not distinguishable as specific chromosomes yet until division • when cell divides chromosomes pack further • Nucleolus make ribosomes - make rRNA (ribosomal RNA) - Proteins imported from the cytoplasm assembled with rRNA to make subunits of ribosomes - exit into the cytoplasm via pores and make actual ribosomes • Nucleus make mRNA - mRNA exit into the cytoplasm via nuclear pores - Ribosome translate mRNA to make polypeptide chains Ribosomes: Protein Factories Jercell Respicio Bio • • Made up of rRNA and protein are components that carry out protein synthesis - Cells that have high rates of protein synthesis have a large number of ribosomes • Cells active in protein synthesis have a prominent nucleoli • Two Cytoplasmic Locations for Ribosomes - Free ribosomes: suspended in the cytosol • usually make proteins that stay in the cytosol - for ex:) enzymes for sugar breakdown - Bound ribosomes: attached to the outside of the endoplasmic reticulum or nuclear envelope. • make proteins that are for packaging or export or membrane components • Both kinds are structurally identical and can be interchangeable Concept Check 4.3 Ribosomes translate mRNA to polypeptide chains making proteins 1. 2. Consists of DNA and the rRNA replicated from DNA and other proteins. These make small ribosomal sub units. These are secreted out into the cytosol to make actual ribosomes. 3. Chromatin (chromosomes plus proteins). Chromatin pack tighter when cell is about to divide. 4.4 The endomembrane system regulates protein traffic and performs metabollic functions in the cell • Endomembrane System includes: nuclear envelope, the endoplasmic reticulum, the lysosomes, various kinds of vesicles and vacuoles, and the plasma membrane • Carries out functions such as - Protein synthesis - Detoxification of poisons - Transport of proteins into membranes or out of the cell - Metabolism and movement of lipids • Could me tiny vesicles (mini membranes) or continuous membranes The Endoplasmic Reticulum • consists of networks of little tubules and sacs called cisternae • ER membrane separates the inside of the ER (lumen) from the cytosol • ER is continuous with the nuclear envelope - The space between the two membranes of the envelop is continuous with the ER • Smooth ER: lack of ribosomes • Rough ER: studded with ribosomes Jercell Respicio Bio • Functions of the Smooth ER • functions in diverse metabollic processes (vary with cell type) • Synthesis of lipids, metabolism of carbohydrates, detoxification of drugs and poisons and storage of calcium ions • Important in the synthesis of lipids including - Oils - Phospholipids - Steroids • For ex: In animal cells, smooth ER produces steroids like sex hormones and other steroid hormones secreted by adrenal glands • Cells that secrete these hormones (testes and ovaries for ex) are rich in smooth ER - Other enzymes of the smooth ER help detoxify drugs and poisons Ex) Liver Cells • • Enzymes detoxify drug molecules by adding a hydroxyl group to them making them more soluble and easier to get out of the body - Ex:) drugs like barbiturates is metabolized by the liver by adding OH group. - Results in proliferation of SER and it’s associated detoxification enzymes - Increases tolerance, so higher doses are required - Can result in tolerance of other drugs - Barbituate abuse can result in decrease effectiveness of antibiotics or other useful drugs • Smooth ER contains calcium ions - For ex:) in muscle cells smooth ER membrane pumps calcium ions from the cytosol into the ER lumen. when muscle cell is stimulated by a nerve impulse calcium ions rush back • across the ER membrane and back to the cytosol and trigger the contraction of the muscle cell. Functions of the Rough ER • Types of cells secrete proteins produced in the ribosome - For Ex:) pancreatic cells synthesize the protein insulin and secretes this into the bloodstream • As polypeptide chain grows in the bound ribosome, the chain is threaded into ER lumen through a pore formed by a protein complex in the ER membrane • As this polypeptide chain enter the lumen, it folds into its functional shape • Most of these secretory proteins are glycoproteins - proteins that have carbohydrates covalently bonded to them - carbohydrates are attached to the proteins in the ER by enzymes built into the ER membrane • ER membrane keeps secretory proteins separate from the proteins made by free ribosomes (which will remain in the cytosol). • Secretory exit by being in the vesicles that bud like bubbles in the transitional ER - called transport vesicles Jercell Respicio Bio • • Rough ER is also a membrane factory - grows in place by adding membrane proteins and phospholipids to its own membrane - as membrane