11. Given your knowledge on mutations and proteins, develop hypotheses to explain how the changes in a rock pocket mouse's Mc1r protein's amino acid sequence might affect its function.
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- 16. Consider the following original coding sequence of a gene that codes for a short 3-amino acid polypeptide: 5'-ATGTGGTCATGA-3' Using the genetic code and the amino acid table below, which of the following sequences arises from a non-conservative missense mutation in the original sequence shown above? First base in codon U A UUU UUC- UUA UUG- CUU CUC CUA CUG- AUU- ACU AUC Ile (1) ACC AUA- ACA AUG Met (M) start ACG GUU GCU GUC GCC GUA GCA GUG- GCG H₂N- U Phe (F) Leu (L) Leu (L) Nonpolar side chains; hydrophobic Val (V) Side chain (R group) H H₂N-C-C-0- HO Glycine (Gly or G) CH₂ H₂N*- CH₂ CH₂ H O Methionine (Met or M) Polar side chains; hydrophilic 0 CH₂ Second base in codon H O Aspartic acid (Asp or D) UCU UCC UCA UCG CCU CCC CCA CCG Alanine (Ala or A) OH CH₂ H₂N-C C 0 H₂N-C C 0 H O Serine (Ser or S) H O Threonine (Thr or T) Electrically charged side chains; hydrophilic OH CH3 CH -0- H₂N+- Acidic (negatively charged) CH₂ H₂N-C-C-O HO C Ser (S) Pro (P) CH₂ CH₂ Thr (T) CH₂ H₂N-C Ala (A)…6. You are performing site-directed mutagenesis to test predictions about which residues are critical for the function of a protein. Which of each pair of amino acid substitutions below would you expect to disrupt protein structure the most? Briefly explain your answers. (a) Ile replaced by Leu or Tyr (b) Val replaced by Ala or Phe (c) Lys replaced by Asp or Arg3. A missense mutation results in the presence of a different amino acid than was encoded by the parental sequence. This type of mutation can have a drastic effect or no effect at all depending on the importance of the amino acid and the type of amino acid that replaces it. Some amino acids are structurally similar and may be able to act as viable substitutes for each other. For example, changing one acidic amino acid to another may not affect the final protein, but changing a polar amino acid to a nonpolar amino acid will likely disrupt the structure. Please explain what mutations occur in HBB gene of abnormal hemoglobin and their effect on the function of the protein.
- 11. Determine the genetic codes for the following sequence of 3 amino acids: Asn-Glu-Lys. a. Provide one possible mRNA sequence for this peptide segment. b. Provide the corresponding tRNA anticodon for each amino acid. c. Provide the template DNA sequence for that mRNA. Table 1: Table of codons for amino acids. 1st position (5' end) C 2 G 2nd position (middle) U Phe F Phe F Leu L Leu L Leu L Leu L Leu L Leu L lle 1 lle 1 lle 1 START/Me tM Val V Val V Val V Val V. C Ser S Ser S Ser S Ser S Pro P Pro P Pro P Pro P The T The T The T The T Ala A Ala A Ala A Ala A Tyr Y Tyr Y STOP STOP His Hi His H Gln Q Gin Q Asa N Asa N Lys K Lys K Asp D Asp D Glu E Glu E G Cys C CVS C STOP Trp W Arg R Arg R Arg R Arg R Ser S Ser S Arg R Arg R Gly, G Saly, G Gly G G Gly *START codon signals the initiation of a peptide chain. *STOP codons signal the end of a peptide chain. 3rd position (3' end) JUAG C DURG C SCAG DUAG CDo you think each of the following types of mutationswould have very severe effects, mild effects, or no effectat all?a. Nonsense mutations occurring in the sequences encoding amino acids near the N terminus of the proteinb. Nonsense mutations occurring in the sequences encoding amino acids near the C terminus of the proteinc. Frameshift mutations occurring in the sequences encoding amino acids near the N terminus of the protein d. Frameshift mutations occurring in the sequencesencoding amino acids near the C terminus of theproteine. Silent mutationsf. Conservative missense mutationsg. Nonconservative missense mutations affecting theactive site of the proteinh. Nonconservative missense mutations not in the active site of the protein1. Given the DNA sequence below: 5’-ACATGTGTACAGGCTTTGTCTGAATGGCTT-3’ 3’-TGTACACATGTCCGAAACAGACTTACCGAA-5’ Translate the mRNA. (Using the 3-letter code for amino acids, write the primary structure of the peptide that will be produced.) 2. Given the DNA sequence below: 5’-ACATGTGTACAGGCTTTGTCTGAATGGCTT-3’ 3’-TGTACACATGTCCGAAACAGACTTACCGAA-5’ Translate the mRNA. (Using the 3-letter code for amino acids, write the primary structure of the peptide that will be produced.)
