Lecture 10 - The Genetic Code

Question 1

using three nucleotides, we are able to:

Answer 1

code for all the amino acids as well as for stop signals

Question 2

tRNA (transfer RNA):

Answer 2

most common non-coding RNA, complex structure that allows for codon recognition and amino acid binding

Question 3

how does the tRNA recognise the codon?

Answer 3

tRNA recognises the codons on the mRNA through a sequence on the tRNA called the anticodon

Question 4

how do amino acids interact with tRNA molecules?

Answer 4

amino acids are attached to the tRNA to be used during protein synthesis

Question 5

what structural element of tRNA molecules allow them to attach to their complimentary codon?

Answer 5

within the sequence of the tRNA at the base of the structure, there is a stretch of three nucleotides whose role is to recognise and bind to the three nucleotides of the codon

as such, the anticodon has a complementary sequence to the mRNA

Question 6

Exact tRNA Sequences Would Be Inefficient:

Answer 6

if each the anticodon of each tRNA had to match exactly, we would require 64 different types of tRNA molecule in order to cover all the possibilities of codon sequence - this would be highly inefficient

Question 7

The Anticodon Third Base can “Wobble”:

Answer 7

to increase efficiency, the third base of the anticodon can wobble - this means that it can actually bind to a nucleotide base that is not its normal partner, this is called non-watson-crick base pairing

• G can bind to C or U
• U can bind to A or G

Question 8

why can anticodon 3rd base “wobbling” occur?

Answer 8

– there is additional space at the third position which allows the bit of RNA to move away from the complementary strand

– there can be a sixth nucleotide that can be included: inosine (I)

Question 9

inosine:

Answer 9

is a modified form of adenosine, processed by a tRNA specific deaminase

inosine is able to engage in many base pairings wether they are crick-watson or non-crick-watson base pairing

with this, it allows for the wobble to occur on the tRNA and allows for less different types of tRNA to exist.

Question 10

high level of redundancy in the system:

Answer 10

most amino acids can be coded by more than one codon

Question 11

what are the two exceptions to the genetic code that can only be encoded with one codon?

Answer 11

methionine and tryptophan are the exception with one codon each

Question 12

Methionine:

Answer 12

the amino acid that all proteins start with as it is the start codon

Question 13

Tryptophan:

Answer 13

the least abundant amino acid and is rare in the proteome

Question 14

most amino acids with similar properties have similar:

Answer 14

codons which means that if there is a change in sequence, it may have a minimal impact

Question 15

The Genetic Code is Nearly Universal:

Answer 15

Mitochondrial genomes have evolved differences in the genetic code:
–UGA is not a stop but codes for tryptophan
–Internal methionine is encoded by AUG and AUA
–In mammalian mitochondria AGA and AGG are not arginine codons but are stop codons.
–In fruit fly mitochondria AGA and AGG are not arginine codons but are serine codons

Question 16

Through wobbles in the anticodon as a result of inosine and other non-Crick-Watson base pairings, we can:

Answer 16

reduce the number of different types of tRNA required to match each codon

Question 17

point mutation:

Answer 17

point mutations are where a there is a change in the sequence of a gene

•These changes can be:

(1) Substitution – where a nucleotide is replaced with another

(2) Insertion – where a nucleotide is added to the sequence

(3) Deletion – where a nucleotide is removed from the sequence

•Can actually be up to three nucleotides

Question 18

4 types of mutation:

Answer 18

silent, missense, nonsense, and frame-shift

Question 19

silent mutation:

Answer 19

mutations that don’t cause a change in amino acid, generally in the third nucleotide of the codon and sometimes second but never first

Question 20

why are silent point mutations possible:

Answer 20

possible due to the wobbles in the anticodon of the tRNA and the high level of redundancy that exists

Question 21

missense mutation:

Answer 21

where there is a change in nucleotide which then changes the amino acid that is coded

often happens with the mutation is in the first nucleotide of the codon, but can happen anywhere within the codon

Question 22

Missense Mutations Can be Conservative:

