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BIOL 1010 Final: cumulative review

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BIOL 1010

CUMULATIVE REVIEW Ch. 1 Science of Biology 1. Describe the fundamental properties of life 1.2.1 ▯ Cellular organization: all composed of one or more cells ▯ Energy utilization: all use energy ▯ Homeostasis: all maintain relatively constant internal conditions ▯ Growth, development, and reproduction: all grow and reproduce ▯ Heredity: all posses a genetic system that is based on replication and duplication of DNA 2. Describe the hierarchical nature of living systems. 1.2.2 CELLULAR: 1. Atoms 2. Molecules 3. Macromolecule 4. Organelle 5. Cell ORGANISMAL: 6. Tissue 7. Organ 8. Organ System 9. Organism POPULATIONAL: 10. Population 11. Species 12. Community 13. Ecosystem 14. Biosphere 3. Explain emergent properties and give some examples. 1.2.3 ▯ Emergent properties: properties that result from the way components interact o EX. Metabolism, consciousness in brain 4. Distinguish between descriptive and hypothesis-driven science. 1.3 ▯ Descriptive: observations lead to hypothesis, deductive reasoning o EX. Study of biodiversity ▯ Hypothesis-driven: suggested explanation that accounts for observation is tested experimentally, inductive reasoning 5. Distinguish between a hypothesis and scientific theory. 1.3 ▯ Hypothesis: suggested explanation that accounts for scientific observation. ▯ Scientific theory: deductive form – proposed explanation for natural phenomenon based on general principles; inductive form – body of interconnected concepts supported by inductive scientific reasoning and experimental evidence. 6. Describe Darwin's theory of evolution by natural selection. 1.4.3 ▯ Evolution's primary mechanism is natural selection, I.e the survival of the most beneficial traits, leading to adaptations and an overall shift in species. 7. Distinguish between artificial and natural selection. 1.4.3 ▯ Essentially, the artificial selection in man-made while natural selection is a result of survival fitness. 8. Identify the major types of evidence supporting evolution and phylogenetic trees. 1.4.4 ▯ Fossil record: transitional forms, microscopic fossils, and fossils overall give evidence for evolution from simple to complex organisms ▯ Comparative anatomy: homologus (same evolutionary origin with different structure and function in present day) and analogous (similar function but different origins) provide evidence ▯ Molecular evidence: comparing genomes of different groups of animals or plants 9. Explain how evolution accounts for both the unity and diversity of life. 1.5.1 ▯ The underlying unity of biochemistry and genetics that all life has evolved from the same origin event. The diversity we see today has arisen by evolutionary change, visible in fossil record. The retention of certain characteristics shared by all organisms, such as DNA being the storage for hereditary info, supports a long line of descent from a common origin. 10. Describe the three domains of life. 22.5.1 ▯ Domain archaea: archaea ▯ Domain bacteria: bacteria ▯ Domain eukarya: eukaryotes – includes Kingdom Plantae, Kingdom Fungi, Kingdom Animalia, and Protists (not a kingdom) CH. 2 MOLECULES AND WATER 1. Describe the general structure of atoms and the properties of their constituent particles. 2.1.1 ▯ Atoms: central nucleus containing cluster of neutrons and protons with electron cloud surrounding ▯ Proton: positive subatomic particle ▯ Neutron: neutral subatomic particle ▯ Electron: negative subatomic particle 2. Distinguish between essential elements and trace elements. 2.2.1 ▯ Essential elements: needed in significant amounts order to live healthy life, a deficiency causes abnormal development or functioning ▯ Trace elements: needed in amounts 7 is basic 10. Distinguish between an acid and a base. 2.5.1 ▯ Acid: any substance that dissociates in water to increase H+ and lower pH ▯ Base: any substance that combines with H+ when dissolved in water, lowering H+ and increasing pH 11. Explain how buffers, such as the bicarbonate buffer system, stabilize the pH of solutions. 