BSCi105 Final Exam Study Guide
BSCi105 Final Exam Study Guide BSCI 105 - 5666
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This 21 page Study Guide was uploaded by Natania Lipp on Sunday March 27, 2016. The Study Guide belongs to BSCI 105 - 5666 at University of Maryland - College Park taught by Dr. Michael Keller in Winter 2016. Since its upload, it has received 18 views.
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Date Created: 03/27/16
Big Ideas: 1. Emergent properties: Arise when lower level units of matter combine and demonstrate new characteristics or abilities that would not be predicted by studying units separately. Ex: alone, ants can’t accomplish much. As a colony, they can do so many things that would not be discovered by studying just one ant. 2. The relationship of structure and function: The physical form dictates what objects are capable of Everything in biology has a structure which sets the limitation on possible functions Structure determines function Ex: we know that dinosaurs had similar posture to mammals and birds because they have similar pelvic structures. 3. Regulatory mechanisms: Regulatory mechanisms are processes that dictate what happens, when it happens, and for how long Then, the mechanism has to function on its own and be able to communicate and respond to other regulatory systems Ex: the handle for the faucet in a sink is necessary so that the water doesn’t just flow out of the faucet the handle is there so that the water can be used as it is needed. 4. Science as a process: Everything we study is a product of scientific process Each idea is the result of a careful study/documentation that has been tested throughout history 5. Evolution: Affects organisms at a cellular level Would not happen without basic material of life upon which it acts Systems and pathways often change between groups of organisms that provide examples of evolution Evolution = change over time This class covers: ● What is life and how do we study it? ● Chemistry ● Structure and function of cells ● Structure, function, and synthesis of molecules ● The Central Dogma of Molecular Biology ● Metabolism Exam I Material Chapter 1: Properties of Life ● “Life” is defined as a combination of recognizable properties: Living things… Are organizes Consume energy Reproduce Selfregulate Sense and respond to the environment Evolve (Evolution = the process of change over time) ● Life operates at differelevels of organization: Molecule → organelle → cell → tissue → organ/organ systems → organisms → populations → communities → ecosystems → biosphere ● Higher levels of organization exhibtmergent properties Emergent properties: the result of properties in lower levels acting in unpredictable ways Emerge at a level, due to arrangement and interactions between parts as complexity increases ● Organisms transform energy and recycle nutrients. ● The structure of living organisms, cells, and molecules reflects their function. ● 3 Domains of life: ○ Bacteria: most diverse and widespread prokaryotes ○ Archaea: live in Earth’s most extreme environments ○ Eukarya: organisms with eukaryotic cells, singlecelled protists or multicellular; 3 kingdoms: plantae, fungi, and animalia ● The cell is the basic unit of life. ● All living things share a common ancestry Evolution everything evolves from the same place ● Living processes are regulated at all levels organization Chapter 6: A Brief Tour of the Cell ● Cell theory: All living things are made of cells All cells come from preexisting cells ● 2 major groups or types of cells: Prokaryotes : no membranes, no real nucleus, DNA is a circular loop Eukaryotes: membranebound organelles, complex DNA, more complex cells ● All cells have: plasma membrane enclosing cytoplasm (cytosol), DNA, membranes, ribosomes, and protein ● Evolution of eukaryotic cells: evolved from prokaryotic by internalization of membrane, developed interconnected set of organelles the Endomembrane System (made up of the nuclear envelope, ER, golgi, and vesicles) ○ Modern eukaryotes have membrane bound organelles, i.e. mitochondria and chloroplasts, acquired through endosymbiosis ○ Eukaryotes evolved in an internal cytoskeleton made of microfilaments, microtubules, and intermediate filaments that support and organize the plasma membrane, organelles, and cytoplasmic components ● Endomembrane system and cytoskeleton allow eukaryotes to compartmentalize processes within cell ○ Function of endomembrane: synthesis of proteins, transport of proteins, movement of lipids, detoxification of poisons ○ Cytoskeleton of eukaryotes: includes cilia (beats back and forth; may act as antennae), flagella (1 percell; move in the same direction as axis i.e. sperm) ● (See pg. 100 and 101 for full pictures of plant and animal cells and their parts) ● Larger organisms have more cells,not bigger cells ● Cell theory All living things are made of cells; all cells come from preexisting cells Membrane A selective barrier that allows passage of enough oxygen, nutrients, and wastes to service the entire cell that all cells are bounded by Endomembrane A system of membranes inside and surrounding a eukaryotic cell, including the plasma membrane, nuclear envelope, the smooth and rough endoplasmic reticulum, the Golgi apparatus, lysosomes, vesicles, and vacuoles. Function: synthesis of proteins, transport of proteins, movement of lipids, detoxification of poisons Prokaryote A cell where the DNA is located in a nucleoid (a region that is not membraneenclosed) Eukaryote A cell where most of the DNA is in the nucleus. Organelle Several