Brainscape's Knowledge GenomeTM


Top Flashcards (Certified)
All Flashcards

Molecular Biology > Protein List > Flashcards

Protein List Flashcards

(85 cards)

Start Studying
1
Q

CPSF

A

Recognizes poly A signal, cleaves when Poly A Pol binds

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

Poly A signal

A

AAUAA upstream cleavage site, GU downstream cleavage site

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

CstF

A

Recognizes downstream GU

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

PABPII (Poly A binding protein)

A

Binds to short A sequence, hyperdrives Poly A Pol, protects 3’ end, stays on mRNA

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

Decapping enzyme

A

Recognizes 5’ triphosphate

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

XNRI

A

Exonuclease for 5’ mRNA

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

Exosome

A

Degrades 3’ end once poly A tail shorter than 10

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

U snRNA

A

Mimics structure of group II self splicing intron

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

U1:

A

Binds to 5’ splice site, replaced by U6, carried by SR proteins recruited during transcription

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

U2:

A

Binds Branch A, base pairs with U6 to make active site

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

U4

A

Bound to U5 and U6 which inhibits U6. Leaves before 1st transesterification, departure makes B*

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

U5

A

Binds to U4 to help inhibit U6, stays on spliceosome, weak interactions with the exons near
the 5’ss, 3’ss. Brings important proteins, like PrP8, for the 2 nd transesterification step. Acts as a
scaffold

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

U6

A

Binds to 5’ splice site when making B*. Part of active site. Base pairs with U2.
Contains Sm proteins which encircle the Sm sequence that is in each U protein.

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

B complex

A

U4 and U5 bound to U6. U1 is bound to 5’ splice site. U2 is bound to BSA (branched A?)

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

B*

A

U2, U5, U6 bound, leads to first transesterification

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

C

A

U2, U5, U6 bound, leads to transesterification reaction after a large conformational change

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

Helicase for spliceosome

A

Uses ATP to induce large conformation change in spliceosome and release of ligated exons and lariat

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

Debranching enzyme

A

Cleaves the 2’ phosphodiester bond at the BSA to linearized the intron

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

Self splicing group I intron

A

Needs a G, magnesium ion.

No ATP, circularizes intron at the end. Very old

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

ICS

A

Internal guide sequence. purine rich intron base pairs with pyrimidine rich exon to align splice sites. Prevents 2nd reaction from reversing

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
21
Q

Self splicing group II

A

Does not require G, product is lariat. Similar to spliceosome

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

Hammerhead ribozyme:

