Molecular Biology Exam 2 Flashcards
1
Q
The structure in a prokaryotic cell that contains the genome. The DNA is bound to proteins and is not enclosed by a membrane.
A
Nucleoid
2
Q
The state of nuclear DNA and its associated proteins
A
Chromatin
3
Q
A discrete unit of the genome carrying many genes. Each consists of a very long molecule of duplex DNA and an approximately equal mass of proteins. It is visible as a morphological entity only during cell division.
A
Chromosome
4
Q
True or False: DNA primarily exists as condensed units rather than loose, double helices.
A
True.
The actual state of DNA is highly compacted genetic material via proteins.
5
Q
Active process in which DNA is driven into the head of a virus by an adenosine triphosphate (ATP) dependent mechanism.
A
Translocation
6
Q
An enzyme that cleaves multimers of a viral genome and then uses hydrolysis of ATP to provide the energy to translocate the DNA into an empty viral capsid with the cleaved end,
A
Terminase
7
Q
True or False: The bacterial genome is a supercoiled nucleoid
A
True
8
Q
In reference to a chromosome, this refers either to a discrete structural entity defined at a region within which supercoiling is independent of other regions, or to an extensive region including an expressed gene that has a heightened sensitivity to degradation by the enzyme DNase.
In a protein, it is a discrete continuous part of
the amino acid sequence that
can be equated with a particular
function
A
Domain
9
Q
Most domains in terms of of a chromosome are __ kb (kilobases) in length.
A
- Recent research suggests they may be 10kb in length, however.
10
Q
NAPs stands for
A
Nucleoid-associated proteins
11
Q
Interphase chromatin consists of a tangled mass with topologically isolated domains which average around ________ kb (kilobases)
A
85kb
12
Q
DNA attached to proteinaceous structures in interphase nuclei are called ____ _____ ______.
A
Matrix attachment regions (MARs) or Scaffold attachment regions (SARs)
13
Q
MARs sequences are usually ___ rich.
A
A-T rich
14
Q
The form of chromatin that comprises most of the genome in the interphase nucleus, which is less tightly coiled than heterochromatin and contains most of the active or potentially active single-copy genes.
A
Euchromatin
15
Q
Regions of the genome that are highly condensed, less transcribed, and late replicating. It is divided into two types, constitutive and facultative.
A
Heterochromatin
16
Q
The common form of heterochromatin that always remains heterochromatic is called _____ _____.
A
Constitutive chromatin
It is near permanently condensed, replicated late in S phase and has a reduced frequency of genetic recombinations.
Consists of multiple repeats.
17
Q
Type of chromatin in which regions of euchromatin are converted to a heterochromatic state.
A
Heterochromatin
18
Q
Bands generated on eukaryotic chromosomes by staining techniques that appear as a series of lateral striations.
They are used for karyotyping (identifying chromosomes and chromosomal regions by the banding pattern)
Stained with Giemsa dye.
A
G-bands
19
Q
Densely staining granules visible in chromosomes under certain conditions, especially in meiosis.
A
Chromomeres
20
Q
True or False: Telomeres do not have simple repeating sequences.
A
False. Telomeres DO have simple repeating sequences.
21
Q
We know that telomeres must be a special structure because chromosome ends generated by breakage are “sticky”, and tend to react with other chromosomes, whereas natural ends are stable.
A
22
Q
The single stranded ___ rich tail of the telomere can form a G-quadruplex because ______ bases have the ability to associate with one another.
A
G-rich
Guanine
23
Q
The human centromere consists of _____ satellites or ____ satellite repeats.
A
Alpha, alpha
24
Q
How do eukaryotes resolve the telomere shortening problem?
A
With telomerase, which is an enzyme that adds repeating units to the 3’ end of the telomere. Primarily active only in germ cells and stem cells.
25
Telomerase is a special ______ _____, or reverse transcriptase.
DNA polymerase.
26
Unusually large chromosomes in diptera in certain tissues. Dark bands represent ______ while lighter bands represent _______.
