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Biology 207 > Chapter 12 > Flashcards

Chapter 12 Flashcards

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AP® Biology flashcards Biology 101 flashcards
1
Q

Conservative Model

A

Entire DNA strands remain or are used as a template to synthesize new strands

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2
Q

Semi-Conservative Model

A

Each nucleotide gets conserved, this means that equal base paring in each strand

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3
Q

Explain Meselson and Stahl’s Experiment

A

Meselson and Stahl grew a culture of E.coli in a medium that contained N15 isotope of Nitrogen

They took a sample of these bacteria, switched the rest of the bacteria to a medium that contained only N14 nitrogen

Meselson ada Stahl distinguished between the heavy and light isotope by using an equilibrium density gradient centrifugation

A single strand band was produced after one generation that was intermediate of the two isotopes – this went against the conservative model

In the second generation, a N14 band and a hybrid band was formed – this went for the semi-conservative model and again the dispersive model

Hence, DNA semi-conservatively replicates

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4
Q

Replicon

A

A segment of DNA that undergoes replication

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5
Q

Origin of Replication

A

Each replicon contains and origin of replication, replication starts at the origin and continues until the entire replicon has been replicated

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6
Q

Theta Replication

A

A replication that occurs in circular DNA common in bacteria, which has an intermediate stage that looks like the greek letter theta

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7
Q

Replication Bubble

A

The unwinding of the double helix generates a loop known as the replication bubble

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8
Q

Replication Fork

A

The point of unwinding where the two strands separate

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9
Q

Bidirectional Bubble

A

In theta replication, where the two strands separate from the double helix

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10
Q

Who discovered theta replication?

A

John Cairns – who used an electron microscope technique to detect radioactive DNA replication

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11
Q

Rolling Circle Replication

A

https://www.youtube.com/watch?v=ZDqsojQ8A5k
Plasmids, Viruses, Bacteria Chromosomes
1. Initiator Protein repA binds to the double-stranded DNA at the origin of replication – ORI
2. RepA breaks one strand of the DNA
3. The RepA protein holds on the 5’-PO4- group
4. The 3’ end hydroxyl group serves as a primer for a host DNA polymerase
5. The DNA polymerase gets to replicate the intact complementary strand
6. The RepA protein recruits Helicase to unwind the DNA
7. The inside strand replicates
8. The outside strand gets cleaved off to form a circular DNA
9. The circular DNA replicates itself
10. You have accomplished two new replicated strands…

***For more info –> watch the Link above
Circular DNA molecules that undergo theta or rolling circle replication have a single origin of replication

This cycle may repeat

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12
Q

Explain why Linear Eukaryotic Replication happens faster

A

They have multiple origins of replication
1. Each chromosome contains numerous origins
2. At the origin, the DNA unwinds, producing a replication bubble
3. DNA synthesis takes place on both strands at each end of the bubble as the replication forks proceed outwards
4. Eventually, the forks of adjacent bubbles run into each other and the segments of DNA fuse..
5. Producing two identical linear DNA molecules

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13
Q

Characteristic of ___ replication
1. Theta
2. Rolling Circle
3. Linear Eukaryotic

A

Theta (circular DNA template, No breakage of nucleotide, 1 replicon, uni/bidirectional, two circular molecules as products)

Rolling Circle (circular DNA template, yes breakage of nucleotides, 1 replicon, unidirectional, and products include one circular and one linear molecule)

Linear Eukaryotic(Linear template, No breakage of nucleotide, many replicons, bidirectional, and two linear molecules as products)

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14
Q

What are the requirements of replication?

A
  1. A template consisting of single-stranded DNA
  2. Raw material – substrates – to be assembled into a new nucleotide strand
  3. Enzymes and other proteins that read the template and assemble the substrates

substrates - dNTPS
Enzymes – DNA polymerases, RNA polymerases, DNA gyrase, etc.

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15
Q

Which end are dNTPs added?

A

“The 3’-OH end”

“The 3’-OH group of the last nucleotide attacks the 5’phosphate on the incoming dNTP”

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16
Q

What bond is created between DNA nucleotides?

A

Phosphodiester bonds

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17
Q

Leading Strand

A

The template strand for the leading strand runs in the 3’ –> 5’ direction, and so the new strand can be synthesized continuously towards the replication fork in the 5’ –> 3’ direction

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18
Q

Lagging Strand

A

The template strands runs in the 5’—> 3’ direction, so the new strand must be built discontinuously in the 5’–> 3’ direction away from the replication fork

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19
Q

Okazaki Fragments

A

The short lengths of DNA when produced discontinuously on the lagging strand

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20
Q

What are 4 stages of bacterial replication?

A

Initiation, Unwinding, Elongation, and Termination

21
Q

Initiator Proteins

A

DNAa – bind to OriC and cause a short section of the DNA to unwind

22
Q

DNA Helicase

A

Breaks the Hydrogen Bonds that exists between the bases of the DNA molecules

**Helicase binds to the lagging strand only, and it moves in the 5’–> 3’ direction
**Helicase needs the help of initiator proteins too separate

23
Q

Single-stranded binding proteins

A

Protect single stranded nucleotides, prevent the formation of secondary structures such as hairpins

24
Q

DNA Gyrase

A

It relives tension ahead of the replication fork
AKA: Topisomerase II

25
Q

Topoisomerase I

A

Alter the supercoiling by making single-stranded breaks

26
Q

Topoisomerase II

A

Creates double-stranded breaks using ATP

27
Q

Place the order to which the enzymes used in Initiation: DNA gyrase, helicase, initiator proteins, Single-stranded binding proteins

A

Initiator Proteins, Helicase, Single-Stranded Binding proteins, and DNA Gyrase

28
Q

Primase

A

Synthesizes short stretches of RNA nucleotides or Primers…which provide a 3’-OH group to which DNA polymerase can attach DNA nucleotides

***new primer is required in each Okazaki fragment

29
Q

DNA Polymerase III

A

Synthesizes DNA by adding nucleotides to the 3’ end of a growing DNA strand

30
Q

When does DNA polymerase move 3’–>5’?

