DNA and Membranes

what bond is between a base and a sugar in a nucleotide?

N-glycosidic

what bond is between a phosphate and a sugar in a nucleotide?

phosphodiester

on what carbon does the base join in a nucleotide?

1'

on what carbon does a phosphate join in a nucleotide?

5'

on what carbon does the second nucleotide join?

3'

what direction is dna read in?

5’ to 3’

what are the purine bases?

A and G

what are the pyrimidine bases?

C and T

how many rings do purines have?

2

what type of replication is involved in DNA?

semi-conservative

what is the entire genome in prokaryotes?

a circular chromosome

what phase of the cell cycle does DNA replicate in?

synthesis

what phase of the cell cycle is gene expression?

G1 and G2

what are the grooves in DNA called?

major and minor

what. are the stages of dna replication?

1. helicase unwinds helix
2. SSBPs bind and stabilise single strands
3. primase adds ribonucleoside triphosphates to synthesise rna primer
4. dna polymerase proceeds in 5' to 3' direction
5. exonuclease removes nucleotides from end (primers)
6. primase fills in gaps
7. ligase joins ends of single dna strands

what does primase do?

synthesizes RNA primer

what direction does primase go?

3' to 5'

what does exonuclease do?

removes RNA primer

what strand contains okazaki fragments?

lagging strand

what are origins of replication?

where the two DNA strands are separated, opening up a replication bubble

what joins origins of replication?

ligase

what does topoisomerase do?

relaxes supercoiling in front of the replication fork

what does telomerase do?

uses short rna primer to add short dna repeats to the end of the chromosome, protecting coding region

what is an enhancer?

short region of dna that can be bound to by proteins to start transcription of specific gene

what is a promoter?

regulatory region of dna located upstream providing control point for regulated gene transcription

what is a TATA box?

sequence of dna consisting of TATAAA located in promoter region around 25bps before transcription site

do most genes contain a TATA box?

no

what do transcription factors recognise in genes without a TATA box?

other promoter sequences

what. is at the start. and end of mRNA?

5' cap and 3' poly-A tail

what is a leader?

UTR before AUG

what is a trailer?

UTR after stop codon

where is the reading frame?

between leader and trailer

how much does a ribosome and each subunit sediment?

80S, large = 60S and small = 40S

where does AUG dock to in a ribosome?

P site

where do all amino acids following methionine dock in a ribosome?

A site

what is present on the 3' end of tRNA and what occurs here?

CCA where amino acid attaches

what. adds correct amino acid to tRNA?

aminoacyl-tRNA synthetase

how many aminoacyl-tRNA synthetases are there?

20

what are the steps to charge a tRNA molecule?

1. amino acid binds to aminoacyl-tRNA synthetase
2. ATP also binds and changes enzymes shape preventing other amino acids binding
3. ATP loses 2 phosphates to form AMP
4. tRNA binds to enzyme replacing AMP
5. amino acid covalently binds to tRNA
6. charged tRNA then released and enzyme returns to original shape

where does the covalent bond form between amino acids and tRNA?

carboxyl group of amino acid and hydroxyl group of pentose sugar in tRNA

what are the steps of translation?

1. 40S moves along mRNA until AUG and then stalls
2. binding of 1st tRNA in A site requiring ATP
3. 60S binds to 40S to form intact ribosome
4. next tRNA binds in A site
5. release factor binds at stop codon and releases polypeptide

what shifts in bases 'rare forms'?

protons

what pairings form between 'rare forms' of bases?

C 2 A and G 3 T

what percent of errors can DNA polymerases proofreading ability fix?

