bchm 218 module 03

if a DNA solution was in standard conditions and its %GC=40, what is the approximate Tm value in degrees celcius? Tm = 0.41 (%GC) + 69.3 a) 85 b) 105 c) 125 d) 145 e) none of the above

a) 85

the number of purines and pyrimidines in RNA are equal a) true b) false

b) false

which of the following histone variants stabilize the open state of chromatin? a) H2AZ b) macroH2AZ c) H3.3 d) both a & c e) both b & c

d) both a & c

Which chemical forces stabilize DNA ? a) van der Waals interactions b) ionic interactions c) hydrogen bonding d) hydrophobic interactions e) all of the above

e) all of the above

Fill in the blanks. As double stranded DNA melts, 260 nm absorbance ______________ and SYBR green fluorescence ____________. a) increases, increases b) remains unchanged, decreases c) decreases, decreases d) decreases, increases e) increases, decreases

e) increases, decreases

three separate PCR products, "A" (300bp), "B" (600bp) and "C" (900bp) are run on gel electrophoresis. what is their order of migration from the wells to the end of the gel? a) A, B, C b) A, C, B c) B, C, A d) C, B, A

a) A, B, C

Proteins that bind to acetylated lysine residues in the histone tail contain: a) Bromodomains b) DNA-binding domains c) Chromodomains d) Kinase domains e) Histone-fold motifs

a) Bromodomains

Reverse transcription PCR (RT-PCR) is a process that results in: a) The conversion of protein-coding RNA to DNA b)The amplification and quantification of a specific mRNA transcript c) Determination of the melting temperature of a specific segment of DNA d) Determination of the amino acid sequence of the protein encoded by a specific mRNA e) none of the above

a) The conversion of protein-coding RNA to DNA

which of the following accurately describes a ribose of a nucleic acid a) its 2' carbon is bonded o a -OH group b) its 4' carbon is bonded to a phosphate group c) the 1' can be bonded to thymine d) all of the above e) none of the above

a) its 2' carbon is bonded o a -OH group

Using Chargaff's rule, if a strand of DNA contained 12% guanine, which statement is correct? a) there is 38% adenine b) there is 24% cytosine c) there is 38% GC content d) there is 12% thymine

a) there is 38% adenine

which of the following is false about human chromosomes? a) there is a total of 23 autosomal pairs b) they are composed of a short p-arm and a long q-arm, separated by a centromere c) euchromatin is a region that is actively expressed d) they have fewer protein coding genes than a rice plant e) none of the above

a) there is a total of 23 autosomal pairs

true or false: ddNTPs have an -H group at both 2' and 3' positions on their pentose sugar a) true b) false

a) true

if the adenine content in a sample of DNA is found to be 32%, what is the cytosine content? a) 32% b) 18% c) 64% d) 50% e) none of the above

b) 18%

If a DNA sample has an A260 value of 1.0, what is its concentration? (Note: the path length is 1cm, and the molar extinction coefficient for DNA is 0.020 g-1cm-1L) a) 100 g/L b) 50 mg/mL c) 25 mg/mL d) 1.25 mg/L e) 50 g/L

b) 50 mg/mL

A typical sequencing reaction the amount of dNTPs is much greater than of the ddNTPs. If equal amounts of both types of nucleotides were used in each reaction, how might that affect the outcome? a) After gel electrophoresis and visualization of the results mostly long fragments would be present and no sequence could be read close to the primer. b) After gel electrophoresis and visualization of the results mostly short fragments would be present and only sequences very close to the primer could be read. c) After gel electrophoresis and visualization of the results the sequence could be read normally; the dNTP/ddNTP ratio does not affect the products of the reaction. d) After gel electrophoresis and visualization of the results only the purine reactions would show termination and be read from the gel. e) After gel electrophoresis and visualization of the results no bands would be visible because the high concentration of ddNTPs would inhibit the activity of the polymerase.

b) After gel electrophoresis and visualization of the results mostly short fragments would be present and only sequences very close to the primer could be read.

