BIO 325 Final Exam Review
XXY male would have ____ Barr body(ies)
1
Given: A DNA template strand with the nucleotide sequence 3′-ATTGCGTAC-5′. The RNA transcribed from this template strand will have the nucleotide sequence:
5′-UAACGCAUG-3′
Which of the following is NOT involved in RNA interference processes? A. RISC B. Drosha C. RNA Polymerase I D. Dicer
C (RNA Polymerase I)
Vectors such as pUC18 contain a large number of restriction enzyme sites clustered in one region. What is that site called? A) palindrome B) consensus sequence C) polylinker D) beta-galactosidase E) complementation
C (polylinker)
Which of the following procedures can benefit from "microarray" ? A. ASO analysis B. Differential gene expression in cancer cells C. Differential gene expression during development D. Differential gene expression by environment changes E. all of the above
E (All of the above)
5) In restriction mapping, map units are expressed as m.u. T / F
F
T/F: A common term for a plasmid or other DNA element that serves as a cloning vehicle is vector.
T
Collection of undifferentiated cells in plants is called the _____
apical meristem
If there are 20 amino acids to choose from, the chances of getting the correct polypeptide by random chance alone are __________ where n = number of amino acids in the polypeptide. (a) 1 in n^20 (b) 1 in 20^n (c) 1 in 20 x n (d) 1 in 20^20 (e) 1 in 2^n
b (1 in 20^n; 20 aa to choose from; n = # of amino acids in the polypeptide)
You wish to probe a human cDNA library to find out which insert has the β- globin gene. Which of the following would be a good choice as your probe (assume in all cases your probe is labeled)? a) A 30 base oligonucleotide corresponding to intron 1 b) A 30 base oligonucleotide corresponding to exon 1 c) A 30 base oligonucleotide corresponding to a β-globin gene enhancer d) An antibody specific for a β-globin epitope e) A heme molecule
b (A 30 base oligonucleotide corresponding to exon 1)
The most recent estimates predict ~20 000 genes in the human genome yet many, many more proteins are predicted to function in cells during the course of human development. Although numerous mechanisms are likely involved in generating what is know as 'protein diversity, one we have studied is: a) Codon bias b) Alternative splicing c) Intron shuffling d) Horizontal gene transfer e) Retrotransposition
b (Alternative splicing)
The primary role(s) of Hox genes during normal Drosophila development is to: a) Form segments b) Determine the identity of segments c) Promote cell division d) Maintain functional homeostasis e) Establish anteroposterior axis
b (Determine the identity of segments)
The nuclear genomes of higher eukaryotes are littered with repetitive DNA generated by numerous mechanisms making assembly of sequence data very challenging. To facilitate assembly of draft quality whole genome data researches employ: a) PCR amplification of homologous sequences in prokaryotes b) Paired-end reads from long insert vectors c) Information available in EST databases d) Sequence information derived from cloning of psuedogenes e) Automated sequencing facilities to achieve 10-fold coverage for each nucleotide in the genome.
b (Paired-end reads from long insert vectors)
A single strand of RNA: (a) is composed of the bases adenine, uracil, guanine, and cytosine (b) is composed of ribose sugars and phosphates (c) can form double‐stranded regions (e.g., stem loops) in which complementary bases are paired, (d) a & b (e) a, b & c
e (a, b & c)
A viral genome can be composed of: (a) double‐stranded DNA, (b) single‐stranded DNA, (c) double‐stranded RNA, (d) single‐stranded RNA, (e) all of the above
e (all of the above)
E. coli's heat shock response is controlled by alternative ______ factors that recognize different promoter sequences.
sigma
What is the probability that a gamete produced by a human female will contain only maternal chromosomes?
(1/2)^23 or about 1 in 8.4 million
DNA Template strand runs: __' → __'
3' → 5'
Codon: 5' UUC 3' Anticodon: 3' AAG 5' Translated in __' → __' direction
5' → 3'
ddNTPs are used in which of the following biochemical reaction? A) restriction digestion B) DNA sequencing C) Electron transport D) PCR E) Plaque hybridization
B (DNA sequencing)
The cellular organelles plastids and mitochondria, are thought to have arisen via endosymbiosis of a free living prokaryote by a primitive eukaryote. Strong evidence for the endosymbiotic theory includes: a) The number and nature of organelle outer membranes b) Variability in organelle genome sizes in different organisms c) Organization of organelle genes in operons d) A and C e) All of the above
D (A and C)
Which of the following is property of Enhancer? A. it is one of tran-acting components in gene regulation. B. it is always located immediate 5' end of a gene. C. it is always located immediate 3' end of a gene. D. its orientation is not important.
