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BIOCHEMISTRY EXAM REVIEW
Part 1- MCQ:
- Which of the following amino acids is likely responsible for most transamination reactions in a cell? A. Glutamate. B. Glutamine. C. Aspartate. D. Alanine.
- The amino acid biosynthetic pathways that are missing in humans and thus lead to requirements for ' essential ' amino acids: A. Are for amino acids made from citric-acid-cycle intermediates. B. Are for amino acids made from glycolytic intermediates. C. Are for amino acids that are derived in whole or in part from erythrose-4- phosphate. D. Are for amino acids that are derived from a diverse group of metabolic intermediates.
- Which of the following compounds is phenylpyruvate?
- One of the amino groups of urea comes from carbamoyl phosphate; the other comes from aspartate. Both are ultimately derived from glutamate. How does the amino group make its way from glutamate to aspartate? A. Glutamate dehydrogenase generates a free amine from glutamate, and the free amine reacts with oxaloacetate to aspartate. B. Glutamate is converted to glutamine by glutamine synthase, and glutamine reacts with oxaloacetate to make aspartate. C. Glutamine and asparagine freely exchange amino groups, resulting in the production of aspartate. D. A transamination reaction between glutamate and oxaloacetate results in the production of aspartate.
- Nitric oxide is synthesized from which amino acid? A. Arginine B. Lysine. C. Histidine. D. Tryptophan.
- Ubiquitination of proteins occurs via: A. An amide bond with the epsilon -ε-amino group of lysine. B. An amide bond with the alpha amino group of a protein. C. An ester bond with the terminal carboxylate of a protein. D. An ester bond with the gamma carboxylate group of glutamate.
- Lesch-Nyhan syndrome can result from a deficiency in hypoxanthine- guanosine ribosyl transferase (HGPRTase) and a resultant buildup in: A. Urea. B. Adenosine. C. Guanosine. D. Uric Acid.
- One of the ultimate effects of the purine nucleotide cycle in muscle is to: A. Produce more AMP to increase the free energy of ATP hydrolysis. B. Convert GTP into ATP. C. Convert Aspartate into Fumarate for use in the Krebs cycle. D. Avoid the buildup of uric acid, which could deposit in joints.
- Which of the following compounds is a general inhibitor of deoxyribonucleotide biosynthesis? A. dATP. B. ATP. C. dTTP. D. UDP.
- The effect of GTP on the conversion of UTP to CTP is: A. To i ncrease the production of CTP. B. To decrease the production of CTP. C. There is no reason to believe that GTP should have an effect on the production of CTP. D. This question cannot be answered without also knowing the cellular level of ATP.
- The additional steps required for the biosynthesis of deoxyribonucleotides that are not present in the biosynthesis of ribonucleotides include: A. Reduction of the 2' position of ribose. B. Modification of the 6' position of adenosine. C. Modification of the 5' position of uridine. D. (a) and (b). E. (a) and (c).
- Which of the following nucleotides does not undergo a ring deamination during catabolism? A. GMP B. AMP C. CMP D. UMP.
- Which of the following substrates or cofactors is not used for the transfer or incorporation of an amino group during nucleotide biosynthesis? A. Aspartate. B. Glycine. C. Glutamine. D. Pyridoxal Phosphate.
- How many carbons are donated by Folate Cofactors in a DNA molecule? A. 2 for every purine. B. 2 for guanosine, 1 for adenosine, 1 for thymidine. C. 1 for every purine, 1 for thymidine. D. 2 for every purine, 1 for thymidine.
