final exam questions.docx

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Department
Biology
Course
BIOLOGY 285
Professor
Dan Chase
Semester
Fall

Description
In order for translation to initiate, a charged tRNA must be placed into which of the following site in the ribosome 1) A 2) P 3) E The newly translated amino acid is attached to which of the following terminus of the growing polypeptide? 1) Amino terminus 2) Carboxyl terminus Are all tRNA's identical? a) True b) False During the hybrid state of the ribosome which of the following G protein is required to elongate translation by shifting the tRNAs? 1) EF-Tu 2) IF2 3) EF-G lacZ, lacY, and lacA are expressed at high levels only when ________ is available and ________ is not. A. glucose, lactose B. lactose, glucose C. lactose, CAMP D. operator, a CAP site DNA is composed of polynucleotides chains. * a) True b) False What is the difference between general and regulatory transcription factors? * A. Regulatory transcription factors are necessary for transcription but general transcription factors are not B. Regulatory transcription factors must bind directly on the promoter sequence but general transcription factors can bind anywhere along the DNA. C. Regulatory transcription factors enhance and inhibit transcription but general transcription factors are necessary for transcription. D. Regulatory transcription factors and general transcription factors are both necessary for transcription. The main difference between DNA and RNA is that DNA does not contain a Hydroxyl group at the 2' position while RNA does . A) True B) False What is something that PCNA does NOT do? * a. It uses ATP to load and unload proteins onto the DNA. b. It keeps all the transcription factors bound to DNA. c. It will recruit RNase H and DNA polymerase 1 when they are needed. d. It keeps DNA polymerase 3 bound to the DNA. SSB proteins are sequence specific. A. True B. False The bond between GC is more stronger than AT. A) True B) False Complementary DNA strands are held together by covalent bonds. A) True B) False (hydrogen bonds) What enzyme is used to repair nicks in the DNA backbone? A) DNA Polymerase I B) primase C) ligase D) helicase Transposons have the ability to copy themselves, take the sequence out of the chromosome and replace it in a different point on the chromosome. A. true B. false Heterochromatin are chromatin that appear to be more relaxed and are being actively transcribed. A. true B. false _________ are adapter molecules that transfer genetic information to amino acid sequence. A. tRNAs B. mRNAs C. snRNAs Which of the following are required for DNA polymerase III to begin to replicate DNA in the cell? 1- Helicase 2- Primase 3- RNaseH 4-Magnesium ions 5-Sliding Clamp a) 1, 2, 4 b) 1, 2, 3, 4 c) 1, 2, 5 d) 2, 3, 4, 5 e) 1, 2, 4, 5 How many hydrogen bonds are created between CG and AT respectively? a) 2, 3 b) 1, 2 c) 3, 2 d) 2, 2 How is double-stranded DNA with high G/C content different from DNA with low G/C content? a) It runs faster on an agarose gel via electrophoresis b) It runs slower on an agarose gel via electrophoresis c) It melts at a lower temperature d) It melts at a higher temperature Which of the following pieces of DNA would bind most tightly to the following 11mer? 5'-TTATTCGGATC-3' a) 5'-GATCCGGGTAA-3' b) 5'-AATAAGCCTAG-3' c) 5'-AATAAGAATAA-3' d) 5'-AATCCGAATAA-3' The role of the topoisomerases is to break positively supercoiled DNA and reseal them during DNA replication. a) True b) False Both telomerase and the ribosome are made up of both RNAs and protein. a) True b) False Why isn't DNA replication reversible? a) absence of DNA polymerase b) high strength of inter-nucleotide bonds c) formation of phosphodiester backbone d) hydrolysis of pyrophosphate DNA synthesis is a highly complex and involved process. In order to begin you must first separate the strands. Which enzyme is involved in separation? a. helicase b. topoisomerase c. RNAseH d. PCNA Of the following forms of ATP, which is the "energy molecule"? a. dATP b. rATP c. ddATP d. None of the above Why doesn't RNA synthesis have to be accurate? a. There are many copies of RNA b. Many codons code for 1 protein (amino acid) c. There are coding and non-coding regions, exons & introns d. All of the above e. Only B and C In the final step of transcription initiation, RNA polymerase leaves the promoter and begins transcribing the gene. This step is known as_____. A. Promoter escape B. Open complex C. closed complex The lac operon is active when: A) lactose and glucose are present B) lactose and glucose are absent C) lactose is present