Answer 22

can be conservative or non-conservative based on what the new anticodon is:
–If the animo acids is similar in properties, then they are considered conservative
–If they are not similar in properties, then they are considered non-conservative

even if the amino acid changes the protein can still remain functional

Question 23

amino acid properties:

Answer 23

depending on the amino acid:
- charge
- hydrophilicity / hydrophobicity
- size
- function groups

Question 24

Non-conservative missense mutations often:

Answer 24

change the structure of a protein

Question 25

Nonsense Mutations Truncate Proteins:

Answer 25

nonsense mutations introduce a stop code in the middle of a protein, as so the protein is truncated and often means it wont function properly / at all - one of the most serious mutations out there

Question 26

reading frames:

Answer 26

RNA can be read in groups of three nucleotides depending on where you start, and these are called reading frames, very important that it is read in the beginning at the right point as only one form of the reading frame will five the correct amino acid sequence

Question 27

frameshift mutation:

Answer 27

frameshift mutations are where there has been an insertion or deletion of a nucleotide which means that the framing of the codons change

this will change the amino acid that will be coded, the location of the stop codon, which combined can changed the protein structure dramatically – often the protein will be nonfunctional as well

Question 28

what form of frameshift is less harmful than a singular addition / subtraction?

Answer 28

an entire codon can be added and removed which will add or remove an amino acid and this itself can cause issues and change the structure of a protein

Question 29

Silent Point Mutations Can Still Be Bad:

Answer 29

Not all codons are equal as there are not equal amounts of tRNA with their anticodons, some anticodons are more prevalent and so this means that during translation, there is no issue in amino acid availability

however, if a mutation changes the codon to one that is rare, this can impede translation by making it slower and affect gene expression

Question 30

point mutation:

Answer 30

where there is a change in the nucleotide sequence that affect what the codon is and then change which amino acid is added to the chai

Question 31

Silent and missense mutations can result in ___ ____ but:

Answer 31

functional proteins

but they may have slowed translation or slightly altered structure dependent on what amino acids are incorporated

Question 32

worst type of mutation & why:

Answer 32

Nonsense and frameshift mutations are the worst type of mutation as they normally end up with incomplete and non-functional proteins

Question 33

Amino Acid Activation:

Answer 33

in order to interact with tRNA, amino acids must be activated - activation of an amino acid means that it is bound to ATP via the enzyme aminoacyl adenylate intermediate

Question 34

tRNA charging:

Answer 34

aminoacyl adenylate intermediate undergoes a nucleophilic attack by an uncharged tRNA to then be joined by an ester bond, thus charging the tRNA

Aminoacyl-tRNA synthetase, the same enzyme involved in amino acid activation, facilitates this reaction

The tRNA now has an amino acid attached ready for translation

Question 35

Aminoacyl-tRNA Synthetase:

Answer 35

20 types (one for each a.a), they recognise anticodon of tRNA via complimentary binding sites within the enzyme

each one also has a synthesis site that has specific affinity for each amino acid and is where activation and charging occurs

also have editing functions so they can check and correct the wrong amino acids being added to the tRNA

Question 36

ribosomes:

Answer 36

made up of both proteins and RNA

responsible for moving along the mRNA and reading the codons, and capture the matching tRNA to allow for the synthesis of the amino acid chain to make a protein

Question 37

Both prokaryotes and eukaryotes have similar ribosomal structures and components:

Answer 37

– one large and one small protein subunit

– two or three ribosomal RNA transcripts associate with the large protein subunit

– one ribosomal RNA transcript with the small protein subunit

Question 38

ribosomal structure:

Answer 38

•The small subunit provides a scaffolding for tRNA anticodons to be matched to mRNA codons
•The large subunit catalyses the formation of the peptide bonds between amino acids during protein synthesis
•The two subunits are separate until they associate with a mRNA for translation.
•When they combine, this provides the room for the binding of the mRNA and the tRNA, and the growing chain of the protein chain

Question 39

The Ribosome as a Ribozyme:

Answer 39

•The ribosomal proteins cover the periphery of the ribosome and provide structural integrity

•Most of the ribosome is RNA, with the transcripts forming the catalytic core that enables peptide bond formation

this is why the ribosome is a ribonucleic acid enzyme (ribozyme).