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Advanced Biochemistry delves into the molecular mechanisms that govern biological processes, with an emphasis on the structure, function, and dynamics of proteins, nucleic acids, and biomembranes. The course explores enzyme kinetics and mechanisms, metabolic pathways and their regulation, signal transduction, and the techniques used to analyze biomolecules at the atomic and molecular levels. Students will critically examine recent research developments, apply quantitative and computational approaches to biochemical problem-solving, and understand the biochemical basis of disease and therapeutic interventions. This course is designed to deepen theoretical knowledge and enhance experimental skills for advanced studies in biochemistry and related fields.
Recommended Textbook
Biochemistry 4th Edition by Christopher K. Mathews
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Q1) Which of the following organelles is found in plant cells,but not in animal cells
A)chloroplast
B)Golgi apparatus
C)mitochondrion
D)smooth endoplasmic reticulum
E)rough endoplasmic reticulum
Answer: A
Q2) Of the following biomolecules,which is found only in a monomeric form as opposed to a polymeric form?
A)amino acids
B)carbohydrates
C)lipids
D)nucleotides
E)none of the above
Answer: C
Q3) The molecule pyruvic acid is found at the crossroads of several biochemical pathways.Pyruvic acid is also known as 2-oxopropanoic acid.Based upon this name,draw the molecule.
Answer: 11ea8a11_436d_60c5_8b44_bfd5f6b258f9_TB4872_00
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Q1) Which of the following would likely form micelles in an aqueous solution?
A)hexane
B)glucose
C)glutamic acid
D)dodecanoic acid
E)none of the above
Answer: D
Q2) If gastric juice has a pH of about 1.5,which of the following would be predominantly deprotonated in the stomach?
A)phenol (pK<sub>a</sub> = 9.9)
B)acetic acid (pK<sub>a</sub> = 4.7)
C)lactic acid, (pK<sub>a</sub> = 3.9)
D)phosphoric acid (pK<sub>a</sub> = 2.1)
E)hydrochloric acid (pK<sub>a</sub> = -6)
Answer: E
Q3) Imidazole is a commonly used buffer in biochemistry labs.With a pK<sub>a</sub> of 7.0,what would be the ratio of base to acid at pH 7.4?
Answer: 2.5 11ea8a11_436e_4b29_8b44_234f570e4c48_TB4872_00
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Q1) Based on the half reactions given below,which of the following reactants is the strongest reducing agent?
A)NADH \(\to\) NAD<sup>+</sup> + H<sup>+</sup> + 2e<sup>-</sup> (ES1U1P1\(\circ\)S1S1P0' = + 0.32 V)
B)dihydrolipoic acid \(\to\) lipoic acid + 2H<sup>+</sup> + 2e<sup>-</sup>
(ES1U1P1\(\circ\)S1S1P0' = + 0.29 V)
C)FADH<sub>2</sub> \(\to\) FAD + 2H<sup>+</sup> + 2e<sup>-</sup>
(ES1U1P1\(\circ\)S1S1P0' = + 0.22 V)
D)lactate \(\to\) pyruvate + 2H<sup>+</sup> + 2e<sup>-</sup> (ES1U1P1\(\circ\)S1S1P0' = + 0.18 V)
E)succinate \(\to\) fumarate + 2H<sup>+</sup> + 2e<sup>-</sup>
(ES1U1P1\(\circ\)S1S1P0' = - 0.03 V)
Answer: A
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Q1) Which of the following secondary structures is correctly identified?
A)Z-DNA: left-handed DNA with pyrimidines in the syn conformation and purines in the anti conformation
B)hairpin structure: self-complimentary single stranded molecules that form a parallel helix
C)cruciform: a double hairpin formed in a region of palindromic DNA
D)H-DNA: triple helical structure that results when Watson-Crick base pairing does not form and instead,Hoogsteen base pairing occurs E)none of the above
Q2) While RNA is often single stranded,transfer RNA (tRNA)is usually found with some double stranded structure.Which of the following explains this?
