
Course Introduction
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Course Introduction
Biological Chemistry is an interdisciplinary course that explores the chemical principles underlying biological processes and systems. Students will examine the structure and function of biomolecules such as proteins, nucleic acids, carbohydrates, and lipids, as well as the mechanisms of enzyme action and regulation. The course integrates fundamental concepts from general and organic chemistry to explain metabolic pathways, bioenergetics, and molecular signaling in living organisms. Emphasis is placed on understanding how chemical interactions and reactions drive cellular processes, providing a foundation for studies in biochemistry, molecular biology, and related biomedical fields.
Recommended Textbook
Biochemistry 1st Canadian Edition by Reginald Garrett
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Q1) Which of the following is NOT a specialized structure of the internal membrane of eukaryotic cells?
A)nucleus
B)endoplasmic reticulum
C)ribosome
D)mitochondrion
Answer: C
Q2) Which of the following is the sequence for making complex biomolecules from the following major precursors?
A)metabolites,building blocks,macromolecules,supramolecular complexes
B)macromolecules,building blocks,metabolites,supramolecular complexes
C)building blocks,macromolecules,supramolecular complexes,metabolites
D)supramolecular complexes,metabolites,macromolecules,building blocks
Answer: A
Q3) Which of the following is NOT correct regarding prion diseases?
A)They include atherosclerosis.
B)They are genetic and infectious.
C)Their occurrence may be sporadic.
D)They are dominantly inherited.
Answer: A

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Q1) Which of the following is the purpose of the physiological mechanism of hyperventilation?
A)to lower [CO (g)] in the blood and increase blood pH
B)to raise [CO (g)] in the blood and increase blood pH
C)to lower [CO (g)] in the blood and decrease blood pH
D)to raise [CO (g)] in the blood and decrease blood pH
Answer: A
Q2) The enzyme fumarase has a pH optimum of about 7.6.Which of the following would be the buffer of choice to study this enzyme?
A)tris-hydroxymethyl aminomethane (K<sub>a</sub> = 8.32 × 10<sup>-9</sup>,pK<sub>a</sub> = 8.07)
B)lactic acid (K<sub>a</sub> = 1.38 × 10<sup>-4</sup>,pK<sub>a</sub> = 3.86)
C)bicarbonate (K<sub>a </sub>= 6.3 × 10<sup>-11</sup>,pK<sub>a </sub>= 10.24)
D)acetic acid (K<sub>a</sub> = 1.74 × 10<sup>-5</sup>,pK<sub>a</sub> = 4.76)
Answer: A
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Q1) Which statement best explains the large G° for the hydrolysis of phosphoenolpyruvate?
A)hydrolysis of the phosphoanhydride bond along with the conversion of the enol to the keto form of pyruvate
B)the hydrolysis of the phosphoanhydride bond
C)conversion from the enol to the keto form of pyruvate
D)strong bond energy along with a change in the stereochemistry of the molecule
Answer: A
Q2) Which thermodynamic property of a biochemical process is measured by calorimetry?
A)heat absorbed or given off,?H
B)overall change in ?G°
C)entropy change,?S
D)volume change,?V
Answer: A
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Q1) Which of the following does <b>NOT</b> react with the -SH group on cysteine?
A)N-ethylmaleimide
B)benzaldehyde
C)acrylonitrile
D)iodoacetate
Q2) Which of the following amino acids has more than 1 chiral carbon?
A)serine
B)lysine
C)threonine
D)cysteine
Q3) At what pH is the cysteine side-chain sulfhydryl group 11% dissociated if its pK value is 8.32?
A)3.2
B)7.4
C)8.5
D)10.2
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Q1) Which of these atoms would be found in the amide plane of the peptide backbone?
A)H bound to the amide nitrogen
B)side chain carbons
C)C<sub> </sub>-carbon
D)O bound to the carbonyl carbon
Q2) Suppose a protein is treated with trypsin.Which of the following techniques could be used to determine its identity by peptide mass fingerprinting?
A)NMR
B)MALDI-TOF mass spectrometry
C)HPLC
D)gel electrophoresis
Q3) Which of the following is a characteristic of all molecules of a given protein?
