7.012 Quiz 1 Answers A≥87 ~25% of test takers B≥73 ~34% of test takers C≥60 ~24.3% of test takers D≥50 ~10.1% of test takers F≥49 ~6.5% of test takers Regrade requests (with a note attached indicating the problem and part you want looked at) Monday 10/04/04 Question Value Score 1 16 2 20 3 16 4 16 5 15 6 17 100 MIT Biology Department 7.012: Introductory Biology - Fall 2004 Instructors: Professor Eric Lander, Professor Robert A. Weinberg, Dr. Claudette Gardel?? Question 1 a) Match each boxed chemical interaction in the structures below with the appropriate description. 10 pts _____B_____ peptide bond _______E___ ionic bond ____A_____ van der Waal’s interaction ______D____ phosphodiester bond _____C_____ hydrogen bond C A B D E 2 Name________________________________ b) Which one of the following structural features is NOT based on hydrogen bonds? Circle all that apply. 3 pts i) complementary base pairing in DNA ii) protein primary structure iii) protein secondary structure iv) complementary base pairing in RNA c) Your friend tried to remove some writing on a plastic box. He used a napkin dampened with water, which did not work. Then as you advised, he used ethanol (instead of water), and successfully removed the writing. Circle why ethanol was better than water in this case. 3 pts [formula of ethanol: CH 3 -CH 2 -OH] i) Ethanol has a greater surface tension, so it extracts the ink molecules better from the plastic. ii) Ethanol can form hydrogen bonds with the ink molecules. iii) One end of ethanol is non-polar. This makes ethanol a better solvent for the ink molecules. iv) Ethanol is more hydrophilic, so it washes off the writing more efficiently. 3 Question 2 a) Fill in the percentages. If the value can’t be determined write “ND”. 6 points i) According to Chargaff’s rule, if the DNA content of a cell was composed of 15% A, then C would make up ____35______% , G would make up ___35______%, and T would make up____15%_______ % of the cell’s DNA. ii) If the RNA content of a cell was composed of 15% A, then C would make up ____ND______%, G would make up ____ND_____%, and T would make up____0%_______ % of the cell’s DNA. b) Match the following with all that apply. 6 points A. Lowers the activation energy of a reaction ___ace___ Lactase B. Raises the activation energy of a reaction C. Breaks down milk sugar to galactose and glucose ____ag___ ribozyme D. Lipid E. Protein ___f______ “TheTransforming Principle” F. DNA G. RNA c) Fill in the blanks. 2 pts each i) DNA is synthesized in the _________ direction. Circle one. C?N 3’?5’ O?P N?C 5’?3’ P?O ii) Proteins are synthesized in the _________ direction. Circle onel. . C?N 3’?5’ O?P N?C 5’?3’ P?O d) Which of the following is used to make deoxyribonucleic acid? Circle all that apply.4 points H N OH H 4 x x x Name________________________________ Question 3 Eukaryotes have proteins called histones that are involved in tightly packing DNA. Below is a schematic of the interaction between a molecule of DNA and the surface of a histone protein. “X” represents an amino acid side chain sticking out from the surface of the protein towards the DNA backbone. x x x Figure by MIT OCW. a) Circle the type(s) of amino acids you would expect to find with side chains in the positions marked “X”? negatively non-polar positively hydrophobic charged charged 2 pts. b) Circle the strongest interaction between the DNA backbone and the histone protein. hydrogen ionic van der Waals X-linked 2 pts 5 Eight histone proteins function as subunits in a multi-protein complex called a nucleosome. Portions of two subunits (HA and HB) interact in the core of the nucleosome. The figure below shows the α? helices where these two proteins interact. Trp Trp Trp Trp rp rp rp rp 72 HBHA 72 HA Phe Ile Phe Ile Figure by MIT OCW. c) Based on the amino acids labeled in the diagram, what interactions keeps HA and HB together? Circle all that apply. 3 pts covalent hydrogen hydrophobic ionic van der Waals d) If tryptophan 72 mutates to become an arginine residue, indicate how the interaction between HA and HB would change. 2 pts. becomes stronger becomes weaker remains the same can not be determined e) Explain your answer in d) in twelve (12) words or less. 3 pts Positive charged does’nt interact with hydrophobic side chain. f) Based on the information given, circle all levels of structure possessed by histones within a nucleosome. 