7.1 DNA Structure Flashcards

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1
Q

What problem did scientists in the mid-twentieth century relating to genetic material?

A

In the mid-twentieth century, scientists were still unsure as to whether DNA or protein was the genetic material of the cell

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2
Q

Why did scientists had trouble deciding whether protein or DNA were the genetic material?

A

It was known that some viruses consisted solely of DNA and a protein coat and could transfer their genetic material into hosts

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3
Q

Who carried out an experiment to determine whether DNA or protein is the genetic material of the cell?

A

In 1952, Alfred Hershey and Martha Chase conducted a series of experiments to prove that DNA was the genetic material

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4
Q
  1. What was grown to prove DNA was the genetic material?
A

Viruses (T2 bacteriophage) were grown in one of two isotopic mediums in order to radioactively label a specific viral component

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5
Q
  1. What were the 2 conditions in which the viruses were grown?
A

Viruses grown in radioactive sulfur (35S) had radiolabelled proteins

Viruses grown in radioactive phosphorus (32P) had radiolabeled DNA

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6
Q

Why were some of the viruses grown in sulfur?

h&c

A

sulfur is present in proteins but not DNA

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7
Q

Why were some of the viruses grown in phosphorus?

h&c

A

phosphorus is present in DNA but not proteins

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8
Q
  1. What were the viruses then allowed to do? h & c
A

The viruses were then allowed to infect a bacterium (E. coli) and then the virus and bacteria were separated via centrifugation

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9
Q
  1. What happened during the centrifugation? h&c
A

The larger bacteria formed a solid pellet while the smaller viruses remained in the supernatant

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10
Q
  1. What were the results? h&c
A

The bacterial pellet was found to be radioactive when infected by the 32P–viruses (DNA) but not the 35S–viruses (protein)

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11
Q
  1. What could they conclude? h&c
A

This demonstrated that DNA, not protein, was the genetic material because DNA was transferred to the bacteria

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12
Q

Who researched the structure of DNA? What did they use?

A

Rosalind Franklin and Maurice Wilkins used a method of X-ray diffraction to investigate the structure of DNA

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13
Q
  1. What is the first step of x-ray diffraction?
A

DNA was purified and then fibres were stretched in a thin glass tube (to make most of the strands parallel)

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14
Q
  1. What is concentrated on the DNA? x-ray
A

The DNA was targeted by a X-ray beam, which was diffracted when it contacted an atom

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15
Q
  1. What does the x-ray diffraction show?
A

The scattering pattern of the X-ray was recorded on a film and used to elucidate details of molecular structure

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16
Q

What 3 things can be determined from the x-ray diffraction?

A

composition
orientation
shape

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17
Q

What was concluded about the composition of DNA from the x-ray diffraction?

A

DNA is a double stranded molecule

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18
Q

What was concluded about the orientation of DNA from the x-ray diffraction?

A

Nitrogenous bases are closely packed together on the inside and phosphates form an outer backbone

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19
Q

What was concluded about the shape of DNA from the x-ray diffraction?

A

The DNA molecule twists at regular intervals (every 34 Angstrom) to form a helix (two strands = double helix)

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20
Q

What did Franklin’s research conclude?

A

Franklin’s x-ray diffraction experiments demonstrated that the DNA helix is both tightly packed and regular in structure

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21
Q

What is the structure of DNA?

A

Phosphates (and sugars) form an outer backbone and nitrogenous bases are packaged within the interior

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22
Q

What did Chargriff determine?

A

Chargaff had also demonstrated that DNA is composed of an equal number of purines (A + G) and pyrimidines (C + T)

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23
Q

What can be inferred from Chargraff’s findings?

A

This indicates that these nitrogenous bases are paired (purine + pyrimidine) within the double helix

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24
Q

How did Chargraff’s findings help in determining the directions of the DNA strands?

A

In order for this pairing between purines and pyrimidines to occur, the two strands must run in antiparallel directions

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25
Q

What information about the hydrogen bonds was concluded by Watson and Crick?

A

When Watson & Crick were developing their DNA model, they discovered that an A–T bond was the same length as a G–C bond

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26
Q

How many bonds are formed between A and T, G and C?

A

Adenine and thymine paired via two hydrogen bonds, whereas guanine and cytosine paired via three hydrogen bonds

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27
Q

What does the DNA structure suggest about the 2 mechanisms for DNA replication?

A

Replication occurs via complementary base pairing (adenine pairs with thymine, guanine pairs with cytosine)

Replication is bi-directional (proceeds in opposite directions on the two strands) due to the antiparallel nature of the strands

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28
Q

What type of process is DNA replication?

A

DNA replication is a semi-conservative process that is carried out by a complex system of enzymes

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29
Q

What is helicase’s role in DNA replication?

A

Helicase unwinds and separates the double-stranded DNA by breaking the hydrogen bonds between base pairs

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30
Q

Where does helicase unwind DNA?

A

This occurs at specific regions (origins of replication), creating a replication fork of two strands running in antiparallel directions

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31
Q

What is the role of DNA gyrase?

