Midterm Exam II in Biology 231 (16 October 2006), Exams of Cell Biology

Download Midterm Exam II in Biology 231 (16 October 2006) and more Exams Cell Biology in PDF only on Docsity! NAME: _______________________________ MIDTERM EXAM II BIOLOGY 231 16 October 2006 ________________________________________________________________________________ -1- GENERAL INSTRUCTIONS: 1. Answer all questions IN INK. 2. NO CALCULATORS. 3. Confine each answer to the BOX or SPACE provided. You are free to use the backs of the pages for scratch work, but ONLY what is written in the box or space will be graded! 4. SHOW YOUR WORK IN ALL CALCULATIONS. 5. Make sure that your name is PRINTED LEGIBLY on EACH PAGE. 6. This exam consists of 10 problems on 15 pages and it is worth a total of 100 points. 7. Take your time, check your work, good luck! Information that might be useful: ! A codon or anticodon is comprised of 3 consecutive bases. There are 64 codons, 61 of which encode amino acids and 3 of which terminate translation. ! because of “wobble” pairing between mRNA codons and tRNA anticodons, U in the 5' position of an anticodon can pair with A or G in the mRNA codon, and G in the 5' position of an anticodon can pair with C or U in the mRNA codon. ! for a transmembrane gradient of any solute X, the Gibbs free energy of the gradient is found by: )GX = RT ln([X]in/[X]out) + zFVm = 5.7 kJ/mol A log([X]in/[X]out) + zFVm “in” = cytoplasmic; “out” = extracellular or non-cytoplasmic space; z = valence of the ion; F = Faraday constant = 102 kJ/VAmole ! the equilibrium potential for an ion, X: VX = (59mV/z) @ log([X]out/[X]in) ! for a gradient of a charged molecule, X: )GX = zF(Vm ! VX) ! for a proton gradient: )G = F()p), where the protonmotive force, )p = R ! (59mV A )pH) and where R = Vm of inner mitochondrial membrane, and )pH = (pHIMS ! pHmatrix) ! for mitochondria, IMM = inner mitochondrial membrane; IMS = intermembrane space ! when a negative number increases, it becomes more positive ! when a positively charged ion leaves the cytoplasm, the Vm becomes more negative ! On this date in 1859, John Brown led an ill-fated raid on the federal armory at Harper’s Ferry, VA NAME: _______________________________ MIDTERM EXAM II BIOLOGY 231 16 October 2006 ________________________________________________________________________________ -2- THE GENETIC CODE (Single letter abbreviations for amino acids) 2nd U C A G 1st 3rd U F S Y C U F S Y C C L S term. term. A L S term. W G C L P H R U L P H R C L P Q R A L P Q R G A I T N S U I T N S C I T K R A M (init.) T K R G G V A D G U V A D G C V A E G A V A E G G NAME: _______________________________ MIDTERM EXAM II BIOLOGY 231 16 October 2006 ________________________________________________________________________________ -5- (3) The double stranded DNA below contains just ONE open reading frame, encoding a protein of MW . 1000 D. The DNA is repeated at the bottom of the page so that you can work on it as needed. 5 ' C C A T G A C C A G A G C T A T T A A C A T A G A G A G A T A G G T A G 3 ' 3 ' G G T A C T G G T C T C G A T A A T T G T A T C T C T C T A T C C A T C 5 ' (a) 5 pts. Identify which strand contains the open reading frame and WRITE in the box below the mRNA that will be transcribed from that strand. Assume that the ENTIRE STRAND is transcribed into mRNA. LABEL the 5’ and 3’ ends. UNDERLINE the initiation and termination codons. (b) 4 pts. Using the single letter abbreviations for amino acids, WRITE below the deduced amino acid sequence of the small protein encoded by this open-reading frame. Be sure to LABEL the N- and C-termini. 5 ' C C A T G A C C A G A G C T A T T A A C A T A G A G A G A T A G G T A G 3 ' 3 ' G G T A C T G G T C T C G A T A A T T G T A T C T C T C T A T C C A T C 5 ' NAME: _______________________________ MIDTERM EXAM II BIOLOGY 231 16 October 2006 ________________________________________________________________________________ -6- (c) 3 pts. Could you mutate a single DNA base pair in the gene for this protein that would result in the protein being EXACTLY ONE AMINO ACID RESIDUE shorter? (Answer Yes or No in the blank). If Yes, EXPLAIN exactly which base you would change, what you would change it to, and HOW that would effect the mRNA sequence. If No, EXPLAIN WHY this is not possible for this gene sequence. 