Brainscape's Knowledge GenomeTM

Browse over 1 million classes created by top students, professors, publishers, and experts.


See full index

M2M > Unit 1 > Flashcards

Unit 1 Flashcards

1
Q

What are the different forms of energy and their sources?

A

Kinetic (radiant, thermal, mechanical, electrical)

Potential (chemical bonds, concentration gradients, charge separation, redox pairs)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
2
Q

What is the 1st law of thermodynamics?

A

Energy is always conserved. It can be converted, but not created/destroyed

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
3
Q

What is the 2nd law of thermodynamics?

A

Entropy of the universe always increases

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
4
Q

Gibbs Free Energy equation

A

del_G = del_H - T*del_S

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
5
Q

Negative del_G means _____

A

reaction is favorable. Will occur spontaneously.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
6
Q

Positive del_G means ______

A

reaction is unfavorable. Will not occur spontaneously.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
7
Q

Rate of a reaction is determined by _____

A

activation energy

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
8
Q

Gibbs Free Energy (redox)

A

del_G = -nFdel_E

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
9
Q

2 classes of high energy bonds

A

Thioester & Phosphate (phosphoanhydride)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
10
Q

In hydrolysis of high energy bonds, the free energy of products is _______ than that of reactents

A

less

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
11
Q

As electrons pass from compounds with low to high E, free energy is _____

A

released

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
12
Q

Purines

A

Adenine & Guanine

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
13
Q

Pyrimidines

A

Thymine & Cytosine

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
14
Q

Solubility of nucleotide components

A

nucleotide > nucleoside > base

pyrimidines > purines

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
15
Q

Diseases related to nucleotide solubility

A

Gout & Lesch-Nyhan

accumulation of purines

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
16
Q

Phosphodiester bonds are between _____ and _____ of nucleotides

A

5’ phosphate and 3’ hydroxyl

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
17
Q

Polarity of DNA/RNA is ______ to ______ because ______

A

5’ to 3’

Replication/transcription are 5’ to 3’

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
18
Q

DNA was established as genetic material through experiment involving _____

A

live, nonvirulent bacteria and DNA from dead, virulent bacteria in solution resulted in live, virulent bacteria

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
19
Q

Chargaff’s Rule

A

purines (A+G) = pyrimidines (T+C)
G=C
A=T
G+C / A+T is different for each organism

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
20
Q

Describe DNA structure

A 
right-handed double helix
strands are anti-parallel
sugar/phosphate is on outside of helix
bases are inside of helix
geometry allows only A:T and G:C base pairs
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
21
Q

How is DNA structure stable?

A

H-bonding between base pairs and stacking energy (hydrophobic interactions) balance the negative charge from phosphates

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
22
Q

_____ G:C content increases the stability of DNA because _____

A

higher

G:C base pairs have 3 H-bonds

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
23
Q

What are 7 types of DNA damage?

A

Methylation, Deamination, Depurination, UV, hydroxylation, alkylation, intercalation

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
24
Q

What drug acts like an alkylating agent?

A

cisplatin

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
25
Q

What drug is an intercalating agent (alters structure of DNA)?

A

Actinomycin D

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
26
Q

UV light damages DNA by creating _____

A

thymine dimers

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
27
Q

Deamination of 5’-methylcystosine results in _____

A

Thymine

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
28
Q

Deamination of cytosine results in _____

A

Uracil

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
29
Q

What factors affect melting temperature of DNA?

A

salt concentration (direct)
pH extremes
DNA chain length (direct)
GC content (direct)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
30
Q

RNA is more prone to hydrolyzation because _____

A

2’ hydroxyl is prone to nucleophilic attack

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
31
Q

RNA is usually _____ stranded

A

single

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
32
Q

What is puromycin and how does it work?

A

nucleotide analogue that mimics tRNA acceptor stem (3’ end). inhibits translation.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
33
Q

The _____ of a ribosome does not contain proteins

A

core

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
34
Q

Translation occurs in _____ of ribosome

A

large subunit

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
35
Q

During translation, mRNA slides along the _____ of ribosome

A

small subunit

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
36
Q

What are the classes and types of RNA?

