MCB Final Exam Document Flashcards
(132 cards)
1
Q
What is the primary replicating enzyme?
A
DNA polymerase delta
2
Q
What is the prokaryotic ortholog for DNA polymerase delta?
A
DNA polymerase III
3
Q
What is responsible for RNA primer synthesis?
A
Primase
4
Q
What is PCNA?
A
Sliding clamp
5
Q
What is the prokaryotic ortholog for PCNA?
A
Beta subunit
6
Q
What is the RFC?
A
The clamp loader (RFC - reload the fucking clamp)
7
Q
Prokaryotic ortholog for RFC
A
Gamma complex
8
Q
What is the role of RPA?
A
Maintain and protect ssDNA
9
Q
What is the prokaryotic ortholog for RPA?
A
SSB
10
Q
What are MCM and CDC6?
A
Helicase and helicase loader respectively
11
Q
What is the prokaryotic ortholog for MCM and CDC6?
A
DnaB and DnaC respectively
12
Q
What is the function of ligase?
A
Links adjacent Okazaki fragments
13
Q
FEN1/RNaseH does what?
A
Removes RNA primer
14
Q
What is the prokaryotic ortholog for FEN1/RNaseH?
A
DNA polymerase I
15
Q
What is the role of DNA polymerase epsilon?
A
Fills in gap left by primer
16
Q
What is the prokaryotic ortholog for DNA polymerase epsilon?
A
DNA polymerase I
17
Q
Which topoisomerase nicks DNA, does not require ATP, and removes supercoils one at a time?
A
Topoisomerase type I
18
Q
Which topoisomerase cuts double stranded DNA, requires ATP, can induce or remove supercoils (2 at a time)
A
Topoisomerase type II
19
Q
What enzyme plays a role in chromatin remodeling by cartelizing the removal of acetyl groups from lysine and arginine residues?
A
HDACs
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
21
Q
____________ prevents chromatin from folding in compact structures, maintaining euchromatic state
A
Acetylation
22
Q
Enzymes that covalently modify the core histone son nucleosomes are?
A
HATs and HDACs
23
Q
Which enzymes remodel nucleosomes on DNA by actively moving or displacing nucleosomes?
A
SWI/SNF complexes
24
Q
Which enzymes use ATP to remodel nucleosomes on the DNA?
A
SWI/SNF complexes
25
How do SWI/SNF complexes actively move or displace nucleosomes?
By creating hypersensitive sites in DNA which stimulate binding of TFs
26
Mismatch repair occurs in which phase of the cell cycle?
G2 cycle
27
What is occurring in the G2 phase of the cell cycle?
Cell is preparing to divide
28
Nucleotide excision repair occurs in which phase of the cell cycle?
G1 phase
29
What is occurring in the G1 phase of the cell cycle?
The cell grows
30
When in the cell cycle does proofreading occur?
S phase
31
What is occurring in the S phase of the cell cycle?
DNA is being replicated
32
What proteins recognize mismatches by DNA polymerase?
MutS and MutL, these require ATP
33
DNA is threaded through MutS/MutL complex until it reaches MutH protein bound to a ______________________, then what happens?
Hemimethylated GATC site, MutH nicks the newly synthesized strand
34
After nick from MutH, and cleavage from helicase and exonuclease activity, _________________ will resynthesize the strand and ______________ will fix the nick
DNA polymerase III, DNA ligase
35
Nucleotide excision repair removes bulky lesions such as?
Pyrimidine dimers and nucleotides with chemicals attached
36
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
Transcription coupled pathway (part of NER)
37
_____ and _____ are DNA ____________ in NER that act to unwind the region of DNA
XPB and XPD, helicases
38
Which type of eukaryotic RNA polymerase is found in nucleolus and has cellular transcripts 18S, 5.8S, 28S rRNA?
Polymerase type I
39
Which type of eukaryotic polymerase is found in the nucleoplasm and has the cellular transcripts: mRNA precursors and snRNA?
RNA polymerase type II
40
Which type of eukaryotic polymerase is found in the nucleoplasm and has tRNA and 5S rRNA cellular transcripts?
RNA polymerase type III
41
Effects of amanitin on eukaryotic RNA polymerase type I, II, and III?
