Lecture 17 (Gene expression - translation)

Question 1

How does DNA code for proteins?

Answer 1

DNA has the code for a protein which mRNA has to copy and then take that copy out of the nucleus to an other organelle called a ribosome. There the copy is translated into the protein.

Question 2

Codon

Answer 2

A group of 3 bases (triplet) coding for an amino acid

Question 3

Anticodon

Answer 3

An anticodon is a trinucleotide sequence complementary to that of a corresponding codon in a messenger RNA (mRNA) sequence. An anticodon is found at one end of a transfer RNA (tRNA) molecule.

Question 4

Triplet

Answer 4

three nucleotides—called a triplet or codon—codes for one particular amino acid in the protein.

Question 5

Triplet codon hypothesis

Answer 5

The genetic code must be at least triplet based

Question 6

Genetic code

Answer 6

The sequence of bases on DNA codes for the sequence of amino acids in proteins. A group of three bases coding for an amino acid is called a codon, on the mRNA and the meaning of each of the 64 codons is called the genetic code

Question 7

Redundancy of the genetic code

Answer 7

Redundancy in the genetic code means that most amino acids are specified by more than one mRNA codon. When a mutation changes a codon so it codes for the wrong amino acid, the proteins made from that gene may lose their function. However, the redundancy of the genetic code reduces the chance that a mutation in the DNA will change the amino acid it codes for.

Question 8

Number of possible combinations with 4 bases and 20 amino acids

Answer 8

4^3 = 64

Question 9

Key features of the genetic code include…

Answer 9

61 of a possible 64 codons specify as amino acid (3 of them are stop codons which essentially make translation stop

Most amino acids have more than one codon

Three codons specific stop (UAA,UAG,UGA)

One codon specifies start (AUG - this codon also specifies methionine)

Question 10

Start codon(s)?

Answer 10

AUG

Question 11

Stop codon(s)?

Answer 11

UAA
UAG
UGA

Question 12

Reading a codon

Answer 12

Always read the codon as it is in the 5’ to 3’

Question 13

tRNA

Answer 13

Transfer ribonucleic acid (tRNA) is a type of RNA molecule that helps decode a messenger RNA (mRNA) sequence into a protein.

An adaptor molecule of a small RNA molecule which is named tRNA

Single strand of RNA

70-80 nucleotides in length

At least on tRNA for each amino acid

Each tRNA has a region which can bind to an amino acid AND a region which can interact with mRNA

Question 14

tRNA and anticodon

Answer 14

An anticodon is a unit made up of three nucleotides that correspond to the three bases of the codon on the mRNA. Each tRNA contains a distinct anticodon triplet sequence that can form 3 complementary base pairs to one or more codons for an amino acid.

Question 15

Direction of anticodon

Answer 15

The middle loop of tRNA carries a nucleotide triplet called the anticodon, whose job it is to bind with a specific codon in the mRNA by specific RNA-to-RNA base pairing. Since codons in mRNA are read in the 5′ → 3′direction, anticodons are oriented in the 3′ → 5′ direction

Question 16

Steps involved in ‘charging’ a tRNA

Answer 16

Before an amino acid can be incorporated into a growing polypeptide, it must first be attached to a molecule called transfer RNA, or tRNA, in a process known as tRNA charging. The charged tRNA will then carry the activated amino acid to the ribosome.

An enzyme (aminoacyl-tRNA synthetase), recognises both a specific amino acid and the correct tRNA for this amino acid and joins them together. There are 20 different (aminoacyl-tRNA synthetase) enzymes, one for each amino acid. This enzyme has a binding sit for the amino acid as well as a binding site for the tRNA.

Question 17

charged tRNA

Answer 17

tRNA with an amino acid attached to it

Question 18

Translation

Answer 18

Translation is the synthesis of proteins by ribosomes using mRNA as a set of instructions

Ribosomes contain both ribosomal RNA (rRNA) and proteins

Question 19

Anatomy of a ribosome

Answer 19

Large and small subunit - A ribosome is made up of a large subunit and a small subunit. Within the large subunit are three large binding sites (the kind of binding sites for the tRNAs). mRNA is sandwiched between the large and small subunit. The small ribosomal subunit programs protein synthesis; it binds mRNA and mediates the interaction between mRNA codons and tRNA anticodons. The large subunit takes care of production.

