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My M2M > Unit I > Flashcards

Unit I 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)

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2
Q

What is the 1st law of thermodynamics?

A

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

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3
Q

What is the 2nd law of thermodynamics?

A

Entropy of the universe always increases

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4
Q

Gibbs Free Energy equation

A

del_G = del_H - T*del_S

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5
Q

Negative del_G means _____

A

reaction is favorable. Will occur spontaneously.

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6
Q

Positive del_G means ______

A

reaction is unfavorable. Will not occur spontaneously.

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7
Q

Rate of a reaction is determined by _____

A

activation energy

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8
Q

Gibbs Free Energy (redox)

A

del_G = -n*F*del_E

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9
Q

2 classes of high energy bonds

A

Thioester & Phosphate (phosphoanhydride)

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10
Q

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

A

less

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11
Q

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

A

released

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12
Q

Purines

A

Adenine & Guanine

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13
Q

Pyrimidines

A

Thymine & Cytosine

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14
Q

Solubility of nucleotide components

A

nucleotide > nucleoside > base pyrimidines > purines

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15
Q

Diseases related to nucleotide solubility

A

Gout & Lesch-Nyhan (accumulation of purines)

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16
Q

Phosphodiester bonds are between _____ and _____ of nucleotides

A

5’ phosphate and 3’ hydroxyl

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17
Q

Polarity of DNA/RNA is ______ to ______ because ______

A

5’ to 3’; Replication/transcription are 5’ to 3’

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18
Q

DNA was established as genetic material through experiment involving _____

A

live-nonvirulent bacteria and DNA from dead-virulent bacteria placed in solution. This resulted in live, virulent bacteria.

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19
Q

Chargaff’s Rule

A

–> purines = pyrimidines

i. e. : (A+G) = (T+C) and in base pairing: G=C, A=T
- The ratio of G+C / A+T is different for each organism

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20
Q

Describe DNA structure

A
  • right-handed double helix strands are anti-parallel
  • The sugar/phosphate is on outside of the helix
  • bases are inside of helix geometry, this allows only A:T and G:C base pairs
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21
Q

How is DNA structure stable?

A

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

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22
Q

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

A
  • higher
  • G:C base-pairs have 3 H-bonds
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23
Q

What are 7 types of DNA damage?

A

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

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24
Q

What drug acts like an alkylating agent?

A

cisplatin

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25
Q

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

A

Actinomycin D

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26
Q

UV light damages DNA by creating _____

A

thymine dimers

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27
Q

Deamination of 5’-methylcystosine results in _____

A

Thymine

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28
Q

Deamination of cytosine results in _____

A

Uracil

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29
Q

What factors affect melting temperature of DNA?

A
  • salt concentration (direct)
  • pH extremes
  • DNA chain length (direct)
  • G:C content (direct)
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30
Q

RNA is more prone to hydrolyzation because _____

A

2’ hydroxyl is prone to nucleophilic attack

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31
Q

RNA is usually _____ stranded

A

single

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32
Q

What is puromycin and how does it work?

A

it is a nucleotide analogue that mimics tRNA acceptor stem (3’ end), thus it inhibits translation.

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33
Q

The _____ of a ribosome does not contain proteins.

A

the core

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34
Q

Translation occurs in _____ of ribosome

A

the large subunit

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35
Q

During translation, mRNA slides along the _____ of the ribosome

A

small subunit

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36
Q

What are the classes and types of RNA?

A
  • Structural (rRNA, tRNA, snRNA, snoRNA)
  • Regulatory (miRNA, siRNA)
  • Informational (mRNA)
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37
Q

Regulatory RNAs are made from _____ parts of genome

A

-non-coding

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38
Q

Replication origins are recognized by _____

A

origin binding proteins

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39
Q

DNA is melted/unwound by _____

A

DNA helicase

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40
Q

Torsional stress is continually relaxed at the replication fork by _____

A

DNA gyrase

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41
Q

What do SSB proteins do?

A

protect unwound, single-stranded DNA during replication

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42
Q

The RNA primer used for replication is made by _____

A

Primase

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43
Q

Elongation of DNA during replication is done by _____

A

DNA Pol III

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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)

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45
Q

What does DNA ligase do?