5 ' C C A T G A C C A G A G C T A T T A A C A T A G A G A G A T A G G T A G 3 ' 3 ' G G T A C T G G T C T C G A T A A T T G T A T C T C T C T A T C C A T C 5 ' (d) 4 pts. Two of the proteins (amino acid sequences) below could result from the deletion of a SINGLE base-pair from the DNA of the original gene, above. CIRCLE those two sequences below: Nterm - M T R A I N I E - Cterm Nterm - M S R A I N I E R - Cterm Nterm - M P E L L T - Cterm Nterm - M Q S Y - Cterm Nterm - M T R A I N I E R - Cterm NAME: _______________________________ MIDTERM EXAM II BIOLOGY 231 16 October 2006 ________________________________________________________________________________ -7- (4) Examine this picture of a ribosome translating a strand of mRNA, and using it as the starting point, answer the questions below about the process by which the ribosome translates mRNA into a polypeptide chain. (a) 2 pts. What is the anticodon of the tRNA in the A site if the ribosome? WRITE it in the box below, labeling the 3' and 5' ends. (b) 2 pts. What amino acid will be coupled to the tRNA in the A site? (c) 2 pts. What will happen next to the tRNA with the anticodon 3'AAA5' ? NAME: _______________________________ MIDTERM EXAM II BIOLOGY 231 16 October 2006 ________________________________________________________________________________ -10- (b) 4 pts. Calculate the potential energy of the glucose gradient in kJ/mole: (c) 6 pts. If this cell had in its plasma membrane a transporter that could use the energy of the K+ gradient to build the glucose gradient, what would its properties be? Name the type of transporter, the stoichiometry, and the directions of movement of the two species. Show your work. NAME: _______________________________ MIDTERM EXAM II BIOLOGY 231 16 October 2006 ________________________________________________________________________________ -11- (6) We saw in lecture that the electrical properties of neurons are mainly generated by specific integral membrane proteins. (a) 2 pts. What are the two membrane proteins or protein complexes that are responsible for the neuron’s RESTING POTENTIAL? (b) 3 pts. What are the two membrane proteins responsible for the threshold behavior and pattern of the action potential? (c) 3 pts. What property, of which membrane proteins, is responsible for the unidirectional nature of the propagated action potential? NAME: _______________________________ MIDTERM EXAM II BIOLOGY 231 16 October 2006 ________________________________________________________________________________ -12- (7) 8 pts. Below is a schematic diagram of a cell containing one very large mitochondrion. On the drawing, add the labels described below as clearly and accurately as possible. Think before you draw - ambiguous answers will not be given credit: LABEL the site where the TCA cycle occurs with an (A) LABEL the site where glycolysis occurs with a (B) LABEL the location of the electron transport chain with a (C) LABEL the location of ATP synthase with a (D) LABEL the location of CO2 production with an (E) LABEL the location where the pH increases during oxidative metabolism with an (F) ADD AN ARROW clearly indicating the direction in which protons are pumped during redox reactions, and LABEL it (G). ADD AN ARROW clearly indicating the direction in which protons flow down their electrochemical gradient during ATP synthesis, and LABEL it (H) NAME: _______________________________ MIDTERM EXAM II BIOLOGY 231 16 October 2006 ________________________________________________________________________________ -15- (10) 7 pts. You are working with isolated mitochondria, in a test tube, under conditions where you can manipulate the solution [H+] and measure R, the transmembrane potential of the IMM. You determine that under your experimental conditions: R = 82 mV pHmatrix = 8 )G for ATP synthesis = 80 kJ/mole ATP synthase produces 3 ATP for every 12 H+ that pass through. At WHAT pH must you set the solution/IMS in order for there to be ATP synthesis? SHOW YOUR WORK. NAME: __________KEY_______________ MIDTERM EXAM II BIOLOGY 231 16 October 2006 ________________________________________________________________________________ -1- GENERAL INSTRUCTIONS: 1. Answer all questions IN INK. 2. NO CALCULATORS. 