membraneenclosed structures with specialized functions, suspended in the cytosol of eukaryotic cells. Cytoskeleton A network of microtubules, microfilaments, and intermediate filaments that extend throughout the cytoplasm and serve a variety of mechanical, transport, and signaling functions. Endosymbiont the theory that mitochondria and plastids, including chloroplasts, originated as prokaryotic theory cells engulfed by a host cell. The engulfed cell and its host cell then evolved into a single organism. Chloroplast A photosynthetic organelle; converts energy of sunlight to chemical energy stored in sugar molecules. Mitochondria Organelle where cellular respiration occurs and most ATP is regenerated. Nucleus The atom’s central core that contains chromosomes (genetic material) in a eukaryotic cell and is made up of neurons. Nuclear Envelope In a eukaryotic cells, the double membrane that surrounds the nucleus, perforated with pores and the regulate traffic with the cytoplasm. The outer membrane is continuous with the endoplasmic reticulum. DNA A nucleic acid molecule, usually in a doublestranded helix, that is capable of being replicated and determining the inherited structure of a cell’s proteins. RNA Ribonucleic acid, including a nitrogenous base, ribose sugar, and phosphate Protein A biologically functional molecule consisting of one r more polypeptides folded and coiled into a specific threedimensional structure Ribosome Complexes made of ribosomal RNA and protein, the cellular components that carry out protein synthesis. Cytoplasm The interior of the cell bounded by the plasma membrane; in eukaryotes, the portion exclusive of the nucleus. Endoplasmic A network of membranous sacs and tubes; active in membrane synthesis and other Reticulum synthetic and metabolic processes; has rough (ribosomestudded) and smooth regions Lumen Measure of the total quantity of visible light emitted by a source Golgi The warehouse of receiving, sorting, shipping, and even some manufacturing. Especially extensive in cells specialized for secretion. Vesicles Sacs made of membrane Vacuole Large vesicles derived from the endoplasmic reticulum and Golgi apparatus. There are food vacuoles, contractile vacuoles (pump excess water out of the cell to maintain the right amount of ions and molecules.); central vacuole (develops by the coalescence of smaller vacuoles) Lysosome A membrane sac of hydrolytic enzymes that many eukaryotic cells use to digest (hydrolyze) macromolecules. Actin Globular protein molecules that make up microfilaments. Microfilament Thin solid rods; twisted double chain of active subunits that can form structural networks when certain proteins bind along the side of such filament and allow a new filament to extend as a branch. Tubulin Proteins of the microtubules; atubulin and btubulin Microtubule small hollow tubes; maintain cell shape; cell motility; chromosome movements in cell division Keratin A family of fibrous structures of proteins that protect epithelial cells from damage/stress Intermediate Have a larger diameter than microfilaments but smaller than microtubules; only found in the Filament cells of animals; specialized for bearing tension and are a diverse class of cytoskeletal elements. Chapter 2: Atoms and simple molecules ● Elements are made of atoms ○ Elements are substances that cannot be broken down anymore ○ 4 main elements: O, C, H, N make up 96% of living matter ● Atom: the smallest unit of matter that haps properties of the elements ● Each element has a unique atomic number and mass depending on number of neutrons. Atomic number: # of protons (also # of electrons) Mass number: sum of protons + neutrons Mass # atomic # = # of neutrons ● Isotopes are elements/atoms with extra neutrons ● Electrons are arranged in shells around the atomic nucleus ○ 2 electrons in each orbital ○ 2 electrons in the first shell, and max of 8 electrons in each shell after ○ Orbital 3D space where an electron is 90% of the time First shell: 1s orbital 2nd shell: 2s, three 2p orbitals Each orbital holds 2 electrons ○ First shell (closest to nucleus) holds 2 electrons ○ Second shell holds up to 8 electrons (4 orbitals) ○ Valence electrons are the electrons on the outer shell ○ Complete valence shell = 2 or 8 electrons; stable and unreactive = inert ● The # of bond an atom forms w/ other atoms depends on how many unpaired valence electrons are in outermost shell ● Atoms find partners for unpaired valence electrons by sharing electrons through bonds ● Electronegativities differs through elements, create unequal sharing of electrons and result in emergence of different types of bonds ○ Nonpolar covalent bonds: equal sharing of electrons, similar electronegativities; strong bond ○ Polar covalent bonds: unequal sharing; different electronegativities ○ Large differences in electronegativities → weak ionic bonds, held together by electrostatic forces after one element strips electrons from another ○ Ionic bond: strong; 2 oppositelycharged atoms → the more charged atom takes electrons from less charged atom (between cation(+) and anion ()) ○ Hydrogen bonds: covalent bond between H and a highly electronegative atom (N/O/F) (Ex: H2O, NH3) ○ Van der Waals interactions: weak; only occur when atoms/molecules are v close together Causes everchanging regions of +/ charge that help all atoms to stick together → how a gecko can walk up a wall ● Compounds or molecules are formed by atoms bonding together and can have different shapes depending on interactions between orbitals ○ Form → function ○ 2 atoms are always linear; 3+ atoms