Nucleic Acid Biochemistry Flashcards
When comparing different species, which of the following best predict the relative number of genes in each species?
a. the size of the organism
b. the complexity of the organism
c. the size of its brain
d. the size of the genome
e. the number of chromosomes
d. the size of the genome.
The number of chromosomes is roughly correlated as well.
Chromatin in which of the following states is the most euchromatic?
a. in a Barr body
b. in the centromere
c. in a transcribed gene during G1
d. in a silenced gene during M phase
e. in a sperm nucleus
c. in a transcribed gene during G1
Genes must be euchromatic (decondensed) in order for transcription factors to have access to them. Chromatin is highly condensed during mitosis, when packed in the sperm head, when part of an inactivated X chromosome (Barr body) and in structural, non-expressed regions of a chromosome such as the centromere.
Which of the following would be expected for a genetic disease based on a mutation in mitochondrial DNA?
a. it would be more common in men
b. it would be more common in women
c. it would be inherited maternally
d. it would be easy to diagnose based on symptoms
e. it would affect multiple organ systems
c. it would be inherited maternally
e. it would affect multiple organ systems
Mitochondria is maternally inherited but unlike X-linked disorders, will affect both men and women who inherit defective genes. Because of heteroplasmy, different people are affected in different organs and to different extents, making diagnosis tricky. However, since mitochondrial function is essential to so many tissues, symptoms typically arise in multiple organs.
Which of the following modifications to histone H3 promote gene silencing?
a. acetylation
b. deacetylation
c. demethylation
d. methylation
e. phosphorylation
b. deacetylation
d. methylation
A typical eukaryotic gene consists of which of the following elements?
a. internal ribosome binding sites
b. introns
c. exons
d. enhancers
b. introns
c. exons
d. enhancers
Multiple mRNAs can arise from a primary transcript by use of alternative
a. splicing.
b. poly(A) sites.
c. promoters.
d. ribosome binding sites.
a. splicing.
b. poly(A) sites.
c. promoters.
Which of the following is (are) encoded by multiple genes present in the human genome?
a. ribosomal RNA
b. transfer RNA
c. histone
d. lysozyme
a. ribosomal RNA
b. transfer RNA
c. histone
Which of the following statements is (are) true of the human genome?
a. 1.5 percent of the genome corresponds to protein coding sequences.
b. The median length of an intron is 10 kb.
c. 10 percent of the genome is transcribed into pre mRNA precursors.
d. Most human exons contain 500–1000 base pairs.
a. 1.5 percent of the genome corresponds to protein coding sequences.
DNA fingerprinting is a technique based on differences in the
a. length of introns.
b. number of tandem copies of a simple sequence repeat.
c. number of tandem ribosomal RNA genes.
d. size of protein coding genes.
b. number of tandem copies of a simple sequence repeat.
Transposition by a bacterial insertion element
a. occurs at a frequency of approximately 1 in 103 cells per generation.
b. can inactivate an essential gene.
c. is mediated through a RNA intermediate.
d. requires the enzyme transposase.
b. can inactivate an essential gene.
d. requires the enzyme transposase.
Transposition by a retrotransposon requires activity of which of the following enzymes?
a. RNA polymerase
b. reverse transcriptase
c. DNA methylase
d. DNA polymerase
a. RNA polymerase
b. reverse transcriptase
LINES (long interspersed elements)
a. are retrotransposons that lack LTRs.
b. are approximately 300 base pairs long.
c. are a rare class of mobile elements in mammals.
d. use the enzyme transposase for transposition.
a. are retrotransposons that lack LTRs.
Human mitochondrial DNA
a. uses the standard genetic code.
b. encodes its own ribosomal RNAs.
c. contains introns like nuclear genes.
d. is larger than yeast mitochondrial DNA.
b. encodes its own ribosomal RNAs.
Plant mitochondrial DNA
a. is the same size as human mitochondrial DNA.
b. encodes a 5S mitochondrial rRNA.
c. contains multiple copies that recombine with each other.
d. uses the standard genetic code.
b. encodes a 5S mitochondrial rRNA.
c. contains multiple copies that recombine with each other.
d. uses the standard genetic code.