A)tRNAs contain self-complimentary stem-loop structures
B)after synthesis,tRNA molecules are hydrolyzed in specific places to allow double stranded structures to form
C)regions of tRNAs become supercoiled,thus forcing formation of double stranded regions
D)tRNAs adopt a form much like Z-DNA allowing double stranded regions to form E)none of the above
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Q1) Which of the following amino acids is derived from another amino acid by the addition of an amine group?
A)lysine
B)asparagine
C)arginine
D)histidine
E)none of the above
Q2) What is the pI for the following peptide: Ala-Glu-Val-Asp-Lys-Leu
Q3) Draw each of the structures of aspartic acid that predominate at pH 1,3,7,and 11.
Q4) Which of the following events occurs after the formation of disulfide bonds during the conversion of preproinsulin to mature insulin?
A)folding of proinsulin into a stable conformation
B)transport of the molecule through the membranes
C)cleavage of the peptide sequence that joins the A and B chains
D)cleavage of the leader sequence
E)posttranslational modification of specific proline residues
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Q1) In an \(\alpha\)-helix,a hydrogen bond is formed between the carbonyl oxygen of the i<sup>th</sup> residue and the amide hydrogen _____ residues away
A)i + 1
B)i + 2
C)i + 3
D)i + 4
E)i + 5
Q2) Which of the following causes denaturation of a protein when disulfide bonds are present?
A)heat
B)pH changes
C)reducing agent
D)detergent
E)all of the above
Q3) What type of interaction occurs between the \(\beta\)-sheets of fibroin?
A)charge-dipole interaction
B)dipole-dipole interaction
C)dipole-induced dipole interaction
D)van der Waals interaction
E)hydrogen bonding
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Q1) Changes in hemoglobin's oxygen affinity are primarily the result of changes in the _________ structure of the protein.
A)primary
B)secondary
C)tertiary
D)quaternary
E)all of the above
Q2) The binding of oxygen to hemoglobin is said to be _______________.
A)high affinity
B)low affinity
C)sigmoidal
D)cooperative
E)sequential
Q3) Using the following sequence from the coding strand of DNA,determine the amino acid sequence of the corresponding protein.Make three different mutations: (1)silent, (2)missense with little or no effect upon the protein structure (indicate the amino acid substitution)and (3)nonsense.

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Q1) Which portion of the myosin protein found in muscle is responsible for both ATP and actin binding?
A)heavy-chain coiled-coiled tails
B)heavy-chain stalk
C)heavy-chain globular head
D)essential light chain
E)regulatory light chain
Q2) Which of the following motor proteins is correctly paired with its primary function?
A)myosin V: muscle contraction
B)myosin II: cargo transport
C)cytoplasmic dynein: bending of cilia or flagella
D)axonemal dynein: cargo transport
E)none of the above
Q3) Which form of myosin is found in striated muscle?
A)I B)II C)IV
D)VI
E)all of the above
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Q1) Which of the following polysaccharides contains exclusively glucose in \(\beta\)(1\(\to\)4)glycosidic bonds?
A)amylose
B)amylopectin
C)glycogen
D)cellulose
E)chitin
Q2) All glycosaminoglycans contain which of the following?
A)a sulfate ester
B)a \(\beta\)(1\(\to\)4)glycosidic bond
C)a carboxylate
D)an amine group that is either acetylated or sulfated E)all of the above
Q3) How many carbon atoms are found in the smallest molecules that are classified as carbohydrates?

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Q1) The fatty acid designated 18:2c\(\Delta\)9,12 is best described as a _______ fatty acid.
A)saturated B)unsaturated C)polyunsaturated D)hydrogenated
E)partially hydrogenated
Q2) Movement of ions across a cell membrane by the Na/K ATPase is best described as
A)sodium moved outside to inside,potassium inside to outside
B)sodium moved inside to outside,potassium outside to inside
C)sodium moved inside to outside,potassium inside to outside
D)sodium moved outside to inside,potassium outside to inside E)none of the above
Q3) A ceramide is derived from which combination of the following?
