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PHA111 > Nucleic Acid Biochemistry > Flashcards

Nucleic Acid Biochemistry Flashcards

1
Q

what actually is DNA?

A
  • genetic material of cell
  • arranged into functional units = genes
  • duplex of 2 anti-parallel strands
  • helix conformation
  • comp base pairing
  • duplex forms templates for replication
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2
Q

DNA

A
  • info store of life
  • simple mol
  • can direct its own replication
  • remarkably stable
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3
Q

RNA

A
  • simple mol
  • forms stable structures
  • performs catalytic functions (ribozymes)
  • imp regulator of gene expression
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4
Q

what are nucleotides briefly?

A

repeating monomers

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5
Q

what are nucleotides made from?

A
  • sugar
  • base
  • phosphate group
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6
Q

what are nucleosides made from?

A
  • sugar

- base

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7
Q

the bases of DNA and RNA are …. (C and N containing) aromatic rings

A

heterocyclic

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8
Q

what does bicyclic mean?

A

2 fused rings

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9
Q

what is thymine also known as?

A

5 methyl uracil

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10
Q

what are the 2 purines?

A

adenine + guanine

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11
Q

what are the 2 pyrimidines?

A

cytosine + thymine/uracil

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12
Q

in the purine bases, what are the 2 nitrogen containing heterocycles?

A

imidiazole + pyrimidine

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13
Q

what is adenine also known as?

A

6 amino purine

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14
Q

adenine is a ….. base than purine & ……. at N-1 only

A

stronger

protonates

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15
Q

what is guanine also known as?

A

2 amino 6 hydroxypurine

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16
Q

what does guanine exist as?

A

a carbonyl tautomer

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17
Q

what is tautomerism?

A

any reaction that involves INTRAMOLECULAR transfer of proton

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18
Q

what is tautomerisation catalysed by?

A

acid + base

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19
Q

give an example of tautomerism?

A

1,3 dicarbonyl compounds

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20
Q

in tautomerism a kete form will become what?

A

enol form

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21
Q

in RNA what is the sugar?

A

ribose (R group = OH)

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22
Q

in DNA what is the sugar?

A

2 deoxyribose (R group = H)

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23
Q

in nucleosides, what is the point of attachment to the base?

A

1-position (N-1) of pyrimidines + 9-position (N-9) of purines

bond between bases and sugars = GLYCOSYLIC (or glycosidic bond)

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24
Q

what is a nucleoside?

A

a base covalently attached to the 1-position of a pentose sugar ring

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25
Q

what is a nucleotide?

A

a nucleoside with one/more phosphate group bound covalently to the 3-, 5-, or (in ribonucleotides ONLY) the 2- position

26
Q

if the sugar is deoxyribose, what are the compounds termed?

A

deoxynucleotides

27
Q

chemically what are nucleotides known as?

A

phosphate esters

28
Q

describe the 2’OH group in ribose?

A
  • acts as nucleophile
  • rna = MORE chem reactive than DNA (single stranded RNA spontaneously cleaves in sol

DNA doesn’t have this 2’OH

29
Q

what is a phosphodiester bond?

A

covalent linkage of a phosphate group between 5’-hydroxyl of one ribose and 3’-hydroxyl of next nucleotide

30
Q

what are nucleic acids?

A

strings of nucleotides attached together by phosphodiester bonds

31
Q

each phosphatase group has what type of single charge?

A

single negative charge

32
Q

nucleic acids are … of strong acids?

A

anions

they are HIGHLY charged proteins

33
Q

what is the most common helical form of DNA

A

B form

34
Q

how many phosphates does the B form have?

A

10 per turn (360 degrees)

35
Q

describe the structure of DNA?

A
  • neg charged sugar-phosphate backbone of mol on outside
  • planar bases of each strand stack on top of each other (on inside so = protected)
  • between backbone strands runs major and minor grooves which follow helical path
  • strands joined non- covalently by HB between bases on opposite strands = base pairs
36
Q

describe the antiparallel feature of DNA?

A

2 strands oriented in opposite directions

5—> 3 direction
2 strands = complementary in terms of sequence

bases HB to each other as purine-pyrimidine pairs —> have similar geometry + dimensions

37
Q

what is the biological significance of the double strandedness?

A
  • have 2 comp strands that act as templates —> copy genetic info
  • second strands serves as template for repair of damaged strand
  • double-helix provides chemically stable enviro —> stores genetic info
38
Q

what is the helical repeat of DNA?

A

10 bp/turn

real dna = 10.5 bp/turn

39
Q

DNA can be induced to form an alternative helix

what is this known as?

A

A form

formed under conditions of low humidity

40
Q

describe the A form?

A
  • right handed
  • wider, more compressed structure (bp tilted to helix axis + lie off axis)
  • 11 bp/turn
  • adopted in vivo
  • helix formed by RNA and DNA-RNA hybrids (imposs to fit 2’OH of RNA into more stable B form)
41
Q

describe the Z form of DNA?

A
  • left handed
  • creates alternating pyrimidine-purine sequence
  • pyrimidine and purine adopt different conformations
  • purine nucleotides adopt syn conformation (purine base lies above deoxyribose ring)
  • zig zag appearance
  • 12 bp/turn
  • not easily formed in DNA
42
Q

why is the Z form not easily formed in dna?

A

boundaries between left handed z form + surrounding b form = v unstable

43
Q

what are prokaryote genomes exemplified by?

A

e.coli chromosome

44
Q

describe the packaging of dna in prokaryotes?

A
  • dna packaged into nucleoid
  • nucleiod has v high DNA conc (30-50 mg/ml)
  • in normal growth, 2 copies of genome per cell made when growth at max rate
45
Q

what does the bulk of DNA in e.coli consist of?

A

single closed-circular dna molecule of length 4.6 million base pairs

46
Q

where may important (and related genes) be found?

A

on same loop/domain

47
Q

describe the domains/loops within prokaryotic dna?

A
  • dna consists of 50-100 domains/loops
  • ends = constrained by ending to structure which consists of proteins attached to part of cell membrane
  • loops = 50-100 kb in size
48
Q

describe the packaging of dna in eukaryotes?

A
  • made up of chromosomes
  • dna = single, linear mol
  • chromsome have high dna conc (200mg/ml)
  • packing accomplished by chromatin
49
Q

what is chromatin?

A

highly organised complex of dna + protein

50
Q

more than …% of the mass of chromatin = protein

A

50

51
Q

through which phase of the cell cycle do chromosomes greatly alter their level of compactness?

A

metaphase

sometimes interphase

52
Q

most of the protein in eukaryotic chromatin consists of…

A

histones

53
Q

what are histones?

A

small proteins with masses bet. 10 and 20 kDa (10,000-20,000 g/mole)

54
Q

what kind of charge do histones have?

A

large, positive charge

55
Q

name the 2 basic amino acids histone sequences consist of?

A
  • lysine

- arginine

56
Q

what are histones assembled into?

A

octamers (8 subunits)

57
Q

what are telomeres?

A

specialised DNA sequences that form ends of linear DNA molecules of eukaryotic chromosomes

58
Q

what is a gene?

A
  • functional unit of hereditary
  • gene sequence that holds info to make RNA mol
  • gene sequence that holds info to make RNA mol —. turned into protein
59
Q

what are the functions of genes?

A
  • regulate RNA seq (transcription)

- mRNA sequences (transcription) —> proteins (translation)

60
Q

what is genetic info stored as?

A

polymer of nucleotides

PHA111 (30 decks)

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