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Biology HL IB 2020-22 > 7.1 DNA structure and replication (HL) > Flashcards

7.1 DNA structure and replication (HL) Flashcards

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1
Q

Why did the Hershey-Chase experiment come about?

A

Scientists weren’t sure whether protein or DNA was genetic material

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2
Q

Why were viruses used in Hershey-Chase?

A

It was known that they could transfer genetic material to hosts so that host (bacteria) can replicate the virus. They also had DNA and a protein coat.

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3
Q

Hershey-Chase: Why was sulphur used in one while phosphorus in the other?

A

Used to label and distinguish between protein and DNA. Proteins have sulfur but no phosphorus while DNA has phosphorus but no sulfur

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4
Q

Hershey-Chase: Which viruses were used?

A

T2 bacteriophages

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5
Q

Hershey-Chase: Where were the viruses grown?

A

They were grown in one of two isotopic mediums to label component radioactively

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6
Q

Hershey-Chase: Which isotopic mediums were used?

A

S-35 and P-32

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7
Q

Hershey-Chase: What happened after viruses were labelled and what was the separation process called?

A

They were allowed to infect E. coli and then the virus and bacteria were separated through centrifugation

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8
Q

Hershey-Chase: What is a supernatant?

A

It is the liquid lying above the residue after precipitation or centrifugation

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9
Q

Hershey-Chase: What was the result of centrifugation and why was it done?

A

Larger bacteria formed a pellet (sedimentation) because it was heavier while viruses remained in the supernatant. This means genetic material should be in pellet while non-genetic material remains in supernatant.

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10
Q

Hershey-Chase: Which isotope was found in pellet and which in supernatant? What does it show?

A
  • In P-32 condition, the pellet was radioactive
  • In S-35 condition, the supernatant was radioactive
  • This showed that DNA was genetic material as viruses only transfer genetic material while proteins were not
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11
Q

Franklin-Wilkins: What do X-rays do when they pass through a substance?

A

They diffract and scatter

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12
Q

Franklin-Wilkins: What should the material be for X-ray diffraction to work well and why?

A

They should ideally be crystallized so that repeating pattern causes diffraction to occur in a regular way

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13
Q

Franklin-Wilkins: What could be deduced from X-shaped pattern?

A

Shows that DNA was a helix

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14
Q

Franklin-Wilkins: What can be deduced from regular nature of pattern?

A

Dimensions of helix were consistent eg. diameter of helix and distance between strands

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15
Q

Franklin-Wilkins: What does vertical distance between horizontal bars show and what was the measurement?

A

Shows distance between two stacked base pairs. Each distance was 3.4 angstroms

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16
Q

Franklin-Wilkins: What does the distance from middle of image to top measure show in DNA?

A

Height of a helical turn (34 angstroms)

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17
Q

Franklin-Wilkins: How can you deduce number of bases in a helical turn?

A

Height of turn/ Distance between horizontal bars. i.e. 34/3.4= 10 base pairs per turn

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18
Q

Franklin-Wilkins: What can be deduced from angle between horizontal axis and arms of X-shaped pattern?

A

The helix’s pitch or degree of its rise

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19
Q

Franklin-Wilkins: From the images, what deduction did Franklin make about positions of molecular units within helical structure?

A

She deduced that phosphate groups were on the outside

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20
Q

What mechanism aids DNA replication?

A

Complementary base pairing

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21
Q

Why can C only pair with G and A only with T?

A

Electrical charges of adenine and thymine are compatible as they are opposing (2 H bonds). Same for cytosine and guanine (3 H bonds)

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22
Q

Why is prokaryotic DNA considered naked?

A

Although DNA is supercoiled, they don’t have histones to be wrapped around like eukaryotes

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23
Q

What are histones?

A

Proteins used by cell to package DNA

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24
Q

What does a nucleosome consist of?

A
  1. Central core of 8 histones (octomer)
  2. Core DNA+ short linker DNA
  3. Additional histone called H1 which binds DNA to core histones for further packing
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25
Q

What are nucleosomes bunched together usually known as?

A

30nm fibers or solenoid

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26
Q

What is supercoiling?

A

When a DNA strand has been wound back on itself so molecule becomes compact

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27
Q

How many times is DNA wound around histone?

A

Twice

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28
Q

Charges of DNA and histones

A

DNA is negatively charged and acidic while histones are positively charged and basic

29
Q

Why is it essential to supercoil chromosomes?

A
  • Packs genetic material into tiny nucleus
  • Allows chromosomes to be mobile in mitosis and meiosis
  • DNA cannot be transcribed for protein synthesis (controls expression)
  • Allows cells to specialize by permanently supercoiling DNA that’s not required
30
Q

Which part of cell cycle is DNA most supercoiled in?

A

Meiosis and mitosis

31
Q

Which part of cell cycle is DNA most supercoiled in?

A

Meiosis and mitosis

32
Q

What is a primer

A

They are short stranded sections of DNA/RNA.

33
Q

Difference between RNA and DNA primers

A

RNA primers initiate activity of DNA polymerase while DNA primers are used in PCR

34
Q

Which direction does DNA polymerase move along template strand?

