Quiz 2 Flashcards
(101 cards)
1
Q
What are the 4 requirements for DNA replication to start?
A
- Single Stranded Exposed DNA
- Primer needs free 3’ OH
- Nucleotides
- 3’ OH performs nucleophilic attack on phosphate
2
Q
DNA Synthesis moves in what direction
A
5’-3’
3
Q
Whbat is a processive enzyme
A
an enzyme that catalzie multiple rounds of elongation/ digestion of a polymer while polymer stays bound
4
Q
Which DNA Polymerase (I or III) has 5’ to 3’ exonuclease activity?
A
I
5
Q
Which DNA Polymerase (I or III) does the bulk of DNA synthesis
A
Pol III
6
Q
DNA Polymerase III does how many nucleotides/minute
A
30,000
7
Q
DNA Polymerase I does how many nucleotides/minute
A
600
8
Q
Which DNA polymerase ( I or III) has 3’ to 5’ exonuclease activity?
A
both
9
Q
Which DNA polymerase ( I or III) fills in Okazaki frags
A
I
10
Q
How is DNA synthesis on leading and lagging strand coordinated?
A
DNA polymerases for both strands are physically connected to each other
11
Q
How often does DNA polymerase add an incorrect base
A
1 in 10,000
12
Q
backward strand slippage causes
A
insertion
13
Q
forward strand slippage causes
A
deletion
14
Q
4 main differences between prok/euk DNA replication
A
- Replication is regulated by cell cycle in Euks
- Euks have multiple origins of replication=
- Eukes have mtDNA replication
- Euks have telomeres because Euk chromosomes are linear, not circular
- Euk DNA is more tightly packed/ chromatin
15
Q
Is Mito DNA replication linear/circular
A
circular
16
Q
Is MtDNA synthesis uni/bi-directional
A
uni
17
Q
What is different between regulation of regular euk DNA synth and MtDNA synth
A
MtDNA replication is not cell cycle regulated …can have multiple copies
18
Q
Incorrect base
- What is the cause
- What is the repair pathway
A
- DNA replication error
- Base excision repair
19
Q
Oxidized base
- What is the cause
- What is the repair pathway
A
- reactive oxygen species
- base excision repair
20
Q
Missing base
- What is the cause
- What is the repair pathway
A
- removal of purines by acid or uracil by glycosylases
- base excision repair
21
Q
Altered base
- What is the cause (2)
- What is the repair pathway
A
- ionizing readiation, alkylating agents
- nucleotide excision repair
22
Q
Bulge
- What is the cause
- What is the repair pathway
A
- intercalatin gagents
- nucleotide excision repair
23
Q
Linked Pyrimidies
- What is the cause
- What is the repair pathway (2)
A
- UV irradiation
- nucleotide excision repair –Translesion DNA syntesis
24
Q
Cross-linked strands
- What is the cause
- What is the repair pathway
A
- bifunctional alkylating agenst
- Nucleotide excision repair—translesion DNA synthesis
25
single or double stranded breaks
## Footnote
1. What is the cause
2. What is the repair pathway
1. ionizing radiation
chemotherapy
2. homologous recombination, non homologous end joining
26
What is difference between mutation and DNA damage
DNA damage can lead to mutation
mutation is when one WC bp is changed to another WC bp
27
mismatch repair recognizes and repairs ....
normal bases that are improperly matched
28
What is first step in DNA repair
recognizing mismatch
29
- In bacteria what protein recognizes DNA damage
- What distinguishes b/w daughter and template strand?
MutS
Mut L
30
Mut L does what
after distinguishin daughter and template strand, uses endonuclease activity to cut phosphodiester bond on daughter strand
31
Most agents damage DNA by modifying...
covalent structure
32
Nucleotide excision repair recognizes what?
Structural distortions
33
What does cis-platin do?
forms crosslinks
34
Xeroderma Pigmentosum is caused by
mutation in genes involved in nucleotide excision repair
35
Trichothoiodystropy and is caused by
mutation in genes involved in nucleotide excision repair
36
difference between mutagen and carcinogen
mutagen causes mutation in DNA, but does not always cause cancer, so not always a carcinogen
carcinogen causes cancer, so it's always a mutagen
37
what is used to distinguish direct/indirect mutagens in Ames test
liver extract
38
What happens in reciprocal chormosomal translocation
pieces of different chromosomes are stuck together
39
What happens during chromosomal Inversion
incorrect pieces of one chromosome fuse
40
Where is centra dogma of molecular biology regulated the most?
transcription
41
major difference between prok and euk transcrip/translation
in prok... transcription and translation are happening at the same place
42
Is coding/non-coding used as template
non-coding
43
Which position on ribose distinguises DNA from RNA
2'
44
What is diff b/w uracil and thymine.
thymine has extra methyl group on 5' position
45
can RNA polymerase proofread and why
no it does not have 3' to 5' exonuclease activity
46
does RNA polymerase require a primer?