bound proteins grow in the Ribosomes they are inserted into the Er membrane itself and is anchored by their hydrophobic portions • Assembles membrane phospholipids from precursors in the cytosol • ER membrane continously expands and some are transformed to transport vesicles to other components to other components of the endomembrane system The Golgi Apparatus: Shipping and Receiving Center • After leaving the ER many transport vesicles travel to the Golgi Apparatus • Warehouse for - Receiving - Sorting - Shipping • Some manufacturing • Products of the ER such as proteins are modified and stored and then sent to specific locations • Golgi Apparatus is prominent in cells that involve secretion • Consists of flattened membranous sacs-cisternae • Many of these stacks (separated from the cytosol) • Vesicles concentrated on the vicinity of golgi are engaged in transfer of materials between golgi and other structures • Have a cis face that receives and a trans face that secretes • Golgi Cisternae themselves mature and move along to trans side as they transport things • Some vesicles recycle enzymes that have already moved forward back to a part that requires more maturation • Products of ER are modified in the ER itself and then as they pass along the Golgi - Golgi removes some sugar monomers of glycoproteins and substitutes other producing a large variety of carbohydrates - Membrane phospholipids may also be altered in golgi • Can also manufacture some macromolecules • Many polysaccharides are secreted by golgi - For example:) pectins and certain other non cellulose polysaccharides are made in the golgi of plant cells and the incorporated along with cellulose into their cell walls • Transport vesicles budded from golgi may have external molecules on their membranes that recognize “docking sites” on the surface of specific organelles or on the plasma membrane Lysosomes: Digestive Compartments • Membranous sac that hydrolyzes macromolecules - contains hydrolytic enzymes Jercell Respicio Bio • Lysosomal enzymes work best in the acidic environment found in lysosomes • • If a lysosome breaks open the enzymes don’t work well in the neutral ph but if enough is leaked out it can destroy the whole cell by self-digestion • Hydrolytic enzymes and lysosomal membrane are made by Rough ER and then transferred to Golgi for further processing. • Lysosomal proteins aren’t destroyed because they have protection in vulnerable bonds from enzymatic attacks • Amoeba and other types of protists eat by phagocytosis - Lysosome engulf food particles - Food vacuole fuses with lysosome which digested the food - Digested products (monomers) secreted into the cytosol to become nutrients for the cell • Human cells have macrophages a type of white blood cell that engulfs bacteria and other invaders • Lysosomes also use their hydrolytic enzymes to recycle the cell’s own organic material - autophagy - takes a damaged organelle or small amount of cytosol fused by a membrane digesting it’s products recycling the small organic compounds to the cytosol for use With the help of these, the cell is able to renew itself • - for ex) human liver cell recycles half of its macromolecules each week - for ex) cells of people with lysosomal storage disease lack a functioning hydrolytic enzyme. Lysosomes are engorged with indigestible material • For ex) tay sachs disease, lipid is invading the brain because lysosomes don’t have required hydrolytic enzyme required to hydrolyze it Vacuoles: Diverse Maintenance Compartments • Vacuoles are large vesicles derived from ER and GolgApp • Integral Parts of the endomembrane system Selective in transporting solutes; as a result, solution inside a vacuole differes from • composition of liquid in the cytosol • Food Vacuoles • Contractile Vacuoles that pump excess water out of the cell mainting a suitable concretion of ions and molecules inside cell • Some vacuoles in plants and fungi carry out enzymatic hydrolysis much like lysosomes do in animal cells • In plants small vacuoles can hold reserves of important organic compounds suc as proteins stockpiled in the storage cells in seeds. • May also help protect the plant against herbivores by storing compounds unpalatable to animals some plant vacuoles contain pigments that hep attract pollinating insects • Large Plants usually have a large central vacuole - coalescence of small vacuoles • Solution inside the central vacuole is called the cell sap Jercell Respicio Bio • - contains cells repository of inorganic ions, including potassium and chloride • Central vacuole is important in the growth of plant cells which enlarge as the vacuole absorbs water Concept Check 4.4 1. Difference between smooth and rough ER