determine shape by positions of atoms’ orbitals Chapter 3: Properties of water ● Live evolved in water ● Water = the solvent in which the chemistry of life occurs ● Water is very polar electrons of covalent bond are closer to oxygen than hydrogen because oxygen is more electronegative (polar covalent bond) ● Hydrogen bonding between water molecules → e mergent properties of water: ○ Cohesion: ability for water to bond to other water molecules by hydrogen bonding ○ Adhesion: clinging of one substance to another ○ Surface tension: how difficult it is to break the surface of a liquid (high for H2O) ○ High heat capacity: the amount of heat that causes 1g of water to change temperature by 1ºC (hard to change water temp) ○ Evaporative cooling: high heat of vaporization amount of heat 1g of liquid must absorb to change from liquid to gas ○ Less dense as a solid ice floats on water ● Water polar solvent; can dissolve ionic bonds and keep large polar (hydrophilic) molecules in solution because of the formatiydration shellaround individual ions or molecules ● Hydrophobic molecules: repels water; nonpolar molecules that do not remain in solution with water; don’t have affinity for water ● Hydrophilic molecules: attracts water; polar molecules that bond in water molecules; break and reform constantly ● Dissociation of water generates hydrogen ions and hydroxide ions ● pH: a measure of concentration of hydrogen ion in water on a log scale ○ Acids: high concentration of hydrogen ions relative to hydroxide ions (low pH); releases protons and accepts H+ ions; pH < 7 ○ Bases: low concentration of hydrogen ions relative to hydroxide ions (high pH); absorbs protons; pH > 7 Chapters 2 & 4: Chemistry with carbon ● Carbon has 4 unpaired valence electrons, so it is the basis for organic molecules ○ The most diversity of molecules that can bond to it and make 3dimensional shapes ● Bonds in carbon backbone of organic molecules can be rearranged in different ways the same combinatino of elements can make different structural isomers ● Double bonds inhibit rotation of carbon backbone → different organization in side groups ● Asymmetric carbons with 4 different side groups can arrange as enantiomers with mirror image symmetry ● Functional side groups = compounds added to the carbon backbone that modify the properties of function of organic molecules ○ Hydroxyl (OH) ○ Carbonyl (doublebond O) ○ Carboxyl (Carbonyl + Hydroxyl off same carbon) ○ Amino (Nitrogen) ○ Phosphate (Phosphorus with THREE Oxygens) ○ Sulfhydryl (Sulfur) ○ Methyl (additional carbon) ● Hydroxyl, carbonyl, carboxyl, amino and phosphate groups all make molecules polar and more hydrophilic ● Carboxyl groups act as acids drop a hydrogen ion in solution ● Amino groups act as bases take up extra hydrogen ion in solution ● Sulfhydryl groups bond to other sulfyhdryl groups, linking molecules together with strong disulfide bonds ● Phosphate groups involved in transferring energy between molecules ● Methyl groups act as “tags” modify the functions of molecules Carbon An element that can form diverse molecules by bonding to 4 other carbon atoms Tetrahedral The shape that carbon molecules form when they attach to for other molecules Isomers One of several compounds with the same molecular formula but different structures and therefore different properties. Structural isomer Differ in covalent arrangements of their atoms. They have the same molecular formula but can differ in branching or location of double bonds. The bigger the skeleton, the more isotopes are possible. Geometric Aka cistrans isomers; have the same bonds to atoms, but different spatial arrangements due to inflexibility of bonds Single bonds can rotate freely without changing the compound, but double bonds can be different if atoms are attached in different places. Enantiomers Isomers that are mirror images of each other and that differ in shape due to the presence of a symmetric carbon (attach to 4 diff atoms or groups of atoms) Asymmetric carbon A carbon atom that is attached to four different types of atoms or group of atoms Functional side groups A specific configuration of atoms commonly attached to the carbon skeletons of organic molecules and involved in chemical reactions. Hydroxyl Addition of OH or HO; polar, forms hydrogen bonds with water, helps dissolve compounds Example: ethanol Carbonyl Ketone (carbonyl within skeleton) or aldehyde (outside) Ketone/aldehyde may be structural isomers Found in sugars; give rise to aldoses and ketoses Carboxyl Acts as acid and donates H+ bc of polar bond b/w O & H Amino Acts as base, accepts H+; typically has charge of 1+ under cellular conditions Sulfhydryl Thiol, 2 SH groups can react and form a crosslink Phosphate Charge = 1 inside phosphate chain, 2 on end of chain Methyl Affects gene expression when bound to DNA, affects shape/function of sex hormones Exam II Material Chapter 7: Membrane Structure and Function ● All cells are defined by cell membrane ● Membrane establishes “inside” versus “outside” ● Cell membrane = “fluid mosaic” of 2 types of molecules: ○ Membrane lipids the structural part of the membrane ○ Amphipathic phospholipids abilayedouble layer) of hydrophobic tails that face each other ● Membrane fluidity the degree of movement/”gapiness” of a membrane ○ Determined by thaturationnd length of fatty acid tailes. Unsaturated fatty acids more fluid membranes Saturated fatty acids more viscous membranes Cholesterol can be added to modulate membrane fluidity, making it either more fluid or more viscous as needed ● Membrane proteins determine the