601 - Exam 2 > 3.2 Replication > Flashcards

3.2 Replication Flashcards

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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
Define heterochromatin
Tightly packed DNA
26
What is facultative heterochromatin?
Heterochromatin that encodes for genes and can be expressed - Heterochromatin that is transcribed but constantly turned over via RNA induced silencing
27
What are the components of eukaryotic chromosomes?
- DNA bound to histones - Chromatin - Nucleosomes - Solenoid - Heterochromatin
28
DNA polymerase needs a ___ and can't synthesize ___
Template De novo (can only extend the chain)
29
DNA gyrase works in front of
The replication fork
30
DNA grows in what direction
5' to 3' - DNA pol only works in 1 direction
31
Define DNA polymerase
Catalyzes elongation of the chain based on the template strand - Multiple in every organism
32
How many DNA polymerase's are in E. coli?
5 DNAP (DNA III = major)
33
How many DNA polymerase are in humans?
15 (Pol delta and PolE)
34
Define topoisomerases (Class II)
Relieve stress due to positive supercoiling and reintroduce negative supercoiling
35
Define helicase
Breaking of H-bonds between bases
36
Define primase
Synthesis of RNA primers that provide 3'OH for DNAP
37
What removes RNA primers?
DNAP 1 Flap endonuclease I (FEN1) and RNase H (eukaryotes)
38
Define DNA ligase
Joining of DNA via phosphodiester bond
39
Define Proliferating cell nuclear antigens (PCNA)
- Only in eukaryotes - DNA clamp that enhances DNAP activity at the replication fork - Diagnostic marker for proliferating cells - Important cancer diagnostic marker
40
Most bacteria have ___ chromosomes with 1 ___
Circular chromosomes 1 oriC
41
oriC is ___rich
AT-rich (meaning A-T) - Easier to open up
42
Steps for bacterial DNA replication:
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
DNA pol I can exonuclease and has activity in what direciton?
5' to 3' direction
44
Leading strand
DNA synthesizes new strand in 5' to 3' direction as 1 long strand
45
Lagging strand
Synthesized in short fragments b/c orientation of template strand is opposite to the direction of DNA synthesis
46
How many base pairs are okazaki fragments in bacteria and eukaryotes?
~1,000 bp in bacteria ~150 - 200 bp in eukaryotes
47
Trombone model of DNA replication
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
How many RNA primers for leading and lagging strand?
1 for leading and many for lagging
49
How many termination sites are there in e. coli?
6
50
Majority of DNA replication occur during what phase?
S phase
51
Pol__ for leading strand and Pol ___ for lagging strand
Pol E for leading Poldelta and Polalpha for lagging
52
Define telomeres
Repeating sequence that may be repeated thousands of times - Aging associated with shortened telomeres
53
Define telomerase
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
Define mutations
Heritable changes in genetic makeup that can be beneficial, harmful, or silent
55
When can mutations be acquired?
During replication or post-replication (damages) - Many are during
56
Types of mutations:
Base pair change Py:Py dimers Chemical alteration of bases Insertions Deletions
57
Define base pair change
Substitution of one base for another - Most common - Ex: A-C instead of A-T
58
Insertions and deletions cause
Frameshifts
59
Define mutagens and what are the 3 types?
Agents that cause mutations Types: chemical, physical, biological
60
Chemical mutagen examples
ROS (reactive oxygen species), deaminating agents, alkylating agents, base analogs, metals
61
Example of physical mutagen
UV
62
Example of biological mutagens
Transposons, plasmids and viruses
63
What is the proof reading/editing function of DNAP?
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
Mismatch repair proteins in e coli
MutH MutL MutS
65
Define mismatch repair proteins
Bind and catalyze removal of a segment of newly synthesized DNA including the mismatch
66
How does mismatch repair distinguish the parents strand in bacteria?
Methylation at GmATC - Knows not to nick there
67
Steps for nucleotide excision repair
1. Specific endonucleases cleave the strand with the mutations and it's removed 2. Gap repaired by DNAP 3. Ligase repairs the break
68
Steps for base excision repair:
1. removal of altered base by specific N-glycosylase 2. AP endonuclease removes sugar and P 3. Repair of gap
69
Define recombination
Breaking and rejoining of DNA molecules in new combination
70
What are the 2 types of recombination?
Homologous and site-specific (like transposons)
71
Define homologous recombination
Occurs between identical or very similar sequences and needs extensive region of homology - Holiday junction
72
Define transposable elements (transposons)
Genetic elements that can "move" or "hop" around - They're important for evolution of organisms
73
Define transposition and give example
Movement of DNA mediated by transposable elements (transposons) - Ex: nonhomologous recombination
74
Define transposase
The enzyme that catalyzes transposition
75
Describe reverse transcription
RNA to DNA - catalyzed by reverse transcriptase - replication strategy of retroviruses
601 - Exam 2
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