A. High carbohydrate, very low protein. B. Very high carbohydrate, no protein, no fat. C) Very high fat, high carbohydrate, no protein. D. Very high fat, very low protein. E. Very low carbohydrate, very high protein. 23 ． Serine or cysteine may enter the citric acid cycle as acetyl-CoA after conversion to: A. Oxaloacetate. B. Propionate. C. Pyruvate. D. Succinate. E. Succinyl-CoA. 24 ．The human genetic disease phenylketonuria (PKU) can result from: A. Deficiency of protein in the diet. B. Inability to catabolize ketone bodies. C. Inability to convert phenylalanine to tyrosine. D. Inability to synthesize phenylalanine. E. Production of enzymes containing no phenylalanine.
- One essential amino acid; A. Are amino acids other than those required for protein synthesis. B. Are not utilized in mammalian proteins. C. Are synthesized by plants and bacteria, but not by humans. D. Can be synthesized in humans as well as in bacteria. E. May be substituted with other amino acids in proteins.
- Glutamine, arginine, and proline: A. Do not have a common precursor. B. May all be derived from a Citric Acid Cycle Intermediate. C. May all be derived from a Cori cycle intermediate. D. May all be derived from a glycolytic intermediate. E. May all be derived from a Urea Cycle Intermediate.
- In which group are all the amino acids closely interrelated metabolically? A. Arginine, hydroxyproline, and histidine. B. Arginine, tyrosine, and glutamate. C. Glycine, valine, glutamine, and aspartate. D. Ornithine, alanine, glycine, and valine. E. Ornithine, proline, arginine, and glutamate.
- Which of the amino acids is an essential one for human body? A. Glutamate. B. Aspartate. C. Leucine. D. Glutamine.E. Asparagine. 29 ． Which type of chemical modifications usually happens for the last step targeting a protein to the proteosome degradation pathway?
A. Phosphorylation. B. Methylation. C. Acetylation. D. Ubiquitination. E. None of the above.
- Which of the following sets of enzymatic activities could be used to repair mutations in DNA due to cytidine deamination (section 20.7B)? A. Uracil N-glycosylase, AP endonuclease, DNA polymerase, and DNA ligase. B. Uracil N-glycosylase, proofreading activity of DNA polymerase, DNA polymerase, DNA ligase. C. DNA photolyase, AP endonuclease, DNA polymerase, DNA ligase. D. DNA photolyase, Uvr ABC endonuclease, DNA ligase.
- You are examining DNA replication in cells whose division has been synchronized. You grow the bacteria in the presence of radiolabeled nucleotides. You examine the cells after one round of replication and find: A. That only one out of every two cells is labeled. B. That most cells in the dividing culture are labeled equally. C. That most cells in the dividing culture are labeled, but one half contains more radioactivity than the other. D. That the majority of the cells in the dividing culture contain no radioactivity, while a few contain most of the radioactivity. E. That none of the cells are labeled.
- Which of the following types of enzymes may not be involved in excision- repair; A. DNA polymerase. B. RNA polymerase. C. DNA ligase D. Helicase. E. Exonuclease.
- The reaction catalyzed by DNA photolyase is an example of: A. Excision repair. B. Direct repair. C. Recombination repair. D. Replicative repair. E. Mismatch repair.
- Which of the following is not a mechanism for avoiding or correcting mutations? A. Recombination. B. Proofreading by DNA polymerases. C. Okazaki fragment synthesis. D. Discrimination between nucleotides during polymerization by DNA polymerases.
- Which of the following statements about DNA replication in prokaryotes is false? A. DNA synthesis proceeds along both strands at the same time. B. DNA synthesis proceeds in both directions from an origin
- Which is the carrier for transportation of acyl CoA into the mitochondria? A. Co-A B. Co-Q. C. Carnitine. D. ACP.
- Which enzyme help acyl CoA to be transported into the mitochondria? A. AcylCoA Synthetase B. HMG-CoA synthase C. carnitine acyltransferase D. Ketoacyl CoA transferase
- Which one is not products of the β-oxidation? A. FADH 2 B. NADH C. CO 2 D. acetyl CoA.