A

Structural (rRNA, tRNA, snRNA, snoRNA)
Regulatory (miRNA, siRNA)
Information (mRNA)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
37
Q

Regulatory RNAs are made from _____ parts of genome

A

non-coding

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
38
Q

Replication origins are recognized by _____

A

origin binding proteins

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
39
Q

DNA is melted/unwound by _____

A

DNA helicase

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
40
Q

Torsional stress is continually relaxed at the replication fork by _____

A

DNA gyrase

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
41
Q

What do SSB proteins do?

A

protect unwound, single-stranded DNA during replication

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
42
Q

The RNA primer used for replication is made by _____

A

Primase

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
43
Q

Elongation of DNA during replication is done by _____

A

DNA Pol III

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
44
Q

What are the functions of DNA pol I?

A

5’ to 3’ exonuclease (remove RNA primer)
5’ to 3’ DNA synthesis
3’ to 5’ exonuclease (proofreading)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
45
Q

What does DNA ligase do?

A

Join Okazaki fragments together after RNA primer has been overwritten by DNA pol I

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
46
Q

DNA pol III is processive because _____

A

holds on to DNA via sliding clamp (high replication rate)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
47
Q

Describe steps of DNA replication

A
  1. origin binding proteins bind to replication origin (AT rich sequence)
  2. DNA Helicase unwinds DNA
  3. SSB proteins and DNA Gyrase bind to each DNA strand.
  4. Primase synthesizes RNA primer
  5. DNA Pol III extends leading and lagging strands
  6. DNA Pol I replaces RNA primer
  7. DNA Ligase ligates DNA fragments together
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
48
Q

What is the error rate of DNA pol?

A

10^-6 ~ 10^-8

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
49
Q

Telomerase is a _____ dependent _____ polymerase (aka reverse transcriptase)

A

RNA; DNA

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
50
Q

How does DNA Pol know which base to incorporate into growing DNA chain?

A

Presence of correct H-bonds between bases & common geometry of base pairs

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
51
Q

Telomerase is only active in _____ cells

A

stem and cancer

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
52
Q

Direct reversal repairs what kind of DNA damage?

A

thymidine dimers
alkylation
strand break

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
53
Q

What repairs DNA strand breaks?

A

DNA Ligase

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
54
Q

what repairs thymidine dimers?

A

photolyase

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
55
Q

What repairs guanine alkylation?

A

MGMT

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
56
Q

How does excision repair work?

A
  1. recognize damage
  2. endonuclease cuts strand on each side of damage
  3. endo/exonuclease removes damage
  4. DNA pol I/III replaces with correct bases
  5. DNA ligase reattaches strand
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
57
Q

What types of damage does BER repair?

A

base lose
deamination
alkylation
base oxidation

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
58
Q

How does BER work?

A

glycosylase recognizes damage and cleaves base from sugar. endonucleases repair.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
59
Q

What types of damage does NER repair?

A

Thymidine dimers
insertion/deletion
chemical adducts
crosslinks

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
60
Q

How does NER work?

A
  1. recognize damage
  2. protein complex binds
  3. unwind DNA
  4. endonuclease removal of damage
  5. DNA pol I/III replaces with correct bases
  6. DNA ligase reattaches strands
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
61
Q

_____ NER recognizes damage anywhere in genome and defects lead to _____

A

Global Genome

Cancer (Xeroderma pigmentosum)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
62
Q

_____ NER recognizes damage in transcribed genome and defects lead to _____

A 
Transcription Coupled
CNS disorder (Cockayne syndrome)
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
63
Q

What types of damage does MMR repair?

A

mismatch
alkylation
oxidation

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
64
Q

How does MMR work?

A
  1. recognize damage by MSH protein complexe
  2. Cleave by MLH protein complex
  3. DNA helicase unwinds strands
  4. DNA pol I/III replaces with correct bases
  5. DNA ligase reattaches strand
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
65
Q

How does MMR recognize daughter strand instead of parent strand?

