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
2
Q
DNA
A
- info store of life
- simple mol
- can direct its own replication
- remarkably stable
3
Q
RNA
A
- simple mol
- forms stable structures
- performs catalytic functions (ribozymes)
- imp regulator of gene expression
4
Q
what are nucleotides briefly?
A
repeating monomers
5
Q
what are nucleotides made from?
A
- sugar
- base
- phosphate group
6
Q
what are nucleosides made from?
A
- sugar
- base
7
Q
the bases of DNA and RNA are …. (C and N containing) aromatic rings
A
heterocyclic
8
Q
what does bicyclic mean?
A
2 fused rings
9
Q
what is thymine also known as?
A
5 methyl uracil
10
Q
what are the 2 purines?
A
adenine + guanine
11
Q
what are the 2 pyrimidines?
A
cytosine + thymine/uracil
12
Q
in the purine bases, what are the 2 nitrogen containing heterocycles?
A
imidiazole + pyrimidine
13
Q
what is adenine also known as?
A
6 amino purine
14
Q
adenine is a ….. base than purine & ……. at N-1 only
A
stronger
protonates
15
Q
what is guanine also known as?
A
2 amino 6 hydroxypurine
16
Q
what does guanine exist as?
A
a carbonyl tautomer
17
Q
what is tautomerism?
A
any reaction that involves INTRAMOLECULAR transfer of proton
18
Q
what is tautomerisation catalysed by?
A
acid + base
19
Q
give an example of tautomerism?
A
1,3 dicarbonyl compounds
20
Q
in tautomerism a kete form will become what?
A
enol form
21
Q
in RNA what is the sugar?
A
ribose (R group = OH)
22
Q
in DNA what is the sugar?
A
2 deoxyribose (R group = H)
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)
24
Q
what is a nucleoside?
A
a base covalently attached to the 1-position of a pentose sugar ring
25
what is a nucleotide?
a nucleoside with one/more phosphate group bound covalently to the 3-, 5-, or (in ribonucleotides ONLY) the 2- position
26
if the sugar is deoxyribose, what are the compounds termed?
deoxynucleotides
27
chemically what are nucleotides known as?
phosphate esters
28
describe the 2'OH group in ribose?
- acts as nucleophile
- rna = MORE chem reactive than DNA (single stranded RNA spontaneously cleaves in sol
DNA doesn't have this 2'OH
29
what is a phosphodiester bond?
covalent linkage of a phosphate group between 5'-hydroxyl of one ribose and 3'-hydroxyl of next nucleotide
30
what are nucleic acids?
strings of nucleotides attached together by phosphodiester bonds
31
each phosphatase group has what type of single charge?
single negative charge
32
nucleic acids are … of strong acids?
anions
they are HIGHLY charged proteins
33
what is the most common helical form of DNA
B form
34
how many phosphates does the B form have?
10 per turn (360 degrees)
35
describe the structure of DNA?
- 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
describe the antiparallel feature of DNA?
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
what is the biological significance of the double strandedness?
- 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
what is the helical repeat of DNA?
10 bp/turn
real dna = 10.5 bp/turn
39
DNA can be induced to form an alternative helix
what is this known as?
A form
formed under conditions of low humidity
40
describe the A form?
- 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
describe the Z form of DNA?
- 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
why is the Z form not easily formed in dna?
boundaries between left handed z form + surrounding b form = v unstable
43
what are prokaryote genomes exemplified by?
e.coli chromosome
44
describe the packaging of dna in prokaryotes?
- 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
what does the bulk of DNA in e.coli consist of?
single closed-circular dna molecule of length 4.6 million base pairs
46
where may important (and related genes) be found?
on same loop/domain
47
describe the domains/loops within prokaryotic dna?
- 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
describe the packaging of dna in eukaryotes?
- made up of chromosomes
- dna = single, linear mol
- chromsome have high dna conc (200mg/ml)
- packing accomplished by chromatin
49
what is chromatin?
highly organised complex of dna + protein
50
more than …% of the mass of chromatin = protein
50
51
through which phase of the cell cycle do chromosomes greatly alter their level of compactness?
metaphase
sometimes interphase
52
most of the protein in eukaryotic chromatin consists of...
histones
53
what are histones?
small proteins with masses bet. 10 and 20 kDa (10,000-20,000 g/mole)
54
what kind of charge do histones have?
large, positive charge
55
name the 2 basic amino acids histone sequences consist of?
- lysine
| - arginine
56
what are histones assembled into?
octamers (8 subunits)
57
what are telomeres?
specialised DNA sequences that form ends of linear DNA molecules of eukaryotic chromosomes
58
what is a gene?
- 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
what are the functions of genes?
- regulate RNA seq (transcription)
| - mRNA sequences (transcription) —> proteins (translation)
60
what is genetic info stored as?
polymer of nucleotides