are the studded ribosomes 1. Both types make phospholipids but membrane bound proteins and and secretory proteins are made in the rough ER. Smooth ER functions in the detoxification, carbohydrate metabolism, and storage of calcium ions 4.5 Mitochondria and Choloroplasts change energy from one form to another • Mitochondria - sites of cellular respiration - Metabolic process that uses oxygen to generate ATP by taking energy from sugars, fats, and other fuels • Sugars->energy (ATP) by use of 02 - Chloroplasts • photosynthesis Conversion of solar energy to chemical energy • • absorption of sunlight to drive synthesis of organic compounds such as sugars from Co2 and H20 • Share same evolutionary origins - peroxisome is an oxidative organelle Jercell Respicio Bio • Evolutionary Origins of Mitochondria and Chloroplasts Endosymbiotic theory • - early eukaryote engulfed something like a mitochondria • Oxygen using prokaryote • host cell formed a close relationship with the cell and became an endosymbiont (cell living in another cell) • overtime they merged to become a single organism - This new cell engulfed a photosynthetic prokaryote • ancestor of chloroplasts containing cells • Evidence that these were independent cells - double membrane (unlike other endomembrane organelles) • chloroplasts have an internal system of membranous sacs - they contain their own ribosomes as well as other circular forms of DNA they have their own genetic code • produces own proteins • - Autonomous (somewhat independent) can reproduce and grow on their own Mitochondria: Chemical energy conversion • Double membrane with a multitude of proteins - Outer membrane is smooth, inner membrane is convoluted • convolution are called cristae • Inner membrane - called mitochondrial matrix encloses different enzymes as well as the mitochondrial DNA and ribosomes - • Enzymes help catalyze cellular respiration • some of the enzymes like the one that makes ATP is embedded into the inner membrane - the highly folded cristae increases surface area which enhances ATP production (mitochondrial productivity) • Mitochondria are in all eukaryotic cells - plants - fungi - animal - most protists • Some cells have on large mitochondrial but most of them have hundreds or thousands of mitochondria - number correlates with cell’s metabolic activity • For ex:) cells that contract and move have a large number of mitochondria • Mitochondria aren’t static structures - Move around - Changing their shapes - Fusing and dividing in two Jercell Respicio Bio • Chloroplasts: Capture of Light Energy • Chloroplasts contain the green pigment chlorophyll - contain enzymes and other molecules that function in the photosynthetic production of sugar • These lens shaped organelles - 3-6 micro meters are found in leaves and other green organs of plants and in algae • Has a double membrane separated by an intramembranous space - Inside the chloroplast is another membranous system in the form of thylakoids (membranous sacs that are interconnected) - Each stack is called a granum - The fluid that is within the inner membrane is called the stroma • contains DNA, ribosomes, and enzymes • The membranes of the chloroplasts separate the chloroplasts into three sections - Intramembranous space - Stroma - Thylakoid space • This organization allows for the conversion of sunlight into energy • Are dynamic non-stagnant organelles that travel along the cytoskeleton Chloroplasts belong in a family called plastids • - a type of plastic is amyoplast, a colorless organelle that stores starch (amylose) particularly in roots and tubers - chromoplats have pigments that give fruits and flowers their orange and yellow hues Peroxisomes: Oxidation • Peroxisome: specialized metabolic compartment - one membrane - contain ezymes that oxidize removes hydrogen atoms from certain molecules and transfer them to oxygen • producing hydrogen peroxide (H202) - For ex:) peroxisomes in the liver cells • peroxisomes detoxify things in the liver cell such as alcohol and other harmful compounds by taking a hydrogen from them and transferring them to oxygen making H202 and then transferring that to water - the enzymes that destroy these compounds and make hydrogen peroxide are sequestered from other cellular components that can be damaged • Peroxisomes increase in size as by incorporating proteins made within the cytosol, and ER as well as lipids made in the ER and within the peroxisome itself Concept Check 4.5 1. Chloroplasts and mitochondrion Jercell Respicio Bio • 1. double membrane, both the chloroplasts and the mitochondrion have a double membrane with an intramembraneous space. They also both deal with energy conversion. Mitochondria deals with conversion of organic molecules to ATP with the use of oxygen; cellular respiration and in chloroplasts, the synthesis of chemical energy from solar energy. Absorbs sunlight and drives synthesis or sugars via C02 and H20. The compartments in each allow for these reactions to occur. Cristae in mitochondria allow for more surface area for metabolic productivity. Thylakoids are compartments that help carry out photosynthesis, and usually appear in interconnected stacks called granum. Each compartment has enzymes imbedded in the membrane that help carry out metabolic function. 