Protein synthesis

What is translation in the context of protein synthesis?

The biological process where a protein is synthesised from the information contained in a messenger RNA (mRNA) molecule.

What type of functional role do transcription factors play as proteins?

Regulatory function

What type of functional protein is ATP synthase classified as?

Transport protein

Keratin and cellulose are examples of proteins fulfilling which functional category?

Structural function

What are the monomeric building blocks of proteins?

Amino acids

Which five chemical components form the core structure of every amino acid?

A central carbon atom covalently bonded to: an amino group (−NH2​), a carboxyl group (−COOH), a hydrogen atom (−H), and a variable R group (side chain).

Which part of an amino acid dictates its specific size, shape, charge, and polarity?

The R group (side chain)

How do non-essential amino acids differ from essential amino acids in human nutrition?

Non-essential amino acids can be synthesised by the body, whereas essential amino acids cannot be synthesised and must be obtained through the diet.

What specific covalent bond links amino acids together in a polypeptide chain?

Peptide bond

What defines the primary structure of a protein?

The specific linear sequence of amino acids in the polypeptide chain.

What type of chemical bonding causes a polypeptide backbone to fold into secondary structures like alpha helices or beta pleated sheets?

Hydrogen bonding along the peptide backbone.

What drives the three-dimensional tertiary folding pattern of a protein?

Interactions and reactions between the amino acid R groups (side chains).

What constitutes the quaternary structure of a protein?

The overall protein structure formed when it consists of more than one amino acid chain.

In protein structural biology, what is a discrete domain?

A self-contained functional unit within a protein molecule.

What is the basic unit of the genetic code?

A codon, which consists of a sequence of three nucleotides.

Of the 64 total possible codons in the genetic code, how many are sense codons and how many are stop codons?

61 sense codons and 3 stop (termination) codons.

What is meant by the statement that the genetic code is 'degenerate'?

More than one distinct codon may specify the exact same amino acid.

What is meant by the statement that the genetic code is 'not ambiguous'?

No single codon can ever specify more than one amino acid.

Why must mRNA codons be read in the correct reading frame during translation?

Reading in an incorrect frame shifts triplet groupings, resulting in the production of an incorrect or non-functional polypeptide.

What evolutionary feature of the genetic code allows genes from one species to be transcribed and translated when transferred into another species?

The genetic code is almost universal across all organisms, from simple bacteria to complex animals.

What primary adapter function does transfer RNA (tRNA) serve in translation?

It acts as the physical link between the genetic code on mRNA and amino acids by transporting a specific amino acid to the ribosome.

How many distinct amino acid species can a single individual tRNA molecule bind?

Only one specific amino acid.

How do modified nitrogenous bases beyond the 4 classical RNA bases arise in mature tRNA?

They are produced post-transcriptionally by specialised tRNA-modifying enzymes.

What is the structural function of the anticodon loop in tRNA?

It contains a three-base sequence that is complementary to a specific codon on the mRNA strand.

What biological roles do the D-loop and T-arm serve in tRNA function?

They enable enzymatic recognition by aminoacyl-tRNA synthetases and mediate tRNA binding to the ribosome.

What proportion of total cellular RNA is made up of ribosomal RNA (rRNA)?

Roughly 80% of all RNA inside the cell.

What physical properties determine a macromolecule's Svedberg unit (S) value during centrifugation?

Its molecular weight and its three-dimensional shape.

Why are Svedberg sedimentation units (S) non-additive when ribosomal subunits combine?

Because sedimentation rate depends on both mass and three-dimensional surface shape, which changes when subunits assemble.

Which three eukaryotic rRNAs are produced from the single master strand copied from the large rDNA gene unit?

18S, 5.8S, and 28S rRNA.

How is the eukaryotic 5S rRNA transcribed relative to the large rDNA gene unit?

It is transcribed separately as an independent, single small gene unit.

In which direction is a protein synthesised regarding its chemical ends?

From the amino terminus (N-terminus) to the carboxyl terminus (C-terminus).

What are the four sequential stages of translation?

1. tRNA charging

2. Initiation

3. Elongation

4. Termination

What conserved three-nucleotide sequence is present at the 3' end of all mature tRNA molecules?

CCA

To which exact site on a tRNA molecule is the amino acid attached during tRNA charging?

The carboxyl group of the amino acid binds to the nitrogenous base adenine (A) located at the 3' end of the tRNA.

Which class of enzymes is responsible for matching and attaching the correct amino acid to its corresponding tRNA?

