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Molecules to Medicine Unit 1 > DNA > Flashcards

DNA Flashcards

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1
Q

Mitochondrial DNA is passed down from the….

A

Mother

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2
Q

The shape of a nuclear chromosome

A

Linear

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3
Q

The shape of mitochondrial chromosome

A

Circular

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4
Q

The three units of DNA include:

A
  1. deoxyribose 2. a nitrogen containing base 3. phosphate group
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5
Q

Purine base

A

Has two rings and includes adenine and guanine

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6
Q

Pyrimidine base

A

Has one ring and include thymine and cytosine

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7
Q

Ribose

A

Five carbon sugar which a hydroxyl group on the 2’ position, repelling the negative charge in the phosphate group and making RNA less stable than DNA.

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8
Q

At what point on the 5-carbon sugar is the differentiating factor between DNA and RNA?

A

2’

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9
Q

At what point on the 5-carbon sugar is the phosphate group attached?

A

3’ and 5’

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10
Q

Deoxyribose ribose

A

A 5-carbon sugar with a hydrogen on the 2’ position

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11
Q

Deoxyribonucleoside

A

In DNA, purine or pyrimidine linked with deoxyribose, without a phosphate group

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12
Q

Ribonucleoside

A

In RNA, purine or pyrimidine linked with a ribose, without a phosphate group

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13
Q

Nucleotide

A

Composed of a base, a sugar and at least one phosphate. They are the monomer building block of DNA or RNA. POlymerize into long polynucleotide chains in the 5’-3’ phosphodiester bonds formed between adjacent deoxyribose units.

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14
Q

Relative solubility of components of nucleotides.

A

A base is less soluble than a nucleoside which is less soluble than a nucleotide. Purine is less soluble than pyrimidine.

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15
Q

Gout/ Lesch Nyhan

A

Both diseases have a defect in enzymes making the bases build-up, There is especially an accumulation of purine due to its insolubility

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16
Q

What did Fred Griffith discover around WWI?

A

He characterized different strands of pneumonia - one with a capsule (which killed mice) and one without (which did not kill mice).

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17
Q

Describe the study of Avery, McCloud and McCarty.

A

They looked at the virulent strain and the non-vvirulent stain and observe that the non-virulent strain was transformed by the virulent strain.

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18
Q

What did Rosalind Franklin and Maurice Wilkins discover?

A

X-ray diffraction of moist DNA fibers showed a helical structure

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19
Q

What are the implications of Chargaff’s rules?

A

Equal percentages of A/G and C/T in every cellular organism meaning there is base pairing!

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20
Q

Two strands of DNA intertwine in a _________ helix.

A

Right-handed

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21
Q

DNA strands’ backbones are oriented ________ to one another.

A

Antiparallel

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22
Q

The base pairs are bonded by ___________.

A

Hydrogen bonding

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23
Q

If you count ________ base pairs, you will end up in the same position.

A

10

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24
Q

Name the factors which negate the repelling energy of the phosphate groups on the DNA helical structure. (3)

A
  1. Hydrophobic interaction/ stacking energy between adjacent base pairs 2. Hydrogen bonding between complementary bases 3. Positive ions floating in the cells which neutralize the negative charge of the phosphate
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25
Q

Factors that affect DNA melting/ melting temperature.

A
  1. Salt concentration 2.pH 3. DNA chain length 4. GC content
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26
Q

Methylation

A

The major covalent modification of human DNA is methylation of Cytocine, which occurs naturally, allowing enzymes to differentiate between the parent and daughter strans

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27
Q

Deamination

A

Deamination of bases is a major cause of mutation, sped up by nitrous acid. Water reacts with an amino group to release ammonia. This occurs spontaneously.

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28
Q

Deamination is an issue if it alters _________ to _________.

A

5-methylcytosine to thymine; but enzymes can recognize a difference in strands and remedy

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29
Q

Depurination

A

This causes the phosphate back to be sensitive to breakage

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30
Q

UV damage

A

Covalently links thymines, creating diner or kinks in the double helix

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31
Q

DNA intercalation

A

DNA intercalation occurs when ligands of appropriate size and chemical nature insert themselves in between base pairs. An example is doxorubicin.

32
Q

Nucleoside analogs

A

Nucleoside analogs mimic actual nucleoside and are phosphorylated and incorporated into the growing DNA strand where they can act as chain terminators and stop DNA polymerase.

33
Q

What does semi-concervative mean?

A

A newly replicated double helix contains one parental strand and one newly synthesized daughter strand.

34
Q

Birectionality in DNA replication

A

Replication begins at a site of origin and simultaneously moves out in both directions

35
Q

What are the three conserved features of the origin of replication?

A
  1. They are unique DNA segments with multiple short repeats 2. They can be recognized by multimeric origin-binding proteins 3. They are usually rich in A/T base pairs
36
Q

What is the function of origin binding proteins?

A

Origin binding proteins recognizes and binds to the origin of replication

37
Q

In humans, the origin binding protein is called ________.

A

ORC

38
Q

What is the function of single-strand binding proteins?

A

When helices unwinds the double-helix, single-strand binding proteins bind to each single strand of DNA, holding it in that conformation.