functions of a cell membrane ○ Peripheral membrane proteins associate w/ membrane; don’t enter membrane ○ Integra membrane proteins insert into bilayer; either partially (monotopic) or all the way through (transmembrane) ○ Transmembrane proteins provide mechanisms for the transport of solutes across the cell membrane in a regulated fashion, making meselectively permeable ● Passive transpor when solutes are moving “down” a concentration gradient ○ Cell usesfacilita diffusiothrough eithehannelproteins oarrier proteins to allow them to cross the membrane without using energy. ● Active transport cells moving “up” concentration gradient; uses energy ○ Uses protein pumps ○ Most are in 3 categories: Unipor moves one solute through the membrane Antipor: two solutes move at the same time through the membrane in opposit directions Symport: two solutes move at the same time through the membrane in thesame direction ● Bulk transport moves large cargos across the membrane ○ Endocytosis: moves material into the cell, in 3 main mechanisms Phagocytosis consumes objects Pinocytosi: consumes water Receptor mediated endocytosi specific consumption ○ Exocytosis movement of material out of the cell Chapters 8 and 9: Energy, Enzymes, and Reaction Coupling ● Metabolism = the sum of anabolic + catabolic reactions in an organism ○ Metabolic pathways assemble these reactions in intersecting networks ● Energy = ability to do work ○ Kineti: transferred between objects in motion ○ Potentia: stored in an object; must be released; due to position Stored in the bonds between atoms ○ Free: the released potential energy available to do work ● First Law of Thermodynamics: energy cannot be created nor destroyed, only transferred ● Second Law of Thermodynamics: every energy transfer increases the entropy of the universe ● Free energy (G) chemical energy available to do work; expressed as the difference between enthalpy and entropy (∆G = ∆H T∆S) ● All reactions involve a change in energy the direction of change in free energy (aka if there is more enthalpy or entropy) tells whether the reaction is exergonic (spontaneous) or endergonic ○ Exergonic net release of free energy, ∆G, spontaneous Spontaneous = energetically favorable ○ Endergonic absorbs free energy, +∆G ** Be able to draw and label endergonic and exergonic reaction bar graphs ● Enzymes are proteins that reduce the activation energy of a reaction, making them go faster ** Be able to draw a graph of the effect of enzymes ● Enzyme specificity and function are the result of the structure and shape of the protein. ○ Substrates interact w/ enzymes atactive site Form enzymesubstrate complex w/ a close interaction thnduced fit ○ Shape determines specificity of enzymes ● Environmental factors interfere with tertiary or quaternary structure of enzymes, impacting activity. Optimal levels (where max activity occurs): ○ pH: tends to be 68 ○ Temperature: usually 3540ºC (body temp) ● Enzymes adapt, evolve, and diversify over generations, and enzymes have different optima conditions they work best in ● Some enzymes require cofactors (i.e. metal ions) ○ Cofactor bound to enzyme, nonprotein helps that aid enzymes (zinc, iron, copper ions) ○ Coenzyme: organic cofactor (vitamins) ● Competitive inhibitor: reduce enzyme activity and compete with substrates for active site ○ Called “competitive” inhibition b/c they resemble normal substrate molecules and compete for admission to the active site ○ Noncompetitive inhibitor bind to another part of the enzyme causing it to change shape which makes the active site less effective ● Allosteric effecto: bind somewhere other than the active site and alter the shape of the protein to eitinhibor ctivat the enzyme function ○ Cooperativity: a substrate molecule binds to one active site in a multisubunit enzyme and triggers a shape change in all subunits which increases the catalytic activity at other active sites ● Metabolic pathways can be regulated at different steps depending on the demands of the cell. ○ Negative feedback(feedback inhibition): uses the product of a pathway to inhibit enzyme at the beginning of the pathway ● Reaction couplingdrives negative ∆G with positive ∆G to give a net overal negative ∆G for the combined reactions. ○ ATP is the most common example of energy coupling Stress bonds between oxygenrich phosphate groups; easy to break; yield a ∆G = 7.3 kcal/mole ○ ATP is continuously used and regenerated from ADP ○ Substratelevel phosphorylatioor edoxdriven oxidative phosphorylation make ATP ○ NADH (or NADPH) is another impt. energy couple that shuttles electrons between redox reactions ○ Electron transport chains (ETextract small amounts of energy from redox reactions Exam III Material Chapter 10: Photosynthesis ● Photosynthesis is a part of an anaboliccatabolic cycle ○ Transforms light energy → chemical energy ○ Chemical energy is stored in the covalent bonds of chemical compounds ○ ● Eukaryotes photosynthesis in the chloroplasts ● Photosynthesis has 2 major components: light and dark reactions ○ Light reactions require light energy ○ Dark reactions (aka Calvin Cycle) do not require light energy ● Photosynthesis uses two photosystems to capture light ○ Chlorophyll a, chloropyll b and cartenoids are the primary pigments of photosynthesis ○ Cartenoids (accessory pigments) are for photoprotection absorb and dissipate excessive light energy that would otherwise damage chlorophyll or interact with oxygen forming reactive oxidative molecules that are dangerous to the cell. Also may broaden the spectrum of pigments that can drive photosynthesis ● The