Proteins
Section: 11. Organic Chemistry | Syllabus: Cambridge AS Level Physics 9702
Introduction to Proteins Proteins Natural polymers formed by condensation polymerization of amino acids. They are also called polyamides or polypeptides because they contain many amide (peptide) linkages.
Proteins are essential biological macromolecules found in all living organisms. They perform a vast array of functions within cells and are critical for life. Key Fact Proteins are the most diverse group of biological molecules.
The human body contains over 100,000 different types of proteins, each with a specific structure and function. Amino Acids - The Monomers of Proteins Amino Acids The monomers that join together to make proteins.
Each amino acid contains an amino group (-NH₂) and a carboxylic acid group (-COOH) attached to the same carbon atom. Diagram Placeholder [DIAGRAM: General structure of an amino acid showing: - Central carbon atom (alpha carbon) - Amino group (-NH₂) on one side - Carboxyl group (-COOH) on another side - Hydrogen atom (-H) - Variable R group (side chain) Label each component and use color coding to highlight functional groups] General Formula All amino acids have the same basic structure: Formula H₂N-CHR-COOH Where R represents the side chain (variable group) that differs between amino acids.
The 20 Natural Amino Acids There are 20 different naturally-occurring amino acids that make up proteins in living organisms. Each has a different R group, which gives it unique properties. Image Placeholder [INTERACTIVE: Click-through gallery of all 20 amino acids showing: - Full structural formula with R group highlighted - 3-letter code (e.g., Gly, Ala, Val) - 1-letter code (e.g., G, A, V) - Properties of R group (polar, non-polar, acidic, basic, neutral) - Example of where this amino acid is commonly found Examples to include: Glycine (simplest - R = H), Alanine (R = CH₃), Valine, Cysteine (contains sulfur), etc.] Amino acids are amphoteric - they can act as both acids and bases because they contain both acidic (-COOH) and basic (-NH₂) groups In solution, amino acids exist as zwitterions (ions with both positive and negative charges) The properties of the R group determine the amino acid's characteristics (e.g., hydrophobic, hydrophilic, charged) Different combinations and sequences of these 20 amino acids create the enormous variety of proteins Formation of Proteins - Condensation Polymerization Peptide Bond (Amide Linkage) The covalent bond that forms between the carboxyl group of one amino acid and the amino group of another amino acid during condensation polymerization.
A molecule of water is eliminated in the process. Diagram Placeholder [ANIMATED DIAGRAM: Formation of peptide bond showing: Step 1: Two amino acids approaching each other Step 2: -OH from COOH group and -H from NH₂ group highlighted Step 3: H₂O molecule being eliminated (shown leaving) Step 4: Formation of C-N bond (peptide/amide linkage -CONH-) Step 5: Resulting dipeptide with peptide bond highlighted in color Include curly arrow mechanisms to show electron movement] The Peptide Linkage The characteristic feature of all proteins is the peptide (amide) linkage: -CO-NH- Important Each time an amino acid is added to a growing protein chain, one molecule of water is released.
This makes protein formation a condensation polymerization reaction, similar to the formation of polyesters and nylon. From Amino Acids to Proteins Dipeptide - formed when 2 amino acids join (1 peptide bond) Tripeptide - formed when 3 amino acids join (2 peptide bonds) Polypeptide - formed when many amino acids join (many peptide bonds) Protein - a polypeptide chain (or multiple chains) with a specific biological function Interactive Placeholder [INTERACTIVE: Build-a-Protein tool where students: - Select amino acids from a dropdown menu - Click "Add" to join them via peptide bond formation - See water molecule being eliminated with each addition - View the growing polypeptide chain - Identify all peptide linkages in the final structure - Option to show 2D structure or simplified representation] Protein Structure Proteins have four levels of structural organization, each contributing to their final 3D shape and function.
Structure Level Description Bonds/Forces Involved Primary Structure The sequence of amino acids in the polypeptide chain (determined by DNA) Peptide bonds (strong covalent) Secondary Structure Folding of the chain into regular patterns: - α-helix (spiral shape) - β-pleated sheet (zigzag folds) Hydrogen bonds between C=O and N-H groups Tertiary Structure The overall 3D shape of the entire protein formed by further folding and coiling - Disulfide bridges (S-S covalent bonds between cysteine residues) - Hydrogen bonds - Ionic interactions - Hydrophobic interactions Quaternary Structure Association of two or more polypeptide chains (subunits) to form a functional protein Same as tertiary structure interactions 3D Model Placeholder [INTERACTIVE 3D MODELS: Four separate rotatable models showing: 1.
Primary structure - linear chain wi…
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