The second lecture exam will concentrate on material discussed in lecture since 2/29/16; however, certain basic information can also be a subject of questions. You should review all the quizzes and study guides after the first lecture exam (quizzes 6, 7, 8 and 9), but you should also review the information from quiz 1 and the information covered in the PowerPoint presentations in the Background Review in the Information section of Blackboard. Make sure to look at the Answers, explanations and additional questions for quizzes 6, 7, 8 and 9 that have been posted to Blackboard. This study guide is meant to be a supplement to previous study guides and quizzes and lecture materials, and it is not meant to be comprehensive.
We also discuss several other topics like What are non-renewable resources?
1. In what direction does RNA synthesis occur? In what direction does protein synthesis occur? During translation, in what direction are mRNA molecules read?
∙ RNA synthesis occurs in the 5’ to 3’ direction
∙ Protein synthesis occurs in the amino to carboxy direction
∙ During translation, mRNA molecules are read in the 5’ to 3’ direction Don't forget about the age old question of What is risk aversion?
2. How does the stability of DNA, RNA and proteins compare? Is it necessary that replication occur shortly before transcription? Is it necessary that transcription occur shortly before translation? How about translation before replication? Don't forget about the age old question of What is the marginal propensity to consume (mpc)?
∙ DNA is the most stable
∙ It is not necessary that transcription occur shortly before translation. It just has to have occurred at some point
∙ It is necessary that translation occur shortly before replication because the proteins needed for replication to occur are made during translation and they have a short half life.
3. How does translation initiate, what role does the 5’ cap play, and what happens when capdependent translation is no longer possible? What role do the 5’ and 3’ UTRs play in controlling gene expression? Can the polyA tail play a role in initiating translation? Must the small ribosome binding site be 5’ to the start codon? What causes termination of translation?
∙ Translation initiates when the small ribosomal subunit binds to an AUG codon and establishes the reading frame. Translation begins after the large subunit also binds.
∙ The 5’ cap can be a binding site for the small subunit and also plays a role in stability
∙ When cap dependent translation is no longer possible, it can bind to the tail or the IRES sequence if there is one If you want to learn more check out What is te mechanical activity of heart?
∙ The polyA tail can also be a binding site for the small subunit
∙ The small ribosomebinding site doesn’t have to be 5’ to the start codon. The mRNA can fold and loop so that the subunit lines up where it is supposed to in order to begin translation
∙ Termination of translation occurs when the stop codon is in the reading frame
4. Which type of mRNA would be more stable, an mRNA coding for a housekeeping protein, or an mRNA coding for a protein in a signaling response pathway? What role do the 5’cap and the polyA tail play in mRNA stability? Suppose you found a highly conserved endonuclease cleavage site in the 3’UTR of an mRNA; what would that tell you about the stability of that mRNA? Would you expect it to code for a housekeeping protein?
∙ An mRNA coding for a housekeeping protein will be more stable than one coding for a protein in a signaling response pathway
∙ The 5’ cap and polyA tail increase the stability of the mRNA molecule. If they are cleaved off, the mRNA degrades rapidly
∙ If there is a highly conserved region in the mRNA that would tell you that the mRNA is probably very stable because that gene is necessary for survival. We also discuss several other topics like What is hubble’s law all about?
∙ I would expect it to code for a housekeeping protein
5. What role do aminoacyltRNA synthetases play in translation? What is the error rate of tRNA charging and how is that achieved? If the active site of an aminoacyltRNA synthetase involved in charging the tRNA has a very low error rate (< 104), would you expect that synthtase to have a proof reading function? Please explain your answer. If the active site of an aminoacyltRNA synthetase involved in charging the tRNA made a mistake and added the wrong amino acid to a tRNA, would this necessarily result in incorporation of the wrong amino acid during protein synthesis? Please explain.
∙ AminoacyltRNA synthetases attach amino acids to tRNAs
∙ The error rate is 104 and it is achieved through a proofreading site that is distinct from the charging catalytic site and will hydrolyze incorrectly charged tRNAs
∙ If the tRNA has a very low error rate, you would not expect that synthase to have a proofreading site because the error rate for the proofreading site does not go below 104 and if the error rate is less than that, the proofreading function wouldn’t help
∙ If the aminoacyltRNA synthetase involved in charging the tRNA made a mistake and added the wrong amino acid to the tRNA, this would not necessarily result in incorporation of the wrong amino acid during protein synthesis. The proofreading site is distinct from the charging site and could correct the mistake before it is added Don't forget about the age old question of What is the spontaneous ion in chemistry?
6. Explain how the arrangement of the genetic code minimizes the impact of mutations. In what codon position are changes most likely to be silent? What types of changes in this position are more likely to be silent? What are conservative changes?