zscheme shows the relationship between components of the light reactions and the energy levels of the excited electrons as well as how electrons move through the system ○ Electrons are at their highest energy state at the primary acceptor of Photosystem II where they are excited by a photon of light ● Photosystem II captures light to boost electrons that supply a short ETC to indirectly power ATP production by photophosphorylation ○ Water oxidized in photosystem II ○ PQ reduced ○ When electrons move through the ETC they are moved through the PQ which is reduced to PQ2 ○ Pc is reduced to Fd which reduces NADP+ to NADPH ● Photosystem I accepts the low energy electrons and reexcites them back to high energy level so NADP reductase can pass them to NADPH ○ Photosystems get new electrons to keep light reactiosn going splitting of water produces 2 electrons which replace the ones that get excited and move through ETC ● First ETC generates an H+ gradient across the thylakoid membrane, flow of H+ back across the membrane powers ATP synthase ○ Considred indirect means to power ATP synthase diffusion creates the energy which is passive ● Electrons leave light reactions in NADPH, new electrons obtained by the splitting of water through photolysis ○ H+ ions also a product of photolysis ○ Oxygen gas byproduct of photolysis ● The dark reactions use the Calvin Cycle to fix inorganic carbon from CO2 in the form of organic carbon chains, store energy in chemical bonds ○ Calvin Cycles is powered by light reactions’ production of ATP and NADPH ● CO2 is covalently bonded to the 5C molecle RuBP by the enzyme Rubisco ○ Generates two 3C organic molecules in the “carbon fixation” phase ● Product of the reduction phase = glyceraldehyde3phosphate (G3P), wi molecule being exported while molecules go back to the “regeneration” phase and are made back into RuBP ○ If regeneration didn’t happen, the cycle would end b/c there would be no RuBP to fuel the next few stages of the cycle and to receive CO2 again ● The G3P from photosynthesis is used to make starch in the chloroplast stroma and sucrose in the cytoplasm ○ Glucose comes from the food we eat ○ G3P is the precursor to other organic molecules including lipids, amino acids, and nucleic acids Photosynthesis The process of light being converted to chemical energy Chloroplast An organelle in plants that absorbs sunlight and uses it to drive the synthesis of organic compounds from carbon dioxide and water. Stroma The dense fluid in the chloroplast Thylakoids A group of sacs in the chloroplast that make up a membrane separate from the stroma Chlorophyll The green pigment that gives leaves their color Light reactions The first stage of photosynthesis Dark reactions The second stage of photosynthesis, also called the Calvin Cycle, uses the electrons from NADPH and energy from ATP to convert CO2 to glucose Wavelength The distance between the crests of elecromagnetic waves Visible light The radiation between 380 nm to 750 nm Pigment Substances that absorb visible light Spectrophotometer An instrument that can measure various wavelengths of light Absorption spectrum The graph that plots each pigment’s light absorption versus wavelength Action spectrum Profiles the relative effectiveness of different wavelengths of radiation in driving photosynthesis. Cartenoid An accessory pigment that absorb bluegreen light (so they’re yellow and orange) and are an important function for photoprotection. Photoprotection Absorbing and dissipating excessive light energy that would otherwise damage chlorophyll or interact with oxygen, forming reactive oxidative molecules that are dangerous to the cell. Photosystem A lightcapturing unit that is composed of a reactioncenter complex and surrounded by lightharvesting complexes. Photosystem I A lightcapturing unit in the chloroplast’s thylakoid membrane that has 2 molecules of P700 chlorophyl a at its reaction center Photosystem II The first light capturing unit of the chloroplast in the thylakoid membrane, has 2 molecules of P680 chlorophyl a at it reaction center Linear electron flow The flow of electrons through the photosystems and other molecular components in the thylakoid membrane that energizes two photosystems and allows for the synthesis of ATP and NADPH Cyclic electron flow An alternative path (to linear electron flow) that only uses Photosystem I, not II. It does not include production of NADPH and Chemiosmosis Energy coupling mechanism that uses energy stored in the form of a hydrogen ion gradient across ta membrane to drive cellular work The Calvin Cycle Aka dark reactions, the second of the two major stages of photosynthesis involving the fixation of carbon Carbon fixation The initial incorporation of carbon from CO2 into an organic compound Autotrophs Organisms that obtain organic food molecules without eating other organisms Heterotrophs Organism that obtain their energy from eating other organisms Chlorophyll a A photosynthetic pigment that converts solar energy to chemical energy Chlorophyll b An accessory pigment to photosynthesis that transfers energy to chlorophyll a Reactioncenter complex A complex in the center of the photosystem that tigers the light reactions of photosynthesis Glyceraldehyde The 3carbon carb that is the direct product of the Calvin cycle (and an 3phosphate intermediate in glycolysis) Chapter 5: Carbohydrates Carbohydrates: sugars and polymers of sugars Monosaccharides = sugar monomers Polysaccharides = sugar polymers Polysaccharides are assembled by dehydration synthesis forming glycosidic bonds 14 glycosidic bonds