Ribosome structure & function - Week 5

Question 1

what is translation

Answer 1

Translation is the mechanism by which a protein is formed using the information stored in mRNA.

Question 2

what components play a role in translation

Answer 2

Translation is a complex process as it involves the function of many different components, which are:
- mRNA
- Ribosomal RNA (rRNA)
- transfer RNA (tRNA)
- ribosomes
- proteins
- enzymes
All these components play a distinct role during the process

Question 3

what is the outcome of translation

Answer 3

The outcome of translation is the formation of a polypeptide, which is made up of a chain of amino acids, and each amino acid is covalently linked to each other via a peptide bond.

Question 4

what happens after polypeptide is formed

Answer 4

After the polypeptide is formed in the cytosol, it is also subject to further modifications, such as phosphorylation, cleavage, and folding, to form a functional protein.

Question 5

what is an amino acid made up of

Answer 5

The components of a single amino acid is a:
- amine group
- carboxylic group
- side-chain, which is specific to each amino acid (it is indicated as R)

Question 6

why is the R group specific to each amino acid

Answer 6

The side chain (R group) is specific to each amino acid because the R group gives the amino acid a particular chemical property.

Question 7

what groups are the 20 amino acids divided up into

Answer 7

There are 20 different amino acids that are found in different polypeptides.

These 20 amino acids are divided into groups according to the chemical property of the R group.
The different groups that the amino acids are divided into are the:
- non-polar group
- polar group
- electrically charged group

Question 8

what is the chemical property of non-polar and polar amino acids

Answer 8

The non-polar group consists of amino acids like glycine, alanine, etc. They do not associate with water. Thus they are ‘water-fearing’.
The polar group consists of amino acids like serine, threonine, etc. They are able to associate with water. Thus they are ‘water-loving’.

Question 9

where are the polar and non-polar amino acids usually located

Answer 9

Usually, the non-polar amino acids are present in the interior of a folded protein, and the polar amino acids are present on the surface of a protein.

Question 10

what is the function of the R-group

Answer 10

the R group is the side chain of an amino acid which gives a unique chemical property to an amino acid and determines the function of the polypeptide.

Question 11

how is a peptide bond formed

Answer 11

The formation of a peptide bond is an example of a condensation reaction. So 2 different amino acids are linked together with the release of water.
The peptide bond formation is by a link of the carboxyl group of a 1 amino acid and the amino group of another amino acid.

Question 12

which direction is the formation of a polypeptide

Answer 12

The formation of the polypeptide has directionality. The polypeptide chain is formed in the amino-carboxyl direction, which corresponds to the 5’-3’ orientation of the codons in mRNA.

Question 13

where does translation take place

Answer 13

The process of translation occurs at the ribosome.

Question 14

where are ribosomes found

Answer 14

Ribosomes are small organelles:
they are found in the endoplasmic reticulum
- ‘Rough’ part of the rough endoplasmic reticulum is the ribosomes.
or ribosomes exist freely in the cytoplasm

Question 15

what is a ribosome composed of

Answer 15

A ribosome is approximatively composed of 60% of ribosomal RNA (rRNA) and 40% of protein.

Question 16

how many ribosomes are there in a cell

Answer 16

there are millions of ribosomes in each cell

Question 17

what are the 2 subunits in a ribosome and what is their function in translation

Answer 17

A ribosome consists of 2 subunits:
- 1 large subunit
- 1 small subunit

These 2 subunits have different functions during translation. The smaller ribosome subunit reads the mRNA, the larger ribosome subunit is involved in the formation of the peptide bond thus the larger subunit is involved in joining the amino acids together to form a polypeptide chain.

Question 18

what is the difference between eukaryotic and bacterial ribosome

Answer 18

In bacteria, such as E.coli, ribosomes are smaller in comparison to eukaryotic ribosomes.

Question 19

what type of ribosome do the ribosomes in mitochondria and chloroplast resemble

Answer 19

Ribosomes of mitochondria and chloroplasts resemble prokaryotic ribosomes

Question 20

what Sverdberg value is the smaller and larger subunit of bacteria and what does the Svergberg value indicate

Answer 20

In bacteria, the smaller subunit of the ribosome is called the 30S and the larger subunit is called 50S, S stands for Sverdberg value.

Question 21

what is the Sverdberg value of the ribosome in eukaryotes

Answer 21

In eukaryotes, the 2 subunits of ribosomes form an 80S ribosome. The smaller one is a 40S subunit and the larger one is a 60S subunit. S stands for Sverdberg value.

