Gene/Protein Expression

Question 1

what are the examples of molecules that don’t follow the central dogma of molecular biology?

Answer 1

retroviruses
non-coding RNA (rRNA, tRNA)

Question 2

what is the definition of DNA?

Answer 2

a polymer molecule made up of a string of deoxyribonucleic acids - the sequence contains info to generate new organisms

Question 3

define the genome

Answer 3

sequence of all DNA in an organism (genes + non-coding regions)

Question 4

define the gene

Answer 4

unit of inheritance - many code for proteins but not all

Question 5

what addition sites are added to the gene in the untranslated region?

Answer 5

cap addition site and polyA addition site

Question 6

what are the 3 steps of transcription?

Answer 6

initiation - RNA polymerate 2 comes to the start of the gene and the DNA strand is pulled apart
elongation - RNA gets longer (forms transcription bubble)
termination - RNA synthesis stops

Question 7

how is RNA processed into mRNA?

Answer 7

the 5’ cap and 3’ polyA tail is added
introns are removed by splicing using splicosome
mRNA exported to cytoplasm for translation

Question 8

what are transcription factors?

Answer 8

proteins binding to specific DNA sequences affecting transcription rate

Question 9

what are the 2 types of transcription factors?

Answer 9

activators and repressors

Question 10

name 4 examples of transcription factors

Answer 10

p53 and E2F (cell cycle control)
steroids (act on TFs)
nuclear hormone receptors (oestrogen/testosterone)

Question 11

what is the transcription initiation complex?

Answer 11

transcription factors act as bridge between DNA and RNA polymerase to allow them to bind

Question 12

where do TFs further stabilise TIC?

Answer 12

upstream enhancer elements

Question 13

what are enhancers and silencers? where are they found? what do they do?

Answer 13

DNA sequences where TFs bind to affect transcription rate
can be upstream/downstream of a gene, close or far away
make it more likely (enhancer) or less likely (silencer) that a promoter is activated
genes often have several enhancers bound by several TFs

Question 14

what does p53 activate and repress the transcription of?

Answer 14

activates transcription of p21 (cell cycle arrest/DNA repair)
represses transcription of survivin (apoptosis)

Question 15

what does ‘closed state’ DNA mean?

Answer 15

TFs have no access to the DNA

Question 16

how does DNA ‘close’?

Answer 16

wrapped around histones to form nucleosomes, forms a scaffold complex

Question 17

what are locus control regions? and how do they work?

Answer 17

open chromatin spanning several genes (e.g globin genes)
TFs bind to globin LCR in erythrocytes opening DNA of all globin genes making gene expression possible

Question 18

what is constitutive gene expression? and give some examples

Answer 18

genes expressed in all cells, all the time, at constant levels
e.g ribosomal proteins and basal TFs

Question 19

what do all constitutive genes have?

Answer 19

a constitutive promoter

Question 20

what is inducible gene expression? give examples

Answer 20

genes only expressed in certain tissues/cells at certain times (spatiotemporal gene expression)
e.g CD4/8, collagen type 1, melatonin, inflammatory cytokines

Question 21

how can one gene produce different products?

Answer 21

splicing (intron removal by splicosome)

Question 22

what is alternative splicing?

Answer 22

when 1 gene can make more than 1 sequence of mRNA (different isoforms)

Question 23

name an example of a gene which undergoes alternate splicing

Answer 23

CD45

Question 24

name an example where alternate splicing can result in disease

Answer 24

the CFTR gene = modifies severity of cystic fibrosis

Question 25

define the transcriptome

Answer 25

the collection of all RNA transcripts in a cell

Question 26

define the proteome

Answer 26

all proteins in any one cell

Question 27

what can the transcriptome be used for?

Answer 27

can differenciate between different diseases
can identify signalling pathways acting in cell/tissue

Question 28

what can the genome be used for?

Answer 28

can tell how many proteins someone may be able to express
can tell if someone will express normal or mutated proteins

Question 29

what can the proteome be used for?

Answer 29

used for diagnosis, prognosis and treatment selection

Question 30

what is the start codon for translation?

Answer 30

AUG

Question 31

what differences can R-groups have?

Answer 31

size
branching
aromatic or aliphatic
polarity
charge
functional groups (-OH, -S)