Which of the following is a non-covalent interaction that stabilizes the helical structure of double stranded DNA? a) Hydrogen bonding between adjacent sugar groups b) Hydrophobic base stacking c) Stem loops involving greater than 5 bases and less than 10 d) Phosphodiester bonds in the DNA backbone e) Repulsion between the negatively charged phosphate groups of the DNA backbone

b) Hydrophobic base stacking

what is the most frequent genetic difference between individuals of the same species a) chromosomal inversions b) single nucleotide polymorphisms c) chromosomal fusions

b) single nucleotide polymorphisms

Which of the following regarding RNA features is FALSE? a) In RNA: the base G can pair with U b) In RNA: hydrogen bonding can involve 3 bases simultaneously c) RNA is more resistant to degradation d) RNA contains an -OH group on the 2' sugar carbon that becomes chemically reactive at high pH e) RNA can form helical structures

c) RNA is more resistant to degradation

Which of the following is TRUE about quantitative PCR: a) Amplification products are run on an agarose gel containing ethidium bromide to quantify them. b) SYBR green added to the reaction mix emits fluorescence when bound to mRNA. c) Reaction products are quantified after every PCR cycle. d) The threshold cycle is used to indicate when the reaction plateaus after all reagents have been consumed. e) The reaction involves the amplification of genomic DNA.

c) Reaction products are quantified after every PCR cycle.

Which statement regarding Sanger DNA sequencing (using 4 separate reactions) is FALSE? a) All reactions require dATP + dCTP + dGTP + dTTP b) A primer is required to anneal to the template DNA strand c) Reaction termination depends on a mixture of dideoxynucleotides coupled with fluorescent tags d) Reaction products are typically separated by gel electrophoresis e) Reaction products of longest length migrate the least by electrophoresis

c) Reaction termination depends on a mixture of dideoxynucleotides coupled with fluorescent tags

DNA is resistant to hydrolysis under alkaline conditions because: a) DNA lacks the 3' hydroxyl group on the pentose ring, which participates in hydrolysis. b) Deoxyribose is able to form furanose rings without an oxygen, which makes the ring more stable. c) The 2' hydroxyl of the pentose sugar is directly involved in the hydrolysis reaction, and DNA lacks this group. d) DNA does not contain uracil, and the methyl group of uracil in RNA is directly involved in the hydrolysis reaction. e) None of these choices is correct.

c) The 2' hydroxyl of the pentose sugar is directly involved in the hydrolysis reaction, and DNA lacks this group.

which of the following external factors can destabilize nucleic acid structure? a) increase in salt concentrations b) decrease in organic solvents c) increase in temperature d) all of the above

c) increase in temperature

which of the following about histone modification is false? a) trans-acting modifications lead to recruit of chromatin remodelling/transcription factors b) cis acting-modifications directly lead to loosening/tightening nucleosome arrangement c) the histone modification enzymes non-covalently alter histone proteins d) the histone modification enzymes can impart multiple modifications on a single histone

c) the histone modification enzymes non-covalently alter histone proteins

You performed multiple experiments to analyze histone H2A levels linked to your gene of interest. You found out that region A has much higher frequency of H2AZ variant than region B. What is a possible conclusion from this result? a) The region A has more ongoing DNA repair or genetic recombination because H2AZ is thought to recruit DNA repair proteins. b) The region A has less ongoing DNA repair or genetic recombination because H2AZ is thought to protect DNA from damage or recombination. c) The region A is less actively transcribed region because H2AZ is thought to destabilize the open state of chromatin. d) The region A is more actively transcribed region because H2AZ is thought to stabilize the open state of chromatin. e) The result is not reliable because H2AZ is known to be scattered throughout the genome in modest amounts.

d) The region A is more actively transcribed region because H2AZ is thought to stabilize the open state of chromatin.