A

In prokaryotes, daughter strand is not yet methylated

In eukaryotes, daughter strand has more nicks

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
66
Q

Mutations in MMR machinery cause _____

A

HNPCC

colorectal cancer

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
67
Q

How does TLS repair work?

A

When damage is too great for other repair mechanisms, bypass DNA pol with less specificity synthesizes new strand from damaged template strand.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
68
Q

How are bypass DNA pol different from regular DNA pol?

A

Don’t have 3’ to 5’ exonuclease activity (proofreading)

Are more error-prone

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
69
Q

How are double strand breaks repaired?

A

NHEJ: no homology, inaccurate
HR: requires homology, accurate

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
70
Q

_____ regulate the DNA damage checkpoint

A

checkpoint kinases

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
71
Q

Primary mRNA transcripts have _____ at their 5’ end

A

3 phosphates

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
72
Q

mRNA primary transcript is _____ to DNA template strand and _____ to DNA coding strand

A

complementary

similar

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
73
Q

The initiation codon for transcription is _____

A

ATG

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
74
Q

RNA pol I is in the _____ and transcribes _____

A

nucleolus

rRNA

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
75
Q

RNA pol II transcribes _____

A

mRNA, snRNA, miRNA

76
Q

RNA pol III transcribes _____

A

tRNA, rRNA

77
Q

Describe steps of transcription

A
  1. RNA pol binds to promoter on duplex DNA
  2. RNA pol melts DNA, forms open complex (isomerization)
  3. RNA pol elongates transcript 5’ to 3’
  4. At stop site, RNA pol releases and transcription complex dissociates
78
Q

RNA pol uses a ____, which makes it processive

A

sliding clamp

79
Q

How does alpha-amanitin work?

A

binds to bridge helix on RNA pol II and halts transcription

80
Q

What drug blocks the RNA exit channel on bacterial RNA pol and halts transcription?

A

rifampicin

81
Q

What sequence is conserved in promoters?

A

TATA box

82
Q

What are the transcriptional control elements on DNA?

A

Core promoter
Promoter proximal elements
Enhancer/Repressors

83
Q

What diseases result from mutations in TFIIH?

A

Xeroderma pigmentosum
Cockaynes syndrome
Trichothiodystrophy

84
Q

What are the components of RNA pol pre-initiation complex?

A

RNA pol
Mediator
Transcription factors (TFIID/H)
Promoter DNA

85
Q

How is a 5’ cap added to pre-mRNA?

A
  1. Triphosphatase cleaves gamma phosphate from 5’ end of pre-mRNA
  2. Guanylyltransferase adds guanosine+P
  3. Guanine 7 methyl transferase adds methyl group to 7’ of guanosine
86
Q

The functions of 5’ cap are _____

A

stabilizes RNA
nuclear export
translational regulation
splicing

87
Q

The conserved sequence at 5’ splice site is _____

A

GU

88
Q

The conserved sequence at 3’ splice site is _____

A

AG

89
Q

The nucleotide at the splicing branch point is _____

A

A

90
Q

_____ attaches to the 5’ splice site

A

U1 snRNA

91
Q

_____ attaches to the splicing branch point

A

U2 snRNA

92
Q

What are the 5 types of alternative splicing?

A 
Exon inclusion/exclusion
Intron inclusion/exclusion
Mutually exclusive exons
5' Exon truncation/extension
3' Exon truncation/extension
93
Q

_____ is an example of a genetic disorder caused by splicing defects

A

spinal muscular atrophy (SMN1)

94
Q

How is 3’ polyA tail made?

A
  1. endonuclease cleaves part of 3’ end of pre-mRNA

2. polyA pol adds string of A to 3’ end

95
Q

What are the 2 functions of polyA tail?

A

stabilizes mRNA

stabilizes translation on ribosome

96
Q

How is polyA tail synthesis associated with termination of transcription?

