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BioChem Exam 3 > CH 23: Anabolism of nucleic Acid (DNA Synthesis/DNA replication) > Flashcards

CH 23: Anabolism of nucleic Acid (DNA Synthesis/DNA replication) Flashcards

1
Q

DNA Replication

What is the template for DNA?

A

The Parent DNA, 2 strands allows for 2 templates using DNA synthase

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2
Q

DNA Replication

How is DNA replication semiconservative?

A

Half of the new templates is from the parent and half is newly synthesized DNA (so not fully new)

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3
Q

DNA Replication

What direction is the DNA replication?

A

5’ to 3’

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4
Q

DNA Replication

Is base pairing more determined by hydrogren bonds or shape?

A

by shape (A to T, C to G)

learned by testing with similar shaped analong that cannot hydrogen bond but it would still recuit the same pairing as if it was the correct molecule

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5
Q

DNA Replication begins at the origin site

How many origin sites so bacteria have?

A

1

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6
Q

DNA Replication begins at the origin site

Do the replication forks go the same direction or opposite?

A

opposite

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7
Q

DNA polymerase catalyzes DNA synthesis

How many structural classes of DNA polymerase do E.coli have?

A

at least 5

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8
Q

DNA polymerase catalyzes DNA synthesis

Which polymerase number is the main for replication (E.coli)?

A

DNA Polymerase III: principal replication

Polymerase I (most abundant): clean RNA primers

Polymerase II, IV, and V: DNA repair

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9
Q

Eukaryotic DNA Polymerase

How many polymerase have we found so far for Eukaryotes?

A

6 (5 in nucleus and 1 in mitochondria. 3 for replication and 3 for repair)

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10
Q

Errors during synthesis

How are errors during DNA synthesis corrected?

A

using 3’ to 5’ exonuclease activity (proofreeds for mismatched base pairs, it gets rid of just placed nucleotide so the polymerase can try again)

RNA polymerase doesn’t have a proofreeding function

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11
Q

Beginning DNA Synthesis

What is needed to start DNA Synthesis?

A

Primers (Primase synthesises RNA Primer)

RNA Fragment that is used to extend DNA polymerase

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12
Q

Beginning DNA Synthesis

What removes this RNA fragment?

A

DNA pol I removes the RNA then it gets replaced by DNA and is sealed by DNA ligase

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13
Q

NIck or Gap

What is the difference between a nick and a gap?

A

Nick: breakage in phophdiester bond between nucleotides

Gap: one to multi-nucleotide spacing in DNA strand

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14
Q

Leading and Lagging Strand Synthesis

How is the template read for DNA synthesis?

A

From 3’ to 5’

SInce DNA must be synthesized 5’ to 3’

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15
Q

Leading and Lagging Strand Synthesis

What is the leading strand?

A

DNA strand being continuously replicated, only needs 1 primer

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16
Q

Leading and Lagging Strand Synthesis

What is the lagging strand?

A

DNA strand being synthesized discontinuously in short sections (okazaki fragments) opposite to where the replication fork moves
Many primers needed

17
Q

Other Necessary Proteins at a Replication Fork

What does Helicase do?

A

opens the double helix and uncoils it using ATP

18
Q

Other Necessary Proteins at a Replication Fork

What does Single-strand binding proteins (SSB) do?

A

keep strands seperated (large amount of protein needed)

19
Q

Other Necessary Proteins at a Replication Fork

What does the sliding clamp (B2 subunit of DNA pol III in E.coli) do?

A

Helps the polymerase slide along the strand processively

20
Q

Other Necessary Proteins at a Replication Fork

What does Topoisomerase do?

A

breaks the covalent bonds of the backbone to allow unwinding ahead of the replication fork and relieves stress by relaxing the supercoils

Type I: cleaves one strand, doesnt require ATP
Type II: cleaves both strands, requires ATP

21
Q

Eukaryotic Chromosomes

What does telomere/telomerase do in eukaryokes regarding the primer areas?

A

The telomerase will replicate the 3’ end of the linear chromosomes using a built in template

22
Q

Types of DNA Damage

Mismatches

A

arise frmo occasional incorporation of incorrect nucleotides

23
Q

Types of DNA Damage

Abnormal bases

A

arise from spontaneous deamination, chemical alkylation, or exposure to free radicals

24
Q

Types of DNA Damage

Pyrimidine Dimers

A

form when DNA is exposed to UV light

25
Q

Types of DNA Damage

Backbone lesions

A

occur frmo exposure to ionizing radiation, free radicals

26
Q

DNA recombination

DNA recombination

A

segments of DNA rearrange their location (either within or between chromosomes)

27
Q

DNA Recombination

What are the 3 classes of DNA recombination?

A

Homologous/general: exchange between 2 DNAs that share an extended region of similar sequence

Site Specific: exchange only at a particular sequence

DNA Transposition: short DNAs that can move from one chromosome to another

BioChem Exam 3 (7 decks)

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