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Biochem w/ Farooq > Test 4 > Flashcards

Flashcards in Test 4 Deck (65):
1

Chemical Agents that can induce DNA damage

HNO2
OH*
H2O2

2

IMP to GMP requires what?

ATP to power
NAD+ to oxidize
Glutamine - Q as amino donor
H20 - hydrolyze

3

RNAPII synthesizes

mRNA

4

I (hypoxanthine) leads to what sub in DNA?

I pairs with C, results in G

5

Intron Removal process

Nuc Attk of 2'-OH of an intronic adenosine on the 5'-phosphate at 5' end of same intron

Nuc Attck of 3'-OH of one exon on the 5'-phosphate located at 5' end of another exon

Formation of intronic 2'-5' phosphodiester bond, lasso

6

elF4A

Unwinds 5'-UTR of mRNA

7

SH2 docks

Phosphotyrosine (pY)

8

DNA Helicase

Unwinds DNA

9

Electrostatic Polarization
Describe domains
What kind of interactions?
Docks in which groove(s)?

DB Domains basic (+) and polarized
Ionic interactions (NOT E-static) + H-bonding - specificity
Major groove

10

Ribonucleotide reductase does NOT reduce?

T

11

dUMP to dTMP occurs by

Methylation
(Thymine is 5-methyluracil)

12

DNA Measurements
Diameter
Pitch
Major/Minor Groove
Density
Twist
Base Tilt
Rise

Diameter - 20 A
Pitch - 34 A/Turn (= major + minor)
Minor Groove - 12 A
Major Groove - 22 A
Density - 10 bp/turn
Twist - 36 degrees
Base Tilt - 6 degrees
Rise - 3.4 A/bp

13

R5P to IMP requires

ATP
Glutamine - Q
Glycine - G

14

elF4G

Recognizes poly(A) tail of mRNA

15

RNAPIII synthesizes

tRNA

16

Bromodomain docks

AcK (acetylated residues)

17

RNA vs DNA

RNA differences:
Single stranded
2'-OH
Uracil
NEVER HELICAL (can be ss, ds, or stem loop)

18

Helix-turn-helix
Made of?
Structure?
What else? (direction)
Docks in which groove(s)?

Two α-helices
Extended and Ordered Structure
Turns and reverses direction
Two consecutive major grooves

19

elF4E

Recognizes 5'-cap of mRNA

20

B-DNA differs from A-DNA:

Fewer base pairs per helical turn
Smaller base tilt
Wider major groove

21

8-Oxoguanine (O) causes what sub in DNA?

O pairs with C and A, sub can result in T

22

Telomere regeneration requires

Telomeric DNA
Telomerase RNA Primer
Telomerase reverse transcriptase

23

DNA Methylation:

Occurs on C
Chromatin Condensation
Transcriptional Repression

24

Transcription/Replication RNA types

sno,tel,sn

25

DNA Denaturation causes

DECREASE in viscosity
INCREASE in hyperchromicity/absorbance
LOSS of double-helix

26

Bonds in a single nucleotide

N-glycosidic bonds
Phosphoester bond
Phosphoanhydride bond

27

In translation initiation, 43S complex (PIC) has

elF3

28

elF2

Recruits metionyl-tRNAi^Met to P site

29

SH3 docks

Proline-rich residues (PPXP)

30

Cleavage of the peptidyl moeity of peptidyl-tRNA at the ribosomal P-site mediated by

eRF1

31

LZ - Leucine Zipper
Made of?
How often is L?
How many heptads?
Docks in which groove(s)?

Two α helices wrapped in tight coil
L at each 7th position
5 successive heptads
Major groove

32

nucleotide sequence of mRNA identical to:
(list all three names and opposites)

Coding Strand
Sense Strand
Nontemplate Strand

33

Gene Regulation RNA types

pi,mi,inc,si

34

In context of DNA replication, RNA primers removed by which ribonuclease?

Ribonuclease H

35

Chromodomain docks

MeK/MeR (methylated residues)

36

R5P to UMP requires

ATP
Glutamine - Q,
Aspartate - D
Bicarbonate

37

RNAPI synthesizes

rRNA

38

snoRNA

modifying RNA nucleotides (ie methylation)

39

INR recruits

TFIID (like TATA)

40

SSB Proteins

Prevent re-annealing

41

Petidyl transferase
What is it?
Component(s) of what S?

RNA Catalytic enzyme - Ribozyme
Component of 28S RNA
Component of 60S subunit

42

TFIIA binds

helps bind TFIID to TATA

43

miRNA involved in

Gene regulation - silencing/degradation

44

DNA Polymerase α

w/ DNA Primase
Low processivity (10-20 nt)
NO 3-5 NOR proofread

45

Helical Rise

length of turn / bps per helical turn
in DNA = 3.4 A/bp

46

DNA Polymerase δ

Requires DNA clamp
Okazaki Fragments
High processivity
3-5 activity/proofreads

47

Zinc Finger
Made of?
Coordinated how?
Docks in which groove(s)?

ZN2+ ion b/w two anti-p β sheets and a α-helix (ββα)
Tetrahedrally coordinated by 4 ligands (C4 or C2H2)
Two consecutive major grooves

48

TFIIE binds

TFIIF and TFIIH

49

Topoisomerase

Relieves supercoil strain

50

IMP Precursor for

AMP and GMP

51

UTP Precursor for

CTP by transamination (CTP synthetase, ATP and H20)

52

"Physical" things that damage DNA

Gamma, X-Rays, UV light

53

Helix-Loop-Helix (HLH)
Made of?
Structure?
What else? (folds)
Docks in which groove(s)?

Two consecutive α-helixes interrupted by loop
Highly flexible or disordered structure
Folds back on each other
Major groove

54

snRNA involved in

Post-transcriptional RNA splicing (part of spliceosome)

55

Histone PTMs Gene Effect (on and/or off)

AcK
MeRK
PSTT
All histone modifications can be - On or off

56

5' capping involves

Adding 7-MG to 5' end of mRNA

Triphosphate bridge linking 5'-OH of 7-MG to 5'-OH of nucleoside at mRNA 5' end (Triphosphate - three 5s)

Methylation - 2'-OH group of NUCLEOSIDE at mRNA 5' end

57

Contour length formula =

Length * Rise
Rise = 3.4 angstrom/bp
angstrom = 10^-10m

58

CAAT recruits

Basal TFs like NFs

59

Three ways to call the sugar in a nucleoside/nucleotide

Ribose
Pentose
Furanose

60

DNA Polymerase ε

Extends Leading Strand
High processivity
3-5 activity/proofreads

61

Stop and Start Codons

Stop - UAA, UAG, UGA
Start - AUG

62

BRE recruits

TFIIB

63

TATA Box binds?
Substitutes are?

TATA Box binds TFIID
INR
MTE
DPE

64

eEF1A/B

Recruits aminoacyl-tRNA to A site

65

Nucleosome
Which Histones
How many turns, what direction?
Contour?

2 x H2A, H2B, H3, H4
Two NEG superhelical turns
Contour - 80 A. (680 is whole wrap around)