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DNA Flashcards

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1
Q

What gene mutation is associated with xeroderma pigmentosa? How does this mutation lead to the associated disorder?

A

A mutation in the NER gene - this gene codes for an enzyme which is used nucleotide excision repair - a dysfunctional gene here won’t recognise and replace abnormal DNA - UV induced DNA damage is not adequately repaired, so a prolonged exposure to ultraviolet light leads to a greater propensity to developing skin cancer

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2
Q

Describe 2 ways in which chemotherapy may actually be more harmful to a cancer patient.

A

Chemotherapy-induced damage - where the chemotherapy itself may be causing DNA damage that is beneficial to the growth and survival of the cancer cell germ line
Differential sensitivity -

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3
Q

Describe how DNA helicase functions.

A

DNA helicase breaks the hydrogen bonds that hold the alpha helical DNA molecule in its secondary structure, unraveling the DNA

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4
Q

What is the end-replication problem? How is this resolved?

A

The end-replication problem relates to the fact that no primer can be put at the end of a bit of DNA to copy the full sequence - therefore every time DNA will be lost - DNA telomerase resolves this by adding G & C repeats onto the end of DNA fragments in order to extend it, allowing primers to bind to copy the remaining bit of coding DNA

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5
Q

How may chemotherapy actually be detrimental to the patient?

A

The chemicals involved in chemotherapy itself may actually induce harmful mutations to a patients DNA

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6
Q

Why after continued chemotherapy treatment may a cancer begin to proliferate again?

A

The chemotherapy may be acting only one a specific cell within the cancer, whereas cells within the cancer itself may have mutated and formed various phenotypes which may be resistant to chemotherapy

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7
Q

How may inhibitors of DNA synthesis be used as antibiotics?

A

They may inhibit the enzymes responsible for the synthesis of DNA

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8
Q

What is non-homologous end joining? What is a potential problem with this repair mechanism?

A

Non-homologous end-joining involves the joining of the DNA flanking gap in a double stranded DNA break - this however will lead to deletion of the sequence which has been lost from the original DNA strand

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9
Q

What is an inversion?

A

A reversal of the order of a sequence of genes in a chromosome from their original/normal order

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10
Q

What is a translocation?

A

A translocation is the interchanging of genetic sequences between 2 non-homologous chromosomes

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11
Q

List 2 types of inversion. How do they differ?

A

Pericentric inversion - an inversion that involves reversing the order of a genetic sequence that includes the centromere
Paracentric inversion - an inversion that reverses the order of a genetic sequence that does not include the centromere

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12
Q

What is an inversion?

A

A reversal of the order of a sequence of genes in a chromosome from their original/normal order

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13
Q

What is a translocation?

A

A translocation is the interchanging of genetic sequences between 2 non-homologous chromosomes

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14
Q

List 2 types of inversion. How do they differ?

A

Pericentric inversion - an inversion that involves reversing the order of a genetic sequence that includes the centromere
Paracentric inversion - an inversion that reverses the order of a genetic sequence that does not include the centromere

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15
Q

How many bases are their every turn of the DNA double helix?

A

10

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16
Q

What is a TATA box?

A

A sequence of nucleotides within a promoter region specifying where transcription will begin

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17
Q

How far upstream from the actual transcription site is the TATA box located?

A

Around -10 base pairs upstream

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18
Q

Within a TATA box what is the sequence of bases?

A

TATAAA

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19
Q

What is the difference between pre-mRNA and mature mRNA?

A

Mature RNA exists after certain modes of protection have been added to pre-mRNA

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20
Q

List 3 ways in which pre-mRNA is transformed to mature mRNA.

A
  • 5’ cap
  • addition of a polyA tail
  • splicing
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21
Q

What are the non-coding parts of DNA called? What are the coding parts called?

A

Non-coding parts are called introns - the coding parts are called exons

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22
Q

At which ends of the pre-mRNA does capping and polyadenylation occur? What is the supposed mechanism of these processes?

A

Capping occurs at the 5’ end (producing a 5’ cap) and polyadenylation occurs at the 3’ end (producing a 3’ polyA tail) - these processes both act to protect the mRNA from degradation

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23
Q

What is splicing?