4 pts primary secondary tertiary quaternary quinternary 6 - - - - - - - - Name________________________________ STRUCTURES OF AMINO ACIDS at pH 7.0 - - O O O O O C O O O C O C C H O H C CH 3 H C CH 2 CH 2 CH 2 N C H C CH 2 C H C CH 2 C NH 3 O - NH 3 NH 3 NH 2 NH 3 NH 2 + + NH 2 + + + ALANINE ARGININE ASPARAGINE ASPARTIC ACID (ala) (arg) (asn) (asp) - - O O O O O O O O C O C C C C O H C CH 2 SH H C CH 2 CH 2 O H C CH 2 CH 2 C H C H - NH 3 NH 2 NH 3 + + + + NH 3 NH 3 CYSTEINE GLUTAMIC ACID GLUTAMINE GLYCINE (gly) (cys) (glu) (gln) - O O - H O O O O O O C N + H C H C H C C + H C C CH 2 CH 3 H C CH 2 C CH 3 H C CH 2 CH 2 CH 2 CH 2 NH 3 H C CH 2 NH 3 C N H NH 3 CH 3 NH 3 CH 3 + NH 3 + + + H ISOLEUCINE LEUCINE LYSINE HISTIDINE (ile) (leu) (lys) (his) O O O O - H H O C O - O O C C C H C CH 2 CH 2 S CH 3 H C CH 2 H H C CH 2 H C CH 2 OH HNH 3 NH 3 CH 2 CH 2 NH 3 + + N + + METHIONINE H H H (met) PHENYLALANINE PROLINE SERINE (phe) (pro) (ser) - H H O O - - O O H H H O O O O - C C CH 3 C H H C CH 2 C N H H C H C CH 2 OH H C C + H C C CH 3 NH 3 NH 3 NH 3 H CH 3 NH 3 OH + + H + H THREONINE TRYPTOPHAN H VALINE (thr) (trp) TYROSINE (val) (tyr) 7 Question 4 Polydactyly is a trait where an individual develops more than five fingers per hand or toes per foot. The pattern of inheritance of polydactyly is shown in the following pedigree. Assume that all individuals marrying in from outside the family do not carry a disease allele. Assume complete penetrance. KEY: normal male normal female affected male affected female 1* 3* 4* 2* ? a) What is the mode of inheritance of this trait? Circle all that apply. 4 pts Autosomal Dominant Mitochondrial Recessive Sex-limited X-linked Y-linked b) What are the genotypes of the numbered individuals? If more than one genotype is possible, write all. Only show the genotype relating to the disease phenotype. Use the letters D, d, X D , X d , Y D , Y d , M D or M d to indicate the genotype corresponding to the polydactyly alleles. 8 pts 1*______Dd_____ 2*_____dd______ 3*____dd_______ 4*_____Dd_____ c) What is the probability that the unborn individual marked with (?) will have polydactyly, 4 pts if it were male?___0%______ if it were female?______0%___ 8 Name________________________________ Question 5 You are studying flies with different eye colors, so you cross them to determine the mode of inheritance. Using standard nomenclature, fill in the blanks with all possible genotypes of the flies described. Use the letters B, b, G, g, H, h, A, a , R and/or r to designate the alleles. If sex chromosomes are involved, use the format ?X B , X b , X G , X g , Y B , Y b , etc. 7 pts a) F 0 : Black-eyed flies ____ gg__ x Gray-eyed flies__ Gg_______ F 1 253 Black-eyed flies____ gg __________ 228 Gray-eyed flies_____ Gg__________ Gray-eyed flies x Gray-eyed flies (F 1 flies) F 2 138 Black-eyed flies ____ gg________ 284 Gray-eyed flies ____ Gg_________ 124 Hazel-eyed flies ____ GG_________ b) F 0 : Amber-eyed male flies ___X r Y__ x Red-eyed female flies ___X R X R _ 8 pts F 1 : All red-eyed __X R Xr, X R Y_______ Red-eyed male F 1 x Red-eyed female F 1 F 2 354 Red eyed males_____X R Y_________ 355 Amber-eyed males_____X r Y_______ 706 Red-eyed females___X R X R , X R Xr____ 9 Question 6 You have a strain of yeast that glows purple when compound A is added to the medium. You suspect that compound A is a precursor of the “glowing” pathway. You mutagenize the original haploid strain and isolate six mutants that do not glow purple in the presence of compound A. Since haploid yeast can be mated to make diploids, you mate each mutant strain with your original WT purple yeast to determine whether the mutant phenotypes are dominant or recessive. You also mate each mutant strain with each other to see which strains can complement each others’ phenotypes. The results are summarized below. (“+” means colonies glow purple, “-“ means they do not glow purple) Strains Mated m1 m2 m3 m4 m5 m6 WT m1 - - + + + - + m2 - + + + - + m3 - + - + + m4 - + + + m5 - + + m6 - + a) Are all the mutant phenotypes recessive? Yes. No. 2 pts. If no, indicate the mutants having dominant phenotypes. b) Place the mutants into complementation groups. 6 pts m1 m2 m6 m3 m5 m4 c) How many genes have you identified that are involved in this pathway? 2 pts 10 3 Name________________________________ In the presence of compound A, the different mutants glow different colors (other than purple). You suspect that these colors may be due to a buildup of different compounds in a biochemical pathway. To figure out this novel biochemical pathway, you make the following observations. °When you add compound A to mutant 1, the strain accumulates compound R and glows red. °When you add compound A to mutant 4, the strain accumulates compound B and glows blue. °When you add either compound B or R to Mutant 5, the strain glows purple. °When you add compound A to a double-mutant yeast strain having both Mutation 2 and Mutation 4, it glows blue. Based on these results solve the biochemical pathway. Circle the model that is consistent with your epistasis data. Note that “Enz 1” denotes the enzyme encoded by the gene mutated in the m1 strain. Model 1 Compound A Enz 5 Compound B Enz 4 Compound R Enz 6 Purple Model 2 Compound R Enz 2 Compound B Enz 5 Compound A Enz 4 Purple Model 3 Compound A Enz 4 Compound R Enz 2 Compound B Enz 5 Purple Model 4 Compound A Enz 1 Compound R Enz 5 Compound B Enz 4 Purple Model 5 Compound A Enz 5 Compound R Enz 4 Compound B Enz 3 Purple Model 6 Compound A Enz 3 Compound R Enz 6 Compound B Enz 4 Purple 7 pts 11