A

-Joins Okazaki fragments together after the RNA primer has been overwritten by DNA pol I

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46
Q

DNA pol III is processive because _____

A

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

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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
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48
Q

What is the error rate of DNA pol?

A

10^-6 ~ 10^-8

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49
Q

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

A

RNA; DNA

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50
Q

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

A

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

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51
Q

Telomerase is only active in _____ cells

A

stem cells and cancer

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52
Q

Direct reversal repairs what kind of DNA damage?

A

thymidine dimers alkylation strand break

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53
Q

What repairs DNA strand breaks?

A

DNA Ligase

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54
Q

what repairs thymidine dimers?

A

-photolyase–> these are DNA repair enzymes that repair damage caused by exposure to ultraviolet light.

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55
Q

What repairs guanine alkylation?

A

MGMT (methylguanine methyltransferase)

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56
Q

How does excision repair work?

A
  1. recognize damage
  2. endonuclease cuts the strand on each side of the damage
  3. endo/exonuclease removes the damage
  4. DNA pol I/III replaces it with correct bases
  5. DNA ligase reattaches the strand
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57
Q

What types of damage does BER repair?

A

base lose

deamination

alkylation

base oxidation

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58
Q

How does BER work?

A

glycosylase recognizes the damage and cleaves the base from the sugar. Then endonucleases make the repair.

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59
Q

What types of damage does NER repair?

A

-Thymidine dimers, insertion/deletion, chemical adducts, crosslinks

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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
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61
Q

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

A

Global Genome Cancer (Xeroderma pigmentosum)

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62
Q

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

A
  • Transcription Coupled
  • CNS disorder (Cockayne syndrome)
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63
Q

What types of damage does MMR repair?

A

-mismatch, alkylation, oxidation

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64
Q

How does MMR work?

A
  1. recognize damage by MSH protein complexe
  2. Cleavage by MLH protein complex
  3. DNA helicase unwinds strands
  4. DNA pol I/III replaces with correct bases
  5. DNA ligase reattaches strand
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65
Q

How does MMR recognize daughter strand instead of parent strand?

A
  • In prokaryotes, the daughter strand is not yet methylated
  • In eukaryotes, daughter strand has more nicks
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66
Q

Mutations in MMR machinery cause _____

A

HNPCC (colorectal cancer)

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67
Q

How does TLS repair work?

A

“Translesion synthesis”–> When damage is too great for other repair mechanisms, Bypass-DNA-pol (with less specificity) synthesizes new strand from damaged template strand.

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68
Q

How are bypass DNA pol different from regular DNA pol?

A

-Don’t have 3’ to 5’ exonuclease activity (proofreading) thus the bypass DNA pol is more error-prone

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69
Q

How are double strand breaks repaired?

A

NHEJ: no homology required, inaccurate.

HR: requires homology, accurate

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70
Q

_____ regulate the DNA damage checkpoint

A

checkpoint kinases

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71
Q

Primary mRNA transcripts have _____ at their 5’ end

A

3 phosphates that are connected 5’ to 5’

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72
Q

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

A

–> complementary; similar

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73
Q

The initiation codon for transcription is _____

A

ATG

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74
Q

RNA pol I is in the _____ and transcribes _____

A

nucleolus; rRNA ( the most abundant)

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75
Q

RNA pol II transcribes _____

A
  • mRNA (informational)
  • snRNA, miRNA (regulatory)
76
Q

RNA pol III transcribes _____

A

tRNA (the smallest RNA)

77
Q

Describe steps of transcription

A
  1. RNA pol binds to the promoter on duplex DNA
  2. RNA pol melts DNA and forms the open complex (isomerization)
  3. RNA pol elongates the 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 the 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

the 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 the 5’ end of pre-mRNA
  2. Guanylyltransferase adds guanosine+P
  3. Guanine 7 methyltransferase 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 the 3’ end of pre-mRNA
  2. polyA pol adds a string of A to 3’ end
95
Q

What are the 2 functions of polyA tail?

A
  • stabilizes mRNA
  • stabilizes translation on the 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
  • Hemophelia 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

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