A)a molecule of sphingosine and a monosaccharide
B)a molecule of sphingosine and a molecule of phosphocholine
C)a molecule of sphingosine and a fatty acid
D)a molecule of sphingosine and two fatty acids
E)a molecule of sphingosine,a fatty acid and a monosaccharide
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Q1) What must be true if K<sub>M</sub> is truly a measure of the affinity of enzyme and substrate?
A)k<sub>c</sub><sub>at</sub> must be larger than K<sub>M</sub>
B)k<sub>cat</sub> must be smaller than K<sub>M</sub>
C)k<sub>cat</sub> must be about equal to k<sub>1</sub>
D)k<sub>cat</sub> must be much smaller than k<sub>-1</sub>
E)k<sub>cat</sub> must be much larger than k<sub>-1</sub>
Q2) An enzymatic reaction has a V<sub>max</sub> of 100 \(\mu\)M/min.At a substrate concentration of 5 \(\mu\)M,the velocity is 25 \(\mu\)M/min.What is the K<sub>M</sub> for the reaction?
A)5 \(\mu\)M
B)10 \(\mu\)M
C)15 \(\mu\)M
D)20 \(\mu\)M
E)none of the above
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Q1) Of the following,which would have the most reduced state of carbon,and therefore,would yield the largest amount of energy per gram?
A)glucose
B)glycogen
C)alanine
D)stearic acid
E)all of the above would have identical energy yields
Q2) The phosphorylation of creatine (Cr)by ATP forming creatine phosphate (Cr-P)is rather endergonic (\(\Delta\)G°´ = + 12.6 kJ/mol).Which of the following explains how this reaction proceeds in a typical muscle cell?
A)in the cytosol,[ATP] is high and [Cr] is high allowing the reaction to proceed
B)in the mitochondria,[ATP] is high and [Cr-P] is low allowing the reaction to proceed
C)Cr-P is rapidly transported across the cellular membrane allowing for high levels of Cr-P in the cytosol
D)in the mitochondria,[ADP] is high allowing phosphorylation of Cr to occur
E)none of the above
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Q1) The conversion of phosphoenolpyruvate and ADP to pyruvate and ATP occurs in two distinct steps,first the transfer of the phosphate from PEP to ADP,then the conversion of enolpyruvate to pyruvate.Which of the following describes the reversibility of this process?
A)both steps are freely reversible
B)step 1 is freely reversible,step 2 is irreversible
C)step 1 is irreversible,step 2 is freely reversible
D)both steps are irreversible
E)the reversibility of the reaction depends completely upon the concentrations of products and reactants
Q2) Under conditions of strenuous exercise,gluconeogenesis occurs primarily in the _______ using _______ formed in the skeletal muscle
A)kidney;alanine
B)muscle;glycerol
C)liver;propionate
D)kidney;acetyl-CoA
E)liver;lactate
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Q1) Which of the following is an inhibitor of citrate synthase,isocitrate dehydrogenase,and \(\alpha\)-ketoglutarate dehydrogenase?
A)NADH
B)succinyl-CoA
C)ATP
D)acetyl-CoA
E)none of the above
Q2) __________ activates __________,thereby inhibiting pyruvate dehydrogenase.
A)NADH;pyruvate dehydrogenase phosphatase
B)Ca<sup>2+</sup>;pyruvate dehydrogenase phosphatase
C)NAD<sup>+</sup>;pyruvate dehydrogenase kinase
D)ATP;pyruvate dehydrogenase kinase
E)pyruvate;pyruvate dehydrogenase kinase
Q3) Which of the following is an equilibrium-controlled reaction of the citric acid cycle?
A)citrate synthase
B)isocitrate dehydrogenase
C)\(\alpha\)-ketoglutarate dehydrogenase
D)succinate dehydrogenase
E)all of the above
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Q1) Within the electron transport chain,complex _____ represents the entry point for electrons from NADH while complex _____ represents the entry point for electrons from FADH<sub>2</sub>.