3. Confine each answer to the BOX or SPACE provided. You are free to use the backs of the pages for scratch work, but ONLY what is written in the box or space will be graded! 4. SHOW YOUR WORK IN ALL CALCULATIONS. 5. Make sure that your name is PRINTED LEGIBLY on EACH PAGE. 6. This exam consists of 10 problems on 15 pages and it is worth a total of 100 points. 7. Take your time, check your work, good luck! Information that might be useful: ! A codon or anticodon is comprised of 3 consecutive bases. There are 64 codons, 61 of which encode amino acids and 3 of which terminate translation. ! because of “wobble” pairing between mRNA codons and tRNA anticodons, U in the 5' position of an anticodon can pair with A or G in the mRNA codon, and G in the 5' position of an anticodon can pair with C or U in the mRNA codon. ! for a transmembrane gradient of any solute X, the Gibbs free energy of the gradient is found by: )GX = RT ln([X]in/[X]out) + zFVm = 5.7 kJ/mol A log([X]in/[X]out) + zFVm “in” = cytoplasmic; “out” = extracellular or non-cytoplasmic space; z = valence of the ion; F = Faraday constant = 102 kJ/VAmole ! the equilibrium potential for an ion, X: VX = (59mV/z) @ log([X]out/[X]in) ! for a gradient of a charged molecule, X: )GX = zF(Vm ! VX) ! for a proton gradient: )G = F()p), where the protonmotive force, )p = R ! (59mV A )pH) and where R = Vm of inner mitochondrial membrane, and )pH = (pHIMS ! pHmatrix) ! for mitochondria, IMM = inner mitochondrial membrane; IMS = intermembrane space ! when a negative number increases, it becomes more positive ! when a positively charged ion leaves the cytoplasm, the Vm becomes more negative ! On this date in 1859, John Brown led an ill-fated raid on the federal armory at Harper’s Ferry, VA NAME: __________KEY_______________ MIDTERM EXAM II BIOLOGY 231 16 October 2006 ________________________________________________________________________________ -2- THE GENETIC CODE (Single letter abbreviations for amino acids) 2nd U C A G 1st 3rd U F S Y C U F S Y C C L S term. term. A L S term. W G C L P H R U L P H R C L P Q R A L P Q R G A I T N S U I T N S C I T K R A M (init.) T K R G G V A D G U V A D G C V A E G A V A E G G NAME: __________KEY_______________ MIDTERM EXAM II BIOLOGY 231 16 October 2006 ________________________________________________________________________________ -5- (3) The double stranded DNA below contains just ONE open reading frame, encoding a protein of MW . 1000 D. The DNA is repeated at the bottom of the page so that you can work on it as needed. 5 ' C C A T G A C C A G A G C T A T T A A C A T A G A G A G A T A G G T A G 3 ' 3 ' G G T A C T G G T C T C G A T A A T T G T A T C T C T C T A T C C A T C 5 ' (a) 5 pts. Identify which strand contains the open reading frame and WRITE in the box below the mRNA that will be transcribed from that strand. Assume that the ENTIRE STRAND is transcribed into mRNA. LABEL the 5’ and 3’ ends. UNDERLINE the initiation and termination codons. 5' CC AUG ACC AGA GCU AUU AAC AUA GAG AGA UAG GUAG 3' (transcribe the bottom strand, top strand has no ORF) (b) 4 pts. Using the single letter abbreviations for amino acids, WRITE below the deduced amino acid sequence of the small protein encoded by this open-reading frame. Be sure to LABEL the N- and C-termini. Nterm - M T R A I N I E R - Cterm 5 ' C C A T G A C C A G A G C T A T T A A C A T A G A G A G A T A G G T A G 3 ' 3 ' G G T A C T G G T C T C G A T A A T T G T A T C T C T C T A T C C A T C 5 ' NAME: __________KEY_______________ MIDTERM EXAM II BIOLOGY 231 16 October 2006 ________________________________________________________________________________ -6- (c) 3 pts. Could you mutate a single DNA base in the gene for this protein that would result in the protein being EXACTLY ONE AMINO ACID RESIDUE shorter? (Answer Yes or No in the blank). If Yes, EXPLAIN exactly which base you would change, what you would change it to, and HOW that would effect the mRNA sequence. If No, EXPLAIN WHY this is not possible for this gene sequence. YES If you change the codon for the last amino acid, R, from AGA to UGA, it will result in a new stop codon, making the protein shorter by one residue. There is one way to do this: replace a “T” with an “A” in the bottom (transcribed) DNA strand (at base pair 27 in the sequence). 