which of the following changes could increase risk of cancer? a) inactivation of a HAT enzyme could increase histone acetylation and decrease expression of a critical regulatory gene b) activation of a HAT enzyme could increase histone acetylation and decrease expression of a critical regulatory gene c) inactivation of a HAT enzyme could decrease histone acetylation and increase expression of a critical regulatory gene d) inactivation of a HAT enzyme could decrease histone acetylation and decrease expression of a critical regulatory gene e) all of the above

d) inactivation of a HAT enzyme could decrease histone acetylation and decrease expression of a critical regulatory gene

What information is contained in genomic DNA? a) control signals for gene expression activation b) signals for chromatin assembly c) start sites for gene transcription d) protein coding sequences e) all of the above are true

e) all of the above are true

identify the correct statement: a) a protein containing a bromodomain linked to a HAT domain would propagated chromosome histone acetylation b) a protein containing a bromodomain linked to a HAT domain would increase histone acetylation c) a protein containing a bromodomain linked to a HAT domain would likely promote gene expression d) bromodomains recognize acetylation modification of histones e) all of the above are true

e) all of the above are true

Which of the following is NOT TRUE of Histone H1: a) It regulates the entry and exit angles of nucleosome-associated DNA b) It dimerizes with histone 2A during DNA compaction c) Provides an extra 6-7-fold compaction of DNA beyond what is achieved by histone octamers alone d) Is present in chromatin at the following molar ratio H1:H2A:H2B:H3:H4 = 1:2:2:2:2 e) It is not one of the "core" histone proteins that assemble into octamers

b) It dimerizes with histone 2A during DNA compaction

TRUE or FALSE: Choose the best combination of answers for the following three statements concerning the chromatin remodeling complexes. I. They can introduce histone variants. II. There are two types of complexes: Cis acting and trans acting. III. They can block a promoter on a gene and repress transcription of the gene. a) T-T-T b) T-F-T c) F-T-F d) F-F-T e) F-F-F

b) T-F-T

Which of the following is NOT a way chromatin remodeling complexes are able to influence nucleosomes? a) They can slide a nucleosome to a different location b) They can modify the N-terminal tails of histones c) They can eject a nucleosome from the DNA d) They can replace the nucleosome with a new nucleosome that contains a variant histone e) All of these choices are correct

b) They can modify the N-terminal tails of histones

what is the composition of a nucleosome core a) a histone octamer composed of two copies of each: H1, H2, H3, H4 b) a histone octamer composed of two copies of each: H2A, H2B, H3, H4 c) a histone tetramer composed of one copy of H2A, H2B, H3, and H4 d) none of the above

b) a histone octamer composed of two copies of each: H2A, H2B, H3

a gene for leptin, a hormone involved in appetite, appears in both humans (LEP) and mice (Lep) and has a high degree of sequence similarity. these genes can be best described as: a) homologs b) orthologs c) paralogs

b) orthologs

Which of the following correctly describes general characteristics of histones? a) negative and acidic proteins that are homologous across eukaryotes b) positive and basic proteins that are homologous across eukaryotes c) negative and acidic proteins that are only found in higher eukaryotes d) positive and basic proteins that are only found in higher eukaryotes e) Contains additional RNA binding activity.

b) positive and basic proteins that are homologous across eukaryotes

When cloning a DNA gene fragment into the PstI site of plasmid pBR322, which statement is correct? a) bacterial colonies containing the gene fragment will grow on media plates containing ampicillin AND grow on plates containing tetracycline b) bacterial colonies containing the gene fragment will grow on media plates containing ampicillin BUT NOT grow on plates containing tetracycline c) bacterial colonies containing the gene fragment will NOT grow on media plates containing ampicillin BUT grow on plates containing tetracycline d) bacterial colonies containing the gene fragment will NOT grow on media plates containing ampicillin AND ALSO NOT grow on plates containing tetracycline e) all of the above are incorrect

c) bacterial colonies containing the gene fragment will NOT grow on media plates containing ampicillin BUT grow on plates containing tetracycline

which of the following series of transitions would have a hyperchromic effect throughout? a) ssDNA -> dsDNA -> free nucleotides b) free nucleotides -> ssDNA -> dsDNA c) dsDNA -> ssDNA -> free nucleotides d) dsDNA -> free nucleotides -> ssDNA

c) dsDNA -> ssDNA -> free nucleotides

which of the following statements regarding the h1 histone is false? a) h1 possesses 2 dna binding sites and stabilizes linker DNA once bound b) h1 supports gene expression by increasing DNA compaction and forms chromatosomes once bound c) h1 is a key element of the histone core and is needed for nucleosome formation d) h1 is needed to produce higher order chromatin structure e) all of the above

c) h1 is a key element of the histone core and is needed for nucleosome formation

