Weeks 1-3

Question 1

where Dna is found in eukaryotes and prokaryotes

Answer 1

E - nucleus, mitochondria, chloroplasts
P - circular chromosome in nucleoid, plasmids

Question 2

pyrimidines and purines

Answer 2

pyrimidines are nitrogenous bases with 1 ring, eg C, T and U. Purines have 2 rings, eg A and G

Question 3

Direction of replication, ratio of bases

Answer 3

5’ to 3’
ratio of A to T and C to G is always the same. Varies between species

Question 4

Eukaryotic vs prokaryotic chromosomes

Answer 4

Prokaryotic - single chromosome, fewer histones
Eukaryotic - multiple, linear so faster to replicate, more histones - forms chromatin

Question 5

Active vs inactive chromatin

Answer 5

Euchromatin - loose structure, active for transcription
Heterochromatin - condensed structure, inactive for transcription

Question 6

gene and genome definition

Answer 6

sequence of nucleotides that encodes the synthesis of a gene product, either RNA or proteim.

genome - the complete set of genetic material present in a cell or organism

Question 7

ORI and replication forks

Answer 7

Origin of replication - 1 in bacteria chromosome, 1000s in eukaryotes.
Replication fork - active area where DNA strands split and replication takes place

Question 8

Replication of chromosome ends

Answer 8

Telomeres are the ends of eukaryotic chromosomes, they consist of many short repeats. The leading strand gets fully replicated but the lagging strand is not, so the chromosome gets shorter after each replication. Repeats are added by telomerase

Question 9

Antiparallel elongation

Answer 9

Leading strand is synthesised continuously. The lagging strand is not, it’s made in pieces - okazaki fragments, joined by DNA ligase.

Question 10

Replication process

Answer 10

topoisomerase unwinds DNA helix to form ladder shape. Helicase unzips DNA. Single stranded binding proteins stabilise the DNA. Primase enzyme forms RNA primers. DNA polymerase (3) adds new nucleotides and DNA ligase joins them together

Question 11

Central Dogma

Answer 11

Term for the idea of genes to RNA to DNA

Question 12

Transcription

Answer 12

In eukaryotes transcription factors bind to the promoter region, in the TATA box. In prokaryotes RNA pol binds straight to the promoter/sigma factor. Then RNA pol binds and separates the DNA strands. It joins together complementary RNA nucleotides. 5’ to 3’ direction

Question 13

mRNA processing in eukaryotes

Answer 13

5’ cap is added - protects transcription, promotes translation and signals nuclear export.
Poly A tail - Adenine bases are added to the 3’ end - protects transcription.
Splicing occurs to remove introns.
Alternative splicing can occur, so 1 gene can code for more than 1 protein

Question 14

types of RNA

Answer 14

ribosomal/ rRNA
small nuclear RNA/ snRNA - involved in nuclear processing of pre-mRNA
SRP RNA - signal recognition particle - mediates protein synthesis
Small RNAs - involved in control of gene expression

Question 15

PCR method

Answer 15

Heat to 95 for 1 minute to unzip DNA
Cool to 60 so primers can bind
Heat to 72 for Taq polymerase (used because it’s heat resistant) to work

Question 16

Gene cloning

Answer 16

Isolate gene of interest, insert into plasmid vector using restriction enzymes. plasmid is inserted into bacteria (transformation). DNA ligase seals the strands. Recognition sites are palindromic.
Transformation is done chemically (heat shock) or by electroporation (electric shock which makes temporary holes in the plasma membrane)

Question 17

Features of a typical cloning vector

Answer 17

Will have an antibiotic resistance gene so can check plasmid was transformed.
Has a colour gene in it’s multiple cloning site (place where there are multiple restriction sites) so can check if gene was inserted

Question 18

Why do you use liquid nitrogen for protein extraction

Answer 18

It prevents degradation so proteins stay intact
Makes samples brittle and easier to grind

Question 19

what do Chelex beads do

Answer 19

Protect sample from DNases which may break down DNA

Question 20

polyacrylamide gel electrophoresis and agarose gel electrophoresis

Answer 20

Polycrylamide is for proteins
Agarose is for DNA

Question 21

Translation - initiation + process

Answer 21

Small and large ribosome subunits assemble when attached to mRNA - forms translation initiation complex
All proteins start with methyonine
Special initiator tRNa has methyonine attached
P site - binds to tRNA holding growing polypeptide chain
A site - binds to tRNA holding new amino acid
E site - binds to tRNA that already unloaded the amino acid
Translocation occurs when the tRNA moves site
Peptide bonds catalysed by peptidyl transferase

Question 22

Termination of translation

Answer 22

A release factor binds directly to the stop codon in the A site. H2O is added instead of an amino acid - hydrolysis

Question 23

Polyribosomes

Answer 23

several ribosomes cab simultaneously translate 1 mRNA

Question 24

Open reading frames

Answer 24

multiple start and stop codons in each gene
different protein made depending on which nucleotide you start from
each gene has 6 frames

Question 25

lac operon

Answer 25

Operons are regions of DNA containing a cluster of genes, under the control of a single promoter - can all be activated with a single transcription factor No lactose - repressor binds to promoter and RNA pol can't bind Lactose - allolactose binds to repressor so it is removed

Question 26

Prokaryotic vs eukaryotic gene expression

Answer 26

in bacteria several genes can be transcribed into 1 mRNA, 1 gene per mRNA in eukaryotes

Question 27

Wobble pairing

Answer 27

fewer tRNAs than codons, pairing between codon and anticodon is flexible. So single tRNA can read more than one codon

Question 28

Gene expression definition

Answer 28

the overall process of producing a protein from the gene that encodes the protein

