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Biology HL > 7.1 DNA Structure And Replication > Flashcards

7.1 DNA Structure And Replication Flashcards

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1
Q

Who found out that DNA was the genetic material of the cell?

A

Hershey and Chase

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2
Q

How did Hershey and Chase discover that DNA was the genetic material of the cell and not proteins? (The experiment) (5)

A
  1. Viruses were grown and radioactively labelled with either:
    Radioactive Sulphur (proteins)
    Radioactive phosphorous (DNA)
  2. Virus infect E.coli and they are then separated via centrifugation
  3. Bacteria formed pellet and virus remained in supernatant
  4. Bacteria was found to be radioactive when infected with P(DNA) but not S(protein)
  5. Showed DNA was genetically material because DNA was transferred to bacteria
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3
Q

Who used X-ray diffraction to investigate the structure of DNA?

A

Franklin and Wilkins

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4
Q

How does X-ray diffraction work? (3 steps)

A
  1. DNA purified and fibres stretched in thin glass tube (to make parallel)
  2. DNA targeted by X-ray beam, which diffracted when contacted with atom
  3. Scattering astern of the X-ray was recorded on film and used to analyse molecular structure
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5
Q

What inferences could be made about the DNA model after crystallography? (3 things)

A

= Composition: DNA is a double stranded molecule
= Orientation: nitrogenous bases are closely packed together on the inside and phosphate from an outer backbone
= Shape: DNA molecule twists at regular intervals to form a helix

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6
Q

What number of hydrogen bonds do adenine and thymine have?

A

2

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7
Q

What number of hydrogen bonds does guanine and cytosine have?

A

3

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8
Q

What two things does the DNA structures suggest about two mechanisms for DNA replication?

A

Replication occurs via complementary base pairings
Replication is bi-directional (due to antiparallel nature of strands)

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9
Q

What is the process of DNA replication? (11 steps)

A
  1. P1: DNA helicase unwinds & separated the double helix by breaking H bonds
  2. Gyrase prevents it from supercooling by reducing torsional strain
  3. Strands now expose, act as templates (semi-conservative)
  4. Single Stranded Binding proteins bind to DNA strand after separation to prevent re-annealing
  5. As synthesis occurs in 5’->3’ direction synthesis continuos on the leading strand & discontinuous on lagging strand
  6. P2: RNA primer is synthesised on parent DNA using RNA primase
  7. DNA polymerase III adds nucleotide to 3’ end according to complementary base pairing (A-T & C-G)
  8. Nucleotides added are in the form as deoxynucleoside triphosphate (2 phosphate groups are released from each nucleotide & energy is used to join nucleotides
  9. DNA polymerase I removes RNA primers & replaces them with DNA nucleotides
  10. DNA ligand joins Okazaki fragments on lagging strand
  11. Each new DNA molecule contains both parent & newly synthesised DNA strand -> semi conservative
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10
Q

What does helicase do?

A
  • Unwinds and separates double stranded DNA by breaking hydrogen bonds between base pairs
  • Occurs at specific regions, creating a replication fork of 2 strands in anti parallel directions
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11
Q

What does DNA gyrase do?

A

Reduces torsional strain created by the unwinding of DNA helicase
By relaxing positive supercojls

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12
Q

What do Single Stranded Binding Proteins do?

A
  • SSB proteins bind to DNA strand after their separation and prevent re-annealing
  • Help prevent DNA from being digested by nucleases
  • Dislodges from strand when new complementary strand is synthesised by DNA polymerase III
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13
Q

What does DNA primase do?

A
  • Generates a short RNA primer on each template strand (-10-15 nucleotides)
  • RNA primer provides an initiation pointer for DNA polymerase which can extend nucleotide chain (but doesn’t start one)
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14
Q

What does DNA polymerase III do?

A

Free nucleotides align opposite their complementary base pairings
- Attaches to 3’ end of primer and covalently join free nucleotides in 5’->3’
Moves in opposite directions on 2 strands
- leading towards replication fork and continuously
- lagging move away from fork and synthesis in pieces (Okazaki fragments)

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15
Q

What does DNA polymerase I do?

A
  • As the lagging strand is synthesised in a series of short fragments, it has multiple RNA primers along its length
  • DNA pol I removes the RNA primers from the lagging strand and replaces them with DNA nucleotides
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16
Q

What does DNA lignase do?

A

Joins Okazaki fragments together to form continuous strand
By covalently joining sugar-phosphate backbones together with phosphodiester bonds

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17
Q

what can DNA polymerase not do?

A

cannot initiate replication
only add new nucleotides to an existing strand

18
Q

what must occur before DNA replication can occur?

A

RNA primer must first be synthesised to provide an attachment point for DNA polymerase

19
Q

how do free nucleotides exist as? (2)

A

deoxynucleoside triphosphate (dNTPs)
they have 3 phosphate groups

20
Q

how does DNA polymerase use dNTPs/ deoxynucleoside triphosphates?