2.5.1 ▯ Buffers exist in solutions to maintain pH by releasing acid when too much base is present and, in a reciprocal manner, releasing base when too much acid is present. CH. 3/6 CARBS, NUCLEOTIDES, & ENZYMES 1. Recognize the general structures of monosaccharides, amino acids, and nucleotides, and describe the chemical properties of each. 3.2.1, 3.3.2, 3.4.1 ▯ Monosaccharides: simplest sugar, C-H bonds with as few as 3 carbon atoms (plays central role in energy storage=6 carbons); linked by covalent bonds – structural isomers determine sweetness ▯ Amino acids: central carbon atom, amino group (-NH2), carboxyl group (-COOH), functional side group R; linked by peptide bonds – chemical character is determined by R group ▯ Nucleotides: 5 carbon sugar (ribose or deoxyribose), phosphate group, nitrogenous base (purines- AG or pyrimidines- CT); linked by phosphodiester bonds – OH on sugar ring = RNA, H on sugar ring = DNA 2. Differentiate between glycosidic linkage, peptide bond, and phosphodiester bond. ▯ Glycosidic linkage: covalent bond between a sugar molecules and another group (may or may not be carbohydrate) ▯ Peptide bond: covalent bond between amino acids ▯ Phosphodiester bond: covalent bond between nucleotides to form nucleic acids 3. Describe the functions of carbohydrates in cells. 3.2 ▯ Building blocks for carbon skeletons ▯ Cell identity on outer surface ▯ Energy storage (glucose, glycogen, starch – alpha linkage) ▯ Structure (cellulose, chitin – beta linkage) 4. How do the structures of starch, glycogen and cellulose affect their functions? 3.2 ▯ Starch and glycogen: alpha branching, allows for longer food reserve, easier to be broken due to branching rather than linkage ▯ Cellulose: beta linkage, stronger than alpha branching a linkage is better for structures; resists tension, compression, and hydrolysis 5. Describe the functions of nucleotides in cells. 3.4.4 ▯ Nucleic acid building blocks (DNA, RNA) ▯ Cellular energy carriers (ATP, GTP) ▯ Electron acceptor/donor (NAD, NADP, FAD) ▯ Carrier of chemical groups (ATP, CoA, UDP) ▯ Regulatory (signaling) molecules (GTP, cAMP) 6. Explain how a catalyst increased the rate of a chemical reaction. 6.4.1 ▯ A catalyst lowers activation energy and makes the transition state more stable 7. Describe the characteristics of enzymes. 6.4.2 ▯ Mostly proteins, some RNA ▯ Lowers activation energy by stressing specific bonds ▯ Different enzymes catalyze different, specific reactions ▯ Can be reused 8. Explain how enzymes lower activation energies. 6.4.2 ▯ Enzymes stress specific chemical bonds in order to allow new bonds to form more easily. 9. Distinguish between substrate, active site, enzyme-substrate complex, and induced fit. 6.4.3 ▯ Substrate: the ligand that binds to an enzyme ▯ Active site: the site where the substrate (ligand) binds to an enzyme ▯ Enzyme-substrate complex: the substrate fits into the enzyme and binds ▯ Induced-fit: the term that describes how the enzyme must alter its shape slightly for the substrate to fit and bind properly 10. Identify the different types of molecules that may act as enzymes. 6.4.4 ▯ RNA: ribosomes may catalyze other molecules (intermolecular catalysis) or themselves (intramolecular catalysis) - rRNAplay a key catalytic role in RNA production, with proteins providing the framework to correctly orient RNA subunits with respect to each other 11. Distinguish between enzyme cofactors and coenzymes. 6.4.4 ▯ Cofactor: additional chemical component, often metal ions found in active site, that assist enzyme function ▯ Coenzyme: cofactor that is a nonprotein, organic molecule 12. Explain the effects of pH and temperature on enzyme activity. 6.4.5 ▯ PH: when pH is not at optimal pH, the rate is not as fast as it has the potential to be. High pH=ionization, low pH=nonionization (affects ionization of R groups) ▯ Temperature: increase in temp increases collisions, thereby speeding up rate, BUT when the temperature gets too high, the protein will change shape (denaturation/unfolding) - an increase in temperature can cause renaturation/refolding in some cases 13. Distinguish between competitive and noncompetitive enzyme inhibition. 