A

polyA tail formation triggers termination of transcription

97
Q

The conserved sequence in polyA tail is _____

A

AAUAAA

98
Q

_____ is an example of how alternative polyA sites can lead to multiple proteins from a single gene

A

IgM (membrane-bound vs. secreted forms)

99
Q

List 3 diseases that are due to defects in DNA control elements

A

Beta-thalassemia
Hemphelia Beta-Leyden
Fragile X syndrome

100
Q

Describe domains of sequence-specific DNA binding protein

A

DNA binding domain (conserved)
Activation domain
flexible protein domain

101
Q

List major families of sequence-specific DNA binding proteins

A

Homeodomain
Zinc finger
basic leucine zipper
Helix Loop Helix

102
Q

List 3 diseases that are due to defects in sequence-specific DNA binding proteins

A

craniosynostosis
AIS
Waardenburg syndrome

103
Q

_____ is when sequence specific DNA binding proteins homo/heterodimerize to regulate gene expression

A

combinatorial control

104
Q

what are the 2 classes of chromatin modifying factors?

A

DNA-dependent ATPase

HAT/HDAC

105
Q

How do HAT/HDAC work?

A

HATs acetylate K on histones, remove positive charge, activate transcription.
HDACs reverse this process.

106
Q

specificity of transcriptional regulation is due to _____

A

binding of transcription factors to DNA control elements

107
Q

List 5 ways sequence-specific DNA binding proteins are regulated

A
  1. ligand binding
  2. nuclear entry
  3. amount of TF
  4. DNA binding
  5. phosphorylation
108
Q

how is tamoxifen involved in breast cancer therapy?

A

binds to estrogen receptor and recruits HDACs (instead of HATs that bound estrogen recruits)

109
Q

Describe mechanism of Nf-kB

A

TF that is normally in cytoplasm and bound to IkB. IkB normally masks the NLS on NF-kB. During inflammatory response, IkB is degraded, so Nf-kB migrates into nucleus

110
Q

_____ controls (lowers) the amount of p53 and regulates its function (DNA damage control)

A

MDM2

111
Q

Give an example of how DNA binding activity of a sequence-specific DNA binding protein can be regulated

A

Ebox proteins homodimerize due to presence of basic domains and promote cell differentiation. Id proteins form heterodimers with Ebox and prevent DNA binding due to absence of basic domains

112
Q

Phosphorylation of _____ promotes transcription by allowing it to bind with a HAT

A

CREB

113
Q

Other than transcriptional regulation, how else is gene expression regulated?

A
  1. mRNA nuclear export
  2. mRNA degradation
  3. translational regulation
  4. miRNAs
  5. protein degradation
114
Q

_____ describes multiple codons coding for a single amino acid

A

degeneracy

115
Q

_____ describes when the first 2 nucleotides determine which amino acid is coded by the codon and the third is insignificant

A

wobble

116
Q

describe prokaryotic translation initiation

A

IF1+IF3 bind mRNA to small subunit at SD sequence. IF2 brings first tRNA to P site. GTP hydrolysis dissociates initiation factors and binds large subunit.

117
Q

describe eukaryotic translation initiation

A

5’ cap recruits initiation factors that recruit small subunit. small subunit scans mRNA for AUG in 5’ to 3’ direction and binds to it. initial tRNA is loaded into P site. large subunit binds

118
Q

Why is cap-independent (IRES-driven) translation important in eukaryotes?

A

can shut down translation machinary when invaded by virus, but still maintain translation of certain, specific mRNA.

119
Q

_____ of eIF-2alpha due to environmental stimuli prevents delivery of initial tRNA to P site.

A

phosphorylation

120
Q

Describe the function of interferon

A

when virus invades cell, cell releases interferon that signal neighboring cells to turn off translation

121
Q

_____ is an example of an mRNA that is specifically edited to encode 2 different proteins depending on cell type.

A

apoB

122
Q

The strength of a start codon in eukaryotes is related to how much the sequence matches the _____

A

Kozak sequence

123
Q

What does rapamycin do?

A

halt translation by binding/sequestering eIF-4E

124
Q

When iron is _____ in the cell, _____ binds to _____ on _____ and prevents degradation of the mRNA and thus allows for coding of _____, which brings iron into the cell

A 
low
IRE-BP
IRE
3' UTR
Transferrin Receptor
125
Q

When iron is _____ in the cell, _____ binds to _____, so that the mRNA is exposed and degraded.

