a. Direct repeats. An example of a direct repeat is: 5' GAGTTA GAGTTA 3' (Note: This represents the sequence across the top strand of the DNA double helix; dots indicate the DNA between the repeats)
b. Direct repeats. An example of a direct repeat is: 5' GAGTTC. TTAGGG 3'
c. Inverted repeats. An example of an inverted repeat is: 5' GAGTTA TAACTC 3'
d. Inverted repeats. An example of an inverted repeat is: 5' GAGTTA ATTGAG 3'
e. Inverted repeats. An example of an inverted repeat is: 5' GAGTTA CTCAAT 3'
2) Which of the following concepts is illustrated by the figure below? (Please note that more than one of the answers may be true statements, but only one is demonstrated by the picture.)
a) Bacterial cells contain multiple origins of replication
b) Eukaryotic cells contain multiple origins of replication
c) Multiple RNA polymerases can simultaneously transcribe a single gene
d) Holliday junctions are essential intermediates in recombination
e) Nucleosomes are important for packaging DNA
3) Which of the following is true about post-translational modifications of histones?
a. The modifications are irreversible
b. Each of the core histones can only be modified on one specific site
c. The modifications do not seem to have any effect on chromatin compaction
d. The modifications are mostly in the tails
4) Which of the following accurately describes euchromatin?
a. It is the more condensed, transcriptionally inactive regions of chromatin
b. It is the less condensed, transcriptionally inactive regions of chromatin
c. It is the more condensed, transcriptionally active regions of chromatin
d. It is the less condensed, transcriptionally active regions of chromatin
5) Which of the following statements about eukaryotic chromosomes is true?
a. Eukaryotic chromosomes are circular
b. Eukaryotic chromosomes are present in their most condensed state only in certain stages of the cell cycle.
c. All eukaryotes are haploid
d. Eukaryotic DNA is only associated with histones during interphase
e. Eukaryotic chromosomes always come in pairs
6) How many base pairs of DNA are wrapped around a nucleosome?
a. 96 base pairs of DNA
b. 147 base pairs of DNA
C. nw 1000 base pairs of DNA
d. A variable amount (from 50-300 bp) of DNA, depending on the organism
7) Which of the following is not true of bacterial plasmids?
a. The frequently carry essential genes, such as those encoding for DNA polymerase
b. They provide a common mode for transmitting antibiotic resistance between bacteria
c. They are often present in multiple copies per cell
d. They are circular, and composed of double-stranded DNA
8) Histones are
a. Acidic (negatively charged) proteins
b. Neutral proteins
c. Not proteins, but lipids.
d. Basic (positively charged) proteins
9) Which of the following histones is NOT a 'core histone' (that is, an integral part of the nucleosome)?
10) Which of the following is a difference between how core histones and transcriptional activator proteins interact with DNA?
a. The core histones predominantly interact with the phosphodiester backbone of DNA, while activator proteins form specific interactions with the DNA bases
b. The core histone proteins primarily interact with the bases of the DNA, while activator proteins predominantly interact with the phosphodiester backbone of DNA
c. The core histone form highly sequence-specific interactions with the DNA, while activator proteinsbind in a sequence independent manner
d. The core histones interact with the 3' OH group of DNA, while activator proteins interact with the 2° OH group
e. Both B and C
11) Which of the following sequences is hkely to serve as a recognition site for a restriction enzyme?
a. GGATCC - CCTACG
b. TAGTAG - ATCATC
c. COCC - GGUG
d. ATCOTA - TAGDAT
e. none of these
Which of the following is true about histone acetylation:
a. It neutralizes the positive charge on lysine, and tends to promote formation of heteroctromation
b. It neutralizes the positive charge en lysine, and tends to promote formation of euchromatin
c. It increases the positive charge of the histone, and tends to promote formation of euchromatin
d. It increases the positive charge of the histone, and tends to promote formation of heterochromatile
e. It increases the negative charge of the histome, and tends to promote formation of heterochromatio,
13) Which of the following is the natural function of the CRISPR system?
a. Protecting bacterials cell against invading viruses
b. Destroging the DNA when the cell dies
c. Protecting the eukaryotic cell against invading bacteria
d. Turnover of mRNA in bacteria
e. Repairing DINA
14) A plasmid used for DNA cloning contains all of the following EXCEPT:
a. A gene for antibiotic resistance
b. An origin of replication
c. A unique restriction site
d. A telomere at both ends of the DNA molecule
15) Which of the following statements is FALSE about the sequencing of the human genome, and the differences
between the public (NIH) and Celera approaches:
a. The method employed by the public group was more stepwise, but also more laborious than the Celera method
b. If a lab were to do whole-genome sequencing on patient samples, they would be more likely to use the method employed by the public group
c. The public approach mapped the fragments before sequencing while the Celera approached mapped after sequencing
d. The method used by Celera has faces greater challenges dealing with repetitive elements
16) You wish to use PCR to add restriction sites to the ends of a DNA fragments to facilitate cloning into a plasmid. Which of the following is true:
a. You would add a restriction site to the 5' end of the forward primer, and the 3' end of the reverse primer.