An open reading frame (ORF) is defined as a DNA sequence that
a. begins with a start codon.
b. ends with a stop codon.
c. contains 50 codons.
d. contains approximately an equal frequency of A, T, G, and C.
a. begins with a start codon.
b. ends with a stop codon.
Two related genes that are derived from a gene duplication event are considered to be
a. homologous.
b. paralogous.
c. orthologous.
d. members of a gene family.
a. homologous.
b. paralogous.
d. members of a gene family.
A transcriptionally active gene compared with a transcriptionally inactive gene would be expected to
a. contain acetylated histones.
b. contain unacetylated histones.
c. be sensitive to DNase I.
d. be resistant to DNase I.
a. contain acetylated histones.
c. be sensitive to DNase I.
Scaffold-associated regions
a. are the chromosome attachment points for the mitotic spindle.
b. can insulate transcription units from each other.
c. are the points at which DNA interacts with histone proteins.
d. are found between transcription units.
b. can insulate transcription units from each other.
d. are found between transcription units.
Metaphase chromosomes can be identified
a. by shape.
b. by the size and number of introns.
c. by banding patterns with Giemsa reagent.
d. by chromosome painting.
a. by shape.
c. by banding patterns with Giemsa reagent.
d. by chromosome painting.
Telomerase
a. extends DNA strands during DNA synthesis.
b. has reverse transcriptase activity.
c. is a protein-RNA complex.
d. replicates repetitious DNA located at the centromere.
b. has reverse transcriptase activity.
c. is a protein-RNA complex.
Compare and contrast simple transcription units and complex transcription units.
A simple transcription unit produces a single monocistronic mRNA, which is translated into a single protein. A complex transcription unit produces primary transcripts that can be processed in alternative ways and translated into multiple proteins.
Describe the three different ways that multiple mRNAs can arise from a complex transcription unit in eukaryotes.
A complex transcription unit is transcribed into multiple mRNAs by using alternative promoters, poly(A) sites, and splicing. The use of alternative promoters produces mRNAs with different 5´ exons but common 3´ exons. The use of alternative poly(A) sites produces mRNAs with common 5´ exons but different 3´ exons. The use of alternative splice sites produces mRNAs with common 5´ and 3´ exons but different combinations of internal exons.
Describe the general organization of the human genome in terms of protein-coding and functional RNA genes, repetitious DNA, and spacer DNA.
The human genome consists of protein-coding and functional RNA genes, repetitious DNA, and spacer DNA. Protein-coding genes and functional RNA genes make up approximately 30 percent of the genome. Protein-coding genes can exist as solitary genes or duplicated genes. Functional RNAs such as tRNA, rRNA, and snRNA are present as tandemly repeated genes. Repetitious DNA makes up almost half of the human genome and is usually concentrated at specific chromosomal locations, e.g., at the centromere. The remainder of the genome consists of spacer or intergenic DNA.
Describe the molecular basis for the DNA fingerprinting technique. How can this be used to differentiate between two individuals?
The DNA fingerprinting technique is based on differences in the length of simple-sequence DNAs. Simple-sequence DNA usually occurs in tandem arrays. The number of simple-sequence repeat units at a given genetic locus varies between individuals, and thus the total length of the tandem array differs. These differences in the length of tandem arrays throughout the genome are unique to an individual and is the basis for an individual’s unique DNA fingerprint.
Describe the structural features of bacterial insertion sequences and transposons.
Bacterial insertion sequences (IS) are about 1–2 kilobases long. At each end of the IS element is an approximately 50-base-pair inverted repeat. Between the inverted repeats is a region that encodes the enzyme transposase—which is required for transposition or the “cut and paste” operation of the element—to a new site in the genome.
Describe the possible role that mobile DNA elements played in evolution.
