Mod 7: The genetic code

Question 1

how many amino acids are there and why is this counted as degenerate

Answer 1

20 amino acids

a 3 nucleotide (triplet) code is used to make amino acid = codon

(wouldn’t work if it was 2 since = only 16 combos could be made ie 4^2)

but 3 makes 4^3 = 64 combinations, and only 20 AAs so degenerate code

Question 2

experiment to break the genetic code - the Nirenberg-Matthaei experiment

Answer 2

• an extract of bacteria in a test tube
• added a poly-U mRNA sequence to it (UUUUUUUUU)
• and added 19 amino acids + 1 radioactivelly labelled AA
• there were 20 tubes, so in each tube a different AA was labelled
• if the polypeptide formed is radioactive, then that means the UUUUUmRNA sequence was used to make it
• found that only when phenylalanine was radioactevely used, they could make a protein
• in the others, no protein was made
• so determined that UUU = phe

https://www.youtube.com/watch?v=I4cfvbmlFD4

Question 3

what does poly A code for

Answer 3

lysine

Question 4

what does poly C code for

Answer 4

proline

(see onenote for the other sequences and how they were determined)

Question 5

how many out of 64 codons were gfound to code for AAs?

Answer 5

61,
the other 3 were determined to be stop codons

Question 6

which position in a codon tends to be the most variable?

Answer 6

the 3rd position
so usually the 1st two nucleotides play a role in determination and the 3rd can be any (hence degeneracy)
not always tho depends on AA

Question 7

which 2 AAs are only coded for by 1 code

Answer 7

methianine (Met)
and
tryptophan (Trp - the same in the TRP operon)

Question 8

what is an open reading frame

Answer 8

sequence of codons that goes from specific start point to a specific stop point
important where u read from czu it could change the seq

Question 9

what code should an open reading frame start with

Answer 9

AUG - codes for Methionine (not all met codons are equal apparently, see next lecture notes)

Question 10

what code should an open reading frame start and end with

Answer 10

start from AUG - codes for Methionine (not all met codons are equal apparently, see next lecture notes)

end at any stop codon

Question 11

what are the 3 stop codons

Answer 11

UAA
UGA
UAG

Question 12

tRNA strucure: whats the name of the arm that the amino acid joins onto

Answer 12

Acceptor arm
on the 3’ end

Question 13

what is the TΨC arm and why is it called that

Answer 13

all you need to know if that it contains modified bases (e.g. pseudouridine) alongside normal bases to form the arm

Question 14

what is the V loop

Answer 14

start with a Y base (pyrimidine) and some tRNAs have the loops others dont, thats all u need

Question 15

what is the anticodon arm

Answer 15

has complementary anticodon sequence which binds the the codon
alongside a D arm that u dont need to know much about

Question 16

what is the overall function of tRNA

Answer 16

to link a specific AA and to recognise a codon in the mRNA
ensures AA-codon match

Question 17

what enxyme is necassary to ensure each tRNA bind to the correct AA

Answer 17

aminoacyl-tRNA synthetase

very specific to what tRNA and AA it binds to

Question 18

how does aminoacyl-tRNA sythetase ensure this

Answer 18

theres ~20 of then, each specific for an AA and a tRNA
then once both are bound to the enzyme, it allows for tRNA and AA to bind to each other

Question 19

why is this tRNA to AA system not always perfect

Answer 19

some tRNAs bind to more than one AA
but not 61 so not enough for all AA

so some tRNAs have to recognise more than one codon

Question 20

what is G-U base pariing and how does it allow tRNA to bind to more than 1 codon

Answer 20

via wobble -
there’s sometimes some leniency on the 3rd base pairing between tRNA and the codon, which means it doesn’t evne have to be complementary it can still bind

see onenote for eg

Question 21

what is inosine and how does it allow tRNA to bind to more than 1 codon

Answer 21

inosine = modified version of guanine
can happily bind to any pyrimidine (so C and U)
but can also pair with A
so A C and U can pair with I
and the variation will still only occur in 3rd position wehre the variability is

used in Isoleucine codons cuz it has so many codons that make this AA

see onenote x

Question 22

what is wobble

Answer 22

the process that allows this unconventional base pairing between the 3rd base in the codon and the 1st base in the anticodon
as seen in the last 2 flashcards