b. You would add a restriction site to the 3' end of the forward primer, and the 5' end of the reverse primer.
c. You would add a restriction site to the 3' end of each primer
d. You would add a restriction site to the 5' end of each primer
e. None of the above. Your primers need to perfectly match the sequence that they are amplifying, so PCR cannot be used to add restriction sites
17) During DNA replication in cells, helicase is required to unwind the DNA. is it likewise necessary to add helicase to a PCR reaction? Why or why not?
a. Yes, helicase is also required to unwind the DNA for PCR
b. Yes, but while helicase is essential for unwinding the DNA in cells, it performs a different function in PCR preventing tangling of the DNA strands
c. No, because the 95°C step in a PCR reaction performs the same function as helicase
d. No, because helicase is only required for synthesis in the S' to 3' direction, but DNA synthesis in a PCR reaction is 3' to 5'
e. No, because the 55°C step in a PCR reaction performs the same function as helicase
18) cDNA is
a. DNA found at the ends of each chromosome
b. DNA that is copied from genomic sequences
c. DNA found at a centromere
d. DNA that is copied from mRNA by reverse transcription
19) Which of the following is true about PCR?
a. 30 cycles should increase the amount of your specific DNA sequence by approximately 1000-fold
b. ddNTPs are added to ensure that the PCR products are the proper length
c. The top strand is replicated 5' to 3', while the bottom strand is replicated 3' to 5'
d. A thermostable polymerase is required to withstand repeated cycles of denaturation and annealing
20) Forward genetic techniques have been used extensively in molecular biology labs. Which sequence below best describes Forwards Genetics?
a. isolation of a naturally-occurring phenotypic mutant, followed by mapping of the mutation to the
b. genome random mutagenesis of the genome by exposure to a mutagen, isolation of phenotypic mutants, followed by mapping of the mutation to the genome
c. mutagenesis of a gene, followed by screening for phenotypes derived from the mutations to identify
d. targeted sequencing the genomes of related organisms, followed by in silico sequence alignments similarities and differences.
e. Both A and B
21) Reverse genetic techniques are increasingly common in modern molecular biology laboratories. Which sequence below best describes Reverse Genetics?
a. isolation of a naturally-occurring phenotypic mutant followed by mapping of the mutation to the genome
b. random mutagenesis of the genome by exposure to a mutagen, isolation of phenotypic mutants, mapping of the mutations to the genome
c. targeted mutagenesis of the gene, followed by screening for phenotypes derived from the mutations
d. sequencing the genomes of related organisms, followed by in silico sequence alignments identify similarities and differences.
e. Both A and B
22) The amount of ddATP added to a sequencing reaction is
a. Just enough to saturate the DNA polymerase
b. About 50% more than the amount of dATP
c. Much less than the amount of dATP
d. Much more than the amount of dATP
e. About the same as the amount of dATP
23) Why are bacteria grown in the presence of an antibiotic in DNA cloning experiments?
a. To kill all of the bacteria that have not taken up the cloning plasmid
b. To prevent laboratory workers from becoming infected with the bacteria
c. To slow down the growth of the bacteria
d. To kill any dangerous bacteria that may have been created
e. To kill viruses that might destroy the bacteria
24) You have identified a' new transcriptional activator protein, and are interested in screening a library to identify the activator's binding site. Which of the following is true?
a. You would want to screen a cDNA library, because genomic libraries contain so much junk DNA.
b. You would want to screen a cDNA library, because genomic libraries only contain the genes expressed in the specific cell type that the genomic DNA was isolated from.
c. You would want to screen a genomic library, because the activator binding sites is unlikely to be present
d. You would want to screen a genomic library, because cDNA libraries contain so much junk DNA. in.a.cDNA library.
25) Dideoxynucleotides (ddNTPs) are used in DNA sequencing to
a. Incorporate radioactivity into DNA
b. Introduce double strand breaks in the DNA
c. Terminate the polymerization reaction
d. Slow down the reaction rate of the polymerase
e. You would like to amplify the entirety of the DNA sequence shown below using PCR. Which pair of primers
26) DNA will be to required? be amplified (the sequence represents one strand of the DNA duplex that you will be amplifying): 5' Possible primers (note: all primers are written in the 5' to 3' direction).
a. CAATGACTTCG and CCCTAACTAGG
b. GCTTCAGTAAC and CCTAGTTAGGG
c. GTTACTGAAGC and CCTAGTTAGGG
d. GCTTCAGTAAC and GGATCAATCCC
e. GTTACTGAAGO and GGATCAATCCC
27) compared the genomes of two unrelated individuals, which of the following would likely be the most common you source of differences?