Mobile DNA elements are hypothesized to have had a profound effect on the evolution of organisms. Insertion of a mobile DNA element into or near a gene can cause a mutation in the gene. Some evidence suggests that recombination between repeat sequences (e.g., mobile elements) of two separate genes can generate a novel combination of exons, a process known as exon shuffling. Unequal crossing over between repeat sequences can result in gene duplication. Furthermore, transposition of DNA adjacent to mobile DNA elements can move transcriptional control elements to new regions of the genome.
How does plant mitochondrial DNA differ from mammalian mitochondrial DNA?
Plant mitochondrial and animal mitochondrial DNA are circular molecules that encode for tRNA, rRNA, and essential mitochondrial proteins. In contrast to mammals, plants contain multiple mitochondrial DNAs that appear to recombine with one another. Plant mitochondrial DNAs are much larger and more variable in size than those of other organisms. Plant mitochondrial DNA also encode a 5S mitochondrial rRNA, which is present only in plant mitochondrial ribosomes, and the α subunit of the F1 ATPase. Furthermore, plant mitochondrial DNA uses the standard genetic code, whereas mammalian mitochondria use a modified code.
What is a BLAST search and how can it be used to help determine the function of an unknown cloned gene?
The BLAST (basic local alignment and search tool) program searches the DNA/protein databases for significant matches between a query sequence and stored sequences. The search program then assigns a score based on the extent of the match. For an unknown cloned gene, the DNA sequence or predicted amino acid sequence can be used as the query sequence for the BLAST search. If a known gene or protein in the database shows significant similarity to the query sequence, then it is likely that the unknown cloned gene is functionally similar to the known gene.
What are the applications of DNA microarrays?
A DNA microarray consists of thousands of individual, closely packed, gene-specific sequences attached to a surface such as glass or a nylon membrane. The power of the microarray is its ability to examine the expression of thousands of genes simultaneously. It is the functional equivalent of performing thousands of Northern blots at one time.
Describe the role that nonhistone proteins play in organizing chromosome structure.
Nonhistone proteins provide a structural scaffold for organizing chromatin loops. The chromosome scaffold, which has the shape of a metaphase chromosome, consists of nonhistone proteins that serve as binding sites for chromatin loops.
How does chromatin differ between transcriptionally inactive and transcriptionally active regions of DNA?
Experimental evidence indicates that transcriptionally inactive DNA has a condensed chromatin structure. This structure makes the DNA inaccessible to RNA polymerase. In contrast, actively transcribed DNA is present in a more extended, “beads-on-a-string” form of chromatin. DNA with this more open conformation is more accessible to RNA polymerase and other proteins required for transcription.
What three functional elements are required for replication and stabilization of chromosomes?
Eukaryotic chromosomes require origins of replication to initiate DNA replication, a centromere for proper segregation of chromosomes during mitosis, and telomeres to stabilize the ends.
How many base pairs make up the human genome? A. 3.3 million B. 5.1 billion C. 3.3 billion D. 5.1 million
C. 3.3 billion
When was Sanger sequencing developed and what is another name for it?
1975, chain terminator
What is the typical read length for a Sanger sequencing product?
A. 300-800 bps
B. 500-1,000 bps
C. 100-300 bps
A. 300-800 bps
What are the major differences between Sanger sequencing and massively parallel sequencing?
- Longer read length with Sanger
- Single template read for Sanger, many template reads with MPS
- Sanger cannot be used for gene expression or quantitative assays
- No prior knowledge of the genome is required for MPS
Which of the following mutations can result in a reduction of β-galactosidase?
a. a mutation in adenylate cyclase
b. a mutation in catabolite activator protein (CAP)
c. a mutation in the CAP site in the lac control region
d. a mutation in the repressor binding site in the operator
a. a mutation in adenylate cyclase
Specific DNA control elements in promoters can
a. interact with general transcription factors.
b. interact with repressor proteins.
c. interact with activator proteins.
d. remain unavailable because of condensed chromatin.
a. interact with general transcription factors.b. interact with repressor proteins.c. interact with activator proteins.d. remain unavailable because of condensed chromatin.
