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Biomedical Sciences > Proteins > Flashcards

Proteins Flashcards

(97 cards)

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1
Q

A-carboxyl

A

PKa- 2

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2
Q

Aspartate

A

4

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3
Q

Glutamate

A

4

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4
Q

Histidine

A

6

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5
Q

A-amino

A

9

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6
Q

Lysine

A

10

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7
Q

Arginine

A

12

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8
Q

Alpha helix

A

Right handed
H bonds every n+4
Most are amphipathic +/-

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9
Q

Beta Sheet

A

Parallel- hydrophobic

Anti- amphipathic

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10
Q

Stabilizing forces

A

Van der waals
Ionic
Disulfide
H bonds

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11
Q

Myoglobin

A

1 globin
Hyperbolic curve
Let’s go of O2 at low []

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12
Q

Hb Forcea

A

Lys, Arg, Asp salt bridges

Uses cooperative O2 binding

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13
Q

Bohr effect

A

Acidity brings His and Asp closer together, T state

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14
Q

DNA adenine methylase

A

Methylates genes on bacterial DNA

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15
Q

Nuclease

A

Hydrolyzes phosphodiester bonds

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16
Q

Exonucleases

A

Cut at ends of polynucleotide chains

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17
Q

Endonucleases

A

Cut in polynucleotide

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18
Q

Topoisomerase

A

Relaxes DNA strand
Adds swivel points
Changes tertiary structure

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19
Q

Bacterial DNA Gyrase

A

Unusual Top II
Makes positive and negative supercoils
Needs ATP
Can be selectively suppressed

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20
Q

Histones

A

Help package DNA
H1 (in between)
H2A H2B H3 H4 (2 of each)
Called nucleosomes when together

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21
Q

DNA Helicase

A

Unwinds double helix

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22
Q

Primase

A

Synthesizes RNA primers for Okazaki fragments

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23
Q

DNA Pol III

A 
Chain elongation
5'-3'
Forms phosphodiester bond 
Proofreading
3'-5'
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24
Q

DNA Pol I

A

Excises RNA primers
Fills in strand gap
5’-3’

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25
Ligase
Binds nicks in fragments | Phosphodiester bonds
26
Lyase
Peels out nucleotide
27
Pol a
Primer synthesis-contains primase
28
Pol b
Base Excision Repair
29
Pol y
Mitochondrial replication
30
Pol d
Lagging strand synthesis | MMR, NER
31
Pol e
Leading strand synthesis | MMR, NER
32
Telomerase
Uses RNA strand as template for repetitions | Reverse transcriptase activity
33
P53
DNA damage sensor
34
MMR
``` Endo Exo Helicase Pol Ligase ```
35
BER
``` Glycosylase Endo Lyase Pol Ligase ```
36
NER
Helicase Exo Polymerase Ligase
37
SSB
Hydrolase/Tranferase Polymerase Ligase
38
DSB NHEJ
Broken DNA sensor nuclease Polymerase Ligase
39
DSB HR
Recombinase | Endo
40
Cytochrome p450
``` Liver detox Bilirubin Cholesterol Bile and bile acids Vitamin D ```
41
Porphyrin precursors
ALA, PBG Water soluble Inactive
42
Porphyrinogens
Solubility depends on COO-'s Active Reduced form
43
ALAS
Succinyl CoA +Glycine Regulated step B6 coenzyme
44
ALAD
ALA to PBG Inhibited by LEAD Uses zinc
45
PBGD
Uses 4 PBG's | Issues in AIP
46
Ferrochelatase
Adds Fe In mitochondria Makes Fe protophyrin IX Inhibited by LEAD
47
PGC 1a
Induces ALAS transcription
48
RNA polymerase
Haloenzyme | Uses sigma promotors to find locus
49
Rho Protein
Makes contact with RNAP and dissociates it
50
DNA Pol I
Does rRNA synthesis
51
DNA Pol II
Does mRNA synthesis
52
DNA Pol III
Does tRNA synthesis
53
CPG
Proximal promoter
54
TATA box
Core promoter
55
Pol II Core Promotor Elements
BRE- TFIIB recognition TATA Box-binds TBP--- INR- initiator --TAF1 TAF2 DPE-downstream promoter TAF6 TAF9
56
Pol II Pre Initiation Complex (PIC)
There are multiple transcription factors
57
RNA Pol II Main Points
12 subunits No sigma-like counterpoint Uses GTF's instead
58
7-methylguanosine
5' cap on mRNA
59
A-amanatin
Binds on RNA Pol II tightly and prevents transcription | Similar to rifampcin in bacteria
60
Splicosome
Takes out introns SNURPS U1, U2
61
DMTase
Demethylates DNA
62
AUG
Start Codon | Methionine
63
AGA, UAA, UAG
STOP codons
64
tRNA
Translates mRNA to protein | Needs to be acylated
65
tRNA Synthetase
Makes and edits aminoacyl tRNA
66
Pre-initiation complex
- MET tRNA - eIF2 - eIF4G - eIF4E
67
Action of eEf1A
Binds all canonical tRNA's
68
Action of eEF2
Ribosomal transferase | Hydrolyzes GTP
69
Prokaryotic mRNA
Polycistronic
70
4EBP
Regulates translation by binding to 5' cap on mRNA | Regulated by mTOR
71
GroEl Chaperone
Assists in the folding repair of denatured proteins
72
Ump1
Brings proteosome together
73
Molten globule
Not a defined structure, but a family of structures | Goal is to exclude water, to bring hydrophobics together
74
Hierarchical model
1 to 2 to 3 fold
75
Nucleation-Condensation model
1 gives 2 and 3
76
Hydrophobic collapse
Molten globule model
77
Agents that promote unfolding
``` Temperature Change in pH Urea Guanidine Organic solvents ```
78
Protein disulfide isomerase
Changes the locations of disulfide bonds in a strand
79
ERAD
ER associated degradation | Retrotranslocates the protein strand out of the ER and into a proteosome
80
Ubiquitous
Conserved Attaches to E1 then E2/E3, then to substrate Dissociated by 19S Reacts with carboxy terminus, lysine residues, hydrophobic residues Expressed in a chain
81
Ub Carboxy Terminal Hydrolase
De-polymerizes ubiquitin strands
82
Ub Activating Enzyme
Activates Ub through de-polymerization | Uses 1 ATP
83
Ub Conjugating Enzyme
Attaches Ub to E1, E2/3, and then substrate
84
Ub-Protein Ligase
Attaches Ub to a protein via a thioester bond
85
Next E3 Ligase
An E3 attached to an E2
86
RING E3 Ligase
An associated ring system that binds Ub
87
19S Regulatory Particle
Unfolds protein Binds and dissociates Ub Binds regulatory proteins 6 members ring of ATPases
88
HIF1
Induces hypoxia metabolic pathways
89
F6-Kinase and mTOR
Induces HiF1 translation
90
VDU and VHL
Promote HiF1 degradation
91
VHL
Component of complex E3 Ligase
92
IF2
Like eIF2
93
EFTu
Like eEF1A
94
EFG
Like eEF2
95
HbA2
A2d2
96
HbF
A2y2
97
HbH
B4

Biomedical Sciences (4 decks)

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