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in a nucleic-acid chain, a subunit that consists of a sugar, a phosphate, and a nitrogenous base
nucleotide
a five-carbon sugar that is a component of DNA nucleotides
deoxyribose
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an organic base that contains nitrogen, such as a purine or pyrimidine; a subunit of a nucleotide in DNA and RNA
nitrogenous base
a nitrogenous base that has a double-ring structure; one of the two general categories of nitrogenous bases found in DNA and RNA; either adenine or guanine
purine
a nitrogenous base that has a single-ring structure; one of the two general categories of nitrogenous bases found in DNA and RNA; thymine, cytosine, or uracil
pyrimidine
the rules stating that in DNA cytosine pairs with guanine and adenine pairs with thymine and that in RNA cytosine pairs with guanine and adenine pairs with uracil
base pairing rules
the nucleotide bases in one strand of DNA or RNA that are paired with those of another strand; adenine pairs with thymine or uracil, and guanine pairs with cytosine
complementary base pair
the order of nitrogenous bases on a DNA chain
base sequence
the process of making a copy of DNA
DNA replication
an enzyme that separates DNA strands
helicase
an enzyme that catalyzes the formation of the DNA molecule
DNA polymerase
a Y-shaped point that results when the two strands of a DNA double helix separate so that the DNA molecule can be replicated
replication fork
in each new DNA double helix, one strand is from the original molecule, and one strand is new
semi-conservative replication
a change in the nucleotide-base sequence of a gene or DNA molecule
mutation
a natural polymer that is present in all living cells and that plays a role in protein synthesis; ribonucleic acid
RNA
the process of forming a nucleic acid by using another molecule as a template; particularly the process of synthesizing RNA by using one strand of a DNA molecule as a template
transcription
the portion of protein synthesis that takes place at ribosomes and that uses the codons in mRNA molecules to specify the sequence of amino acids in polypeptide chains
translation
the formation of proteins by using information contained in DNA and carried by mRNA
protein synthesis
a five-carbon sugar present in RNA
ribose
a single-stranded RNA molecule that encodes the information to make a protein; messenger RNA
mRNA
an organelle that contains most of the RNA in the cell and that is responsible for ribosome function; ribosomal RNA
rRNA
transfers amino acids to the ribosome to make protein.
tRNA
an enzyme that starts (catalyzes) the formation of RNA by using a strand of a DNA molecule as a template
RNA polymerase
a nucleotide sequence on a DNA molecule to which an RNA polymerase molecule binds, which initiates the transcription of a specific gene
promoter
a specific sequence of nucleotides that marks the end of a gene
termination signal
the rule that describes how a sequence of nucleotides, read in groups of three consecutive nucleotides (triplets) that correspond to specific amino acids, specifies the amino acid sequence of a protein
genetic code
in DNA and mRNA, a three-nucleotide sequence that encodes an amino acid or signifies a start signal or a stop signal
codon
a region of a tRNA molecule that consists of a sequence of three bases that is complementary to an mRNA codon
anticodon
the complete genetic material contained in an individual or species
genome
Semi-Conservative Replication: the strands of DNA are separated, and one “parental” DNA strand is conserved, acting as a template for a complete newly synthesized “daughter” strand. DNA synthesis is semi-discontinuous: Leading strand synthesis is continuous 5′-3′ Lagging strand synthesis is discontinuous 5′-3′
Define the terms, semi-conservative and semi-discontinuous replication.
Helicase is a DNA unwinding protein, it hydrolyzes ~2 ATP per base pair
separated. With upwards of 4.2 million base pairs in E.coli and 3+billion in humans unwinding DNA can
be a very expensive process!
DNA helicase (an ATPase):
SSBPs have a high affinity for singlestranded DNA (ssDNA). They stabilize unwound ssDNA and prevents its shearing. SSBPs
also promote increased DNA helicase and enhance DNA polymerase activity
Single Stranded DNA Binding Proteins (SSBP)
DNA dependent RNA polymerase (primase), lays down an RNA primer essential to initiation of DNA synthesis. RNA primase is essential at the origin of initiation for overall leading strand DNA synthesis and for the initiation of each Okazaki fragment on the lagging
strand of DNA synthesis. The primer RNA is usually only 3 to 5 nucleotides long. In eukaryotes and 5 to 8 nucleotides long in prokaryotes. Primase is a component of the active DNA polymerase complex.
Primase:
This enzyme seals “nicks” or breaks in the DNA phosphodiester backbone
using 5’PO4 from one nucleotide and an adjacent 3’OH from another nucleotide. This is a key enzyme
involved in DNA synthesis for resolution of Okazaki fragments, general repair of DNA strand breaks and DNA recombination reactions. Human ligase uses ATP as an
energy source, whereas bacteria tend to use NAD to power these reactions.
DNA Ligase
djusts supercoil density by relaxing supercoil tension around DNA’s
helical axis thereby relieving structural stress generated by the unwinding of the DNA helix during
replication
DNA Gyrase / Topoisomerase –
Nicks one strand, passes the opposite strand through cut site, and religates the phosphodiester bond, this removes one supercoil, relaxing tension.
Type I topoisomerase (topo-I)
Breaks in both strands, passes another region of dsDNA through the
break, and then the DNA strands are re-ligated.
Type II topoisomerase (topo-II) –
r cancer chemotherapy (campothecan, topothecan,