A

DNA gyrase reduces the torsional strain created by the unwinding of DNA by helicase

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32
Q

How does DNA gyrase reduce the torsional strain?

A

It does this by relaxing positive supercoils (via negative supercoiling) that would otherwise form during the unwinding of DNA

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33
Q

What 7 proteins are involved in DNA replication?

A
helicase
DNA gyrase
SSB Proteins (single-stranded binding proteins)
DNA primase
DNA polymerase III
DNA polymerase I
DNA Ligase
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34
Q

What is the role of SSB’s in DNA replication?

A

SSB proteins bind to the DNA strands after they have been separated and prevent the strands from re-annealing

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35
Q

Apart from separating the DNA strands, what is the role of SSB’s?

A

These proteins also help to prevent the single stranded DNA from being digested by nucleases

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36
Q

What happens to SSBs once DNA replication is finished?

A

SSB proteins will be dislodged from the strand when a new complementary strand is synthesised by DNA polymerase III

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37
Q

What is the role of DNA primase?

A

DNA primase generates a short RNA primer (~10–15 nucleotides) on each of the template strands

38
Q

What is the role of RNA primer?

A

The RNA primer provides an initiation point for DNA polymerase III, which can extend a nucleotide chain but not start one

39
Q

How is the new DNA strand created?

A

Free nucleotides align opposite their complementary base partners (A = T ; G = C)

40
Q

What is the role of DNA Polymerase III?

A

DNA pol III attaches to the 3’-end of the primer and covalently joins the free nucleotides together in a 5’ → 3’ direction

41
Q

In what ways does DNA Polymerase III move?

A

As DNA strands are antiparallel, DNA pol III moves in opposite directions on the two strands

42
Q

How does DNA P III work on the leading strand 3’ to 5’?

A

On the leading strand, DNA pol III is moving towards the replication fork and can synthesise continuously

43
Q

How does DNA P III work on the lagging strand 5’ to 3’?

A

On the lagging strand, DNA pol III is moving away from the replication fork and synthesises in pieces (Okazaki fragments)

44
Q

What is the role of DNA polymerase I?

A

DNA pol I removes the RNA primers from the lagging strand and replaces them with DNA nucleotides

45
Q

Which strand has more RNA primers?

A

As the lagging strand is synthesised in a series of short fragments, it has multiple RNA primers along its length

46
Q

What is the role of DNA ligase?

A

DNA ligase joins the Okazaki fragments together to form a continuous strand

47
Q

How does DNA ligase join the Okazaki fragments?

A

It does this by covalently joining the sugar-phosphate backbones together with a phosphodiester bond

48
Q

Can DNA Polymerase simply initiate replication?

A

NO

DNA polymerase cannot initiate replication, it can only add new nucleotides to an existing strand

49
Q

What must first happen for DNA replication to occur?

A

For DNA replication to occur, an RNA primer must first be synthesised to provide an attachment point for DNA polymerase

50
Q

What does DNA polymerase do to initiate replication?

A

DNA polymerase adds nucleotides to the 3’ end of a primer, extending the new chain in a 5’ → 3’ direction

51
Q

In what form do free nucleotides exist in?

A

Free nucleotides exist as deoxynucleoside triphosphates (dNTPs) – they have 3 phosphate groups

52
Q

How does DNA polymerase create the chain?

A

DNA polymerase cleaves the two additional phosphates and uses the energy released to form a phosphodiester bond with the 3’ end of a nucleotide chain

53
Q

Why does DNA polymerase move in different directions?

A

Because double-stranded DNA is antiparallel, DNA polymerase must move in opposite directions on the two strands

54
Q

In what direction does DNA polymerase move on the leading strand?

A

On the leading strand, DNA polymerase is moving towards the replication fork and so can copy continuously

55
Q

In what direction does DNA polymerase move on the lagging strand?

A

On the lagging strand, DNA polymerase is moving away from the replication fork, meaning copying is discontinuous

56
Q

Why is the lagging strand discontinuous?

A

As DNA polymerase is moving away from helicase, it must constantly return to copy newly separated stretches of DNA

57
Q

What is the lagging strand built up in?

A

This means the lagging strand is copied as a series of short fragments (Okazaki fragments), each preceded by a primer

58
Q

What must be done before the Okazaki fragments can be joined?

A

The primers are replaced with DNA bases and the fragments joined together by a combination of DNA pol I and DNA ligase

59
Q

What is DNA sequencing?

A

DNA sequencing refers to the process by which the base order of a nucleotide sequence is elucidated

60
Q

What is the most widely used method for DNA sequencing?

A

The most widely used method for DNA sequencing involves the use of chain-terminating dideoxynucleotides

61
Q

How are dideoxynucleotides unique?

A

Dideoxynucleotides (ddNTPs) lack the 3’-hydroxyl group necessary for forming a phosphodiester bond (structure)

62
Q

How do dideoxynucleotides affect the DNA chain?

A

Consequently, ddNTPs prevent further elongation of a nucleotide chain and effectively terminate replication

63
Q

What is the point of using dideoxynucleotides?