6.4.5 ▯ Competitive enzyme: will block substrate at active site ▯ Noncompetitve enzyme: will block substrate by entering enzyme at different site than where substrate binds 14. Explain allosteric regulation of enzymes 6.4.5 ▯ Allosteric regulation can activate or inhibit enzymes – can bind to an area other an active site to stabilize an active form or inactive form (noncovalent/reversible) 15. Explain the control of protein function by phosphorylation. 9.1.3 ▯ Phosphorylation acts as a switch; if the protein is "off" before adding a phosphate, phosphorylation will turn it "on" and vice versa. The concentration of kinase will affect amount of phosphorylation (lots of kinase=lots of phosphorylation). LEARNING OBJECTIVES FOR ENERGY AND METABOLISM (CH.6) 1. Define energy and distinguish between potential and kinetic energy. 6.1.1 ▯ Energy: capacity to do work ▯ Potential energy: energy of motion (active energy) ▯ Kinetic energy: stored energy (energy at rest) 2. State the First Law of Thermodynamics. 6.2.1 ▯ Energy cannot be created or destroyed; it can only change from one form to another (e.g. potential to kinetic) 3. State the Second Law of Thermodynamics and describe how it applies to biological systems. 6.2.2 ▯ Disorder in the universe (I.e. entropy) is continually increasing. 4. Define entropy, enthalpy and free energy. Explain how chemical reactions can be predicted based on changes in free energy. 6.2.3 ▯ Entropy (S): disorder in the universe ▯ Enthalpy (H): total energy contained in a molecule's chemical bonds ▯ Free energy: availability of energy to do work with temperature and pressure constant; a positive change in free energy means the reaction will not be spontaneous/not favorable while a negative change in free energy means the reaction will be spontaneous/favorable. 5. Distinguish between endergonic and exergonic reactions. Explain what is meant by a spontaneous reaction. 6.2.3 ▯ Endergonic: requires energy, not spontaneous, typically +deltaG/ +deltaH/ -deltaS ▯ Exergonic: doesn't require energy to occur, spontaneous, typically -deltaG/-deltaH/+deltaS ▯ Spontaneous reaction: additional energy is not required for the reaction to occur 6. Recognize the general structures of nucleotides and describe their chemical properties. 3.4.1 ▯ 5 carbon sugar (ribose or deoxyribose), phosphate group, nitrogenous base (purines - AG or pyrimidines-CT); linked by phosphodiester bonds – OH on sugar ring = RNA, H on sugar ring = DNA 7. Describe the functions of nucleotides in cells. 3.4.4 ▯ Nucleic acid building blocks (DNA, RNA) ▯ Cellular energy carriers (ATP, GTP) ▯ Electron acceptor/donor (NAD, NADP, FAD) ▯ Carrier of chemical groups (ATP, CoA, UDP) ▯ Regulatory (signaling) molecules (GTP, cAMP) 8. Describe the three main kinds of work carried out by cells. ▯ Chemical: biosynthesis, bioluminescence ▯ Transport: voltage, concentration ▯ Mechanical: movement 9. Describe the structure of ATP and explain how ATP hydrolysis drives endergonic reactions. 6.3.1 ▯ Structure: 5-carbon sugar (ribose), 2 carbon-nitrogen rings (adenine), 3 phosphates ▯ ATP hydrolysis driving endergonic reactions: if cleavage of ATP's terminal high-energy bond releases more energy than the other reaction consumes, the two reactions can be coupled, resulting in a net release of energy (-deltaG) -- almost all endergonic reactions require less energy than released by ATP hydrolysis, so ATP is able to provide most energy a cell needs. 10. Describe energy coupling using ATP hydrolysis ▯ Energy coupling is the transfer of energy from an exergonic process to an endergonic process. Free energy from ATP hydrolysis is used to drive endergonic reactions. CH 7 CELL RESPIRATION 1. Distinguish between oxidation and reduction reactions. 6.1.2, 7.1.1 ▯ LEO says GER (Lose Electrons Oxidation/Gain Electrons Reduction) ▯ Oxidation: process by which an atom or molecule loses an electron – Lose Electrons Oxidation; atom or molecule that accepts an electron is an oxidizing agent ▯ Reduction: process by which an atom or molecule gains an electron – Gains Electrons Reduction; atom or molecule that donates or gives away an electron is a reducing agent 2. Describe the structure of NAD, its role, and the role of B vitamins in energy metabolism. 