Dark bands = chromomeres, inactive
Light Bands = interbands, active
27
Polytene chromosomes undergo ______, which arises from multiple rounds of replication, but sister chromatids remain synapsed (adhered) to each other.
Endoreduplication
28
In terms of polytene chromosomes, what physical change occurs that signifies gene expression being induced.
Puffs, or rather when the bands expand in response to gene expression. They quite literally "puff" up.
29
Replication of DNA involves the stages of ____, _____, and, _____.
Initiation, elongation, and termination.
30
Before initiation can occur, the replication origin region of the chromosome must be negatively supercoiled or _____.
Unwound
31
What enzyme is responsible for the negative supercoiling at the replication origin and the subsequent relaxation of positive supercoils ahead of the moving replication fork?
Topoisomerase
32
Read: Initiation involves recognition of an origin via a large protein complex. Before DNA synthesis can begin, the parental strands must be separated and transiently stabilized in the single-stranded state, creating a replication bubble.
33
What is a multiprotein structure that assembles at the bacterial replication fork to undertake synthesis of DNA?
It contains DNA polymerase and other enzymes.
Replisome (It's in the name, dummy)
34
After initiation begins, ____ can begin. It is undertaken by another complex of proteins known as ______.
Elongation
Replisome
35
The replisome exists as a persistent protein unit OR de novo and reassembled at the origin for each replication cycle.
Choose one.
The replisome exists de novo and is reassembled at the origin for each replication cycle.
36
DNA Polymerases are the enzymes which make _______.
DNA
37
Some DNA polymerases involved in replication have nuclease activity in addition to the ability to synthesize DNA. Which way do they excise DNA?
3' to 5' exonuclease activity or 5' to 3' exonuclease?
Both. DNA polymerase 1 has a unique 5' to 3' exonuclease activity in addition to its 5' to 3' synthetic and 3' to 5' exonuclease activities.
38
How many subclasses of errors exist that DNA polymerases can make during replication?
2.
1. Substitutions: improperly paired nucleotide incorporation. The error frequency is determined by the efficiency of proofreading.
2. Frameshifts: When an extra nucleotide is inserted OR one is omitted.
39
A site in the genome of which the frequency of mutation (or recombination) is very much increased, usually by at least an order of magnitude relative to neighboring sites.
Mutation hotspots
40
DNA polymerases replicate ____ to ____ (direction).
5' to 3'
41
In MAMMALS, the origin of replication does or does not have an identifiable sequence?
In mammals, the origin of replication does not have an identifiable sequence.
42
The region or unit of DNA or RNA that replicates from a single origin of replication.
Prokaryotes typically have one.
Eukaryotes typically have multiple.
The Replicon
43
Replication strand growth can be unidirectional, bidirectional, or both?
Both
44
DNA replication requires priming. Therefor, DNA polymerase requires a ______ to initiate DNA synthesis.
3'-OH
45
Primase is needed for primer synthesis ---> Short RNA primer is synthesized ---> DNA is synthesized by DNA polymerase.
46
What are other mechanisms of priming? Name three.
1. A preformed RNA (tRNA) can be used common to some retroviruses.
2. A nick is introduced in DNA --rolling circle
3. A protein covalently linked to a nucleotide (this is used by some viruses, it's called a priming protein)
47
Once unwound, DNA strands have different modes of synthesis.
One, is _______ while the other is ______.
Discontinuous
Continuoius
48
Topisomerase 1 is involved in cutting one strand of DNA.
Topoisomerase 2 cuts 2 strands.
49
Recombinase is similar to _____________.
Topoisomerase 1
50
attB/attP, the b = bacteria, the p = phage
51
Lysogenic cycle leads to
Genome integration prophage
52
Lytic cycle leads to
Replication, packaging and cell lysis
53
Integrase is an enzyme involved in
Phage integration
54
Xis factor involved in integrated genome does what?