90

what is mismatch repair?

errors fixed after replication as replication stalled by exposed OH group in wrong position because of incorrect nucleotide

what is strand slippage?

run of identical bases bunch up out of sequence with pairing underneath

what is a point mutation?

single base pair change

what. are the two types of substitution?

transition and transversion

what is transition substitution?

purine replaces purine or pyrimidine replaces pyrimidine

what is transversion substitution?

purine replaces pyrimidine or vice versa

what is a silent mutation?

alters a base but does not change the amino acid

what is a missense mutation?

changes amino acid sequence

what is a nonsense mutation?

change resulting in early stop codon

what is an extensive missense mutation?

removes stop codon

what is a conservative change?

replaces amino acid with similar amino aid

what is a non-conservative change?

replaces amino acid with an amino acid with different properties

what is the ratio of dna to histones?

1:1

what are the core histones?

H2A, H2B, H3, H4

what charge do the core histones have?

highly positive

what histone is more conserved?

core histones

what is the linker histone?

H1

what is the base unit of chromatin?

nucleosome

how many base pairs on dna in a nucleoosme?

146

how many superhelical turns in a nucleosome?

1.8

what dna around a histone is inaccessible?

touching the histone

where does H1 bind?

dyad

what. is the purpose of H1?

lock histone in place

what are common variants of H2A?

H2A.X, macroH2A and H2A.Z

what are common variants of H3?

cenpA and H3.3

what are the depths of the chromosome?

nucleosome - 10nm fibre - 30nm solenoid - 300nm solenoid - 700nm fibre - metaphase chromosome

what is the packing ratio of the 30nm solenoid?

40

what is the packing ratio of the 300nm solenoid?

680

what is the packing ratio of the 700nm fibre (coiled coil)?

10^4

where is transcription not available from?

300nm onwards

what are telomeres and centromeres made from?

repetitive patterns of bases - heterochromatin

what chromatin contains dna?

euchromatin

what. is constitutive heterchromatin?

chromatin that is always heterochromatic in all cells at all times

what is facultative heterchromatin?

not consistent between cells

what is X chromosome inactivation?

facultative heterochromatin as random expression of paternal or maternal chromosome

what is euchromatin?

more open than heterochromatin and replicated early in S phase, transcriptionally active and inactive genes with different histone modifications

why are phospholipids amphipathic?

polar head and non-polar tail

is the phospholipid tail hydrophobic or hydrophilic?

hydrophobic

what phospholipid concentrates on cytosolic layer?

phosphatidylserine

what is phosphatidylserine important for?

protein kinase C activity

what to bacteria and yeast synthesise in cold conditions and why?

shorter fatty acids and increase saturation - decreases interactions b/w fatty acids so membrane remains fluid

what does cholesterol do?

tightens packing in the bilayer and decreases membrane permeability to small molecules

what do intracellular signal transduction lipids do?

rapidly generated and destroyed by enzymes to bind to regions in proteins to induce conformational or localisational changes

what transports fatty acids that have been assembled in the cytosol to smooth ER?

FABP

where is the bilayer assembled?

smooth ER

what is added to fatty acids in the membrane?

glycerol, phosphate and choline

what are the steps of lipid bilayer synthesis?

1. occurs in outer cytosolic leaflet in ER membrane
2. ER scramblase flips phospholipids from outer to inner leaflets to distribute evenly
3. new membrane transported to plasma membrane in vesicles
4. plasma membrane enzyme flippase flips phospholipids from extracellular to cytosolic to create asymmetrical bilayer

where does glycosylation occur?

lumen of Golgi

what are glycolipids and glycoproteins important for?

cell recognition, inflammatory response and protection

where do the sugar residues of glycoproteins lie?

extracellularly

what is the glycocalyx?

carb rich layer of glycolipids/proteins surrounding cells

what is the function of the glycocalyx?

protects cells against chemical and mechanical damage

what molecules are most likely to diffuse through the membrane?

small, uncharged, hydrophobic

are uniporters faster or slower than channel proteins?

slower

in a Na+/glucose symporter, what is the binding of glucose dependent on?

Na+

what are the 5 body fluid compartments?

intracellular fluid, interstitial fluid, fat, blood plasma and transcellular fluid