and glucose is absent D) lactose is absent and glucose is present Which of the following is a reason why certain things in the cell are conserved throughout evolution? A. They are not necessary with any processes in the cell. B. They are necessary for many processes that are essential for life and organisms would die without them. C. They are not used often within the cell, so there is no reason to change them. D. You could not make these things any better, so they stay the same. Which of the following is true about replication and transcription? None of the above A. They both use primers. B. They are both transient copies of RNA or DNA C. They both only copy part of the genome. D. They both synthesis a strand of DNA in a 5' to 3' direction. Which of the following proteins bind in to a specific sequence? A. SSB Proteins B. RF1 C. Histones D. SR proteins E. B and D What is tRNA? A. translated RNA B. transcribed RNA C. transfer RNA D. None of the above. During elongation, FACT is activated and removes a portion of the histone in eukaryotic organisms. Which portion is removed A) H2A/H2B dimer B) H3/H4 tetramer Promoter melting in ________ requires hydrolysis of ATP. A. eukaryotes B. prokaryotes C. both D. neither Which of the five molecules in the cell does NOT participate in the process of recognizing proper splice sites. A) U2 B) TFIIE C) U6 D) U2AF E) U1 Transcriptional activators often bind cooperatively to increase levels of expression. Which of the following is another example of a protein that also binds cooperatively? a. DSB protein b. SSB protein c. TBP d. Topoisomerase Adenine binds with _______ and cytosine binds with ______. A. adenine/thymine B. thymine/guanine C. thymine/adenine D. guanine/thymine Which of the following can be used to unwind DNA? A. primase B. helicase C. topoisomerase D. Pol III Bacteria ______ their DNA to protect it from degradation by enzymes that break down foreign DNA. a. phophoryate b. methylate c. acetylate d. ligate Which of the following bind cooperatively I. single stranded binding proteins II. SR binding proteins III. transcriptional activators a. I only b. II only c. I and II d. I and III e. all of the above Histones bind to specific sequences in DNA a. True b. False In a DNA strand, G-C base pairs are more stable than A-T base pair. A. True B. False During RNA splicing, ____ are removed and _____ are retained in the mature RNA. A. exons, introns B. introns, exons In DNA, the nucleotides can be catagorized into purines and pyrimidines. The purines are ______ and _______. A. guanine, cytosine B. adenine, thymine C. guanine, adenine D. cytosine, thymine DNA is dissolved in two solutions with varying salt concentrations at a pH of 7.0. If the G+C content is the same in both pieces of DNA, in which of the solutions will the DNA denature at a lower temperature? A. High salt concentration B. Low salt concentration RNA contains the nucleotide _____ in place of the nucleotide _______ which appears in DNA. A. uracil, cytosine B. thymine, uracil C. uracil, thymine D. uracil, adenine Which of the histones is referred to as the linker histone which is not part of the nucleosome core particle? A. H1 B. H2A C. H2B D. H3 E. H4 ________ is more compacted showing less gene expression, whereas _______ is more open allowing for more gene expression. A. Euchromatin, Heterochromatin B. Heterochromatin, Euchromatin The H2A and H2B bind together to form a _____ on the newly synthesized daughter strand and the H3 and H4 bind together to form a ______. A. dimer, tetramer B. tetramer, dimer C. dimer, dimer D. tetramer, tetramer Which of the following base pairs form dimers when exposed to UV radiation? A. G-A B. C-T C. U-A D. A-T During DNA replication, which strand of DNA is synthesized discontinuously? A. Leading Strand B. Lagging Strand C. Okazaki Strand (fragments) During DNA replication, _____ bind to the DNA cooperatively to ensure that the newly generated ssDNA remains free of base pairing until DNA synthesis. A. SSB B. Topoisomerase C. Primase Which of the following ensure high processivity of the DNA polymerase? A. SSB B. Primase C. DNA Helicase D. sliding DNA clamps Telomeres exist in humans as A. dsDNA B. ssDNA C. both D. neither DNA synthesis is dependent on the presence of A. the four deoxynucleoside triphosphates B. The primer: template junction C. the DNA Pol III holoenzyme D. A + B E. All of the above Transcription and DNA Replication are equally accurate A. True B. False Rho-dependent termination uses ATP to induce termination and Rho-independent termination does not. A. True B. False ____ enhance splicing at