A

Exonuclease activity –> allows it to remove incorrect nucleotides in the 3’–> 5’ direction (proofreading)

31
Q

B - beta sliding clamp

A

The ring-shaped polypeptide encircles the DNA and allows polymerase to slide easily along the DNA template strand during replication

This polypeptide is part of DNA polymerase enzyme

32
Q

DNA Polymerase I

A

5’–>3’ polymerase and 3’–>5’ exonuclease which allows to synthesize and to correct DNA

***DNA POL I also possess 5’–>3’ exonuclease activity which is used to remove primers and replace them with DNA nucleotides synthesized in the 5’–>3’ direction

33
Q

What are the functions of DNA polymerases?

A
  • Synthesize any sequence specified by the template strand
  • Synthesize in the 5’–>3’ direction by adding nucleotides to a 3’-OH group
  • Use dNTPs to synthesize new DNA
  • Require a 3’-OH group to initiate synthesis
  • Catalyzes the phosphodiester bonds, and cleaves two phosphates from the end
  • Produce newly synthesized strands that are complementary and antiparallel to the template strand
  • Are associated with a number of proteins
34
Q

DNA Ligase

A

DNA Ligase seals the gap with a phosphodiester bond between the 5’-phosphate group of the initial nucleotide aded by DNA polymerase III and the 3’-OH group of the final nucleotide added by DNA polymerase I

35
Q

How many units of DNA Pol III at the replication fork?

A

Two for each strand

36
Q

How does replication termination occur in E.coli bacteria?

A
  1. Specific termination sequence – Ter – blocks further replication
  2. A termination protein TUS binds to the TER sequence creating TER-TUS complex
  3. This complex blocks the movement of helicase
  4. The complex stalls the replication fork and prevents further DNA replication
  5. The complex only blocks the replication fork moving in one direction not the other
37
Q

Explain the steps of proofreading

A
  1. DNA polymerase inserts an incorrect nucleotide into the growing strand
  2. The 3’-OH group is not correctly position in the active site of DNA Polymerase Enzyme
  3. The incorrect positioning stalls the polymerization reaction
  4. The 3’–>5’ exonuclease activity of DNA polymerase removes the incorrectly paired nucleotide
  5. DNA polymerase than inserts the correct nucleotide
38
Q

Explain the steps of Mismatch Repair

A
  1. Any incorrectly paired nucleotide remaining after replication produce a deformity in the secondary structure of DNA
  2. The deformity is recognized by enzymes – DNA POL
  3. Removes incorrect nucleotide
  4. Uses the original template strand to replace the incorrectly paired nucleotide
  5. DNA is fixed!

Things to know:
***Occurs after replication, methyl groups are added to the original parent strand to make it easy to fix the new strand of DNA

39
Q

Why are Eukaryotic chromosomes more challenging than prokaryotic chromosomes?

A

A) Bigger Genome
B) Linear Chromosome
C) Histone Proteins

40
Q

Origin Recognition Complex – ORC

A

Serves as the initiator by binding to defined organs than are actually used during DNA synthesis

41
Q

Difference Between Bacteria and Eukaryotic Origin of Replication

A

—> In Bacteria, helicase is unable to bind to the double-stranded DNA…initiator protein first melts DNA
—> In Eukaryotes, Initiator ORC recruits and loads helicase onto double-stranded DNA at the origin…takes place in G1…where in S…helicase activates

42
Q

What is the telomeric DNA?

A

5’-TTAGGG-3’

43
Q

G-rich 3’overhang

A

The single stranded protruding end of the telomere DNA

44
Q

Telomerase

A

An enzyme that build telomeres…and is composed of RNA and protein

45
Q

Explain The Activity of Telomerase

A
  1. The telomere has a protruding end with a G-rich sequence – TTAGGG
  2. The RNA part of telomerase is complementary to the G-rich strand and pairs with it
  3. Nucleotides are added to the 3’ end of the sequence
  4. The telomerase is removed
  5. Synthesis of the complementary strand occurs during replication
46
Q

How does Initiating start in Eukaryotic Organism DNA replication?

A
  1. In GAP 1 - G1 - Initiator protein called ORC binds to the DNA double helix
  2. The Initiator protein recruits licensing proteins and helicase
  3. The whole complex recruits MCM2-7 complex
  4. Then in S-phase…these complexes help activate helicase to start doing replication
47
Q

Replication Licensing System

A

It ensures that the DNA is not replicated again until after the cell has passed through mitosis

48
Q

Autonomously replicating sequences – ARS

A

They enable DNA that were attached to them to replicate

49
Q

What are the different DNA polymerases and their functions in Eukaryotic organism?

A
  1. DNA polymerase alpha – Primate activity and initiates nuclear DNA synthesis by synthesizing RNA primers
  2. DNA polymerase delta – completes replication of the lagging strand
  3. DNA polymerase epsilon – completes replication of the leading strand

Biology 207 (11 decks)

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