RNA

Question 1

what is the difference between a nucleotide and a nucleoside?

Answer 1

nucleotide- this a base bonded to a 5-membered ribose ring
nucleoside - this is a nucleoside bonded to one or more phosphates (they’re the same apart from the phosphates in the nucleoside)

Question 2

what is DNA made up of?

Answer 2

its made up of bases, you know the bases and 2 antiparallel strands, the stands have a sugar-phosphate backbone on the outside, whilst the bases are on the inside

Question 3

how are the strands of DNA kept together?

Answer 3

by H bonds and van der waals forces

Question 4

what phase of the cell cycle does DNA replication take place in?

Answer 4

the S phase of the cell cycle

Question 5

what is primase and what does it do?

Answer 5

its an enzyme that makes random primers to provide a free 3’ end for DNA replication
it also proof reads the strand to make sure there’s no mistakes

Question 6

what way does the newly formed DNA grow?

Answer 6

it grows from 5’ to 3’
but it copies a complimentary copy of the DNA going from the 3’ end towards the 5’ end

Question 7

what type of fragments grow on the lagging strand?

Answer 7

Okazaki fragments

Question 8

what is mRNA?

Answer 8

it is the template for the synthesis of proteins and is transcribed by RNA polymerase II

Question 9

what is mRNA transcribed by?

Answer 9

RNA polymerase II

Question 10

what is tRNA?

Answer 10

it carries amino acids to the ribosome

Question 11

what is tRNA transcribed by?

Answer 11

RNA polymerase III

Question 12

what is rRNA?

Answer 12

it is a component of ribosomes

Question 13

what is rRNA transcribed by?

Answer 13

RNA polymerase I

Question 14

describe the steps of tRNA synthesis?

Answer 14

there are 3 steps
1. the amino acid activation step
2. the transfer of amino-acyl-AMP to a specific tRNA
3. the process is driven by hydrolysis of PPi

Question 15

what is the overall word equation for tRNA synthesis?

Answer 15

amino acid + ATP + tRNA + H2O > amino-acyl-tRNA + AMP + 2 Pi

Question 16

what does the anti-codon pair with in tRNA synthesis and why does it do that?

Answer 16

it pairs with the codon to ensure specificity and that the correct amino acid is brought to the ribosome

Question 17

what are tRNA synthetases?

Answer 17

they link the amino acid with the specific tRNA
they also have proof reading ability in the CCA arm, it can read the amino acid to check its the right one

Question 18

what is the structure of tRNA?

Answer 18

its a clover leaf structure

Question 19

what are the names of the steps in mRNA synthesis?

Answer 19

initiation
elongation
termination

Question 20

what happens in initiation in mRNA synthesis?

Answer 20

RNA polymerase and transcription factors gather at promoter sites then synthesis is initiated

Question 21

where does initistion occur on the DNA strand?

Answer 21

at the promoters, these are places that have any number of boxes at them

Question 22

what are the names of the boxes and where are they on the template strand in mRNA polymerase?

Answer 22

TATA box- found at -25 bp from synthesis site
CAAT box- found at -75bp from synthesis site
GC box- found wherever GGCCGG is

Question 23

where does initaition begin for mRNA synthesis

Answer 23

it starts at +1 because that is where the TATA box is telling it to start

Question 24

In what direction is mRNA synthesised along the DNA strand and what synthesises it?

Answer 24

5’>3’ by RNA polymerase II

Question 25

what happens in termination in mRNA synthesis?

Answer 25

the RNA polymerase stops at a defined site

Question 26

what is splicing for?

Answer 26

it to get rid of introns and stop the mRNA from degrading

Question 27

how is the mRNA transcript stabilised?

Answer 27

the mRNA transcript is stabilised by modifications by adding a cap at the 5' end and a poly A tail at the 3' end - this happens by the methylation of bases at either side of the coding region a 5' to 5' triphospahte also protects it

Question 28

when does capping happen?

Answer 28

it happens when the pre-mRNA is ~25 nucleotides long the process involves specific proteins which enhance the stability`

Question 29

what does every intron begin with and end with?

Answer 29

begins with AG and ends with G

Question 30

what molecule is key to splicing?

Answer 30

pyrimidine-rich tract (Py)n with a specific adeninie

Question 31

what do splicing proteins recognise?

Answer 31

they recognise different sites by the bases that are there

Question 32

how is a splicosome created?

Answer 32

by splicing proteins recruiting other proteins into a complex

Question 33

what is alternative splicing?

Answer 33

it is the creation of different mRNA transcripts which can have different functions for the proteins they create

Question 34

what is an example of a protein made by alternative splicing?

Answer 34

antibodies on the cell surface are examples

Question 35

is the effect of controlling RNA splicing by RNA binding proteins positive or negative?

Answer 35

trick question it can be both if it isn't controlled though, mutations can occur and cause disease by affecting splicing

Question 36

how do RNA molecules self-slice and how is it a good thing?

Answer 36

they can act as enzymes to slice themselves by folding into distinct structures the short sequences of nucleotides can base-pair with others to cause it to fold and can drive slicing of the structure

Question 37

how can RNA interference be exploited? and how can it be used in cell biology?

Answer 37

it can be exploited to 'silence' the expression of specific genes in different organisms its used in cell biology to examine the function of a particular gene product

Question 38

what happens ex-vivo in CRISPR?

Answer 38

the cells are isolated from the patient and treated, edited and then re-engrafted back into the patient the target cells are then able to survive in vitro and go back to the target tissue after being transplanted back in the body

Question 39

what happens in vivo in CRISPR?

Answer 39

engineered nucleases are deeliveded by both viral and non-viral approaches they're directly injected into the patient for systemic/ targeted tissue effect

Question 40

what happens in CAR-T therapy?

Answer 40

t cells are collected by the patient then they're isolated, engineered and modified, then they're bound to an antigen then CAR can transmit signals and activate the modified t cells CAR recognition can allow the t cells to bypass MHC limitation and give it an advantage towards tumours

Question 41

what are enhancers?

Answer 41

they control the transcription process far away from the promoter

Question 42

how do enhancers work?

Answer 42

they turn on/off genes theyre also sites that transcription factors can bind to this can all influence gene expression

Question 43

what is the transcription start site in protein synthesis?

Answer 43

it is the AGU on the mRNA which is the GO codon

Question 44

what is the initiation codon for translation?

Answer 44

MET

Question 45

what is mRNA read in at the ribosome?

Answer 45

its read in lots of 3 nucleotides which make up codons

Question 46

what subunits make up the ribosomes?

Answer 46

50S and 30S rRNA subunits

Question 47

what are the P, A and E sites?

Answer 47

P site- where the peptode grows from A site - the tRNA binds to this part and brings in the next amino acid E site- this is where the tRNAs exit the ribosome

Question 48

where is the growing polypeptide released from in the ribosome?

Answer 48

the tunnel

Question 49

what is the complex in tanslation made up of?

Answer 49

its made up of the initiation factors, the tRNA bound to the MET, GTP and the 30S ribosome subunit

Question 50

what does the complex formed in translation do?

Answer 50

it scans the mRNA looking for the AGU (GO) codon then when it finds the codon, the other ribosomal units are recruited with more initiation factors to make the 80S initiation complex

Question 51

how many codons is MET coded for?

Answer 51

1

Question 52

what is involved in the selective control of gene expression?

Answer 52

enhancers DNA modifications epigenetics

Question 53

what are the regulatory steps you can take for DNA replication?

Answer 53

selective control of gene expression control of mRNA synthesis rates mRNA stability mRNA processing protein synthesis and degradation rates