∙ The genetic code minimizes the impact of mutations because of the way it is organized. Codons that differ in the third base position, or the wobble position of the codon often times code for the same amino acid or one similar in structure. Therefore, if there is a mutation in this position it doesn’t change the amino acid that is charged
∙ Bases in the third position of the codon are more likely to be silent, and transitions are more likely to be silent
∙ Conservative changes are when a mutation changes the amino acid that is charged, but it is one similar in structure
7. How does splicing differ between mRNA, rRNA and tRNA molecules? What drives splicing in each case? In mRNA splicing, what happens if the splicesome cannot find the 3’ splice site in the first intron? What are the advantages of alternative splicing? What is a constitutive intron?
∙ The introns of nuclear mRNA precursors are spliced out in two step reactions carried out by splicesomes ∙ The introns of some rRNA precursors are removed auto catalytically in a unique reaction mediated by the RNA molecule itself (self splicing)
∙ The introns of tRNA precursors are excised by precise endobucleolytic cleavage and ligation reactions catalyzed by special splicing
∙ If the splicesome can’t find the 3’ splice site in the first intron, it will bind to the 5’ splice site and continue scanning to the next 3’ splice site. The whole region in between will get cut out.
∙ A constitutive intron is an intron that is always an intron, not matter how it is spliced
8. What types of RNA are necessary for translation?
∙ rRNA, tRNA, and mRNA are necessary for translation
9. What happens when proteins misfold and why is that dangerous for cells? What fraction of proteins misfold? How does protein synthesis and protein folding compare in eukaryotes and prokaryotes? How does protein size compare in eukaryotes and prokaryotes?
∙ When proteins misfold, the hydrophobic regions are on the outside and the hydrophilic regions are on the inside
∙ They are toxic to cells because they can become prions, which recruit other normally folded proteins to misfold
∙ ¼ to ½ of all proteins are misfolded and must be destroyed
∙ Translation and folding rates are 410 times higher in prokaryotes than eukaryotes
∙ In prokaryotes, folding is posttranslational and in eukaryotes, folding is cotranslational. ∙ Eukaryotic proteins tend to be larger than prokaryotic proteins
10. Explain how chaperone proteins could mask the effect of mutations.
∙ Chaperone proteins assist with folding the proteins, and are therefore able to prevent misfolding ∙ They can mask the effect of nonconservative mutations by how they fold the protein.
∙ Mutations in the amino acid sequence could code for a different folding of the protein, but chaperone proteins are able to fold it correctly
11. Suppose there was a mutation that resulted in a transition in the third position of UGG codon. Why might that be a very significant change? Which amino acids would you expect to have two tRNAs in mitochondria?
∙ It might be a very significant change because it could introduce a stop codon and create a truncated protein
∙ Amino acids that take up the entire box require at least two tRNAs
12. What are prions, and how do they replicate themselves? Are they ever adaptive (that is, can they ever increase fitness of organisms)? Please explain. How would a tRNA with the anticodon 5’IUA3’ that was charged with tyrosine be similar to the PSI+ phenotype in yeast?
∙ Prions are misfolded proteins and they replicate by recruiting other proteins to misfold ∙ They are not adaptive often because they are usually associated with disease, but there are situations where they could be adaptive in stress enviornments.
∙ A tRNA with that anticodon could code for both an amino acid and a stop codon. The tRNA would have to guess which amino acid to charge, and if it is supposed to be a stop codon but the amino acid is charged instead, that would cause a readthrough. It is the same situation that causes the PSI+ phenotype in yeast.
13. How would you expect gene size (that is exons plus introns) to compare in humans and worms? What about the genome sizes of humans and worms? Approximately what fraction of the human genome codes for proteins? The genomes of some salamanders are ten times the size of the genomes of humans. Approximately what fraction of the genomes of those salamanders would you expect to code for proteins? What is the exome? What is the proteome?
∙ I would expect the gene size in humans to be larger than the gene size in worms
∙ I would expect the genome size to also be larger in humans than in worms
∙ Approximately 1.53%, or 22,287 genes in the human genome code for proteins
∙ I would expect less than 1.5% of the genome of salamanders to code for proteins
∙ The exome is the part of the genome formed by exons
∙ The proteome is the part of the genome formed by proteins, or all the proteins coded for in the human genome
14. Why would large introns make the evolution of large complex proteins easier? What is the evidence that Alu elements may have played a role in human evolution?
