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Biochemistry > Nucleic acids L1 L2 > Flashcards

Nucleic acids L1 L2 Flashcards

1
Q

what is the biochemical role of nucleotides

A

Chemical energy (metabolism)
Product of photphosphorylation and cellular respiration
Used by enzymes, and structural proteins and biosynthetic reactions (motility and cell division)
Signal transduction pathways and 2nd messenger systems (cAMP)

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2
Q

what is the biochemical role of nucleic acids

A

Fundamental process of information transfer (genetics)
DNA the genetic information within cells
RNA serves in expression of information through transcription and translation (protein synthesis)

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3
Q

what is photophosphorylation

A

use of light energy from photosynthesis to provide the energy to convert ADP to ATP

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4
Q

what can nucleotides be used by

A

enzymes
structural proteins
biosynthetic reactions

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5
Q

what is a nucleoside

A

sugar and base

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6
Q

what is a nucleotide

A

sugar, base and phosphate

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7
Q

what is a nucleic acid

A

polynucleotides, linear polymers of nucleotides: of sugar, base and phosphate
linked by phosphodiester bridges

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8
Q

what joins base and sugar

A

glycosidic bond in beta conformation

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9
Q

where is a nucleotide derived from

A

when phosphoric acid is esterified to a sugar OH group of a nucleoside

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10
Q

what are the types of nucleic acids

A

DNA

RNA

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11
Q

what does a pyrimidine contain

A

6 membered heterocyclic rings containing 2 nitrogen atoms

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12
Q

what does a purine contain

A

2 rings of atoms (1 resembling the pyrimidine ring and the other an imidazole ring)

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13
Q

which bases are purines

A

adenine

guanine

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14
Q

which bases are pyrimidine

A

cytosine
uracil
thymine

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15
Q

what is the ribose sugar like

A

5 carbon sugar usually in furanose form

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16
Q

what is the deoxyribose sugar like

A

5 carbon sugar usually in furanose form except that on C2’ the OH group replaced with H

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17
Q

what is furanose

A

collective term for a 5 membered ring structure, with 4 carbon atoms and one oxygen atom

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18
Q

what is the difference between ribose and deoxyribose

A

carbon 2 of deoxyribose the OH group is replaced with a lone hydrogen

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19
Q

how is a sugar linked to a purine base

A

linked via a n-glycosyl (glycosidic N) bond between carbon 1 of the sugar and nitrogen 9 of adenosine

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20
Q

what happens to adenosine when bound through a glycosidic bond

A

becomes adenonine

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21
Q

how is a sugar linked to a pyrimidine base

A

glycosidic N bond, but the bond is situated between carbon 1 of the sugar and nitrogen 1 of the base

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22
Q

where are phosphates added on to nucleosides

A

5’ carbon of sugar

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23
Q

what linked polynucleotides sugar phosphate backbone

A

phosphodiester bonds

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24
Q

what types of DNA are there

A

Some viruses are single stranded DNA
Viruses, bacteria, mitochondria, chloroplasts are double stranded loop
most eukaryotic cells are double stranded linear

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25
Q

what was Erwin Chargaffs findings

A

four bases commonly found in DNA (ATCG) don’t occur in equimolar amounts and that the amounts vary across different species
he did note that certain bases paired together lead to base pairing

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26
Q

what did Waston and Crick find

A

took advantage of Chargraffs rule and x-ray diffraction studies on the structure of DNA to conclude that DNA was a complementary double helix
two strands held together by bonding interactions between unique base pairs always consisting of a purine in one strand and a pyrimidine in the other
DNA is essentially 2 antiparallel chains (2 chains that run in opposite directions). The sequence of bases in one DNA strand is complementary to the bases in the other.

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27
Q

what is chromatin

A

DNA and protein

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28
Q

what are the ‘bead’ like structures of chromatin seen under a microscope

A

Nucleosomes- protein core, DNA wrapped around outside

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29
Q

what are the primary functions of chromatin

A

1) package DNA into a smaller volume to fit in the cell
2) reinforce DNA macromolecule to allow mitosis
3) prevent DNA damage
4) control gene expression and DNA replication

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30
Q

what are the primary components of chromatin

A

histones that compact the DNA

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31
Q

where is chromatin found

A

only in eukaryotic cells (cells with defined nuclei)

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32
Q

what is the structure of a chromosome

A

Nucleosomes folded into a fibre DNA binds round
Fibres organised on structural scaffold as superloops
All the nucleosomes together