A

The resulting length of a DNA sequence will reflect the specific nucleotide position at which the ddNTP was incorporated
For example, if a ddGTP terminates a sequence after 8 nucleotides, then the 8th nucleotide in the sequence is a cytosine

64
Q

What method is used to determine the DNA sequence using dideoxynucleotides?

A

Dideoxynucleotides can be used to determine DNA sequence using the Sanger method

65
Q

What is set up? Sanger method 1

A

Four PCR mixes are set up, each containing stocks of normal nucleotides plus one dideoxynucleotide (ddA, ddT, ddC or ddG)

66
Q
  1. Why are PSR mixes used? sanger method
A

As a typical PCR will generate over 1 billion DNA molecules, each PCR mix should generate all the possible terminating fragments for that particular base

67
Q
  1. How are the fragments seperated? Sanger method
A

When the fragments are separated using gel electrophoresis, the base sequence can be determined by ordering fragments according to length

68
Q
  1. What can be done to the fragments to make detection easier?
A

If a distinct radioactive or fluorescently labelled primer is included in each mix, the fragments can be detected by automated sequencing machines

69
Q

What will happen if the sanger method is conducted on the coding strand?

A

If the Sanger method is conducted on the coding strand (non-template strand), the resulting sequence elucidated will be identical to the template strand

70
Q

What is the vast majority of human genome composed of?

A

The vast majority of the human genome is comprised of non-coding DNA (genes only account for ~ 1.5% of the total sequence)

71
Q

What are the 5 types of noncoding DNA?

A
satellite DNA
Telomeres
Introns
Non-coding RNA genes
Gene regulatory sequences

STING

72
Q

What are 3 characteristics of satellite DNA?

A

tandemly repeating sequences of DNA
structural component of heterochromatin and centromeres
commonly used for DNA Profiling

73
Q

What are 2 characteristics of telomeres?

role and structure

A

regions of repetitive DNA at the end of a chromosome

Protects against chromosomal deterioration during replication

74
Q

What are 2 characteristics of introns?

role and structure

A

non-coding sequences within genes

are removed by RNA splicing prior to the formation of mRNA

75
Q

What are 2 characteristics of non-coding RNA Genes?

role and structure

A

codes for RNA molecules that are not translated into protein

e.g genes for tRNA

76
Q

What are 2 characteristics of gene regulatory sequences?

role and structure

A

sequences that are involve din the process of transcription

includes promoters, enhancers and silencers

77
Q

What is DNA profiling?

A

DNA profiling is a technique by which individuals can be identified and compared via their respective DNA profiles

78
Q

What is identified in DNA profiling?

A

Within the non-coding regions of an individual’s genome there exists satellite DNA – long stretches of DNA made up of repeating elements called short tandem repeats (STRs)

79
Q

How can tandem repeats be excised? DNA profiling

A

Tandem repeats can be excised using restriction enzymes and then separated with gel electrophoresis for comparison

80
Q

Why are DNA profiles unique?

A

As individuals will likely have different numbers of repeats at a given satellite DNA locus, they will generate unique DNA profiles

Longer repeats will generate larger fragments, while shorter repeats will generate smaller fragments

81
Q

How is DNA packaged in eukaryotic organisms?

A

In eukaryotic organisms, the DNA is packaged with histone proteins to create a compacted structure called a nucleosome

82
Q

What is the role of nucleosomes?

A

Nucleosomes help to supercoil the DNA, resulting in a greatly compacted structure that allows for more efficient storage

83
Q

What is the role of supercoiling?

A

Supercoiling helps to protect the DNA from damage and also allows chromosomes to be mobile during mitosis and meiosis

84
Q

What is the DNA complexed with and what does it form?

A

The DNA is complexed with eight histone proteins (an octamer) to form a complex called a nucleosome

85
Q

What are nucleosomes linked by and what do they form?

A

Nucleosomes are linked by an additional histone protein (H1 histone) to form a string of chromatosomes

86
Q

What does a string of chromatosomes form?

A

These then coil to form a solenoid structure (~6 chromatosomes per turn) which is condensed to form a 30 nm fibre

87
Q

What is done to the fibres and what do they form? organisation of eukaryotic dna

A

These fibres then form loops, which are compressed and folded around a protein scaffold to form chromatin

88
Q

What is the final step of the organisation of eukaryotic DNA, involving chromatin?

A

Chromatin will then supercoil during cell division to form chromosomes that are visible (when stained) under microscope

89
Q

What is the structure of a nucleosome?

A

A nucleosome consists of a molecule of DNA wrapped around a core of eight histone proteins (an octamer)

90
Q

How are the charges arranged in a histone?

A

The negatively charged DNA associates with positively charged amino acids on the surface of the histone proteins

91
Q

What extrudes from the histone?

A

The histone proteins have N-terminal tails which extrude outwards from the nucleosome

92
Q

What happens during chromosomal condensation?

A

During chromosomal condensation, tails from adjacent histone octamers link up and draw the nucleosomes closer together