BIOL 107 Midterm and Final Review: Cell Structure, Metabolism and Gene Expression

Terms in this set (35)

1. Prokaryotic vs eukaryotic cells: what is the key structural difference?Prokaryotes (bacteria and archaea) have no nucleus or membrane-bound organelles; their DNA sits in a nucleoid region and they have 70S ribosomes. Eukaryotes have a nucleus, an endomembrane system, mitochondria and 80S cytosolic ribosomes.
2. Name the four major classes of biological macromolecules and their building blocks.Proteins (amino acids), nucleic acids (nucleotides), carbohydrates (monosaccharides) and lipids. Lipids are not true polymers; a triglyceride is glycerol plus three fatty acids.
3. Dehydration synthesis vs hydrolysisDehydration synthesis joins monomers by removing a water molecule to form a covalent bond. Hydrolysis breaks that bond by adding water. Polymers are built by dehydration and digested by hydrolysis.
4. What are the four levels of protein structure?Primary: amino acid sequence. Secondary: alpha helices and beta sheets held by backbone hydrogen bonds. Tertiary: overall 3D fold from R-group interactions. Quaternary: assembly of two or more polypeptide subunits.
5. What determines whether an amino acid is nonpolar, polar, acidic or basic?Its R group (side chain). The amino and carboxyl groups are common to all amino acids, so only the side chain changes the chemical properties.
6. Saturated vs unsaturated fatty acidsSaturated fatty acids have no C=C double bonds, pack tightly and are solid at room temperature. Unsaturated fatty acids have one or more cis double bonds that kink the chain, so they pack loosely and tend to be liquid.
7. Why do phospholipids spontaneously form a bilayer in water?They are amphipathic: a hydrophilic phosphate head and two hydrophobic fatty acid tails. In water the tails cluster away from water and the heads face the aqueous surroundings on both sides.
8. What does the fluid mosaic model describe?A membrane is a fluid phospholipid bilayer in which proteins, cholesterol and glycolipids are embedded or attached and can move laterally, forming a mosaic of components.
9. What factors increase membrane fluidity?Higher temperature and more unsaturated (kinked) or shorter fatty acid tails. Cholesterol acts as a buffer: it reduces fluidity at warm temperatures and prevents tight packing at cold temperatures.
10. Simple diffusion vs facilitated diffusion vs active transportSimple diffusion: small nonpolar molecules cross the bilayer down their gradient. Facilitated diffusion: channel or carrier proteins move solutes down their gradient with no energy input. Active transport: pumps move solutes against their gradient using energy such as ATP.
11. An animal cell is placed in a hypertonic solution. What happens?Water leaves the cell by osmosis toward the higher solute concentration, so the cell shrinks (crenates). In a hypotonic solution an animal cell swells and may lyse, while a plant cell becomes turgid.
12. What evidence supports the endosymbiotic origin of mitochondria and chloroplasts?They have double membranes, their own circular DNA, 70S bacteria-like ribosomes, divide by binary fission, and their genes are most similar to those of bacteria.
13. Rough ER vs smooth ERRough ER is studded with ribosomes and makes secreted and membrane proteins. Smooth ER lacks ribosomes and synthesizes lipids, detoxifies drugs, and stores calcium ions.
14. What is the function of the Golgi apparatus?It receives proteins and lipids from the ER, modifies them (for example by adding or trimming carbohydrates), sorts them and packages them in vesicles for delivery to the plasma membrane, lysosomes or secretion.
15. What do lysosomes do?They are acidic, membrane-bound compartments containing hydrolytic enzymes that digest macromolecules, worn-out organelles (autophagy) and material taken in by phagocytosis.
16. What does a negative delta G tell you about a reaction?The reaction is exergonic and spontaneous: it releases free energy. It says nothing about speed; a spontaneous reaction can still be very slow without a catalyst.
17. How do enzymes speed up reactions?They lower the activation energy by stabilizing the transition state. They do not change delta G or the equilibrium position, and they are not consumed by the reaction.
