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BIOC0005 - Molecular Biology
Polymers of Molecular Biology
Sketch labelled, updated central dogma of molecular biology given what we know
now?
#note RNA to DNA e.g retroviruses #note RNA to RNA e.g dsRNA viruses
Sketch and label a single RNA molecule, showing the prime C?
Identify which bases are purines vs pyrimidines?
Purines —> A and G have two rings (they are "pure" royals)
BIOC0005 - Molecular Biology 1
, Pyrimidines —> C, U and T have one ring (they have been "CUT" down to a single
ring)
Sketch all 5 bases and label their carbons?
Direction of Biological vs Chemical DNA synthesis?
Biological i.e natural —> always 5' to 3' so bases only added to 3' end
Chemical i.e artificial —> 3' to 5' so bases added to 5' end
Explain importance of bases molecular shape in terms of distance between two
polyphosphate chains by considering what would happen if backbones were closer or
further apart?
Molecular shape of four bases means larger purine always pairs with smaller
pyrimidine = maintains equal and optimal distance between two backbones
regardless of which pair...
If backbones closer = polyanionic backbones repel due to P
If backbones further = H-bonds between bases break/don't form
Pairing of the bases only works if the chains are ___?
Antiparallel
Explain two causes of DNA twisting into ds helix?
twisting DNA strands into helix reduces rise between adjacent base pairs i.e rise
between adjacent bases < rise between adjacent ribosugars...
BIOC0005 - Molecular Biology 2
, a) bases very hydrophobic so energetically favourable for them to be closer to other
hydrophobes i.e each other and shielded from surrounding hydrophilic cell fluid
b) promotes base stacking via π-π interactions from delocalised rings of e- since
non-covalent interactions only occur over short distances
What is pi aka π–π stacking?
attractive, non-covalent interactions between pi bond-containing aromatic rings
#namely dispersion and dipole-induced interactions
Describe 4 possible forms of DNA, including handedness?
B-DNA —> most common = right-handed anti-parallel double helix
A-DNA —> right-handed form seen when B-DNA dehydrated
Z-DNA —> left-handed form seen if B-DNA modified in specific way
Triple-helical DNA —> result of incorporating third strand into B-DNA
Describe B-DNA helix in terms of bp/turn, turn rise, width and grooves?
10.5 bp/turn 3.3nm rise i.e height per turn 2.0nm width
alternating major and minor grooves
how much is 1 Angstrom?
10−10 m
How to use hand to visualise helix handedness?
Right-hand = right-handed and vice versa
BIOC0005 - Molecular Biology 3
, Describe E.coli chromosome?
single, circular DNA molecule
#4.6 million bp
Calculate length : width ratio of E.coli chromosome using values from prev.
flashcards?
Length = no. of turns x rise
= (4.6 million bp/10.5 bp per turn) x 3.3nm
= ~438095 turns x 3.3nm per turn
= ~1445714nm
Width = 2.0nm
Ratio = 1445714 : 2 —> 7.3 x 10^5 : 1
Which 3 bases can be methylated and where?
#diagrams don't show but in reality methyl groups buried inside helix
BIOC0005 - Molecular Biology 4
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