- Which one is the donor of two-carbon unit in fatty acid synthesis? A. CO 2 B. HCO 3 -^ C. Malonyl-CoA. D. acetyl CoA
- Which one is not derived from cholesterol? A. Steroid hormones. B Bile Salts. C. Eicosanoids. D vitamin D
- Which is the prosthetic group of Acetyl CoA Carboxylase? A FMN B FAD C biotin D vitamin B
- ETC exisits in; A cell membrane B the OM of mito. C the Inner Membrane of mito. D microsome
- Which one is not the components of the NADH pathway of ETC? A. FMN B. FAD C. Co-Q D. Fe-S E. Cyto c
- The main form of ATP production is; A phosphorylation of creatine. B oxidative phosphorylation C phosphorylation of glucose D substrate level phosphorylation
- 1 molecule of FADH 2 will produce (?) ATP through ECT; A 1 B 2 C 3 D 4 E 0
- Which enzyme donate electron to O 2? A PDH B succinate dehydragenase C cyto c oxidase D SOD
- About H+^ concentration in the intermembrane space, which one is right; A higher than matrix B lower than matrix C pass freely into matrix D actively transported into matrix
- Which metal ions take part in ETC; A Fe B Mg C Zn D. none
- Of the 4 complexes, which is not proton pump; A Ⅰ B Ⅱ C Ⅲ D Ⅳ
- Except iron, Cyt aa 3 contains (?) ion; A Zn B Mg C Cu D Ca
- The right electron transport sequence is; A b→c→c 1 →aa 3 →O 2 B c 1 →c→b→aa 3 →O 2 C c→c 1 →b→aa 3 →O 2 D c→b→c 1 →aa 3 →O 2 E b→c 1 →c→aa 3 →O 2
- About ATP Synthase, which are right? A. Embeded in IM，called complex V. B. Contain F 1 and F 0. C. F 0 is proton channel. D. ATP synthesis is on the β-subunit of F1. E. F 1 is hydrophobic, embedded in the IM.
- About Co-Q, which are right? A Hydrophilic. B Can diffuse freely in IM. C No component of ETC complex. D Converging point of NADH and FADH 2 etc.
- About cytochrome, which are right? A Contains Heme. B Has color. C Electron-carrier. D Inhibited by CN. E Chemically a protein.
- Which contain Fe-S as a prosthetic group in ETC? A Complex-Ⅰ B Complex-Ⅱ C Complex Ⅲ D Complex Ⅳ E Cyt c
- Where does the phosphorylation couple with the oxidation and can produce ATP? A. NADH→CoQ. B. CoQ→Cyt b. C. CoQ→Cyt c. D. FADH 2 →CoQ. E. Cyt aa 3 →O 2.
Part 3- Glossary Definition / Short Answer Questions: Lipid Mobilization; in adipose tissue TAGs are hydrolyzed to fatty acids plus glycerol. Or in places where there is fat, fatty acid is taken out from TAG. Ketone bodies; are water-soluble fuels normally produced and exported by the liver including acetoacetate , β-hydroxybutyrate , and acetone. Or, are molecules which can dissolve in water, and contain enough carbon-carbon bonds that break to give energy. They are produced in the liver. Electron Transport Chain; a series of enzyme complexes and associated cofactors that are electron carriers, passing electrons from reduced coenzymes or substrates to molecular oxygen (O 2 ), the terminal electron acceptor of aerobic metabolism. Or, the chain refers to the fact that there are a series of enzyme complexes (+ cofactors) which carry the electron from NADH and FADH 2 to molecular oxygen, and on the way getting redoxed. Oxidative phosphorylation; is a set of reactions in which compounds such as NADH and reduced ubiquinone (QH 2 ) are aerobically oxidized and ATP is generated from ADP and Pi. Oxidative phosphorylation consists of two tightly coupled phenomena:
- Oxidation of substrates by the respiratory electron-transport chain , accompanied by the translocation of protons across the inner mitochondria membrane to generate a proton concentration gradient.
