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MCB 1 > MCB Final Exam Document > Flashcards

MCB Final Exam Document Flashcards

1
Q

What is the primary replicating enzyme?

A

DNA polymerase delta

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2
Q

What is the prokaryotic ortholog for DNA polymerase delta?

A

DNA polymerase III

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3
Q

What is responsible for RNA primer synthesis?

A

Primase

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4
Q

What is PCNA?

A

Sliding clamp

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5
Q

What is the prokaryotic ortholog for PCNA?

A

Beta subunit

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6
Q

What is the RFC?

A

The clamp loader (RFC - reload the fucking clamp)

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7
Q

Prokaryotic ortholog for RFC

A

Gamma complex

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8
Q

What is the role of RPA?

A

Maintain and protect ssDNA

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9
Q

What is the prokaryotic ortholog for RPA?

A

SSB

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10
Q

What are MCM and CDC6?

A

Helicase and helicase loader respectively

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11
Q

What is the prokaryotic ortholog for MCM and CDC6?

A

DnaB and DnaC respectively

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12
Q

What is the function of ligase?

A

Links adjacent Okazaki fragments

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13
Q

FEN1/RNaseH does what?

A

Removes RNA primer

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14
Q

What is the prokaryotic ortholog for FEN1/RNaseH?

A

DNA polymerase I

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15
Q

What is the role of DNA polymerase epsilon?

A

Fills in gap left by primer

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16
Q

What is the prokaryotic ortholog for DNA polymerase epsilon?

A

DNA polymerase I

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17
Q

Which topoisomerase nicks DNA, does not require ATP, and removes supercoils one at a time?

A

Topoisomerase type I

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18
Q

Which topoisomerase cuts double stranded DNA, requires ATP, can induce or remove supercoils (2 at a time)

A

Topoisomerase type II

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19
Q

What enzyme plays a role in chromatin remodeling by cartelizing the removal of acetyl groups from lysine and arginine residues?

A

HDACs

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20
Q

Which enzymes play a role in chromatin remodeling by catalyzing transfer of acetyl groups from acetyl CoA to various lysine and arginine residues in amino terminal regions of histone proteins?

A

HATs

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21
Q

____________ prevents chromatin from folding in compact structures, maintaining euchromatic state

A

Acetylation

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22
Q

Enzymes that covalently modify the core histone son nucleosomes are?

A

HATs and HDACs

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23
Q

Which enzymes remodel nucleosomes on DNA by actively moving or displacing nucleosomes?

A

SWI/SNF complexes

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24
Q

Which enzymes use ATP to remodel nucleosomes on the DNA?

A

SWI/SNF complexes

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25
Q

How do SWI/SNF complexes actively move or displace nucleosomes?

A

By creating hypersensitive sites in DNA which stimulate binding of TFs

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26
Q

Mismatch repair occurs in which phase of the cell cycle?

A

G2 cycle

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27
Q

What is occurring in the G2 phase of the cell cycle?

A

Cell is preparing to divide

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28
Q

Nucleotide excision repair occurs in which phase of the cell cycle?

A

G1 phase

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29
Q

What is occurring in the G1 phase of the cell cycle?

A

The cell grows

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30
Q

When in the cell cycle does proofreading occur?

A

S phase

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31
Q

What is occurring in the S phase of the cell cycle?

A

DNA is being replicated

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32
Q

What proteins recognize mismatches by DNA polymerase?

A

MutS and MutL, these require ATP

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33
Q

DNA is threaded through MutS/MutL complex until it reaches MutH protein bound to a ______________________, then what happens?

A

Hemimethylated GATC site, MutH nicks the newly synthesized strand

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34
Q

After nick from MutH, and cleavage from helicase and exonuclease activity, _________________ will resynthesize the strand and ______________ will fix the nick

A

DNA polymerase III, DNA ligase

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35
Q

Nucleotide excision repair removes bulky lesions such as?

A

Pyrimidine dimers and nucleotides with chemicals attached

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36
Q

What is the preferential repair of template strand where RNA polymerase has stalled? It has CSB protein involvement which is a component of TFIIH complex

A

Transcription coupled pathway (part of NER)

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37
Q

_____ and _____ are DNA ____________ in NER that act to unwind the region of DNA

A

XPB and XPD, helicases

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38
Q

Which type of eukaryotic RNA polymerase is found in nucleolus and has cellular transcripts 18S, 5.8S, 28S rRNA?

A

Polymerase type I

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39
Q

Which type of eukaryotic polymerase is found in the nucleoplasm and has the cellular transcripts: mRNA precursors and snRNA?

A

RNA polymerase type II

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40
Q

Which type of eukaryotic polymerase is found in the nucleoplasm and has tRNA and 5S rRNA cellular transcripts?

A

RNA polymerase type III

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41
Q

Effects of amanitin on eukaryotic RNA polymerase type I, II, and III?

