Protein synthesis

From Nucleic Acids to Proteins

Lecture Information

  • Lecture presented by Dr. Susanna Cogo, University of Reading.

  • Email: s.cogo@reading.ac.uk

Intended Learning Outcomes (ILOs)

  • At the end of this lecture you will be able to:

    • Discuss the structure and functions of proteins.

    • Explain the genetic code.

    • Describe the structure and function of transfer RNA (tRNA) and ribosomal RNA (rRNA).

    • Outline the main steps of translation.

Overview of Translation

Process of Translation

  • Translation is the process by which a protein is synthesized from the information contained in a molecule of messenger RNA (mRNA).

Functions of Proteins

  • Proteins serve various functions, illustrated as follows:

    • Enzymatic: Catalyze biochemical reactions.

    • Example: Lactase enzyme breaking down lactose into glucose and galactose.

    • Regulatory: Involved in gene expression, such as proteins that act as repressor or activator in transcription.

    • Structural: Provide structural support, such as collagen molecules forming collagen fibers.

    • Transport: Facilitate the movement of ions and molecules across cell membranes, for example through active transport proteins.

Amino Acids: The Building Blocks of Proteins

Basics of Amino Acids

  • Amino acids (aa) are the monomers of proteins. The general structure consists of:

    • Carboxyl group: COOH.

    • Amine group: NH2.

    • Variable group (R): Determines the properties of the amino acid.

Classification of Amino Acids

1. Amino Acids with Electrically Charged Side Chains:

  • Negative: Aspartic acid (Asp), Glutamic acid (Glu).

  • Positive: Arginine (Arg), Histidine (His), Lysine (Lys).

2. Amino Acids with Polar Uncharged Side Chains:

  • Asparagine (Asn), Serine (Ser), Threonine (Thr), Glutamine (Gln), Cysteine (Cys), Proline (Pro).

3. Amino Acids with Hydrophobic Side Chains:

  • Alanine (Ala), Valine (Val), Leucine (Leu), Isoleucine (Ile), Methionine (Met), Phenylalanine (Phe), Tyrosine (Tyr), Tryptophan (Trp).

Essential vs Non-Essential Amino Acids

  • Non-essential amino acids: can be synthesized by the body (e.g., Alanine, Serine, Proline).

  • Essential amino acids: must be obtained from the diet (e.g., Isoleucine, Methionine, Phenylalanine).

Structure of Proteins

Peptide Bonds

  • Polypeptide chains are formed via peptide bonds, linking amino acids together.

  • The sequence of amino acids in a protein represents its primary structure.

Protein Folding and Structure

  • Secondary Structure: Interaction with neighboring amino acids leads to folded structures such as alpha-helices and beta-pleated sheets.

  • Tertiary Structure: Interaction of secondary structures leads to the overall 3D conformation.

  • Quaternary Structure: Association of multiple polypeptide chains, potentially forming functional units called domains.

The Genetic Code

Codons

  • The basic unit of the genetic code is called a codon, with each codon comprised of three nucleotides (Triplets)

  • Established by Crick and colleagues in 1961, this triplet code outlines the relationship between nucleotides and amino acids.

Breaking the Genetic Code

  • Total Codons: 64 possible codons are identified:

    • 3 Stop Codons: UAA, UAG, UGA.

    • 61 Sense(normal) Codons: Each coding for specific amino acids.

  • The genetic code is described as:

    • Degenerate: More than one codon may specify a particular amino acid.

    • Not Ambiguous: No codon specifies more than one amino acid.

  • Reading Frame: Codons must be read sequentially without overlap, starting from a designated initiation codon (AUG).

Universality of the Genetic Code

  • The genetic code is nearly universal across organisms

  • Genes cna be transcribed and translated after being transferred from one species to another

Classes of RNA in Protein Synthesis

Types of RNA

  • Three main classes involved in translating genetic information:

    • Messenger RNA (mRNA): Carries genetic information from the nucleus to the ribosome.

    • Ribosomal RNA (rRNA): Component of ribosomes, facilitating protein synthesis.

    • Transfer RNA (tRNA): Links amino acids to codons on the mRNA during translation.

Transfer RNAs (tRNA)

Function and Structure

  • tRNA functions as the bridge between the genetic code and the amino acids in proteins.

  • Each tRNA carries a specific amino acid and binds to the correct codon on the mRNA through its anticodon.

  • Structural Features:

    • 74-95 nucleotides long, with a shared CCA sequence at 3' end.

    • Anticodon loop contains a three-base sequence complementary to the mRNA codon.

    • D-loop and T-arm assist enzyme recognition and ribosome binding.

Ribosomal RNA (rRNA)

Composition and Function

  • Ribosomes consist of over 50 RNA molecules and proteins, acting as the site for translation.

  • Abundant in cells (>20,000 ribosomes/cell), comprising 80% of the total RNA.

  • rRNA is categorized based on size (measured in Svedberg units).

Eukaryotic Ribosomal RNA Genes

  • Multiple copies of rRNA genes are clustered, coding for:

    • Large rRNA (28S, 18S, 5.8S)

    • Small rRNA (5S)

The Stages of Translation

When and Where Translation Occurs

  • What: mRNA is translated into proteins.

  • When: Translation occurs after mRNA is transported from the nucleus to the cytoplasm.

  • Where: Ribosomes, starting near the 5' end of mRNA.

Stages of Translation

  1. tRNA Charging: Binding of tRNAs to their corresponding amino acids.

  2. Initiation: Assembly of all necessary components at the ribosome.

  3. Elongation: Addition of amino acids to the growing polypeptide chain.

  4. Termination: Completion of protein synthesis at stop codons.

tRNA Charging

  • The CCA sequence is present in all tRNAs, with amino acids attached to the 3' end.

  • Specificity determined by aminoacyl-tRNA synthetases based on nucleotide sequences and properties of amino acids.

  • recognition of tRNA by the aminoacyl-tRNA synthesis is mediated by the nucleotide sequence

  • Recognition of amino acid by the aminoacyl-tRNAsynthesis is mediated by size, charge and R groups

  • Aminoacyl-tRNA synthesis (or aminoacylation) is the process of attaching an amino acid to its correct tRNA.

Initiation of Translation

  1. Binding of Components: mRNA, ribosomal subunits, initiation factors, and initiator tRNA.

  2. Pre-initiation Complex (43S): Recognizes the 5' cap on mRNA and scans for AUG codon.

  3. Kozak Sequence: Surrounding sequence that aids in recognizing the initiation codon.

Elongation of the Polypeptide Chain

  • Involves binding of charged tRNA to A site, formation of peptide bonds mediated by rRNA, and movement of ribosome (translocation).

Termination of Translation

  • Occurs upon reaching a stop codon, with no corresponding tRNA, and facilitated by release factors.

Implications of Translation Defects

  • Protein synthesis errors can lead to diseases, including Diphtheria, caused by toxins that disrupt translation processes.

Research References on Diseases Related to Translation

  1. Scheper et al., "Translation matters: protein synthesis defects in inherited disease", Nature Reviews Genetics, 2007.

  2. Jia et al., "Protein translation: biological processes and therapeutic strategies for human diseases", Signal Transduction and Targeted Therapy, 2024.

Exceptions to the Central Dogma

  • Examples include prion diseases and mechanisms that subvert typical genetic information flow, highlighting unique biological phenomena.

Suggested Further Reading

  • Chapters 4-7 from course materials provide context on DNA, replication, gene expression, and protein translation.