nearby splice sites and ____ repress splicing at nearby splice sites. A. ESE, ISE B. ISE, ESE C. ESS, ISS D. ESE, ESS DNA synthesis proceeds by primer extension. A. True B. False ________ relieve the super-coiling of DNA ahead of the replication fork. A. RNASE B. Polymerases c. Topoisomerases DNA________ replicates the chromosome. A. Polymerase I B. Polymerase III C. Polymerase II Replication is restricted to once per cell cycle A. True B. False Which of the following statements about transposons are true? A) They compose roughly 45% of the human genome B) They are capable of causing knockout mutations by inserting themselves in the middle of a gene C) Transposons are a major cause of gene duplication D) All of the above are true statements Which of the following domains bind methylated histones? I. Chromodomains II. Bromodomains III. TUDOR domains A) I only B) II only C) I and II D) I and III E) I, II and III Which of the following proteins do NOT require ATP? A) Transcription Coupled Repair Factor B) Nucleosome Remodeling Complexes C) EF-Tu D) Rho factor Which of the following proteins does NOT interact with the PCNA sliding clamp? A) Helicase B) RNAse H C) Ligase D) DNA Polymerase I In the MutSLH repair pathway, MutH performs what action? A) Recruits MutS to cleave the phosphate backbone B) Functions as a helicase to remove nicked DNA C) Nicks the phosphate backbone of damaged DNA D) Removes damaged bases but leaves the backbone intact Methylation of histones can: A) disrupt or enhance interactions with DNA B) disrupt or enhance the formation of the 30 nm fiber C) promote modification of nearby histones D) all of the above After DNA replication, exonuclease repair, and mismatch repair, there is only one mistake per 10^10 nucleotides added. If both the proofreading exonuclease and mismatch repair systems were nonfunctional, at what frequency would mistakes be expected? A) 1:10^10 B) 1:10^7 C) 1:10^5 D) 1:10^3 A _____ has a 2' and a 3' hydroxyl group (-OH). a) ribonucleotide b) deoxyribonucleotide During DNA replication, what is the order in which the following proteins act ? 1. DNA primase 2. DNA polymerase 3. DNA ligase 4. DNA helicase 5. Nuclease A. 1,2,3,4,5 B. 4,1,2,3,5 C. 4,1,2,5,3 D. 5,4,3,2,1 The primary enzyme of transcription is the _________. A. RNA polymerase B. DNA polymerase c. Primer Most transcription factors interact with the __________ groove of the DNA helix? A. Major B. Minor In a eukaryote, which area of the cell are you most likely to find DNA in? a. cytoplasm b. nucleus In order to charge a tRNA you must... a) perform a condensation reaction b) adenylate the amino acid c) perform an acyl linkage d) break a phosphodiester bond A transposon is an example of a pseudogene. a) true b) false Primase activity increases when it interacts with______? a) ligase b) RNaseH c) helicase d) topoisomerase The weakest nucleotide pairing is: A) AT B) GC C) AU D) AG E) CT Which of the following is the correct order for the three stages of the Polymerase Chain Reaction? A. Extension, Annealing, Denaturation B. Denaturation, Annealing, Extension C. Denaturation, Extension, Annealing D. Annealing, Extension, Denaturation DNA is always synthesized in the 5' --> 3' direction A. True B. False During DNA replication, Okazaki fragments make up the _______ strand. A. Leading B. Lagging Mutations in intron sequences of a gene cannot be harmful for proper protein synthesis. A) True B) False Which of the following bind cooperatively? 1) DNA single stranded binding proteins 2) regulatory transcription factors 3) transcriptional activators 4) snRNP's involved with splicing A. 1 B. 2 C. 3 D. 1,3 E. 1,3,4 A codon is made up of _______ nucleotides A. 1 B. 2 C. 3 D. 4 E. 5 You are looking at an mRNA strand which includes the following: a tri-phosphate group at the 5’ end, multiple start and stops codons, and multiple Shine Delgarno sequences. Which of the following is the correct classification of this mRNA? a. Eukaryote, monocistronic b. Prokaryote, polycistronic c. Eukaryote, polycistronic d. Prokaryote, monocistronic mRNA is the only species that codes for protein A-) True B-) False ------- seperates the two strands by breaking Hydrogen bonds while ----------- relieves supercoiling a-) Helicase,helicase b-) Helicase, topoisomerase I c-) Topoisomerase type I, topoisomerase type II d-)Helicase, Topoisomerase type II What is a molecule called that binds a receptor? A. Transcription factor B. Trasposon C. Ligand D. Polymerase ------- is a motor protein that uses ATP to scan DNA looking for stalled Polymerase a-) PCNA b-) Protein Rho c-) TCRF d-) DNA polymerase