etoposide ), and antibiotics (ciprofloxin), there is no DNA synthesis without supercoil relaxation.
Topoisomerase is a target for what and why?
A DNA repair enzyme -e enzyme
contains:
a. 5’3′ exonuclease activity to clear damaged DNA or RNA primers,
b. 3’5′ exonuclease activity as a proof reading function, editing enzyme mistakes as it goes along.
Functions: ssDNA gap filling, mismatch repair, short-patch repair, Okazaki RNA primer repair.
DNA Polymerase I (polA): A
A DNA repair enzyme – a ssDNA gap filling repair enzyme. Replaces RNA primer regions in Okazaki fragments only after the RNA has been cleared out by a special primer-RNase enzyme.
DNA pol II has 3’5′ exonuclease proof reading function adjacent to the
active site in order to fix polymerase enzyme mistakes. This enzyme has no
5′ 3′ exonuclease activity. It just fills in gapped ssDNA.
DNA polymerase II (polB):
Essential for replication -Contains a beta-subunit dimer or ATP dependent sliding clamp loading
onto DNApol III, inducing processivity/speed to support rapid DNA synthesis.
DNA polymerase III (polC):
c. RNA-primer w/3’OH required for initiation. (RNA primase activity
occurs first)
what is required for DNA replication
5′ phosphate of an appropriate dNTP (w/ Mg+2) reacts with the 3’OH
terminal of growing chain via nucleophilic attack. (5′ to 3′ is direction
of new DNA chain growth). The 3′ OH initiates the nucleophilic attack
on the incoming dNTP 5’phosphate. dNTP = deoxynucleotide
triphosphate
nucleophilic attack
s are formed on the lagging strand during DNA synthesis as generated by the DNA pol III complex. Okazaki fragments are approximately ~2000 nucleotides (nt) in prokaryotes vs only ~200-300 nt in eukaryotes for each fragment. RNA primers are required for initiating DNA synthesis of each Okazaki fragment.
Okazaki Fragments
5′ phosphate of an appropriate dNTP (w/ Mg+2) reacts with the 3’OH
terminal of growing chain via nucleophilic attack. (5′ to 3′ is direction
of new DNA chain growth). The 3′ OH initiates the nucleophilic attack
on the incoming dNTP 5’phosphate. dNTP = deoxynucleotide
triphosphate
why 5′ to 3′
Replicons are continuous regions of DNA duplicated under the influence of a single origin of
replication.
Replicons:
are sequence specific domains of
DNA that are intimately involved with initiation of DNA synthesis. Origins have multiple DNA sequence
components. The Origin Recognition Element (ORE) is a DNA sequence (20-100nt). DNA Unwinding
Elements (DUE) are AT-rich regions (245bp in E.coli) that flank either side of the ORE. Replication
initiation factors (proteins) bind these sequence elements and open the DNA double helix
Origins of replication
: A DNA-protein complex assembles at the origin of replication unwinding the dsDNA to
ssDNA. SSBPs and other protein factors bind ssDNA establishing a docking site for primase (replication
dependent -RNA polymerase). The primase – RNA polymerase synthesizes a short primer RNA called
oriRNA
Primosomes:
The active DNA replication fork, including all its various protein factors,
leaves the origin (ORE) and becomes a replisome complex. This results in bidirectional replication forks moving away from the origin (2 replication forks = 2 replisomes)
Replisome:
increases processivity and replication fork moves forward in a 5’3’direction continuously synthesizing a new leading DNA strand complementary to the pre-existing template strand
sliding clamp,
A telomer protects the end of the chromosome as redundant DNA sequences fold up to form an
intricate 4-way H-bonding network between the multiple guanosines, sealing the end of the chromosome. This structure is further stabilized and protected by the binding of numerous telomere specific stabilization proteins.
Describe the purpose of a telomere in eukaryotic linear chromosomes.
is a ribonuclear protein enzyme that constructs redundant DNA sequences at
the end of linear chromosomes using an RNA molecule as a template in the telomerase enzyme’s active
site. It’s a reverse trascriptase, copying DNA from an RNA template!
Telomerase
Constitutive (high fidelity, normal) vs Inducible (low fidelity, emergency) repair mechanisms
Constitutive vs Inducible
A. Direct Reversal of DNA Damage (very efficient):B. Excision Repair: C. Recombination Repair – D. Post-Replication Repair – SOS Repair (
DNA Repair Mechanisms:
is
extremely important in monitoring DNA fidelity, and inducing the expression
of repair systems. Interestingly, p53 is found to be mutated in nearly 60% of
all cancers; literally taking the brakes off growth control and DNA repair
stringency, promoting genomic instability and cancer
p53 protein
Abl and Bcr are the names of two specific protein coding genes that are altered during a recombination event. These altered proteins induce a
cancerous growth state in white bloods cells.
Philadelphia Chromosome Translocation (#22 – #9; abl-bcr)
True or False: DNA replication occurs in the 5′ to 3′ direction; that is, new nucleoside triphosphates are added to the 3′ end.
True
True or False: DNA strand replication begins with an RNA primer.
True
True or False: In general, DNA replicates semi-conservatively and bidirectionally.
True
True or False: In ligase-deficient strains of E. coli, DNA and chromosomal replication is unaltered because ligase is not involved in DNA replication.
False
True or False: During replication, primase adds a DNA primer to RNA.
False
True or False: DNA polymerase III is an enzyme that adds nucleotides to the 3′ end of each growing DNA strand.
True
An endonuclease is involved in removing bases sequentially from one end of DNA or the other.
False
True or False: DNA replicates conservatively, which means that one of the two daughter double helices is “old” and the other is “new.”
False
The basic structure of a nucleotide includes the following components:

a) base, sugar, and phosphate.
b) phosphorus and sulfur.
c) tryptophan and leucine.
d) amino acids.
e) mRNA, rRNA, and tRNA.

a) base, sugar, and phosphate.
The classic Hershey and Chase (1952) experiment that offered evidence in support of DNA being the genetic material in bacteriophages made use of the following labeled components:

a) hydrogen.
b) phosphorus and sulfur.
c) nitrogen and oxygen.
d) tritium.
e) none of the above

b) phosphorus and sulfur.
Reverse transcriptase is an enzyme found in association with retroviral activity. It has the property of:

a) synthesis of DNA from an RNA template.
b) translation.
c) requiring no template.
d) most lysozymes.
e) synthesis of RNA from a DNA template.

a) synthesis of DNA from an RNA template.
What are the two major components of the Tobacco Mosaic Virus?

a) DNA and protein
b) RNA and protein
c) Carbohydrates and nucleic acids
d) Lipids and nucleic acids
e) RNA and DNA

b) RNA and protein
In the structure of double-stranded DNA, what kinds of bonds hold one complementary strand to the other?

a) van der Waals
b) hydrogen
c) covalent
d) ionic
e) hydrophobic and hydrophilic

b) hydrogen
Regarding the structure of DNA, the covalently arranged combination of a deoxyribose and a nitrogenous base is called a:

a) ribonucleotide.
b) nucleoside.
c) nucleotide.
d) monophospate nucleoside.

b) nucleoside.
In the classic experiment conducted by Hershey and Chase, why was the pellet radioactive in the centrifuge tube that contained bacteria with viruses, which had been grown on medium containing 32P?

a) The radioactive viruses (coats plus DNA) were in the pellet.

b) The bacteria were in the pellet, and many contained the radioactive viral DNA.

c) The radioactive viruses were in the pellet, and the bacteria were in the supernatant.

d) The radioactive protein coats of the viruses were in the pellet.

e) The bacteria were in the pellet, and they had incorporated radioactive proteins into their cell membranes.

b) The bacteria were in the pellet, and many contained the radioactive viral DNA.
If 15 percent of the nitrogenous bases in a sample of DNA from a particular organism is thymine, what percentage should be cytosine?

a) 15 percent
b) 35 percent
c) 70 percent
d) 30 percent
e) 40 percent

b) 35 percent
In an analysis of the nucleotide composition of double-stranded DNA to see which bases are equivalent in concentration, which of the following would be true?

a) A = G and C = T
b) A + T = G + C
c) A + C = G + T
d) A = C
e) Both B and C are true.

c) A + C = G + T
Which of the following clusters of terms accurately describes DNA as it is generally viewed to exist in prokaryotes and eukaryotes?

a) double-stranded, parallel, (A + T)/C + G) = 1.0, (A + G)/(C + T) = 1.0

b) double-stranded, parallel, (A + T)/C + G) = variable, (A + G)/(C + T) = 1.0

c) double-stranded, antiparallel, (A + T)/C + G) = variable, (A + G)/(C + T) = variable

d) double-stranded, antiparallel, (A + T)/C + G) = variable, (A + G)/(C+ T) = 1.0

e) single-stranded, antiparallel, (A + T)/C + G) = 1.0, (A + G)/(C + T) = 1.0

d) double-stranded, antiparallel, (A + T)/C + G) = variable, (A + G)/(C+ T) = 1.0
Which of the following terms accurately describes the replication of DNA in vivo?

a) nonreciprocal
b) semidiscontinuous
c) dispersive
d) nonlinear
e) conservative

b) semidiscontinuous
DNA polymerase III adds nucleotides

a) in the place of the primer RNA after it is removed.
b) to internal sites in the DNA template.
c) to the 5′ end of the RNA primer.
d) to the 3′ end of the RNA primer.
e) to both ends of the RNA primer.

d) to the 3′ end of the RNA primer.
DNA polymerase I is thought to add nucleotides

a) on single-stranded templates without need for an RNA primer.
b) in a 5′ to 5′ direction.
c) to the 5′ end of the primer.
d) in the place of the primer RNA after it is removed.
e) to the 3′ end of the primer.

d) in the place of the primer RNA after it is removed.
Which cluster of terms accurately reflects the nature of DNA replication in prokaryotes?

a) fixed point of initiation, bidirectional, conservative
b) random point of initiation, unidirectional, semiconservative
c) fixed point of initiation, bidirectional, semiconservative
d) fixed point of initiation, unidirectional, conservative
e) random point of initiation, bidirectional, semiconservative

c) fixed point of initiation, bidirectional, semiconservative
The discontinuous aspect of replication of DNA in vivo is caused by

a) polymerase slippage.
b) trinucleotide repeats.
c) topoisomerases cutting the DNA in a random fashion.
d) sister-chromatid exchanges.
e) the 5′ to 3′ polarity restriction.

e) the 5′ to 3′ polarity restriction.
Use the pGEM-T Easy vector map in your laboratory manual to the following question.
A DNA fragment was excised from some source DNA using SacI and SphI and ligated to pGem-T easy cut with the same restriction enzymes. The DNA fragment contains a gene whose open-reading frame (ORF) runs in the direction SphI àSacI. The gene in this construct is:

a) under the control of T7 promoter.
b) under the control of the lac promoter.
c) under the control of the SP6 promoter.
d) It is not possible to determine the orientation of the gene in this instance.

a) under the control of T7 promoter.
*** Use the pGEM-T Easy vector map in your laboratory manual to the following question.***
Which of the following restriction enzyme/s would allow you to remove a PCR generated insert from the multiple cloning site.

a) EcoRI
b) SpeI
c) AatII & NcoI
d) SpeI & SalI

a) EcoRI
Words such as “Mom,””Dad,” and “liveevil” might have special significance when considering the fundamental tools of recombinant DNA technology. What term would be used to describe such words in the context of recombinant DNA technology? (See Problems and Discussion Questions for a description.)

a) insertion
b) prototrophic
c) conjugation
d) lysogenic
e) palindromic

e) palindromic
Restriction endonucleases are especially useful if they generate “sticky” ends. What makes an end sticky?

a) blunt ends
b) poly-A sequences
c) 5′ cap
d) single-stranded complementary tails
e) interference

d) single-stranded complementary tails
Which of the following would you expect to be especially useful characteristics of cloning vectors?

a) high copy number and antibiotic resistance gene(s)
b) ability to integrate into the host chromosome and then cause a lytic cycle
c) virulence and lysogenicity
d) reverse transcriptase and ligase activities
e) nonautonomous replication and transposition

a) high copy number and antibiotic resistance gene(s)
Some vectors such as pUC18 and others of the pUC series contain a large number of restriction enzyme sites clustered in one region. What term is given to this advantageous arrangement of restriction sites?