a. Single nucleotide polymorphisms
b. Structural rearrangements
c. Copy number variants
d. Changes in chromosome number
e. Short tandem repeats
29) Which of the following is NOT a property of eukaryotic RNA polymerase II?
a. It synthesizes RNA in the nucleus of the cell
b. It requires a primer to initiate RNA synthesis
c. The C terminal domain is phosphorylated during transcriptional elongation
d. It is unable to bind to a promoter in the absence of general transcription factors
e. It transcribes protein-coding genes
30) A mutation in which of the following would be most likely shut off transcription of the Tryptophan operon:
a. The gene for the Lac repressor
b. The Trp operator sequence
c. The gene for the CAP protein
d. The -35 site
e. Mutation of the CAP binding site
31) Polycistronic messages:
a. have the potential to encode at least two proteins
b. are only made in eukaryotes
c. are more rapidly exported from the nucleus
d. are always alternatively spliced
32) In an experiment in the test tube, pure DNA (no histones) containing a wild-type eukaryotic gene (with all of its transcriptional regulatory sequences) is incubated with pure RNA polymerase II, the necessary general transcription factors and NTPs. Addition of activator proteins only leads to a 10 fold stimulation of transcription. In the cell, the same gene is activated over 5000 fold. Why is the degree activation much greater in the cell than in the test tube?
a. Activated transcription cannot be achieved in a test tube
b. Activators do function in a test tube, but very poorly, so you can only achieve weak transcription
c. In the absence of activators, pure DNA is likely to show higher levels of transcription than the same gene in the cell.
d. Sigma factor works synergistically with activators in eukaryotic cells to achieve much stronger transcriptional activation
33) If you were to insert a full length bacterial gene (including its promoter and terminator) into a mammalian chromosome, which of the following would you expect?
a. It would be constantly expressed at high levels, because the eukaryotic regulatory factors would be unable to regulate its expression
b. It would be expressed at a level similar to its expression in bacteria, because the genetic code is the same in eukaryotes and prokaryotes
c. It would not be expressed, because eukaryotic RNA polymerase cannot transcribe from a bacterial promoter
d. It would not be expressed, because the genetic code is different in eukaryotes and prokaryotes
e. It would be expressed at higher levels than in prokaryotes, because prokaryotes utilize repressors to regulation transcription, but eukaryotes only use activators
34) Which of the following is a function of the transcription factor TFIIH?
a. Phosphorylation of the talk of Pol II, allowing for RNA synthesis
b. Bending of the DNA molecule at the TATA box
c. Creating a sharp bend in the DNA to facilitate the assembly of general transcription factors
d. Termination of transcription in eukaryotes
e. Recruiting sigma factor, thereby facilitating polymerase binding
35) You identify a new chemical that you name traxoline. You discover that traxoline is essential for bacterial survival, and you identify the operon responsible for traxoline's synthesis. Which of the following mechanisms is most likely to regulate this operon?
a. Traxoline binds to a repressor protein, preventing the repressor from binding to the operon
b. Traxoline binds to a repressor protein, promoting the repressor's binding to the operon
c. Traxoline binds to an acetyl transferase (an enzyme responsible for acetylation), promoting acetylation of the chromatin containing this operon
d. Traxoline bind to an activator protein, promoting the activator's binding to the operon
e. Both A and D
36) What determines which DNA strand serves as a template for transcription?
a. Most genes can use either to top or the bottom strand, and switch between them in response to environmental signals.
b. The position and orientation of the promoter determines which strand acts as a template
c. The top strand is always used as a template, since RNA polymerase works in the 5' to 3' direction
d. The bottom strand is always used as a template, since RNA polymerase works in the 3' to 5' direction
37) You identify two promoters in a strain of bacteria. One has -35 and -10 regions that perfectly match the consensus sequence, while the other one differs from the consensus at a few positions. Which of the following would you expect to be true?
a. Only the promoter that perfectly matches the consensus sequence will be recognized by sigma factor
b. Both promoters will be transcribed at equal levels, because sigma factor is relatively insensitive to the sequence of the -35 and -10 elements
c. The promoter with -35 and 10 elements that matches the consensus is likely to be the stronger promoter, and is likely to be regulated by positive regulation
d. The promoter with -35 and -10 elements that matches the consensus is likely to be the stronger promoter, and is likely to be regulated by negative regulation
e. The promoter with -35 and -10 elements that matches the consensus is likely to be the weaker promoter, and is likely to be regulated by positive regulation
38) Bacterial RNA polymerase transcribes the following genes:
a. rRNA genes
b. tRNA genes
c. mRNA genes
d. all of the above
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