A

high
IRE-BP
Iron

126
Q

When iron is _____ in the cell, IRE-BP binds to IRE on 5’ UTR and prevents translation of _____

A

low

ferritin

127
Q

When iron is _____ in the cell, IRE-BP binds to iron, so _____ is made and iron is sequestered

A

high

ferritin

128
Q

When pH is _____ than pKa, the protonated acid form of amino acids dominates

A

less

129
Q

Under _____ conditions C forms disulfide bonds that form inter/intra chain links

A

oxidizing

130
Q

List post-translational modifications and diseases/drugs associated with each.

A
  1. Hydroxylation (scurvy)
  2. Carboxylation (bleeding)
  3. Glycosylation (CDG)
  4. Acetylation/Methylation (HDAC inhibitors)
  5. Phosphorylation (Gleevac/leukemia)
  6. Ubiquitination (proteasome inhibitor/myeloma)
131
Q

Primary protein structures are formed by _____ bonds, while secondary, tertiary, and quatrenary structures are formed by _____ bonds

A

covalent

non-covalent (H-bond, ionic/hydrophobic/Van der Waal interactions)

132
Q

H-bonds between NH on _____ amino acid and CO on _____ amino acid form alpha helix.

A

1st

5th

133
Q

_____ and _____ are alpha helix formers, while _____ and _____ are helix breakers

A

A & L

P & G

134
Q

_____ allows hemoglobin to be an effective oxygen transporter

A

cooperativity

135
Q

What can denature proteins?

A

heat, pH extremes, chemicals

136
Q

The ribonuclease refolding experiment showed that _____

A

protein primary structure determines its function

137
Q

_____ help proteins to fold

A

chaperones

138
Q

The two main classes of chaperones are _____ and _____

A

Hsp (bind hydrophobic areas of unfolded proteins to prevent degradation)
GroEL/GroES (hydrolyzes ATP to fold/refold proteins. nonspecific)

139
Q

_____ help with protein folding by replacing improper disulfide bonds with correct ones.

A

protein disulfide isomerases

140
Q

_____ help with protein folding by changing the configuration of P residues

A

peptide prolyl isomerases

141
Q

Protein misfolding causes _____

A

prion disease
Alzheimer’s
Parkinson’s
amyloidosis

142
Q

Describe what happens in prion disease

A

PrP misfold (beta sheet instead of alpha helix) causes it to become resistant to protease activity

143
Q

What are the 7 ways proteins can be purified?

A
  1. Gel filtration chromatography (size)
  2. Ion exchange chromatography (charge)
  3. Affinity chromatography (ligand binding)
  4. SDS-PAGE (size)
  5. Mass spectrometry (size/charge)
  6. Edman degradation (N-terminal sequencing)
  7. Western blot (immunology)
144
Q

miRNA are derived from _____

A

imperfectly matched dsRNA (dicer and drosha dependent)

145
Q

When miRNA have an imperfect match to their target mRNA, the target is _____

A

translationally repressed

146
Q

When miRNA have a perfect match to their target mRNA, the target is _____

A

degraded

147
Q

What is the mechanism of action of miRNA?

A

RISC/Argonaute mediated cleavage
deadenylation/decapping
block translation initiation/elongation

148
Q

siRNA are derived from _____

A

perfect match dsRNA (dicer dependent)

149
Q

siRNA always _____ match their target RNA

A

perfect

150
Q

piRNA is derived from _____

A

ssRNA (dicer independent)

151
Q

siRNA functions relate to _____

A

defense/immunity (mRNA degredation)

152
Q

piRNA functions relate to _____

A

gametes and control of mobile elements

153
Q

What are the functions of lncRNAs?

A 
scaffold
regulate alternative splicing
transcriptional repression
regulate miRNA
DNA mimicry
154
Q

Describe the mechanism of action of ASOs

A

bind to target mRNA and mediate cleavage by RNase
bind to splice site and force translation of alternative protein
siRNA: RISC mediated cleavage
anti-miR: inhibit miRNA

155
Q

What are the 3 general features of cloning vectors?