Excises the gene placed there (or target gene)
Knockout
55
Somatic recombination
Eukaryotic recombination that occurs in non-germ cells (not in meiosis)
Yeast mating type switching
V(D)J recombination of immunoglobulin genes in immune system
56
Must be two different types of yeast cells to mate. One is ___ and the other is ___.
a
alpha
Two a cells cannot mate. Two alpha cells cannot mate. They have receptors on their surface which recognize the other variant.
57
In yeast, the mating type information is encoded at the ______.
Mating Type Locus
58
With yeast cells, each subsequent generation becomes the opposite type. a to alpha, alpha to a, etc.
True
59
Three loci in yeast for mating information, HMLalpha, MAT, HMLa.
Which expresses identity?
MAT.
60
In yeast, the mating type switching occurs by replacement of _______ locus with opposite ______ cassette. This is non reciprocal.
MAT, MAT
61
HO endonuclease used for cutting open two strands, just like SPOI11 for switching mechanism in
Yeast
62
Because MATa/alpha is not identical, HMLa and HMLalpha are found via flanking (side) genes of the middle MATa/alpha
63
What happens to a yeast cell of mating type "a" when its HO gene is mutated?
It will remain as mating type "a".
64
Fragmented pieces of DNA part of the discontinuous strand
Okazaki Fragments
65
What is used to link okazaki fragments?
DNA Ligase
66
What is the name of the E. coli origin?
oriC
67
On the leading strand, or forward strand, DNA synthesis can proceed (continuously or in fragments) toward the 5' to 3' direction.
However, on the lagging strand, synthesis can proceed (continuously or in fragments).
Continuously
in fragments
68
Fragments of DNA that must be annealed back together with ligase enzymatic activity.
Okazaki fragments
69
E.coli origin, oriC, is ____ bp in length.
245 bp
70
Why is oriC A-T rich instead of G-C rich?
Easier to melt/denature.
71
During initiation, _____ binds to the 9mers, bends the DNA, and then proceeds to unwind the ____.
DnaA-ATP tetramer (four ATP)
unwinds at the 13mers
72
DnaA recruits ______ and __________.
DnaA recruits DnaB and DnaC.
73
DnaB is an ___________.
ATP dependent 5'-3' helicase.
74
DnaC is a _____________.
Chaperone and suppressor of DnaB.
75
in terms of regulation of initiation, what is the inactive form of DnaA-ATP?
DnaA-ADP.
When converted to this, it dissociates from oriC.
76
DnaG acts as a ________ at the initiation site?
A primase. DnaG generals small RNA primers.
77
DnaG binds to ____ which causes ______ to dissociate, consequently activating _______.
This is called the _______ ________.
DnaG binds to DnaB which causes DnaC to dissociate through ATP inactivation, consequently activating DnaB.
This is called the initiation complex.
78
What are the three other factors (proteins) involved/required for initiation?
Hu: DNA binding protein
Gyrase: Type II topoisomerase
SSB: Single stranded binding protein
79
Initiation builds how many replication forks?
Two. Once the DNA is "melted" and unwound, two replication forks are formed inside the replisome at opposite ends.
80
How many 13bp and 9bp repeats does oriC have?
Three 13mer and four 9mer repeats.
81
DNA synthesis in eukaryotic organisms requires a licensing factor. What exactly do the licensing factors do?
They control replication. A licensing factor is present in the nucleus prior to replication, removed, inactivated or destroyed by replication and then later resynthesized in the cytoplasm.
82
What are ARS?
Autonomously replicating sequences
83
What is the ORC?
The origin of replication complex.
84
What is the likely purpose of ORC?
To identify origin for the replication machinery. Well conserved.
85
What is Cdc6?
A licensing factor made in G1 phase and binds to ORC.
86
Does ORC remain attached to the origin all the time?
Yes.
87
The ability of a phage to survive in a bacterium as a stable prophage component of the bacterial genome.
Lysogeny.
In simpler terms, the phage lives as part of the chromosome, awaiting synthesis.