7.1.2 ▯ Structure: 2 nucleotides (nicotinamide monophosphate-NMP + adenosine monophosphate – AMP) joined head to head; NMP is active part – readily reduced (accepts electrons) ▯ NAD role: major electron; when NAD is reduced by accepting 2 B vitamin role: B vitamins act as coenzymes that are crucial in aiding enzymes in ATP and fatty acid production 3. Explain the process of glycolysis, including reactants, products, and energy yield. 7.2.1 ▯ Process: anaerobic; glucose is converted into 2 pyruvates; each molecule of glucose yields 2 ATP in this process; consists of 10 rxns, first 5 in energy investment phase (splitting, exergonic) ▯ Reactants: glucose, 2NAD+, 4 electrons, 2 ATP, 4H+ ▯ Products: 2H+, pyruvate, 2H2O, 4 ATP (total yield of 2 ATP), 2NADH ▯ Energy yield: 2 ATP 4. Describe two ways in which ATP is generated in cellular respiration. 7.1.3 (p. 134-135) ▯ Substrate-level phosphorylation: ATP is formed by transferring a phosphate group directly to ADP from a phosphate-bearing intermediate or substrate; in glycolysis, the chemical bonds of glucose are shifted around in reactions that provide the energy required to form ATP by substrate-level phosphorylation ▯ Oxidative phosphorylation: ATP is synthesized by ATP synthase (which is both an enzyme and a channel) using energy from a proton gradient that is formed by high-energy electrons harvested by the oxidation of glucose and passing down an electron transport chain ( how ATP is produced most by eukaryotes and aerobic prokaryotes 5. Name and describe the four stages of cellular respiration, identifying specifically where in the cell (prokaryotic and eukaryotic) each occures. ▯ Glycolysis: eytoplasm in euk and prok ▯ Pyruvate oxidation: mitochondria in euk, in cytoplasm and at plasma membrane in prok ▯ Krebs cylcle/citric acidcycle/TCA: mitochondrial matrix/inner membrane of mitochondria in euk, cytosol in prok ▯ Oxidative Phosphorylation: mitochondrial cristae in euk, cell membrane in prok 6. Describe two different metabolic pathways that pyruvate can enter. ▯ Oxidation of pyruvates – cleaves off one of pyruvate's 3 carbons which becomes CO2, remaining 2-carbon compound (acetyl) attaches to coenzyme A to produce acetyl-CoA. In this rxn, 2 nd electrons and 1 proton are transferred to NAD+ to reduce it to NADH with a 2 proton donated. ▯ Fermentation – uses reduction of all or part of pyruvates to oxidize NADH back to NAD+, executed copiously by bacteria 7. Identify the reactants and products of pyruvate oxidation. 7.3.1 ▯ Reactants: pyruvates, NAD+, CoA ▯ Products: acetyl-CoA, NADH, Co2, H+ 8. Identify the reactants and products of the Krebs cycle and describe its role. 7.3.2 ▯ Reactants: acetyl-CoA, 3NAD+, FAD, ADP + P, OAA ▯ Products: 1 ATP, 3 NADH, 1 FADH2, CO2, CoA-SH, OAA 9. Describe how the movement of electrons along the electron transport chain generates a proton gradient. 7.4.1 ▯ The first protein to receive the electrons is the membrane-embedded enzyme NADH dehydrogenase ▯ A carrier called ubiquinone then passes the electrons to a protein-cytochrome complex called the bc1 complex ▯ The electrons are then carried by cytochrome C to the cytochrome oxidase complex. This complex uses 4 electrons to reduce a molecule of oxygen; each oxygen then combines with 2 protons to form water. ▯ Protons are produced when electrons are transferred to NAD+ ▯ As the electrons are passed along the ETC, the energy they release transports protons out of the matrix and into the intermembrane space (concentration gradient) ▯ The flow of highly energetic electrons induces a change in the shape of pump proteins, causing them to transport protons across the membrane. The increasing electronegativity with each pump propels the protons down the ETC. 10. Explain chemiosmosis, including a description of how ATP synthase works. 7.4.2 ▯ Chemiosmosis: ATP is driven by a diffusion force similar to osmosis. Because the mitochondrial matrix is negative compared with the intermembrane space, protons are attracted to the matrix. The higher outer concentration of protons drives protons back in by diffusion , but because membranes are relatively impermeable to ions, this occurs slowly. ▯ ATP synthase: enzyme channel that uses the energy of the gradient to catalyze the synthesis of ATP; the new ATP is transported by facilitated diffusion to the many places in the cell where enzymes require energy to drive endergonic reactions. 