A)a variable amino acid composition
B)a random amino acid sequence
C)a nucleotide sequence from which they are encoded
D)an amino acid sequence read from C-terminal end to N-terminal end
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Q1) Which characteristic of a peptide contains all the information necessary for folding the peptide chain into its "native" structure?
A)its amino acid sequence
B)its amino acid composition
C)its configuration
D)its amino acid side chain charges
Q2) Which of the following does NOT determine secondary and higher orders of structure?
A)hydrophobic interactions
B)hydrogen bonds
C)van der Waals forces
D)peptide bonds
Q3) How are the parallel -sheets in a -barrel connected?
A)by regions of -helix
B)by -turns
C)by electrostatic interactions
D)by disulfide bonds
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Q1) Which of the following compounds has a glycosidic bond?
A) -D-galactosamine
B)methyl- -D-glucoside
C) -D-glucose-6-phosphate
D) -D-fructose-1,6-bisphosphate
Q2) Which of the following are important components of the vitreous humour of the eye and of synovial fluid that lubricates the joints?
A)heparins
B)hyaluronates
C)chondroitins
D)keratin sulfates
Q3) Which of the following disaccharides is NOT a reducing sugar?
A)lactose
B)maltose
C)sucrose
D)cellulose
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Q1) Which of the following products are generated when triacylglycerols undergo saponification?
A)fatty acid and glycerol
B)fatty alcohols and fatty acids
C)salts of fatty acids and fatty alcohols
D)salts of fatty acids and glycerol
Q2) Why are lipids the biomolecules of choice for storage of metabolic energy?
A)They are soluble in water.
B)They yield a large amount of energy upon oxidation.
C)They are highly oxidized.
D)They are easily hydrolyzed and therefore offer quick energy yield.
Q3) Which of the following would contain the largest amount of fatty acids with trans double bonds?
A)the fatty acid on carbon #1 of the glycerol of phosphatidylcholine
B)butter
C)canola oil
D)a 900 gram package of cookies containing partially hydrogenated cottonseed
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Q1) Which of the following is correctly paired with its precursor?
A)cholesterol palmitic acid
B)arachidonic acid prostaglandins
C)testosterone progesterone
D)aldosterone cholic acid
Q2) What is the major circulatory complex for cholesterol and cholesterol esters ("bad cholesterol")?
A)chylomicron
B)HDL
C)LDL
D)VLDL
Q3) Which lipoprotein has the highest density?
A)chylomicrons
B)HDL
C)LDL
D)VLDL
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Q1) In the Na ,K -ATPase mechanism,which of the following processes does NOT involve ATP?
A)binding E2 to change conformation to E1 and release of K
B)binding E<sub>1</sub> to facilitate binding of Na+
C)transferring a phosphate group to make sodium phosphate
D)hydrolysis to ADP and E<sub>1</sub>-P
Q2) Which of the following describes the energy and transport systems,respectively,associated with passive diffusion?
A)kinetically favoured;using a transport protein
B)kinetically favoured;without a specific transport system/molecule
C)thermodynamically favoured;using a transport protein
D)thermodynamically favoured;without a specific transport system/molecule
Q3) Which of the following terms represent 12-TMS?
A)12-trans-methyl synthase
B)12-tris-methyl sulfate
C)12-trans-model symmetry
D)12-transmembrane segments
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Q1) Which of the following regarding hormones is correct?
A)Progesterone is a polypeptide hormone.
B)Epinephrine is an amino acid.
C)Steroid hormones can enter cells and regulate translation.
D)Insulin is a polypeptide hormone.
Q2) Which of the following second messengers is produced from the hydrolysis of PIP that activates the increase of Ca² concentrations in the cytoplasm?
A)diacylglycerol (DAG)
B)phosphatidylinositol (PI)
C)phosphatidylinositol-4,5-bisphosphate (PIP<sub>2</sub>)
D)inositol-1,4,5-trisphosphate (IP<sub>3</sub>)
Q3) Calcium-binding proteins all possess 2 or more characteristic peptide domains for Ca² binding that consist of a short a-helix,a loop of 12 amino acids,and a second a-helix (helix-loop-helix).Which of the following motifs best describes these peptide domains?
