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Protein Synthesis and Folding — Notes

Synthesis of Polypeptides and the Ribosome

  • Overview: One amino acid linked to another via dehydration synthesis to form a covalent bond; the small molecule water (H₂O) is released in the process. The key idea is that amino acids are joined to make a polymer called a polypeptide, which can fold into a functional protein.
  • Dehydration reaction and water release:
    • Two amino acids come together, with the carboxyl group (–COOH) of one reacting with the amino group (–NH₂) of the next.
    • The reaction releases water, forming a peptide bond between the carbonyl carbon of the first amino acid and the amide nitrogen of the next.
    • Generic representation:
      ext{Amino acid}1{-}COOH + ext{Amino acid}2{-}NH2 \rightarrow ext{Amino acid}1{-}CO{-}NH{-} ext{Amino acid}2 + \mathrm{H2O}
    • In the cell, this process occurs inside the ribosome, described as a giant enzyme complex around the growing polypeptide.
  • Role of ribosome and tRNA:
    • The ribosome acts as the molecular machine that catalyzes peptide bond formation.
    • Transfer RNA (tRNA) brings the specific amino acids to the ribosome, matching codons in mRNA to the correct amino acid.
    • The growing chain is attached to the tRNA, and successive amino acids are added one by one to build a polypeptide.
  • Polypeptide vs. protein:
    • A polypeptide is a chain of amino acids linked together.
    • Once the polypeptide folds into a specific three-dimensional shape, it becomes a protein.
  • Backbone vs. side chains:
    • The backbone is the repeating sequence of the amino group, α-carbon, and carboxyl group (–N–Cα–C(=O)–).
    • The side chains (R groups) extend outward from the backbone and determine the protein’s chemical properties.
  • Example of a short sequence (five amino acids) shown in the lecture:
    • Threonine: polar
    • Alanine: nonpolar
    • Aspartic acid: negatively charged
    • Lysine: positively charged
    • The remaining fifth amino acid is not named in the transcript excerpt.
  • Why polarity matters:
    • Polar amino acids tend to be hydrophilic and interact with water; they are generally found on the outside in an aqueous environment.
    • Nonpolar amino acids are hydrophobic and tend to hide inside the protein core away from water.
    • Charged amino acids (like aspartic acid and lysine) participate in ionic interactions, potentially attracting one another and stabilizing structure.
  • Visualizing the polypeptide backbone and R groups:
    • The backbone (the repeating parts) is uniform across the chain.
    • The R groups (the side chains) hang off the bottom and are responsible for the diversity of amino acids and the protein’s properties.
  • Typical protein size:
    • Proteins usually contain thousands of amino acids in a single polypeptide chain.
    • An example mentioned is hemoglobin, a well-known blood protein consisting of multiple subunits.
  • Summary takeaway:
    • A polypeptide is the sequence of amino acids; once folded into a particular three-dimensional shape, it becomes a functional protein.

Four Levels of Protein Structure (Overview)

  • Primary structure
    • Definition: The linear order of amino acids in the polypeptide chain.
    • This order determines all higher-level structure and ultimately function.
  • Secondary structure
    • Includes alpha helices and beta pleated sheets.
    • Alpha helix: a right-handed coil stabilized mainly by hydrogen bonds along the backbone.
    • Beta pleated sheet: consists of beta strands running side by side with hydrogen bonds between adjacent strands.
    • Hydrogen bonds in secondary structure are primarily between the carbonyl oxygen (C=O) of one peptide bond and the amide hydrogen (N–H) of another in a neighboring segment:
      ext{C}=O \cdots \text{H}-N
  • Tertiary structure
    • The three-dimensional folding of a single polypeptide chain.
    • Driven by interactions among R groups: hydrophobic cores, hydrophilic surfaces, ionic bonds (positive–negative), disulfide bonds, etc.
    • Examples of stabilizing features:
    • Hydrophobic residues often cluster inside; polar/hydrophilic residues on the outside interact with the aqueous environment.
    • Possible disulfide bonds (–S–S–) between cysteine residues.
  • Quaternary structure
    • Arises when two or more polypeptide chains assemble into a functional protein complex.
    • Hemoglobin is given as an example: a protein made of multiple subunits (often described as two alpha and two beta subunits in adults) forming a tetramer.
  • Key concept:
    • Proteins are not just a random collection of amino acids; their concrete three-dimensional shapes determine their functions.