D (its orientation is not important)
T/F: Some tRNAs recognize more than one codon for amino acids they carry. This is due to the wobble position created at the 3' end of anticodon of tRNA.
False (wobble position on mRNA codon)
Ribosomal genes are transcribed by RNA Polymerase ___
I
T/F: After meiosis I, chromosome set number is n.
True
p53 can induce programmed cell death if the damage cannot be repaired through a process called ______ .
apoptosis
If you had a mutation affecting anterior-posterior patterning of the Drosophila embryo in which every other segment of the developing mutant larva was missing, would you consider it a mutation in: a) a gap gene b) a pair-rule gene c) a segment-polarity gene d) a segment-identity (i.e Hox) gene e) cannot be deterimined from information given
b (a pair-rule gene)
The protein coat that encloses the viral genome is called the: (a) nucleoid, (b) capsid, (c) envelope, (d) side chain, (e) ribozyme
b (capsid)
The initiation stage of translation in prokaryotes involves (among other things) the binding of ______ by its ______ to the ________ ribosomal subunit. (a) mRNA by its Shine‐Dalgarno sequence to the large (50S) ribosomal subunit, (b) mRNA by its Shine‐Dalgarno sequence to the small (30S) ribosomal subunit, (c) rRNA by its Shine‐Dalgarno sequence to the large (50S) ribosomal subunit, (d) rRNA by its Shine‐Dalgarno sequence to the small (30S) ribosomal subunit, (e) tRNA by its anti-codon to the large (50S ) ribosomal subunit.
b (mRNA by its Shine‐Dalgarno sequence to the small (30S) ribosomal subunit)
Which of the following is not involved in RNA interference processes? A. RISC B. Drosha C. RNA polymerase I D. Dicer E. All of these play a role in RNA interference processes.
c (RNA polymerase I)
In Prokaryotes, cluster of genes can be regulated together as operon. Each operon produces a single ________ mRNA, which contains multiple genes.
polycistronic
A short single-stranded piece of DNA that is labeled and used in hybridization experiments is called a(n) ________
probe
In humans, brachydactyly is a dominant condition. Six thousand four hundred people in a population of 10,000 show the disease (1,600 are BB, 4,800 are Bb) and 3,600 are normal phenotypes (bb). The frequency of the b allele is A. 0.6 B. 0.4 C. 0.36 D. 0.48 E. 0.16
A (0.6)
ddNTP lacks ..............at the ........end. A) methyl group, 3' B) OH group, 3' C) OH group, 5' D) Carboxyl group, 3' E) None of the above
B (OH group, 3')
The most critical step in the regulation of most bacterial genes is the binding of ____ _____ to the _____ .
RNA Polymerase; promoter
T/F: A man with blood type "A," whose father was blood type "O," married a woman of blood type "B" whose mother was blood type "O." Children of this couple can have all possible blood types
True
In eukaryotes, ________ replicates the leading strand in a processive manner. (a) DNA polymerase ε, (b) DNA polymerase δ, (c) DNA polymerase α, (d) DNA polymerase III, (e) DNA polymerase III + Primase.
a (DNA polymerase ε - epsilon)
You have a 3 kb piece of DNA corresponding to a portion of the human dystrophin gene. You also have a 3 kb plasmid vector (for cloning in E. coli). Which of the following is likely common to both of these DNA fragments? a) Restriction enzyme sites b) A polylinker (multiple cloning site) c) A selectable marker d) An origin of replication e) None of the above
a (Restriction enzyme sites)
The primary control point at which gene expression is regulated is initiation of: a) Transcription b) Splicing c) Nucleus-to-cytosol transport d) Translation e) Post-translational modification
a (Transcription)
Anabolic pathways involved in the synthesis of essential molecules are usually regulated by A. end product of the pathway. B. substrate of the pathway. C. other metabolites that are limiting. D. all of the above. E. none of the above.
a (end product of the pathway)
Compaction of a bacterial chromosome involves the formation of: (a) looped domains, (b) nucleosomes, (c) 30‐nm fibers, (d) b & c (e) a, b & c
a (looped domains)
As a general principle of gene regulation through operons regulatory genes encode: A. trans-acting proteins that interact with cis-acting DNA elements. B. cis-acting proteins that interact with cis-acting DNA elements. C. cis-acting proteins that interact with trans-acting DNA elements. D. trans-acting proteins that interact with trans-acting DNA elements. E. trans-acting DNA elements that interact with cis-acting proteins.
a (trans-acting proteins that interact with cis-acting DNA elements.)