2. Plant cells do have mitochondria. Plants still need an abundant amount of ATP to perform cellular function. Chloroplasts are there for production of food, as for animals this ins done through ingestion. ATP is still needed. 1. Chloroplasts form the sugar needed but mitochondria produce ATP from these sugars 3. Chloroplasts and mitochondrion are not part of the endomembrane system because they have characteristics that differentiate them from the rest of the endomembrane system such as: 1. they contain own DNA, ribosomes, and proteins 2. They are autonomous which means they are somewhat independent, able to grown and reproduce on their own 3. they have a double membrane 4.6 The cytoskeleton is a network of fibers that organizes structures and activities and activities in the cell Roles of the Cytoskeleton: Support and Motility • Provide mechanical support to the cell and maintain its shape • This is important for animal cells because they lack cell walls Like a tent, the cytoskeleton is stabilized by opposing forces exerted by its element • • Provide a lot of anchorage for many organelles and cytosolic enzyme molecules • Cytoskeleton is dynamic - can be quickly dismantled and taken apart and reassembled in a new location, changing the cell’s shape • Involved in Cell Motility - encompasses both changes in cell location and movements of parts of the cell - cytoskeleton interacts with motor proteins • Cytoskeletal elements and motor proteins work together with plasma membrane molecules to allow whole cells to move along fibers outside the cell - For Ex:) this is how vesicles containing neurotransmitter molecules get to the tips of axons which release these molecules as chemical signals to adjacent cell walls • Vesicles that bud off from the ER travel along the cytoskelelton to the Golgi Jercell Respicio Bio • • The plasma membrane is also manipulated by the cytoskeleton to form food vacuoles and other phagocytic vesicles Components of the Cytoskeleton: • Three main types of fibers that compose the cytoskeleton - Microtubules: thickest - Intermediate filaments: fibers with diameters in the middle range - Microfilaments (actin filaments): thinnest • Microtubules - all eukaryotic cells have microtubules • hollow rods constructed from globular protein called tubulin - Each tubulin protein is called a dimer, a molecule made up of two protein subunits each tubulin dimer consists of two types of polypeptides • - alpha tubulin and beta tubulin - microtubules grow in length by adding more tubulin dimers • can also be disassembled and re-assembled in other parts of the cell - Microtubules act as tracks (shape and support) • In which Organelles equipped with motor proteins can move along - Also involved in the separation of chromosomes during cell division • Centrosomes and Centrioles - In animal cells, microtubules root from the centrosomes • located near the nucleus “microtubule organizing center” • These microtubules act as compression-resisiting girders of the cytoskeleton - Within the centrosome is a pair of centrioles each composed of nine sets of three microtubules arranged in a ring - • Before an animal cell divides, the centrioles replicate - Not all eukaryotes have the centrioles within centrosomes • plants and fungi lack centrosomes with centrioles but have other microtubule organizing centers that substitute its role Jercell Respicio Bio • • Microtubules are responsible of the beating of flagella and cilia - Microtubules contain extensions that project from the cells • When Cilia and flagella extend from cells that are part of a tissue layer, the cells are able to move fluid across their surface of the tissie - For ex: mucous is swept from the lungs by the lining of the trachea - In a women’s reproductive system, the ciliated lining of the oviducts help move the egg toward the uterus • Significant amount of cilia lining the cell’s surfaces - flagella is limited to one or a few cells - flagella and cillia differ in their beating patterns • flagella like a fish tail • Cillia work like oars with alternating power and recovery strokes - Cillia may also act as a signal