A

Splicing is the removal of non-coding sections of DNA from the mRNA sequence

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24
Q

Describe briefly the structure of the 5’ cap.

A

A guanosine is methylated on the 7 position

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25
Q

Briefly describe the process of polyadenylation.

A

Endonuclease activity initially cleaves the mRNA molecule at a specific site, where polyA polymerase acts to add as many as 200 adenine bases

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26
Q

How many adenine bases may be in an mRNA polyA tail?

A

As many as 200

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27
Q

What is a polysome/polyribosome?

A

A collection of ribosomes held together by a strand of mRNA which they’re all helping to translate

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28
Q

What, and how many, molecules make up the basic structure of a eukaryotic ribosome? What 2 subunits do they compose?

A

4 rRNA’s and 82 proteins - these make up the 40s and 60s subunits

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29
Q

What, and how many, molecules make up the basic structure of a prokaryotic ribosome? What 2 subunits do they compose?

A

3 rRNA’s and 56 proteins - these make up the 30s and 50s subunits

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30
Q

What are the seperate names for the prokaryotic and eukaryotic ribosomes?

A

The prokaryotic ribosome is called the 70s ribosome, while the eukaryotic ribosome is called the 80s ribosome

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31
Q

Which triplet in the DNA code is used to initiate translation? What amino acid does this code?

A

AUG - this codes for a methionine

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32
Q

Describe specifically what makes up each subunit in the 80s ribosome? Is this ribosome eukaryotic or prokaryotic?

A

The 80s ribosome is eukaryotic and is composed of:

  • a 60s subunit which is composed of:
    • 5s RNA, 5.8s RNA, 28s RNA, and 49 proteins
  • a 40s subunit which is composed of:
    • 18s RNA and 33 proteins
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33
Q

Which nucleotide triplets code for a stop codon? What amino acids do these code for?

A

UAA, UAG, & UGA - these triplets don’t actually code for any amino acid

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34
Q

In tRNA structures, how are the stem loops held in conformation?

A

The anti-parallel sequences that make up the stem loop are held together by hydrogen bonds

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35
Q

How does tRNA interact with mRNA?

A

The anti-codon of a tRNA is complementary to a codon (a sequence of 3 RNA nucleotides) and so will bind it - the tRNA carries a specific amino acid which is coded for by the codon sequence, and tRNA binding via the anti-codon ensures that this amino acid will be incorporated into the protein being translated in order

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36
Q

What is the wobble hypothesis?

A

This concept states that the 3rd nucleotide of a codon may bind to the 1st nucleotide in the anti-codon using non-Watson-Crick base-pairing

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37
Q

What is an anticodon?

A

A complemtary 3 base code on the tRNA to the codon on an mRNA

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38
Q

Which enzyme catalyses the transfer of an amino acid onto a tRNA molecule? Where is this attachment site?

A

Aminoacetyl-tRNA synthetase - they are attached to the 3’ end of the tRNA

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39
Q

What are the P-site and A-site in a ribosome?

A

The A site (aminoacyl) is the first binding site of a tRNA molecule, and the p site (peptidyl) is the second binding site of a tRNA molecule

40
Q

What initiates termination of translation?

A

A stop codon, which is recognised by a release factor, which binds and results in the release of the polypeptide chain created by the ribosome

41
Q

What triplet code gives rise to a start codon? What amino acid does this code for?

A

AUG - this codes for a methionine

42
Q

A DNA sequence is often decried as comma-less, what does this mean?

A

There are no gaps in the reading frame of the DNA sequence

43
Q

How many nucleotides code for a single amino acid? What is this called?

A

3 - this is called the triplet code

44
Q

Why are there so few rRNA’s, and so many mRNA’s?

A

Ribosomes show relatively little variation, so the rRNA that comprises them also shows little variation across different times - mRNA code proteins that show an extraordinary amount of variation, and so encompass a huge volume

45
Q

Why do DNA polymerases shave a greater proof-reading capacity than RNA polymerases?

