Nucleic acids

Question 1

phosphate group

Answer 1

charge of -2 as H+ dissociates at physiological pH, hydrophyllic

Question 2

pentose sugar

Answer 2

exist as either straight chains or furan rings, furan rings for nucleotide
naming: 1’ C is the one bonded to the base
deoxy - only has one hydroxyl group

Question 3

nitrogenous bases classification

Answer 3

pyrimidine rings: single ring made of 6 atoms (CTU)
purine rings: 2 rings made of 9 atoms (AG)

Question 4

nitrogenous base properties

Answer 4

resonance occurs, electrons are no longer localised over 2 atoms, spread over more atoms –> very stable, absorbs UV light
resonance results in bonds having a partial double bond character
due to double bonds, very planar or almost planar

Question 5

nitrogenous base naming

Answer 5

nucleoside, nucleotide
purines: -osine, -ylate
pyrimidines: -idine, idylate
add deoxy in front for DNA

Question 6

function of nucleic acids and derivatives

Answer 6

storage and retrieval of genetic information for determining AA sequence during protein synthesis
RNA is either structural or functional

ATP: storage of energy
NAD+ : important co factor for cellular processes
cAMP: signalling molecule

Question 7

other bases

Answer 7

minor bases in cells, even cyclic nucleotides

Question 8

nucleoside

Answer 8

base and sugar bonded together via glycosidic bond (N)

Question 9

nucleotide

Answer 9

phsophate group bonded to other nucleoside via phosphoester bond

Question 10

DNA structure

Answer 10

double helix, 2 strands running anti-parallel (5’ to 3’ and 3’ to 5’)
phosphate group of 1 nucleotide joins with ribose sugar at 3’ carbon via phosphodiester bond

Question 11

H bonding between bases

Answer 11

hydrogen bonding between bases occurs, strongest when all 3 molecules are in a straight line, hence AT (2 H bond) CG (3 H bond)
other base pairings H bonding are not as strong
2 purines or 2 pyrimidines cause overlaps or gaps

Question 12

hydrophobic effect in DNA

Answer 12

bases are hydrophobic, project inside the double helix to reduce contact area with water, more energetically favourable
planar bases –> stacking very efficient packing
meanwhile hydrophyllic sugar phosphate backgbone is on the outside of the helix

Question 13

primary and secondary structure

Answer 13

primary: sequence of nucleotides 5’ to 3’
secondary: 2 strands running antiparallel : double helix with complete turn every 3.4 nm, diameter of 2nm

Question 14

what did Chargaff discover

Answer 14

DNA contains same amount of phosphate and pentose, different base sequence varies across species
sum purines = sum pyrimidines
A=T, C=G
same species has identical DNA in different cells, does not change

Question 15

X ray measurements discoveries

Answer 15

regular structure of a helix,
density measurements: helix must have 2 chains

Question 16

Griffith 1928 experiment

Answer 16

S strain has polysaccharide capsules, R does not
S strain live cells: mouse dies
R strain live cells: mouse lives
heat killed S strain cells, mouse lives
R strain and heat killed S strain, mouse dies
S strain DNA was taken up by the R strain cells –> transformation

Question 17

Avery 1944 experiment

Answer 17

mouse lives when S strain DNA is destroyed, hence DNA carries genetic information

Question 18

1952 phage experiment procedure

Answer 18

• grow bacteria in either radioactive 35S or 32P
• infect bacteria with phage to get phage with hot (radioactive) proteins or DA
• infect fresh bacteria with phage that have hot proteins or DNA
• protein coat of phage is sheared off, phages separated from cells
• 35S not found in new phage, 32P found in bacterial cells and new phages –> DNA passed down

Question 19

fundamental features of DNA double helix

Answer 19

right handed helix
major and minor grooves to allow proteins and ions to interact with DNA
3 forms of helices, most common is B form, 10 base pairs per full turn

Question 20

denaturation annealing hybridisation

Answer 20

denaturing - separating double helix into single strands of DNA
annealing - 2 single strands of DNA rewind to form double helix spontaneous process if more than 10 base pairs are still intact
hybridisation - when strands from different species that have similar bases anneal

Question 21

how can DNA be denatured

Answer 21

break H bonds –> high temperature, extreme pH

Question 22

how to measure % denaturation

Answer 22

viscosity, increase denaturation, decrease viscosity
hyperchromism, single stranded DNA absorbs UV light more readily than double stranded DNA

Question 23

Tm definition

Answer 23

temperature at which DNA has reached half total max denaturation

Question 24

base composition and Tm

Answer 24

CG 3 H bonds, AT 2 H bonds, increase CG content, increase Tm

Question 25

ionic strength and Tm

Answer 25

repulstion between sections of sugar phosphate backbone is the main destabilising force for helix increase salt concentration, increase interactions with phosphate ions, decrease repulsion, stabilisation of helix

Question 26

Tm and pH

Answer 26

large change in protonisation states, decrease H bonding, decrease Tm mildly alkaline pH is preferred for denaturation

Question 27

Tm and in vitro H bonds

Answer 27

decrease Tm, forms H bonds with bases, prevents reannealing needs high concentrations though

Question 28

DNA palindromes and hairpin formation

Answer 28

sequence of bases that reads the same forwards and backwards self-complimentary bases within each strand --> intrastrand H bonding occurs, forming hairpin structures

Question 29

nuclear vs mitochondrial DNA

Answer 29

linear vs circular

Question 30

When does DNA replication occur and what it relies on

Answer 30

S phase of cell cycle complementary base pairing