are straight chained polysaccharides 16 bonds form branches Polysaccharides can have digestible alpha glycosidic bonds (starch, glycogen) or indigestible beta glycosidic bonds (cellulose) Alpha bond has hydroxyl group on the s ame side as the OH; all monomers have the same orientation Beta has hydroxyl group on o ppositeside; every monomer is upside down with its neighbor Dehydration reaction A chemical reaction in which two molecules become covalently bonded to each other with the removal of a water molecule. Hydrolysis Adds a water molecule, breaking it down Types of biological macromolecules Carbohydrates, proteins, lipids, and nucleic acids Polysaccharides A bunch of monosaccharides Monomers Smaller molecules that are the “building blocks” for polymers Polymers A long molecule consisting of many similar or identical building blocks linked by covalent bonds Glycosidic bonds A covalent bond formed between two monosaccharides by a dehydration reaction (forms disaccharides) Chapter 9: Cellular Respiration Cellular respiration: the process of breaking down glucose to make ATP using substratelevel and oxidative phosphorylation Major metabolic pathways: glycolysis, Krebs Cycle, oxidative phosphorylation SLP when there is enough energy for reaction coupling Oxidative phosphorylation when there is not enough energy, uses the energy from the H+ gradient to form ATP Glycolysis in the cytosol; anaerobic Cytric acid cycle in the mitochondria; aerobic Oxidative phosphorylation in the mitochondria ETC aerobic Fermentation anaerobic Glycolysis first process in cellular respiration Takes in glucose and makes ATP (substrate level phosphorylation), NADH, and pyruvate Divided into investment and payout Investment = cell spends ATP Payout = ATP is produced by substratelevel phosphorylation and NAD+ is reduced to NADH by electrons released from the oxidation of glucose Per glucose 1ATP, 3 NADH Pyruvate is important to mitochondria in the transition step, getting converted into acetylCoA at the same time Pyruvate’s carboxyl group is removed and gives off a molecule of CO2 at the same time Pyruvate dehydrogenase complex: mutlienzyme complex involved in conversion of pyruvate AcetylCoA enters Krebs Cycle, oxidized down to CO2 and used to make ATP, NADH, and FADH2 Makes 1 ATP, 3 NADH, and 1 FADH2 The NADH and FADH2 from glycolysis, the transition step, and the Kreb’s ycle donate high energy electrons to the mitochondrial ETC which uses energy to pump H+ ions into the intermembrane space, generation the “proton motive force” across the inner membrane Know how to draw the mitochondrial ETC and to label it with Complexes IIV, X, and cytC, and where electrons enter from NADH and FADH2 FADH2 generates fewer ATP than NADH comes in later in the ETC Enters at complex II instead of I so has a lower energy level and is only responsible for enough H+ for the synthesis of 1.5 ATP (NADH = 2.5) Complex IV = final electron acceptor Flow of hydrogen ions across the membrane power production of ATP by the ATP synthase through chemiosmosis (oxidative phosphorylation) Oxidative phosphorylation is driven by indirect energy source Driven by H+ gradient, fueled by protonmotive fource DNP = an uncoupler that allows H+ to flow freely back through the membrane doesn’t power ATP synthase → inhibits creation of ATP Makes 2628 ATP When ETC doesn’t work, (i.e. when O is limited), ATP can only be produced by glycolysis supported by fermentation Fermentation allows for cells to use ATP w/o oxygen Without fermentation, glycolysis would run out of NADP+ and die Organic molecule is the final electron acceptor 2 main kinds of fermentation: Lactic acid: causes lactate to go back to the liver and is recycled as pyruvate (happens in muscles when you exercise lactic acid buildup) Alcoholic: Pyruvate is converted to ethanol by releasing CO2 from pyruvate (how beer is made) Organic molecules used by cellular respiration if glucose is not available Sugars and glycerol go into glycolysis Beta oxidation breaks down fatty acids into twocarbon fragments, which enter the citric acid cycle as acetyl CoA NADH and FADH2 also generated and can enter the ETC leading to more ATP production Diff amino acids can feed into diff parts of the Krebs Cycle Fermentation A catabolic process; partial degradation of sugars or other organic molecules without the use of oxygen Aerobic respiration The most efficient catabolic pathway where oxygen is consumed as a reactant along with organic fuel Redox reactions The transfer of one or more electrons from one reactant to another (aka oxidationreduction reactions) Reducing agent The electron donor that reduces another element (adds electrons) Oxidizing agent The electron acceptor that removes the other element’s electron (oxidizes) Electron transport chain A number of molecules, mostly proteins, built into the inner membrane of the mitochondria of eukaryotic cells Glycolysis The first stage of cellular respiration; occurs in the cytosol; breaks down glucose and 2 molecules of pyruvate, sending pyruvate to the mitochondria to oxidize to acetyl CoA Citric acid cycle Second stage where breakdown of glucose to carbon dioxide is completed Oxidative ETC and chemiosmosis occur; a mode of ATP synthesis powered by the redox phosphorylation reactions of the ETC Acetyl CoA An acetyl coenzyme; the entry compound for the citric acid cycle in cellular respiration, formed from a twocarbon fragment of pyruvate attached to a coenzyme. ATP synthase Enzyme throughout the inner membrane of the mitochondrion/plasma membrane that makes ATP from ADP and