A

Abnormal DNA would produce universally abnormal proteins downstream which could potentially affect the viability of the cell and the organism - they will also be passed onto daughter cells - therefore DNA changes hold a greater priority in terms of having to be corrected - abnormal RNA will only affect a few proteins downstream, won’t affect any daughter cells, and so is no as great a priority to correct as the universal changes cause by abnormal DNA

46
Q

How many RNA polymerase do prokaryotes have in comparison to eukaryotes?

A

Prokaryotes have just 1, whereas eukaryotes have 3

47
Q

Does the anticodon of tRNA bind to the A site or P site of a ribosome?

A

It binds to the A site

48
Q

What occurs at the P site?

A

Covalent bonds (peptide) are formed between the existing amino acid polypeptide and the amino acid attached to the tRNA occupying the A site

49
Q

What performs splicing?

A

The spliceosome

50
Q

What is thought to control splicing? How may mutations here affect splicing?

A

Specific sequences in introns promote splicing - mutations here may mean they are not recognised as introns and as such not spliced

51
Q

In which area of the cell does transcription occur? In which compartment does translation occur?

A

Transcription occurs in the nucleus - translation occurs in the cytoplasm

52
Q

State how the antibiotics tetracyclin, chloramphenicol, and erythromycin affect the ribosome.

A
  • tetracyclin - binds the 30s subunit - prevents aminoacyl tRNA binding - the A site therefore cannot be occupied
  • chloramphenicol - binds the 50s subunit - affects peptidyl transferase action - peptide bonds can’t form between amino acids
  • erythromycin - binds the 50s subunit - affects translocation from the A site to the P site - the A site therefore remains occupied
53
Q

What base pair is formed using 3 hydrogen bonds?

A

Cytosine & guanine

54
Q

What base pair is formed using 2 hydrogen bonds?

A

Adenine & thymine

55
Q

What nuclear bases are purines?

A

Adenine & guanine

56
Q

What nuclear bases are pyrimidines?

A

Thymine & cytosine

57
Q

DNA is often described as having a ‘twisted-rope ladder’ structure. What molecules would form the steps and ropes of the ladder?

A
  • the nitrogenous bases would make up the steps

- the phosphodiester bonds that join the 5’ -phosphate group and the 3’ -hydroxyl group

58
Q

Where do most DNA-binding proteins bind the DNA alpha helix? Why?

A

At the major groove - it has a greater area for DNA to bind

59
Q

Does euchromatin stain dark or light?

A

Light

60
Q

Does heterochromatin stain dark or light?

A

Dark

61
Q

What is the genome?

A

The complete set of information an organism carries in its genes

62
Q

How is a nucleosome composed?

A

It is composed a a histone octamer (8 histones) which the DNA strand is wrapped around

63
Q

What does the ‘beads on a string’ describe?

A

The histone octamers that form the nucleosome, and the DNA wrapped round it, with linker DNA joining adjacent histone octamers

64
Q

What keeps the DNA wrapped round a histone octamer?

A

Histones contain various positive amino acid residues in their structure, such as lysine and arginine, which attracts the negatively charged DNA sequence - hydrogen bonds are also formed between the 2 structures

65
Q

Is euchromatin or heterochromatin highly condensed?

A

Heterochromatin is highly condensed

66
Q

What is the short arm of a chromosome called? What is the long arm called?

A

A chromosomes short arm is called the p arm - a chromosomes long arm is called the q arm

67
Q

What determines whether a nucleic acid is a nucleotide or a nucleoside? What then is the difference between the 2?

A

Whether the nucleic acid has an attached phosphate group - a nucleotide contains this phosphate group, while a nucleoside doesn’t

68
Q

What is a nucleic acid with an attached phosphate group called?

A

A nucleotide

69
Q

What 3 structures comprise a nucleotide? What bond joins them together?

A

A nuclear base, sugar (pentode sugar), and a phosphate group - these are all joined by covalent bonds

70
Q

What pentode sugar is found in DNA? What pentode sugar is found in RNA

A

2-deoxyribose is found in DNA - ribose is found in RNA

71
Q

Draw the structure of 2-deoxyribose. How does this differ to the structure of a ribose sugar?

