Bioc385-Exam1-Spr2016-KEY - BIOC 385 Spring 2016 Exam 1 KEY...

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Unformatted text preview: BIOC 385 Spring 2016, Exam 1 KEY Name________________________ Preceptor/Team_____________ 1 BIOC 385 Spring 2016, Exam 1 KEY Name________________________ Preceptor/Team_____________ 1. (6 pts.) There are four major biomolecules in living cells;; simple sugars, nucleotides, fatty acids, and amino acids. Match the TWO examples of each of the four representative biomolecules by writing the number on the lines. Choose one each from Column 1/1’ and one each from Column 2/2’. Biomolecule Column 1 Column 2 Representative examples Column 1’ Column 2’ Nucleotides (1)___D____ (2)____H___ A. alanine E. palmitate Fatty acids (3)____B___ (4)____E____ B. oleate F. fructose Amino acids (5)____A___ (6)____G____ C. galactose G. aspartate Simple sugars (7)____C___ (8)____F____ D. adenosine H. thymidine The correct order from #1 à #8 is: A) B, G, D, E, A, H, C, F B) A, H, B, E, D, G, C, F C) D, H, B, F, A, G, C, E D) D, H, B, E, A, G, C, F E) D, H, B, C, A, G, E, F 2. (6 pts) Membrane receptors are _______ that are activated by ligand binding, which in turn, causes a _______________ change in the cytoplasmic region of the receptor. This can lead to altered rates of ________ transport, increased protein synthesis, and changes in enzyme activity. Ligand binding to receptor proteins is _______ and a function of extracellular ligand concentration, which means that when ligand concentrations ________, receptor proteins return to the inactive conformation. Fill in the blanks above with the best answers provided below. A. hormones, symmetrical, iron, transitory, solute B. proteins, conformational, ion, reversible, decrease C. ions, conformational, hormone, irreversible, solvent D. proteins, reciprocal, cAMP, reversible, solvent E. transmitters, permanent, ligand, covalent, solute 3. (5 pts.) Biochemistry is an applied science that follows the hierarchical structure of life on Earth. Number the following hierarchical levels starting with simplest (#1) and ending with the most complex (#8). ___7__ (A) Desert ___6__ (B) Lizard ___3__ (C) Hexokinase ___5__ (D) Muscle cell ___2__ (F) Fructose ___4__ (G) Glycolysis ___1__ (H) Hydroxyl group ___8__ (I) Earth The correct order from letters A à I is: A) B, F, C, G, D, H, A, I B) H, F, C, D, G, B, I, A C) C, F, H, G, D, B, A, I D) H, C, F, G, B, D, A, I E) H, F, C, G, D, B, A, I 4. (5 pts.) What is the most important lesson about protein function that can be learned from studying the jellyfish Green Fluorescent Protein (GFP)? Choose the one best answer. A. The fluorescence properties of proteins at 470 nm are a function of the number of aromatic amino acids. B. The primary function of a beta barrel protein conformation is to provide a scaffold for chromophores C. The primary amino acid sequence encodes information needed for protein structure and function. D. The Pacific Northwest Jellyfish has evolved a unique mechanism to combine a chromophore with NaCl. E. Aequorin and coelenterazine are required for green fluorescence when blue light bulbs are not available. 2 BIOC 385 Spring 2016, Exam 1 KEY Name________________________ Preceptor/Team_____________ 5. (5 pts.) Match the 8 amino acid structures below with each of the four chemical groups. Each amino acid fits into only one chemical group (HB, C, HL, A), and each chemical group has 2 amino acids represented. Hydrophobic (HB), Charged (C), Hydrophilic (HL), Aromatic (A) The correct order from numbers 1 à 8 is: A) A, C, HB, HL, HL, B) HB, C, HB, HL, HL, C) A, HB, C, HL, A, D) C, A, HB, C, HL, E) A, C, HB, HB, HL, A, A, HL, A, A, C, C, C, HL, C, HB A HB HB HL 6. (5 pts.) Which one of the following statements about enzyme structure and function is the most true? A. Enzymes that are RNA (ribozymes) function at higher temperatures than enzymes that are proteins. B. Enzymes increase the rates of biochemical reactions without changing the equilibrium constant. C. Disulfide bonds are required for enzymes to catalyze biochemical reactions involving sulfur. D. Eukaryotic enzymes are all multisubunit complexes requiring either cofactors, coenzymes, or metal ions. E. Enzyme catalyzed reactions take seconds not years because the equilibrium constant is increased. 