7.012: Introductory Biology-Fall 2004 Instructors: Professor Eric Lander, Professor Robert A Weinberg, Dr. Claudette Gardel 7.012 Quiz 1 Answers A287 25% of test takers B273 w34% of test takers C260 24.3% of test takers D≥50 w10.1% of test takers F249 6.5% of test taker Regrade requests (with a note attached indicating the problem and part you want looked at) Monday 10/04/04 Question Value Score 16 2 20 3 16 16 5 15 6 17 100
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 van der Waals interaction phosphodiester bond hydrogen H H H CH CHa OH -H NH H OH A B 0-P=0 OH
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
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 1) protein primary structure i)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 case3 pts [formula of ethanol: CH3-CH2-OH] i)Ethanol has a greater surface tension, so it extracts the ink molecules better from the plastic i 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 molech iv)Ethanol is more hydrophilic, so it washes off the writing more efficiently
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: CH3-CH2-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 1) According to Chargaffs rule, if the dna content of a cell was composed of 15% a then C would make up %o, G would make up__35_%, and T would make up__15% of the cell's DNA i)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 0% of the cells dna b)Match the following with all that apply. 6 points A. Lowers the activation energy of a reaction Lactase B. Raises the activation energy of a reaction C. Breaks down milk sugar to galactose and glucose ribozyme D. Lipid E. Protei The Transforming 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 CN 3÷5 o→PN>C5÷3 P→O d Which of the following is used to make deoxyribonucleic acid? circle all that pply 4 points HOH, CH,OH O
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. CN 3’5’ OP NC 5’3’ PO ii) Proteins are synthesized in the _________ direction. Circle onel. . CN 3’5’ OP NC 5’3’ PO d) Which of the following is used to make deoxyribonucleic acid? Circle all that apply.4 points H N OH H 4
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 Figure by MIT Oc a)Circle the type(s)of amino acids you would expect to find with side chains in the positions marked"? negative non-polar tively hydrophobic chargea charge d b)Circle the strongest interaction between the dna backbone and the histone protein van der Waals X-linked 2 pts
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 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 a- helices where these two proteins interact Trp 72 Ph Trp p HA HB 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 drogen nyaropnoDIc IonIc an 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 an 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 seconda tertiary quaternary quinternary 6
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 Trp Trp Trp Trp 72 HA HB 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
STRUCTURES OF AMINO ACIDS at pH7.0 H-C-CH3 H-C—CH,CH,CH H-C-CH NH, NH3 ALANINE ARGININE ASPARAGINE ASPARTIC ACID g asn H-C-CH,-SH H-(H-c=0 H-C-CH,CH-c NH3 NH3 CYSTEINE GLUTAMIC ACID GLUTAMINE GLYCINE glu (gln) (gly) -CH -C-C-CH,CI H--C-CH2-C-CH3 H-C-CH2 CH, CH CH2-NH3- NH NH3 ISOLEUCINE LEUCINE LYSINE HISTIDINE (leu) CH, CH,-S-CH3 H-C-CH, H-C-CH,-OH CH, NH3 METHIONINE H+ CH (met) PHENYLALANINE PROLINE SERINE (phe) (ser) H-C-CH H-C-CH OH H THREONINE TRYPTOPHAN VALINE (trp) TYROSINE (val) (tyr)
- - - - - - - - Name________________________________ STRUCTURES OF AMINO ACIDS at pH 7.0 - - O O O O O C O O O C C C H O O H C CH3 H C CH2CH2CH2 N C H C CH2 C H C CH2 C NH3 O- NH3 NH3 NH2 NH3 NH2 + + NH2 + + + 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 CH2 SH H C CH2CH2 O H C CH2CH2 C H C H - NH3 NH2 NH3 + + + + NH3 NH3 CYSTEINE GLUTAMIC ACID GLUTAMINE GLYCINE (gly) (cys) (glu) (gln) - - H O O O O O O O O C N + H C H C H C C + H C C CH2CH3 H C CH2 C CH3 H C CH2CH2CH2CH2 NH3 H C CH2 NH3 C N H NH3 CH3 NH3 CH3 + NH3 + + + 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 CH2CH2 S CH3 H C CH2 H H C CH2 H C CH2 OH NH3 NH H 3 CH2 + CH2 NH3 + N + METHIONINE H H H + (met) PHENYLALANINE PROLINE SERINE (phe) (pro) (ser) - H H O O - - O O H O O- C H H O O C H H C CH C CH3 2 C N H H C H C CH2 OH H C C + H C C CH3 NH3 NH3 NH3 H CH3 NH3 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 er 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: D normal male ○ normal female affected male affected female ●●■■ a)What is the mode of inheritance of this trait? Circle all that apply. 4 pts Autosomal minant Mitochondrial cessive 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, x, y, yo, M or M to indicate the genotype corresponding to the polydactyly alleles. 8 pts dd Dd c)What is the probability that the unborn individual marked with(?)will have polydactyly, 4 pt if it were male? 0% if it were female? 0%
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, XD, Xd , YD, Yd , MD or Md 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
Question 5 you are studying f lies 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, x,X6, x9, y, yb, etc. 7 pts Fo: Black-eyed flies_99__ x Gray-eyed flies__ 253 Black-eyed flies 228 Gray-eyed flies ray-eyed flies x Gray-eyed flies(F1 flies F 138 Black-eyed flies __99 Gray-eyed flies_ Gg 124 Hazel-eyed flies GG b) Fo: Amber-eyed male flies_Xy x Red-eyed female flies_XXR_8 pts FI All red-eyed_X Xr, X y Red-eyed male F1 x Red-eyed female F1 F2 354 Red eyed males Xy 355 Amber-eyed males 706Red- eyed females_ x2×,×
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 XB , Xb , XG , Xg , YB , Yb , etc. 7 pts a) F0: Black-eyed flies ____ gg__ x Gray-eyed flies__ Gg_______ F1 253 Black-eyed flies____ gg __________ 228 Gray-eyed flies_____ Gg__________ Gray-eyed flies x Gray-eyed flies (F1 flies) F2 138 Black-eyed flies ____ gg________ 284 Gray-eyed flies ____ Gg_________ 124 Hazel-eyed flies ____ GG_________ b) F0: Amber-eyed male flies ___Xr Y__ x Red-eyed female flies ___XR XR _ 8 pts F1: All red-eyed __XR Xr, XR Y_______ Red-eyed male F1 x Red-eyed female F1 F2 354 Red eyed males_____XR Y_________ 355 Amber-eyed males_____Xr Y_______ 706 Red-eyed females___XR XR , XR 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 complement each others' phenotypes. The results are summarized below ta ominant or 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 C+means colonies glow purpl means they do not glow purple) Strains m1 WT Mated + a)Are all the mutant phenotypes recessive? es. 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 c)How many genes have you identified that are involved in this pathway? 2 pts
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
