Chapter 9: The Molecular Biology of Translation – Study Notes

Polypeptides and Amino Acids

Polypeptides Are Composed of Amino Acid Chains Assembled at Ribosomes

Polypeptides are linear chains of amino acids that are synthesized by ribosomes during the process of translation. The unique properties of each amino acid contribute to the structure and function of proteins.

• Twenty different amino acids serve as the building blocks of polypeptides.

• Covalent peptide bonds form between the carboxyl group of one amino acid and the amino group of the next, creating a polypeptide chain.

• The distinctive R-groups of amino acids allow them to participate in specific chemical reactions and determine whether they are hydrophobic or hydrophilic.

Amino Acid Structure

All amino acids share a common structure but differ in their side chains (R-groups), which determine their chemical properties.

• Each amino acid contains a central (α) carbon, an amino group (–NH2), and a carboxyl group (–COOH).

• The ribosome catalyzes the formation of a peptide bond between the carboxyl group of one amino acid and the amino group of the next.

• The R-group is unique for each amino acid and can be nonpolar, polar, or electrically charged.

Figure: Amino Acids and Peptide Bond Formation

Peptide bond formation involves the removal of a water molecule (dehydration synthesis) as the bond forms between amino acids.

Amino Acids Grouped by Side Chain Properties

Amino acids are classified based on the properties of their side chains at physiological pH (7.0).

Type	Amino Acids	Properties
Nonpolar side chains	Alanine (Ala), Cysteine (Cys), Glycine (Gly), Isoleucine (Ile), Leucine (Leu), Methionine (Met), Phenylalanine (Phe), Proline (Pro), Tryptophan (Trp), Valine (Val)	No charged or electronegative atoms; hydrophobic
Polar side chains	Asparagine (Asn), Glutamine (Gln), Serine (Ser), Threonine (Thr), Tyrosine (Tyr)	Partial charges; can form hydrogen bonds
Basic side chains	Arginine (Arg), Histidine (His), Lysine (Lys)	Positively charged; can form ionic bonds
Acidic side chains	Aspartate (Asp), Glutamate (Glu)	Negatively charged; can form ionic bonds

Polypeptide and Transcript Structure

Polypeptide Synthesis and Ribosome Function

Polypeptides are synthesized by ribosomes, which are complex molecular machines composed of ribosomal RNA (rRNA) and proteins.

• Ribosomes translate mRNA in the 5'-to-3' direction, reading each triplet codon and assembling amino acids in the specified order.

• The mRNA sequence determines the amino acid sequence of the resulting polypeptide.

• Translation boundaries are defined by a start codon (N-terminus) and a stop codon (C-terminus).

• The 5' untranslated region (5' UTR) and 3' UTR are segments of mRNA outside the translated region.

Levels of Polypeptide Structure

Level	Description	Stabilized by	Example
Primary	Sequence of amino acids	Peptide bonds	Hemoglobin α-chain
Secondary	Formation of α-helices and β-pleated sheets	Hydrogen bonding	One α-helix of hemoglobin
Tertiary	Three-dimensional shape of a polypeptide	Bonds and interactions between R-groups	One hemoglobin subunit
Quaternary	Shape produced by combinations of polypeptides	Bonds and other interactions between polypeptides	Hemoglobin (four subunits)

Ribosome Structure and Function

Tasks of Ribosomes

• Bind mRNA and identify the start codon.

• Facilitate complementary base pairing between mRNA codons and tRNA anticodons.

• Catalyze peptide bond formation between amino acids.

Important Ribosomal Sites

• P site (peptidyl site): Holds the tRNA with the growing polypeptide chain.

• A site (aminoacyl site): Binds new tRNA carrying the next amino acid.

• E site (exit site): Provides an exit for tRNA after its amino acid is added.

• The large subunit contains a channel for the emerging polypeptide chain.

Ribosomes in Different Domains

• Bacterial ribosomes: 70S (50S large + 30S small subunits)

• Eukaryotic ribosomes: 80S (60S large + 40S small subunits)

• Archaeal ribosomes: Similar rRNA to bacteria, but protein composition differs

Three-Dimensional Structure

• Ribosomes are ~25 nm in diameter.

• Cryo-electron microscopy is used to visualize ribosome structure in detail.

Phases of Translation

Overview

Translation occurs in three main phases: initiation, elongation, and termination. While the overall process is conserved, there are differences between bacteria, archaea, and eukaryotes, especially in initiation.

Initiation

• The small ribosomal subunit binds near the 5' end of mRNA and identifies the start codon.

• The initiator tRNA, carrying the first amino acid, binds to the start codon.

• The large subunit joins to form the complete ribosome.

• Initiation factors and GTP are required for proper assembly.

• tRNAs carrying amino acids are called charged tRNAs; those without are uncharged.

Bacterial Initiation

• The Shine-Dalgarno sequence in mRNA base pairs with the 16S rRNA to position the ribosome.

• The initiator tRNA carries N-formylmethionine (fMet).

• Formation of the 30S initiation complex is followed by joining of the 50S subunit to form the 70S initiation complex.

Eukaryotic Initiation

• The 40S subunit binds initiation factors (eIF1, eIF1A, eIF3) to form the preinitiation complex.

• The Kozak sequence (5'-ACCAUGG-3') helps identify the correct start codon (AUG).

• The 60S subunit joins, completing the 80S ribosome.

Archaeal Initiation

• Archaeal initiation is more similar to eukaryotes than bacteria.

• Methionine is the first amino acid, and some mRNAs have Shine-Dalgarno sequences.

Additional info:

Further details on elongation, termination, and the genetic code are covered in subsequent slides and text, including the roles of elongation factors, release factors, and the universality of the genetic code.