a) complementation
b) palindrome
c) polylinker
d) β-galactosidase
e) consensus sequence

c) polylinker
One of the primary reasons for the necessity of generating a large number of clones in a eukaryotic genomic library is that

a) each cosmid replicates nonautomously.
b) lysogenic phages continue to integrate their DNA into the host chromosome, thus reducing the number of desired recombinant clones.
c) each vector can take up only a very small fraction of the eukaryotic DNA.
d) the host range of the vector is limited.
e) each ligation product is sequence-specific.

c) each vector can take up only a very small fraction of the eukaryotic DNA.
Assume that a circular plasmid is 3200 base pairs in length and has restriction sites at the following locations: 400, 700, 1400, 2600. Give the expected sizes of the restriction fragments following complete digestion.

a) 300, 700, 1000, 1200
b) 400, 1200, 1600
c) 700, 400, 1400, 2600
d) 300, 700, 2200
e) 400, 800, 1000 (two of these)

a) 300, 700, 1000, 1200
The PCR (polymerase chain reaction) protocol that is currently used in laboratories was facilitated by the discovery of a bacterium called Thermus aquaticus in a hot spring inside Yellowstone National Park, Wyoming. This organism contains a heat-stable form of DNA polymerase known as Taq polymerase, which continues to function even after it has been heated to 95C. Why would such a heat-stable polymerase be beneficial in PCR?

a) Each cycle includes a “hot” denaturation phase (95C), which separates the hydrogen bonds that hold the strands of the template DNA together.
b) Each cycle includes a “hot” saturation phase (95C), which allows the primers to anneal to the target DNA.
c) Each cycle includes a “hot” denaturation phase (95C), which serves to sterilize the culture.
d) Each cycle includes a “hot” denaturation phase (95C), which activates the Taq polymerase.
e) More than one of the above is correct.

a) Each cycle includes a “hot” denaturation phase (95C), which separates the hydrogen bonds that hold the strands of the template DNA together.
What is the name given to the three bases in a messenger RNA that bind to the anticodon of tRNA to specify an amino acid placement in a protein?

a) protein
b) codon
c) rho
d) anti-anticodon
e) cistron

b) codon
An intron is a section of

a) carbohydrate that serves as a signal for RNA transport.
b) RNA that is removed during RNA processing.
c) transfer RNA that binds to the anticodon.
d) protein that is clipped out posttranslationally.
e) DNA that is removed during DNA processing.

b) RNA that is removed during RNA processing.
The genetic code is fairly consistent among all organisms. The term often used to describe such consistency in the code is

a) overlapping.
b) universal.
c) exceptional.
d) trans-specific.
e) none of the above

b) universal.
Which of the following sets of two terms relates most closely to split genes?
a) elongation, termination
b) 5′-cap, 3′-poly-A tail
c) heteroduplex, homoduplex
d) introns, exons
e) transcription, translation
d) introns, exons
Significant in the deciphering of the genetic code was the discovery of the enzyme polynucleotide phosphorylase. What was this enzyme used for?
a) production of ribosomal proteins
b) the manufacture of synthetic RNA for cell-free systems
c) degradation of RNA
d) ribosomal translocation
e) peptide bond formation
b) the manufacture of synthetic RNA for cell-free systems
In 1964, Nirenberg and Leder used the triplet binding assay to determine specific codon assignments. A complex of which of the following components was trapped in the nitrocellulose filter?
a) uncharged tRNAs and ribosomes
b) free tRNAs
c) sense and antisense strands of DNA
d) ribosomes and DNA
e) charged tRNA, RNA triplet, and ribosome
e) charged tRNA, RNA triplet, and ribosome
What is the initiator triplet in both prokaryotes and eukaryotes? What amino acid is recruited by this triplet?
a) AUG; arginine
b) UAA; methionine
c) UAA or UGA; arginine
d) UAA; no amino acid called in
e) AUG; methionine
e) AUG; methionine
Select three posttranscriptional modifications often seen in the maturation of mRNA in eukaryotes.
a) 3′-capping, 5′-poly(A) tail addition, splicing
b) 5′-poly(A) tail addition, insertion of introns, capping
c) heteroduplex formation, base modification, capping
d) 5′-capping, 3′-poly(A) tail addition, splicing
e) removal of exons, insertion of introns, capping
d) 5′-capping, 3′-poly(A) tail addition, splicing
The genetic code is said to be triplet, meaning that
a) there are three amino acids per base in mRNA.
b) there are three bases in mRNA that code for an amino acid.
c) there are three “nonsense” triplets.
d) there may be three ways in which an amino acid may terminate a chain.
e) none of the above
b) there are three bases in mRNA that code for an amino acid.
When scientists were attempting to determine the structure of the genetic code, Crick and co-workers found that when three base additions or three base deletions occurred in a single gene, the wild-type phenotype was sometimes restored. These data supported the hypothesis that
a) AUG is the initiating triplet.
b) there are three amino acids per base.
c) the code contains internal punctuation.
d) the code is overlapping.
e) the code is triplet.
e) the code is triplet.
When examining the genetic code, it is apparent that
a) AUG is a terminating codon.
b) there can be more than one amino acid for a particular codon.
c) there can be more than one codon for a particular amino acid.
d) the code is ambiguous in that the same codon can code for two or more amino acids.
e) there are 44 stop codons because there are only 20 amino acids.
c) there can be more than one codon for a particular amino acid.
The relationship between a gene and a messenger RNA is that
a) mRNAs are made from genes.
b) genes are made from mRNAs.
c) messenger RNA is directly responsible for making Okazaki fragments.
d) all genes are made from mRNAs.
e) mRNAs make proteins, which then code for genes.
a) mRNAs are made from genes.
Introns are known to contain termination codons (UAA, UGA, or UAG), yet these codons do not interrupt the coding of a particular protein. Why?
a) UAA, UGA, and UAG are initiator codons, not termination codons.
b) More than one termination codon is needed to stop translation.
c) Exons are spliced out of mRNA before translation.
d) Introns are removed from mRNA before translation.
e) These triplets cause frameshift mutations, but not termination.
d) Introns are removed from mRNA before translation.
It has been recently determined that the gene for Duchenne muscular dystrophy (DMD) is over 2000 kb (kilobases) in length; however, the mRNA produced by this gene is only about 17 kb long. What is a likely cause of this discrepancy?
a) There are more amino acids coded for by the DNA than the mRNA.
b) The introns have been spliced out during mRNA processing.
c) When the mRNA is produced, it is highly folded and therefore less long.
d) The exons have been spliced out during mRNA processing.
e) The DNA represents a double-stranded structure, while the RNA is single-stranded.
b) The introns have been spliced out during mRNA processing.
If one compares the base sequences of related genes from different species, one is likely to find that corresponding ________ are usually conserved, but the sequences of ________ are much less well conserved.
a) introns; proteins
b) exons; introns
c) introns; chaperons
d) chaperons; exons
e) introns; exons
b) exons; introns
Three posttranscriptional modifications often seen in the maturation of mRNA in eukaryotes occur in which cellular organelle?
a) cytoplasm
b) nucleus
c) mitochondrion
d) lysosome
e) Golgi
b) nucleus
The triplet AUG is commonly used as a start codon during translation.
a) True
b) False
a) True
The term peptidyltransferase relates to
a) 5′ capping of mRNA.
b) discontinuous strand replication.
c) peptide bond formation during protein synthesis.
d) elongation factors binding to the large ribosomal subunit.
e) base additions during mRNA synthesis.
c) peptide bond formation during protein synthesis.
The primary structure of a protein is determined by
a) hydrogen bonds formed between the components of the peptide linkage.
b) covalent bonds formed between fibroin residues.
c) a series of helical domains.
d) pleated sheets.
e) the sequence of amino acids.
e) the sequence of amino acids.
A protein is 300 amino acids long. Which of the following is the minimum number of nucleotides in the section of DNA that codes for this protein? (Remember, DNA is double-stranded.)
a) 300
b) 1800
c) 500
d) 100
e) 3
b) 1800
A short segment of an mRNA molecule is shown below. The polypeptide it codes for is also shown:

5′-AUGGUGCUGAAG : methionine-valine-leucine-lysine

Assume that a mutation in the DNA occurs so that the fourth base (counting from the 5′ end) of the messenger RNA now reads A rather than G. What sequence of amino acids will the mRNA now code for? (You do not need a copy of the genetic code to the question.)

a) methionine-lysine-leucine-lysine
b) methionine-valine-methionine-lysine
c) methionine-leucine-leucine-lysine
d) methionine-valine-leucine-lysine
e) methionine-methionine-leucine-lysine

e) methionine-methionine-leucine-lysine
RFLPs and minisatellites are commonly used in recombinant DNA technology to

a) identify alleles and generate DNA fingerprints.
b) substitute for oligonucleotides.
c) serve as recombinant DNA vectors.
d) generate pharmaceutical products of interest.
e) cleave DNA of interest.

a) identify alleles and generate DNA fingerprints.
VNTRs are sections of DNA with the following characteristics:

a) various nucleotides transcribed repeatedly, homogeneous.
b) variable amino acid substitutions, highly heterogeneous.
c) variable numbers of tandem repeats, variable in the population.
d) very noteworthy transcribed regions, lethal genes.
e) variable numbers of tandem repeats, highly uniform in the population.

c) variable numbers of tandem repeats, variable in the population.
RFLPs are commonly used in gene mapping as

a) supplements for restriction endonucleases.
b) genetic markers.
c) substitutes for VNTRs in gene therapy.
d) primers for PCR.
e) in situ hybridization probes.

b) genetic markers.
A DNA microarray (also called a DNA chip) can be used to

a) scan a population of nucleic acids for abundance and mutations.
b) isolate genes from eukaryotic cell nuclei.
c) trap genes that are both active and inactive.
d) assay protein output from a genomic database.
e) mutate genes of interest.

a) scan a population of nucleic acids for abundance and mutations.
Under strictly controlled conditions, a probe can be used that will hybridize only with its complementary sequence and not with other sequences that may vary by as little as one nucleotide. What are such probes called?

a) generation-specific probes
b) VNTRs
c) microsatellites
d) short, variable repeats
e) allele-specific oligonucleotides (ASOs)

e) allele-specific oligonucleotides (ASOs)
In DNA sequencing, after the ddNTP is incorporated into the growing strand, DNA chain extension stops because:

a) DNA polymerase requires a free 3′ OH group, missing on the ddNTP, to extend the chain.
b) The dye linked to each base disrupts chain extension.
c) DNA polymerase requires a free 2’OH group, missing on the ddNTP, to extend the chain.
d) The ddNTPs contain a 2’OH group that prevents DNA polymerase from attaching another nucleotide.