Which of the following is FALSE about histone modification? a) bromodomains recognize acetylated Lys residues b) chromodomains recognize methylated Lys residues c) methylation always leads to gene repression d) acetylation leads to higher levels of gene expression e) both acetylation and methylation modifications are reversible

c) methylation always leads to gene repression

actively expressed gene regions are most likely: a) darkly stained with Giemsa stain b) predominantly methylated on histone tails c) predominantly acetylated on histone tails d) darkly stained with Giemsa stain and predominantly methylated on histone tails e) darkly stained with Giemsa stain and predominantly acetylated on histone tails

c) predominantly acetylated on histone tails

Which of the following is NOT a common external factor which influences DNA stability? a) temperature b) salt c) pressure d) proteins e) organic solvents

c) pressure

! The long floppy N-terminal tails of histones are important because: a) they fix the DNA to the nuclear matrix b) they bind Giemsa to allow visualization of chromosome banding patterns c) their negatively charged residues repel the phosphate backbone of DNA d) they act to join adjacent nucleosomes together e) none of the above

c) their negatively charged residues repel the phosphate backbone of DNA

You have sequenced a genome. The reference genome has a size of 5,000,000 bp and your raw output includes 2,500,000 reads. The average read length is 100 bp. What is the depth of coverage? a) 200x b) 100x c) 150x d) 50x e) 25x

d) 50x

Which of the following is TRUE about the human genome? a) The human genome is larger than that of any other known organism. b) There is a larger proportion of gene-related sequences than there is intergenic and repeat DNA. c) All genes code for functional proteins. d) Exons represent a very small proportion of the human genome. e) The genome is made up of all chromosomal and mitochondrial DNA in the cell.

d) Exons represent a very small proportion of the human genome.

Which of the following statements, regarding the levels of organization within a chromosome, is FALSE? a) The mitotic chromosome represents the highest level of organization. b) A nucleosome consists of a DNA strand wound around a histone core. c) Packaging the genome requires a high degree of condensation while also permitting precise binding of regulatory factors to DNA. d) Histones are the only proteins required for formation of a chromosome. e) Chromatin is a filamentous complex that constitutes eukaryotic chromosomes.

d) Histones are the only proteins required for formation of a chromosome.

Using Beer's equation: if a sample gives a A260 reading of 0.650, which of the following is correct? a) If the extinction coefficient is 0.02 g(-1)cm(-1) L , the concentration equals 8 g L(-1) b) If the extinction coefficient is 0.02 g(-1)cm(-1) L , the concentration equals 16 g L(-1) c) If the extinction coefficient is 0.04 g(-1)cm(-1) L , the concentration equals 32 g L(-1) d) If the extinction coefficient is 0.04 g(-1)cm(-1) L , the concentration equals 16 g L(-1)

d) If the extinction coefficient is 0.04 g(-1)cm(-1) L , the concentration equals 16 g L(-1)

Which proteins transfer epigenetic information to progeny after DNA replication ? a) Marked histone H1 b) Unmarked histone H2A:H4 dimers c) Unmarked histone H3:H4 dimers d) Marked histone H3:H4 dimers e) Marked histone H2A:H4 dimers

d) Marked histone H3:H4 dimers

Which of the following statements concerning nucleosomes is correct? a) A local abundance of G-C base pairs at histone binding sites facilitates compression and tight wrapping of DNA. b) The binding of H1 does not substantially impact the degree of DNA compaction. c) The last stage of DNA condensation involves the observable formation of the 30 nm filament. d) Nucleosomes represent the organized units into which DNA is packed; they typically each encompass ~200 base pairs of genomic DNA. e) Revealed through electron microscopy, nucleosomes resemble a curved yet uniform string.

d) Nucleosomes represent the organized units into which DNA is packed; they typically each encompass ~200 base pairs of genomic DNA.