A

5’ to 3’ direction

35
Q

What is difference between lead and lagging strand?

A

Replication is continuous on lead strand and discontinuous on lagging due to anti-parallel nature. Can only move from 3’ to 5’ hence why primers are required on lagging strand and creates fragments

36
Q

DNA helicase

A

Unwinds and separates DNA by breaking H bonds between bases. Helps create the fork of two strands

37
Q

DNA gyrase/ topoisomerase

A

Reduces strain created by unwinding of DNA by helicase. (Extra: Uses -ve supercoiling to relax +ve supercoils)

38
Q

DNA primase

A

Generates short RNA primer on template to provide initiation point for DNA polymerase III.

39
Q

DNA polymerase III

A

Forms covalent bonds between nucleotides as they are added to polynucleotide

40
Q

DNA polymerase I

A

Lagging strand has multiple RNA primers so they remove them and replace with DNA nucleotides

41
Q

DNA ligase

A

Joins Okazaki fragments to form continuous strands. Covalently joins sugar and phosphates with phosphodiester bond.

42
Q

SSB proteins

A

Stands for Single Stranded Binding proteins. They prevent template strands from reconnecting so they can be replicated

43
Q

Okazaki fragments

A

They are the RNA primers + DNA fragments

44
Q

Difference between coding and non-coding regions of DNA

A
  • Coding regions contain sequences for polypeptide production
  • Non-coding regions make up most of genome and help regulate gene expression.
45
Q

How do non-coding regions regulate gene expression?

A

They act as enhancers or inhibitors for genes which affects the genes that get transcribed to mRNA

46
Q

Which regions of DNA have highly repetitive sequences and what is their function?

A

Telomeres. They are the end of chromosomes and prevent degradation of DNA during replication

47
Q

What was known as ‘junk DNA’ and why?

A

Non-coding regions as they were thought to have no function

48
Q

Non-coding regions: Introns

A

They are within the gene and removed by splicing prior to formation of mRNA They do not contribute to polypeptide production

49
Q

Non-coding regions: Gene regulatory sequences

A

Sequences involved in the process of transcription. Includes promoters, enhancers and silencers

50
Q

Non-coding regions: Non-coding RNA genes

A

They code for RNA molecules that do not get translated eg. forming tRNA molecules

51
Q

How does dideoxyribonucleic acid affect DNA replication?

A

DNA polymerase requires a nucleotide with a 3’ OH group to form bond however ddNTP only has 3’ H group so it stops replication

52
Q

What does ddNTP stand for?

A

Dideoxyribonucleic triphosphates

53
Q

What is attached to ddNTP during base sequencing?

A

Fluorescent markers so base present when replication stops is identified

54
Q

What is it known as when DNA synthesis stops due to ddNTP?

A

Chain termination method or dideoxy DNA sequencing

55
Q

Sanger sequencing: How many reactions take place and what do they consist of?

A

4 reactions occur parallelly. They contain copies of DNA template strand, radiolabeled primers, DNA polymerase and all forms of dNTP (dATP, dCTP, dGTP and dTTP). One type of ddNTP will be added to each

56
Q

Sanger sequencing: How are multiple DNA molecules generated?

A

PCR

57
Q

Sanger sequencing: If sequence is TACGGATGATC and ddATP is added, what will all fragments look like?

A
  • 5’ A 3’
  • 5’ ATGCCTA 3’
  • 5’ ATGCCTACTA 3’
    Hence we know T is first, seventh and tenth in sequence
58
Q

Sanger sequencing: What are the contents of each reaction loaded into?

A

DNA electrophoresis gel

59
Q

Sanger sequencing: How do contents separate in electrophoresis gel?

A

They separate on basis of their length. Smallest fragments travel down the most.

60
Q

Sanger sequencing: What is autoradiography?

A

It is a photograph of gel produced by radiation. It labels lanes according to dNTP with which each fragment should end.

61
Q

Sanger sequencing: How do you read sequence in the gel?

A

Read it from bottom to top. This is newly synthesized strand. Old template strand will be complementary to the fragments in the gel

62
Q

What is VNTR?

A

Variable number tandem repeats. They are short nucleotide sequences that show variations between individuals in terms of number of times sequences is repeated consecutively.

63
Q

Where is VNTR used?

A

They can be used for genealogical investigations using allele combinations

64
Q

What is a locus?

A

Physical location of heritable element on chromosome

65
Q

2 different sources of DNA used in parental profiling

A
  • Paternal lineage: Short tandem repeats from Y chromosome

- Maternal lineage: Mitochondrial DNA variations in single nucleotides in hyper-variable regions

66
Q

Why are non-coding regions more useful in DNA profiling?

A

They are used for gene expression and so we can compare differences in alleles

67
Q

Why are tandem repeats used in DNA profiling?

A

Everyone has different tandem repeats so they can be combined to map a DNA profile and match individuals.

68
Q

How many tandem repeats in GTCTACTACTACTATGGT?

A

CTA is repeated 4 times

69
Q

What should you look for when given a question on matching DNA profiles (like parentage)?

A

Look at which profile doesn’t have a lone allele as child will inherit different VNTRs from both parents

Biology HL IB 2020-22 (24 decks)

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