a) DNA polymerase requires a free 3′ OH group, missing on the ddNTP, to extend the chain.
True or False: A restriction fragment is generated by the action of a restriction enzyme (endonuclease).
True
What term refers to a contiguous genetic complex that is under coordinated control?
a) prototroph
b) operon
c) lysogen
d) attenuation
e) allosteric
b) operon
5'CCTAAG3'
You are interested in the sequence of a 15-base segment of a gene. Using the dideoxy-chain-termination method, you obtain the above results after gel electrophoresis. The bands are of smaller molecular weight towards the bottom of the page. What is the sequence of the gene segment? Be sure to indicate the 3′ and 5′ orientation of the sequence.
5’CCTAAG3′
It is common to use ddNTPs (dideoxyribonucleoside triphosphates) in which of the following biochemical reactions?
a) DNA sequencing
b) plasmolysis
c) citric acid cycle
d) electron transport
e) restriction digestion
a) DNA sequencing
ddNTP, used often in DNA sequencing, lacks a ________ at the ________ and ________ carbons.
a) methyl; 2′; 3′
b) carboxyl; 5′; 3′
c) hydroxyl; 2′; 3′
d) hydroxyl; 2′; 5′
e) None of the above are correct.
c) hydroxyl; 2′; 3′
When two proteins show a 50 to 70 percent match in amino acid sequence, it is likely that
a) the two proteins have identical functions.
b) the two proteins have no common origin.
c) the two proteins have identical tertiary structures.
d) the primary structures may differ but the secondary structures are identical.
e) the two proteins share a common ancestry.
e) the two proteins share a common ancestry.
Name the two strategic methods that scientists are using to sequence genomes.
clone-by-clone method and shotgun cloning
ORF analysis of a DNA sequence often gives a number of ORFs many of which are NOT protein coding. Explain why such a result is often observed.
The analysis simply looks for potential start codons in all six reading reading frames and “translates” from each potential start codon until a stop codon is encountered. Many of the potential start codons are simply fortuitous as are the potential stop codons.
What term refers to a contiguous genetic complex that is under coordinated control?
a) prototroph
b) operon
c) lysogen
d) attenuation
e) allosteric
b) operon
Genetic regulation in eukaryotes can take place at a variety of levels from transcriptional to posttranslational. At what level is genetic regulation considered most likely in prokaryotes?
a) capping
b) exon processing
c) polyadenylation of the 3′ end of the mRNAs
d) transcriptional
e) intron processing
d) transcriptional
What term would be applied to a regulatory condition that occurs when protein is associated with a particular section of DNA and greatly reduces transcription?

a) negative control
b) positive control
c) stimulation
d) activation
e) induction

a) negative control
Which term most appropriately refers to a regulatory protein in prokaryotes?
a) DNA binding protein
b) gyrase action
c) RNA processing
d) helicase activation
e) translation
a) DNA binding protein
In the lac operon, the product of structural gene lacZ is capable of:

a) forming ATP from pyruvate.
b) forming lactose from two glucose molecules.
c) nonautonomous replication.
d) replacing hexokinase in the early steps of glycolysis.
e) splitting the ß-linkage of lactose.

e) splitting the ß-linkage of lactose.
Which of the following terms best characterizes catabolite repression associated with the lac operon in E. coli?
a) repressible system
b) inducible system
c) negative control
d) constitutive
e) positive control
e) positive control
When referring to attenuation in regulation of the trp operon, it would be safe to say that when there are high levels of tryptophan available to the organism,
a) translational termination is likely.
b) the trp operon is being transcribed at relatively high levels.
c) transcriptional termination is likely.
d) ribosomes are stalling during translation of the attenuator region.
e) tryptophan is inactivating the repressor protein.
c) transcriptional termination is likely.
positive
In the diagram what type of control, positive or negative, is operating?
positive
The lac operon consists of three structural genes as well as the adjacent region of DNA known as the regulator.

True or False?

False
Regarding the lactose utilization system in E. coli, a constitutive mutant is one in which the three enzymes are produced regardless of the presence or absence of lactose.

True or False?

True
Regarding the lactose utilization system in E. coli, a gratuitous inducer is a molecule that is chemically analogous to lactose and induces the operon, but is not a substrate for the enzymes of the lac operon.

True or False?

True
Under a system of negative control, genetic expression occurs unless such expression is shut off by some form of regulator.

True or False?

True
Under a system of positive control, transcription does not occur unless a regulator molecule directly stimulates RNA production.

True or False?

True
The enzyme permease cleaves the linkage between glucose and galactose residues in lactose.

True or False?

False
The trp operon is typically characterized as being both under negative control and repressible.

True or False?

True
Attenuation is known to occur in the lac operon.

True or False?

False
Attenuation involves the termination of mRNA synthesis.

True or False?

True
The trp and lac operons are both subject to forms of control that are typically called negative.

True or False?

True
Regulation of RNA transport through the nuclear membrane is as common in prokaryotes as in eukaryotes.

True or False?

False
DNA methylation may be a significant mode of genetic regulation in eukaryotes. Methylation refers to:

a) altering translational activity, especially of highly methylated tRNAs.
b) addition of methyl groups to the cytosine of CG doublets.
c) alteration of DNA polymerase activity by addition of methyl groups to glycine residues.
d) changes in DNA-DNA hydrogen binding.
e) altering RNA polymerase activity by methylation

b) addition of methyl groups to the cytosine of CG doublets.
What are enhancers?
Enhancers are sections of DNA that regulate transcription of other sections of DNA.
How are siRNA and miRNAs similar?
Both are similarly sized, double-stranded RNAs that silence genes.
True or False: A common term for a plasmid or other DNA element that serves as a cloning vehicle is vector.
True
True or False: Restriction endonucleases typically recognize palindromic DNA sequences and often generate “sticky ends” or single-stranded DNA overhangs at cut sites.
True
True or False: In general, the main goal of cloning is to include as many different genes as possible in a single cloning vector.
False
True or False: The main purpose of a probe is its insertion in plasmid DNA.
False
True or False: To isolate a bacterium with a plasmid that carries a desired DNA fragment cloned within the ampicillin resistance gene, we should grow bacteria in a medium that contains ampicillin.
False
True or False: Some restriction endonucleases are capable of producing blunt ends, while others can generate “sticky” ends.
True
True or False: In recombinant DNA technology, a YAC is an enzyme isolated from a large South American four-legged mammal.
False
True or False: Reverse transcriptase is often used as the heat-stable enzyme in PCR.
False
True or False: In a typical PCR, primers are used to cleave specific regions of the DNA template.
False
True or False: A restriction map provides the location of sites cleaved by restriction enzymes.
True
True or False: During a PCR, heat is provided to inactivate the polymerase enzyme.
False
True or False: pUC18 is a common YAC.
False
True or False: In recombinant DNA technology, YAC, ddNTPs, and pUC18 have identical uses.
False
True or False: In a PCR, primers are complementary to stretches of DNA with which they anneal.
True
True or False: Transcription in eukaryotes is generally influenced by enhancers, just as in prokaryotes.
False
True or False: In the eukaryotic promoters that have it, the CAAT box appears to be critical to the promoter’s ability to facilitate transcription.
True
True or False: Alternative RNA processing generates different mRNAs that can direct the synthesis of different polypeptides.
True
Genetic regulation in eukaryotes can take place at a variety of levels from transcriptional to posttranslational At what level is genetic regulation considered most likely in prokaryotes?
a)capping
b) exon processing
c) polyadenylation of the 3′ end of the mRNAs
d) transcriptional
e) intron processing
d) transcriptional
True or False: Regulation of RNA transport through the nuclear membrane is as common in prokaryotes as in eukaryotes
False
True or False: Transcription factors are proteins with at least two functional domains, one that binds to DNA and one that binds to RNA polymerase or to other transcription factors
True
Regarding eukaryotic and prokaryotic genetic regulation, what process seems to be the most similar between the two?
a) RNA splicing regulation
b) intron/exon shuffling
c) 5′-capping regulation
d) transcriptional regulation
e) poly-A tail addition
d) transcriptional regulation
True or False: Alternative RNA processing can result in different mRNAs that start with different exons
True
Two modular elements that appear as consensus sequences upstream from RNA polymerase II transcription start sites are:

a) rDNA and nucleolar organizers
b) TATA and CAAT
c) enhancers and telomeres
d) microsatellites and transposons
e) TTAA and CCTT

b) TATA and CAAT
DNA methylation may be a significant mode of genetic regulation in eukaryotes Methylation refers to:

a) altering translational activity, especially of highly methylated tRNAs
b) addition of methyl groups to the cytosine of CG doublets
c) alteration of DNA polymerase activity by addition of methyl groups to glycine residues
d) changes in DNA-DNA hydrogen binding
e) altering RNA polymerase activity by methylation

b) addition of methyl groups to the cytosine of CG doublets
Which of the following clusters of terms applies when addressing enhancers as elements associated with eukaryotic genetic regulation?

a) cis-acting, fixed position, fixed orientation
b) cis-acting, variable orientation, variable position
c) trans- and cis-acting, variable position
d) trans-acting, fixed position, fixed orientation
e) cis-acting, variable position, fixed orientation

b) cis-acting, variable orientation, variable position
What term would be applied to a regulatory condition that occurs when protein is associated with a particular section of DNA and greatly reduces transcription?

a) negative control
b) positive control
c) stimulation
d) activation
e) induction

a) negative control
What is a concise definition of proteomics?

a) changing the terminal sequences of proteins to alter their function
b) the process of defining the complete set of proteins encoded by a genome
c) the manipulation of amino acid sequences in proteins to alter their function
d) the rational design of drugs based on protein structure
e) the harvesting of proteins from a cell to determine their economic value

b) the process of defining the complete set of proteins encoded by a genome
A bacterial operon :

a) is void of start (AUG) and termination (UAA, UGA, UAG) triplets.
b) contains information for more than one protein product.
c) contains information for one protein product.
d) is capped at the 5′ end and carries a poly-A tail at the 3′ end.
e) none of the above

b) contains information for more than one protein product.
The Human Genome Project, which got under way in 1990, is an international effort to:

a) collect samples of cells from all parts of the world in order to preserve human genetic diversity.
b) collect plant seeds in order to reduce the impact of human activity on plant extinction.
c) determine the sequence of the 3.3 billion base pairs in the human genome.
d) clone deleterious genes from humans and study their mode of action.
e) clone beneficial genes from humans for eventual use in gene therapy.

c) determine the sequence of the 3.3 billion base pairs in the human genome.
True or False: Typically, bacterial DNA contains less repetitive DNA than eukaryotic DNA.
True
In general, the organization of genes in bacteria is different from that in eukaryotes. In E. coli, approximately 27 percent of all genes are organized into contiguous, functionally related units containing multiple genes under coordinate control that are transcribed as a single unit. Such contiguous gene families are called

a) operons.
b) proteomes.
c) transcriptomes.
d) contigs.
e) pseudogenes.

a) operons.
True or False: The terms proteomics and genomics mean essentially the same thing.
False
Compared with eukaryotic chromosomes, bacterial chromosomes are

a) Large, triple-helix, Z-DNA, organized in monocistronic units with introns.
b) small, mainly organized in monocistronic transcription units with introns.
c) large, mainly organized in monocistronic transcription units without introns.
d) small, with high gene density.
e) large, mainly organized in polycistronic transcription units without introns.

d) small, with high gene density.
True or False: Bacterial genes have introns, and eukaryotic genes lack introns.
False
True or False: There is a general inverse relationship between DNA content and organismic complexity.
False
True or False: Humans have more DNA and more genes than any other organism.
False
Compared with prokaryotic chromosomes, eukaryotic chromosomes are:

a) large, linear, less densely packed with protein-coding genes, mainly organized in single-gene units with introns.
b) small, mainly organized in single-gene transcription units with introns.
c) large, mainly organized in single-gene transcription units without introns.
d) large, mainly organized in multigene transcription units without introns.
e) small, mainly organized in multigene transcription units without introns.

a) large, linear, less densely packed with protein-coding genes, mainly organized in single-gene units with introns.
When two proteins show a 50 to 70 percent match in amino acid sequence, it is likely that

a) the two proteins have identical functions.
b) the two proteins have no common origin.
c) the two proteins have identical tertiary structures.
d) the primary structures may differ but the secondary structures are identical.
e) the two proteins share a common ancestry.