A

Type I: insensitive,
Type 2: strongly inhibited
Type 3: inhibited by high concentrations

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42
Q

What acts indirectly as a bridge between DNA -binding transactivators and complex composed of polymerase II and General TFs?

A

Co-activators

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43
Q

May be thousands of base pairs away from transcription initiation site and make contact with initiator sites through transactivators

A

Enhancers

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44
Q

What limits the action range of enhancers and might bind to nuclear matrix giving looped domains?

A

Insulators

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45
Q

Regulatory elements like promoters and enhancers that are on same chromosome as transcribed gene are acting in _____?

A

Cis

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46
Q

Activator or repressor proteins reach point of action by diffusion and act in ____?

A

Trans

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47
Q

Epinephrine activates what type of receptors?

A

G-protein coupled receptors

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48
Q

Activated G-protein coupled receptors bind to and activate what?

A

Adenylyl cyclase giving increased cAMP levels

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49
Q

cAMP binds to what?

A

Regulatory subunit of protein kinase A (PKA) which moves into the nucleus

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50
Q

After PKA moves into the nucleus, it’s catalytic subunit phosphorylates what?

A

cAMP response element binding proteins (CREB)

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51
Q

P-CREB binds to cAMP response elements in promoter of target genes and binds to coactivator CREB binding protein (CRB) yielding what?

A

Facilitation of transcription via histone acetylation and chromatin remodeling

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52
Q

Wobble position in anticodon is there for what?

A

Steric freedom so other bases may pair

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53
Q

Initiator tRNA is first charged with?

A

Methionine then a formyl group is transferred from N10-formyltetraydrofolate

54
Q

Formylation of methionyl-tRNA ensures what?

A

That this methionine cannot be inserted in growing polypeptide chain

55
Q

Methionine is not formylated in eukaryotes because it travels with?

A

40S subunit

56
Q

In prokaryotic translation, IF3 prevents the premature binding of?

A

50S subunit

57
Q

In prokaryotic translation, IF1 prevents?

A

Usage of A-site in initiation

58
Q

In prokaryotic translation, IF2-GTP complex does what?

A

Brings first tRNA to the P-site

59
Q

The antibiotic streptomycin acts to?

A

Bind the 30S subunit and distorts its structure, interfering with the initiation of protein synthesis

60
Q

IF2-GTP is hydrolyzed and initiation factors are released when _____ subunit arrives to form the ______________?

A

50S, 70S initiation complex

61
Q

Elongation factors act to do what?

A

Direct the binding of appropriate tRNA to the codon in the empty A site

62
Q

EF-Tu GTP does what?

A

Guides tRNA to A site

63
Q

EF-T recycles EF-Tu by?

A

Exchanging GDP for GTP after hydrolysis

64
Q

The antibiotic tetracycline does what?

A

Interacts with small subunit to block access to A site

65
Q

The antibiotic puromycin acts how?

A

Resembles tRNA, and is incorporated in growing polypeptide chain, stopping elongation in prokaryotes and eukaryotes

66
Q

The antibiotic chloramphenicol does what?

A

Inhibits prokaryotic peptidyl-transferase

67
Q

The antibiotic erythromycin acts to?

A

Irreversibly bind to A-site on 50S subunit inhibiting translocation

68
Q

Heme prevents inactivation of eIF2 by?

A

Heme kinase

69
Q

EIF2 makes what?

A

Glob in

70
Q

If heme is up, then eIF2 is _________ and the kinase is __________

A

Active, inactive

71
Q

Ferritin is an?

A

Iron-storage protein required when there is excess of dietary iron

72
Q

Transferrin receptor is involved with?

A

Up-take of transferrin bound iron from blood plasma

73
Q

Ferritin mRNA has IRE in the __________, while transferrin receptor mRNA has IRE located in the ____________

A

5’ UTR, 3’ UTR

74
Q

When there is excess iron what happens to ferritin and transferrin?

A

Ferritin is made, no transferrin is made

75
Q

Nucleolus is the site for?

A

rRNA transcription and rRNA modification by snoRNPs

76
Q

Speckles contain what?

A

snRNPs involved in mRNA production (splicing)

77
Q

Ear signal sequence is located at? And what binds to it to allow for recognition at ER membrane?

A

N-terminus, SRP

78
Q

Proteins destined for lysis me are tagged with _________ in the?

A

M6P take, cis Golgi

79
Q

What extends RNA primer 10-20 nucleotides?

A

DNA polymerase alpha

80
Q

The default signal pathway from the ER goes to?

A

The cytosol

81
Q

NLS signal sequence takes protein to?

A

Nucleus

82
Q

SKL signal sequence takes protein to?

A

Peroxisome

83
Q

KKXX signal sequence takes protein to?

A

Cell membrane

84
Q

Protein going from ER to Golgi need what type of coat?

A

COP II/SAR

85
Q

Protein going from Golgi back to ER needs what coat?

A

COP I/ARF

86
Q

Once vesicle buds off, what happens to coat?