88
What is a plasmid ale to integrate into bacterial DNA called?
An episome.
All episomes are plasmids, but not all plasmids are episomes.
89
How is the dilemma of linear replication solved when initiation would begin at the end of a top strand 5' end?
By converting the replicon into a circular or multimeric molecule.
90
Adenovirus uses strand displacement to....
Grow strands by displacing the previous homologous strand of the duplex.
91
What is a terminal protein?
A protein that allows the replication of a linear phage genome to start at the very end. it attaches to the 5' end of the genome through a covalent bond, and is associated with a DNA polymerase, and contains a cytosine residue that serves as a primer.
92
The dsDNA viruses adenovirus and O29 have terminal proteins which initiate replication by generating a new 5' end.
The newly synthesized strand displaces the corresponding strand of the original duplex.
93
Rolling circles also help solve the issue of terminal end DNA replication/initiation. What do rolling circles produce in terms of a replicon?
Multimers of a replicon.
94
Describe the steps of rolling circle replication.
1. A template of circular duplex DNA is present.
2. A nick at the origin in the strands splits them to reveal a 5' P end and a 3' -OH end.
3. Elongation of growing strands begins and displaces old strands (lead by the 5' end facing out/away)
4. After one revolution, displaced strand reaches unit length
5. Continued elongation generates a displaced strand of multiple unit lengths.
95
What are used to replicate phage genomes?
Rolling circles.
96
The ΦX174 A protein is a (cis or trans) acting relaxase that generates single-stranded circles from the tail produced by rolling
circle replication.
cis
97
Conjugation is mediated by the ____ plasmid.
F plasmid
98
An episome that can be free or integrated in E. coli and that can sponsor conjugation in either form.
F plasmid
99
A segment on the F plasmid that is required for bacterial conjugation.
Transfer region
100
The presence of the F plasmid, whether free or integrated, has important consequences for the host bacterium. Bacteria that are F-positive (contain the episome) are able to conjugate and mate with bacteria that are F-negative.
If the F plasmid exists as a free plasmid in the donor bacterium, what occurs?
It is transferred to the F-negative bacteria and converts it into an F-positive bacteria.
101
What do F-positive bacteria possess on their surfaces?
Surface appendages called pili.
They are encoded by the F plasmid.
102
traA encodes the single subunit protein ____ which is polymerized into the pilus (or multiple pili)
Pilin
103
parA, ParB, parS are involved in proper partitioning in
F plasmid transfer and replication.
104
A set of plasmids unable to coexist in the same bacterial cell.
Compatibility group
105
in the event of a compatibility group within a cell, what is normally the fate?
At cellular division, one cell will get one set of plasmid, whilst the remaining will contain an opposing set.
106
The bacterial ______ plasmid can transfer genes into plants.
Ti plasmid
107
Why is Agrobacterium tumefaciens important?
It is able to act as a parasite and contained gene-editing system. It is capable of changing a plants genes and create new mechanisms in existing structures as a result. Even in the absence of A. tumefaciens, the new genes will continue to be expressed in the plant cells.
108
What is a Ti plasmid?
It is a tumor inducing replicon that caries genes involved in various bacterial and plant cell activities.
109
What three loci on the Agrobacterium chromosome are required for the initial stage of binding the bacterium to the plant cell?
chvA, chvB, and pscA
110
Non-homologous end joining is mainly involved during...
DNA damage
111
Transposable elements jumping can cause a change in
DNA sequences
112
Mutation examples:
Deamination (amino group lost)
UV dimerization (UV light causes thymine dimers formation)
Replication
Alkylation
Depurination
113
Most DNA damage causes what?
Detectable structural distortion
114
Thymine dimerization by UV light fusion creates a cyclobutane ring incorporating the two.
115
Direct repair (in lower organisms) involves
Inappropriate covalent bonds reversed by light dependent enzymes (not in most humans or animals)
Lower organisms, not available in placental mammals
116
Repair mechanisms in higher organisms:
1. Replication repair (Proofreading of newly synthesized DNA)
2. Error-prone repair (Translesion polymerases inserts any base when template base unrecognizable.
117
Polymerase I and III are used in ______ in bacteria.