5 ' C C A T G A C C A G A G C T A T T A A C A T A G A G A G A T A G G T A G 3 ' 3 ' G G T A C T G G T C T C G A T A A T T G T A T C T C T C T A T C C A T C 5 ' (d) 4 pts. Two of the proteins (amino acid sequences) below could result from the deletion of a SINGLE base-pair from the DNA of the original gene, above. CIRCLE those two sequences below: Nterm - M T R A I N I E - Cterm Nterm - M S R A I N I E R - Cterm Nterm - M P E L L T - Cterm (delete A:T 6) Nterm - M Q S Y - Cterm (delete 2 bp) Nterm - M T R A I N I E R - Cterm (Del G:C 33) NAME: __________KEY_______________ MIDTERM EXAM II BIOLOGY 231 16 October 2006 ________________________________________________________________________________ -7- (4) Examine this picture of a ribosome translating a strand of mRNA, and using it as the starting point, answer the questions below about the process by which the ribosome translates mRNA into a polypeptide chain. (a) 2 pts. What is the anticodon of the tRNA in the A site if the ribosome? WRITE it in the box below, labeling the 3' and 5' ends. 3'UUG5' (b) 2 pts. What amino acid will be coupled to the tRNA in the A site? N (asparagine) (c) 2 pts. What will happen next to the tRNA with the anticodon 3'AAA5' ? It will exit the E site of the ribosome. NAME: __________KEY_______________ MIDTERM EXAM II BIOLOGY 231 16 October 2006 ________________________________________________________________________________ -10- (b) 4 pts. Calculate the potential energy of the glucose gradient in kJ/mole: )Gglucose = 5.7 kJ/mol A log([X]in/[X]out) + zFVm (z=0, so 2 nd term = 0) = 5.7 kJ/mol (log(100/1)) = 11.4 kJ/mol (c) 6 pts. If this cell had in its plasma membrane a transporter that could use the energy of the K+ gradient to build the glucose gradient, what would its properties be? Name the type of transporter, the stoichiometry, and the directions of movement of the two species. Show your work. )GK+ = zF(Vm ! VK) = (1)(102 kJ/volt-mol)(!59mV !(!118mV)) = (102 kJ/volt-mol)(0.059V) = +5.9 kJ/mol )GK+ > 0, so the favorable direction of K + flow is out of the cytoplasm. So, we need an ANTIPORTER that moves glucose IN coupled to favorable K+ flow OUT. Since 11.4 kJ/mol is slightly < twice as large as 5.9 kJ.mol, the stoichiometry will be AT LEAST 2:1 moles of K+ to moles of glucose. NAME: __________KEY_______________ MIDTERM EXAM II BIOLOGY 231 16 October 2006 ________________________________________________________________________________ -11- (6) We saw in lecture that the electrical properties of neurons are mainly generated by specific integral membrane proteins. (a) 2 pts. What are the two membrane proteins or protein complexes that are responsible for the neuron’s RESTING POTENTIAL? the Na/K ATPase and K leak channels (b) 3 pts. What are the two membrane proteins responsible for the threshold behavior and pattern of the action potential? voltage-gated Na and K channels (c) 3 pts. What property, of which membrane proteins, is responsible for the unidirectional nature of the propagated action potential? The refractory period of the voltage-gated Na and K channels NAME: __________KEY_______________ MIDTERM EXAM II BIOLOGY 231 16 October 2006 ________________________________________________________________________________ -12- (7) 8 pts. Below is a schematic diagram of a cell containing one very large mitochondrion. On the drawing, add the labels described below as clearly and accurately as possible. Think before you draw - ambiguous answers will not be given credit: LABEL the site where the TCA cycle occurs with an (A) LABEL the site where glycolysis occurs with a (B) LABEL the location of the electron transport chain with a (C) LABEL the location of ATP synthase with a (D) LABEL the location of CO2 production with an (E) LABEL the location where the pH increases during oxidative metabolism with an (F) ADD AN ARROW clearly indicating the direction in which protons are pumped during redox reactions, and LABEL it (G). ADD AN ARROW clearly indicating the direction in which protons flow down their electrochemical gradient during ATP synthesis, and LABEL it (H)