A

by cleaving 2 additional phosphates and uses the energy to form a phosphodiester bond with 3’ end of a nucleotide chain

21
Q

why must DNA polymerase move in opposite directions on 2 strands?

A

because the double-stranded DNA is antiparallel

22
Q

which direction must the DNA polymerase move on the leading strand?

A

DNA polymerase must be moving towards te replication fork and can copy continuously

23
Q

what direction must the DNA polymerase move on the lagging strand?

A

DNA polymerase is moving away from the replication fork and copying is discontinuous

24
Q

what are the steps DNA polymerase moving on the lagging strand? (3 steps)

A
  1. DNA polymerase is moving away from helicase, it must constantly return to copy newly separated stretches of DNA
  2. this means that the lagging strand is copied as a series of short fragments (OKAZAKI fragments) each preceded by a primer
  3. the primers are replaced with DNA bases and the fragments joined together by combination of DNA polymerase I and DNA ligase
25
Q

what is DNA sequencing?

A

the process by which base order of a nucleotide sequence is elucidated (made clear)

26
Q

what are the characteristics of dideoxynucleotides and the consequences? (3)

A
  • dideoxynucleotides (ddNTPs) lack 3’ hydroxyl group necessary for forming a phosphodiester bond
  • so, ddNTPs prevent further elongation of a nucleotide chain and effectively terminate replication
  • the resulting length of DNA sequence will reflect the specific nucleotide position at which the ddNTP was incorporated
    (eg. is ddGTP terminates a sequence after 8 nucleotides, then the 8th nucleotide in the sequence is a cysosine)
27
Q

describe the way that dideoxynucleotides can be used to determine DNA sequencing using the Sanger method (5 steps)

A
  1. four PCR mixes are set up, each containing stocks of normal nucleotides plus one dideoxynucleotide (ddA, ddT,ddC or ddG)
  2. (PCR normally generates over 1 billion copies) so, each PCR mix should generate all the possible terminating fragments for that particular base
  3. when fragments are separated using gel electrophoresis, the base sequence can be determined by ordering fragments according to length
  4. is a distinct radioactive/ fluorescent labelled primer is included in each mix, the fragments can be detected by automated sequencing machines
28
Q

what should occur id the Sanger method is conducted n the coding strand(non-template strand)?

A

the resulting sequence found will be identical to the template strand

29
Q

what are five examples of non-coding regions of DNA?

A

tandemly repeating sequences of DNA (eg. STRs), telomeres, introns, non-coding RNA genes, gene regulatory sequences

30
Q

what are tandemly repeating sequences (eg. STRs) and what do humans used them for? (2)

A

structural component of heterochormatin and centromeres
- used for DNA profiling

31
Q

what are telomeres and what do they do? (2)

A

regions of repetitive DNA at the end of a chromosome
- protects against chromosomal deterioration during replication

32
Q

what are intons and what happens to them? (2)

A

non-coding sequences within genes
- are removed by RNA splicing prior to formation of mRNA

33
Q

what are non-coding RNA genes and an example? (2)

A

codes for RNA molecules that are not translated into proteins
eg, genes for tRNA

34
Q

what are gene regulatory sequences and what is included/examples? (2)

A

sequences are involved in the process of transcription
- includes promoters, enhancers and silencers

35
Q

what is DNA profiling?

A

technique by which individuals can be identified and compared via DNA profiles

36
Q

what is the process of DNA sequencing? (3 steps)

A
  1. within non-coding regions there will be long stretches of DNA made up of short tandem repeats (STRs)
  2. tandem repeats can be excised(cut out) using restriction enzymes and separated suing gel electrophoresis for comparison
  3. individuals will have different number of repeats at a given short tandem repeat locus and will generate unique DNA profiles
    (longer repeats = larger fragments
    shorter repeats = smaller fragments)
37
Q

in Eukaryotes how is DNA packaged?

A

with histone proteins to creat compacted nucleosome structure

38
Q

what do nucleosomes do and why? (2)

A
  • help supercoil DNA resulting in compacted structure, allowing for more efficient storage
  • supercoiling helps protect DNA from damage and allows chromosomes to be mobile during mitosis and meiosis
39
Q

what is the organisation of Eukaryotic DNA? (5)

A
  • DNA is complexed w/ 8 histone proteins (octamer) to form a nucleosome
  • nucleosomes are linked by an additional histone protein (H1 histone) which is condensed to form a string of chromosomes
  • these coil around a solenoid structure which is condensed to form a 30nm fibre
  • the fibres from loops which are compressed and folded around protein scaffold to form chromatin
  • chromatin will supercoil during cell division to from chromosomes that are visible (when stained) under microscope
40
Q

what does a nucleosome consist of? (4)

A

a molecule of DNA wrapped around a core of 8 histones
- the negatively charged DNA associates with positively charged amino acids on the surface of histone proteins
- the histone proteins have N-terminal tails which extrude outwards from the nucleosome
- during chromosomal condensation tails from adjacent histone octamer link up and draw nucleosomes closer together

Biology HL (14 decks)

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