7. (5 pts.) What explains the observation that the rates of a passive transport carrier and an active transport carrier are saturated at high solute concentration? Choose the one best answer. A. Active transport proteins are energized channel proteins that require GTP and ATP to function. B. The rate of carrier protein transport is limited by the stoichiometry of solute binding to protein. C. The rate of solute molecule transport across the membrane is determined by the polarity of the solvent. D. It is difficult to determine without knowing the melting point of the plasma membrane in that region. E. Each time a solute molecule binds to the transport protein it releases redox energy in the form of light. 8. (5 pts.) What is the overall signal amplification in the pathway shown at the right considering that one glucagon molecule activates one glucagon receptor, which leads to the activation of 10 adenylate cyclase molecules, which produces 100 cAMP molecules that activate protein kinase A (PKA) at 2 cAMP per PKA, and each PKA molecule phosphorylates and activates 100 phosphorylase kinase molecules? A. The signal amplification = 200,000 fold B. The signal amplification = 50,000,000 fold C. The signal amplification = 10,000 fold D. The signal amplification = 10,000,000 fold E. The signal amplification = 50,000 fold 3 BIOC 385 Spring 2016, Exam 1 KEY Name________________________ Preceptor/Team_____________ 9. (6 pts). Identify the labeled structures in the DNA double helix by choosing the MOST correct letter label. Note that labels may be used once, more than once, or not used at all. Labels A-­E are features within the DNA helix, and labels F-­I refer to different structural forms of DNA that have been identified. 1. “A form” DNA___H______ 2. DNA backbone___ B ____ 3. Hydrogen bonds___ A ___ 4. “B form” DNA_____ G ___ 5. Base stacking____ C ____ 6. “Z form” DNA_____ F ___ 7. Major groove_____ E___ 8. Minor groove_____ D ___ The correct order for numbers 1 à 8 is: A) I, B, A, F, C, G, E, D B) H, B, A, I, D, F, C, E C) F, B, A, G, C, I, E, D D) H, B, A, G, C, F, E, D E) H, E, B, G, C, F, D, A 10. (5 pts) Determine the missing nucleotides (G, C, A, T, U) in each nucleic acid duplex shown below considering 1) DNA-­DNA duplex, 2) RNA-­DNA duplex, 3) RNA-­RNA duplex, 4) DNA palindrome (a palindrome is a sequence that reads the same 5’ to 3’, e.g., “radar” and “madam” are word palindromes. 1. 5’ T A G C G C T 3’ 3’ A T C G C G A 5’ 3. 5’ U A U A C U C 3’ 3’ A U A U G A G 5’ 2. 3’ T A G A C T C 5’ 5’ A U C U G A G 3’ 4. 5’ G A A T T C 3’ 3’ C T T A A G 5’ The BEST answers for numbers 1 à 4 with top strand listed first for each numbered nucleic acid are: A) 1 G, T;; 2 T, U;; 3 U, A;; 4 T, A B) 1 G, U;; 2 T, T;; 3 U, T;; 4 G, C C) 1 G, T;; 2 T, U;; 3 T, A;; 4 T, A D) 1 C, T;; 2 T, U;; 3 U, A;; 4 C, G E) 1 G, T;; 2 U, U;; 3 U, A;; 4 A, T 11. (6 pts) Choose the word leading strand or lagging strand DNA synthesis in the 2 replication forks below. The correct answers A à D are: A. Lagging, Leading, Leading, Lagging B. Leading, Lagging, Lagging, Leading C. Lagging, Leading, Lagging,Leading D. Leading, Lagging, Lagging, Lagging E. Lagging, Lagging, Leading, Leading 4 BIOC 385 Spring 2016, Exam 1 KEY Name________________________ Preceptor/Team_____________ 12. (6 pts). Why does RNA contain uracil and DNA contain thymine? Choose the one BEST answer. A. Spontaneous cytosine deamination generates uracil, which base pairs with adenine during replication, and thereby converts a C-­G base pair to an A-­T base pair. B. Spontaneous cytosine deamination generates uracil, which base pairs with adenine during replication, and thereby converts a C-­G base pair to a T-­A base pair. C. Spontaneous cytosine deamination generates uracil, which base pairs with adenine during replication, and thereby converts a G-­C base pair to a A-­T base pair. D. RNA transcription base pairs U-­T in the RNA with DNA, whereas this process base pairs A-­T in the RNA with DNA. Therefore, if uracil were present in DNA, then U-­A and A-­U could not be distinguished. E. Uracil deamination to cytosine provides a survival advantage to rapidly evolving species like viruses. 