DNA replication in bacteria.
118
In prokaryotes, Polymerase IV and V are involved in ______.
DNA repair
Error Prone repair
Translesion repair
119
What type of damage are DBS (double strand breaks)?
Severe
120
For DBS, what kind of repair is prefered?
Recombination repair
A last resort is non-homologous end joining.
121
Most eukaryotic cells repair DNA breaks by...
NJEJ pathways (Non-homologous-end joining)
122
When the cells are not dividing, you don't make a copy or pair, so Non-homologous-end-joining will be more prevalent.
When cells are dividing in S phase or G2 phase with DNA replication errors you can find a sister chromosome and copy the information. This is homologous recombination.
123
Mismatch repair does what?
Scrutinizes DNA for appropriate base pairing.
124
Many human cancers are caused by mutations in mismatch repair. What are the most prevalent forms caused by this?
Skin cancer
125
In mismatch repair, the system must know which strand is the daughter strand which strand is the parental strand. Otherwise, what can occur?
Mutations.
126
Base excision repair involves....
directly removing damaged bases
127
Nucleotide excision repairs are more common and involves what?
Removing a small stretch of DNA including the damage. Keyword SMALL
128
Four proteins involved in nucleotide excision repair in prokaryotes (this process accounts for 99% of E.coli repairs):
UvrA (recognizes damage and binds to UvrB)
UvrB (Holds position, UvrA released, UvrC binds)
UvrC (nicks DNA on both sides of damage)
UvrD ( unwinds region, releasing damaged strand)
129
Eukaryotic nucleotide excision repair involves...
XP
Global genome repair -> XPC scanning for mutations --> Ds DNA break by XPG (endonuclease)
130
Eukaryotic base excision repair uses what do remove the base? This enzyme is what separates the system from nucleotide excision repair
DNA Glycosylase
131
What system would deal with repair of Thymine dimers: Base excision repair or nucleotide excision repair
Nucleotide excision repair. Thymine dimerization happens on the same strand and incorporates dimerization horizontally of two thymines. Because of this, the nucleotide excision repair would be best fit.
Base excision repair is ONLY FOR ONE BASE
132
Long patch pathway vs short patch pathway
Long patch = AP endonuclease breaks backbone (APE1 in humans) --> Polymerase extends 2-10 nucleotide displacing bases
Short patch = Lyase opens sugar ring --> Single base repair
133
Protein system mut genes help prevent what
Errors in genome
134
How are strands (parental/daughter) strands distinguished?
-FILL IN LATER-
Involves mut. methylated DNA on daughter, unmethylated on parental strand.
135
What does MutS do?
Recognizes mismatch in DNA and recruits MutL.
136
What does MutL do?
Uses ATP to translocate along DNA to a GATC motif.
Here it recruits endonuclease MutH which cuts the non-methylated strand.
Eukaryotic cells also have this same system.
137
What proteins are required for packaging DNA into a new phage?
Terminase
138
Which of the following protein is associated with bacterial DNA?
Basic proteins
139
What protein is associated with the DNA in maize and the humans ?
Histones
140
Which of the following is true of MARs (Matrix associated Regions) ?
It is often close to Topoisomerase II sites
141
Giemsa staining produces white-black patterns in a chromosome, and FISH can detect the location of a specific piece of DNA. If you compare the Giemsa bands and the FISH signal for a gene of interest, where do you most likely to see a colocalization?
A white band
142
Which of the following has helicase activity ?
DnaG
DnaA
DnaB
DnaC
DnaB
143
Which of the following is the primase in bacteria ?
DnaB
DnaC
DnaA
DnaG
DnaG
144
Which activity does the bacterial primase have ?
RNA polymerase
145
What enzymatic activities does DnaA have?