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33
Q

what makes up a nucleosome

A

8 histones

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34
Q

what are the three main types of RNA

A

tRNA
rRNA
mRNA

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35
Q

what is the structure of RNA

A

Single stranded molecules but can still base pair to form loops and stems

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36
Q

what are examples of single stranded polynucleotides

A

tRNA
rRNA
mRNA
can base pair to form a number of loops and stems

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37
Q

what are the RNAs in E. coli

A

23S, 16S and 5S rRNA

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38
Q

which is the smallest RNA

A

tRNA 75-90 nucleotides

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39
Q

which contains 10% uncommon bases

A

tRNA

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40
Q

what is rRNA structure like

A

very few uncommon bases

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41
Q

rRNA role

A

major component of ribosomes plays a catalytic and structural role in protein synthesis

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42
Q

what determines rRNA size

A

according to their sedimentation behaviour
sedimentation rate of each subunit is affected by its shape as well as mass ( i.e. sedimentation rate is a measure of how fast the particle settles or sediments)
usually done in a test tube in a centrifuge
svedberg unit offers a measure of particle size based on its rate of travel in a tube subjected to high g force

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43
Q

how many mRNAs are there in a cell

A

many hundreds of different types in each cell

each only as a few copies

44
Q

mRNA chain structure

A

very few uncommon bases

45
Q

what is mRNAs heterogenous size population

A

6S-25S

46
Q

what does mRNA have in its structure

A

non-coding sequences - introns (intervene coding regions, exons)
Poly A tails (100-200 adenylic acid residues attached) at their 3’
Cap at 5’

47
Q

function of poly A tail

A

poly A tail makes the RNA molecule more stable and prevents its degradation

48
Q

which is more stable DNA or RNA

A

DNA is generally more stable

49
Q

what chemical factors affect nucleic acids

A

pH (both acid and alkali)
enzymes
chemical modification of DNA bases

50
Q

what physical factors affect nucleic acids

A

heat, (breaks bonds)
UV light
salt concentrations, (manipulating ionic structure – alter physical and chemical properties)

51
Q

how does pH affect nucleic acids

A

affect ionization of amino acids, can have direct impact on how a protein will interact with another protein

52
Q

how can hydroxyl groups affect nucleic acids

A

Hydroxyl groups in carbohydrates can ionize (polar functional groups)

53
Q

how can electron cloud dispersion affect nucleic acids

A

Dispersion of electron clouds, pH could change the spread of electrons

54
Q

what is the problem with compacting the DNA

A

more difficult to access specific sites

55
Q

what enzyme is used to cut DNA

A

restriction endonucleases

56
Q

what is an example of a polymeric molecule

A

DNA

57
Q

when is an oligonucleotide formed

A

when several phosphodiester bond bonds

58
Q

what are phosphodiester groups at physiological pH (7.4)

A

each phosphodiester group exists as an anion

59
Q

what are nucleic acids at physiological pH (7.4)

A

highly charged polyanionic molecules

60
Q

what gives nucleic acid chains directionality

A

One end of a nucleic acid strand has a 5′-hydroxyl group (primary hydroxyl) and the other end has a 3′-hydroxyl group (secondary hydroxyl)

61
Q

which are the non-covalent interactions

A

van der Waals
ionic
hydrogen bond

62
Q

which are the covalent bonds

A

C-C
C=C
hydrolysis of ATP phosphoanhydride bond

63
Q

what holds the anti-parallel DNA strands together

A

weak bonds between complementary base pairs

64
Q

what can separate a few base pairs

A

only small amounts of energy are needed to separate a few base pairs, and so, DNA can open up to its
single strand confirmation

65
Q

where are glycosidic bonds

A

Link between the sugar and base

66
Q

where are phosphodiester bonds

A

Links between the sugar and phosphate groups

in the DNA backbone very strong, broken by specific nucleases enzyme

67
Q

where are hydrogen bonds

A

links between the complementary bases of the two polynucleotide strands relatively weak and can be disrupted by different factors such as heat

68
Q

what temperature will denature DNA

A

90 degrees C

called DNA melting

69
Q

how can DNA melting process be followed

A

spectrophotometrically

by monitoring the absorbance of the at 260nm

70
Q

what absorbs light in UV region

A

Nucleotides contain conjugated double bonds

and these bonds absorb light in the UV region

71
Q

why can single stranded molecules absorb over 260nm

A

exposure of bases

72
Q

what is the hyperchromic effect

A

single strand absorbs more than the double stranded as the nitrogenous bases accessible so will absorb more light
means more colour