e) the two proteins share a common ancestry.
What is one major limitation of two-dimensional gel electrophoresis (2DGE)?
a) Only the most abundant products are detected.
b) When products are separated, they tend to leach out of the gel matrix.
c) 2DGE is only useful in separating eukaryotic gene products.
d) It is extremely costly to execute in a typical molecular biology laboratory.
e) 2DGE can only be run on nucleic acids.
a) Only the most abundant products are detected.
True or False: Introns are found only in prokaryotic genomes.
False
Comparisons of DNA and amino acid sequences between different organisms reveal evolutionary relationships
molecular biology
Study and comparison of genomes within a single species or among different species.
genomics
the branch of genetics that studies the full set of proteins encoded by a genome
proteomics
Application of mathematics and computer science to store, retrieve, and analyze biological data
bioinformatics
A technology that includes the process of manipulating or altering the genetic material of a cell resulting in desirable functions or outcomes that would not occur naturally.
genetic engineering
An approach to studying biology that aims to model the dynamic behavior of whole biological systems based on a study of the interactions among the system’s parts.
system biology
A system in which at least one of the equations is not linear
nonlinear system
molecule reproduced itself, by chance, in the ocean where all conditions were available for life
origins of life
-parasites of plants, animals, and bacteria that often cause disease and that consist essentially of a core of RNA or DNA surrounded by a protein coa
viruses
A plant pathogen composed of molecules of naked, circular RNA several hundred nucleotides long., A plant pathogen composed of molecules of naked, circular RNA several hundred nucleotides long.
viroids
An circular self-replicating non-chromosomal DNA molecule found in many bacteria, capable of transfer between bacterial cells of the same species, and occasionally of different species. Antibiotic resistance genes are frequently located on plasmids. Plasmids are particularly important as vectors for genetic engineering
plasmids
infectious agents composed only of single-stranded RNA. They are unable to replicate without the aid of specific viruses that coinfect the host cell.
virusoids
An organism whose cells do not have an enclosed nucleus, such as bacteria.
prokaryotic
A cell characterized by the presence of a nucleus and other membrane-bound organelles. Eukaryotes can be unicellular (protists) or multicellular (fungi, plants and animals).
eukaryotic
The aqueous part of the cytoplasm within which various particles and organelles are suspended
cytosol
A part of the cell containing DNA and RNA and responsible for growth and reproduction
nucleus
A cell organelle constructed in the nucleolus and functioning as the site of protein synthesis in the cytoplasm; consists of rRNA and protein molecules, which make up two subunits.
ribosomes
An organelle found in large numbers in most cells, in which the biochemical processes of respiration and energy production occur.
mitochondria
a protein that goes from one side of a membrane through to the other side of the membrane
trans-membrane proteins
(genetics) cell division that produces reproductive cells in sexually reproducing organisms
meiosis
A sequence of electron carrier molecules (membrane proteins) that shuttle electrons during the redox reactions that release energy used to make ATP.
electron transport chain
occurs in cytoplasm; converts one glucose into 2 pyruvic acids, makes 2 ATP and NADH
glycolisis
Chemical process that converts lactate and pyruvate back into glucose.
gluconeogenesis
A series of chemical reactions that either builds a complex molecule or breaks down a complex molecule into simpler compounds
metabolic pathways
Take place in the chloroplasts of plants and algae
photosynthetic reactions
(biochemistry) a long linear polymer found in the nucleus of a cell and formed from nucleotides and shaped like a double helix
dna
(biochemistry) a long linear polymer of nucleotides found in the nucleus but mainly in the cytoplasm of a cell where it is associated with microsomes
rna
to maintain integrityy of genome; 2 types: direct reversal, indirect reversal – removal of damaged bases then replacement with new DNA, double helix structure aids in repairing provides match
dna repair
Consists of structural DNA alteration, cell proliferation that fixes the DNA damage, and DNA repair that either directly repairs the alkylated bases or bases or results in the removal of larger segments of the DNA
mutagenesis
A macromolecule serving as a catalyst, a chemical agent that changes the rate of a reaction without being consumed by the reaction.
enzyme
Proteins that are important for holding cells and organisms together, such as the proteins that make up the cell membrane, muscles, tendons, and blood
structural proteins
Health care utilizing advances made by genomics and molecular biology. Genomic medicine holds the promise of personalized therapies.
genomic medicine
The insertion of working copies of a gene into the cells of a person with a genetic disorder in an attempt to correct the disorder
gene therapy
-genetic manipulation of organisms to generate either live attenuated or inactivated vaccine
recombinant vaccines
Attempts to change the instructions to cancer cells by reactivating genes (half of patients in trial went into remission)
epigenetic therapy
plants are infected with bacteria whose plasmids usually cause tumors in plants. the tumor producing gene is inactivated and the bacterial plasmid insted only introduces the desired donor gene
transgenic plants
DNA can be injected directly into the cells or host genes can be replaced (knocked out) with the donor gene. extra growth hormone gene creates cattle with more meat, chickens may be given genes to resist bacterial infections that poison food.
transgenic animals
The process of implanting an early embryo into the uterus of a surrogate mother. The resulting animal will be genetically identical to the donor of the nucleus.
reproductive cloning
Cells that divide and remain undifferentiated. Three types are totipotent, pluripotent, and multi-potent.
stem cell
(polymerase chain reaction) multiple copies of a specific segment of DNA
PCR
A quantitive in vitro test for an antibody or antigen in which the test material is absorbed on a surface and exposed either to a complex of an enzyme linked to an antibody specific for the antigen or an enzyme linked to an anti-immunoglobulin specific to the antibody followed by reaction of the enzyme with a substrate to yield a colored product corresponding to the concentration of the test material.
ELISA
Fluoresence In Situ Hybridization (FISH)
fluorescent molecular scan
Method of isoenzyme separation
electrophoretic separation
Similar in concept to a DNA microarray, a solid surface with a microscopic grid with thousands of spaces containing probes for analyzing the proteome, the complete set of proteins encoded by the genome of an organism. Also referred to as a protein chip.
protein microarray
guanine
guanine
adenine
adenine
thymine
thymine
cytosine
cytosine
uracil
uracil
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