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Genetics > Genetics Chapter 13.1-13.5 > Flashcards

Genetics Chapter 13.1-13.5 Flashcards

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1
Q

Structural features of DNA that enable it to be replicated

A

The goal of DNA replication is to make an exact copy of the DNA

Double helix composed of two strands
The AT/GC rule

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2
Q

Parental strands of DNA

A

The two original ones

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3
Q

Daughter strands of DNA

A

The two newly made strands

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4
Q

Template strands of DNA

A

is the leading strand

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5
Q

Leading strands of DNA

A

synthesized continuously, continues along the RNA primer

Extends in the SAME direction of DNA polymerase

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6
Q

lagging strands of DNA

A

synthesized discontinuously

Opens up in the OPPOSITE direction to DNA polymerase

Okazaki fragments are synthesized on the lagging strand and Okazaki fragments are joined together by DNA ligase

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7
Q

Conservative Model

A

results in 1 molecules containing both the original strand (identical to the original)

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8
Q

Semi-conservative Model: DNA replication is semi-conservative!

A

Each strand of DNA acts as a template

Results: 2 DNA molecules with 1 original strand & 1 new strand

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9
Q

Dispersive Model

A

every round of replication results in hybrids/mixtures

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10
Q

Meselson and Stahl’s experiment
What it is and results

A

Conducted experiments to distinguish between these models by growing different generations of bacteria in heavy or light nitrogen

models:
Conservative Model
Semi-conservative Model
Dispersive Model

Results: experiment demonstrated that DNA replicates semi-conservatively: each strand in a DNA molecule serves as a template for synthesis of a new, complementary strand.

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11
Q

Meselson and Stahl’s experiment steps

A
  1. Grow bacteria in heavy 15N for many generations (all DNA contains 15N)
  2. Add light 14N to bacteria for several generations(all new DNA contains 14N)
  3. Lyse cells to access DNA
  4. Load lysate into CsCl gradient that separates DNA strands by density
  5. Centrifuge DNA strands to reach equilibrium
  6. Examine DNA position using UV light
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12
Q

Origin of replication

A

a sequence of DNA at which replication is initiated on a chromosome

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13
Q

DNA polymerase

A

DNA polymerase adds new nucleotides

Other functions for DNA polymerase: synthesis & repair

Extends the complementary strand in the 5’ → 3’ direction, however, it READ the template strand in the 3’ → 5’ direction

Proofreading to double check and correct eros

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14
Q

RNA primers

A

a short nucleic acid sequence that provides a starting point for DNA synthesis

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15
Q

Primase

A

Places RNA primer at the origin of replication

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16
Q

Give DNA polymerase a 3 hydroxyl group to attach free nucleoside triphosphates to create phosphodiester bond via condensation reaction
Where does the energy for creating these bonds come from?

A

HYDROLYSIS OF 2 PHOSPHATES FROM EACH NEW BASE

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17
Q

Primosome

A

protein complex responsible for creating RNA primers on single stranded DNA during DNA replication.

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18
Q

Replisome

A

a large protein complex that carries our DNA replication, starting at the replication origin

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19
Q

DNA is antiparallel

A

one strand 5’ is attached to the other strand’s 3’ end.

For example: if the template strand is 5’-GTAT-3’, the antiparallel complementary strand will be 3’-CATA-5’

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20
Q

Eukaryotic origins

A

Origins of replication in Saccharomyces cerevisiae are called ARS elements (ARS: Autonomously Replicating Sequence)

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21
Q

Origin of replication, shape, size, where, speed, and whats needed for Prokaryotes?

A

Single origin of replication

Circular, double-stranded DNA

Replicated in cytoplasm

Fast

-DNA gyrase is required

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22
Q

Origin of replication, shape, size, where, speed, and whats needed for Eukaryotes?

