Sub-topic Checklist: at the end of this topic you should be able to:
- Outline how initiation of translation takes place.
- State the name and function of the tRNA binding sites on ribosomes.
- Describe the repeated cycle of events that occur during synthesis of the polypeptide chain.
- Outline how the disassembly of the translation components leads to termination of the process.
- Use molecular visualisation software to analyse the structure of eukaryotic ribosomes and a tRNA molecule.
- Explain how tRNA-activating enzymes illustrate enzyme–substrate specificity.
- Explain the role of phosphorylation in binding of amino acids to tRNA molecules.
- Outline that free ribosomes synthesise proteins for use primarily within the cell.
- Outline that bound ribosomes synthesise proteins primarily for secretion or for use in lysosomes.
- Outline that translation can occur immediately after transcription in prokaryotes, due to the absence of a nuclear membrane.
- Identify polysomes in electron micrographs of prokaryotes and eukaryotes.
- Outline that the sequence and number of amino acids in the polypeptide is the primary structure.
- Outline that the secondary structure is the formation of alpha helices and beta pleated sheets, stabilised by hydrogen bonding.
- Outline that the tertiary structure is the further folding of the polypeptide, stabilised by interactions between R groups.
- Outline that the quaternary structure exists in proteins with more than one polypeptide chain.
Lesson one: Translation
Objectives: know the three steps of translation and how they are triggered. describe how the primary, secondary, tertiary and quaternary structure of proteins is derived.
- translation: the synthesis of a polypeptide, based on the sequence of codons on an mRNA sequence
- tRNA: a ‘clover shaped’ piece of RNA that brings a specific amino acid to a ribosome
- mRNA: a single stranded RNA copy of the sense strand of DNA
- aminoacyl-tRNA-synthetase: an enzyme which activates a tRNA molecule (attaches an amino acid)
- ribosome: an organelle which is the site of translation and therefore protein synthesis
- P and A sites on a ribosome: The spaces occupied by two tRNA molecules. The amino acid from the tRNA molecule is transferred from the tRNA at the P site, to the growing chain at the A site.
The three steps of translation
The three steps of translation are:
1)Initiation. Initiation of translation comes as a response to a ‘start codon’, which is often AUG (memory trigger, schools begin in August). The amino acid met (methionine) binds to the start codon to begin translation.
2) Elongation. The growing chain of amino acids joined together by polypeptides forms. As we will see later, often a protein is formed of more than one polypeptide chain.
3) Termination. Translation ends as a response to a ‘stop codon’ which may be UUA (memory trigger, OOhAAh think I’ll stop now). It may also be UGA, UAG
Activation of the tRNA:
This simply means attaching a specific amino acid to a tRNA molecule. This requires ATP, and an enzyme called amino acyl-tRNA-synthetase (may not have to remember it but should be familiar)
The binding sitre for mRNA is on the small ribosome sub-unit.
The binding sites for tRNA:
The sites are on the small sub-unit of the ribosome. There are three positions in the binding site:
- A site – aminoacyl-tRNA-transferase site (memory trigger Arrival). This is the first position occupited
- P site – peptide site. This is the position of the growing polypeptide chain
- E site – exit site. This position is occupied by the tRNA molecule that is leaving, having contributed an amino acid to the growing amino acid chain.
Each tRNA molecule occupies the A, P, E site sequentially. Watch this video to understand how it works:
The complex structure of a protein
Describing the structure of such subtlety complex molecules of proteins presents a challenge. Look at haemoglobin for example, a transport protein that binds to four molecules of oxygen. Red blood cells (erythrocytes), contain 250 million molecules of haemoglobin (so how much oxygen?).
It is composed of four different polypeptide chains, all folded tightly on themselves, and compacted together to produce a ‘globular shape’. This dense shape, and the presence of polar groups on the outside of the molecule, account for the solubility of haemoglobin.
How could you describe the structure of haemoglobin in a systematic way?
1. Primary structure: Primary structure deals with the basic amino acid sequence.
2. Secondary structure: A polypeptide chain once formed, may adopt two forms:
- It can spiral, forming a helix, this is called an alpha helix.
- Or it can fold on itself at regular intervals, this is called a B-pleated sheet.
3. Tertiary structure: The polypeptide chain can fold on itself, forming specific bonds to hold this new configuration.
Bonds: include so called sulphur bridges, which are covalent bonds formed between sulphur molecules. This makes amino acids that contain sulphur, e.g.. methionine, important for tertiary structure.
4. Quarternary structure: More than one polypeptide chain can be involved. In haemoglobin, four polypeptide chains are involved, 2 alpha chains, and 2 beta chains.
Q) What is the difference between the alpha and beta chains?
New feature: Example questions with mark scheme:
Draw molecular diagrams to show the condensation reaction between two amino acids to form a dipeptide.
a. each amino acid with a COO–/COOH group at one end AND a NH2/NH3+ at the other
mp a requires the double bond to be shown between the C and O.
b. CH in middle with H or R group attached
c. peptide bond correctly drawn between N and C=0
d. COO–/COOH group at one end of dipeptide AND NH2/NH3+ at other end
e. loss of water
a. A, P and E binding sites are on the large subunit of the ribosome
b. initiation of translation starts with binding of met-tRNA to the start codon
c. large sub-unit binds with «start» tRNA in the P site
d. A binding site holds the tRNA with the next amino acid to be added
e. peptide bond is formed between the amino acids of the A site and the polypeptide at the P site
f. polypeptide is transferred to the tRNA in the A site
g. the tRNA «with polypeptide» in A site then moves to P site
P binding site holds the tRNA attached to the growing polypeptide
h. E binding site «exit» is where the tRNA «from P site without amino acid» leaves the ribosome
Accept annotated diagrams of the sites.