bio 111 exam #2
TRANSCRIPT
A1
Bio 111 Exam #2 Version A 11/13/06
Your Name: TA's Name: Lab Section Write your initials on every page in the space provided. This exam has 11 pages including this coversheet. Check that you have pages 1-11. This exam has five questions. You may want to read all questions before starting to write. Make your answers as clear and precise as possible. Answer all questions in the space provided.
Question Value Score 1 23 2 19 3 18 4 15 5 25 TOTAL: 100
Solutions can be found in the Biochemistry 5 handout.
Initials
A2
Question 1: Chemistry (23 points) Note that a summary of chemistry can be found on page 10 of this exam. Consider the following three molecules:
SHNH3
Molecule #1 Molecule #3Molecule #2
a) Rank the three molecules in order from the most hydrophobic to the most hydrophilic. Note that they are not amino acids. Write your answers in the blanks below (9 pts.) Most Most Hydrophobic Hydrophilic b) Draw a molecule in the space below which is similar to the molecules above and is more hydrophilic than the most hydrophilic molecule you indicated above. Make sure that your molecule obeys the bonding rules described in lecture and includes all hydrogen atoms. Note that there are many possible correct answers here. (8 pts)
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Question 1, continued: c) Shown below is a molecule of beta-mercapto-ethanol. Draw a single water molecule making a single hydrogen bond to an appropriate part of the beta-mercapto-ethanol molecule. Indicate the hydrogen bond with a dashed line ( ). (6 pts)
H S C C O H
H H
H H
Initials
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Question 2: Protein Structure I (19 points) Note that structures of amino acids can be found on page 11 of this exam. You are designing a protein to bind to a small molecule, Molecule X. Molecule X is shown below with three parts circled: Part A Part B Part C
H3NOH
a) Consider Part A. Choose an amino acid that has a side-chain that can only form a van derWaals bond with Part A of Molecule X. If more than one is possible, give only one. Explain why these two can only form a van der Waals bond. (7 pts) Amino acid Explanation: b) Consider Part B. Choose an amino acid that has a side-chain that can form a non-covalent bond with Part B of Molecule X. Give the amino acid and the bond that could form between its side chain and Part B. If more than one is possible, give only one. (6 pts) i) Amino acid ii) Circle the strongest bond that could form between the side chain and Part B. ionic hydrogen hydrophobic van der Waals bond bond interaction bond c) Consider Part C. Choose an amino acid that has a side-chain that can form a non-covalent bond with Part C of Molecule X. Give the amino acid and the bond that could form between its side chain and Part C. If more than one is possible, give only one. (6 pts) i) Amino acid ii) Circle the strongest bond that could form between the side chain and Part C. ionic hydrogen hydrophobic van der Waals bond bond interaction bond
Initials
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Question 3: Protein Structure II (18 points) These structures are relevant to this question:
H3N
CH
CO
O
CH3
H3N
CH
CO
O
CH2 C
O
O
H3N
CH
CO
O
CH2
H3N
CH
CO
O
CH2 OH
alanine
phenylalanineaspartic acid
serine
a) Consider an enzyme with a hydrophobic core. Amino acid #212 is alanine and is part of this hydrophobic core. (6 pts each) i) A mutation that changes amino acid #212 to serine results in an enzyme that is completely inactive. Based on the structures of the two amino acids, provide a plausible explanation for why the mutation results in an inactive enzyme. ii) A mutation that changes amino acid #212 to phenylalanine results in an enzyme that is completely inactive. Based on the structures of the two amino acids, provide a plausible explanation for why the mutation results in an inactive enzyme. iii) Consider a mutation that changes amino acid #212 to aspartic acid. Based on the data given so far, what do you think the effect of this mutation would be? Circle one and explain your reasoning. Inactive Enzyme Active Enzyme Explanation:
Initials
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Question 4: Thermodynamics (15 points) Given that the reaction H2 + O2 ⇒ H2O is spontaneous, answer the following questions. a) Rank the following states of hydrogen and oxygen in order from the highest free energy to the lowest free energy. (8 pts) State Description 1 free H and O atoms not bonded to anything 2 the products (H2O molecules) 3 the reactants (H2 and O2 molecules) 4 the transition state between reactants and products Highest free energy Upper Middle free energy Lower Middle free energy Lowest free energy b) What type(s) of bonds are being broken when going from state (3) to state (1)? Circle all that apply. (3 pts) ionic hydrogen covalent hydrophobic van der Waals bonds bonds bonds interactions bonds c) Suppose that you added a catalyst for this reaction. What effect would adding the catalyst have on the energy of each of the following states? Circle the correct answer. (4 pts) i) State 1: free energy free energy free energy increases unchanged decreases ii) State 2: free energy free energy free energy increases unchanged decreases iii) State 3: free energy free energy free energy increases unchanged decreases iii) State 4: free energy free energy free energy increases unchanged decreases
Initials
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Question 5: Enzymes, Pathways, Glycolysis, & Fermentation (25 points) The reaction pathway for glycolysis and fermentation are shown on pages 8 and 9. Each reaction is indicated by a number. a) Answer the following questions using the numbers from the reactions on pages 8 and 9. There may be more than one right answer to each question; give only one. (4 pts each)
i) Give a number corresponding to a reaction where a phosphate (P) is transferred from another molecule to ADP to make ATP.
ii) Give a number corresponding to a reaction where a single covalent bond connecting two carbon atoms is broken.
