BIO130 Exam Review: Gene Expression, Membranes, Protein Sorting, Cytoskeleton and Cell Cycle

Terms in this set (34)

1. State the central dogma and its best-known exception.Information flows from DNA to RNA (transcription) to protein (translation). Retroviruses such as HIV use reverse transcriptase to copy RNA back into DNA.
2. How does DNA differ from RNA chemically?DNA has deoxyribose (no 2' OH), uses thymine and is usually double-stranded. RNA has ribose (with a 2' OH), uses uracil in place of thymine and is usually single-stranded and less stable.
3. If a DNA sample is 30% adenine, what are the percentages of T, G and C?By Chargaff's rules A = T and G = C. So T = 30%, leaving 40% for G + C: G = 20% and C = 20%.
4. What does it mean that the two DNA strands are antiparallel?They run in opposite directions: one strand runs 5' to 3' and its partner 3' to 5'. The 5' end has a free phosphate and the 3' end a free OH, where new nucleotides are added.
5. What is the end-replication problem, and how does telomerase address it?When the final primer at a linear chromosome end is removed, the lagging strand cannot be completed, so chromosomes shorten each round. Telomerase uses its own RNA template to extend the repetitive telomere DNA, mainly in germ cells, stem cells and many cancers.
6. How do cells keep DNA replication accurate?DNA polymerase has 3' to 5' exonuclease proofreading that removes mispaired nucleotides as it goes. Mismatch repair then fixes errors that escape proofreading by recognizing the newly made strand.
7. What is a nucleosome, and how does euchromatin differ from heterochromatin?A nucleosome is about 147 bp of DNA wrapped around a histone octamer (two copies each of H2A, H2B, H3 and H4). Euchromatin is loosely packed and transcriptionally active. Heterochromatin is densely packed and mostly silent.
8. How do histone acetylation and DNA methylation affect transcription?Acetylation of histone lysines neutralizes their positive charge, loosening chromatin and generally increasing transcription. Methylation of cytosines at CpG sites in promoters generally silences genes.
9. What is needed to start transcription of a eukaryotic protein-coding gene?RNA polymerase II plus general transcription factors assemble at the promoter, often recognizing the TATA box through TFIID (TATA-binding protein), to form the preinitiation complex.
10. How can an enhancer far from a gene increase its transcription?Activator proteins bind the enhancer, and the DNA loops so the activators can contact the promoter complex, often through the Mediator complex and coactivators, which recruit or stabilize RNA polymerase II.
11. When is the lac operon expressed at high levels in E. coli, and why?When lactose is present and glucose is low. Allolactose binds the lac repressor so it releases the operator, and the low glucose raises cAMP, so CAP-cAMP binds and strongly stimulates RNA polymerase.
12. What is alternative splicing?Different combinations of exons from the same pre-mRNA are joined by the spliceosome (snRNPs), so one gene can encode several protein isoforms.
13. What are the key features of the genetic code?Codons are triplets, read without gaps and without overlap. The code is degenerate (most amino acids have several codons) and nearly universal. AUG is the start codon (Met); UAA, UAG and UGA are stop codons.
14. What do aminoacyl-tRNA synthetases do, and why are they crucial?Each one attaches the correct amino acid to its matching tRNAs, using ATP. They make the actual connection between codon and amino acid, so their accuracy determines translation accuracy.
15. Silent vs missense vs nonsense vs frameshift mutationsSilent: the codon changes but the amino acid does not. Missense: a different amino acid. Nonsense: an early stop codon. Frameshift: an insertion or deletion not in multiples of 3 shifts the reading frame and usually ruins the protein.
16. How do secreted proteins enter the ER?An N-terminal signal sequence is bound by the signal recognition particle (SRP) as it emerges from the ribosome. SRP pauses translation and brings the ribosome to the SRP receptor on the ER, where the protein is threaded through a translocon as it is made (cotranslationally).
17. How do proteins get into the nucleus?A nuclear localization signal (NLS) is recognized by importin, which carries the protein through the nuclear pore complex. Ran-GTP in the nucleus releases the cargo, which keeps import one-way.
18. Where are proteins glycosylated as they pass through the secretory pathway?N-linked glycosylation starts in the ER, where a preformed oligosaccharide is added to asparagine. The Golgi then trims and modifies the sugars as the protein moves from the cis face to the trans face.