Visual and Functional Details: 3D Folding and Structure-Function Relationship

  • Backbone and side chains in space:
    • The polypeptide backbone forms the scaffold (the same in all amino acids).
    • The R groups extend outward and drive folding and interactions.
  • Alpha helix details
    • Helix shape is stabilized by hydrogen bonds between the backbone carbonyl and amide groups at regular intervals along the chain.
    • The helix is a recognizable secondary structure feature with a distinctive coil.
  • Beta pleated sheet details
    • Composed of β-strands aligned side by side.
    • Hydrogen bonds form between carbonyl oxygens and amide hydrogens of adjacent strands, stabilizing the sheet.
    • Side chains alternate above and below the plane of the sheet, influencing folding tendencies and core packing.
  • Hydrophobic vs. hydrophilic distribution in tertiary structure
    • Hydrophobic R groups tend to hide in the interior to avoid water.
    • Hydrophilic or charged R groups tend to orient toward the exterior to interact with water or form ionic/stable interactions.
  • Denaturation and its consequences
    • Denaturation: disruption of the three-dimensional structure (caused by heat, changes in pH, or other conditions).
    • Denatured proteins lose their native function because structure governs activity.

Fold It: Protein Folding as a Puzzle

  • Fold It (Foldit) is a game introduced to explore protein folding principles.
    • Players are given a simple polypeptide with an R group, and the goal is to arrange the folding so that the side chains (R groups) are in favorable positions (happy state).
    • Levels: Level 1 already cleared; Level 2 is a more complex puzzle; supports Mac, Linux, and Windows.
  • How it works in the talk:
    • The demonstration shows moving and rearranging R groups to achieve stable conformations; the goal is to satisfy the folds analogous to natural protein folding constraints.
  • Real-world significance and outcomes
    • Foldit players have contributed to actual scientific discovery by solving protein-folding problems that can guide biology and drug design.
    • Notably, Foldit-related efforts helped researchers decode the shape of a crucial enzyme involved in HIV infection.
    • This success story has been highlighted in the media and raised the possibility that human players could contribute to Nobel Prize–level insights in the future.
    • The idea: humans may outperform computers at certain protein-folding tasks because humans can perceive global structure and constraints more intuitively in some cases.

Connections to Core Principles and Real-World Relevance

  • Life uses this process in cells:
    • Amino acids are brought in by tRNAs and assembled by ribosomes into polypeptides, which then fold into proteins with specific functions.
    • The sequence of amino acids (primary structure) and the arrangement of R groups determine the protein’s final three-dimensional shape and function.
  • Structure informs function:
    • The ability of a protein to carry out a given task depends on its precise structure; changing conditions can disrupt function through denaturation.
  • Examples in biology:
    • Hemoglobin as an example of a protein with quaternary structure.
    • The general principle that many proteins adopt specific shapes to interact with other molecules, enzymes, receptors, or structural roles.

Quick Reference: Key Terms and Concepts

  • Dehydration synthesis: removal of water to form a peptide bond between amino acids.
  • Peptide bond: covalent bond linking the carboxyl carbon of one amino acid to the amino nitrogen of the next.
  • Polypeptide: a polymer chain of amino acids; becomes a protein when folded into a functional form.
  • Backbone: repeating sequence of –N–Cα–C(=O)– in the polypeptide chain.
  • R group (side chain): the variable group attached to the α-carbon that determines amino acid properties.
  • Primary structure: linear sequence of amino acids.
  • Secondary structure: local folding patterns (alpha helices and beta pleated sheets).
  • Tertiary structure: overall three-dimensional shape of a single polypeptide chain.
  • Quaternary structure: arrangement of multiple polypeptide chains into a functional protein.
  • Denaturation: loss of structure and function due to disruption of bonds or interactions.
  • Foldit/Fold It: interactive protein-folding game used to study and solve folding problems.
  • Hemoglobin: protein example with multiple subunits (quaternary structure) involved in oxygen transport in the blood.

Important Equations and Notation

  • Dehydration synthesis (peptide bond formation):
    ext{Amino acid}1{-}COOH + ext{Amino acid}2{-}NH2 ightarrow ext{Amino acid}1{-}CO{-}NH{-} ext{Amino acid}2 + ext{H}2 ext{O}
  • Hydrogen bonding in secondary structure (illustrative):
    ext{C=O} \cdots \text{H-N}
  • Water in the reaction is represented as: ext{H}_2 ext{O}