Questions, answers and sum of ideas to prepare you for first test
Questions, answers and sum of ideas to prepare you for first test BCH 6713
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Date Created: 09/05/16
STUDY GUIDE – MOLECULAR BIOLOGY – TEST 1 The followed questions are more likely to be on the first test. Watch out for details given in class, from numbers, names of enzymes and proteins to even the position of each element in a carbon! This study is not in the same order of chapter! Test your skills! After the questions, you have the answers and after that a sum of the main ideas given until this week. Total of 60 multiple questions. 1) All of them are true about Avery’s Bombshell experiment, except: a. Confirmed that RNA can be translated in proteins b. Used pneumonia causing bacteria c. Based on the fact that smooth capsule is necessary for pathogenesis d. One step included destruction of proteins using proteolytic enzymes e. One step included destruction RNA using ribonucleases f. One step included destruction DNA using deoxyribonucleases 2) What is false about DNA structure? a. Each turn occurs every 10.5 base pairs b. Formed by polynucleotide chain c. Double helix is kept by hydrogen bond and van der waals forces d. Major groove has 22A e. Minor groove has 10A 3) Which carbon the hydroxyl group is present on a DNA molecule (more than one can be right): a. C 1 b. C 2 c. C 3 d. C 4 e. C 5 f. C 6 4) All about DNA replication are true, except: a. Uses dNTPS 15 b. Experiments using N labeled on bacterial DNA showed it’s a semiconservative process c. Catalyzed by DNA polymerase III d. Unidirectional process e. Needs primers to start the process of elongation 5) The largest histone on nucleosome structure is: a. H2A b. H2B c. H3 d. H1 e. H4 6) About Hersey-Chase experiment, include T (true) or F (false): 32 a. Based on the fact that P is a marker for protein b. Based on the fact that P is a marker of backbone phosphate on DNA and RNA c. Wanted to prove that bacteria have DNA just like viruses 32 d. Labeled protein from bacteriophages with P e. Replicated bacteriophages in bacteria and notice that only labeled DNA from the bacteriophage was present in the bacteria 7) All are true about Rosalind Franklin experiment, except: a. Use X-ray diffraction to analyze DNA structure b. Helical form of DNA is indicated by the crossways pattern of the X-ray reflection c. Proved DNA have a double-helix structure d. Each turn occurs every 8.5 base pair e. Each turn occurs every 3.4nm 8) The ratio between purines and pyrimidines is: a. 0.5 b. 0.2 c. 2 d. 5 e. 1 9) Which carbon the hydroxyl group is present on a RNA molecule (more than one can be right): a. C 1 b. C 2 c. C 3 d. C 4 e. C 5 f. C 6 10)Study involving the genetic disease of sickle cell anemia showed: a. DNA is responsible for transmitting the information necessary to produce the protein chains b. People with genotype SS don’t develop the disease c. Disease involve a change in the shape of hemoglobin from beta to alpha conformation d. mRNA was used to test that the disease is transmittable e. In the disease valine amino acid is substitute by proline 11) All about the central dogma are true, except: a. Tells how DNA keep the genetic information to be translated into proteins b. DNA can be either translated into RNA or replicated c. RNA can be either translated into proteins or reverse transcribed into cDNA d. Proteins cannot be reversed into RNA nor DNA e. DNA polymerase I is used for DNA replication 12)Write down which type of RNA (mRNA, tRNA or rRNA) is related to the followed characteristic: a. Represents approximately 85% of all RNA in the cell: _________ b. Also known as adaptor: ___________ c. Transport genetic information to sites where proteins are translated: _________ d. Formed mostly by guanine and cytosine bases on its sequence: ____________ e. At least 20 types of this type of RNA exists : ____________ 13) Write T (true) or F (false) about tRNA: a. Found on ribosomes b. It’s the adaptor for the hydrophilic amino acid and hydrophobic base pair c. Recognize and bind to anticodons methionine d. The first amino acid that binds to mRNA is brought by specific tRNA e. Anticodon region is formed by 3 matched base pairs 14)Regarding the genetic code, all are true, except: a. Combination of 3 base pairs can form 20 different amino acids b. Combination of 3 base pairs form a total of 64 codons c. 61 out of 64 codons produce the 20 amino acids d. Start codon is usually AUG e. Stop codons are usually UAA, AUU, UAG 15)Write T (true) or F (false) about DNA: a. A-T base pairing is formed by 3 hydrogen bonds b. C-G base pairing is formed by 3 hydrogen bonds c. Ends on 3’ hydroxyl group and 5’ phosphate group d. Replicated in the direction from 5’ to 3’ e. Phosphodiester linkage is responsible for the polarity of DNA f. Formed by 2 hydroxyl group while RNA is formed by one hydroxyl group g. Diameter is approximately 3 nm 16)Regarding the nucleotide structure, all are true, except: a. Backbone formed by phosphate group and sugar b. Sugar and base are called nucleoside c. Phosphodiester linkage is the result of the reaction from the 3’ hydroxyl group from one nucleotide to the 5’ hydroxyl group from another nucleotide d. 4 types are naturally found in the organism e. Phosphodiester linkage is unstable by nature and bases are responsible to stabilize the structure of the nucleotide 17)The glycosylic bond release one molecular of water in which the OH group comes from the: a. C 1 b. C 2 c. C 3 d. C 4 e. C 5 f. C 6 18)What is true about DNA stability? a. Given by peptide bonds b. Hydrogen bond have a strong bond that gives DNA stability c. Shorter DNA sequences (less than 10 base pairs) are more stable d. Base pairs matching happens at two main points: C and6N from 1urine base and C and N f4om a 3 pyrimidine base e. Hydrophilic interaction between base pairs gives stability to DNA 19)All are true about Mica experiment, except: a. DNA is fixed in a mica surface by its 5’ end b. Concludes that DNA make a turn every 10.5 bases c. After 5.25 base pairs, DNA make a turn of 180° d. Each turn has 3.2nm (size) e. Each base pair display 36° 20)All are true about major grooves, except: a. G-C base pair form a pattern of H bond acceptor (A) and donor (D) as AADH b. G-C base pair form a pattern of H bond acceptor (A), donor (D) and methyl group as ADAM c. A-T base pair form a pattern of H bond acceptor (A), donor (D) and methyl group as ADAM d. Distance of 22A e. Forms an angle of approximately 240° 21)All are true about minor grooves, except: a. G-C base pair form a pattern of H bond acceptor (A) and donor (D) as ADA b. A-T base pair form a pattern of H bond acceptor (A) and nonpolar H (H) as AHA c. Distance of 12A d. Forms an angle of approximately 100° e. Gives less information regarding DNA the base pairing when compared with major groove 22)About double helix conformations, all are true, except: a. B form is found more in RNA molecules b. B form happens in high humidity c. A form happens in low humidity d. A form has one turn each 11 base pairs e. Z form is characterized by zigzag f. Z form often happens in high ionic positively charged environment 23)Write true (T) or false (F) about the nucleosome: a. Have 2 histones 2A b. Have 2 histones 2B c. Have 2 histones 2C d. Have 2 histones 4 e. Composed by only a group of 8 histones 24)All are true about nucleosome, except: a. It’s how DNA is wrapped on eukaryote and prokaryote b. Formed by two main parts: core and linker c. DNA that is not in a nucleosome state (wrapped) is