Match: 1) Probes 2) Sanger's method 3) Plaque hybridization sequence 4) Transfection a) screening of DNA library b) viral vector c) DNA sequencing d) screening of phage library
a, c, d, b
The homeodomain found in all proteins encoded by Hox genes has what function? a) Binding RNA b) Binding histones c) Repressing transcription d) Binding DNA e) Targeting proteins for degradation
d (Binding DNA)
Which of the following polymorphisms is the most efficient for use in population genetics studies? a) Amino acid sequence polymorphisms b) Restriction site variation c) Chromosomal polymorphisms d) Complete sequence variation e) Variable number of tandem repeats
d (Complete sequence variation)
One primary difference between whole shotgun sequencing and so called 'next generation' sequencing approaches is: a) Next generation approaches produce significantly longer sequence reads. b) Next generation approaches rely on DNA polymerase activity. c) Next generation approaches do not utilize all four nucleic acids. d) Next generation approaches eliminate the need to clone genomic fragments. e) Next generation approaches cannot identify DNA binding elements.
d (Next generation approaches eliminate the need to clone genomic fragments.)
In bacterial DNA replication, a lagging strand is synthesized: (a) continuously 3′ to 5′ as a series of Okazaki fragments, (b) continuously 5′ to 3′ as a series of Okazaki fragments, (c) discontinuously 3′ to 5′ as a series of Okazaki fragments, (d) discontinuously 5′ to 3′ as a series of Okazaki fragments, (e) a & c
d (discontinuously 5' to 3')
A homeotic mutation: a) Results in replacement of one normal body part with another. b) Produces unusual phenotypes due to gain-of-function or loss-of- function. c) May cause all segments to have the same identity. d) Affects both pairs of serially reiterated structures. e) All to the above
e (All of the above)
RNA polymerase II in eukaryotes synthesizes ____ using a DNA template.
mRNA
RNA is made __' → __'
5' → 3' (same direction in which New DNA is replicated)
DNA New Strand is made: __' → __'
5' → 3' (same direction in which RNA is made)
In eukaryotes, transcriptional activity is low when: A. DNA is hypermethylated. B. Histone is hyperacetylated. C. Histone H3 Lys 4 is methylated. D. Histone H3 Lys 36 is methylated E. none of the above.
A (DNA is hypermethylated)
_______________ is used to describe a situation in which a gene's expression pattern is dependent upon the parent from which is was inherited. A. Genomic imprinting B. Spermatogenesis C. Heterodimerization D. Homodimerization E. Gender-specific RNA stability
A (Genomic imprinting)
What technique would be used to best study a phenocopy? A. RNAi B. Transgene C. Isolation of mutations D. QTL mapping analysis E. Microarray
A (RNAi)
List two especially useful characteristics of cloning vector A) high copy number and antibiotic-resistance gene B) virulence and lysogenecity C) ability to integrate into host chromosome and cause lysis of the host cell D) nonautonomous replication and transposition E) reverse transcriptase and ligase activity
A (high copy number and antibiotic-resistance gene)
In a southern-blot, one generally A) hybridizes filter-bound DNA with a DNA probe B) hybridizes filter-bound RNA with a DNA probe C) examines amino acid substitutions with radioactive probe D) cleaves RNA with restriction endonuclease E) ligates DNA with DNA ligase
A (hybridizes filter-bound DNA with a DNA probe)
The Rb activity is regulated by A. its phosphorylation state. B. its methylation level C. cyclin A. D. E2F E. its polyA tail.
A (its phosphorylation state)
A codon is a three base sequence of A. mRNA that codes for an amino acid. B. rRNA that codes for an amino acid. C. tRNA that codes for an amino acid. D. DNA that codes for an amino acid.