19. How are enzymes targeted to the lysosome?In the Golgi they are tagged with mannose-6-phosphate. M6P receptors in the trans-Golgi network package them into vesicles bound for endosomes and lysosomes, where the low pH releases them.
20. Constitutive vs regulated secretionConstitutive secretion happens continuously in all cells, for example releasing extracellular matrix proteins. Regulated secretion stores cargo in secretory vesicles until a signal, such as a rise in Ca2+, triggers release (for example insulin or neurotransmitters).
21. What is receptor-mediated endocytosis? Give an example.Ligands bind specific surface receptors that cluster in clathrin-coated pits, which pinch off as vesicles (with the help of dynamin). Cells take up LDL cholesterol this way.
22. Integral vs peripheral membrane proteinsIntegral proteins are embedded in the bilayer, often spanning it with hydrophobic alpha helices of about 20 amino acids; detergents are needed to remove them. Peripheral proteins attach loosely to the surface or to integral proteins.
23. Channels vs transporters (carriers)Channels form a pore that lets specific ions flow rapidly down their gradient, often gated. Transporters bind their solute and change shape to move it across; this is slower and is needed for active transport.
24. What does the Na+/K+ ATPase do, and why is it important?Each ATP hydrolyzed pumps 3 Na+ out of the cell and 2 K+ in. It maintains the ion gradients and membrane potential that power secondary transport, control cell volume and allow nerve signalling.
25. Give an example of secondary active transport.The Na+/glucose symporter in intestinal cells uses Na+ flowing into the cell down its gradient (set up by the Na+/K+ ATPase) to bring glucose in against its own concentration gradient.
26. Compare the three cytoskeletal filament types.Microfilaments (actin, about 7 nm): cell shape, crawling and muscle contraction. Microtubules (tubulin, about 25 nm): tracks for transport, the mitotic spindle, cilia. Intermediate filaments (for example keratins and lamins, about 10 nm): mechanical strength.
27. Kinesin vs dynein vs myosinKinesins mostly walk toward the plus end of microtubules (outward toward the cell periphery). Dyneins walk toward the minus end (toward the centrosome). Myosins move along actin filaments. All use ATP hydrolysis.
28. What is dynamic instability of microtubules?Microtubules switch between growing and rapidly shrinking. A GTP-tubulin cap at the plus end stabilizes growth; if GTP is hydrolyzed faster than new subunits are added, the cap is lost and the microtubule shrinks (catastrophe).
29. How do cyclins and Cdks drive the cell cycle?Cyclin-dependent kinases (Cdks) are active only when bound to a cyclin. Cyclin levels rise and fall through the cycle, so different cyclin-Cdk complexes phosphorylate targets that trigger S phase or mitosis. Cyclins are then destroyed by ubiquitin-mediated proteolysis.
30. What does the spindle assembly checkpoint monitor?It delays anaphase until every kinetochore is properly attached to spindle microtubules. Only then is the APC/C activated to trigger separation of the sister chromatids.
31. Proto-oncogenes vs tumour suppressor genesProto-oncogenes (such as Ras) promote growth; a gain-of-function mutation in one copy can drive cancer. Tumour suppressors (such as p53 and Rb) restrain growth; usually both copies must be lost. p53 halts the cycle or triggers apoptosis after DNA damage.
32. What is apoptosis, and which enzymes carry it out?Programmed cell death that orderly dismantles a cell without inflammation. Caspases (cysteine proteases) are activated in a cascade, for example after cytochrome c is released from mitochondria.
33. Outline G protein-coupled receptor (GPCR) signalling through cAMP.A ligand binds the GPCR, which makes the G alpha subunit swap GDP for GTP. G alpha s activates adenylyl cyclase to make cAMP, which activates protein kinase A (PKA). The signal ends when G alpha hydrolyzes GTP.
34. Outline receptor tyrosine kinase signalling to the MAP kinase pathway.Ligand binding makes the receptors pair up and phosphorylate each other's tyrosines. Adaptor proteins recruit a GEF that activates Ras (GDP to GTP). Ras starts a kinase cascade (Raf, then MEK, then ERK) that changes gene expression and promotes proliferation.