Reporter genes are used to
a. express enzymes that are not easily assayed in cell extracts.
b. express enzymes that are easily assayed in cell extracts.
c. characterize DNA control elements.
d. characterize reporter plasmids.
b. express enzymes that are easily assayed in cell extracts.c. characterize DNA control elements.
The three eukaryotic RNA polymerases can be distinguished by
a. the types of genes they transcribe.
b. the number and types of large subunits.
c. their differential sensitivities to cycloheximide.
d. their differential sensitivities to α-amanitin
a. the types of genes they transcribe.andd. their differential sensitivities to α-amanitin.
“Which of the following can be identified using a series of promoter linker scanning mutations?
a. areas of the promoter that are non-essential
b. areas of the promoter that are essential
c. the presence of separate transcriptional control regions
a. areas of the promoter that are non-essentialb. areas of the promoter that are essentialc. the presence of separate transcriptional control regions
An enhancer
a. can be located upstream of a promoter.
b. can be located downstream of a promoter.
c. can be located a variable distance from the promoter.
d. is always located within 1 kb of the promoter.
e. can be cell-type-specific.
a. can be located upstream of a promoter.b. can be located downstream of a promoter.c. can be located a variable distance from the promoter.e. can be cell-type-specific.
The fact that a specific protein leaves a footprint on a DNA molecule is indicative of
a. a lack of interaction between the specific protein and DNA.
b. protection from DNAse by the specific protein.
c. binding of the specific protein to all types of DNA.
d. binding of the specific protein to a specific sequence of DNA.
b. protection from DNAse by the specific proteinandd. binding of the specific protein to a specific sequence of DNA.
The C-terminal activation domain of transcriptional activators is capable of
a. binding to DNA.
b. stimulating transcription.
c. interaction with other transcriptional machinery.
d. functioning in a fusion with a DNA-binding domain from an unrelated transcriptional activator.
a. binding to DNA.
b. stimulating transcription.
c. interaction with other transcriptional machinery.
d. functioning in a fusion with a DNA-binding domain from an unrelated transcriptional activator.
Which of the following are not found in DNA-binding proteins?
a. homeodomains
b. zinc fingers
c. leucine zippers
d. CpG islands
d. CpG islands
Transcription factors can:
a. exhibit cooperative binding.
b. exist as heterodimers.
c. act to repress transcription of transcription factor genes.
d. undergo conformational changes which alter activity.
e. never interact with co-repressors.
a. exhibit cooperative binding.
b. exist as heterodimers.
c. act to repress transcription of transcription factor genes.
d. undergo conformational changes which alter activity.
Which is the first factor to bind at the promoter of eukaryotic genes?
a. RNA polymerase
b. TFIIA
c. TFIIB
d. TFIID
e. TATA box binding protein
d. TFIID,
e. TATA box binding protein
Which of the following occur(s) during Pol II transcription preinitiation complex formation?
a. TFIIA binds to TFIIB.
b. TFIIB unwinds the DNA.
c. TFIIB contacts both TATA box binding factor and DNA.
d. DNA bends.
c. TFIIB contacts both TATA box binding factor and DNA.
d. DNA bends.
Chromatin-mediated repression of transcription involves
a. modification of lysine residues in histones.
b. large, multiprotein complexes.
c. acetylation of histone tails.
d. deacetylation of histone tails.
a. modification of lysine residues in histones.
b. large, multiprotein complexes.
c. acetylation of histone tails.
Which of the following does (do) not require a DNA helicase activity?
a. SWI/SNF function
b. Pol II open-complex formation
c. transcription-factor binding to DNA
d. deacetylation of histone tails
c. transcription-factor binding to DNA
d. deacetylation of histone tails
The yeast two-hybrid system can be used to identify
a. proteins that interact with a known or unknown protein.
b. proteins that interact with a kinase domain.
c. cDNAs that encode interacting proteins.
d. co-activators and co-repressors.
a. proteins that interact with a known or unknown protein.
c. cDNAs that encode interacting proteins.
d. co-activators and co-repressors.
The expression of which gene(s) is (are) regulated by promoter proximal pausing?
a. hsp70
b. lac operon
c. tat
d. none of the above
a. hsp70