A

It dissociates, exposing V SNARE to all binding with T SNARE on target membrane

87
Q

In transcytosis what determines the direction of the vesicle, and give an example.

A

pH determines direction, seen in maternal IgG antibodies

88
Q

What regulates the binding of V and T SNARE?

A

RAB-GTP

89
Q

What is the role of NSF/SNAPs?

A

Binds and induces membrane fusion, the ATPase activity disassembles snares

90
Q

What are the names of the v and t snares in neuronal cells?

A

Synaptobrevin and syntaxin respectively

91
Q

What are Ca sensors that interact with t-snare to trigger fusion?

A

Synaptotagmins

92
Q

Clathrin coated pits can be described as?

A

Receptor mediated endocytosis

93
Q

What is the role of adaptin?

A

Concentrate cargo in lipid raft and trigger assembly of clathrin

94
Q

What is the role of dynamin?

A

Vesicle constriction to allow for budding off

95
Q

What is the function of the G-protein RAN?

A

Nuclear import and export

96
Q

What is the function of the G-protein RAS?

A

Signal transduction of growth factor signals

97
Q

RAS is important for what pathway?

A

MAPK for cell proliferation

98
Q

What is the function of the G-protein RHO?

A

Regulation of actin cytoskeleton, actin stress fibers and local adhesion formation

99
Q

What is the function of RAC?

A

Lamelipodia formation

100
Q

What is the function of CDC42?

A

Filopodia formation

101
Q

RAS and RHO transducer signals from where?

A

The cell surface?

102
Q

Gq is activated by binding to?

A

GPCR

103
Q

Phospholipase C (PLC) breaks down membrane inositol into what?

A

IP3 and DAG (second messengers)

104
Q

What is the role of IP3?

A

Increase Ca out of ER, which binds to PKC and activates it

105
Q

What is the role of DAG?

A

Binds PKC together with Ca, activates TFs

106
Q

What is special about the PI3K pathway?

A

Cell survival through apoptosis inhibition

107
Q

RTK activation does what? And why is this important?

A

Reveals docking site for proteins GRB2, cell growth through growth factors

108
Q

Intracellular receptors are also called?

A

Steroid hormone receptors

109
Q

What is special about steroid hormone receptors?

A

Lipid soluble ligand that crosses membrane to bind receptor-chaperone complex, enters nucleus, receptor = TF

110
Q

Microtubules are made of what?

A

Alpha and beta tubulin dimers in a linear arrangement

111
Q

Are Microtubules polar or nonpolar tubes?

A

Polar because the alpha (- end) contacts beta (+ end) on next dimer

112
Q

If GDP tubulin reaches the + end what happens?

A

Depolymerization, “catastrophe”

113
Q

Describe the dynamic instability of Microtubules

A

Dimers continually add and subtract from hollow tube, growth rate is proportional to GTP dimers

114
Q

What is the structural role of intermediate filaments?

A

Tensile strength, resistance to stretch, connect to IFs of other cells and ECM components (anchoring junctions)

115
Q

Is there polarity associated with Intermediate filaments?

A

No

116
Q

What is special about actin microfilaments?

A

Both ends are growing, + end faster than - end, this allows for polarity

117
Q

What is treadmilling?

A

Seen in low concentrations of ATP-G actin, so monomers come off - end and add to + end, so length of filament remains the same

118
Q

Describe alpha actin

A

Loose packing, contractile, found in stress fibers

119
Q

What is the role of dystrophin in muscle cells?

A

Links actin cytoskeleton to integral membrane glycoprotein complex

120
Q

Dystrophin acts to?

A

Transduce contractile forces from intracellular sarcomeres to ECM

121
Q

What is unique about collagen?

A

There is a glycine at every 3rd turn

122
Q

The glycine arrangement in collagen allows for what?

A

H-bonding between its backbone and adjacent helix

123
Q

What is the role of hydroxyproline in collagen?

A

Make kinks, assist in helix formation

124
Q

Collagen chains are first synthesized as long precursors known as?

A

Preprocollagen

125
Q

Ascorbic acid (vit c) is needed for?

A

Hydroxylation of proline

126
Q

____________ remove N and C propeptides turning procollagen into collagen

A

Peptidases

127
Q

Collagen VII is considered what? And what is its function?

A

Anchoring fibril, anchors basal lamina to underlying ECM

128
Q

What is unique about FACITs?

A

The 3 stranded structure is interrupted by no helical domains making it more flexible than fibrillar collagen

129
Q

What is the function of Zn-dependent enzymes?

A

Degrade the ECM

130
Q

What are hemidesmosomes?

A

Strongest anchor between cell and ECM, bind to intermediate filaments (keratins) and are anchored by collagen VII fibrils in ECM

131
Q

What is the role of lamins?

A

Anchor epithelial cells to basal lamina

132
Q

What is fibronectin?

A

Large adhesive glycoprotein that causes cell to assume normal shape and grow in right direction

MCB 1 (11 decks)

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