11. Explain the maximum yield of ATP from a molecule of glucose and the efficiency of this energy conversion. 7.5 ▯ The maximum yield is approx. 30-32 ATP. 12. Explain why the maximum yield of ATP is rarely obtained. ▯ The max yield is limited by the fractional number of ATP produced by NAHD and FADH2, which NADH shuttle transported to the mitochondria, the other uses the proton motor force is used for (moving ADP to matrix, proton symport), and intermediates in anabolism. 13. Explain feedback regulation and describe two keys points at which it is used to regulate cellular respiration. 6.5.2 ▯ Feedback regulation: control mechanism whereby an increase in the concentration of some molecules inhibits the synthesis of that molecule. o In glycolysis: control point a phosphofructokinase (which catalyzes the conversion of fructose phosphate to fructose bisphosphate); first reaction of glycolysis that is not readily reversible; ATP itself and citrate (Krebs cycle intermediate) are allosteric inhibitors – high levels of both ATP and citrate inhibit phosphofructokinase. When ATP is in excess or when the Krebs cycle is producing citrate faster than it is being consumed, glycolysis slowed. o In pyruvate oxidation: control point at pyruvate dehydrogenase (which converts pyruvate to acetyl-CoA); inhibited by high levels of NADH; another control point in the Krebs cycle is citrate synthetase (which catalyzes the first reaction, the conversion of oxaloacetate and acetyl-CoA into citrate) -- high levels of ATP inhibit citrate synthetase (as well as phosphofructokinase, pyruvate dehydrogenase, and two other Krebs cycle enzymes), slowing down the entire catabolic pathway. 14. Describe two ways that prokaryotes can produce ATP entirely anaerobically. 7.7 ▯ Anaerobic respiration: many prokaryotes use sulfur, nitrate, carbon dioxide, or even inorganic metals as the final electron acceptor in place of oxygen – amount of free energy released is lower than with oxygen because of lower electronegativity; ATP production is less ▯ Fermentation: the electrons generated by glycolysis are donated to organic molecules 15. Describe fermentation, explain its role, and distinguish between ethanol and lactic acid fermentation. 7.7.2 ▯ Fermentation: anaerobic process that occurs after pyruvate has been produced through glycolysis; allows cells to regenerate NAD+ for glycolysis ▯ Ethanol fermentation: occurs in yeast, the molecule that accepts electrons from NADH is derived from pyruvates, the end-product of glycolysis, yeast enzymes remove a terminal CO2 group from pyruvate through decarboxylation, producing a 2-carbon molecule called acetaldehyde. The CO2 released causes bread made with yeast to rise. The acetaldehyde accepts a pair of electrons from NADH, producing NAD+ and ethanol, source of the ethanol in wine and beer. ▯ Lactic acid fermentation: regeneration of NAD+ in the absence of oxygen without decarboxylation; for example, muscles use the enzyme lactate dehydrogenase to transfer electrons from NADH back to the pyruvates that is produced by glycolysis. This reaction converts pyruvates into lactic acid and regenerates NAD+ from NADH, allowing glycolysis to continue as long as glucose is available. 16. Briefly describe how proteins and fats can be used to make ATP in cellular respiration. 7.8 ▯ Proteins: first broken down into their individual amino acid (deanimation), and a series of reaction converts the carbon chain that remains into a molecule that enters glycolysis or the Krebs cycle. The reactions of cellular respiration then extract the high-energy electrons from these molecules and put them to work making ATP ▯ Fats: broken down into fatty acids plus glycerol, oxidized in the matrix of the mitochondrion. Enzymes progressively remove 2-carbon acetyl groups from the terminus of each fatty acid, nibbling away at the end until the entire fatty acid is converted into acetyl groups. Each acetyl group is combined with coenzyme A to form acetyl-CoA (known as beta oxidation) CHAPTER 8 Photosynthesis 1. Describe the four ways that organisms obtain carbon and energy. 