13. (4 pts) Choose 3 reasons below why RNA is a dynamic biomolecule, and in that way, distinct from DNA. 1. RNA is synthesized and degraded within the nucleus, where it functions to control biochemical processes 2. RNA forms base pairs with complementary nucleotides and transmits information in a predictable way. 3. RNA tertiary structure is altered by the binding of protein and small molecule ligands. 4. RNA forms a double helical structure between anti-­parallel strands with 5’ -­ 3’ and 3’ – 5’ polarity. 5. RNA is able to participate in transitory functional base pairing interactions with RNA or DNA. 6. RNA contains a ribose sugar, a nucleotide base attached to the ribose, and phosphate groups. 7. RNA can be degraded in the 5’ to 3’ direction or in the 3’ to 5’ direction, and it can be cleaved internally. A. 1, 4, 6 B. 3, 5, 7 C. 4, 5, 7 D. 2, 4, 6 E. 1, 3, 5 14) (7 points) Refer to the diagram at right showing RNA and protein synthesis. Circle one choice for each label in the diagram. Letter Circle one of these choices A 5’ NH3+ 3’ COO-­ -­ + B COO 3’ NH3 5’ + C NH3 3’ 5’ COO-­ à ß D ß à E F. The diagram shows a process in….. F eukaryotes prokaryotes A. B. C. D. E. (A) 5’;; (A) 5’;; (A) COO-­;; (A) NH3+;; (A) 5’;; (B);; COO-­;; (B);; NH3+;; (B);; 5’;; (B);; 5’;; (B);; COO-­;; (C) NH3+;; (C) 3’;; (C) 3’;; (C) 5’;; (C) 3’;; (D) à;; (D) à;; (D) ß;; (D) ß;; (D) à;; (E) ß;; (E) à;; (E) ß;; (E) à;; (E) à;; (F) eukaryotes (F) prokaryotes (F) prokaryotes (F) eukaryotes (F) eukaryotes 15. (5 pts) What explains why ~25,000 human genes are able to encode >150,000 human proteins? A. There are ~6 times more proteins than genes because each gene makes 6 different proteins. B. Some genes are transcribed from both strands of the DNA, which is 6x more proteins. C. Polypeptide subunits of the same protein complexes are often differentially cleaved by ribozymes. D. Differentially spliced mRNA transcripts can be generated from the same gene. E. Most proteins belong to multisubunit complexes, so 2 x 3 combinations of complexes is 6x more. 5 BIOC 385 Spring 2016, Exam 1 KEY Name________________________ Preceptor/Team_____________ For questions 16-­18 use the nine nucleotide DNA base pairs below to determine the mRNA, three tRNAs, and protein sequences. Write your answers in the blanks. The Genetic Code is contained on page 1 of the exam. The section of DNA sequence shown is located in the middle of the gene (…), it is not at the 5’ end. 5’……. CCA TAC CGG …….3’ PROMOTER TERMINATION 3’……. GGT ATG GCC….….5’ 16. (5 pts.) mRNA 5’….. _C_ _C_ __A__ __U__ __A__ __C__ __C__ __G__ _G__...3’ codon 1 codon 2 codon 3 The correct order for codons 1, 2, and 3 written 5’ to 3’ on the mRNA strand is: A) CCA, UAC, CGG B) GGT, AUG, GCC C) CCA, TAC, CGG D) CCG, GUA, UGG E) None of these answers are correct. 17. (5 pts.) tRNAs 5’ _U_ _G_ __G__ 3’ 5’ _G_ _U_ __A__ 3 5’ __C_ _C_ __G___ 3’ anticodon 1 anticodon 2 anticodon 3 The correct order for tRNA anticodons 1, 2, and 3 written each in the 5’ to 3’ orientation is: A) GUU, AUG, GCC B) CCA, UAC, CGG C) GCC, AUG, GGU D) UGG, GUA, CCG E) None of these answers are correct. 18. (5 pts.) protein NH3+….. __Pro__ -­ ___ Tyr ___ -­ __ Arg __.....COO-­ amino acid 1 amino acid 2 amino acid 3 The correct order for amino acids 1, 2, and 3 written in the NH3+ to COO-­ orientation is: A) Val, Met, Ala B) Pro, Tyr, Arg C) Gly, Val, STOP D) Pro, Phe, Met E) None of these answers are correct. 19. (4 pts) What happens during protein synthesis if a tRNA is charged with the wrong amino acid? A. The protein will contain the wrong amino acid in the corresponding codon position. B. The tRNA will be excluded from the A site of the ribosome but not from the P site. C. The amino acid will be removed by a ribozyme that cleaves tRNA molecules at the CCA end. D. The protein will not be synthesized because the incorrectly charged tRNA will be stuck in the P site. E. Protein synthesis will continue, however the RNA splicing reaction will be blocked by the amino acid. 6 ...
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