Which of the following is a unique feature of next generation DNA sequencing? a) Reactions require dATP + dCTP + dGTP + dTTP b) A primer is required to anneal to the template DNA strands c) Reaction detection depends on nucleotides coupled with fluorescent tags d) Sequence detection depends on reversible chemical groups on nucleotides e) Reaction products are detected following laser excitation

d) Sequence detection depends on reversible chemical groups on nucleotides

You have isolated a DNA sample and wish to amplify it. Before you run your PCR however, you want to check the purity of your DNA. Instead of checking absorbance at just 260nm, you determine the optical density of your samples across a range of wavelengths. The absorbance curve for your sample is below. https://bhsc01.it.meds.queensu.ca/portal/api/serve-learning-object.api.php?id=472&filename=Annotation+2020-07-08+133627+BCHM+218.png a) This sample is pure, and can be used for PCR. b) This sample is pure, but cannot be used for PCR. c) The sample is contaminated with a protein containing only aliphatic amino acids, d) The sample is contaminated with protein containing some nonpolar, aromatic amino acids. e) The sample is contaminated with RNA, and the 260/280 ratio is 2.0.

d) The sample is contaminated with protein containing some nonpolar, aromatic amino acids.

Fill in the blanks, euchromatin will be predominately ________ on histone tails and will appear ________ when stained with Giemsa dye. a) acetylated, dark b) methylated, light c) methylated, dark d) acetylated, light e) none of the above

d) acetylated, light

the stringency of DNA hybridization can be a) lowered by high salt concentration b) increased by the rise of temperature to Tm c) lowered by the absence of organic solvents d) all of the above e) none of the above

d) all of the above

which of the following is not a function of histone H1 a) stabilizing nucleosomes b) promoting higher order chromosome structure c) enhancing the repression of transcription by nucleosomes d) binding to regions undergoing active RNA synthesis

d) binding to regions undergoing active RNA synthesis

which function for histone variant forms is correct? a) histone h3.3 can be phosphorylated at s139 to recruit DNA repair proteins b) histone h2ax: critical for X chromosome inactivation c) histone h2az: leads to nucleosome associated with actively transcribing genes d) cenpa: associated with kinetocore for chromosome separation during cell division e) all of the above are true

d) cenpa: associated with kinetocore for chromosome separation during cell division

Identify the FALSE statement a) the haploid genome size (DNA base pair length) of the fern plant is greater than that of humans b) the human haploid genome is ~3,000,000,000 DNA base pairs c) human cells typically have 22 pairs of autosomal chromosomes d) chromosome p-arms are bigger than chromosome q-arms e) chromosome regions staining darkly with Giemsa contain regions of low gene transcriptional activity

d) chromosome p-arms are bigger than chromosome q-arms

which of the following is used in dye-terminator but not in traditional Sanger sequencing? a) gel electrophoresis b) heat denaturation of dsDNA c) four reaction mixtures to add each ddNTP separately d) fluorescently labeled ddNTPs e) none of the above

d) fluorescently labeled ddNTPs

Which function for histone variant forms is correct? a) CENPA: stabilises open chromatin state for active gene transcription b) histone H2AX: associated with kinetocore for chromosome separation during cell division c) histone H3.3 can be phosphorylated at S139 to recruit DNA repair proteins d) histone H2AZ macro: X chromosome inactivation e) all of the above are true

d) histone H2AZ macro: X chromosome inactivation

Next generation sequencing uses which of the following modified nucleotides? a) Fluorescently labeled dideoxynucleotides b) nucleotides bearing an irreversible 2' block and a cleavable fluorescent label c) dideoxynucleotides bearing a cleavable fluorescent label d) nucleotides bearing a reversible 3' block and a cleavable fluorescent label e) nucleotides bearing a reversible 2' block and a cleavable fluorescent label