A

Multiple origins of replication

Bidirectional

Origin recognition complex (ORC) binds to the DNA sequence of the origin
MCM helicase, Cdt1, and Cdc6 bind to ORC to trigger DNA replication licensing. These proteins make up the pre replication complex (preRC).
Protein phosphorylation releases the preRC from the origin. MCM helicase unwinds the DNA double helix.

Linear, double-stranded DNA
-origins in animals may be due to features of chromatin structure

Replicates in the nucleus

Slow

DNA gyrase isn’t required

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23
Q

Eukaryotes Contain Many Different DNA Polymerases

What are the four?

A

alpha (a), delta (d), epsilon (e) and gamma (g) have the primary function of replicating DNA

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24
Q

alpha, delta, and epsilon

A

Nuclear DNA

translesion-replicating polymerases

They can cross over regions of damage

Can induce DNA mutations

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25
Q

epsilon

A

synthesizes the leading strand

26
Q

delta

A

synthesizes the lagging strand

27
Q

gamma

A

Mitochondrial DNA

28
Q

Ligation of Okazaki fragments require a

A

flap endonucleases

29
Q

Ligation of Okazaki fragments require a

A

flap endonucleases

30
Q

DNA pol delta elongates Okazaki fragments until it runs in the RNA primer of the adjacent fragment→

A

RNA to form a small flap

31
Q

Flap endonucleases

A

removes the flap & DNA pol delta generates a new one process repeats

32
Q

What is the Ends replication problem?

A

DNA polymerases synthesize DNA only in the 5’ to 3’ direction

Cannot initiate DNA synthesis without a primer

33
Q

Telomeres

A

Moderately repetitive tandem arrays

3’ overhang that is 12-16 nucleotides long

Each species has a variation of the sequence: G&T rich

34
Q

What are telomerases?

A

Enzyme

They reverse transcriptase (TERT)+ telomerase RNA component (TERC)

The RNA complementary to the DNA sequence found in the telomeric repeat

Reverse transcriptase makes DNA from RNA

RNA to DNA

35
Q

Mechanism Telomerase

A

Binding to 3’ overhang region

Telomerase polymerizes repeat

Telmoerase translocates to end of new repeat to start again

Primase, DNA polymerase, ligase finish job

36
Q

What protects the chromosome ends

A

T-loops form to project the chromosome ends

37
Q

The five differences that Eukaryotes have and not Prokaryotes?

A

Multiple origins of replication (difference #1)

origins in animals may be due to features of chromatin structure (difference #2)

Eukaryotes Contain Many Different DNA Polymerases (difference #3)

Ligation of Okazaki fragments require a flap endonucleases (difference #4)

Telomeres (difference #5)

38
Q

Processivity

A

ability of DNA polymerase to carry out continuous DNA synthesis on a template DNA without frequent dissociation

DNA replication exhibits a high degree of fidelity (DNA polymerase refers to its ability to accurately replicate a template)

39
Q

The beta subunit acts as a clamp for

A

polymerase processivity

40
Q

induced fit

A

DNA polymerase active site changes shape when the correct nucleotides are bound

41
Q

Proofreading

A

function of DNA polymerase using 3’-5’ exonuclease

42
Q

Prokaryotes proof reads during

A

Prokaryotes proof reads during replication by DNA polymerase 3
polymerase & exonuclease

While adding nucleotides, the polymerase closely monitors the correct base pairing

43
Q

lagging strands

A

Lagging strand is synthesized discontinuously, opposite direction to how DNA polymerase is traveling

Small Okazaki fragments make up the discontinuous strand and one RNA primer is required for each fragment

44
Q

leading strand

A

As the replication fork opens, the LEADING STRAND is synthesized continuously from a single RNA primer

Leading strand is extending the same direction as the DNA polymerase

Leading strand is the template strand

45
Q

Bacterial DNA Replication
DNA synthesis begins at the ——-
Only — origin of replication in bacteria; the origin of replication in E. coli is termed —-

A

origin of replication
Only
oriC (origin of Chromosomal replication)