A

~have to check structure drawing for yourself~

72
Q

What charge does a phosphate group on a nucleotide?

A

A negative charge

73
Q

Is DNA hydrophobic or hydrophilic? Why is this?

A

DNA is hydrophilic (it attracts water) as it has an overall negative charge, as a result of the attached phosphate group

74
Q

What type of bond are the nucleotides in a linear sequence joined by?

A

A phosphodiester bond

75
Q

Draw the structures of adenine, guanine, cytosine, and thymine.

A

~check slides~

76
Q

Name the 4 nucleosides and corresponding nucleotides found in RNA.

A
  • guanosine - guanosine monophosphate
  • adenosine - adenosine monophosphate
  • cytidine - cytidine monophosphate
  • uridine - uridine monophosphate
77
Q

Name the 4 nucleosides and corresponding nucleotides found in DNA.

A
  • deoxyadenosine - deoxyadenosine monophosphate
  • deoxyguanosine - deoxyguanosine monophosphate
  • deoxycytidine - deoxycytidine monophosphate
  • deoxythymidine - deoxythymidine monophosphate
78
Q

What nuclear base replaces thymine in RNA?

A

Uracil

79
Q

What links the nuclear bases on opposing strands?

A

Hydrogen bonds

80
Q

What base does adenine bind in RNA? How many hydrogen bonds link the 2 nuclear bases?

A

Uracil - they are linked by 2 hydrogen bonds

81
Q

DNA strands in a double helix are said to be anti-parallel. What does this mean?

A

The opposite strands run in a way where the polarity of one strand is orientated in the opposite direction to the other

82
Q

How is a single nucleotide universally read?

A

5’ to 3’ left to right

83
Q

What happens to the strand of DNA that is copied for DNA synthesis?

A

A strand from this sequence will go into 1 daughter strand each

84
Q

How are Okazaki fragments sealed together?

A

By DNA ligase

85
Q

In the classical X-shaped chromosome after replication, what is the number of chromosomes, chromatids, and DNA molecules?

A
  • 1 chromosome
  • 2 chromatids
  • 2 DNA molecules
86
Q

What is the function of DNA helicase?

A

DNA helicase breaks the hydrogen bonds joining the 2 DNA sequences, unraveling the DNA alpha helix

87
Q

What structures are formed by DNA polymerase on the lagging strand in DNA replication?

A

Okazaki fragments

88
Q

How is DNA replication elongated in the plasmids of prokaryotes?

A

Via 2 replication forks

89
Q

What is chromatin?

A

Chromatin is the combination of protein and DNA

90
Q

Why are nucleoside analogues often used in antiviral drugs as opposed to nucleotides analogues?

A

Nucleoside analogues are missing the 5’ phosphate group - therefore they cannot be incorporated into the DNA of invading pathogens, and they will not be able to multiply and replicate

91
Q

What is the difference between an exonuclease and an endonuclease?

A

Exonucleases cleave external phosphodiester bonds at the end of a nucleotide sequence - endonucleases cleave internal phosphodiester chains within the nucleotide sequence

92
Q

What type of restriction activity is present in DNA polymerase? What is its role?

A

DNA polymerase contains innate endonuclease activity - this acts as a proof-reading merchants and can correct any incorrect base pairing at the 3’ OH- end

93
Q

What is the function of topoisomerase?

A

Topoisomerase prevents DNA from overwinding during replication, by introducing single-strand breaks (these are resealed after completion of transcription)

94
Q

What is the role of DNA primase?

A

This adds an RNA primer for DNA polymerase to instigate DNA synthesis

95
Q

What is a transition?

A

A substitution mutation involving the exchange of a purine for another purine or a pyrimidine for a pyrimidine

96
Q

What is a transversion?

A

Asubstitution mutation involving the exchange of a purine for a pyrimidine or a pyrimidine for a purine

97
Q

What are the terms ‘A site’ and ‘P site’ abbreviations of?

A
  • A site = aminoacyl site

- p site = peptidyl site

Medical Cell Biology & Genetics (11 decks)

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