b) Consider enzyme (1) in the glycolysis pathway. Suppose that there are two forms of this molecule encoded by two different alleles of the gene: allele enzyme (1) encoded G fully-functional enzyme (1) g non-functional enzyme (1) i) Complete the following table with numbers as appropriate: (6 pts)
Genotype % of Enzyme (1) that is functional % of Enzyme (1) that is non-functional GG
gg
Gg ii) Individuals with the genotype gg are dead. Explain why this genotype would be lethal. (5 pts) ii) What is the most likely phenotype of a Gg individual? (circle one) live dead Explain your reasoning. (6 pts)
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Reactions of Glycolysis & Fermentation I
3 phosphoglycerate
ADP
ATP
ADP
ATP
(7)
O
HPO
H2C
H O
O
CC C C C
O O O
H
HH
H P
O
1,3-di-phosphoglycerate
PiPi
C C C
O O O
H
HH
H P
OP
C C
O
OH
H2C
OP H
O P
(6)(borrow an "O" for each piece)
(move H to NAD)
NAD +
NADH
NAD +
NADH
3-phospho-glyceraldehyde
(5)
+ C C C
O O O
H
HHH
H P3-phospho-glyceraldehyde
C C
O
OH
H2C
OP
H
H
3-phospho-glyceraldehyde
di-hydroxy-acetonephosphate
fructose-1,6-di-phosphatefructose-6-phosphate
+
+ H+
+ H+
C C C
O O O
H
HHH
H P
C C
O H
O
H
H2C
OP
H
(4)
C C C C C
O H O
H
O O
H
HHHO
H
H P
H2C
OP
C C C C C
O H O
H
O O
H
HHHO
H
H P
H2C
O
H(3)
ATP ADP
(2)
glucoseglucose-6-phosphate
ADPATP
(1)
CH
O
C C C C C
O
H
H O
H
O O
H
HHHO
H
H
H P
CH
O
C C C C C
O
H
H O
H
O O
H
H
HHHO
H
H
H
Initials
A9
Reactions of Glycolysis & Fermentation II
(pick up H +'s as needed)
(pick up H +'s as needed)
(pick up H +'s as needed)
(save H's as H +'sreturn the O's)
ethanolH3C
O
C H
H
H
H
H
O
CC
H
H
H
H
(12)NADH
NAD +
NADH
NAD +
H
H
O
CC
H
HH3C
O
C H
carbondioxide
carbondioxide
acetaldehyde
(11)C
O
O
C
O
O
pyruvateO
H
H
OO
CCC
H
OH3C
O
O
CC
ADP
ATP
ADP
ATP
(10)
(9)
phospho-enol-pyruvate
2-phosphoglycerate
P
OH2C
O
O
CC
P
O
H
H
OO
CCC
P
O
H
H H
H
OOO
CCC
P
O
HO
H2C
H O
O
CC
(8)
H2OH2O
3-phosphoglycerate+C C
O
OH
H2C
OP H
O C C C
O O O
H
HH
H P
O
Initials
A10
Summary Chart:
If you see.. You should think.... Part of molecule Properties
C–C non-polar ‘phobic no no yes C–H non-polar ‘phobic no no yes C–N polar ‘philic ª ‡ no C–O polar ‘philic ª ‡ no C–S non-polar ‘phobic no no yes
O–H polar ‘philic ª yes no N–H polar ‘philic ª yes no P–O polar ‘philic ª ‡ no S–H non-polar ‘phobic no no yes S–O polar ‘philic ª ‡ no
N
§ ‘philic no yes no
N
§ ‘philic yes no no
O
§ ‘philic no yes no
O
§ ‘philic yes yes no
S
§ ‘phobic no no yes
Notes: * Assuming a suitable partner is nearby. ª If the O or N is charged, “yes”; if not “no”. ‡ Yes, if the N or O has a lone pair available. § Since this is an atom, not a bond, it is neither polar nor non-polar.
Initials
A11
ALANINE(ala)
ARGININE(arg)
ASPARAGINE(asN)
C
C
OO
H
NH3
CH3
-
+
C
C
OO
H
NH3
C
H
CH3
CH3
-
+
C
C
OO
H
NH3
CH2CH2CH2 N
H
CNH2
NH2
-
++
C
C
OO
H
NH3
CH2 C
O
NH2
-
+
C
C
OO
H
NH3
CH2 C
O
O
-
+
-
ASPARTIC ACID(asp)
C
C
OO
H
NH3
CH2 SH
-
+
CYSTEINE(cys)
C
C
OO
H
NH3
CH2CH2
O
O
C
-
+
-C
C
OO
H
NH3
CH2CH2
O
C
NH2
-
+
C
C
OO
H
NH3
H
-
+
C
C
OO
H
NH3
CH2
CN
CN
H
H
H
H
-
+
+
C
C
OO
H
NH3
C
H
CH3
CH2CH3
-
+
C
C
OO
H
NH3
CH2 C
H
CH3
CH3
-
+
C
C
OO
H
NH3
CH2CH2CH2CH2 NH3+
-
+
C
C
OO
H
NH3
CH2CH2 S CH3
-
+
C
C
OO
H
NH3
CH2
H H
H
HH
-
+
C
NCH2
CH2
CH2
H
H
H
-
C
OO
+
C
C
OO
H
NH3
CH2 OH
-
+
C
C
OO
H
NH3
C
H
OH
CH3
-
+
C
C
OO
H
NH3
CH2
-
+C
C
OO
H
NH3
CH2 OH
H H
HH
-
+
GLUTAMIC ACID(glu)
GLUTAMINE(glN)
GLYCINE(gly)
HISTIDINE(his)
ISOLEUCINE(ile)
LEUCINE(leu)
LYSINE(lys)
METHIONINE(met) PHENYLALANINE
(phe)PROLINE(pro)
SERINE(ser)
THREONINE(thr)
TRYPTOPHAN(trp) TYROSINE
(tyr)
VALINE(val)
STRUCTURES OF AMINO ACIDS
C
N
H
H
H
H
HH
Initials
A12