A)I;III
B)II;III
C)I;II
D)II;I
E)IV;III
Q2) Which of the following pathways takes place primarily within the inner mitochondrial membrane?
A)fatty acid \(\beta\)-oxidation
B)electron transport
C)glycolysis
D)citric acid cycle
E)pentose phosphate pathway
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Q1) In the mechanism of Rubisco,what role does the Mg<sup>2+</sup> play?
A)neutralizes negative charges of active site Asp and Glu,enabling ionization of CO<sub>2</sub>
B)activates water molecule that hydrates the carboxy-\(\beta\)-keto intermediate C)complexes with the phosphate on C-1 to hold ribulose-1,5-bisphosphate in the active site
D)repels the product,3-phosphoglycerate,allowing it to leave the active site more rapidly E)none of the above
Q2) Which of the following acts as a corepressor for the transcription of chloroplast genes?
A)3-phosphoglycerate
B)fructose-1,6-bisphosphate
C)CO<sub>2</sub>
D)sucrose
E)none of the above
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Q1) What enzyme activities are found in the mitochondrial trifunctional protein that metabolizes long chain (LC)fatty acids?
A)LC-enoyl-CoA hydratase,LC-hydroxyacyl-CoA dehydrogenase,LC-thiolase
B)LC-acyl-CoA synthetase,LC-acyl-CoA dehydrogenase,LC-enoyl-CoA hydratase
C)LC-carnitine acyltransferase II,LC-acyl-CoA dehydrogenase,LC-enoyl-CoA hydratase
D)LC-acyl-CoA dehydrogenase,LC-enoyl-CoA hydratase,LC-hydroxyacyl-CoA dehydrogenase
E)LC-acyl-CoA dehydrogenase,LC-hydroxyacyl-CoA dehydrogenase,LC-thiolase
Q2) Which of the following lipoproteins distributes dietary lipids?
A)chylomicron
B)very low density lipoprotein
C)intermediate density lipoprotein
D)low density lipoprotein
E)high density lipoprotein
Q3) If gadoleic acid (20:1c\(\Delta\)9)underwent complete mitochondrial oxidation to CO<sub>2</sub>,how many ATP could be produced assuming that all reduced electron carriers are re-oxidized by the mitochondrial electron transport chain?
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Q1) Which of the following hormones is correctly described?
A)ghrelin: produced in pancreas,stimulates appetite
B)adiponectin: produced in adipose tissue,stimulates appetite
C)insulin: produced in pancreas,stimulates appetite
D)leptin: produced in intestines,suppresses appetite
E)none of the above
Q2) What process in the brain consumes most of the ATP that is produced?
A)movement of actin/myosin
B)maintenance of membrane potentials
C)active transport of glucose and amino acids
D)cellular growth
E)none of the above
Q3) For skeletal muscle,which of the following correctly pairs the activity state with the source of energy?
A)resting: glucose
B)resting: amino acids
C)exertion: glucose
D)exertion: fatty acids
E)none of the above

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Q1) Tay-Sachs disease is caused by a deficiency of __________ which results in an accumulation of ___________.
A)sphingomyelinase;sphingomyelin
B)ceramidase;ceramide
C)\(\alpha\)-galactosidase A;GM<sub>1</sub> ganglioside
D)lysosomal N-acetylhexosaminidase A;GM<sub>2</sub> ganglioside
E)\(\beta\)-glucosidase;glucosylceramide
Q2) The synthesis of phosphatidylethanolamine in prokaryotes involves _________________ while in mammals _______________ occurs.
A)reaction of CDP-diacylglycerol with ethanolamine;decarboxylation of phosphatidylserine
B)decarboxylation of phosphatidylserine;reaction of CDP-ethanolamine with diacylglycerol
C)reaction of phosphoethanolamine with diacylglycerol;reaction of CDP-ethanolamine with diacylglycerol
D)decarboxylation of phosphatidylserine;reaction of CDP-diacylglycerol with ethanolamine
E)reaction of CDP-diacylglycerol with ethanolamine;reaction of phosphoethanolamine with diacylglycerol
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Q1) Which of the following is an essential amino acid for humans?
