* Your assessment is very important for improving the workof artificial intelligence, which forms the content of this project
Download Biology 321 Spring 2011 Answers to Assignment Set #5
Site-specific recombinase technology wikipedia , lookup
Genomic library wikipedia , lookup
Oncogenomics wikipedia , lookup
Messenger RNA wikipedia , lookup
Zinc finger nuclease wikipedia , lookup
Mitochondrial DNA wikipedia , lookup
Epitranscriptome wikipedia , lookup
SNP genotyping wikipedia , lookup
Expanded genetic code wikipedia , lookup
Gel electrophoresis of nucleic acids wikipedia , lookup
United Kingdom National DNA Database wikipedia , lookup
Genealogical DNA test wikipedia , lookup
Bisulfite sequencing wikipedia , lookup
DNA polymerase wikipedia , lookup
Epigenomics wikipedia , lookup
DNA vaccination wikipedia , lookup
Cancer epigenetics wikipedia , lookup
Molecular cloning wikipedia , lookup
DNA replication wikipedia , lookup
No-SCAR (Scarless Cas9 Assisted Recombineering) Genome Editing wikipedia , lookup
History of genetic engineering wikipedia , lookup
Vectors in gene therapy wikipedia , lookup
Non-coding DNA wikipedia , lookup
Extrachromosomal DNA wikipedia , lookup
DNA supercoil wikipedia , lookup
Cre-Lox recombination wikipedia , lookup
Microsatellite wikipedia , lookup
Nucleic acid double helix wikipedia , lookup
DNA damage theory of aging wikipedia , lookup
Therapeutic gene modulation wikipedia , lookup
Microevolution wikipedia , lookup
Cell-free fetal DNA wikipedia , lookup
Primary transcript wikipedia , lookup
Helitron (biology) wikipedia , lookup
Artificial gene synthesis wikipedia , lookup
Genetic code wikipedia , lookup
Nucleic acid analogue wikipedia , lookup
Deoxyribozyme wikipedia , lookup
Biology 321 Spring 2011 Answers to Assignment Set #5 Answers to questions in Griffiths 10th edition Chapter 7 8. NOTE: primes used in the lab are short polymers of DNA (15-30 bases long) Chapter 8 19. 21. Chapter 9 12 1 1 14 18 38 2 2 Chapter 16 9. 10. 13 21. d. A nonsense mutation causes premature termination of translation. A frameshift mutation shifts the reading frame and often results in a truncated polypeptide due to the presence of a stop codon in the new reading frame. 3 3 22. 31. Answers to Biology 205 review questions: 1. peptide bonds 2. tertiary 3. isoleucine & phenylalanine 3B 4 & 5 4. The tertiary structure of a globular protein is determined in part by the hydrophobic effect – nonpolar amino acid side chains are sequestered in the interior of a protein. Polar side chains will typically be on the surface of the protein (interacting with water). This mutation has resulted in the 4 4 substitution of an amino acid with a polar side chain for an aa with a non-polar side chain and might very well affect the stability and/or foramtion of the proper tertiary structure. 5. & 6. single-stranded DNA 5’ carbon is at the top of the chain – with 3 phosphates; 3’ carbon is at the bottom with the free hydroxy 7. a. 8. a 9. c 10. c 11. b & c 12. c 13. a 14A a. A b. no anticodon will H-bond here since the 5’ UAA 3’codon is a stop codon and will terminate polypeptide synthesis c. mRNA is written and translated 5’ 3’ d. protein is synthesized from N-terminal to C-terminal 14B: e. 15: a. nucleoside = nucleotide without a phosphate b. 1. carbonyl 2. pyrimidine 3. hydroxyl 4. modified deoxyribose 16. DNA consists of two polymers; adenine base-pairs with thymine and guanine with cytosine 17. the top pyrimidine 18. Watson drew guanine in its rare tautomeric form which (due to its pattern of H-bond donor and acceptors) H-bonds with thymine not cytosine 19. 5’ GUU 3’ anticodon will base-pair with a 5’ AAC 3’ codon which specifies asparagine (ASN) 20. promoter 21. a&b. see problem 20 c. specific sequences which are typically high in A’s and T’s (TATA box) 22. 5 translation begins at the first AUG and ends with the first inframe stop codon: UAA 23. DNA is the permanent archive of the genetic database; RNAs typically have a short half-life. Errors made during DNA synthesis in a multicellular organism (that remain unrepaired) are passed onto the next generation of cells (if somatic) or progeny (if in the germline) 24. The codon is 5’ UAC 3’ and will specify tyrosine 25. See text description of mRNA, tRNA and rRNA 26. b 27. d 28. See lecture notes and text 29. T T F 30. a. ase means the protein has catalytic activity b. transcript in the standard context means an RNA molecule that is generated from a DNA template C. the retrovirus infection cycle involves generating DNA molecules using RNA as a template – the reverse of what usually happens in the cell during transcription 31. Answer is a. The mRNA reads 5’ CGUAAUCAUG…. etc. (antiparallel to the template). Translation starts with the first AUG and ends with the first in-frame stop codon: UAG 5 5 Additional Problems Problem 1 The mutation rate per gamete in Drosophila represents mutations that have accumulated after a series of mitoses that gave rise to the germline in the embryo and to the cells that eventually under go meiosis. So more DNA replication events are represented by the per gamete rate. Problem 2 The 3’-5’ exonuclease activity associated with DNA polymerases corrects most mistakes that occur during the DNA chain elonation process. DNA mismatch repair systems correct errors that remain post-DNA synthesis. RNA polymerases do not have proofreading capabilities and there are no RNA repair systems. Why does this make sense in the context of the different roles of DNA and RNA in the cell? Problem 3 Answer: c Problem 4 a. See lecture notes for labelling of the carbons. b. dideoxy means that there is no hydroxyl group on either the 2’ or 3’ carbon. c. This compound must be converted into the triphosphate form (added to the 5’ carbon) before it can serve as a substrate for viral DNA polymerase d. The TP version