involved on gene expression d. Formed by 8 histones and the wrapped DNA e. Nucleosome does not have specificity to DNA, but high affinity 25)Write true (T) or false (F) about the core DNA: a. It’s more stable and constant structure than linker b. Presents around 120 base pairs c. Formed by one of each of the following histones: H2A, H2B, H3 and H4 d. Present a disk shape when in contact with DNA e. High percentage of lysine and arginine on its protein structure 26)How much base pairs the linker DNA often includes? a. 20-30 bp b. 20-40 bp c. 40-60 bp d. 20-60 bp e. 30-60 bp 27)All are false about allostery, except: a. Responsible for changing the protein structure b. It means change structure c. Function is changed by structure d. Lac repressor is an effector that acts by phosphorylation e. There are 3 main ways of changing protein shape 28)What is wrong about the histone 1? a. Only one H1 exists per nucleosome b. At least 20% of amino acid are lysine and arginine c. The amount of H1 in the cell is 1/4 of the other types of histones d. Presented at the linker DNA e. Size is approximately 21 kD 29)What is the true binging process on the nucleosome? a. Heterodimers H1 and H4 bind together, forming a tetramer of H1+H1+H4+H4. After that each dimer is joined together, H2A and H2B. b. Heterodimers H2A and H2B bind together, forming a tetramer of H2A+H2A+H2B+H2B. After that each dimer is joined together, H3 and H4. c. Heterodimers H2 and H3 bind together, forming a tetramer of H3+H3+H2+H2. After that each dimer is joined together, H4 and H2B. d. Heterodimers H1 and H2 bind together, forming a tetramer of H1+H1+H2+H2. After that each dimer is joined together, H3 and H4. e. Heterodimers H3 and H4 bind together, forming a tetramer of H3+H3+H4+H4. After that each dimer is joined together, H2A and H2B. 30)How many distinct sites of contact between DNA and histones has? a. 7 b. 14 c. 8 d. 12 e. 16 31)All are true about histones bind characteristics at regions of DNA, except: a. H2A and H2B interacts with 30 bp of DNA b. Binding sites are on the major groove of the DNA c. H3 and H4 tetramer interacts with 60bp of DNA d. Approximately 40 H bonds are made between DNA and histones e. Binding sites are on the minor groove of the DNA 32)All are true about amino terminal tails, except: a. Tails wrap around DNA to the histone in right handed way b. H2A and H4 tails emerge either above or below 2 DNA helices c. H2B and H3 tails emerge between 2 DNA helices d. It is not necessary for DNA association with histones e. They are sites of extensive modification 33)How many times DNA is wrapped around the histone? a. 1 b. 2 c. 1.5 d. 1.65 e. 1.56 34)All are true about chromosomal regions, except: a. Formed mainly by two regions b. Heterochromatin has a dense and condense appearing c. Euchromatin has a dense and condense appearing d. Euchromatin is a less organized structure e. Heterochromatin is a less expressed region of DNA 35) Regarding the diameter of DNA, nucleosome and the fiber, respectively, which one is true: a. 20A, 10 nm and 30nm b. 2 nm, 10nm and 30nm c. 1nm, 20nm and 30 nm d. 0.1 nm, 20 nm and 30 nm e. 0.1 nm, 10 nm and 30 nm 36)All are true about H1 binding to DNA structure, except: a. Can bind to two distinctive regions of DNA duplex b. Gives additional protection to 40bp of DNA sequence from nuclease digestion c. In increased salt concentration forms the fiber d. Gives a zigzag appearance to the structure e. 2 models of fiber can be found: solenoid and zigzag 37)All are true about nuclear scaffold, except: a. Fiber compacts the DNA in approximately 40 fold b. Topoisomerase II held DNA at the base of the loops c. SMC held DNA at the base of the loops d. SMC holds sister chromatins together after chromosome duplication e. It’s a level up from