Biochem Ii Exam 2.1

Front 1

Central dogma

Back 1

DNA - Replication - Transcription to RNA - Translation to Protein

Front 2

Semiconservative DNA replication

Back 2

In new DNA, one strand is conserved from parent and one strand is new

Front 3

Direction of DNA replication?

Back 3

Bi-directional - bubble is created and has two replication forks

Front 4

DNA elongation occurs in which direction, and why?

Back 4

5' to 3' only; Because can add only to the hydroxyl group, which is on the 3'

Front 5

DNA replication origin sites for prokaryote/eukaryote

Back 5

Multiple in eukaryote (thousands); single site in prokaryote

Front 6

DNA Shapes - prok, euk

Back 6

Prok: circular; Euk: long and linear and circular (mitochondrial)

Front 7

DNAa?

Back 7

Enzyme that unwinds prokaryotic chromosome during replication

Front 8

Speed of prokaryote DNA replication

Back 8

1000 bases/sec, 4 million bases, about 40 minutes

Front 9

Anti-parallel nature of DNA

Back 9

Direction of the sugar - 3' to 5' on one strand, 5' to 3' in the other.

Front 10

Direction of DNA replication problem, solution

Back 10

Antiparallel strands and DNA polymerase can only add bases 5' to 3'. So, semi-discontinuous replication used. One strand is continuous (leading) and one is discontinuous (1000 bp segments, Okazaki)

Front 11

DNA Template

Back 11

The strands, both leading and lagging from the parent DNA

Front 12

RNA Primers needed for leading strand, lagging

Back 12

One, multiple

Front 13

DNA polymerase I

Back 13

prokaryotic

Front 14

DNA polymerase III

Back 14

prokaryotic

Front 15

DNA pol α

Back 15

Eukaryotic

Front 16

DNA pol δ

Back 16

Eukaryotic

Front 17

Delete RNA primer and adds DNA

Back 17

DNA pol I

Front 18

This unwinds DNA

Back 18

Helicase

Front 19

Main enzyme responsible for leading strand synth

Back 19

DNA pol III

Front 20

Main enzyme responsible for lagging strand synth

Back 20

DNA pol III

Front 21

Topoisomerases

Back 21

Relieve coil winding

Front 22

DNA polymerase initiation

Back 22

Cannot initiate without RNA primer

Front 23

What to DNA polymerases do?

Back 23

Catalyze a template directed synthesis

Front 24

For DNA elongation, what is required?

Back 24

1.DNA or RNA Primer attached to 3' OH ( "3' END"); 2.Nucleotides (dNTP); 3.DNA template - from parent DNA

Front 25

DNA/RNA primer - difference?

Back 25

?

Front 26

Reverse Transcriptase

Back 26

RNA Dependent DNA polymerase

Front 27

AZT

Back 27

Reverse transcriptase inhibitor; Is incorporated into DNA synthesis, but lack the 3' OH so blocks synthesis.

Front 28

Differentiate Pol I & Pol III

Back 28

Both (every) polymerase has 3' to 5' exonuclease activity; Only pol I has 5' to 3' exonuclease activity; Pol III very fast.

Front 29

Which Pol has 5' to 3' exonuclease activity and why important

Back 29

Only Pol I has this; ??Has to remove primer.

Front 30

What is exonuclease activity?

Back 30

Ability to cleave nucleotide/DNA from the terminus (end)

Front 31

What is endonuclease activity?

Back 31

Ability to cleave nucleotide from the middle

Front 32

Processivity in DNA

Back 32

# of nucleotides made in a certain amount of time

Front 33

Processivity of Pol I & Pol III

Back 33

Pol I 40 - 200; Pol III > 500,000

Front 34

General Function of DNA Polymerases

Back 34

Bind template; Bind correct dNTP substrate

Back 35

Cata;yse phosphoryltransfer; Remove mismatched bases (3' to 5' exonuclease activity)

Front 36

Architecture of T7 DNA

Back 36

Bacteriophage DNA polymerase with; A form architecture (widened minpr groove); .Allows enzyme to recognize the H-bonding pattern; Universal Minor Grove H-Bonding recognition motif

