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Biomedical Sciences > Proteins > Flashcards

Proteins Flashcards

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
Q

Ligase

A

Binds nicks in fragments

Phosphodiester bonds

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26
Q

Lyase

A

Peels out nucleotide

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27
Q

Pol a

A

Primer synthesis-contains primase

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28
Q

Pol b

A

Base Excision Repair

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29
Q

Pol y

A

Mitochondrial replication

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30
Q

Pol d

A

Lagging strand synthesis

MMR, NER

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31
Q

Pol e

A

Leading strand synthesis

MMR, NER

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32
Q

Telomerase

A

Uses RNA strand as template for repetitions

Reverse transcriptase activity

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33
Q

P53

A

DNA damage sensor

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34
Q

MMR

A 
Endo
Exo
Helicase 
Pol
Ligase
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35
Q

BER

A 
Glycosylase 
Endo
Lyase 
Pol
Ligase
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36
Q

NER

A

Helicase
Exo
Polymerase
Ligase

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37
Q

SSB

A

Hydrolase/Tranferase
Polymerase
Ligase

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38
Q

DSB NHEJ

A

Broken DNA sensor nuclease
Polymerase
Ligase

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39
Q

DSB HR

A

Recombinase

Endo

40
Q

Cytochrome p450

A 
Liver detox
Bilirubin 
Cholesterol
Bile and bile acids 
Vitamin D
41
Q

Porphyrin precursors

A

ALA, PBG
Water soluble
Inactive

42
Q

Porphyrinogens

A

Solubility depends on COO-‘s
Active
Reduced form

43
Q

ALAS

A

Succinyl CoA +Glycine
Regulated step
B6 coenzyme

44
Q

ALAD

A

ALA to PBG
Inhibited by LEAD
Uses zinc

45
Q

PBGD

A

Uses 4 PBG’s

Issues in AIP

46
Q

Ferrochelatase

A

Adds Fe
In mitochondria
Makes Fe protophyrin IX
Inhibited by LEAD

47
Q

PGC 1a

A

Induces ALAS transcription

48
Q

RNA polymerase

A

Haloenzyme

Uses sigma promotors to find locus

49
Q

Rho Protein

A

Makes contact with RNAP and dissociates it

50
Q

DNA Pol I

A

Does rRNA synthesis

51
Q

DNA Pol II

A

Does mRNA synthesis

52
Q

DNA Pol III

A

Does tRNA synthesis

53
Q

CPG

A

Proximal promoter

54
Q

TATA box

A

Core promoter

55
Q

Pol II Core Promotor Elements

A

BRE- TFIIB recognition
TATA Box-binds TBP—
INR- initiator –TAF1 TAF2
DPE-downstream promoter TAF6 TAF9

56
Q

Pol II Pre Initiation Complex (PIC)

A

There are multiple transcription factors

57
Q

RNA Pol II Main Points

A

12 subunits
No sigma-like counterpoint
Uses GTF’s instead

58
Q

7-methylguanosine

A

5’ cap on mRNA

59
Q

A-amanatin

A

Binds on RNA Pol II tightly and prevents transcription

Similar to rifampcin in bacteria

60
Q

Splicosome

A

Takes out introns
SNURPS
U1, U2

61
Q

DMTase

A

Demethylates DNA

62
Q

AUG

A

Start Codon

Methionine

63
Q

AGA, UAA, UAG

A

STOP codons

64
Q

tRNA

A

Translates mRNA to protein

Needs to be acylated

65
Q

tRNA Synthetase

A

Makes and edits aminoacyl tRNA

66
Q

Pre-initiation complex

A
  • MET tRNA
  • eIF2
  • eIF4G
  • eIF4E
67
Q

Action of eEf1A

A

Binds all canonical tRNA’s

68
Q

Action of eEF2

A

Ribosomal transferase

Hydrolyzes GTP

69
Q

Prokaryotic mRNA

A

Polycistronic

70
Q

4EBP

A

Regulates translation by binding to 5’ cap on mRNA

Regulated by mTOR

71
Q

GroEl Chaperone

A

Assists in the folding repair of denatured proteins

72
Q

Ump1

A

Brings proteosome together

73
Q

Molten globule

A

Not a defined structure, but a family of structures

Goal is to exclude water, to bring hydrophobics together

74
Q

Hierarchical model

A

1 to 2 to 3 fold

75
Q

Nucleation-Condensation model

A

1 gives 2 and 3

76
Q

Hydrophobic collapse

A

Molten globule model

77
Q

Agents that promote unfolding

A 
Temperature 
Change in pH
Urea
Guanidine 
Organic solvents
78
Q

Protein disulfide isomerase

A

Changes the locations of disulfide bonds in a strand

79
Q

ERAD

A

ER associated degradation

Retrotranslocates the protein strand out of the ER and into a proteosome

80
Q

Ubiquitous

A

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
Q

Ub Carboxy Terminal Hydrolase

A

De-polymerizes ubiquitin strands

82
Q

Ub Activating Enzyme

A

Activates Ub through de-polymerization

Uses 1 ATP

83
Q

Ub Conjugating Enzyme

A

Attaches Ub to E1, E2/3, and then substrate

84
Q

Ub-Protein Ligase

A

Attaches Ub to a protein via a thioester bond

85
Q

Next E3 Ligase

A

An E3 attached to an E2

86
Q

RING E3 Ligase

A

An associated ring system that binds Ub

87
Q

19S Regulatory Particle

A

Unfolds protein
Binds and dissociates Ub
Binds regulatory proteins
6 members ring of ATPases

88
Q

HIF1

A

Induces hypoxia metabolic pathways

89
Q

F6-Kinase and mTOR

A

Induces HiF1 translation

90
Q

VDU and VHL

A

Promote HiF1 degradation

91
Q

VHL

A

Component of complex E3 Ligase

92
Q

IF2

A

Like eIF2

93
Q

EFTu

A

Like eEF1A

94
Q

EFG

A

Like eEF2

95
Q

HbA2

A

A2d2

96
Q

HbF

A

A2y2

97
Q

HbH

A

B4

Biomedical Sciences (4 decks)

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