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IMS > NUCLEIC ACIDS + DNA REPLICATION > Flashcards

NUCLEIC ACIDS + DNA REPLICATION Flashcards

1
Q

what is a nucleotide?

A

Fundamental biochemical building block of DNA and RNA

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2
Q

what does a nucleotide consist of?

A

3 components

nitrogenous base, pentose sugar, phosphate sugar

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3
Q

what are nitrogenous bases?

A

Pyrimidine (C, T in DNA, U in RNA)

Purine (G, A)

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4
Q

what is pentose sugar?

A

deoxyribose in DNA, ribose in RNA

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5
Q

what is phosphate group?

A

acts a bridge between adjacent ribose/deoxyribose groups

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6
Q

what is adenosine?

A

nucleoside (sugar+base)

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7
Q

what is AMP?

A

nucleoside monophosphate

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8
Q

what is ADP?

A

nucleoside diphosphate

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9
Q

what is ATP?

A

nucleoside triphosphate

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10
Q

how are the bases on complimentary strands held together?

A

Hydrogen bonds

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11
Q

what bases pair up with what base?

A

C-G 3-H bonds

T-A/U-A 2-H bonds

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12
Q

where are the hydrophobic bases found?

A

in the centre od the duplex away from water, stabilised by H bonds

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13
Q

how is the hydrophilic sugar-phosphate backbone stabilised?

A

by electrostatic and H-bonding interactions with water

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14
Q

what is the interaction between stacked bases like?

A

weak transient electrostatic interactions

van der Waal’s forces (pi-pi interactions)

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15
Q

what is the structure of RNA?

A

Single-stranded, adopt secondary structures through base-pairing

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16
Q

how are nucleic acids define by?

A

size and direction

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17
Q

how are polymers described by?

A

sequence and the number of bases

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18
Q

where are nucleotides added?

A

to the 3’- end of a polynucleotide chain

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19
Q

how is a 3-5’ phosphodiester bond formed?

A

the alpha-phosphate of the new nucleotide reacts with the 3’-OH group of the polymer

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20
Q

how does the polypeptide chain grow?

A

in a 5’ to 3’ direction

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21
Q

what does the nucleus contain?

A

DNA and proteins which help compact the DNA

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22
Q

what is chromatin?

A

histone-bound DNA

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23
Q

what is the order of organisation of DNA by increased complexity?

A

DNA duplex, nucleosome, chromatosome, chromosomes

24
Q

what is a nucleosome?

A

DNA wrapped around 8 histones, basic unit of compacted DNA

25
Q

what does a nucleosome contain?

A

Octamer with 2 copies four histone proteins (H2A, H2B, H3, H4)
high arg/lys content (+ve ) to bind to DNA backbone (-ve)

26
Q

what is core DNA?

A

146 bp wrap around histone core

27
Q

what is linker DNA?

A

60-80 bp leads to adjacent nucleosome

28
Q

what does a replicating chromosome contain?

A

2 chromatids linked by a centromere

29
Q

what does a chromatid contain?

A

1 single DNA molecule compacted as chromatosomes

30
Q

what are chromosome territories?

A

nuclear regions in which specific chromosomes are localised

31
Q

what is DNA replication?

A

several steps that involve multiple proteins called replication enzymes and RNA

32
Q

where does DNA replication occur?

A

in the S phase of interphase during the cell cycle

33
Q

why is DNA replication important?

A

vital for cell growth, repair, and reproduction

34
Q

what is semi-conservative replication?

A

the parent strand is separated, creating two single strands used as a template for the complimentary strand

35
Q

what Step 1: Replication Fork Formation?

A

Double stranded DNA “unzipped” into two single strands, base pairs broken by DNA helicase
strands form a Y shaped replication fork which is the template for replication to begin
proteins bind and stabilise unwound single stranded DNA

36
Q

how is the replication fork bi-directional?

A

One strand oriented 3’ to 5’ direction,leading strand

Other oriented 5’ to 3’, lagging strand

37
Q

is each side of the stand replicated differently?

A

Each side is replicated by different processes to accommodate the directional difference

38
Q

what is Step 2: RNA primer binding?

A

A short piece of RNA (primer) binds to the 3’ end of the strand. The primer is the replication starting point, primers generated by the enzyme DNA primase

39
Q

what is Step 3: Elongation?

A

DNA polymerase alpha  binds to the strand at the site of the primer, adds new complementary base pairs to the strand during replication
extends approx 20 base pairs, then elongation taken over by
DNA pol epsilon
DNA pol delta and epsilon have proofreading 3’->5’ exonuclease activity

40
Q

what does Step 3: Elongation prevent?

A

Prevents incorporation of incorrect nucleotides

41
Q

what does Step 3: Elongation result in?

A

the synthesis of one continuous replicated DNA strand in the 5’-3’ direction

42
Q

what happens to the lagging strand?

A

Multiple RNA primers needed, DNA pol delta generates complimentary DNA (Okazaki fragments) to the strand between the RNA primers
Replication discontinuous as the new fragments are not joined

43
Q

what is Step 4: Termination?

A

RNA primers degraded and filled by action of RNAse H and DNA pol delta
DNA ligase joins any breaks in the leading and lagging strands to generate continuous double stranded DNA

44
Q

why does DNA replication occur at multiple sites?

A

Replication cannot just originate from 1 site per chromosome as it would take too long

45
Q

how many origins of replication are needed?

A

Multiple origins of replication with replication forks proceeding in opposite directions necessary
replication bubble

46
Q

how is a replication bubble formed?

A

the enzyme helicase is used to separate the 2 strands. the separated DNA strands form a little open pucker-replication bubble

47
Q

what is a replication bubble?

A

an unwound and open region of a DNA helix where DNA replication occurs

48
Q

what happens in the replication bubble?

A

Histones removed in front of the bubble
H3/H4 tetramers remain intact adjacent to the DNA after synthesis
New H3/H4 tetramer cores bind followed by H2A/H2B.

49
Q

what is epigenetics?

A

heritable changes in phenotype/cell behaviour or gene expression in cells caused by changes other than in the DNA base sequence that control the activity of genes

50
Q

give examples of changes in DNA

A

Histone modifications
E.g. acetylation of Lys, methylation of Lys and Arg
DNA modifications
E.g. methylation of cytosine

51
Q

what does epigenetic modifications alter?

A

alter chromatin structure to control accessibility of transcription factors and co-activators necessary for gene transcription

52
Q

how are epigenetic marks altered?

A

by environmental stimuli

E.g. smoking, nutritional status

53
Q

what do epigenetic markers provide?

A

provides a mechanism for environmental factors to be imprinted genetically

54
Q

what is dutch famine?

A

Fetuses prenatally exposed to famine during 1944-45 had, >50 years later, less DNA methylation on the IGF2 gene compared with unexposed same sex siblings

55
Q

what was the effect of dutch famine?

A

children developed obesity and schizophrenia later in life
Children born to these women 20-30 years later suffered from the same problems despite being conceived and born in a normal dietary state

56
Q

what did dutch famine suggest?

A

Association for exposure just after conception is important in establishing epigenetic marks that persist for generations

57
Q

what are the application of DNA replication?

A

Polymerase chain reaction (PCR)
DNA sequencing
Precision/personalised medicine

IMS (52 decks)

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