fiber structure (DNA > nucleosome > fiber > nuclear scaffold) 38)About histone modification and gene expression, what are the two true sentences: 1. Lysine 8 and lysine 26 can be acetylated and start gene expression 2. Lysine 8 and lysine 9 can be acetylated and start gene expression 3. Only Lysine 8 start gene expression 4. Only Lysine 27 represses transcription 5. Acetylation and phosphorylation are the main ways of reducing the positively charge histones, allowing DNA to be expressed/ transcribed a. 1 and 3 are true b. 1 and 4 are true c. 1 and 5 are true d. 2 and 3 are true e. 2 and 4 are true f. 2 and 5 are true 39)Which protein interacts to acetylated tails? a. PHD fingers b. Bromodomains c. Chromodomains d. TUDOR domains e. Sant domains 40)Match the name of the enzymes and its function: 1. Histone acetyltransferase ( ) Removes methyl group 2. Histone deacetylase ( ) Add methyl group 3. Histone methyltransferase ( ) Removes acetyl group 4. Histone demethylase ( ) Add acetyl group 41) All are false about histones chaperones, except: a. They are positively charged b. Form complexes only with H2A and H2B c. CAF1 only assembles when DNA is replicating d. CAF1 interacts to H2A and H2B e. None of them is true 42) True (T) or false (F) about DNA replication: a. Needs a primer to start replication b. Direction is from 5’ to 3’ c. Nucleotide assembly to the chain release diphosphate group d. Phosphate group from nucleotide is attached to 3’ end of the primer e. Primers are double stranded sequences f. DNA polymerase interacts with DNA by van der Waals force in the sugar ring 43)About DNA polymerase domains, what is false? a. There are 3 main domains b. Palm domain monitors base pairing c. Thumb interacts with DNA d. Finger domain make a 45° turn in the DNA backbone e. Thumb domain maintain primer position 44)What is the composition of the Palm domain: a. Two beta sheet and often Mg and Zn +2 b. One beta sheet and often Mg and Zn +2 c. Two beta sheet and any divalent ions d. One beta sheet and any divalent ions e. Two beta sheet and often Ca and Zn +2 +2 +2 f. One beta sheet and often Ca and Zn 45)All are ways of proofreading DNA, except: a. Exonucleases degrades incorrect base pairing starting from 3’ end b. Size and structure of each base pair does not allow unmatched pairs to get closer to 3’OH for reaction c. Palm domain is responsible for monitoring base pairing by its extensively H bonds interaction on the minor groove d. Finger domain is responsible for monitoring base pairing by opening the interaction for exonuclease interacts to the unmatched base pair e. All are true 46)What is the error rate of the DNA polymerase? a. 1 nucleotide every 10 7 b. 1 nucleotide every 10 5 10 c. 1 nucleotide every 10 20 d. 1 nucleotide every 10 e. It’s never wrong 47)All are true about the replication Fork, except: a. It moves toward the unreplicated DNA b. Regions where the DNA is separated into two single strands c. Region where DNA Polymerase attaches d. Region where SSBs proteins bind to stabilize the single strands e. All are true 48)What is false about Okazaki fragments? a. Its length is 100 -400 bp in eukaryote b. They are fragments of replicated DNA from the lagging strand c. Results from the replication of the antiparallel strand d. It is replicated from 5’ end to 3’ end e. All are true 49)Match each event to its function: 1. Topoisomerase ( ) open DNA and stabilize it 2. Exonuclease ( ) single stranded sequence with 5- 10 nucleotides 3. RNAse H ( ) degrades the primer 4. Primer RNA ( ) reduce supercoil 5. DNA ligase ( ) degrades ribonucleotides at 5’ 6. Primase ( ) ligate Okazaki fragments 7. DNA helicase ( ) build the primer using DNA template 50)True (T) or false (F) about DNA replication process: a. Primase is a RNA polymerase b. DNA