of dideoxyI can be added to the 3’ end of a DNA chain, but DNA replication terminates because there is no 3’ hydroxyl -- which is required for addition of the next nucleotide. Problem 5A a. After a couple of rounds of replication: CG to TA transition b. Thymine replaces uracil in DNA so that the cell can recognize the cytosine deamination product (uracil) as abnormal and initiate a repair process. If uracil were used as adenine’s pairing partner in DNA, there would be a problem differentiating “normal” uracils that should be in the DNA from uracils that are a cytosine decay product. NOTE: I think I remember reading that a G:T repair system was just discovered that changes the T to a C in a GT mismatch. This is not a postreplication mismatch repair system which could change the G to an A OR the T to C depending on which strand was the parental. Problem 5B Problem 6 a. thymine b. a GC to AT transition will result Answer is c. A G C G* C C T A rep G C ___ ____ = apurinic site = the phosphodiester backbone (phosphate –ribosephosphate) is still intact but the ribose doesn’t have a base attached to it 6 6 Problem 7 a. Some spontaneous mutations are the result of mistakes made during DNA replication. Furthermore, many (all of the examples discusssed in class) spontaneous and induced mutations require rounds of replication to establish the error in both strands of DNA. Therefore the more a cell divides, the greater the risk of mutation. Paternal gametes undergo many more rounds of replication than maternal gametes. Since the germline cells divide continually in a male, in an older father, the germ cells will have undergone more round of replication. b. NOTE: the mutation (GGU AGU) is designated in codon jargon, which, by convention, is in RNA language. BUT, we are not talking about a transcription error -- which obviously does not meet the definition of a mutation. diagram on the next page 7 7 Problem 8 See answers to a revised version of this problem: Winter 2010 Take-home quiz (#4) Problem #2. Problem 9 Answer is c. 8 8 Problem 10 MUTANT #1 a. nonsense b. tyr stop tyr UAU --› UAA or UAC --› UAA --› UAG --› UAG each case is a transversion c. a base modifying agent might, depending on which bases it chemically modified and whether an apurinic/apyrimidinic base resulted. MUTANT #2 a. frameshift b. trp UGG =› one of the G's is deleted c. intercalating agent MUTANT #3 a. missense b. tyr UAU --› CAU or UAC --› CAC both are transition mutations c. base analog or base modifying agent d. mutant #3 Problem 11 (i) e (b & c) Mutant 1 could result from (i) UAu/c --> UAG or UAA transversion , (ii) from a deletion of the 3rd base in the tyr codon which would generate a UAA stop codon or (iii) from an insertion of a G or an A after the UA of the tyr codon resulting in a UAA or a UAG stop codon (ii) e (a & b) (iii) a 9 9 Problem 12 a. FH380: missense FH 763: frameshift FH 683: nonsense b. UAU/C tyrosine UGU/G cysteine A to G transition c. mRNA 5’….GUG UAC CAA…. DNA 5’ ….GTG TAC CAA….3’ 3’ ….CAC ATG GTT… 5’ bottom strand serves as the template for mRNA synthesis 5’ ---A--- 3’ 3’ ---T--- 5’ ----G --- --- G------ T* ------ C --- T* = thymine in rare tautomeric form = round of DNA replication (drawing follows one parental strand only) d. I’m going to testify for the defense for the following reasons 1. The father and mother need to be assessed. It is likely that one or the other is heterozygous for the same mutation their son has. Do either have a history of heart attacks? Have their genotypes been determined? 2. Even if the son results from a new mutation it couldn’t have been caused by the father’s exposure to hydroxylamine. The son’s mutation is a AT to GC transition. Hydroxylamine cannot cause this mutation because it only modifies cytosines and would not act at an AT base pair. 3. Defense probably pays more (just kidding) e. Note ARG is specified by 6 different codons. • The mutation could be CGn UAG or AGa/g UAG • The first alternative CGn UAG requires transition mutations in the first two base pairs of the codon (assuming that n=G). Neither aflatoxin or proflavin will accomplish this. The second alternative AGa/g UAG is a possibility. Inserting a T before this codon would result in a UAG and, as an intercalating agent, proflavin could cause this type of mutation. Since both parents are likely to be homozygous wild-type, I’ll go with the prosecutors on this one. 10 10 Problem 18 a. Neutral Sequence variation does not affect the Darwinian fitness of the organism. b. Yes. The alternative sequence variation exceeds 1% c. These sequence variations are not disease causing. You would want to focus your screen on the mutations in Table 2. d. It is in the third codon position so likely to be a same sense or silent mutation e. It is in the first codon position so likely toe be a neutral missense Problem 19 Answer not available just yet. Will post it on FRiday Problem 20 a. Review definition of polymorphism in earlier lecture b. silent or same sense mutation c. Neutral missense mutation (note legend at bottom of table that indicates that all people genotyped were healthy non-NIDDM) d. Examination of a normal control group is important because some sequence variations will be associated with disease and others will have no obvious effect on the encoded protein or on the organismal phenotype. In order to understand how the gene product functions and to assess the phenotypic implications of a particular genotype, it is critical that researchers be able to distinguish between these two types of sequence variations. e. Intron sequences are non-coding – not translated into protein Problem 21 GAU/C (asp) CAU/C transversion GC CG Start here: Have G* pair with G in first round of replication, etc 5’ GAT 3’ 3’ CTA 5’ hhhhhhhhhhhhhhhhhhhh Problem 22 Answer will not be available 11 11