73
Q

what has a linear response

A

More conc solution of molecule is the more absorption occurs – linear response

74
Q

what is the Beer Lamberts law

A

If you have a chemical or a molecule in solution, assuming it has a chromophore (part of its structure will absorb light) if you increasing the concentration of the molecule it will absorb more light

75
Q

in ds DNA what causes a decreased UV absorbance

A

H-bonds between paired nitrogen bases
in double helix limits resonance behaviour of aromatic ring of the bases = (hypochromic effect)
stacked bases in dsDNA structure facilitate
shielding from light (Conceal or cover up)
results less absorbance

76
Q

why does ss DNA have a higher absorbance

A

bases of ssDNA are in free form, and no H-bonds exist between
complementary bases which results in 40% higher absorbance in
ssDNA (hyperchromic) at the same concentration

77
Q

how do you calculate the affects of increased temperature on melting point of two substances
normalised absorbance change for specific temperature

A

absorbance at specific temp - absorbance at room temp / Abs 85 degrees C - absorbance at room temperature

78
Q

how does a lot of CG bases affect thermal stability

A

Lots of CG = more energy as they can form three hydrogen bonds with their adjacent pair

79
Q

what is a tautomer

A

molecule that under differing pH conditions a hydrogen atom in the molecule moves from one part to another, if happens in bases it can cause miss matched pairing

80
Q

what will break in mildly acidic conditions

A

N-glycosyl bond releasing bases from sugar

81
Q

what will break in strongly acidic conditions

A

(pH 3-4) typically break phosphodiester bonds in both DNA and RNA
Hydrolysing sugar moieties and leaving the bases intact

82
Q

what will break in pH 7-8

A

alter the tautomeric state of the bases in DNA

83
Q

what will an amino group (-NH2) tautomerize to

A

imino form (=NH)

84
Q

what will a keto group (-C=O) tautomerize to

A

enol form (=C-OH)

85
Q

what can tautomers form

A

non-standard base pairs that fit into the double helix

86
Q

what do purines and pyrimidines exist as

A

different chemical forms - tautomers

phenomenon arise due to changes in the position of protons in the bases

87
Q

how do tautomers form

A

results in the reversal of base pairing rules

88
Q

what can cause purines and pyrimidines to undergo spontaneous alterations

A

physiological conditions

89
Q

how do some mutagens affect DNA bases

A

chemically modify causing mis-match

90
Q

what is Xeroderma pigmentosum

A

inherited condition where thymine-thymine dimers are not repaired

91
Q

what enzymes cleave nucleic acids

A

exo endonucleases

92
Q

what are exonucleases

A

cleaves at the ends of a polynucleotide chain

93
Q

what are endonucleases

A

cleaves within a polynucleotide chain

94
Q

what are nucleases defined by

A

Substrate (RNA or DNA)

Product (whether they cut at the 3’ or 5’ end)

95
Q

where do restriction endonucleases typically target

A

dsDNA substrates and recognise specific base sequence

96
Q

what can the spectral properties of nucleic acids be used for

A

detection, quantification and assessment of purity

97
Q

what absorption do aromatic amino acids have

A

280nm max

98
Q

what absorption should pure DNA give

A

Pure DNA preparations should give an A260nm/280nm ratio of approx. 1.8 (little contamination from other macromolecules)
lower ratios - contamination by proteins

99
Q

what overall charge is DNA

A

negative

due to phosphate

100
Q

where will DNA move if there is -ve and +ve electrodes

A

to +ve as it is -ve

101
Q

how fast does DNA migrate

A

relative to the size of the DNA fragment (smaller fragments travel faster than larger ones)

102
Q

what happens to DNA in apoptosis

A

dna is broken down ‘cleaned’, can track the rate of apoptosis in group of cells

103
Q

what is the earliest application of flow cytometry

A

Cell cycle analysis by quantitation of DNA content
incorporates the use of a DNA-binding dye called propidium iodide (PI)
PI is impermeable to intact membranes,
PI binds to bases in dsDNA and fluoresces

104
Q

what is PCR

A

technique to amplify a specific region of double-stranded DNA

105
Q

what happens in each PCR cycle

A

heating to denature double-stranded DNA and cooling to allow annealing of excess primer to template and elongation/extension from the primers by the Taq Polymerase

Biochemistry (13 decks)

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