I e-) none of the above RNase H is responsible for: A. removes DNA primer B. removes RNA primer C. adds RNA primer D. fills nick after DNA ligase DNA Helicase uses ATP to move along and open the DNA strand True or False. A. True B. False Which of the following uses cooperative binding? A. Histones B. Telomeres C. ssDNA-binding proteins (SSBs) D. Sliding clamp Glycosylase is an enzyme used in which of the following repair systems A. Nucleotide Excision Repair B. Base Excision Repair C. Photoreactivation D. None of the above When a polymarase leaves the promoter it is said to have: A. escaped B. elongated C. scrunched D. inch-wormed Pyrophosphorolytic editing works by backtracking multiple nucleotides and then cleaving the RNA A. True B. False Antibiotics target the ________ between ribosomes in Eukaryotes and Bacteria A. Similarities B. differences which of the following are sources of mutations a. inaccuracy in DNA replication b. chemical change to the genetic material c. transposons d. a and c e. all of the above RNA polymerase only works in one known way according to FRET. What are the two ways that have been disproven by FRET? A) Inch-worming, Scrunching B) Scrunching, Transient excursion C) Sliding, Scrunching D) Inch-worming, Transient excursion E) None of the above the holoenzyme is a multiprotein complex in which a core enzyme activity is associated with additional components to enhance function. a. true b. false Match the following with their role in translation. g A series of three tRNA bases complementary to a mRNA codon. d The ribozyme that forms peptide bonds between amino acids during translation. a The ribosomal subunit that binds to mRNA to form the initiation complex. i The ribosomal site where an aminoacyl-tRNA first attaches during translation. h The ribosomal site where the growing amino acid chain is temporarily being held by a tRNA as the next codon in the mRNA is being read. f A complex of an amino acid and a tRNA molecule. b The sequence of bases on mRNA to which a 30S or 40S ribosomal subunit first attaches. k A series of three mRNA bases coding for no amino acid and thus terminates the protein chain: UAA, UAG, UGA. c A complex consisting of a 30S or 40S ribosomal subunit, a tRNA having the anticodon UAC and carrying an altered form of the amino acid methionine (N-formylmethionine or f-Met), and proteins called initiation factors. e A three-dimensional, inverted cloverleaf-shaped molecule about 70 nucleotides long to which a specific amino acid can be attached; transports amino acids to the ribosome during translation. a. 30S(prokaryotic) or 40S(eukaryotic) ribosomal subunit ----- b. ribosome binding site ----- c. initiation complex ----- d. 50S or 60S ribosomal subunit ----- e. tRNA ----- f. aminoacyl-tRNA ----- g. anticodon ----- h. P-site of ribosome ----- i. A-site of ribosome ----- j. peptidyl transferase k. nonsense (stop) codon ----- l. release factors m. start codon The stop codon encodes for an amino acid that is incorporated into the polypeptide chain. A)true B)false Promoters in eukaryotes must be downstream of the +1 site A.) True B.) False In eukaryotes, general transcription factor machinery binds to the promoter and recruits RNA polymerase to the promoter. What protein in prokaryotes have the same function? A) Sigma factor B. Poly A Polymerase C. The Mediator Complex D. TATA Binding Protein The energy required to attach an amino acid onto a tRNA comes from which molecule? a. GTP b. Kinase c. ATP d. GDP which bond is broken in order to add an amino acid onto a growing polypeptide chain? A) A B) B C) C D) D E) none of the above Please indicate in the box with a (+) if sugar/s is/are present and a (-) if not present corresponding to the diagram below. Diagram 1: Basal Level of Transcription + + Diagram 2: No Transcription + - Diagram 3: Activated Levels of Transcripton - + Sigma factor binds to... A) The UP element B) -10 element C) -35 element D) Both -10 and -35 elements The U1 snRNP recognizes the... A) 5' splice site B) 3' splice site C) -10 site D) None of the above Promoter melting is facilitated by... A) TFIIB B) TFIIH C) TFIIF D) TFIIA A primer:template junction is made up of ssDNA as well as dsDNA. A. True B. False The following processes require ATP: I. Loading the Sliding Clamp II. Unwinding DNA with DNA Helicase III. DNA Repair via Photoreactivation IV. Binding Sigma Factor A. I and II B. I, II, III C. I, II, IV D. I, III, IV E. All of the above An intron is removed through two successive transesterification reactions in which phosphodiester linkages within the pre-mRNA are broken and new ones