46
Q

DNA replication in bacteria is what direction

A

DNA replication in bacteria is bidirectional from oriC

47
Q

Bacterial DNA Replication Steps

A

Two replication forks move in opposite directions

Replication fork is where the parental strands have separated and new daughter strands are being made

oriC DNA sequence features allow replication initiation

Steps:
- DnaA proteins bind to DnaA boxes
- Additional proteins bind to DnaA that bend the DNA and separate strands at AT rich region
- DNA helicases (DnaB) bind and use ATP to travel 5’ to 3’ to open the double helix
- The DNA replication machinery can now access the DNA strands

48
Q

DNA polymerase

A

DNA polymerase adds new nucleotides
Other functions for DNA polymerase: synthesis & repair
Extends the complementary strand in the 5’ → 3’ direction, however, it READ the template strand in the 3’ → 5’ direction
Proofreading to double check and correct eros

49
Q

Helicase

A

“Unzips: the wound DNA by breaking H-bonds

50
Q

PROKARYOTES PROCESS
begining steps

A

Proteins at the replication fork

Unwinding of the helix

DNA helicase-Breaks the hydrogen bonds between the strands

Topoisomerase II (DNA gyrase)
Relaxes supercoiling in front of DNA helicase

Single-stranded binding proteins
Keep the two strands separated until after they are copied

51
Q

What happens at the replication fork leading strand?
PROKARYOTES

A
  1. Topoisomerase II (DNA gyrase) relieves positive supercoils
  2. DNA helicase (DnaB) moves 5’ to 3’ to open double helix
  3. Single-stranded binding proteins keep the strands separated
  4. Primase makes RNA primer 10—12 nt long at origin
  5. DNA polymerase III uses primer to start adding nucleotides complementary to leading strand
51
Q

What happens at the lagging strand?
PROKARYOTES

A

Primase makes RNA primer on lagging strands as the strands separate

DNA polymerase III uses a primer to start adding nucleotides complementary to lagging strand until it hits the previous Okazaki fragment

DNA polymerase I removes RNA primer with 5’ to 3’ exonuclease activity and adds DNA

DNA ligase joins Okazaki fragments together

52
Q

DNA Polymerases -

A

Enzymes that catalyze the formation of the phosphodiester bond between nucleotides

53
Q

DNA pol III

A

normal replication
10 subunits – holoenzyme
a subunit makes phosphodiester bonds

54
Q

DNA pol I

A

One subunit
Replaces RNA with DNA

Has 5’ to 3’ exonuclease activity

Primarily acts on only the lagging strand to remove RNA from Okazaki fragments

Uses 5’-3’ polymerase activity to replace RNA with DNA

DNA pol I cannot join the small DNA fragments on lagging strand

Accomplished by DNA ligase

55
Q

DNA pol II, IV and V

A

DNA repair and replication of damaged DNA

56
Q

Properties of DNA pol enzyme

A

DNA polymerase cannot link two single nucleotides together

DNA polymerase requires a primer to begin DNA synthesis

DNA polymerase can attach nucleotides ONLY in the 5’ to 3’ direction

Because of these features, the synthesis of the leading and lagging strands are different

57
Q

Biochemical activity of DNA pol

A

The 3ʹ-OH on the previous nucleotide reacts with the phosphate group, and PPi is released

58
Q

What happens if DNA pol makes a mistake in the DNA sequence?

A

DNA replication exhibits a high degree of fidelity. The b subunit acts as a clamp for polymerase processivity.

The DNA polymerase active site changes shape when the correct nucleotides are bound – called induced fit

Proofreading function of DNA polymerase, using a 3′ – 5′ exonuclease

59
Q

DNA Replication Complexes

A

DNA helicase + primase = primosome

Primosome + 2 holoenzymes = replisome

The two proteins form a dimeric DNA polymerase that moves as a unit toward the replication fork

Genetics (5 decks)

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