A)basic region leucine zipper
B)zinc finger
C)EF hand
D)beta-beta
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Q1) Which of the following is NOT correct regarding the transition state of a reaction?
A)The transition state is located at the height of a free energy diagram.
B)The transition state,once reached,indicates that there is a high probability that the reaction will occur.
C)The energy required to raise the average energy of one mole of reactant to the transition state is the free energy of activation.
D)The transition state energy level is the sum of the energy levels of the reactants and products.
Q2) What type of enzyme inactivator is penicillin an example of?
A)competitive inhibitor
B)non-competitive inhibitor
C)suicide substrate
D)uncompetitive inhibitor
Q3) How do enzymes work?
A)by providing an alternate reaction pathway
B)by increasing the spontaneity ( G)of the reaction
C)by lowering the activation energy of the reaction
D)by altering the concentration of the reactants to achieve a favourable G
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Q1) Which of the following pairs below forms a low-barrier hydrogen bond?
A)Asp<sup>102 </sup>and Ser<sup>195</sup>
B)Asp<sup>102</sup> and His<sup>57</sup>
C)His<sup>57</sup> and Ser<sup>195</sup>
D)Ser<sup>195</sup> and carbonyl oxygen in the peptide bond
Q2) Which of the following structures has the greatest complementarity to enzyme active sites?
A)substrate
B)transition state
C)product
D)stable intermediate
Q3) How does HIV-1 protease differ from most mammalian aspartic acid proteases?
A)It has 2 subunits,each with a 2-aspartate active site.
B)It has 2 subunits,each contributing an aspartate to the active site.
C)It has 2 active sites on 1 protein.
D)It has 2 subunits,1 with an active site and the other with a regulatory activity.
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Q1) Which of the following mechanisms explains how carbon dioxide affects O binding to Hb?
A)by directly binding to heme-Fe in the oxygen binding site
B)by forming iron carbonate with the heme-iron
C)by forming HCO -,which combines with H to increase CO binding
D)by forming H + HCO -,where the H is an antagonist to oxygen binding to Hb
Q2) The PDH complex is allosterically activated and inhibited by multiple modes.Which of the following is a correct relation?
A)acetyl-CoA: activation
B)NAD : inhibition
C)NADH: activation
D)CoA-SH: activation
Q3) When O binds,which of the following components of the heme group is drawn into the plane of the porphyrin,causing a conformational change that is transmitted to adjacent subunits,enhancing the affinity for additional O binding?
A)Mg
B)CO
C)His
D)Fe
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Q1) Which of the following does NOT affect microtubule polymerization and is NOT used in cancer chemotherapy?
A)taxol
B)colchicine
C)vinblastine
D)vincristine
Q2) Which component(s)of the 6 polypeptides that make up the thick filament contain(s)the ATPase activity?
A)LC1
B)LC2
C)myosin heavy chains
D)essential light chains
Q3) How does intracellular movement of organelles in axons occur?
A)through axoneme motion through ATP-driven walking of dyneins along microtubules
B)through formation of ring-like structures around tubulin to move organelles
C)through progressive movement along DNA strands
D)through kinesin-mediated ATPase-driven movement along microtubules
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Q1) Which of the following statements defines an amphibolic pathway?
A)a pathway found in animals living in both land and water
B)a pathway that is carried out in both water and organic solvents
C)a pathway found on both sides of the mitochondrial membrane
D)a pathway that is both anabolic and catabolic in nature
Q2) Which of the following is higher in thioesters than in oxygen esters?
A)electronegativity
B)resonance
C)group transfer potential
D)positive G
Q3) Which of the following is NOT a dietary fibre?
A)maltose
B)pectin
C)cellulose
D)lignin
Q4) Which of the following lifeforms is NOT a chemoheterotroph?
A)Staphylococci aureus
B)fungus
C)alga
D)animal

18
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Q1) Which of the following characteristics applies to Class I aldolases?
A)an enediol intermediate
B)a requirement for biotin
C)a Schiff base intermediate
D)coenzyme requirement for thiamine pyrophosphate (TPP)
Q2) Which enzyme is NOT involved in the first 5 steps of glycolysis?