A

restriction sites
origin of replication
selectable marker

156
Q

In gel electrophoresis for DNA separation, the sample is loaded at _____ end

A

cathode (negative)

157
Q

_____ blotting is used to detect DNA

A

southern

158
Q

_____ blotting is used to detect RNA

A

northern

159
Q

What are the 4 characteristics of hybridization probes?

A

Length (determines Tm)
Sequence (determines target)
Marker (for detection)
Quantity (has to be in excess)

160
Q

Describe how microarrays work

A

The array is composed of immobilized, unlabeled probes. target cDNA/DNA is put on array. Fluorescence measured.

161
Q

In PCR, denaturation occurs at _____ degrees, annealing at _____, and elongation at _____

A

95
55
72

162
Q

Describe how sickle cell anemia can be diagnosed using RFLP

A

make probe to whole gene. Add restriction enzyme.
do southern blot.
abnormal sample will be missing a restriction site (only 1 fragment). Normal sample will have 2 fragments.

163
Q

Describe how DNA fingerprinting works

A

make probes to VNTRs on multiple samples. compare on southern blot.

164
Q

Prion strains are due to _____

A

different misfolding patterns

165
Q

BSE is a _____ compared to vCJD

A

different prion strain

166
Q

_____ CDK activity during _____ phase allows for _____ of pre-RC, but not its _____

A

low
G1
formation
activation

167
Q

_____ CDK activity during _____ phase allows for _____ of pre-RC, but not its _____

A

high
S
activation
formation

168
Q

What is the function of the G1 checkpoints?

A

cell growth (w/o division)
cell differentiation
check for DNA damage

169
Q

What is the function of the G2 checkpoint?

A

check new DNA for damage

170
Q

What is the function of the M checkpoint?

A

check function of spindle for correct DNA distribution into daughter cells

171
Q

The read length of Illumina is _____ and its error rate is _____

A

50-250 bases

0.1%

172
Q

The read length of PacBio is _____ and its error rate is _____

A

2500 bases

15%

173
Q

What 3 criteria must be considered when using next-gen sequencing for SNP identification?

A

coverage (i.e. overlap of fragments)
error rate
ploidy (i.e. heterozygosity)

174
Q

Exome sequencing is useful when a mutation is _____ and follows _____

A

rare

mendelian inheritance

175
Q

Since exome sequencing only involves _____, it cannot be used to diagnose mutations in _____ parts of DNA

A

exons

non-coding

176
Q

List 5 causes of DSBs in DNA

A 
immune system rearrangements
SSBs during replication
meiosis
radiation
medical imaging/treatments
177
Q

homologous recombination occurs only during _____ phases of cell cycle

A

S & G2

178
Q

loss of heterozygosity in homologous recombination occurs due to _____

A

use of homolog instead of sister chromatid for DSB repair (depends on Holliday junction)

179
Q

_____ regulates HR, while _____ regulates NHEJ

A

BRCA1

53BP1

180
Q

Describe the 3 classes of proteins involved in DSB repair

A

sensors (ku)
transducers (ATm/ATR)
repair complexes (BRCA1/53BP1)

181
Q

The difference between cofactors and coenzymes is that _____

A

coenzymes are consumed

cofactors are NOT consumed

182
Q

List 5 ways that enzymes can lower activation energy

A 
binding energy (w/ S to form ES)
increase effective concentration of S
metal ion catalysis (cofactor)
acid/base catalysis (w/ transition state)
covalent catalysis (w/ S)
183
Q

irreversible inhibitors _____ change the enzyme structure/function

A

permanently

184
Q

competitive inhibitors bind to _____ and function by _____

A

enzyme

compete with substrate for binding to active site

185
Q

uncompetitive inhibitors act as _____ regulators and bind to _____

A

allosteric

ES (enzyme-substrate complex)

186
Q

mixed inhibitors bind to _____

A

E or ES

187
Q

What are the 4 mechanisms of enzyme regulation?

A

allosteric regulation
covalent modification
proteolytic cleavage
protein binding

M2M (2 decks)

Brainscape helps you reach your goals faster, through stronger study habits.
© 2024 Bold Learning Solutions. Terms and Conditions