polymerase only initiate synthesis where primer is annealed c. Each strand requires one primer to replication occurs d. DNA helicase decrease activity of primase e. RNaseH leaves only one ribonucleotide without degradation f. DNA polymerase only initiate synthesis when primer is removed forming a gap g. DNA helicase has 6 domains, which means it is a hexameric protein 51)Put in order the following events: 1. DNA helicase open the double stranded DNA 2. DNA primase use the DNA as template to produce a primer 5-10 bases long 3. SSBs proteins stabilize the opened DNA, binding to DNA in a cooperative manner 4. Topoisomerase allow DNA helicase to work 5. Primer anneal to single stranded DNA 6. DNA polymerase and sliding clamp fills the gap 7. Exonuclase correct mismatched bases 8. RNAseH degrades primer a. 1, 4, 3, 2, 5, 8, 7, 6 b. 4, 1, 3, 2, 5, 8, 6, 7 c. 4, 1, 2, 3, 5, 8, 6, 7 d. 1, 4, 3, 2, 5, 8, 6, 7 e. 4, 1, 3, 2, 5, 8, 7, 6 52)All about DNA helicase is true, except: a. It is a hexameric protein b. It can open DNA from 5’ end to 3’ end c. It can open DNA from 3’ end to 5’ end d. It has a ring shape e. It has 20A of diameter 53)All are true about the types of DNA polymerase, except: a. DNA polymerase α is responsible for elongation of the leading strand b. DNA polymerase δ is responsible for elongation of the lagging strand c. Eukaryote have 3 main types δ, α and ε d. Prokaryote have 3 main types I, II core and III holoenzyme e. All are true 54)What is false about Sliding Clamp Proteins: a. Have a doughnut shape b. Diameter is bigger enough for a double stranded DNA pass through c. Increase processivity of DNA polymerase d. After replication it is removed from the new double stranded DNA together with DNA polymerase e. Prevents DNA polymerase from diffusing away 55)How many subunits the Clamp loader proteins are made of: a. 4 b. 5 c. 6 d. 7 e. None of the options 56)All are functions of the Clamp loader proteins, except: a. Unwind DNA b. Load DNA helicase c. Unfold proteins d. Disassemble proteins from DNA e. Assemble DNA polymerase to DNA helicase 57)Put in order the following events: 1. Clamp loader releases itself from DNA and Sliding clamp 2. ATP binds to clamp loader changing its conformations 3. Sliding clamp is opened 4. ATP hydrolysis happen 5. Clamp loader recognizes primer-template junction 6. Clamp loader binds to sliding clamp 7. Sliding clamp closes around DNA a. 5, 6, 2, 4, 3, 1, 7 b. 2, 5, 6, 3, 7, 4, 1 c. 5, 6, 2, 3, 4, 7, 1 d. 2, 5, 6, 3, 4, 7, 1 e. 5, 2, 6, 3, 4, 1, 7 58)They are all part of the Polymerase III holoenzyme: a. Sliding clamp b. γ complex Clamp loader c. Polymerase III core d. ȷ protein subunit e. Polymerase I 59)True (T) or false (F) about prokaryote replication: a. DNA helicase interacts with Polymerase III core b. DNA helicase opens DNA into 2 strands and each ȷ protein subunit fits between them c. While DNA is open, primer is formed d. Primase degrades the primer while DNA helicase open DNA e. Clamp loader recognizes the primer-template junction and insert sliding clamp f. Leading strand is replicated from 5’ to 3’ g. Okazaki fragments are shorter than RNA primers h. Trombone model is found only in prokaryote i. Replisome are all proteins that together form the replication fork j. The weak association between DNA helicase and primase regulates the length of Okazaki fragments 60)All about replicon model are true, except: a. Replicon is a replicated DNA b. Replicator is A-T rich sequence c. Initiator recognizes replicator d. Initiator recruits factors e. Eukaryote replicator is shorter/ smaller than prokaryote 61)Match each element to its function: 1. ORC ( ) helicase in prokaryote 2. Dna A ( ) initiator in prokaryote 3. Dna B ( ) replicator in prokaryote 4. Dna C ( ) helicase loader in eukaryote 