Type I: insensitive,
Type 2: strongly inhibited
Type 3: inhibited by high concentrations
42
What acts indirectly as a bridge between DNA -binding transactivators and complex composed of polymerase II and General TFs?
Co-activators
43
May be thousands of base pairs away from transcription initiation site and make contact with initiator sites through transactivators
Enhancers
44
What limits the action range of enhancers and might bind to nuclear matrix giving looped domains?
Insulators
45
Regulatory elements like promoters and enhancers that are on same chromosome as transcribed gene are acting in _____?
Cis
46
Activator or repressor proteins reach point of action by diffusion and act in ____?
Trans
47
Epinephrine activates what type of receptors?
G-protein coupled receptors
48
Activated G-protein coupled receptors bind to and activate what?
Adenylyl cyclase giving increased cAMP levels
49
cAMP binds to what?
Regulatory subunit of protein kinase A (PKA) which moves into the nucleus
50
After PKA moves into the nucleus, it's catalytic subunit phosphorylates what?
cAMP response element binding proteins (CREB)
51
P-CREB binds to cAMP response elements in promoter of target genes and binds to coactivator CREB binding protein (CRB) yielding what?
Facilitation of transcription via histone acetylation and chromatin remodeling
52
Wobble position in anticodon is there for what?
Steric freedom so other bases may pair
53
Initiator tRNA is first charged with?
Methionine then a formyl group is transferred from N10-formyltetraydrofolate
54
Formylation of methionyl-tRNA ensures what?
That this methionine cannot be inserted in growing polypeptide chain
55
Methionine is not formylated in eukaryotes because it travels with?
40S subunit
56
In prokaryotic translation, IF3 prevents the premature binding of?
50S subunit
57
In prokaryotic translation, IF1 prevents?
Usage of A-site in initiation
58
In prokaryotic translation, IF2-GTP complex does what?
Brings first tRNA to the P-site
59
The antibiotic streptomycin acts to?
Bind the 30S subunit and distorts its structure, interfering with the initiation of protein synthesis
60
IF2-GTP is hydrolyzed and initiation factors are released when _____ subunit arrives to form the ______________?
50S, 70S initiation complex
61
Elongation factors act to do what?
Direct the binding of appropriate tRNA to the codon in the empty A site
62
EF-Tu GTP does what?
Guides tRNA to A site
63
EF-T recycles EF-Tu by?
Exchanging GDP for GTP after hydrolysis
64
The antibiotic tetracycline does what?
Interacts with small subunit to block access to A site
65
The antibiotic puromycin acts how?
Resembles tRNA, and is incorporated in growing polypeptide chain, stopping elongation in prokaryotes and eukaryotes
66
The antibiotic chloramphenicol does what?
Inhibits prokaryotic peptidyl-transferase
67
The antibiotic erythromycin acts to?
Irreversibly bind to A-site on 50S subunit inhibiting translocation
68
Heme prevents inactivation of eIF2 by?
Heme kinase
69
EIF2 makes what?
Glob in
70
If heme is up, then eIF2 is _________ and the kinase is __________
Active, inactive
71
Ferritin is an?
Iron-storage protein required when there is excess of dietary iron
72
Transferrin receptor is involved with?
Up-take of transferrin bound iron from blood plasma
73
Ferritin mRNA has IRE in the __________, while transferrin receptor mRNA has IRE located in the ____________
5' UTR, 3' UTR
74
When there is excess iron what happens to ferritin and transferrin?
Ferritin is made, no transferrin is made
75
Nucleolus is the site for?
rRNA transcription and rRNA modification by snoRNPs
76
Speckles contain what?
snRNPs involved in mRNA production (splicing)
77
Ear signal sequence is located at? And what binds to it to allow for recognition at ER membrane?
N-terminus, SRP
78
Proteins destined for lysis me are tagged with _________ in the?
M6P take, cis Golgi
79
What extends RNA primer 10-20 nucleotides?
DNA polymerase alpha
80
The default signal pathway from the ER goes to?
The cytosol
81
NLS signal sequence takes protein to?
Nucleus
82
SKL signal sequence takes protein to?
Peroxisome
83
KKXX signal sequence takes protein to?
Cell membrane
84
Protein going from ER to Golgi need what type of coat?
COP II/SAR
85
Protein going from Golgi back to ER needs what coat?