- Formation of ATP, driven by the flux of proton into the matrix through a channel in F 0 F 1 ATP synthase. Or Is the reaction, powered by the oxidation of the ETC, which by building up a concentration gradient of H+^ in the intermembrane space of the mitochondria, ultimately leads to the phosphorylation of ADP with Pi through the ATP synthase. Chemiosmosis; the movement of protons from their high concentration in the inter-membrane space (IMS) to their low concentration inside the matrix. Chemiosmosis drives ATP synthesis. Proton-motive force; the movement of protons (proton-motive) creates enough energy to drive the ATP synthase. Phenylketonuria (PKU); an autosomal recessive metabolic genetic disorder characterized by a mutation in the gene for the hepatic enzyme phenylalanine hydroxylase (PAH), rendering it nonfunctional. This enzyme is necessary to metabolize the amino acid phenylalanine (Phe) to the amino acid tyrosine. Or a disease in which patients don’t have phenylalanine
hydroxylase and therefore cannot metabolize phenylalanine into tyrosine. A build-up of (PHE) is dangerous for the mental growth of a baby. This disease is considered to be an autosomal recessive metabolic genetic disorder. Albinism; A congenital disorder characterized by the complete or partial absence of pigment in the skin, hair and eyes due to absence or defect of an enzyme involved in the production of melanin. Alkaptonuria; ( Black Urine Disease ); a rare inherited genetic disorder of phenylalanine and tyrosine metabolism. This is an autosomal recessive condition that is due to a defect in the enzyme homogentisate 1,2- dioxygenase , which participates in the degradation of tyrosine. Or, similar to phenylketonuria, this is an autosomal recessive metabolic genetic disease that is one step after the metabolism of pheylalanine into tyrosine. In this disease, tyrosine cannot be degraded due to the absence of the enzyme homogentisate 1,2- dioxygenase. Transamination Reactions (amino-transfer); two chemical reactions between an amino acid and an alpha-keto acid accomplished by enzymes called transaminases. The amino group is transferred from the former to the latter; this results is the amino acid being converted to the corresponding α-keto acid. The reactant α-keto acid is converted to the corresponding amino acid. Or, any reaction in which the amino group of an amino acid is transferred with the help of a transaminase to an α-keto acid making the amino acid an alpha- keto acid and vice versa. Some examples are ALT (Alanine Aminotransferase), AST (Aspartate Aminotransferase), GPT (Glutamate Pyruvate Transaminase), and GOT (Glutamate Oxaloacetate Transaminase) which are important in the diagnoses of heart and liver damage caused by heart attack, drug toxicity, or infection. Urea Cycle; a metabolic cycle consisting of four enzyme-catalyzed reactions that converts nitrogen from ammonia and aspartate, into urea. Four ATP equivalents are consumed during formation of one molecule of urea;
Semi-Continuous (or discontinuos) Replication a.k.a Okazaki Fragments; during the process of DNA replication, the new strands of DNA must be made in a 5' to 3' direction. For one strand (the leading strand ), this is fine and the process occurs in a straight line continuously. However, the second strand (the lagging strand ) must be done is small sections as the direction of replication must still be 5' to 3'. Thus, you get these fragments of DNA called okazaki fragments. These are then later joined together using the enzyme DNA ligase, forming a complete new strand of DNA. Okazaki Fragment; Relatively short single-stranded DNA are produced during discontinuous synthesis of the lagging strand during DNA replication. Replicon; a DNA molecule or RNA molecule, or a region of DNA or RNA, that replicates from a single origin of replication. L eading Strand; the leading strand template is the strand of DNA being replicated continuously or being continuously polymerized towards the replication fork. A polymerase "reads" the template DNA and continuously adds nucleotides to the 3' end of the elongating strand. This polymerase is DNA polymerase III (DNA Pol III) in prokaryotes and presumably Pol ε in eukaryotes. Lagging Strand; The lagging strand grows in the direction opposite to the movement of the growing fork. It grows away from the replication fork and it is synthesized discontinuously. Homologous Recombination; A type of genetic recombination in which nucleotide sequences are exchanged between two similar molecules of DNA.
