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601 - Exam 2 > 3.2 Replication > Flashcards

3.2 Replication Flashcards

1
Q

Why do we care about replication?

A
  • Transmission of genetic info is essential
  • Better understanding of mutations leads to development of better therapeutics, evolution…
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2
Q

Purines are

A

Adenine and guanine
(Have 2 rings)

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3
Q

Pyrimidines are

A

Uracil, Thymine, and Cytosine
(Has 1 ring)

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4
Q

Name for DNA sugar

A

2’-Deoxyribose
(lacks a hydroxyl group at 2’)

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5
Q

Name for RNA sugar

A

Ribose (RNA)

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6
Q

Chargaff’s rule

A

A=T
G=C

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7
Q

A-T binding has how many hydrogen bonds?

A

2

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8
Q

C-G has how many hydrogen bonding?

A

3 H bonds

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9
Q

Chargaff’s rule was instrumental in helping ___ to decipher the structure of DNA using the X-ray crystallography images of the molecule by ___. The idea to use X-ray crystallography belonged to ___.

A

Watson and Crick
Rosalind Franklin
Maurice Wilkins

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10
Q

The double helix is ___ with what types of grooves?

A

Antiparallel

Has major and minor grooves

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11
Q

B-DNA

A

10.5 bp/turn
Relaxed DNA
The typical DNA

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12
Q

A-DNA

A

11 bp/turn
(More tightly wound)

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13
Q

Z-DNA

A

12 bp/turn
Left-handed helix

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14
Q

Most DNA found is nature is ___ supercoiled DNA. It turns in what direction?

A

Negative
- Turns left
- Less than 10 bp/turn

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15
Q

What is overwound DNA called?

A

Positively supercoiled DNA
- More than 10 bp/turn
- Turns right

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16
Q

When is positive supercoiling mostly seen?

A

During replication and transcription

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17
Q

What is nicked DNA?

A

DNA with a broken phosphodiester bond on 1 strand
- ONLY ON 1 STRAND

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18
Q

Define open circle DNA

A

circular DNA with a nick

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19
Q

Describe bacterial chromosomes

A
  • They’re circular and negatively supercoiled
  • Has DNA binding proteins to compact to form supercoiled domains
    (Has histone LIKE proteins, but NO HISTONES)
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20
Q

What is the cytoplasm region with the chromosome called in bacterial chromosomes?

A

Nucleoid

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21
Q

DNA is eukaryotic chromosomes are bound to equal weight of ___. What do these small basic proteins have large amounts of?

A

Histones
Arg and Lys

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22
Q

Define chromatin

A

DNA with protein complex

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23
Q

Define nucleosomes

A

Beads with protruding DNA (beads of nucleosome cores)
- Composed of 8 histones and 140 base pairs

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24
Q

Define solenoid

A

Winding of strings of nucleosomes into helical tubular coil

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25
Q

Define heterochromatin

A

Tightly packed DNA

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26
Q

What is facultative heterochromatin?

A

Heterochromatin that encodes for genes and can be expressed
- Heterochromatin that is transcribed but constantly turned over via RNA induced silencing

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27
Q

What are the components of eukaryotic chromosomes?

A
  • DNA bound to histones
  • Chromatin
  • Nucleosomes
  • Solenoid
  • Heterochromatin
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28
Q

DNA polymerase needs a ___ and can’t synthesize ___

A

Template
De novo (can only extend the chain)

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29
Q

DNA gyrase works in front of

A

The replication fork

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30
Q

DNA grows in what direction

A

5’ to 3’
- DNA pol only works in 1 direction

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31
Q

Define DNA polymerase

A

Catalyzes elongation of the chain based on the template strand
- Multiple in every organism

32
Q

How many DNA polymerase’s are in E. coli?

A

5 DNAP (DNA III = major)

33
Q

How many DNA polymerase are in humans?

A

15 (Pol delta and PolE)

34
Q

Define topoisomerases (Class II)

A

Relieve stress due to positive supercoiling and reintroduce negative supercoiling

35
Q

Define helicase

A

Breaking of H-bonds between bases

36
Q

Define primase

A

Synthesis of RNA primers that provide 3’OH for DNAP

37
Q

What removes RNA primers?