A)phosphofructokinase-1 (PFK-1)
B)phosphoglycerate kinase
C)fructose bisphosphate aldolase
D)triose phosphate isomerase (TPI)
Q3) Which of the of the following covalent modifications does cAMP-dependent protein kinase carry out on pyruvate kinase?
A)carboxylation
B)phosphorolysis
C)phosphorylation
D)decarboxylation
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Q1) Where do glycolysis and the TCA cycle,respectively,occur in eukaryotic cells?
A)cytoplasm;mitochondria
B)mitochondria;mitochondria
C)cytoplasm;cytoplasm
D)mitochondria;ribosomes
Q2) Which molecule is generated between succinyl-CoA and ATP in mammals to "preserve" the energy of the thioester bond?
A)a-ketoglutarate
B)phosphohistidine
C)citrate
D)acetyl-CoA
Q3) Which of the following statements is NOT correct about the reaction catalyzed by the pyruvate dehydrogenase complex?
A)It is the link between glycolysis and the TCA cycle.
B)The activity of the complex is regulated by the phosphorylation of the pyruvate dehydrogenase complex.
C)NAD is the direct oxidant of reduced lipoamide.
D)An FAD is covalently linked to the EDLD,the lipoamide dehydrogenase component.
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Q1) Which of the following is another term used to define Complex II in the electron-transport chain?
A)cytochrome c oxidase
B)NADH-CoQ reductase
C)succinate-CoQ reductase
D)cytochrome b<sub>c1 </sub>complex
Q2) Which of the following is a mobile electron carrier?
A)UQ
B)[FMN]
C)Complex I
D)Complex III
Q3) Which of the following is a property of uncouplers?
A)They enhance the proton gradient.
B)Electron transport continues.
C)ATP/ADP ratio increases.
D)Water is produced.
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Q1) Which of the following is a characteristic of CAM plants?
A)CO is fixed by rubisco during the night.
B)The stomata are closed during the night and open during the day.
C)They try to avoid loss of water by condensation.
D)During the night,dicarboxylic acid is stored within the vacuoles.
Q2) Light-dependent electron flow with the production of ATP can occur without the formation of NADPH.Which of the following photosystems is involved in this cyclic photophosphorylation?
A)P700
B)photosystem II
C)P680
D)ferredoxin
Q3) Which of the following is a property of both the P700 and the P680 reaction centres?
A)involved in light-driven O evolution
B)contain chlorophyll monomers
C)electron acceptors
D)activated by visible light
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Q1) Which of the following enzymes is NOT unique to gluconeogenesis?
A)phosphoglucoisomerase
B)glucose-6-phosphatase
C)fructose-1,6-bisphosphatase
D)PEP carboxykinase
Q2) The polyol pathway is a suspected pathway for diabetes-induced cataract formation.Which enzyme does it involve?
A)aldose reductase
B)glucose-6-phosphate dehydrogenase
C)phosphopentose isomerase
D)transaldolase
Q3) What does the enzyme transketolase catalyze?
A)transfers of 3-carbon units from a ketose to an aldose
B)transfer of ketoses into aldoses
C)TPP-dependent transfer of 2-carbon units to the recipient aldose
D)keto-group transfer from C-2 to C-3
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Q1) In ketone body biosynthesis,the HMG-CoA lyase reaction is mechanistically the reverse of the first half of the reaction catalyzed by a particular TCA enzyme.Which of the following TCA enzymes does it resemble?
A)aconitase
B)citrate synthase
C)malate dehydrogenase
D)succinyl-CoA synthase
Q2) Which of the following hormones does NOT cause fatty acid mobilization in adipose cells?
A)ACTH (adrenocorticotropic hormone)
B)glucagon
C)insulin
D)epinephrine (adrenaline)
Q3) Which of the following lipid components are produced in the duodenum by the enzyme pancreatic lipase during lipid digestion?
A)diacylglycerols and fatty acids
B)fatty acids and glycerol
C)triacylglycerols and glycerol
D)monoacylglycerols and fatty acids
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Q1) Which of the following products is formed from the glutamate synthase-catalyzed reaction?