∙ Large introns would make it more likely for transposable elements to land in the introns instead of the exons and there would be less mutations in the large complex proteins
∙ Alu elements have increased a lot since the division from chimpanzees. Also recently acquired transposable elements are present in human genes but not those of chimpanzees
15. What is the nearly neutral theory of molecular evolution, and why does it have important consequences for small, isolated populations? Why do genomes expand in species with small effective population sizes?
∙ The nearly neutral theory of molecular evolution predicts that mutations behave close to neutrally if s,1/ (2Ne) where s is the selective disadvantage and Ne is the effective population size. Species with higher effective population sizes will be under much greater constraint
∙ This has important consequences for small isolated populations because a change in phenotype doesn’t have a big impact on fitness because of the lack of competition. Because of that, genome sizes can increase much more than in large populations
16. What are transcription factors? What are enhancer sequences, and where are they found in relation to genes? What do we mean by the core promoter?
∙ Transcription factors are proteins that bind to the DNA and help the RNA polymerase bind to the promoter ∙ Enhancer sequences are cis acting sequences that transcription factors will recognize ∙ Enhancer sequences are not found in a specific place. The DNA strand is able to fold over so that the enhancer sequence can help polymerase that ay be further downstream from it.
∙ The core promoter is the region that contains the transcription initiation sites
17. Suppose you wanted to cause a rapid response in a cell; which would you activate – a kinase, a transcription factor, an mRNA binding protein or a translational activator?
∙ If you want to cause a rapid response, you should activate a kinase
18. What effect would you expect HDAC inhibitors to have on gene expression? Why is global methylation more effective than sitespecific methylation? Why is gene expression control by methylation more comprehensive in eukaryotes than prokaryotes? How does control of gene expression by site specific methylation in eukaryotes compare to methylation in prokaryotes?
∙ HDAC inhibitors decrease gene expression by deacetylate histones
∙ Global methylation is more effective than site specific methylation because it methylates the entire area instead of just specific spots
∙ Prokaryotes don’t have histones, so methylation cant completely shut off gene expression ∙ Site specific methylation in eukaryotes and methylation in prokaryotes both cause the gene to be leaky
19. What are CG islands, and what do they indicate? Would you expect to find CG islands in areas of the genome that are rich in transposable elements? Would you expect CG islands to be highly conserved? ∙ CG islands are areas that are rich in CG pairs. They are not methylated and indicate that the gene they code for is being expressed
∙ You would not expect to find CG islands in areas of the genome that are rich in transposable elements ∙ You would expect CG islands to be highly conserved
20. What are APOBECs, and what are they used for? Suppose you discovered that transposable elements were AT rich; how might you explain that observation? Would APOBECs work against DNA transposons? What other antitransposable element mechanism do eukaryotes use? Suppose you found that polyaromatic hydrocarbons did not cause mutations in prokaryotes, but they did cause increased mutations in eukaryotes. How would you explain that observation?
∙ APOBECs are a family of enzymes that deaminate cytosine in RNA molecules
∙ You could explain that transposable elements were AT rich because methylation turns off transposable elements. If they are AT rich, there are less CG areas to be methylated
∙ APOBECs would work agains DNA transposons
∙ Methylation is used as an antitransposable element mechanism
21. Zinc fingers are domains that are typically found on proteins that specifically bind to particular sequences on DNA molecules. In what groove of the DNA molecule would you expect zinc fingers to insert into? Please explain why.
∙ I would expect them to insert into the major groove because you can tell the specific sequence in the major groove, whereas the minor groove you can only see what the base pair is
22. What are miRNA and siRNA? Where do they affect gene expression (do they decrease transcription, translation, etc.)?
∙ miRNA and siRNA are types of single stranded RNA that are small and they match with all or some of an mRNA sequence
∙ miRNA causes translational silencing and siRNA causes cleavage of the mRNA
23. Describe some mutations that might have an impact on gene expression control through the control of mRNA degradation. For instance, would mutations to the 3’ UTR have that effect; how about mutations to the upstream controlling elements such as enhancer sequences?
∙ If there is a mutation that cleaves off the 5’ cap or poly A tail, it could decrease translation ∙ Mutations to the 3’ UTR could decrease gene expression by causing the mRNA molecule to degrad ∙ Mutations upstream such as in the enhancer sequence could decrease gene expression
24. If you could only choose one of DNA, RNA or proteins, which would you pick to make a functional, self replicating entity? Please explain your answer.
∙ I would chose RNA because it can replicate, and form complex structures by folding and can create proteins through translation.
25. Are there genes with microsatellites in their cisregulatory regions? What types of genes would you expect to have microsatellites in their ciscontrolling regions?
∙ There are genes with microsatellites in their cisregulatory regions
∙ Genes involved in fast adaptation such as behavior would be expected to have microsatellites in their cis controlling regions