A (mRNA that codes for an amino acid)
Some restriction endonucleases produce 'sticky' ends. What makes an end sticky? A) blunt ends B) single-stranded complementary tails C) poly-A sequences D) 5' cap E) Interference
B (single-stranded complementary tails)
If grandparents are heterozygous for the trait, what is the probability that a child in question would NOT have the trait (disease). A. 1/4 B. 3/4 C. 1/3 D. 2/3
D (2/3)
Taq polymerase, a heat-stable DNA polymerase, is used in PCR, because A) each PCR cycle includes a 'hot' (95 degree C) denaturation phase, that allows the primer to anneal to the target DNA B) each PCR cycle includes a 'hot' (95 degree C) denaturation phase, that sterilize the culture C) each PCR cycle includes a 'hot' (95 degree C) denaturation phase, that activates the Taq polymerase D) each PCR cycle includes a 'hot' (95 degree C) denaturation phase, that separates the hydrogen bonds which hold the strands of DNA together E) A and C are correct
D (each PCR cycle includes a 'hot' (95 degree C) denaturation phase, that separates the hydrogen bonds which hold the strands of DNA together)
In the trp operon, attenuation occurs through the recognition of two Trp codons in the leader sequence. What would happen if these two codons were mutated to stop codons? A. This operon will be insensitive to attenuation by tryptophan. B. The structural genes will be transcribed in the presence or absence of tryptophan. C. The tryptophan biosynthetic enzymes will be synthesized. D. None of these results (A~C) will take place. E. All of these results (A~C) will take place.
E (All of these results (A~C) will take place)
Regions of DNA are most sensitive to DNAase digestion when A. they are free of histones. B. they are regions devoid of (lacking) genes. C. they are transcriptionally active. D. they are transcriptionally inactive E. a cell is in G0. E. Answers A & C F. All of the above
E (Answers A & C)
________ as cis-acting DNA sequences can function at a distance from the gene they are regulating, either 5' or 3' of the gene.
Enhancers
T/F: In a typical PCR, primers are used to cleave specific regions of the DNA template
F
T/F: Epigenetic changes refer to changes in gene function that are stable due to changes in DNA sequence.
False
T/F: Heterochromatic DNA is DNA that is actively transcribed.
False
T/F: High concentration of Glucose is necessary for the maximum induction of Lac operon genes.
False
T/F: The map of a chromosome interval is A--10 m.u.--B-- 40 m.u.--C. From the cross Abc/aBC × abc/abc, you observed 10 double crossovers from 1000 progeny. In this case, interference is 0.5
False
T/F: The size of population does not affect Hardy-Weinberg Equilibrium.
False
T/F: cDNAs from eukaryotic organisms contain promoter region.
False
"Certain covalent modifications of Histone can dictate the fate of gene expression at given loci" is referred as _____ _____ hypothesis.
Histone Code
T/F: Some restriction endonucleases produce sticky ends, while others produce blunt ends.
T
T/F: To isolate a bacterium with a plasmid that carries a desired DNA fragment along with an ampicillin-resistance gene; we should grow the bacteria in a medium that contains ampicillin.
T
T/F: Genomic imprinting is an example of epigenetic alteration of DNA.
True
T/F: Genotype frequency can change until the population comes to equilibrium.
True
T/F: HIV contains reverse transcriptase.
True
T/F: HIV does not contain DNA in its virus particles.
True
T/F: Nimblegen array uses photo-activating building blocks to construct DNA array on the slide.
True
T/F: Population at Hardy-Weinberg equilibrium assumes that there is no new mutation over generations.
True
T/F: Trimethylation at Histone H3 Lys 27 usually associated with transcriptionally repressed chromatins
True
The expression of 'tool kit' genes is precisely modulated both spatially and temporally by the binding activities of a number of protein factors during the early development of animals. To achieve this level of control tool kit genes: a) Encode splicing enzymes that activate Hox mRNAs b) Contain regions composed of multiple activator and repressor elements that allow context specific control of expression c) Have strictly defined roles in the developmental process in a limited number of organisms d) Are sequentially ordered along the length of the chromosome, from largest to smallest e) Are insensitive to mutations that could modify developmental fate of a given tissue
b (Contain regions composed of multiple activator and repressor elements that allow context specific control of expression)
Why is glucose involved in the catabolite repression of the lactose operon? A. It has nothing to do with regulation of the lactose operon. B. It results in decreased cAMP levels, which in turn leads to decreased CRP binding; its presence thereby signifying the presence of glucose in the cell. C. It is also a substrate for β-galactosidase. D. Its presence in the cell increases the amount of lac repressor in the cell. E. Its presence in the cell decreases the amount of lac repressor in the cell
b (It results in decreased cAMP levels, which in turn leads to decreased CRP binding; its presence thereby signifying the presence of glucose in the cell.)