A)glutamate
B)a-ketoglutarate
C)NADPH
D)N-acetylglutamate
Q2) Which of the following explains why bacterial glutamine synthetase monomers are inactive?
A)They must be phosphorylated for activity.
B)They must be activated by binding glutamine.
C)They must be stacked for interface active site development.
D)They must be combined for allosteric regulation.
Q3) Which of the following amino acid's carbon and nitrogen atoms are all used in the biosynthesis of ornithine?
A)proline
B)valine
C)alanine
D)glutamate
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Q1) Which is of the following is NOT correct for purines and pyrimidines?
A)They are aliphatic.
B)They are nitrogenous bases.
C)They exhibit strong UV absorption.
D)They are capable of keto-enol tautomerization.
Q2) What type of bond links the nitrogenous base to the nucleotide sugar?
A) -anhydride
B) -N-amide
C) -N-acetyl (glycosidic)
D) -N-hemiacetal
Q3) With which of these ions do nucleotide triphosphates and nucleotide diphosphates often form stable complexes?
A)Na
B)Fe<sup>3 </sup>
C)K
D)Mg²
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Q1) Sequencing nucleic acids is now easier than sequencing polypeptides.Which of the following developed technologies facilitates this?
A)restriction endonucleases and polyacrylamide gel electrophoresis
B)base-specific chemical cleavage and autoradiography
C)cytosine methylation and base-specific chemical cleavage
D)double-helix denaturation and restriction endonucleases
Q2) Which of the following statements is NOT correct regarding the linking number?
A)It is a basic parameter characterizing supercoiled DNA.
B)L = T + W.
C)It is the number of times that 2 strands are intertwined,providing both strands remain covalently intact.
D)L = 40 in a relaxed circular DNA duplex of 400 bp.
Q3) Which of the following terms defines the process that occurs when ssDNA reassociates with other ssDNA?
A)diffusion
B)reannealing
C)melting
D)solidifying
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Q1) Which of the following types of bonds is formed in purine biosynthesis when glycine adds to 5-phosphoribosyl- -amine?
A)glycosidic
B)anhydride
C)amine
D)thioester
Q2) Which of the following regarding nucleotides is correct?
A)Uridine nucleotide derivatives of carbohydrates are common intermediates in cellular transformation of carbohydrates.
B)The nitrogenous bases serve as energy sources.
C)Many coenzymes are derivatives of amino acids.
D)They are produced only in eukaroytes.
Q3) Which of the following mechanisms explains how thymidylate synthase synthesizes dTMP from dUMP?
A)by methylation utilizing the coenzyme biotin
B)by carboxylation utilizing the coenzyme THF
C)by phosphorylation utilizing the coenzyme ATP
D)by reduction utilizing the coenzyme ATP
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Q1) How are hybrid proteins or fusion proteins produced?
A)by incubation of 2 proteins with a protease
B)by expression of genes coding for multiple proteins
C)by translation of mRNAs without removing exons
D)by translation of recombinant sequences from expression vectors carrying cDNA inserts cloned directly into the coding sequence of a vector-born protein-coding gene
Q2) Which of the following is a method used to insert or transform cells with a plasmid?
A)add the DNA to bacterial cells that have been lightly treated with lysozyme to produce "holes" in the cell wall
B)add the DNA to a heated suspension of cells at 42°C
C)treat the bacteria with Ca² ,add the DNA,and briefly heat to 42°C
D)incubate the DNA with the cells overnight at 4°C
Q3) Which in vitro process makes it possible to systematically alter the nucleotide sequence of a cloned gene?
A)protein synthesis
B)mRNA synthesis
C)hybridization
D)mutagenesis
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Q1) Which of the following is a property of DNA polymerase III?
A)It is responsible for incorporating most of the nucleotides in the leading strand.
B)It is a large protein complex containing more than 5 subunits.
C)It synthesizes most of the leading strand prior to aiding in the synthesis of the lagging strand.
D)It has lesser processivity than DNA polymerase I.
Q2) Which of the following is an RNA-dependent DNA polymerase that carries the RNA template with it to synthesize repeats at the 3'-ends of chromosomes?