18. Competitive vs noncompetitive inhibitionA competitive inhibitor binds the active site and can be outcompeted by adding more substrate. A noncompetitive inhibitor binds elsewhere on the enzyme and changes its shape, lowering activity no matter how much substrate is present.
19. How do cells use ATP to drive endergonic reactions?Through energy coupling: the exergonic hydrolysis of ATP is linked to the endergonic reaction, often by transferring a phosphate group to a reactant (phosphorylation) so the overall delta G is negative.
20. Glycolysis: location, input and net outputIt takes place in the cytosol. One glucose is split into 2 pyruvate, with a net gain of 2 ATP and 2 NADH. It does not need oxygen.
21. Pyruvate oxidation and the citric acid cycle: where do they occur and what do they make per glucose?Both occur in the mitochondrial matrix. Per glucose they make 2 acetyl CoA, 8 NADH, 2 FADH2, 2 ATP (or GTP) and 6 CO2 in total.
22. How does chemiosmosis produce ATP?The electron transport chain in the inner mitochondrial membrane pumps H+ into the intermembrane space. The H+ flow back into the matrix through ATP synthase, which uses that energy to make ATP. O2 is the final electron acceptor and forms water.
23. Why do cells carry out fermentation when oxygen is absent?To regenerate NAD+ from NADH so glycolysis can continue making ATP. Pyruvate is reduced to lactate (in animals) or to ethanol and CO2 (in yeast).
24. Light reactions vs Calvin cycleThe light reactions occur in the thylakoid membranes: they split water, release O2 and make ATP and NADPH. The Calvin cycle occurs in the stroma and uses that ATP and NADPH to fix CO2 into sugar (G3P).
25. What does rubisco do?Rubisco is the Calvin cycle enzyme that fixes CO2 by attaching it to ribulose bisphosphate (RuBP). It is thought to be the most abundant protein on Earth.
26. What are the phases of the eukaryotic cell cycle, and when is DNA replicated?Interphase (G1, S, G2) followed by M phase (mitosis and cytokinesis). DNA is replicated during S phase.
27. Mitosis vs meiosisMitosis: one division that produces 2 genetically identical diploid cells, used for growth and repair. Meiosis: two divisions that produce 4 genetically different haploid gametes.
28. What two events in meiosis generate genetic variation?Crossing over between homologous chromosomes in prophase I, and independent assortment of homologous pairs at metaphase I. Random fertilization adds further variation.
29. What did the Meselson-Stahl experiment show?That DNA replication is semiconservative: each new double helix has one parental strand and one new strand. They showed this by growing bacteria in heavy 15N and then light 14N medium and separating the DNA by density.
30. Leading vs lagging strandDNA polymerase adds nucleotides only in the 5' to 3' direction. The leading strand is made continuously toward the fork; the lagging strand is made discontinuously as Okazaki fragments that are later joined.
31. State the roles of helicase, primase, DNA ligase and topoisomerase.Helicase unwinds the double helix. Primase lays down RNA primers. DNA ligase seals the nicks between Okazaki fragments. Topoisomerase relieves the supercoiling that builds up ahead of the fork.
32. How does transcription differ from DNA replication in its requirements?RNA polymerase does not need a primer. It reads the template strand 3' to 5', makes RNA 5' to 3' using U instead of T, and copies only one gene or region, not the whole genome.
33. Name three ways eukaryotic pre-mRNA is processed before it leaves the nucleus.A 5' methylguanosine cap is added, a 3' poly-A tail is added, and introns are removed by splicing so that the exons are joined together.
34. In translation, what happens at the A, P and E sites of the ribosome?The A site accepts the incoming aminoacyl-tRNA, the P site holds the tRNA carrying the growing polypeptide, and the E site is where the empty tRNA exits.
35. A template DNA strand reads 3'-TACGGA-5'. Give the mRNA and the amino acids it encodes.The mRNA is 5'-AUGCCU-3', which encodes Met-Pro. AUG is also the start codon.