inorganic phosphate. Alcohol fermentation Pyruvate is converted to ethanol by releasing CO2 from pyruvate → converts to twocarbon compound acetaldehyde, and then NADH reduces that to ethanol Lactic acid fermentation Lactic acid causes lactate to go back to the liver and it’s recycled as pyruvate. Exam IV Material Chapter 5.5: Nucleic Acids Monomer: deoxyribose or ribose Polymer: polynucleotides Nucleic acids linked by hosphodiester linkage phosphate links to nitrogen base Made of nitrogen base + pentose + phosphate group DNA: makes RNA: makes proteins Purine: 6ring carbon/nitrogen fused with 5ring; larger, adenine/guanine Pyrimidine: Smaller, 6ring carbon of C/N, cytosine/thymine/uracil 5’/3’ end cause antiparallel arrangement; 3’ had hydroxyl group and 3carbon; 5’ has phosphate and 5carbon Chapter 16.1: DNA is the genetic material The nucleus controls the phenotype of a cell Phenotype all physical traits of an organism (i.e. anatomy or enzyme function) → concents of the nucleus carry genes that define the genotype of an organism Genotype all information defining and giving rise to phenotype Chromatin: DNA wrapped around histone beads to form nucleosomes; histones wrap into fibre that make up heterochromatin DNA the only molecule that can transform cells Transformation = the genetic alteration of cells Watson and Crick described DNA as: Antiparallel strands Sugar phosphate backbone outside Strict basepairing of nucleotides inside (A:T; C:G) Double helix Concluded that the structure dictated how DNA replicates Semiconservative model: hydrogen bonds btwn A/T and C/G of double helix broken, then each strand is template and creates 2 new strands; after 2 replications, there are 4 strands → none exactly identical to parents Chapter 16.2: DNA Replication DNA replicates with semiconservative replication: parental strand from a double helix is used as a template to make daughter strand Results in two double helices, each having an “old” DNA strand paired with a “new” DNA strand Correct bases get added to daughter strand b/c of strict base pairing DNA requires many proteins to unwind the helix and make new strands: Replication fork: Yshaped region where parental strands of DNA are unwound Helicase: enzyme that untwists 2 strands Singlestrand binding proteins: stabilize unpaired DNA strands Topoisomerase: breaks, swivels, and rejoins DNA strands Primase: enzyme that synthesizes primer (510 nucleotide long RNA chain) from DNA; then adds DNA onto 3’ end of RNA primer DNA polymerase: catalyzes synthesis of new DNA by adding nucleotides to preexisting chain I: removes RNA nucleotides of primer with DNA versions on end of Okazaki frag. (removes from 5’ end) III: add DNA nucleotide to RNA primer then continues w/DNA nucleotides Monomer joins DNA strand → 2 phos. groups lost via exergonic rxn, aka hydrolysis Leading strand: where DNA is made by DNA poly III adding nucleotides to it Lagging strand: creates in Okazaki fragments and joined together by DNA ligase Replication starts at origin DNA double helix begins unwinding Replication bubble forms w/ two replication forks that move away from each other in opposite directions As bubble expands, forks move further apart and new daughter strands are replaced inside the bubble Eukaryotes have many origins of replication; prokaryotes have one Be able to draw and label this process including polarity Always replicate in the correct order bc strict basepairing and hydrogen bonding mediates the process Antiparallel strands of the double helix happen because the nucleotides pair with the opposite nucleotide (i.e. A:T) Antiparallel → lagging strand, result of DNA polymerase ability to only add nucleotides to the 3’ end of a growing polynucleotide → DNA pol III always moves toward helicase and follows replication fork of the leading strand, but moves the away from fork on lagging strand Each time new template DNA is exposed along the lagging strand a new primer is made starting a new daughter strand and resulting in O kazaki fragments Chapter 17/18: Central Dogma of Molecular Biology Central Dogma: DNA makes RNA makes protein Genes organize information encoding proteins on DNA Downstream transcribed regions = templates for making RNA Downstream = away from 5’ Upstream regulatory elements (i.e. promoter) control the production of RNA Upstream = away from 3’ +1 position = where the gene’s transcription begins One strand of DNA acts as a template for the production of an RNA strand by the process of transcription mediated by the enzyme R NA polymerase RNA polymerase unwinds DNA locally and assembles complementary RNA nucleotides along the DNA template strand, linking them with phosphodiester bonds into a polynucleotide RNA pol can also only add to the 3’ end of the polymer 5’ 3’ = coding strand 3’ 5’ = template strand Transcription in eukaryotes makes premRNA that must be processed to mature mRNA Requires 3 things for maturation: Adds 5’ capto 5’ end andpolyA tail to 3’ end Both: facilitate the export of the mature mRNA from the nucleus; protect mRNA from degradation by hydrolytic enzymes; help ribosomes attach to 5’ of the mRNA once the mRNA reaches the cytoplasm RNA splicing takes out exons and joins introns together mRNA encodes peptide sequences using codons which are translated using tRNA tRNA associates with the proper codon on mRNA through its a nticodon. Codons represent a d egenerate code, with more than one codon representing the same amino acid. By reading codons in order, a polypeptide sequence can be determined. Sequence starts with AUG Translation occurs in ribosomes: large multiprotein complexes that interact w/ mRNA and enzymatically assemble polypeptides Small subunit binds to mRNA and recruits the large subunit at the first 5’ AUG (start codon) with its associated methionine tRNA Gene expression is regulated at diff levels Transcriptional regulation the major mode of gene regulation By transcription factors binding to regulatory DNA Prokaryotes “operons” that are controlled by repressors negative regulation Eukaryotes use activators and repressors to control gene expression Through upstream elements Most genes under positive control Proximal promoter that recruits RNA polymerase more distal upstream elements that help determine the when, where, and how much of RNA production Use enhancers to promote robust transcription Coordinate control: group of genes put into 1 transcription unit that respond to one on/off switch Genes on the same chromosomes are coexpressed but have own promoter and are transcribed individually Or On different chromosomes but share a control element combo Operator: switch for controlling transcription Controls access of RNA poly to DNA Has 2 states: repressorbound and not repressorbound Operon: operator + promoter + all genes they control → all of DNA required for enzyme production Repressor: turns operon off; is a protein; blocks attachment of RNA polymerase to promoter Binding repressor to operator is reversible; repressor is active or inactive Regulatory gene: makes repressor; always expressed but at low rate Corepressor: small molecule that works with repressor protein to turn operon off Negative gene regulation Repressible operon: transcription is usually on but can be turned off if a specific molecule binds allosterically to a regulatory protein Ex: trp operon Inducible operon: usually off but can be turned on when a molecule interacts with regulatory protein Ex. lac operon Inducer: inactivates repressor (allolactose for lac operon) Inducible enzyme: induced by chemical signal (enzymes in lactose path) Repressible enzyme: anabolic; synthesis turned off by chemical signal Negative control: operon switched off by active form of repressor protein Positive gene reg: reg. protein interacts w/genome to switch transcription on Activator: binds to DNA and stimulates transcription of gene Ex. cAMP accumulates when glucose is scarce; cAMP binds to regulatory protein and increases transcription rate Gene expression of eukaryotes can be regulated at any stage 20% of genes expressed at all times due to differential gene expression → different genes expressed by cells with same genome Chapter 11: Cell communication and signal transduction Communication the key to evolution of multicellular organisms Allows cells to coordinate activities Secreted signals are detected by receptors expressed by receiving cells Signalling between cells requires transmission of signal from a sending cell through the environment, followed by a reception of the signal by the receiving cell, causes a response Ligand a signaling molecule that interacts with a receptor Transmembrane receptors required to detect hydrophilic ligands, resulting in signal transduction Hydrophobic ligands can be detected by intracellular or nuclear hormone receptors that cause response directly Signal transduction pathway: signal on cell surface is converted, in steps, to a cell response Bacteria: Quorum sensing: sense local density of bacterial cells Biofilms: bacteria form these regions of specialized function Local signaling Cellcell recognition: direct contact b/w cells (gap junction in animals, plasmodesmata in plants) Embryonic development Messenger molecules secreted (growth factors → paracrine signaling) Synaptic: electrical signals move along nerve cell through synapse Longdistance signaling Hormones: endocrine (animal) → specialized cells release hormones Signals through nervous system 3 stages of signaling: discovered by Sutherland; found that epinephrine signals glycogen breakdown, by activating an enzyme only w/intact cells 1. Reception: target cell detects signal molecule from outside when signal mol binds to receptor protein 2. Transduction: receptor protein changes, causes cell response through relay molecules in a signal transduction pathway 3. Response: cell response occurs → like catalysis, activation of gene, etc. Receptors: found in cytoplasm or plasma membrane Plasma membrane: watersoluble membrane binds to RP; signal transmitted by changed RP shape; can cross membrane if very small; 3 types 1. G protein: cancer, heart disease, asthma; widespread, work with G protein and make GTP Active when bound to GTP (replace GDP with GTP); usually “on” Hydrolysis of GTP to GDP terminates activation 2. Receptor tyrosine kinase: attaches phosphates to tyrosines, can activate 10+ signal transduction pathways 3. Ligandgated ion channel: acts as gate when receptor changes shape, opens or closes to allow/block flow of ions Binding affects membrane potential Intracellular: in cytoplasm or nucleus, small/hydrophobic Usually steroid/thyroid hormones Transduction: at each step, signal is changed by phosphorylation Protein kinase: transfers phos. group from ATP to protein Protein phos → transmits signal → shape change Protein phosphatases: enzymes that rapidly remove phos groups (aka dephosphorylation) Make protein kinases reusable Small messengers and ions as 2nd messengers: spread via diffusion Cyclic AMP: ligand fits into adenyl cyclase → cAMP becomes AMP via phosphodiester → activates protein kinase A Ca2+: increased Ca2+ = cell contracti
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