COP I/ARF
86
Once vesicle buds off, what happens to coat?
It dissociates, exposing V SNARE to all binding with T SNARE on target membrane
87
In transcytosis what determines the direction of the vesicle, and give an example.
pH determines direction, seen in maternal IgG antibodies
88
What regulates the binding of V and T SNARE?
RAB-GTP
89
What is the role of NSF/SNAPs?
Binds and induces membrane fusion, the ATPase activity disassembles snares
90
What are the names of the v and t snares in neuronal cells?
Synaptobrevin and syntaxin respectively
91
What are Ca sensors that interact with t-snare to trigger fusion?
Synaptotagmins
92
Clathrin coated pits can be described as?
Receptor mediated endocytosis
93
What is the role of adaptin?
Concentrate cargo in lipid raft and trigger assembly of clathrin
94
What is the role of dynamin?
Vesicle constriction to allow for budding off
95
What is the function of the G-protein RAN?
Nuclear import and export
96
What is the function of the G-protein RAS?
Signal transduction of growth factor signals
97
RAS is important for what pathway?
MAPK for cell proliferation
98
What is the function of the G-protein RHO?
Regulation of actin cytoskeleton, actin stress fibers and local adhesion formation
99
What is the function of RAC?
Lamelipodia formation
100
What is the function of CDC42?
Filopodia formation
101
RAS and RHO transducer signals from where?
The cell surface?
102
Gq is activated by binding to?
GPCR
103
Phospholipase C (PLC) breaks down membrane inositol into what?
IP3 and DAG (second messengers)
104
What is the role of IP3?
Increase Ca out of ER, which binds to PKC and activates it
105
What is the role of DAG?
Binds PKC together with Ca, activates TFs
106
What is special about the PI3K pathway?
Cell survival through apoptosis inhibition
107
RTK activation does what? And why is this important?
Reveals docking site for proteins GRB2, cell growth through growth factors
108
Intracellular receptors are also called?
Steroid hormone receptors
109
What is special about steroid hormone receptors?
Lipid soluble ligand that crosses membrane to bind receptor-chaperone complex, enters nucleus, receptor = TF
110
Microtubules are made of what?
Alpha and beta tubulin dimers in a linear arrangement
111
Are Microtubules polar or nonpolar tubes?
Polar because the alpha (- end) contacts beta (+ end) on next dimer
112
If GDP tubulin reaches the + end what happens?
Depolymerization, "catastrophe"
113
Describe the dynamic instability of Microtubules
Dimers continually add and subtract from hollow tube, growth rate is proportional to GTP dimers
114
What is the structural role of intermediate filaments?
Tensile strength, resistance to stretch, connect to IFs of other cells and ECM components (anchoring junctions)
115
Is there polarity associated with Intermediate filaments?
No
116
What is special about actin microfilaments?
Both ends are growing, + end faster than - end, this allows for polarity
117
What is treadmilling?
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
Describe alpha actin
Loose packing, contractile, found in stress fibers
119
What is the role of dystrophin in muscle cells?
Links actin cytoskeleton to integral membrane glycoprotein complex
120
Dystrophin acts to?
Transduce contractile forces from intracellular sarcomeres to ECM
121
What is unique about collagen?
There is a glycine at every 3rd turn
122
The glycine arrangement in collagen allows for what?
H-bonding between its backbone and adjacent helix
123
What is the role of hydroxyproline in collagen?
Make kinks, assist in helix formation
124
Collagen chains are first synthesized as long precursors known as?
Preprocollagen
125
Ascorbic acid (vit c) is needed for?
Hydroxylation of proline
126
____________ remove N and C propeptides turning procollagen into collagen
Peptidases
127
Collagen VII is considered what? And what is its function?
Anchoring fibril, anchors basal lamina to underlying ECM
128
What is unique about FACITs?
The 3 stranded structure is interrupted by no helical domains making it more flexible than fibrillar collagen
129
What is the function of Zn-dependent enzymes?
Degrade the ECM
130
What are hemidesmosomes?
Strongest anchor between cell and ECM, bind to intermediate filaments (keratins) and are anchored by collagen VII fibrils in ECM
131
What is the role of lamins?
Anchor epithelial cells to basal lamina
132
What is fibronectin?
Large adhesive glycoprotein that causes cell to assume normal shape and grow in right direction