A

DNAP 1
Flap endonuclease I (FEN1) and RNase H (eukaryotes)

38
Q

Define DNA ligase

A

Joining of DNA via phosphodiester bond

39
Q

Define Proliferating cell nuclear antigens (PCNA)

A
  • Only in eukaryotes
  • DNA clamp that enhances DNAP activity at the replication fork
  • Diagnostic marker for proliferating cells
  • Important cancer diagnostic marker
40
Q

Most bacteria have ___ chromosomes with 1 ___

A

Circular chromosomes
1 oriC

41
Q

oriC is ___rich

A

AT-rich (meaning A-T)
- Easier to open up

42
Q

Steps for bacterial DNA replication:

A
  1. Formation of pre-priming complex to open up oriC
  2. SSB bind (protects from zipping back and protects ssDNA)
  3. Replication fork formation and H bonds break
  4. Gyrase relieves pos. supercoiling
  5. Primase
  6. Bidirectional chain elongation
  7. Topoisomerase IV (4) reintroduces neg. supercoiling on new DNA
  8. DNAP 1 removes RNA from Okazaki fragments
  9. DNA ligase joins fragments
  10. Chromosome separation
43
Q

DNA pol I can exonuclease and has activity in what direciton?

A

5’ to 3’ direction

44
Q

Leading strand

A

DNA synthesizes new strand in 5’ to 3’ direction as 1 long strand

45
Q

Lagging strand

A

Synthesized in short fragments b/c orientation of template strand is opposite to the direction of DNA synthesis

46
Q

How many base pairs are okazaki fragments in bacteria and eukaryotes?

A

~1,000 bp in bacteria
~150 - 200 bp in eukaryotes

47
Q

Trombone model of DNA replication

A

DNA of lagging strand loops so it’s in correct orientation for DNA pol
- The leading and lagging strand now contact each other and are replicated at same time

48
Q

How many RNA primers for leading and lagging strand?

A

1 for leading and many for lagging

49
Q

How many termination sites are there in e. coli?

A

6

50
Q

Majority of DNA replication occur during what phase?

A

S phase

51
Q

Pol__ for leading strand and Pol ___ for lagging strand

A

Pol E for leading
Poldelta and Polalpha for lagging

52
Q

Define telomeres

A

Repeating sequence that may be repeated thousands of times
- Aging associated with shortened telomeres

53
Q

Define telomerase

A

RNA dependent DNA polymerase carrying own RNA primer
- Binds to telomere (3’ overhang) and base pairs with it
- Allows for less shrinkage and we can live longer

54
Q

Define mutations

A

Heritable changes in genetic makeup that can be beneficial, harmful, or silent

55
Q

When can mutations be acquired?

A

During replication or post-replication (damages)
- Many are during

56
Q

Types of mutations:

A

Base pair change
Py:Py dimers
Chemical alteration of bases
Insertions
Deletions

57
Q

Define base pair change

A

Substitution of one base for another
- Most common
- Ex: A-C instead of A-T

58
Q

Insertions and deletions cause

A

Frameshifts

59
Q

Define mutagens and what are the 3 types?

A

Agents that cause mutations

Types: chemical, physical, biological

60
Q

Chemical mutagen examples

A

ROS (reactive oxygen species), deaminating agents, alkylating agents, base analogs, metals

61
Q

Example of physical mutagen

A

UV

62
Q

Example of biological mutagens

A

Transposons, plasmids and viruses

63
Q

What is the proof reading/editing function of DNAP?

A

DNAP senses mutations and uses 3’ to 5’ exonuclease activity to chew back and remove the wrong base
THEN uses 5’ to 3’ polymerase activity to synthesize the strand

64
Q

Mismatch repair proteins in e coli

A

MutH
MutL
MutS

65
Q

Define mismatch repair proteins

A

Bind and catalyze removal of a segment of newly synthesized DNA including the mismatch

66
Q

How does mismatch repair distinguish the parents strand in bacteria?

A

Methylation at GmATC
- Knows not to nick there

67
Q

Steps for nucleotide excision repair

A
  1. Specific endonucleases cleave the strand with the mutations and it’s removed
  2. Gap repaired by DNAP
  3. Ligase repairs the break
68
Q

Steps for base excision repair:

A
  1. removal of altered base by specific N-glycosylase
  2. AP endonuclease removes sugar and P
  3. Repair of gap
69
Q

Define recombination

A

Breaking and rejoining of DNA molecules in new combination

70
Q

What are the 2 types of recombination?

A

Homologous and site-specific (like transposons)

71
Q

Define homologous recombination

A

Occurs between identical or very similar sequences and needs extensive region of homology
- Holiday junction

72
Q

Define transposable elements (transposons)

A

Genetic elements that can “move” or “hop” around
- They’re important for evolution of organisms

73
Q

Define transposition and give example

A

Movement of DNA mediated by transposable elements (transposons)
- Ex: nonhomologous recombination

74
Q

Define transposase

A

The enzyme that catalyzes transposition

75
Q

Describe reverse transcription

A

RNA to DNA
- catalyzed by reverse transcriptase
- replication strategy of retroviruses

601 - Exam 2 (11 decks)

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