Nucleic Acids - 7.3 Translation (HL (+ some SL))

Question 1

2.7 understandings (5)

Answer 1

1. translation is the synthesis of polypeptides on ribosomes
2. the amino acid sequence of polypeptides is determined by mRNA according to the genetic code
3. Codons of 3 bases on mRNA correspond to one amino acid in a polypeptide
4. Translation depends on complementary base pairing between codons on mRNA and anticodons on tRNA
5. Translation is the process of building a polypeptide chain from amino acids guided by the sequence of codons on the mRNA

Question 2

7.3 understandings (6)

Answer 2

1. Initiation of translation involves assembly of the components that carry out the process
2. Synthesis of the polypeptide involves a repeated cycle of events
3. Disassembly of the components follows termination of translation
4. Free ribosomes synthesise proteins for use primarily within the cell
5. Bound ribosomes synthesise proteins primarily used for secretion or for us in lysosomes
6. Translation can occur immediately after transcription in prokaryotes due to the absence of a nuclear membrane
7. The sequence and number of amino acids in a polypeptide is the primary structure
8. The secondary structure is the formation of alpha helices and beta pleated sheets stabilised by hydrogen bonding
9. The tertiary structure is the further folding of the polypeptide stabilised by interactions between R groups
10. The quaternary structure exists in proteins with more than one polypeptide chain

Question 3

Structures involved in translation (RNA + RNA + A A + R_)

Answer 3

1. Messenger RNA molecules (mRNA)
   - carries the code from the DNA that will be translated into an amino acid sequence
2. Transfer RNA molecules (tRNA)
   - transport amino acids to their correct position on the mRNA strand (each amino acid has a specific tRNA activating enzyme)
3. Amino acids = polypeptides are constructed from
4. Ribosomes = provide the environment for tRNA attachment and amino acid linage
   (Ribosomes are composed of approx 60% ribosomal RNA (rRNA) and 40% protein)

Question 4

More on Transfer RNA molecules (tRNA) (the arms)

Answer 4

1. Carrier end = for binding to the specific amino acid
2. Anticodon site = for binding to the codon of the mRNA
3. Ribosome site = for attaching to the ribosome
4. Enzyme site = for the tRNA activating enzyme

tRNA molecules fold into a cloverleaf structure with four key regions:

The acceptor stem (3’-CCA) carries an amino acid
The anticodon associates with the mRNA codon (via complementary base pairing)
The T arm associates with the ribosome (via the E, P and A binding sites)
The D arm associates with the tRNA activating enzyme (responsible for adding the amino acid to the acceptor stem)

Question 5

Steps in translation (3+)

Answer 5

1. Initiation
2. Elongation
3. Translocaton
4. Termination

Question 6

Steps in translation - INITIATION

Answer 6

the bringing together of mRNA with the start codon (AUG) - a tRNA bearing the start amino acid of a polypeptide (methionine) and ribosomes

The first stage of translation involves the assembly of the three components that carry out the process (mRNA, tRNA, ribosome)

The small ribosomal subunit binds to the 5’-end of the mRNA and moves along it until it reaches the start codon (AUG)
Next, the appropriate tRNA molecule bind to the codon via its anticodon (according to complementary base pairing)
Finally, the large ribosomal subunit aligns itself to the tRNA molecule at the P site and forms a complex with the small subunit

Question 7

Steps in translation - ELONGATION (6 steps)

Answer 7

amino acids are added (one by one) by tRNAs as the ribosome moves along the mRNA

1. tRNA brings the appropriate amino acid up to the ribosome
2. anticodon on the tRNA matches with the codon on the mRNA
3. new amino acid is joined to the polypeptide chain
4. as step 3 happens, the ribosome nudges the mRNA strand along 3 notches and the next tRNA falls into place
5. peptide bond forms between adjacent amino acids
6. tRNA is released

A second tRNA molecule pairs with the next codon in the ribosomal A site
The amino acid in the P site is covalently attached via a peptide bond (condensation reaction) to the amino acid in the A site
The tRNA in the P site is now deacylated (no amino acid), while the tRNA in the A site carries the peptide chain

Question 8

Steps in translation -TERMINATION

Answer 8

ribosome reaches a stop codon = polypeptide chain disconnects from the ribosome

The final stage of translation involves the disassembly of the components and the release of a polypeptide chain

Elongation and translocation continue in a repeating cycle until the ribosome reaches a stop codon
These codons do not recruit a tRNA molecule, but instead recruit a release factor that signals for translation to stop
The polypeptide is released and the ribosome disassembles back into its two independent subunits

Question 9

Ribosomes in translation

Answer 9

FREE ribosomes synthesize proteins for use primarily within the cell

BOUND ribosomes synthesis proteins primarily for secretion or for use in lysosomes

Question 10

Polysomes in translation

Answer 10

= several ribosomes can translate an mRNA at the same time = POLYSOME
The polysomes will appear as beads on a string (each ‘bead’ represents a ribosome ; the ‘string’ is the mRNA strand)
In prokaryotes, the polysomes may form while the mRNA is still being transcribed from the DNA template
Ribosomes located at the 3’-end of the polysome cluster will have longer polypeptide chains that those at the 5’-end

= more than one ribosome can translate an mRNA at one time = possible to produce many polypeptides simultaneously from a single mRNA

Bit extra:
(In eukaryotes, the ribosomes are separated from the genetic material (DNA and RNA) by the nucleus

After transcription, the mRNA must be transported from the nucleus (via nuclear pores) prior to translation by the ribosome
This transport requires modification to the RNA construct (e.g. 5’-methyl capping and 3’-polyadenylation)