E site (exit site) - The E-site is the third and final binding site for t-RNA in the ribosome during translation, a part of protein synthesis. E site which is the exit site of the now uncharged tRNA after it gives its amino acid to the growing peptide chain.

Exit tunnel - This is the escape route for the proteins being built

P site - The P site is where the peptidyl tRNA is formed in the ribosome.

A site - The A site is the point of entry for the aminoacyl tRNA (except for the first aminoacyl tRNA, which enters at the P site).

Question 20

Talk about the sites on ribosomes

Answer 20

The A site is the point of entry for the aminoacyl tRNA (except for the first aminoacyl tRNA, which enters at the P site). The P site is where the peptidyl tRNA is formed in the ribosome. And the E site which is the exit site of the now uncharged tRNA after it gives its amino acid to the growing peptide chain.

Question 21

Ribosome

Answer 21

A complex of ribosomal RNA and protein molecules that functions as a site of protein synthesis in the cytoplasm.

Question 22

Location of ribosomes

Answer 22

Bound to the rER - synthesise proteins that are used within the plasma membrane or are exocytosed from the cell

Free in the cytosol - synthesise proteins that are released into the cytosol and used within the cell

Question 23

Cytosol and cytoplasm

Answer 23

The cytoplasm is made up of the cytosol and insoluble suspended particles. The cytosol refers to anything that is soluble and dissolved in it autos as ions and soluble proteins. The insoluble things could be ribosomes for example

Question 24

Three stages of translation

Answer 24

Initiation
Elongation
Termination

All three stages require energy input

Question 25

Translation - initiation

Answer 25

1 - The small ribosomal subunits finds the initiation AUG codon on the mRNA. The AUG codon is positioned in the P site of the small ribosomal subunit
2- A tRNA ‘charged’ with the amino acid methionine (Met, M) binds to the P site
3- The large ribosomal subunit attaches

In the beginning, everything is disassembled and nothing is linked together. So what happens in imitation is that the small ribosomal subunit flows around and will recognise the G’ cap and will identify the mRNA in that way. It will now latch on to the mRNA and scan along the mRNA until it finds the first AUG codon (start codon) and this is where translation will begin. Three complimentary bases on the tRNA anticodon which are complimentary to the mRNA. The large ribosomal subunit will then join in and the very first tRNA brings MET into the P-site and that is the end of initiation

Question 26

Translation - elongation

Answer 26

1 - A ‘charged’ tRNA, with an anticodon complementary to the A site codon, lands in the A site (it is only the very 1st tRNA that ends up in the P-site as it is how it is assembled and from then on the rest of the tRNAs enter on to the A site
2- Then two things happen at the same time. Firstly, the ribosome will break the bond that binds the amino acid to the tRNA in the P site, transfer the amino acid to the newly arrived amino acid (attached to the tRNA in the A site) and form peptide bond between them (a tRNA with the growing amino acid chain in the A site and an empty/‘uncharged’ tRNA in the P site). Secondly, while the tRNAs are bound to the mRNA (in the P and A sites), the ribosome moves three nucleotides down the mRNA (the tRNA with the growing amino acid cain up in the P site (was in the active site) so that the chain of amino acids can exit through the tunnel located above the P site. ‘Uncharged’ tRNA in the E site (was in the P site))
3- IN the E site, the ‘uncharged’ tRNA detaches from its anticodon and is expelled
4- A new ‘charged’ tRNA with an anticodon complementary to the next A site codon enters the ribosome at the A site and the elongation process repeats itself

Question 27

Translation - termination

Answer 27

When the ribosome reaches a stop codon, a protein (not a tRNA) called release factor enters the A site (this protein releases everything)

The release factor breaks the bond between the P site tRNA (using water) and the final amino acid. This causes the polypeptide chain to detach from its tRNA and the newly made polypeptide is released

The small and large ribosomal subunits dissociate from the mRNA and each other (so that they can be used again)

Question 28

Genotype

Answer 28

Set of genes and/or DNA combinations that are responsible for a particular trait

Determined at a DNA level

Question 29

Phenotype

Answer 29

The physical expression, or characteristics of a genotype i.e. are traits or characteristics of an organism that can be observed

Defined by what happens at a protein level (together with environmental influences)

Question 30

Mendel’s Pea experiment

Answer 30

Illustrated a relationship between genotype and phenotype I.e. what happens at the DNA level is reflected at the protein level, and that genetic variation commonly leads to phenotypic variation

Question 31

Genotypic variation leads to …

Answer 31

Phenotypic variation