LIFESCI 7A Midterm Review: Biomolecules, Enzymes, Cellular Respiration and Gene Expression

Terms in this set (31)

1. Why is water such a good solvent for ions and polar molecules?Water is polar: its partially negative oxygen and partially positive hydrogens form hydrogen bonds with polar solutes and surround ions in hydration shells, stabilizing them in solution.
2. What is the hydrophobic effect?Nonpolar molecules cluster together in water because this reduces the ordered cage of water molecules around them, increasing water's entropy. It drives lipid bilayer formation and helps proteins fold with nonpolar side chains buried inside.
3. Describe 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 side chain interactions. Quaternary: assembly of two or more polypeptide subunits.
4. How is a peptide bond formed?By a condensation (dehydration) reaction between the carboxyl group of one amino acid and the amino group of the next, releasing water. The chain has a free amino N-terminus and a free carboxyl C-terminus.
5. Saturated vs unsaturated fatty acidsSaturated fatty acids have no C=C double bonds, so straight chains pack tightly (solid fats). Unsaturated fatty acids have cis double bonds that kink the chain, lowering packing and melting point and increasing membrane fluidity.
6. Name three structural differences between DNA and RNA.DNA uses deoxyribose (no 2' OH), thymine, and is usually double-stranded. RNA uses ribose (has a 2' OH), uracil instead of thymine, and is usually single-stranded, often folding into complex shapes.
7. What does it mean that the two strands of DNA are antiparallel, and how do bases pair?One strand runs 5' to 3' while its partner runs 3' to 5'. A pairs with T by 2 hydrogen bonds and G pairs with C by 3 hydrogen bonds, so GC-rich DNA is harder to melt.
8. What does the sign of ΔG tell you, and what is the equation?ΔG = ΔH − TΔS. Negative ΔG means exergonic and spontaneous (but not necessarily fast); positive ΔG means endergonic and requires an energy input to proceed.
9. How do enzymes speed up reactions? What do they NOT change?They lower the activation energy, mainly by stabilizing the transition state. They do not change ΔG or the equilibrium constant; they only help the reaction reach equilibrium faster.
10. Competitive vs noncompetitive inhibition: effect on Km and VmaxCompetitive inhibitors bind the active site: apparent Km rises, Vmax unchanged, overcome by more substrate. Pure noncompetitive inhibitors bind elsewhere: Vmax falls, Km unchanged, not overcome by more substrate.
11. What is Km in Michaelis-Menten kinetics?The substrate concentration at which the reaction rate is half of Vmax. A lower Km means the enzyme reaches half-maximal rate at lower substrate concentration (higher apparent affinity).
12. What is feedback inhibition?The end product of a metabolic pathway binds an allosteric site on an enzyme early in the pathway and inhibits it, so the cell stops making product when it already has enough.
13. How does ATP drive endergonic reactions?ATP hydrolysis to ADP + Pi is strongly exergonic (about −30.5 kJ/mol under standard conditions). The cell couples it to unfavorable reactions, often by transferring the phosphate to a substrate or protein, making the overall ΔG negative.
14. Define oxidation and reduction. What happens to NAD+ in metabolism?Oxidation is loss of electrons; reduction is gain of electrons (OIL RIG). NAD+ is reduced to NADH when it accepts two electrons and a proton from a fuel molecule being oxidized.
15. Glycolysis: location, inputs, and net products per glucoseOccurs in the cytosol and needs no oxygen. One glucose becomes 2 pyruvate, with a net gain of 2 ATP (by substrate-level phosphorylation) and 2 NADH.
16. Pyruvate oxidation and the citric acid cycle: location and productsBoth occur in the mitochondrial matrix. Each pyruvate becomes acetyl-CoA, releasing CO2 and making NADH. Each turn of the cycle releases 2 CO2 and makes 3 NADH, 1 FADH2 and 1 ATP (or GTP).
17. How do the electron transport chain and ATP synthase make ATP?Electrons from NADH and FADH2 pass through inner-membrane complexes to O2, the final acceptor, forming water. The energy pumps H+ into the intermembrane space; H+ flowing back through ATP synthase into the matrix powers ATP synthesis (chemiosmosis).
18. What is the purpose of fermentation?To regenerate NAD+ from NADH so glycolysis can keep making ATP without oxygen. Animals make lactate; yeast make ethanol and CO2. No extra ATP is made beyond glycolysis.
19. What happens to a cell treated with an uncoupler that makes the inner mitochondrial membrane leaky to H+?Electron transport and O2 consumption continue or even increase, but the proton gradient collapses, so ATP synthase makes little ATP. The energy is released as heat.
20. What did the Meselson-Stahl experiment show?DNA replication is semiconservative. Bacteria grown in heavy 15N were moved to 14N: after one generation all DNA had hybrid density; after two generations there were hybrid and light bands, ruling out conservative and dispersive models.
21. Leading vs lagging strand synthesisDNA polymerase only adds nucleotides to a 3' end (builds 5' to 3'). The leading strand is made continuously toward the fork; the lagging strand is made away from the fork in short Okazaki fragments, each started by an RNA primer.
22. Match the replication enzyme to its job: helicase, primase, DNA polymerase, ligase, topoisomeraseHelicase unwinds the double helix. Primase lays down RNA primers. DNA polymerase extends primers and proofreads. Ligase seals nicks between fragments. Topoisomerase relieves supercoiling ahead of the fork.
23. How does transcription differ from DNA replication in terms of direction and primers?RNA polymerase reads the template strand 3' to 5' and builds RNA 5' to 3', like DNA polymerase, but it needs no primer. It starts at a promoter and only copies one gene-sized region rather than the whole genome.
24. What three processing steps convert a eukaryotic pre-mRNA into mature mRNA?Addition of a 5' cap, addition of a 3' poly-A tail, and splicing, in which the spliceosome removes introns and joins exons. Alternative splicing lets one gene encode several proteins.
25. Outline translation at the ribosome.tRNA anticodons pair with mRNA codons. Initiation begins at AUG (methionine). The ribosome moves through the A, P and E sites, forming peptide bonds. A stop codon (UAA, UAG, UGA) is bound by a release factor, freeing the polypeptide.
26. Key properties of the genetic codeTriplet codons read without overlap; redundant (several codons can code the same amino acid); unambiguous (each codon specifies one amino acid); and nearly universal across organisms.
27. Silent vs missense vs nonsense vs frameshift mutationsSilent: codon changes but same amino acid. Missense: one amino acid replaced by another. Nonsense: codon becomes a stop codon, truncating the protein. Frameshift: insertion or deletion not a multiple of 3 shifts every downstream codon.
28. How is the lac operon regulated?Without lactose, the lac repressor binds the operator and blocks transcription. Allolactose binds the repressor and releases it. Strong transcription also needs low glucose, when cAMP-CAP binds near the promoter and recruits RNA polymerase.
29. Inducible vs repressible operons: lac vs trpThe lac operon is inducible: normally off, turned on when lactose is present. The trp operon is repressible: normally on, and tryptophan acts as a corepressor that activates the repressor to shut it off.
30. How do chromatin modifications affect eukaryotic gene expression?Histone acetylation loosens chromatin and generally promotes transcription. DNA methylation (often at CpG sites) and histone deacetylation generally condense chromatin and silence genes.
31. A DNA template strand reads 3'-TAC GGA-5'. What is the mRNA and the encoded dipeptide?The mRNA is 5'-AUG CCU-3', which encodes Met-Pro. The mRNA is complementary and antiparallel to the template, with U in place of T.