23.4.1 ▯ Photoautotroph: energy source= light; carbon source = CO2, HCO3-, or related compound (cynobacteria, bacteriachlorophyll) ▯ Chemlithoautotrophs energy source = light; carbon source = organic molecules (nonsulfur bacteria) ▯ Chemoheterotrophs: energy = organic molecules; carbon source = organic molecules (decomposers, most pathogens, humans, nonphotosynthetic eukaryotes) 2. Write the balanced equation for photosynthesis and identify which molecules are oxidized or reduced. 8.1.1 ▯ 6CO2 + 12H2O + sunlight yields C6H12O6(glucose) + 6H2O + 6O2 ▯ In photosynthesis, CO2 is reduced to glucose using electrons gained from the oxidation of water. The oxidation of H2O and the reduction of CO2 requires energy that is provided by light. 3. Compare the structure of a chloroplast with that of a mitochondrion. 8.1.2 ▯ A mitochondrion's complex structure of internal and external membranes contribute to its function. The same is true for the structure of the chloroplast. The internal membrane of chloroplasts, called the thylakoid membrane, is a continuous phospholipid bilayer organized into flattened sacs that are found stacked on one another in columns called grana (singular, granum). The thylakoid membrane contains chlorophyll and other photosynthetic pigments for capturing light energy along with the machinery to make ATP. Connections between grana are termed stroma lamella. Surrounding the thylakoid membrane system is a semiliquid substance called stroma. The stroma houses the enzymes needed to assemble organic molecules from CO2 using energy from ATP coupled with reduction via NADPH. In the thylakoid membrane, photosynthetic pigments are clustered together to form photosystems, which act as large antennas, gathering the light energy harvested by many individual pigment molecules. 4. Describe the endosymbiotic origin of chloroplasts. 24.1.3 ▯ All chloroplasts are likely derived from a single line of cyanobacteria, but the organisms that host these chloroplasts are not monophyletic. This apparent paradox is resolved by considering the possibility of secondary, and even tertiary endosymbiosis. Red and green algae both obtained their chloroplasts by engulfing photosynthetic cyanobacteria. The brown algae most likely obtained their chloroplasts by engulfing one or more red algae, a process called secondary endosymbiosis. 5. Identify specifically the location of the light reactions and carbon fixation in the chloroplast. ▯ Light reactions: photosystems (photosynthetic pigments clustered together in thylakoid membrane) ▯ Carbon fixation: stroma 6. Identify the reactants and products of the Calvin cycle. 8.6.2 ▯ Reactants: 6CO2, 18ATP, 12NADPH, H2O ▯ Products: 2 G3P, 16PI, 18ADP, 12 NADP+ 7. Describe the three major phases of the Calvin cycle and the role of Rubisco. 8.6.2 ▯ Carbon fixation: generates 2 molecules of PGA o 3 RuBP + 3 CO2 yields 6PGA ▯ Reduction: PGA is reduced to G3P by reverse –glycolysis rxns o 6 PGA + 6 ATP + 6 NADPH yields 6 G3P ▯ Regeneration: PGA is used to regenerate RuBP o 5 G3P + 3 ATP yields 3 RuBP ▯ G3P is product; 3 turns of cycle are needed to produce one molecule of G3P; 6 turns needed to synthesize one glucose molecule ▯ Rubsico: enzyme that carries out carbon fixation; catalyzes primary chemical reaction by which inorganic enters the biosphere; 16-subunit enzyme found in stroma; most abundant protein on earth, though slow 8. Describe the nature of electromagnetic radiation and visible light. 8.3.1 ▯ Light is a form of electromagnetic energy. The wave nature of light produces an electromagnetic spectrum based on wavelength and frequency. The shorter the wavelength, the greater the energy. Visible light occupies a very small part of the spectrum, approx. 400nm to 740 nm 9. identify which wavelengths/colors of visible light are most effective in photosynthesis. 8.3.2 ▯ Chlorophyll a and chlorophyll b absorb violet-blue and red light best. Neither absorb photons
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