A)alanine
B)serine
C)tyrosine
D)cysteine
E)histidine
Q2) Which of the following is seen in the transaminase mechanism?
A)aldimine formed between pyridoxal and lysine residue
B)Schiff base
C)pyridoxamine phosphate that reacts only with an \(\alpha\)-ketoacid
D)a carbanion that is resonance stabilized as a quinonoid intermediate
E)all of the above
Q3) Which of the following amino acids relies upon the synthesis of carbamoyl phosphate?
A)lysine
B)histidine
C)arginine
D)glutamine
E)asparagine

22
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Q1) Threonine is converted into acetyl-CoA and pyruvate while proline is converted into \(\alpha\)-ketoglutarate.Classify each of these amino acids.
A)threonine is ketogenic,proline is ketogenic
B)threonine is ketogenic and glucogenic,proline is ketogenic
C)threonine is ketogenic,proline is glucogenic
D)threonine is ketogenic and glucogenic,proline is glucogenic
E)none of the above
Q2) In the pathway for conversion of phenylalanine to fumarate and acetoacetate,there are two well-known enzyme defects that cause inheritable metabolic diseases.What are the names of these two diseases?
A)homocysteinuria and nonketotic hyperglycinemia
B)phenylketonuria and maple syrup urine disease
C)alkaptonuria and nonketotic hyperglycinemia
D)alkaptonuria and phenylketonuria
E)maple syrup urine disease and homocysteinuria
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Q1) Which of the following correctly explains the relationship between xanthine dehydrogenase (XDH)and xanthine oxidase (XO)?
A)in healthy tissue,XDH is abundant while XO is rarely found
B)conversion of XDH to XO occurs under conditions that damage cells
C)XDH is converted to XO by formation of a disulfide bond
D)XDH is converted to XO by proteolysis
E)all of the above
Q2) What molecule contributes at least two nitrogen atoms to each purine?
A)asparagine
B)10-formyltetrahydrofolate
C)glycine
D)glutamine
E)carbamoyl phosphate
Q3) Which of the following correctly describes the activity or regulation of E coli ribonucleotide reductase?
A)the overall activity of the enzyme is controlled by ATP and dATP
B)the specificity of the enzyme is controlled by all four dNTPs
C)a tyrosine free radical participates in the reaction
D)the reduction is not a result of simple hydride transfer
E)all of the above
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Q1) Which of the following pathways correctly shows how glycogen synthase is activated in response to the activation of IRS-1 by insulin binding?
A)IRS-1 causes activation of protein kinase B which phosphorylates glycogen synthase kinase thus preventing phosphorylation of glycogen synthase
B)IRS-1 activates a cascade that ultimately phosphorylates ERK which then binds to glycogen synthase
C)IRS-1 activates phosphoinositide 3-kinase and the resulting PIP<sub>3</sub> is an allosteric activator of glycogen synthase
D)IRS-1 activates guanylate cyclase and the resulting cGMP binds to glycogen synthase kinase thus preventing phosphorylation of glycogen synthase
E)none of the above
Q2) Insulin activates glycogen synthase while glucagon inhibits glycogen synthase.Explain the intracellular mechanisms that are used to bring about this activity.
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Q1) What term is used to describe a collection of cloned genomic fragments?
A)sequence
B)repository
C)fragmented genome
D)library
E)none of the above
Q2) The alteration in chromatin structure that occurs within the centromere is brought about by the replacement of which histone protein?
A)H1
B)H2A
C)H2B
D)H3
E)H4
Q3) The combination of histone proteins with DNA gives rise to what structure?
A)cohesins
B)telomeres
C)centromeres
D)nuclear scaffold
E)nucleosomes
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Q1) Which of the following is the best description for primase?