39
Q

What is the function of primase?

A

DNA polymerase cannot initiate synthesis of new strand without RNA primer, which is formed by copying of the parental DNA strand.

40
Q

DNA polymerase I

A

DNA Pol I performs the cleanup function in prokaryotes. DNA Pol I mediates replacement of RNA primers

41
Q

DNA polymerase III

A

In prokaryotes, DNA polymerase III is the major replication enzyme because is has a sliding clamp, giving it higher processivity.

42
Q

In eukaryotes, _____________ synthesizes the first 20 deoxyribonucleotides in eukaryotes after the RNA primer and is then swapped for __________ for the lagging strand and __________ for the leading strand.

A

DNA Pol α; Pol δ;Pol ε

43
Q

What is the sliding clamp called in humans?

A

PCNA

44
Q

What is the sliding clamp called in E. Coli?

A

Beta-clamp

45
Q

What is the function of Gyrase?

A

In prokaryotes, relieves torsional strain

46
Q

What is the function of Topoisomerase?

A

In eukaryotes, relieves torsional strain

47
Q

What is the function of Telomerase?

A

Telomerase has reverse transcriptase activity and carries its own RNA template in order to restore the ends of chromosomes (telomeres) in human cancer and stem cells.

48
Q

The leading strand is formed by continuous copying of the parental strand that runs 3’ to 5’ ________ the replication fork.

A

Towards

49
Q

The lagging strand is formed by discontinuous copying of the parental strand that runs 3’ to 5’ __________ from the replication fork.

A

Away

50
Q

What are the two main components which contribute to the fidelity of replication in polymerase activity?

A
  1. The ability to form hydrogen bonds between with bases A and T and G and C 2. Common geometry of the A and T and G and C basepairs
51
Q

DNA damage repair is __________ meaning if one repair mechanism fails, there are back-up options.

A

Redundant

52
Q

What causes oxidative damage to DNA?

A

Oxidative damages to bases are caused by reactive oxygen species that are generated during normal cell metabolism

53
Q

What is base alkylation?

A

Chemical alteration to a base; which can cause a point mutation

54
Q

What is depurination or depyrimidination?

A

Loss of a base

55
Q

What is base deamination?

A

Loss of an amine group which can cause a point mutation

56
Q

What are the two changes in DNA structure which interferes with replication and transcription?

A

DNA strandbreaks and Inter/Intra strand crosslinks

57
Q

What is a point mutation?

A

Substitution of one base for another

58
Q

What is an insertions?

A

Additions of one or more nucleotides within a DNA sequence.

59
Q

What is a deletion?

A

Removal of one or more nucleotides from a DNA sequence.

60
Q

What is nucleotide excision repair?

A

NER removes DNA lesion that distort the DNA structure and block transcription.

61
Q

What are the two types of nucleotide excision repair?

A
  1. Global genome NER which recognizes distorting DNA lesion in any region of the genome 2. transcription-coupled NER which recognizes distorting lesion in regions that are actively transcribed
62
Q

What is base excision repair?

A

BER removes DNA lesions that are missed by the NER process but do not necessarily block polymerase function or distort the DNA structure.

63
Q

Glycosylases are required in __________. They recognize a specific type of altered base and flips the altered base of the helix and removes the damaged base.

A

Base excision repair

64
Q

What are the two types of double-stranded break repairs?

A
  1. Non-homologous end joining (NHEJ): required no sequence homology 2. Homologous recombination: required extensive sequence homology between broken ends and template DNA
65
Q

What is the function of endonuclease in excision repair?

A

Mediates cutting of the phosphodiester backbone flanking the damaged nucleotide

66
Q

What is the pair of homologous protein kinases central to lesion detection?

A

ATM and ATR, which are recruited to the site of DNA damage and initiate the recruitment of downstream proteins.

67
Q

What are the five sources of DNA double-strand breaks?

A
  1. Naturally during Meiosis 2. During generation of immune diversity (VDJ) 3. During DNA replication, when the replication fork encounters a nick in one template strand 4. During insertion of retrovirus 5. From ionizing radiation in the environment
68
Q

Double stranded breaks are sensed by __________ and ___________ kinases.

A

ATM and ATR

69
Q

Positively, Imprecise repair by NHEJ contributes to ___________

A

Antibody diversity

70
Q

NHEJ is __________, ____________, and __________

A

Fast, relatively inaccurate, not sequence dependent

71
Q

Homologous recombination can only occur during _________ and _________ of the cell cycle

A

S; G2

72
Q

Homologous recombination requires____________

A

The nearly identical DNA strands of the unbroken sister chromatid

73
Q

Different resolution of _______________ can lead to exchange of genetic information between the two chromosomes undergoing HR

A

Holliday junction

74
Q

The formation of ___________ is an essential feature of meioses which can lead to gene conversion of crossing over

A

Holliday junction

75
Q

Failure to repair a double-stranded break will lead to cell death. This is exploited by __________

A

Cancer therapy drugs such as bleomycin which causes double-stranded breaks

76
Q

What is resection?

A

Resection is processing in homologous recombination in which broken ends are processed to expose single-strand ending in 3’ OH

Molecules to Medicine Unit 1 (10 decks)

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