In using bioinformatics tools to search for possible genes in the DNA sequence of a prokaryotic genome, which of the following would be good evidence for a region being genic? a) Presence of short (3-30 bp) ORF flanked by a "start" and "stop" codon b) Presence of a long (100 bp or more) ORF flanked by a "start" and "stop" codon c) Presence of an ATG codon (since the "start" codon is invariably ATG). d) Detection of an ORF in more than one reading frame e) Absence of introns
b (Presence of a long (100 bp or more) ORF flanked by a "start" and "stop" codon)
You are a researcher who has tentatively identified a human homolog of a yeast gene. You determine the DNA sequence of cDNAs of both your yeast gene and the human gene and decide to compare the gene sequences, as well as the predicted protein sequence of each, using alignment software. You would expect the greatest sequence identity from comparisons of the: a) cDNA sequences b) Protein sequences c) Genomic DNA sequences d) Both (a) and (b) will give you equivalent sequence similarity e) All will give equivalent sequence similarity
b (Protein sequences)
DNA microarrays are particularly useful to study: a) The changes in expression of a small subset of mRNA over many experiments b) The changes in expression of all mRNA of the cell in response to a given experimental condition c) The differences in protein accumulation under a given experimental condition d) The conservation of binding domains of transcription factors e) The establishment of concentration gradients of maternal effect gene products such as Bicoid
b (The changes in expression of all mRNA of the cell in response to a given experimental condition)
Ubx (Ultrabithorax) is a Drosophila homeotic gene that normally has two key functions: Promote hindwing development and repress forewing development. A nonlethal loss-of-function allele of Ubx might reasonably be expected to: a) Transform the forewing into a hindwing b) Transform the hindwing into a forewing c) Result in no development of either hindwing or forewing d) Result in growth of an eye structure instead of a wing structure e) Transform the forewing into a leg structure
b (Transform the hindwing into a forewing)
Transcription in prokaryotes begins at the: (a) TATA box in the promoter, (b) start site in the promoter, (c) start codon in the promoter, (d) ‐10 sequence in the promoter, (e) ‐35 sequence in the promoter.
b (start site in the promoter)
Catabolic pathways that break down complex substances into more usable units are usually regulated by the A. end products of the pathway. B. substrate of an enzyme in the pathway. C. other metabolites that are limiting. D. all of the above. E. none of the above
b (substrate of an enzyme in the pathway.)
In an old view of heredity, __________ inheritance assumes that parental traits become mixed and forever changed in offspring.
blending
Transcription of eukaryotic structural genes is initiated when _________ and __________ bind to a promoter sequence. (a) RNA polymerase core enzyme and sigma factor, (b) RNA polymerase holoenzyme and primase, (c) RNA polymerase II and general transcription factors, (d) RNA polymerase II and sigma factor, (e) RNA polymerase III and general transcription factors
c ( RNA polymerase II and general transcription factors)
You have isolated and sequenced a protein that appears to possess a DNA binding domain. You would now like to ascertain if indeed your protein binds DNA and determine the sequence element to which it binds in cells. To study these questions you could: a) Synthesize a double stranded RNA, introduce this to cells and knock down expression of the gene that encodes your protein. b) Set up a yeast two-hybrid experiment using your protein as bait. c) Create a cDNA library for your organism following exposure to a pathogen. d) Conduct a chromatin immunoprecipitation (ChIP) assay. e) Clone the N-terminus for your protein upstream of a reporter gene and monitor color development.
c (Create a cDNA library for your organism following exposure to a pathogen.)
Which of the following is strong evidence that a putative gene identified by sequence analysis of the genome functions as a bona fide gene in vivo? a) Presence of introns and exons in the genomic sequence b) Presence of a "start" and "stop" codon in the genomic sequence c) Presence of mRNA in the cell with an ORF that corresponds precisely with the predicted exons in the putative gene d) Presence of orthologous sequences in the genome e) Apparent codon bias is congruent with organism under study
c (Presence of mRNA in the cell with an ORF that corresponds precisely with the predicted exons in the putative gene)
Match: 1) PCR 2) Palindromes 3) Northern blot a) probing of RNA fragment b) recognition c) automated thermocyclers
c, b, a
Generally speaking, cancer is due to abnormal or uncontrolled _____ division
cell
A DNA nucleotide is composed of: (a) a nitrogenous base, (b) the sugar ribose, (c) a phosphate, (d) a, b & c (e) a & c
e (a &c)
In prokaryotes, the RNA polymerase core enzyme is composed of: (a) two α subunits, (b) one β subunit and one β' subunit, (c) one ω subunit, (d) one σ factor, (e) a, b & c
e (a, b & c are correct)
Mutations in either of two sites in operon will produce a constitutive phenotype. These two sites are _____ or ______.
operator, reperessor
In Prokaryotes, cluster of genes can be regulated together. This cluster of genes is called an ____
operon
The region of DNA containing the set of genes that are cotranscribed, along with all the regulatory elements that control the expression of these genes, is called a(n) ____ .
operon