A)a DNA-dependent DNA polymerase
B)an RNA-dependent DNA polymerase
C)a DNA-dependent RNA polymerase
D)an RNA-dependent RNA polymerase
E)none of the above
Q2) Type I topoisomerases break _____ strand(s)of DNA;type II topoisomerases break _____strand(s)of DNA.DNA gyrase is a type ___ topoisomerase.
A)both;1;I
B)both;1;I.
C)both;1;III
D)1;both;I
E)1;both;II
Q3) Which of the following is required for DNA polymerase I activity?
A)3' hydroxyl group
B)ATP,GTP,TTP and CTP
C)Zn<sup>2+</sup>
D)an RNA template
E)all of the above
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Repair,recombination,rearrangement,amplification
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Q1) One mechanism to introduce greater diversity into antibody sequences is somatic hypermutation.What enzyme is responsible for somatic hypermutation in the DNA sequences that code for antibodies?
A)deoxyadenosine deaminase
B)deoxycytidine deaminase
C)deoxyadenosine transaminase
D)purine-pyrimidine transposase
E)none of the above
Q2) Which of the following types of DNA repair is often coupled with transcription?
A)photoreactivation
B)base excision repair
C)replication
D)nucleotide excision repair
E)all of the above
Q3) What is the causative agent in the formation of a cyclobutane thymine dimer?
A)benzo[a]pyrene
B)N-methyl-N'nitro-N-nitrosoguanidine
C)methylnitrosourea
D)ethylmethanesulfonate
E)ultraviolet radiation

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Q1) Which of the following events commonly occur in the processing of eukaryotic mRNA?
A)addition of a 5' cap
B)RNA editing
C)splicing to remove introns
D)alternative splicing to combine different exons into mature mRNA
E)all of the above
Q2) What is the mechanism by which enhancers,despite the fact that they are often several kilobase pairs away from the promoter,activate transcription?
A)DNA unwinding
B)DNA looping
C)chromatin remodeling
D)DNA hairpin formation
E)none of the above
Q3) Give the mRNA sequence that would result from the following sense strand: 5'-A-T-C-T-C-G-A-T-C-G-T-A-C-G-A-T-G-T-C-A-3'
Q4) Draw a transcription bubble,clearly labeling the proteins and nucleic acids involved in the process.
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Q1) What is the energy requirement for the formation of the 70S initiation complex?
A)1 GTP
B)1 ATP
C)1 GTP and 1 ATP
D)2 GTP (from hydrolysis of 1 GTP to GMP)
E)2 ATP (from hydrolysis of 1 ATP to AMP)
Q2) Which of the following explains how an aminoacyl-tRNA synthetase
(AARS)recognizes the correct tRNA?
A)the AARS always recognizes the anticodon
B)the AARS always recognizes elements of the acceptor stem
C)the AARS always recognizes the size and sequence in the variable loop
D)the AARS always recognizes elements in the D loop and T<sub>\(\varPsi\) </sub>C loop
E)the mechanism of AARS recognition varies from one enzyme to another
Q3) A repetitive mRNA of GAG could produce which of the following?
A)polyglutamate
B)polyleucine
C)polyleucine,polyserine,or polyproline
D)polyarginine,polyglycine or polyglutamate
E)none of the above

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Sample Questions
Q1) At the transcriptional level,how does tryptophan control the production of genes within the trp operon?
A)the trp repressor contains a high percentage of Trp residues and is thus only produced when Trp levels are high
B)without sufficient Trp,the production of the trp repressor is truncated,thus producing a protein that cannot bind to the operon,ultimately resulting in structural gene expression C)high levels of Trp cause the repressor to be proteolytically digested D)the trp repressor binds to the operon only when bound to Trp E)none of the above
Q2) Give the sequence and draw the first two residues of a morpholino oligo that would serve as an antisense RNA for the following mRNA sequence (you may use the letter A,C,G and U to denote the bases): 5'-CAUGUCC-3'
Q3) Show how glutamine interacts with an A-T base pair as seen in the cI and Cro repressors.
Q4) Design an antisense RNA that prevents the start of translation for any mRNA in an E.coli cell.
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