- 5. A peptide was cleaved into two smaller peptides with cyanogen bromide (CNBI) and into two different peptides by trypsin (Tryp). Their sequences were as follows: CNB 1: Gly-Thr-Lys-Ala-Glu CNBR 2: Ser-Met Tryp 1: Ser-Met-Gly-Thr-Lys Tryp 2: Ala-Glu What was the sequence of the original peptide?1. Given is the 30 nucleotides in the human gene for hemoglobin (the oxygen-carrying protein in the red blood cells): 3’ TAC-CAC-GTG-GAC-TGA-GGA-CTC-CTC-TTC-AGA 5’ a. What is the amino acid sequence based on this mRNA? b. A very important mutation in human hemoglobin occurs in this DNA sequence, where the T at nucleotide 20 is replace with an A. The mutant hemoglobin is called sickle cell hemoglobin and is associated with severe anemia. What is the amino acid replacement that results in sickle-cell hemoglobin?6. In the following graph, the dashed line shows the level of mRNA for a certain protein, Prot6, at various positions along the anterior-posterior axis of an insect embryo. The solid lines portray the levels of two regulatory proteins, A and B, that control translation of the Prot6 mRNA. A В Position Biology: How Life Works, Second Edition © 2016 W.H. Freeman and Company If both A and B stimulate translation of the Prot6 mRNA, then which graph, from the ones shown below, best approximates the expected level of Prot6 across the embryo? Briefly justify your answer. M K Q Position Position Position Position Position Protein level MRNA level
- 7. If you have aligned orthologous gene sequences from an important, conserved gene; there is a different way you can determine reading frame. a. The following sequences of orthologous copies of the insulin receptor gene (INSR) from four species. The sequences are aligned but the reading frame is unknown. What is the reading frame for these sequences? (ie., Does the first complete codon begin at the first, second, or third nucleotide?) Hint: Think about what you know about the nature of mutations, natural selection and the genetic code. 1. Bear CCTGAAGAGCTACCICCGCICCCIGCGGCCGGAGGCTGAGAATAACCCCGGCCGCCCT 2. Human CCTGAAGAGCTACCICCGTICICIGCGGCCAGAGGCTGAGAATAATCCIGGCCGCCCI 3. Chicken CITGAAAAGCTACCIACGCTCICIGAGACCCGACGCIGAGAATAACCCTGGICGICCA 4. Cow CCTGAAGAGTTACCTCCGTTCCCIGCGGCCTGAGGCTGAGAATAACCCCGGCCGCCCT Answer:1. How would the following affect BOTH transcription and translation of a particular multi- exon gene in a eukaryotic cell (for each address both transcription and translation of a particular multi-exan gene; also treat each independently): A mutation abolishing kinase activity in TFIIH a. b. A mutation abolishing mRNA binding in the snRNP U1 С. A mutation in aminoacyl tRNA synthetase for isoleucine such that it can't bind ATP (assume there is an isoleucine in the code)2. If instead of 20 amino acids there were 200 amino acids, then how many nucleotides would you be minimally needed for each codon? а. 3 b. 4 С. 5 d. 6 е. 7