d) nucleotides bearing a reversible 3' block and a cleavable fluorescent label

A plasmid vector used in molecular cloning typically has which of the following features? a) An origin of replication b) An antibiotic-resistance selectable gene to ensure that the only bacteria growing contain the intact or recombinant vector c) Unique restriction sites for insertion of DNA segments d) Small size to facilitate entry into the cell and biochemical manipulation of the DNA e) All of the above are features of plasmid vectors

e) All of the above are features of plasmid vectors

Which of the following statements regarding traditional Sanger sequencing are false? i) The 3' carbon of a ddNTP bears a -H group. ii) After denaturing a dsDNA target via heat, RNA primers are added to the exposed ssDNA strands. iii) Following the termination of synthesis, the template DNA's sequence is read directly via gel electrophoresis of the resulting fragments. iv) One particular type of ddNTP is added to each of four reaction mixtures alongside a much higher concentration of dNTPs, resulting in all possible lengths of fragments. v) Traditional Sanger sequencing is a common in-vivo technique for determining sequences of lengths 1000-1500. a) i and iii b) i, ii, and iii c) iv and v d) ii, iii, and v e) All statements are true.

e) All statements are true.

Which of the following is NOT a component of a polymerase chain reaction (PCR)? a) dNTPs b) DNA containing the sequences to be amplified c) Primers complementary to each end of the sequence to be amplified d) Heat stable Taq polymerase e) DNA ligase to connect the fragments together

e) DNA ligase to connect the fragments together

A research team is attempting to determine the sequence of a gene in a pathogenic E. coli strain acquired resistance to antibiotics. Upon purifying a large amount of the target sequence by PCR, the researchers conduct Sanger sequencing and run the newly-synthesized DNA fragments through gel electrophoresis, giving the following product: https://bhsc01.it.meds.queensu.ca/portal/api/serve-learning-object.api.php?id=471&filename=BCHM+128+-+Quiz+%23+3.png From this gel data, what is the 5'-3' sequence of the template DNA? a) 5'-CAGCGATTACGCTCAGGATCA-3' b) 3'-TGATCCTGAGCGTAATCGCTG-5' c) 5'-ACTAGGACTCGCATTAGCGAC-3' d) 3'-CAGTACGTACATGGTCAAGCG-5' e) None of the above

e) None of the above

Which of the following is NOT represented in the genome sequence? a) Coding sequences for RNA and protein. b) Signals for initiation of replication. c) Start and stop sites for transcription. d) Sites for histone modifications. e) Signals for chromatin condensation and remodeling.

e) Signals for chromatin condensation and remodeling.

Which of the following is a histone modification mechanism? a) Acetylation of lysines b) Methylation of arginines c) Phosphorylation of serines d) Ubiquitination of lysines e) all of the above

e) all of the above

Which of the following changes could increase risk of cancer? a) activation of a HMT enzyme could increase histone H3 methylation at lysine 9 and decrease expression of a critical regulatory gene b) inactivation of a HMT enzyme could decrease histone H3 methylation at lysine 4 and decrease expression of a critical regulatory gene c) inactivation of a HMT enzyme could decrease histone H3 methylation at lysine 9 and increase expression of a critical regulatory gene d) activation of a HMT enzyme could increase histone H3 methylation at lysine 4 and increase expression of a critical regulatory gene e) all of the above could be true

e) all of the above could be true

Which statement regarding quantitative qPCR is FALSE? a) the dye SYBR green binds more strongly to dsDNA b) the no template control is not expected to reach the Ct threshold during the course of the reaction c) qPCR sequence involves denaturation, annealing and amplification d) the qPCR plateau phase indicates that PCR reagents have been exhausted e) samples that surpass the Ct threshold at low cycle number indicate relatively lower amounts of target cDNA

e) samples that surpass the Ct threshold at low cycle number indicate relatively lower amounts of target cDNA