Question 22

what does the Sverdberg value refer to

Answer 22

the Sverdberg value refers to the rate of sedimentation in a centrifuge.
the S value doesn’t indicate the molecular weight of the ribosome but a coefficient of sedimentation, thus the Sverdberg value depends on the size and shape of a ribosome and not on the molecular weight of the ribosome.

Question 23

What S value ribosome is formed in bacteria and eukaryotes

Answer 23

In bacteria, the 2 subunits of ribosomes form a 70S ribosome.

in eukaryotes, the larger subunit consists of 50 ribosomal proteins that associate with 2 different types of ribosomal RNA. Whereas the smaller subunit in eukaryotes consists of 33 ribosomal proteins that associate with 1 type of ribosomal RNA. Together both subunits form an 80S ribosome.

Question 24

what are the 3 important sites in a ribosome

Answer 24

The ribosome contains 3 important sites, which are:
- A-site
- P-site
- E-site

Question 25

what is the function of tRNA in translation

Answer 25

the process of translation involves the participation of tRNA molecules which serve as the carriers for amino acids that need to be assembled to form a protein.

Question 26

how do the 3 sites in the ribosome link with each other and tRNA in translation

Answer 26

essentially, The 3 different sites of the ribosome binds to the tRNA molecule in the process of translation.
In the process of translation, the tRNA attaches at the aminoacyl (A) site, is transferred into the peptidyl (P) site, and then exits by the exit (E) site, generating a polypeptide chain in the process.

Question 27

what is a tRNA and who discovered it

Answer 27

tRNAs consist of a single nucleotide chain of about 80 nucleotides in length. Also, tRNAs are ‘adaptor’ molecules whose existence was predicted by Francis Crick in 1956.

Question 28

what is the function of tRNA

Answer 28

• The function of a tRNA molecule is to bring a specific amino acid to the ribosome.
• tRNA also helps to read the codons of mRNA.

Question 29

what 2 sites does tRNA have and why are they important

Answer 29

The tRNA molecule has 2 distinct sites which are the 5’ end of tRNA which is phosphorylated and the 3’ end has a free -OH group that is important for the attachment of a specific amino acid.

Question 30

other than the normal bases, what bases does tRNA have

Answer 30

Also in addition to the normal bases, the tRNA molecule contains modified bases as well. which are:
- Inosine.
- Pseudouridine
- Dihydrouridine

Question 31

what is a tRNA molecule made up of

Answer 31

tRNA molecules contain:
- three major loops
- four base-paired regions
- an anticodon triplet, which is important because it pairs with a codon within an mRNA.
- a 3’ terminal sequence of CCA (where the appropriate amino acid can be attached by an ester bond).

Question 32

what 3D structure do tRNAs have and why

Answer 32

All tRNAs have a similar L-shaped 3D structure that allows them to fit into the P and A sites of the ribosome.

Question 33

what is aminoacylation and which enzyme carries out aminoacylation

Answer 33

The 3’ end of a tRNA molecule is the site where an amino acid is attached to the tRNA. The chemical reaction that allows the attachment of the amino acid to the tRNA is called aminoacylation.
Aminoacylation is the process of adding an amino acid to the tRNA at the 3’ end. essentially, The carboxyl group of the residue is altered to form an amino acid ester intermediate

Question 34

what is aminoacylation also called

Answer 34

This event, aminoacylation, is also called the charging of tRNA or activation of tRNA.

Question 35

which enzyme carries out aminoacylation and which 3 components is involved in aminoacylation

Answer 35

The chemical reaction is carried out by a specific enzyme that is called Aminoacyl-tRNA Synthetase. The chemical reaction catalysed by this enzyme involves 3 components:
- a tRNA molecule
- an amino acid
- an ATP

Question 36

what is the 2 step reaction that is taken place to join amino acids to tRNAs

Answer 36

Amino acids are joined to tRNAs by the activity of Aminoacyl-tRNA Synthetases, via a two-part reaction. which are:
Step 1 - Formation of an aminoacyl adenylate
Aminoacyl-tRNA synthetase binds ATP and the amino acid and catalyzes the formation of the aminoacyl-AMP that remains associated with the enzyme
Step 2 - Linking of activated amino acid to tRNA at 2’/3’ position of the ribose sugar (terminal adenine of tRNA).
The amino acid is transferred to the appropriate tRNA and bound covalently to either the 2’OH or 3’OH of the invariant 3’ adenosine terminal of the tRNA molecule.
overall, a tRNA with a specific amino acid attached is formed.