Question 29

Northern Blot

Answer 29

Extract mRNA then run electrophoresis Northern blotting to transfer mRNA onto membrane mRNA is fixed to membrane with UV or heat. Hybridization probes used - complementary to mRNA and labelled with radioactivity or fluoresence Can see labelled RNA on x-ray film semi-quantitative technique

Question 30

RT-PCR*

Answer 30

PolyT primer binds to mRNA tail retrotranscriptase makes ssDNA from mRNA Can select gene of interest using primers and PCR qPCR removes the need to run gels - primer with fluoresence is mixed with RT-PCR reaction, the amount of fluoresense is measured using a laser

Question 31

Microarrays

Answer 31

Each well contains DNA/RNA probes Array is incubated with mRNA or cDNA of a sample Flourescent labelling allows detection of any nucleic acid that binds

Question 32

Measuring amount of protein - Western blot

Answer 32

protein detection can require production of an antibody Mammals are injected with protein of interest and immunoglobulins are extracted Proteins separated by PAGE Protein is treated with a detergent to give it a negative charge It is blotted onto the nitrocellulose membrane Antibody with fluoresent label binds to protein

Question 33

Mutation + polymorphism definition

Answer 33

Mutation - changes in the genome of an organism Polymorphism - genetic differences between individuals in a population More mutations from sperm than egg cell Only mutations in germ line cells (form gametes) are passed onto the next generation

Question 34

Missense and nonsense mutations

Answer 34

Missense - results in different codon in the gene sequence so different amino acid is coded for Can be conservative - the different amino acid is from a similar group and has similar properties, or non conservative Nonsense - introduces an early stop codon so protein synthesis ends early

Question 35

Polyploidy

Answer 35

chromosome duplications drives evolution and speciation because the 1 set may mutate more than the other so will have different functionc can also have whole genome duplications

Question 36

Point, transition and transversion mutation

Answer 36

point alters a single base transition - eg pyrimidine replaces a pyrimidine transversion - eg a purine replaces a pyrimidine

Question 37

mismatch repair

Answer 37

occurs immediately after replication DNA polymerase removes incorrect bases and replaces it Has to distinguish between template and new strand Does this by Methylation of A base in specific palindromic sequence

Question 38

excision repair

Answer 38

Excision repair enzymes recognise damaged DNA uvrABC complex binds to damaged DNA. Damaged strand is removed and resynthesized by DNA polymerase

Question 39

Mutations caused by UV

Answer 39

Can cause thymine dimers (2 thymines covalently bonded). Distorts the helix Photolyase enzymes bind to DNA. Energy from visible light is used to cleave dimer and restore bases

Question 40

Phosphoglyceride bilayer + effect of temperature and saturation

Answer 40

hydrophilic heads face out and hydrophobic tails face in decrease in temp - bilayer forms rigid gel like/ crystalline structure increase - membrane becomes more fluid Fluidity increases as degree of unsaturation increases. Kink from carbon double bond affects how lipids pack into membrane

Question 41

How to isolate membrane enriched cell fractions

Answer 41

Use differential centrifugation Can isolate highly purified membrane fractions using equilibrium density-gradient centrifugation. Organelles settle at particular depth depending on density

Question 42

How plants adapt to reduced temperatures

Answer 42

Increase insertion of PUFAs into membranes. Makes it more fluid. Done by fatty acid desaturase - inserts double bonds

Question 43

Types of membrane protein

Answer 43

Integral - exposed on both sides on membrane, has 3 domains. peripheral proteins bind to integral ones

Question 44

Proving that membrane proteins can move

Answer 44

Use fluroesence recovery after photobleaching Label all proteins with fluoresenct reagent, bleach with laser. Recovery will be 50% because some proteins move and some don't

Question 45

cell surface receptors - properties

Answer 45

made up of 3 domains: extracellular, intracellular and transmembrane Some proteins criss cross membrane and others function by forming dimers Highly specific for their ligand Ligand-receptor binding is reversible Ligand binding induces conformational change in receptor - can then interact with other proteins. Activated receptors can recruit other proteins. High affinity receptor: will bind to ligand even when it's at low concentrations

Question 46

protein modification - phosphorylation

Answer 46

Phosphorylation is catalysed by protein kinases. Phosphate from ATP. Could activate a protein or cause conformational change. Phosphoprotein phosphatases dephosphorylate their substrates

Question 47

CCK signalling pathway (GPCR receptors)

Answer 47

CCK secretion increases when mucosal cells encounter digestion products. CCK binds to it's receptor - single polypeptide with 7 transmembrane helices. This activates the heterotrimeric G protein. G protein activates PLC (phospholipase) PLC hydrolyses plasma membrane lipid PIP2 into DAG and IP3 - 2nd messengers. IP3 diffuses into cytoplasm and binds to receptor on ER - Ca2+ released into cytosol. Increase in Ca2+ causes PKC to move to plasma membrane. Activated by DAG. Activated PKC causes chain reaction so alpha amylase is released. After secretion Ca2+ conc is restored by ATPase enzymes that pump them into ER or out of cell.

Question 48

Synthesis and degradation of cAMP

Answer 48

A G protein activated AC so cAMP is synthesised. Targets protein kinase A Made from ATP, catalysed by adenylyl cyclase Degraded by cAMP-PDE, forming AMP.

Question 49

pulmonate gastropods and mollusc shell

Answer 49

The mantle wall functions as a modified lung Periostracum = organic, resistant to damage Prismatic = prisms of CaCO3 Nacreous = continually excreted, in some is mother of pearl bivalves use ctenidia for feeding Lophotrocozoans have U shaped feeding structures ctenophora - biradial symmetry. Collenchyma is mesohyl equivalent eumetazoans - true tissues

Question 50

microtubule arrangement

Answer 50

2 microtubules in the centre, surrounded by 9 doublets with dynein arms. cross bridging links between proteins.