Site-Specific Recombination; A type of genetic recombination in which DNA strand exchange takes place between segments possessing only a limited degree of sequence homology. Transposition; a mutation in which a chromosomal segment is transferred to a new position on the same or another chromosome. Point Mutation; a type of mutation that causes the replacement of a single base nucleotide with another nucleotide of the genetic material - DNA or RNA -including insertions or deletions of a single base pair. Transition and Transversion; -Transitions : replacement of a purine base with another purine or replacement of a pyrimidine with another pyrimidine. -Transversions : replacement of a purine with a pyrimidine or vice versa. Silent / Missense / Nonsense Mutation; Silent (synonymous change) - A silent mutation has no effect on the functioning of the genome. A single nucleotide can change, but the new codon specifies the same amino acid resulting in an unmutated codon. OR point mutation leads to no change in phenotype because resulting amino acid is the same. Missense (non-synonymous) - A missense mutation changes a codon so that a different protein is created, a change. At times a change to one amino acid in the protein is not detrimental to the organism as a whole. Nonsense - A nonsense mutation converts an amino acid codon into a termination codon. This causes the protein to be shortened because of the stop codon interrupting it's normal code. Frameshift; a genetic mutation caused by indels (insertions or deletions) of a number of nucleotides that is not evenly divisible by three from a DNA sequence, due to the triplet nature of gene expression by codons. Excision-Repair Pathway; repairs bulky helix-distorting lesions. Base Excision Repair (BER) is important for removing damaged bases that could otherwise cause mutations by mispairing or lead to breaks in DNA during replication.
Promoter; the regions of DNA that serve as sites of transcription initiation. Operon; In bacteria, a transcription unit (several genes are often co- transcribed from a single promoter in bacteria). The Direction of Transcription; see long question answer 4. TATA box, -35region; an A/T-rich region, also called a TATA box, is located 19 to 27 bp upstream of the transcription start site and is the site where RNA polymerase II binds to DNA during assembly of the initiation complex. Termination Sequence; Transcription complex disassemble at the 3’ end of genes at specific sequences called termination sequences. Rho Factor Functions; It can bind single-strand RNA. It has activity of ATPase and helicases. It may denature short RNA-DNA hybrid double strands. 3 types of Eukaryotic RNA polymerases and their Functions; Repressor; prevents the transcription. Activator; activates the transcription. Inducer; ligands that bind to and inactivate repressors. Co-repressor; ligands that bind to and activate repressors. The Mechanism of Lactose Operon (lac operon) Regulation; Three genes
form an operon that is transcribed from a single promoter to produce a large mRNA molecule containing three separate protein-coding regions. Lac Y: lactose permease , transport the galactoside into plasma. Lac Z: galactosidase , hydrolyze galactoside. Lac A: thiogalactoside transacetylase , acetylate galactoside. In other words, organization of the genes that encode proteins required to metabolize lactose. The coding regions for three proteins—lacZ, lacY, and lacA— constitute the lac operon and are co-transcribed from a single promoter ( Plac ). The gene that encodes lac repressor, lacI , is located upstream of the lac operon and has its own promoter, P. lac repressor binds to the operators O1 and O2 near Plac .t denotes the transcription termination sequence. RNA Processing; the reactions that transform a primary RNA transcript into a mature RNA molecule. The steps involved are removal of nucleotides from primary RNA transcripts, addition of nucleotide with sequences not encoded by the corresponding genes, and covalent modification of certain bases. Eukaryotic mRNA Processing; the primary mRNA transcript is translated directly, often beginning before transcription is complete in prokaryotes. *Mature eukaryotic mRNA molecules are often derived from much lager primary transcripts *mRNA is processed in the nucleus in eukaryotic cells. 5’ Capping and 3’ Polyadenylation; Capping is carried out in the nucleus before splicing and relates with protein translation. It can protect mRNA 5’- terminal from nuclease.