no
47
What does R do in lac operon
lactose sensor ...blocks operator / prevents transcription of lac genes
48
What does i do in lac operon
makes LacR
49
Does LacR act in trans or cis
trans
50
What does it mean if an effector acts in Tran
doesn't need to near/ part of operon ...position doesn't matter
51
What acts as an effector regarding LacR in lac operon?
lactose
52
what's the relationship between glucose and cAMP
When glucose is low, cAMP is high
53
What is the relationship between cAMP, CAP, and the lac operson
When glucose is low cAMP is high and cAMP binds to CAP and CAP is then able to bind to DNA and helps recurit RNA polymerase and stiumlate transcription
54
Small percentage of exons, and larger percentage of introns is indictaive of what?
importance of regulation of transcription ..regulation leads to complexity
55
What percent of genome is classified as repeats
35
56
Whatis rate of SNP variation
1/1250 bps
57
For genetic disease...are SNPs usually found in introns or exons
introns
58
why is Beta globin gene family an exception
gene family is all in small region
59
Which is the RNA polymerase that produces mRNA in Euks?
RNA Polymerase II
60
Polyadenylation of mRNA assists with
termination
61
Capping of mRNA assits with
translation initiation
62
What is the structure of mRNA cap?
5' cap
5' to 5' linkage with 7-methylguanylate bound to phosphate of terminal RNA nucleotide
63
What is the sequence of the start codon
AUG
64
What are sequences of Stop codons
UAG
UAA
UGA
65
3 components of post transcriptional processing
capping, splicing, and polyadenylation
66
What are 3 cis acting sequencing required for initiating and regulating transcription in vivo?
core promoter elements, promoter proximal sequences, and enhancers
67
What do core promotoer elements do?
close to transcriptional start site and direct the assembly of RNa polymerase and general transcription factors necessary to initiate transcription on the DNA
68
What does promoter proximal sequence do
help assemble general transcription apparatus
69
Enhancers are usually found where?
introns
70
What do enhancers do?
binding site for DNA bound transcription factors that can stimulate or repress transcription of a target gene
71
What is splice donor site sequence
GU
72
What is splie acceptor site sequence?
AG
73
What confers tissue specific gene expression
enhancers
74
What percentage of human genes encode for DNA-binding transcription factors?
10%
75
do enhancers work in cis or trans
cis
76
What targets DNA to be exposed/unwound
acetylation by histone acetyltransferases
77
AA is attached to which end of tRNA
3'
78
anticodon is on mRNA or t-RNA
t-RNA
79
Large subunit of Euk Ribosome is __ S
Small subunit of Euk Ribosome is __ S
Whole Ribosome is \_\_S
60
40
80
80
4 Steps in the process of translation
1. activation
2. initiation
3. Elongation
4. Termination
81
82
how do AA get Activated
1. Amino Acid gets added to ATP to form aminoacyl-AMP
2. Amino Acyl-AMP gets added to tRNA to form Amino Acyl-tRNA
83
What is happening in AA activation and why is it important
AA getting added to tRNA,
no where else in process is AA recognized, rest of process is dependent on RNA recognition, so this step has to be correct for translation to work
84
Is tRNA attached to carboxyl or amino groupof AA
carboxyl
85
4 steps of initiation
1. Initiation factors stabilize association of t-RNA with 40S ribosome unit
2. Initiation factors bind to 7-mehtyl guanosite cap on mRNA and recruit the 40S ribosome to the 5' end of the mRNA
3. 40S subunit scans for mRNA until it finds start codon.
4. Large subunit comes over
86
What happens in vanishing white matter disease
mutations in the gene encoding eIF2B
87
what is unique about catalysis of peptide bond in ribosome?
peptide bond is catalyzed by Ribosomes
88
What proofreads translation in ribosome?
Elongation factor
89
Where does energy come from for insertion of aminoacyl-tRNA and translocation of ribo some to next codon
GTP hydrolysis
90
4. Differences between translation in Euks and Proks
1. coupling of transcription/translation
2. Euks have 60/40 ribosomal and Proks have 50/30
3. Proks iniatiate via f-Met --Euks via 5'cap
4. Proks polycistronic
91
How does streptomycin work
binds to 30s subunit and inhibits initation and causes misreading
92
How does tetracycline work?
Binds 30s subunit and inhibits binding of aminoacyl-tRNA
93
How does Chloramphenicol work?
inhibits peptidyl transferase activity of 50S subunit
94
How does Erythromycin work?
Binds 50S subunit and inhibits translocation
95
What does it mean to say that the genetic code is degenerate
single AA has more than one codon
96
What is wobble effect and how does it cause degeneracy
wobble--unconvetional base pairing caused by the fact that anticodon is in a loop
97
What is a wildtype mutation
single nucleotide change that causes single AA change
98
What is a nonsense mutation
premature stop codon/ peptide shortened
99
What is a Frameshift mutation
insertion/deletion that changes reading frame
--usually also causes a nonsense mutation
100
Mito DNA encodes it's own
tRNA genes
101
