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MBB I > DNA > Flashcards

DNA Flashcards

1
Q

What are the components of DNA?

A

Deoxyribonucleotides

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2
Q

What are the components of a deoxyribonucleotide?

A

Deoxyribose sugar, Phosphate, Nitrogenous base

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3
Q

Name the bases of DNA and RNA.

A

Guanine, Cytosine, Adenine, Thymine, Uracil

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4
Q

What is the difference between Purines and Pyrimidines?

A

Purine = 2 rings. Pyrimidine = 1 ring.

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5
Q

Which bases are Purine?

A

Guanine, Adenine

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6
Q

Which bases are Pyrimidine?

A

Cytosine, Thymine, Uracil (RNA)

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7
Q

What bond do the base and sugar form?

A

Glycosidic bond

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8
Q

What is a nucleoside?

A

When the base and sugar combine without the phosphate

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9
Q

What is the primary structure?

A

DNA sequence

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10
Q

What are the different ends of DNA?

A

3’ end and 5’ end

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11
Q

What is the backbone known as and what does this mean?

A

Polyanion. Has multiple negative charges due to the phosphate groups.

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12
Q

Why is DNA double stranded and why does this help?

A

Due to polarity. Maintains stability.

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13
Q

What does antiparallel mean?

A

5’ and 3’ run in different directions

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14
Q

Explain the hydrogen bonds between the bases?

A

Hydrogen interacts with a negative molecule and becomes more positive. It will be attracted to another negative molecule.

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15
Q

How many hydrogen bonds are between C & G and A & T?

A

C & G = 3 bonds.

A & T = 2 bonds

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16
Q

What are some examples of Non-standard base pairing?

A

Watson-Crick. Hosteen.

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17
Q

Describe Base Stacking.

A
  1. Bases stack and interact
  2. DNA bases has alternating single bonds
  3. Pi orbitals allow free electron movement and overlap to form Pi conjugation
  4. Becomes more stable
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18
Q

Why does DNA twist?

A
  • Having a straight stack creates repulsion
  • Rotates 30 degrees they interact better
  • Twisting makes the DNA helix asymmetrical
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19
Q

What are Major Grooves?

A

Big gaps in the helix. Higher information content. Proteins can interact and bind.

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20
Q

What is the Minor Groove?

A

Small gaps in the helix. Less access to the bases.

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21
Q

What is electrostatic repulsion in the DNA helix?

A

Phosphate groups are negatively charged and repel on another. Can form ionic bonds.

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22
Q

What is ssDNA?

A

Single Stranded DNA - always pushes to become double

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23
Q

What is dsDNA?

A

Double stranded DNA

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24
Q

What is the effect of temperature on DNA?

A

Increases = more DNA becomes single stranded.

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25
Q

What is the melting temperature?

A

When 50% of DNA is single stranded. Below can still anneal

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26
Q

How does DNA anneal?

A

Trial and error

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27
Q

What does the melting temperature depend on?

A

Content of GC base pairs, size of DNA, ionic strength, pH

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28
Q

When does DNA replication happen?

A

During cell division - synthesis

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29
Q

During replication what are the 2 strands known as?

A

Template strand and complementary strand

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30
Q

Explain Semi Conservative replication

A

One parent strand and one new daughter strand

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31
Q

Where does DNA replication start?

A

Origins of replication

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32
Q

What is meant by bidirectional replication bubble?

A

Replicates in both directions. Known as a replication fork.

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33
Q

What enzymes separates the DNA strands?

A

Helicase - breaks hydrogen bonds.

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34
Q

What do SSB proteins do?

A

Straighten and prevent DNA from re-annealing

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35
Q

What is DNA polymerase?

A

Enzyme the catalyses DNA synthesis - there are 3 different ones

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36
Q

What does DNA polymerase need?

A

A template (bases). dNTPs (building blocks). Mg2+ (promotes reaction. Primer

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37
Q

What does DNA primase produce?

A

RNA primer

38
Q

What direction does replication occur?

A

Runs from 5’ to 3’

39
Q

What happens during replication?

A
  • Both strands synthesized at the same time by DNA polymerase III
  • Leading = continuous
  • Lagging - done in fragments
40
Q

What are Okazaki fragments?

A

1000 to 2000 base pairs

41
Q

What is the role of DNA polymerase I?

A

Finishes lagging strand. Removes RNA and replaces it with DNA

42
Q

What is the role of DNA ligase?

A

Joins it together at the end

43
Q

Why does DNA want complementary pairs?

A

More stable than mismatched pairs

44
Q

How does DNA polymerase copy DNA accurately?

A
  • It’s active site prevents bond formation between mismatched pairs
  • Can make contact in minor groove and measure the correct distance
  • Can proofread its own work
  • Editing and synthesizing happens in separate parts of DNA polymerase
45
Q

How does DNA polymerase synthesize the lagging strand?