In other words, the function of subunits of RNA polymerase in E. coli; α-determines which genes are transcribed. β-catalytic site. β’:binds DNA template. σ-recognizes transcription initiation site. Difference Between RNA polymerase and DNA polymerase; RNA polymerase synthesizes RNA, but does not need a primer to initiate synthesis. DNA polymerase synthesizes DNA, but needs a primer in order to initiate synthesis. (Terms from Chapter-22) Translation; it is the process of encoding the genetic information contained in messenger RNA (mRNA) into proteins. Protein synthesis falls into three stages;
- initiation -the assembly of a ribosome on an mRNA molecule.
- elongation -repeated cycles of amino acid addition.
- termination -the release of the new protein chain. Codon; The protein-coding region of the mRNA consists of an ordered series of 3-nt-long units called codons that specify the order of amino acids. Reading Frame; any of the three possible ways of reading a sequence of nucleotides as a series of triplets. Signal peptide; The N-terminal sequence of residues that signals the protein to cross a membrane. SRP; a protein-RNA complex, recognizes and binds to the signal peptides. Glycosylation; add oligosaccharide chains to proteins. P site and A site; Ribosomes contain two aminoacyl-tRNA binding sites; P site: holds peptidyl-tRNA , and A site holds a new aminoacyl-tRNA. Prominent Features of Standard Genetic Code; The standard genetic code is composed of 64 triplet codons. The left-hand column indicates the nucleotide found at the first (5') position of the codon; the top row indicates the nucleotide found at the second (middle) position of the codon; and the right column indicates the nucleotide found at the third (3') position of the codon. The codon AUG specifies methionine (Met) and is also used to initiate protein synthesis. STOP indicates a termination codon.
How to recognize the start codon in prokaryotes and in eukaryotes respectively? Three codons, UAA, UAG, and UGA signify chain termination. The methionine codon, AUG is called the initiation codon. How many phosphoanhydride bonds need to be broken for adding one amino acid during translation? For each amino acid four phosphoanhydride bonds are broken- ATP is hydrolyzed to AMP+2Pi, two GTP are hydrolyzed to 2GDP+2Pi. Aminoacylation of tRNA; Amino acids should attach to tRNA first before adding to polypeptide chain. Aminoacylation of tRNA is a particular amino acid that is covalently attached to the 3’ end of each tRNA molecule. The product is called aminoacyl-tRNA , an energy-rich molecule. Aminoacyl tRNA synthetases Reaction and Steps; A. Aminoacyl tRNA Synthetases Reaction- The overall reaction of the activation of an amino acid is: Amino acid + tRNA + ATP -> Aminoacyl-tRNA+AMP+PPi B. Reaction steps: First, the aminoacyl-tRNA synthetase attaches AMP to the-COOH group of the amino acid utilizing ATP to create an aminoacyl adenylate intermediate. Then, the appropriate tRNA displaces the AMP. Proofreading Activity of Aminoacyl-tRNA Synthetases; Aminoacyl-tRNA formation is very accurate with it’s selection of the correct amino acid. Some enzymes have editing pocket to do proofreading by matching the wrong product and hydrolyzing it. (Terms & Questions from Chapter 23) Recombinant DNA technology; Methods for isolating, manipulating and amplifying identifiable sequences of DNA to study the structure and function of individual genes. Cloning; DNA cloning is to place a gene of interest into a vector and form a recombinant DNA which can be replicated independently of the original genome and normally in other host species. Vector and its Features; A vector is a virus or other agent that is used to deliver DNA to a cell. General features of a vector are that it can- a. Autonomously replicate DNA independent of host’s genome.