5. oriC ( ) initiator in eukaryote 6. cdc 6 ( ) helicase in eukaryote 7. mcm 2 -7 ( ) helicase loader in prokaryote 62)Which elements facilitate and coordinate replication: 1. DNA polymerase 2. topoisomerase 3. SSBs 4. Primer annealing 5. helicase a. 1, 3, 4, 5 b. 2, 3, 5 c. Only 1 d. 1, 2, 5 e. All of them 63)All about replicator motifs are correct, except: a. Prokaryote replicator has a 9 base pair motif and 13 base pare motif b. The 13 mer motif is where the single strand DNA is formed c. Eukaryote replicator has one motif extra than prokaryote d. One of the eukaryote replicator motif repeats 5 times e. All are wrong 64)Put in order all following events about E. coli initiation of replication: ( ) DNA synthesis ( ) DNA Poly III recognizes primer-template junctions ( )Formation of single stranded DNA ( )DnaC is released ( ) DnaA binds to a 9bp repetition on Oric ( )DnaB recruits helicase, one for each strand ( )Separation of DNA strand > 20 base pairs length ( ) Recruiting a complex of 6 DnaB and 6 DnaC ( )DnaA interacts with the 13 mer elements ( )DnaC assembly DnaB around the DNA and directs replication ( )Primase / DNA poly I form the primer 65)What is true about initiation of replication on Eukaryote? a. Occurs at least once during the cell cycle b. Occurs all at S phase c. Occurs all at G phase d. Mediated by kinases e. None is true 66)All are true about the kinase Cdk, except: a. Controls pre RC formation at G1 phase b. At low levels allows formation of pre RC c. At low levels increase activation d. At S phase, its levels are high e. At high levels block formation of pre RC 67)All are true about regulation of replication, except: a. DnaA and ATP levels regulate replication on prokaryote b. Mcm proteins help regulation on eukaryote c. Seq B regulate replication on eukaryote d. Seq A prevents DnaA to bind to OriC sites e. All are true 68)Seq A specific bind to the sequence of the DNA: a. AAA b. GTAC c. GTA d. TATA e. CTGA 69)All are true about finishing the replication, except: a. Circular DNA, daughter and template, are separated by topoisomerase II b. Leading strand is replicated continuously till the end c. Lagging strand uses two ways to finish the replication and form telomeres d. Eukaryote cells form the telomeres with A-T rich sequence e. Protein can be used as final primer to form the end of lagging strand replication 70)All are true about telomerase, except: a. TER size is constant in eukaryotes b. Enzyme with multiple protein subunits plus RNA component c. RNA element from telomerase is called TER d. Acts at the 3’ end of the DNA template e. Telomerase has limit number in the cell that decrease over time STUDY GUIDE – ANSWERS FOR STUDY GUIDE 1) A 2) E 3) C 4) C 5) D 6) A. false b. true c. false d. false e. true 7) D 8) E 9) C and B 10)A 11)B 12)a = RRNA b= trna c= mrna d= rrna e= trna 13)A. true b. false c. false d. true e. true 14)E 15)A. false b. true c. true d. false e. true f. false g. false 16)E 17)A 18)D 19)D 20)B 21)D 22)A 23)A. true b. true c. false d. true e. false 24)A 25)A. true b. false c. false d. true e. true 26)D 27)E 28)C 29)E 30)B 31)B 32)A 33)D 34)C 35)A 36)B 37)C 38)C 39)B 40)4,3,2,1 41)C 42)A. true b. false c. true d. true e. false f. true 43)D 44)A 45)D 46)B 47)E 48)D 49)7,4,3,1,2,5 50)A. true b. true c. false d. false e. true f. true g. true 51)B 52)E 53)A 54)D 55)B 56)E 57)E 58)E 59)A. false b. false c. true d. true e. true f. true g. true h. false i. true 60)E 61)3,2,5,6,1,7,4 62)B 63)D 64)11,10,4,7,1,8,3,5,2,6,9 65)D 66)C 67)C 68)B 69)D 70)A ANY CONCERN OR POSSIBLE FAIL ON PASSING THE RESULTS, PLEASE FEEL FREE TO CONTACT ME BY E-MAIL. DOUBTS ABOUT THE INFORMATION OF THE STUDY GUIDE, PLEASE CONTACT ME. E-MAIL firstname.lastname@example.org
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