A)DNA ligase
B)telomerase
C)topoisomerase
D)DNA polymerase (beta)
Q3) Which of the following mutations can occur when the thymine analog,5-bromouracil,incorporates into DNA normally occupied by thymine?
A)T-A to A-T
B)G-C to C-G
C)U-A to A-U
D)C-G to T-A
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Q1) The non-template strand has the same nucleotide sequence and direction as that of the RNA transcript.Which of the following parts of the mRNA encodes the N-terminus of the protein?
A)non-reducing end
B)reducing end
C)3'-end
D)5'-end
Q2) Which of the following terms defines the huge multi-subunit entities that mediate ATP-dependent conformational changes that peel 50 bp of DNA from the edge of nucleosome core particles,and create a "bulge" in the DNA:core nucleosomes association?
A)histone deacetylase complexes
B)DNA-bound transcriptional activators
C)chromatin-remodelling complexes
D)general transcriptional factors
Q3) Which of the following is NOT a stage in transcription?
A)binding of RNA polymerase holoenzyme at the promoter sites
B)chain elongation
C)DNase I activity on RNA polymerase/DNA complex
D)initiation of polymerization

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Q1) Which of the following is NOT a component required for peptide chain initiation?
A)DNA
B)30S and 50S ribosomal subunits
C)initiation factors
D)GTP and f-Met-tRNAi<sup>fMet</sup>
Q2) Which of the following is NOT classified as a GTP-binding protein?
A)30S rRNA
B)EF-Tu
C)EF-G
D)RF-3
Q3) Which of the following is NOT a feature of the tRNA molecule with the anticodon 5'CAU?
A)It is the anticodon for tRNA<sub>fmet</sub>.
B)The wobble base in the anticodon would be cytosine.
C)Its anticodon can theoretically base pair with up to 3 different codons.
D)Its anticodon can base pair to the codon 5'AUG.
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Q1) Which of the following do miRNAs binds?
A)GREs
B)seed elements
C)AREs
D)core promoters
Q2) Which of the following is a characteristic of non-stop decay (NSD)?
A)It is used to accumulate mRNAs devoid of a stop codon.
B)Stalling of the ribosome at the 5'-end of the transcript recruits the cytoplasmic exosome.
C)The exosome has a number of 5' 3' exonucleases
D)Decay proceeds without the need for deadenylation and decapping.
Q3) Which of the following is a feature of oncoprotein mRNA?
A)The AMD extends the mRNA lifetime of the proto-oncogene.
B)It contains a 3' translated region (3'UTR)rich in A and U elements.
C)It is highly stable.
D)Its decay pathway is through AU-rich mediated decay (AMD).
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Q1) In which of the following macromolecular structures is protein degradation compartmentalized?
A)ribosomes and endoplasmic reticulum
B)ribosomes and Golgi
C)proteasomes and mitochondria
D)proteasomes and lysosomes
Q2) Which of the following is NOT a characteristic of the mammalian translocon?
A)It has Sec61 complex at the core.
B)It is a transmembrane,protein-conducting channel.
C)BiP carries out ATP-dependent protein folding.
D)It is composed of a single transmembrane-spanning (TMS)protein.
Q3) Which of the following pairs forms a common conduit for transfer of the nascent protein through the endoplasmic reticulum membrane?
A)ribosome and translocon
B)signal sequence and plasma membrane
C)EF-G and endoplasmic reticulum
D)chaperonin and plasma membrane
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Q1) Which regulatory enzyme shows greater activity at low energy charge in an energy-producing pathway?
A)hemoglobin
B)phospholipase C
C)PKA
D)PFK-1
Q2) Which of the following is NOT a fuel for contracting muscles during strictly anaerobic metabolism?
A)palmitic acid
B)creatine phosphate
C)glycogen
D)glucose
Q3) Which of the following is NOT a characteristic of brain tissue?
A)Brain tissue is 20% or so of body mass.
B)Twenty percent of oxygen is consumed by the brain.
C)Oxygen consumption is independent of mental activity.
D)Brain tissue has no significant fuel reserves.
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