Front 37

DNA polymerase T7 - an example of substrate discrimination

Back 37

Try526 and Glu480 residues in active site provide tight clearance and prevent an NTP with a 2' OH from binding

Front 38

Unwinding of DNA necessitates the need for this

Back 38

Topoisomerase to relieve the twist (supercoil) stress

Front 39

Topoisomerase types

Back 39

1A, 1B - single strand cuts; 1A - strand passage mechanism; 1B - rotation; 2 - double strand cut, passage mechanism

Front 40

Topoisomerase inhibitor types:

Back 40

Catalytic ; Poisons

Front 41

Novobiocin

Back 41

Catalytic (coumarin) topoisomerase inhibitor

Front 42

Topotecan

Back 42

Poison topoisomerase inhbitor; Stabilizes the cleavage complex; Covalently binds to DNA and prevents religation,

Front 43

NA-protein interaction is useful when?

Back 43

Transcription, translation, DNA repair, DNA cleavage, recombination, methylation

Front 44

Example of protein - DNA interaction

Back 44

GAL4 protein is a Transcription factor binding to DNA in promoter region to turn on lacZ gene. When GAL4 cannot bind, lacZ gene is turned off

Front 45

How does protein DNA interaction start?

Back 45

Recognition of side chain sequence

Front 46

Amide bond of asparagine is

Front 47

Can recognize Hoogsteen face of A-T

Back 47

Asn or Gln

Front 48

Can recognize G-C

Back 48

Arg - the

Front 49

Most common binding motif

Back 49

Alpha helix secondary structure

Front 50

Motifs with alpha helix

Back 50

Leucine zipper, HTH, zinc fingers

Front 51

434 repressor

Back 51

Contains alpha heli x including RECOGNITION HELIC, turn, another helix, recognizes base pairings in major groove

Front 53

HTH

Back 53

Motif with N-terminal, then scaffolding, then turn, then recognition sequence. In many protiens including 434 reressor

Front 54

Homeodomain

Back 54

3 alpha helices connected by short loop. Helices by n terminal are parallel, helix toward c-term is perpendicular, common in transcription factors

Front 55

Basic region leucine zipper

Back 55

Found on some transcription factors

Back 56

Leucine every 7 aminos which allows for dimerization interaction necessary; has basic region - many Arg residues to interact with DNA in the major groove

Front 57

Basic region HLH

Back 57

Motif for DNA interaction; Has two alpha helix regions separated by a loop; Then a dimer forms; Recognizes the MAJOR groove

Front 58

Zinc Finger

Back 58

DNA binding using beta sheet and alpha helix (ββα); Most common structure in eukaryotes; 2 Cys & 2 His residues

Front 59

Zn Finger

Back 59

Reads 3 or 4 bp sequence in major groove of DNA; Alpha helix

Front 60

HAT

Back 60

Histone Acetyl Transferase; Acetylates histones, opens chromatin, allows transcription

Front 61

HDAC

Back 61

Histone deacetyl transferase; Results in tight coiling and closed chromatin - no transcription

Front 62

Nucleosome

Back 62

Fundamental repeating unit in eukaryotic chromatin; Carries epigenetic info - histone modification & DNA methylation

Front 63

Histone structure

Back 63

2 copies of each H2A, H2B, H3, H4. H1 is not part of the "bead" Linker of about 80 bp between the beads (not part of histone)

Front 64

30 nm fiber

Back 64

High level of H1, no gene transcription

Front 65

11 nm fiber

Back 65

Reduced level of H1, gene transcription possible

Front 66

Histone modification location / charges

Back 66

Tail sticks out of the "bead" and has positive charged residues (Lys, Arg).

Front 67

DNA phosphate back bone - the charge?

Back 67

Negative

Front 68

Phosphate backbone causes what kind of interaction between nucleosomes?

Back 68

Repulsive

Front 69

Acetylation of histones does what

Back 69

Lose positive charge on histone tails and the negative charge on the DNA phosphate backbone begins to compact

Front 70

Transcription factor Access when 30 nm form?