are formed. A) True B) False During elongation of the polypeptide in the ribosome the peptide chain is made longer by: a. transferring the existing peptide onto the incoming charged tRNA b. transferring the incoming amino acid onto the existing peptide c. none of the above. Primase is a RNA polymerase dedicated to making short RNA primers on an ssDNA template. A) True B) False Elimination of the Shine-Dalgarno sequence, prevents the translation process from occurring, in prokaryotes. A) True B) False A single gene can make many RNAs, which can be translated by many ribosomes at any given time. a) true b) false IF1, IF2, and IF3 interact with (in order): a) E Site, A site, GTP and IF1 b) E site, GTP and IF1, A site c) A site, GTP and IF1, E site The _ subunit binds RNA, while the _ subunit catalyzes peptidyl reactions. A) Small, Large B) Large, Small C) Amino, Carboxyl D) Carboxyl, Amino The ribosome has a footprint of _ nucelotides, so multiple ribosomes are _ to bind to one RNA. A) 80, able B) 80, unable C) 160, able D) 160, unable The first model of a helix was developed by Linus Pauling for _____. A) Proteins B) DNA C) RNA ______ and _______ suggested the double helix for DNA. A) Crick, Chargoff B) Watson, Crick C) Pauling, Franklin D) Watson, Franklin Adenine binds only to ______. Cytosine binds only to _______. A) Uracil, Guanine B) Guanine, Uracil C) Thymine, Guanine D) Guanine, Thymine What enzyme can put back together DNA that has been cut? A) migase B) digase C) ligase D) rigase In gel electrophoresis, the negatively charged _______ of a strand of DNA is attracted to a positive charge. a. Nitrogenous Base b. Sugar-Phosphate Backbone c. 5' end d. 3' end What is the purpose of the Shine-Delgarno sequence? A. It's a start codon B. It's a stop codon C. It's a ribosome binding site Which of the following is true about a Kozak sequence? I. The sequence that is near the start codon. II. It's the ribosome binding site. III. It encodes several genes. IV. It increases the efficiency of translation. A. I, II, and IV B. I, and IV only C. II, III, and IV D. IV only What is the first step for charging a tRNA? A. Phosphorylation B. Translation C. Adenylation D. Peptidyl transferase During transcription initiation process, the initial binding of polymerase to promoter results in the formation of ________? A. Open Complex B. Closed Complex C. Consensus sequence D. A & B Which of the following happens when lactose is present in a cell? A. Allolactose binds to the operator B. Allolactose binds to the Lac repressor C. Lactose binds to the operator D. Lactose binds to the Lac repressor The 5’ end of a mature prokaryotic mRNA contains A. Phosphate groups B. 5’ cap C. Neither Consider the releasing phase of translation. In this process, RF3, which has a high affinity for GDP, binds to the ribosome only in the presence of a class I releasing factor. In order for the class I releasing factor to be removed, however, the GDP bound to RF3 must be transformed into GTP. Which of the following is most likely to aid this transformation? A. GAPs B. GEFs C. ATP Which is not a difference between transcription and translation? a. replication yields a permanent copy while transcription yields a transient copy b. Both transcription and translation require primer c. one is very accurate and the other is less so d. translation copies the entire gene and transcription only copies part of the gene Which base is this and is it a pyrimidine or purine? (see diagram attached) A) adenine; purine B) cytosine; purine C) guanine; purine D) thymine; pyrimidine Why would regulation occur after the protein is already made? A) It is the most energy efficient way to regulate gene expression. B) So the proteins can be turned on and off quickly in response to cell stimuli. C) All regulation occurs in the transcriptional stage which eliminates the need for protein regulation. Chargaff's rule states that: a) DNA is double helix b) A is paired with T and C is paired with G c) DNA is complimentary and parallel d) there are two hydrogen bonds between A-T and three between C-G The backbone of DNA contains: a) phosphates b) sugars c) neither d) both When there is a pyrimidine dimer the system(s) used to fix this mutation is? A. Nucleotide Excision Repair B. Photoreactivation C. Endonuclease Activity D. Only A and B E. All of the Above Where does the ribosome bind? A. 5' end of DNA B. 3' end of RNA C. 3' end of DNA D. 5' end of RNA DNA is synthesized: a) 3' to 5' b) 5' to 3' If the transient excursion model of initial transcription were true and w
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