receiving antennae for a cell these cells are usually nonmotile and are usually one per cell Vertebrate animals have these kinds of cells and are crucial in embryonic • development and brain function • Cilia and flagella share a common structure - Motile cilium or flagellum has a group of microtubules sheathed in an extension of the plasma membrane • In motile cells, Microtubules are arranged in a ring-like structure surrounding the cell. 3 microtubules in a ring composed of nine of these triplets. There are two mircrotubules in the middle so these are commonly referred to as 9+2. Some don’t have them. • This assembly is anchored back to the main body of the cell via the basal body • This acts as a centriole - basal body of fertilizing sperm flagellum enters egg and becomes centriole Proteins called dynein are attached to adjacent doublets and walk along one, each • doublet is connected like this and thought the use of ATP these proteins can walk along the microtubule and when all dyneins do so, the whole thing bends and causes movement Microfilaments: • Solid rods • Also called actin filamenets because they are made up actin - globular protein • Microfilaments are formed from actin subunits - double chain - can branch out when proteins bind with them for strucutural support Role is to bear tension (pulling forces) • - help structurally - in intestinal cells, lining is filled with microfilaments to increase surface area • Known for their role in motility - thousands of actin filaments and thicker filaments of a protein called myosin interact tor cause contraction of muscle cells Jercell Respicio Bio • Actin myosin relationship causes movement in amoebea and circular flow of • cytoplasm within plants • Overall speeds distribution of materials within cell Intermediate Filaments: • Bigger than microfilaments but smaller than microtubules • Bear Tensions • Are more permanent framework in cells that permanently holds certain structure - for ex) nuclues, nuclear envelop held by intermediate filaments found in keratin • 4.7 Extracellular Components and Connection between cells help coordinate cellular activities Cell Walls of Plants • Maintain shape prevents uptake of too much water • hold up plant against gravity Microfibrils made of cellulose are snythesized by cellulose synthase and released • outside of the cell which binds with other sugars and proteins • Primary cell wall is made by young plants. Between the walls is the middle lamella that help stick adjacent cell walls together • as plant mature they either secrete hardening things to harden their wall or have secondary cell wall like wood • Channels between adjacent cells called plasmodesmata ECM of animal cells • ECM of animal cells are rich in glycoproteins and other carb containing molecules secreted by the cells themselves - glycoprotein: a carb covalently bonded with a protein - most abundant glycoprotein is collagen • form strong fibers outside the cell • collagen makes up 40% of the proteins of the human body • Integrins can transmit signals from ECM to cytoskeleton •integrate changes in an d out of cell Jercell Respicio Bio • • Influential role of ECM in lives • Regulate cell behavior through integrins • reasearch shows that extracellular matrix around cell can influence activity of genes in nucleus • Information reaches nucleus most likely via mechanical and chemical signals - mechanical changes shape of cytoskeleton and invokes a chemical signal Cell Junctions • plasmodesmata connects plant cells • One living continuum • Share nutrients and sometimes proteins and RNA Monday, 28 September 2015 Lecture Notes • Cell theory - Organisms are composed of cells - cells are the smallest living things - Cells arise only from pre-existing cells • All cells today represent a continuous line of descent from the first living cells • Cell size is limited - small due to diffusion of substances in and out of cells - metabolically inactive cells tend to be larger that active ones - Can’t have a volume in which toxins can linger Jercell Respicio Bio • • Surface area to volume ratio - squared is SA volume is cubes - In order to carry out cellular functions, smaller cells are better • Ex) whale cells are the same size as mouse cells just more • Bacterias have a cell wall (not cellulose, but a modified sugar) - called peptidoglycan • Antibiotics break down cell wall - Archaea don’t have peptidoglycan • Eukaryotes - compartamentalize - cytoskeleton 2 Oct. 2015 Lecture Notes - Cystic Fibrosis • Na and Cl imbalance across membrane • Mucous outside is membrane is thick • Protein channel complication - Diamond-Blackafna anemia • bone marrow fails to make red blood cells • Ribosomal defect- 9 different