Back 70

HAT if access, or remodeling with chromatin remodeling complex

Front 71

In some cancers, HDAC is

Back 71

overexpressed

Front 72

RNA structure compared to DNA

Back 72

Shorter, not ds, stem & loop

Front 73

Base pairing in RNA

Front 74

Stabilization in RNA

Back 74

Metal ions

Front 75

Ribosome RNA content

Back 75

2/3 RNA, 1/3 protein

Front 76

Ribozyme

Back 76

Ribosome is a ribozyme, has catalytic function, peptidyl function

Front 77

What kind of a molecule is thymidylate?

Back 77

Nucelotide

Front 78

What kind of a molecule is hypoxanthine?

Back 78

precursor of IMP in salvage (using HGPRT); spontaneous deamination product of adenine

Front 79

What kind of a molecule is guanosine?

Back 79

purine nucleoside, can be phos. To GMP etc.,

Front 80

What kind of a molecule is 5-phosphoribosyl-1-pyrophosphate?

Front 81

ATP dependent?: Transformation of ribose-5-phosphate into phosphoribosyl pyrophosphate (PRPP)

Back 81

Yes

Front 82

ATP dependent?: Transformation of glycinamide ribonucleotide into formylglycinamide ribonucleotide (FGAR)

Back 82

No

Front 83

ATP dependent?: Transformation of xanthine monophosphate (XMP) into guanosine monophosphate (GMP)

Back 83

Yes

Front 84

Reactions requiring PRPP

Back 84

de novo synthesis of purines, de novo synthesis of pyrimidines; salvage pathway for purines (not certain this is complete)

Front 85

PNP is involved in salvage of purines?

Back 85

FALSE

Front 86

Deficiency in PNP

Back 86

Results in SCID

Front 87

Adenosine deaminase (ADA)

Front 88

Hypoxanthine-guanine phosphoribosyl transferase (HGPRT)

Back 88

Lesch-Nyhan

Front 89

Purine nucleoside phosphorylase (PNP)

Front 90

Xanthine oxidase

Back 90

Gout

Front 91

Inosine monophosphate dehyrgenase (IMPDH

Front 92

PNP

Back 92

Purine nucleoside phosphorylase, converts nucleoside to its base and R1P in catabolism, deficiency results in SCID (like ADA deficiency)

Front 93

ADA

Back 93

Adenosine deaminase, catalyzee dA to dInosine, mediates DNA turnover, deficiency

Front 94

Degrade pathways for Pur, pyr

Back 94

Yield uric acid; ammonia

Front 95

Where is most de novo nucleotide synthesis

Back 95

Liver, other areas rely on salvage

Front 96

First steps of de novo Purine synth

Back 96

PRPP - IMP > A/GMP > A/GDP > A/GTP

Front 97

First steps of de novo pyrimidine synth

Back 97

PRPP > orotate > OMP > UMP > UDP . UTP > CTP

Front 98

O6-methylguanine

Back 98

Methylating agent, G:C to A:T transition mutation, removed by MGMT

Front 99

Benzopyrene

Back 99

From burning food, smoking; P450 activation required, alkylator

Front 100

Aflatoxin

Back 100

In peanut fungi, epoxidized by P450; covalently adducts N7 on guanine which is the depurinated to give an abasic site

Front 101

Acrylamide

Back 101

French fries, starch cooked above 120C forms glucose/asparagine adduct, metabolised by P450 to give carcinogenic DNA alkylator

Front 102

O6-methylguanine

Back 102

Methylating agent, G:C to A:T transition mutation, removed by MGMT

Front 103

Benzopyrene

Back 103

From burning food, smoking; P450 activation required, alkylator

Front 104

Base substitution mutations

Back 104

Transition (pur/pyr to another pur/pyr); Transversion (pur/pyr to pyr/pur); or frameshift

Front 105

Spontaneous deamination of DNA/nucleotides

Back 105

Exocyclic amines are hydrolized

Front 106

Spontaneous deamination of C,A,G,MeC

Back 106

U, hypoxantine, xanthine and thymine (thymine is normal base, so it is hardes t to repair!)

Front 107

Spontaneous deamination of C

Back 107

U

Front 108

Spontaneous deamination of A

Back 108

hypoxanthine

Front 109

Spontaneous deamination of G

Back 109

Xanthine

Front 110

Spontaneous deamination of 5-MeC

Back 110

Thymine, causing TG mismatch, CG -> TA transition mutation