A

Needs a free 3’OH to initiate. Requires an RNA primer. RNA primers in the middle are easily removed.

46
Q

What is the End Replication Problem?

A

RNA primers at 5’ cannot be replaced as there is no 3’OH existing. End up with DNA that is a little shorter than the parent. Called the terminal gap. Always shortening.

47
Q

How does the DNA deal with the End Replication Problem?

A

Don’t put important genes at the end of chromosomes. Adds tandem repeats of DNA - don’t have function in gene expression. Repeated multiple times.

48
Q

What are tandem repeats?

A

Telomeres. T and G rich

49
Q

How do telomeres and protein complexes interact?

A

Associate with proteins to form a loop which protects the end of the genome

50
Q

What is the importance of telomeres?

A

They are counted after each replication. Too little telomeres mean the cell will not replicate anymore.

51
Q

What is the role of telomerase?

A

Adds telomeres to the end of DNA. Multicomplex of proteins and RNA - the RNA is complementary to DNA and acts as a template to lengthen the telomeres

52
Q

Where is telomerase active?

A

Germ cells and cancer cells.

53
Q

What is Heterochromatin?

A

Condensed. Few genes. Telomeres. Centromeres. Suppresses gene expression. Stability. Inactive.

54
Q

What is Euchromatin?

A

Less condensed. Expressed genes.

55
Q

What is chromatin?

A

DNA and its packaging

56
Q

What happens if you treat chromatin with low concentrations salt?

A
  • Adding competing bonds
  • Will destabilize the structure
  • Disturbs the intermolecular interactions
57
Q

What happens if you treat chromatin with high concentrations of salt?

A

Will break strong interactions

58
Q

What are you left with if you treat the nucleus with salt?

A

‘beads on a string’

59
Q

What is the string in ‘beads on a string’ structure?

60
Q

What are the beads in ‘beads on a string’ structure?

A

Proteins → histones → nucleosomes

61
Q

What charge would an interacting protein have?

A

Weak positive charged

62
Q

How many histones are in a nucleosome?

63
Q

What are the core histones?

A

H2A, H2B, H3, H4.

64
Q

What is the octameric complex?

A

2 copies of the core histones which come together to form an octameric complex

65
Q

How many base pairs of DNA are wrapped around a histone?

66
Q

What are nucleosomes linked by?

67
Q

Why does DNA need to be packaged?

A

Body will recognise naked DNA like viral DNA

68
Q

How many fold reduction is beads on a string?

69
Q

What is the 40 fold reduction known as?

A

30 nm chromatin fibre. Zigzag structure.

70
Q

What histone clamps the 40 fold reduction?

A

H1 - changes the exit path of DNA from the nucleosome.

71
Q

What fold is the entire mitotic chromosome?

A

10,000 fold shorter than extended DNA

72
Q

What is RNA?

A

Ribonucleic acid

73
Q

What are the roles of RNA?

A

Storage/transfer of genetic information. Structural. Catalytic. Rrgulatory.

74
Q

Why should RNA be less table?

A

Don’t want transcripts to stay forever as there will be no regulatory system. Gene will be constantly expressed

75
Q

Why is RNA less stable than DNA?

A
  1. 2’OH (not H)

2. Single stranded

76
Q

Why does having a 2’OH make RNA unstable?

A

OH can be activated → electrons transferred to phosphate → covalent bond between O and P → P releases its other bond → degrades the chain

77
Q

Describe the secondary structure of RNA

A

Can become double stranded → hydrogen bonds between nucleotides → forms compicated structure → get a bulge, internal loop or a hairpin

78
Q

Why does single stranded RNA twist?

A
  • Promoted by base stacking and is strong

- On an angle = more stable

79
Q

Describe folding of tRNA.

A
  • Have an anticodon loop, interacts with mRNA

- Loop to bring the amino acid to the peptide bond

80
Q

How many classes of histones are there?

81
Q

What does the activity of telomerase do?

A

Avoid loss of chromosome ends

82
Q

What do the daughter strands have in semiconservative DNA replication?

A
  • Contains one of the parent strands

- Has the same (A+T) content as template strand

83
Q

What is the role of helicase?

A

Moves along the DNA to separate strands. At the replication fork helicase is required to separate the strands.

84
Q

What does the proof-reading activity of DNA polymerase increase?

A

Fidelity of replication at least on hundred fold

85
Q

What is the overall dimension of a CG pair very similar to?

A

An AT pair

86
Q

How many hydrogen bonds are formed in ice?

87
Q

How are base pairs arranged in B-DNA?

A
  • Base stacking contrubutes to the stability

- Base pairs are placed across the centre of the double helix

88
Q

How are base pairs arranged in A-DNA?

A

Base stacking contributes to stability

89
Q

How are 5’ and 3’ carbons linked in nucleic acids?

A

Phosphate group

90
Q

What methyl group is located in the major groove?

MBB I (4 decks)

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