Aminoacyl-tRNA synthetases

How many distinct aminoacyl-tRNA synthetase enzymes exist in a standard cell?

20 distinct enzymes (one for each standard amino acid).

In biochemistry, what is an amino acid residue?

A single amino acid unit that has been incorporated into a protein chain.

What feature of a tRNA molecule mediates recognition by its cognate aminoacyl-tRNA synthetase?

Specific nucleotide sequences and key residues on the tRNA.

What molecular features of an amino acid dictate recognition by its specific aminoacyl-tRNA synthetase?

Size, charge, and the specific chemical structure of its R group.

What chemical bond is formed between an amino acid and a tRNA during the catalytic step of tRNA charging?

A covalent ester bond (driven by energy from ATP hydrolysis).

How do aminoacyl-tRNA synthetases ensure high fidelity and prevent incorrect tRNA charging?

They possess intrinsic proofreading activity to detect and hydrolyse incorrectly attached amino acids.

What six general components are required for translation initiation in eukaryotes?

mRNA, small ribosomal subunit, large ribosomal subunit, eukaryotic initiation factors (eIFs), initiator tRNA (Met-tRNAiMet), and GTP.

Which components combine to form the 43S pre-initiation complex in eukaryotic translation?

The small ribosomal subunit (SSU), initiator tRNA (Met-tRNAiMet), and initiation factors.

How does the initial mRNA binding site in eukaryotic initiation differ from bacterial initiation?

Eukaryotic complexes bind directly to the mRNA 5' cap structure, whereas bacterial complexes recognize an internal sequence called the Shine-Dalgarno sequence.

What consensus sequence surrounds the start codon in eukaryotes to facilitate recognition during scanning?

The Kozak sequence (ACCAUGG)

How many initiation factors are required in prokaryotes versus eukaryotes?

Prokaryotes require 3 initiation factors, whereas eukaryotes require at least 12 initiation factors (eIFs).

Why do initiation factors bind to the small ribosomal subunit before mRNA scanning?

To prevent premature binding of the large ribosomal subunit before the correct start site on the mRNA is identified.

What is the primary role of the Cap-Binding Complex (CBC) during nuclear export and the pioneer round of translation?

It facilitates physical mRNA transport across the nuclear membrane and promotes an initial pioneer round of translation to check for structural errors.

Which standard initiation factor replaces the Cap-Binding Complex (CBC) at the 5' cap after a error-free pioneer round of translation?

eIF-4E

How does template circularisation occur in eukaryotic translation?

The 3' poly-A tail interacts with the 5' cap through regulatory proteins, creating a closed loop that stabilises SSU/mRNA binding.

In mRNA translation, what are uORFs?

Upstream Open Reading Frames: short reading frames in the 5' UTR located upstream of the main AUG start codon that can be translated into peptides.

What are the three distinct tRNA binding sites located within a functional ribosome?

1. Aminoacyl (A) site

2. Peptidyl (P) site

3. Exit (E) site

Which ribosomal site is uniquely occupied by the initiator tRNA at the end of translation initiation?

The peptidyl (P) site

Which helper protein complex delivers incoming charged tRNAs to the ribosomal A site during elongation?

The eEF1A-GTP complex

What biochemical event causes the eEF1A-GDP complex to detach from the tRNA and ribosome after entering the A site?

GTP hydrolysis (cleavage of GTP into GDP).

Which ribosomal location and nucleic acid molecule catalyse peptide bond formation during elongation step 2?

It occurs in the large ribosomal subunit (LSU) and is catalysed by the 28S rRNA.

Which helper protein and energy source drive the physical translocation of the ribosome during elongation step 3?

eEF2 using energy provided by GTP hydrolysis.

In which direction and by what distance does the ribosome shift during translocation?

5' to 3' direction along the mRNA by a distance of exactly one codon.

What path do tRNAs take through the ribosomal sites during elongation?

Charged tRNAs enter at the A site, shift to the P site as the peptide chain grows, move to the E site, and are released uncharged into the cytoplasm

How does the small ribosomal subunit resolve secondary structures in the mRNA strand during elongation?

Via intrinsic helicase activity within the small subunit (SSU) that unwinds mRNA structures.

Why does the ribosomal A site remain empty when a termination (stop) codon is reached?

There are no tRNAs with anticodons complementary to stop codons.

What is the primary function of release factor eRF1 during translation termination?

It directly recognizes and binds to the stop codon exposed in the A site.

What function does release factor eRF3 perform in termination?

It supports the GTP-dependent cleavage of the ester bond holding the completed protein chain to the final tRNA at the P site.