A

Self-cleaving RNA, no splicing, needs magnesium ion. Used in viral RNA cleavage

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

medRNA

A

mini exon sequence that is the same in trypanosomes, used in trans splicing

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

transsplicing

A

Uses BSA, product in 2 introns and a spliced exon

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
25
tscA
RNA that helps with self splicing in trans. because a group II self splicing intron. has BSA
26
U2AF
Protein recognizes poly pyrimidine sequence and 3' splice site. Regulation of alternative splicing as it plays a role in regulating the binding of U2
27
Prp8
Recruited by U5, binds to splice sites, poly pyrimidine and BSA. Mediates structural changes after 1st reaction. Holds U2 and U6 together for catalysis. Remains with spliceosome the whole time
28
Brr2
Helicase that unwinds U6 from U4, helps U2 and U6 bp
29
19th/19th related complex
Big complexes that build the structure of the spliceosome
30
Prp2
Helicase that sets up B*
31
M2
Forms after B* is made, located in U6, coordinates 4 phosphate oxygen and the last not of the exon and first not of intron. Froms due to U6 and U2 binding
32
Yju2
Brings BSA to 5' splice site
33
BSA
A H-bonds with U at the 5' splice site. G stacks on A. Magnesium ion makes 2'OH more nucleophilic and stabilizes the negative charge buildup
34
M1:
Conformation change in U2 to a tem loop has to occur before it can form
35
HnRNP
Negative effect on splicing, oligomerizes to block splice sites. Prevents binding of U@AF
36
Intron encoded protein:
For group II self splicing introns, very similar to Prp8. Stabilizes structure of RNA
37
Prp22
After exons are ligated, unwinds at the 5' splicesite and U5. Spliced RNA is release immediately
38
ISS, ISE, ESS, ESE
DNA sequences that show up anywhere, can enhance or silence splicing. Where regulators bind
39
TIAI
Protein that helps U1 bind
40
Sex lethal protein
Prevents binding of U2AF. Subsequence splicing excludes certain exon
41
Tra+Tra2
Promotes binding of U2AF so splicing includes exon. Normally U2AF will not bind to poly pyrimidine sequence on sex differentiating gene
42
CCA
Single stranded 3' end of every tRNA (acceptor stem) Amino acid acceptor binds through the 2' OH of the A
43
3D strucutre of tRNA
L-type structure
44
Anticodon loop
Base pairs are splayed out for binding to codon
45
D-loop
Dihydrouridine, missing a double bond. Where stress is induced in tRNA to prepare for peptide bond formation
46
TuC loop
Pseudo loop
47
Variable loop
Varies for tRNAs
48
Inosine
Mimics a G. Comes from deaminating an A. Promotes degeneracy of genetic code. Recognizes/BP with A U and C
49
Aminoacyl-AMP
Intermediate when loading amino acid on tRNA
50
Activating Site:
IDK
51
Editing site
Cleaves amino acid and AMP. Correct amino acid goes to 2nd step and the wrong amino acid gets hydrolyzed from AMP
52
IF3
Binds small ribsosomal subunit in prokaryotes. Prevents binding to large subunit. Facilitates binding to shine delgarno sequence. Puts AUG in P site. Leaves when large subunit binds
53
Shine delgarno sequence
AGG AGG. Separated from AUG by 8 nts, aligns AUG to the P site
54
IF2
Boudn to GTP. Directs Met-tRNAi-Met to the P site. Does not bind any other tRNAs. Hydrolysis of GTP causes IF2 to dissociate
55
IF1
Blocks the A site so tRNA won't go there
56
EF-Tu
Bound to GTP. Binds the free charge amino acyl tRNA and brings it to a ribosome. Prevents it from entering the active site of the ribosome
57
EF-G
Bound to GTP. Slides tRNA in large subunit from P to E site. Opens A site. Slides tRNa in small subunit from A to P. Binds to the A site at the end and moves the ribosome down the mRNA
58
RF 1/2
Mimics the structure of tRNA. Binds to the A site. Stimulates peptidyl transferase activity. Tether the complete peptide to he tRNA in P site
59
RF3
Causes RF 1/2 to depart from the ribosome
60
RRF
Binds to the A site to undock the ribosome
61
Met-tRNAi-Met
Binds to the P siste, not A site. IF1 blocks the A site, IF3 puts AUG in the P site
62
16s rRNA
Part of the small subunit that binds to the shine delgarno sequence. Aligns the AUG to P site. mediated by IF3
63
Riboswitch
Region of RNa that can bind a cofactor, secondary structure changes so AUG and shine delgarno sequence ar not accessible. Puts in a stem region
64
eIF2
Brings Met-tRNAi-Met to the Small eukaryotic subunit P site. Has beta, gamma, and alpha subunits. Gamma carries the tRNA, alpha binds to GTO and is involved in regulation
65
eIF4
Binds the small subunit to the 5' cap of mRNA
66
Important Subunits of eIF4
4E: cap binding protein 4A: helicase for RNA, cannot san with hairpins 4G: The glue, binds 5' end and PABP, circularizes mRNA and protects it from degradation
67
Kozak sequence
Sequence around AUG that helps with recognition: A/GXXAUGG
68
eIF2B
Exchanges GDP for GTP on eIF2
69
eIF2alpha kinase
phsophorylates the alpha subunit of eIF2, turned on during viral infection so viruses can use host ribosomes
70
Phosphorylated eIF2
Cannot bind to the initiator tRNA. Translation stops
71
m-TOR
A kinase targets the 5' end of the mRNA, turns off in response to stress. When active phosphorylation of 4G activates 4A in eIF4 and phosphorylation of 4E-BP frees 4E so it can make the eIF4 complex
72
IRES
Virus stimulates decapping enzymes, shuts down host protein synthesis, increases available ribosomes so they can bind to viral RNA. Viral RNA does not have a 5' cap, they have internal RNA binding sites
73
Properties of Viral RNA due to internal RNA binding sites
Can recruit the ribosome Can initiate without eIF4E since no cap Can bind without tRNAi
74
Small ribosomal subunit
Decodes mRNA, mediates tRNA-mRNA interactions
75
Large ribosomal subunit
Peptide bond formation between P and A sites. (Makes the peptidyl transferase center
76
EF-Tu, EF-TS interaction
EF-TS exchanges GDP for GTP, EF-G does not need a protein to exchange
77
Codon, Anticodon interaction
Allows tRNA to become distorted
78
Accommodation
Proofreading mechanism before peptide bond formation. Distorts tRNA and ejects it if it is not a match
79
16s A
2 A residues on helix 44 flip up to H bond to the ribose and phosphates of the tRNA:mRNA. Stabilizes
80
16s G
Stacks and stabilizes over A
81
Distortion of tRNA
3' end makes H bonds with rRNA | Thermodynamically favorable
82
Helix 44
Where the A's are located. Undergoes confomration change with perfect base pairing because of negative delta G H-bonds. Involved before GTP hydrolysis and EF-Tu dissociate. Fundamental to decoding and allows h hydrolysis of GTP
83
Paromycin bound ribosome
Binds to helix 44, pushes A's up, no energy requirement. Allows tRNAs to be included. Overall misreading of mRNA
84
Hydrophobic gate on EF-Tu
H2O will hydrolyze GTP once it is activated by His. His is blocked by the gate, which opens when helix 44 changes conformation upon correct codon anticodon binding.
85
Reactions that need ATP
1st transesterification reaction 2nd transesterification for conformational change 1st step of aminoacyl transferase reaction eIF4A for helicase activity

Molecular Biology (2 decks)

Brainscape helps you reach your goals faster, through stronger study habits.
© 2025 Bold Learning Solutions. Terms and Conditions