ATPase
146
What is the licensing factor for DNA replication in eukaryotes?
Cdc6
147
T/F : In yeast, the ARS is bound by ORC only during the initiation of DNA replication
False. It is always bound.
148
E. coli needs 40 minutes to replicate its chromosome and another 20 minutes to divide. For a bacterial culture that doubles its cell number every 35 minutes, how frequently DNA polymerase starts replication?
Every 15 min
149
Which of the following is required for septum formation, and has GTPase activity ?
ftsZ
ParA
ZipA
ftsK
Tus
ftsZ
150
Mutation in which of the following genes would cause the phenotype shown below (mini cells)?
Min C/D
151
Q4. Which of the following is NOT involved in chromosomal segregation in bacteria ?
Tus
OriC
Ter
ZipA
ftsZ
OriC
152
T/F: Plasmid partitioning requires binding of parA and parB to box A and boxB respectively, and bending of the central region of parS by IHF.
False
153
Which of the following extrachromosomal DNA is used for genetic engineering of plants ?
Agrobacteria Ti plasmid
Phage φX174
The circular chromosome in E. coli
Adenovirus
Agrobacteria Ti plasmid
154
True/False: During conjugation between bacteria with and without F plasmid, DNA is transferred as double-stranded DNA.
False
155
True/False: Telomerase is required to complete DNA replication in all living organisms and viruses.
False
156
During agrobacteria infection, which protein nicks the DNA and initiates transfer.
VirD2
None of the others
VirA
VirE2
VirD2
157
True/False: Homologous recombination occurs only in germ cells.
False
158
In yeast, SPO11 is a _____
endonuclease
159
Which of the following protein/protein complex is involved in resolving the holiday junction during homologous recombination?
RAD51
Spo11
The Ruv complex
DNA ligase
The MRN complex
RecA
The Ruv complex
160
Homologous recombination is initiated when a _______ is introduced by an ____.
single-strand break, exonuclease
double-strand break, exonuclease
double-strand break, endonuclease
single-strand break, endonuclease
double-strand break, endonuclease
161
Which of the following proteins is responsible for the invasion of the 3' single-stranded overhang into the double-stranded DNA of its non-sister chromatid during homologous recombination?
Spo11
RecA
The MRN complex
5'-3' exonuclease
The Ruv complex
RecA
162
True/False: During DNA replication, topoisomerase releases the tension in DNA by cutting open the two strands.
False
163
The lamda phage Integrase acts most similarly to_____.
Topoisomerase I
164
The Cre/LoxP system is used by which of the following organism:
Animals
Yeast
Plants
P1 phage
P1 phage
165
T/F: DNA integration and excision mediated by the Cre recombinase is irreversible.
False.
166
T/F: Integrase is required for the insertion of lamda phage into, but not essential to its excision out of the host (bacterial) genome.
False
167
After mating type switching, what would happen to a yeast cell that has a mating type alpha and a nonfunctional HMRa locus (the diffusible mating type product is not functional)?
It cannot mate because it will have a nonfunctional Mata locus
168
If a Thymine dimer is formed in bacterial DNA , it will be recognized by which of the following protein?
UvrC
MutS
UvrB
UvrA
DNA glycosylase
UvrA
169
In bacteria, a G is replaced by a A, it will be recognized by which of the following protein?
UvrB
UvrC
MutS
UvrA
DNA glycosylase
MutS
170
In humans, the equivalent of bacterial UvrA is:
XPG
MutH
XPA
XPC
APE1
XPC
171
If a Thymine dimer is found in the bacterial genome, which of the following enzymes will be recruited for repair?
Pol IV or V
Pol I only
Pol I or III
Pol I, III, IV or V
Pol III only
Pol I should be the right answer, but Pol IV and V are also involved at times.
172
If the DNA is broken in a human epidermal cell (not dividing), which of the following mechanisms will be most likely employed for repair?
Base excision repair
NHEJ
Direct repair
Nucleotide excision repair
Homologous recombination repair
NHEJ