Prokaryotes lack compartmentalised structures (like the nucleus) and so transcription and translation need not be separated

Ribosomes may begin translating the mRNA molecule while it is still being transcribed from the DNA template
This is possible because both transcription and translation occur in a 5’ → 3’ direction )

Question 11

7.3 application (tRNA)

Answer 11

“tRNA-activating enzymes illustrate enzyme-substrate specificity and the role of phosphorylation”

each tRNA molecule is recognised by a tRNA-activating enzyme that attaches a specific amino acid to the tRNA ( = requires energy from ATP_

Question 12

Further understandings (4)

Answer 12

1. the sequence and number of amino acids in the polypeptide is the primary structure
2. the secondary structure is the formation of alpha helices and beta pleated sheets stabilized by hydrogen bonding
3. the tertiary structure is the further folding of thepolypeptide stabilized by interactions between R groups
4. The quaternary structure exists in proteins with more than one polypeptide chain

Question 13

ribosomes

Answer 13

Ribosomes are made of protein (for stability) and ribosomal RNA (for catalytic activity)
They consist of a large and small subunit:
The small subunit contains an mRNA binding site
The large subunit contains three tRNA binding sites – an aminoacyl (A) site, a peptidyl (P) site and an exit (E) site
Ribosomes can be found either freely floating in the cytosol or bound to the rough ER (in eukaryotes)
Ribosomes differ in size in prokaryotes and eukaryotes (prokaryotes = 70S ; eukaryotes = 80S)

Question 14

tRNA activation

Answer 14

Each tRNA molecule binds with a specific amino acid in the cytoplasm in a reaction catalysed by a tRNA-activating enzyme

Each amino acid is recognised by a specific enzyme (the enzyme may recognise multiple tRNA molecules due to degeneracy)

The binding of an amino acid to the tRNA acceptor stem occurs as a result of a two-step process:

The enzyme binds ATP to the amino acid to form an amino acid–AMP complex linked by a high energy bond (PP released)
The amino acid is then coupled to tRNA and the AMP is released – the tRNA molecule is now “charged” and ready for use

The function of the ATP (phosphorylation) is to create a high energy bond that is transferred to the tRNA molecule

This stored energy will provide the majority of the energy required for peptide bond formation during translation

Question 15

steps in translation - TRANSLOCATION

Answer 15

The ribosome moves along the mRNA strand by one codon position (in a 5’ → 3’ direction)
The deacylated tRNA moves into the E site and is released, while the tRNA carrying the peptide chain moves to the P site
Another tRNA molecules attaches to the next codon in the now unoccupied A site and the process is repeated

Question 16

Protein Destinations

Answer 16

Understanding:
• Free ribosomes synthesise proteins for use primarily within the cell
• Bound ribosomes synthesise proteins primarily for secretion or for use in lysosomes

All proteins produced by eukaryotic cells are initially synthesised by ribosomes found freely circulating within the cytosol

If the protein is targeted for intracellular use within the cytosol, the ribosome remains free and unattached
If the protein is targeted for secretion, membrane fixation or use in lysosomes, the ribosome becomes bound to the ER

Protein destination is determined by the presence or absence of an initial signal sequence on a nascent polypeptide chain

https://ib.bioninja.com.au/higher-level/topic-7-nucleic-acids/73-translation/protein-destinations.html

Question 17

Protein Structure

Answer 17

Understanding:
• The sequence and number of amino acids in a polypeptide is the primary structure
• The secondary structure is the formation of α-helices and β-pleated sheets stabilised by hydrogen bonding
• The tertiary structure is the further folding of the polypeptide stabilised by interactions between R groups
• The quaternary structure exists in proteins with more than one polypeptide chain

1. Primary (1º) Structure
2. Secondary (2º) Structure
3. Tertiary (3º) Structure
4. Quaternary (4º) Structure

Question 18

Primary (1º) Structure - protein structure

Answer 18

The first level of structural organisation in a protein is the order / sequence of amino acids which comprise the polypeptide chain

The primary structure is formed by covalent peptide bonds between the amine and carboxyl groups of adjacent amino acids

Primary structure controls all subsequent levels of protein organisation because it determines the nature of the interactions between R groups of different amino acids

Question 19

Secondary (2º) Structure - protein structure

Answer 19

The secondary structure is the way a polypeptide folds in a repeating arrangement to form α-helices and β-pleated sheets

This folding is a result of hydrogen bonding between the amine and carboxyl groups of non-adjacent amino acids

Sequences that do not form either an alpha helix or beta-pleated sheet will exist as a random coil

Secondary structure provides the polypeptide chain with a level of mechanical stability (due to the presence of hydrogen bonds)

In pictures, alpha helices are represented as spirals (purple ; left) and beta-pleated sheets as arrows (blue ; right)

Question 20

Tertiary (3º) Structure - protein structure

Answer 20

The tertiary structure is the way the polypeptide chain coils and turns to form a complex molecular shape (i.e. the 3D shape)

It is caused by interactions between R groups; including H-bonds, disulfide bridges, ionic bonds and hydrophobic interactions

Relative amino acid positions are important (e.g. non-polar amino acids usually avoid exposure to aqueous solutions)

Tertiary structure may be important for the function of the protein (e.g. specificity of active site in enzymes)

Question 21

Quaternary (4º) Structure - protein structure

Answer 21

Multiple polypeptides or prosthetic groups may interact to form a single, larger, biologically active protein (quaternary structure)

A prosthetic group is an inorganic compound involved in protein structure or function (e.g. the heme group in haemoglobin)

A protein containing a prosthetic group is called a conjugated protein

Quaternary structures may be held together by a variety of bonds (similar to tertiary structure)