ribosomal proteins are implicated - 5q syndrome • Severe anemia • Cancer predisposition - Inclusion Cell Disease Abnormal modification of lysosomal protein • - gets excreted instead of sent to lysosome • Lysosomes become overloaded with waste - Pombe Disease • glucosidase lysosomal protein coverts glycogen to glucose • gylcogen accumulates in organs and miscles • Muscle weakneses, respiratory weakness, heart problems • Prognosis depedns on age 5 Oct. 2015 Lecture Notes • Plasma membrane is selectively permeable • Phospholipids are most abundant lipid in the plasma membrane and are amphipathic - have both polar and non polar regions • Fluid Mosaic model - membrane is a fluid structure with a lot of proteins • Things with charges don't want to pass through the membrane - Hydrogen is held out which helps us survive Jercell Respicio Bio • - Na Cl dissolves, are now ions, and the selectively permeable membrane holds them out • Protein are specific passage ways - proteins are amphipathic as well - non polar inside membrane, polar outside • Phospholipids in plasma membrane can move within the bilayer • unsaturated hydrocarbon tails with kinks are less viscous • Cholesterol is a fluidity buffer - at high temperature it holds on to tails to prevent them from moving to fast - at cold temperatures, it acts as a blocking from cells being packed too close • Proteins specify what kind of cell - Peripheral proteins • bound to surface of membrane - Integral penetrate hydrophobic core (transmembrane if they make it all the way • through) • Hydrophobic regionals of an integral protein consist of one or more stretches of non polar amino acids • Six major functions of proteins - Transport • moving things across me - Enzymatic activity • doing chemical work - Signal transduction • telling other cells what to do or receive instructions what to do - Cell-cell recognition self vs. other - • Intercellular joining • sheets of cells like skin - Structural • attachment to the cytoskeleton and extracellular matrix 07 Oct. 2015 Wednesday Lecture Notes • Membrane carbohydrates may be covalenty bonded to proteins - glycoproteins Membrane carbohydrates may be covalently bonded to lips • - glycolipids • more common • Cell to cell recognition • End up on the outside due to how they are assembled Passive Transport • Diffusion of a substance across a biological membrane-requires no energy - Diffusion is tendency for molecules to spread out evenly into an available space Jercell Respicio Bio • - Movement is from an area of high conc. to an area of lower conc. - At equilibrium movement doesn’t stop, but movement is equalized on both sides • Osmosis is the diffusion of water across a selectively permeable membrane • High water conc (low solute conc) to low water conc (high solute conc) • Tonicity: is the ability of a solution to cause a cell to gain or lose water Transport Proteins • Allow passage of hydrophilic substances across the membrane • Carrier proteins - bind to molecules and change shape to shuttle them across the membrane • Channel proteins - have a hydrophilic channel that certain molecules or ions can use as a tunnel - Aquaporins, for facilitated diffusion of water ethanol increases production of these in urinary track • - dehydration, headache - Ion channel that open or close in response to a stimulus Facilitated Diffusion • Transport proteins speed the passive movement of molecules across the plasma membrane - not exerting energy, doesn’t work against gradient Active transport • moves substances against conc. gradient • Requires energy ( form of atp) • Performed by specific proteins embedded in membranes • Allow cells to maintain different concentration gradients from the outside of the cell - for ex:) sodium potassium pump shooting nerve signals due to sodium potassium pump • • polarization of slightly positive outside and and slightly negative inside preps cell for propagation of nerve cell - depolarization Na+ rushes inside the cell and propagates signal - Refractory period is when concentrations are isotonic Chapter 5 Membrane Transport and Cell Signaling 5.1 Cellular Membranes are fluid mosaics of lipids and proteins • Ampiphatic Molecules, containing both hydrophobic and hydrophilic regions • Membrane proteins are the same The Fluidity of Membranes • held my hydrophobic reactions which are weaker than covalent bonds - Lipids and proteins shift laterally • Membranes with unsaturated phospholipid tails that are kinked are more fluid in lower temperatures • Cholesterol has a different effect Jercell Respicio Bio • - In lower temperatures it prevents in from becoming to solid - In higher temperatures in rema


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