Unit 4: Amino Acids and Proteins
Table of Contents
Amino Acids: Structure and Properties
Amino acids are the monomers (building blocks) of proteins. There are 20 standard amino acids used to build proteins in humans.
General Structure
Every amino acid has a central alpha-carbon (α-carbon) bonded to four different groups:
- A Hydrogen Atom (H)
- An Amino Group (-NH2), which is basic.
- A Carboxyl Group (-COOH), which is acidic.
- A Side Chain (R-group), which is different for every amino acid and determines its properties.
Chemical Properties
- Zwitterions: At neutral pH (pH 7.4), the amino group is protonated (NH3+) and the carboxyl group is deprotonated (COO-). This doubly-charged ion is called a zwitterion.
- Amphoteric: Because they have both an acidic and a basic group, they can act as either an acid (donate H+) or a base (accept H+). This makes them excellent buffers.
Classification
Amino acids are classified based on the properties of their R-group.
| Class | Property of R-group | Examples |
|---|---|---|
| Nonpolar, Aliphatic | Hydrocarbon chains (hydrophobic) | Glycine, Alanine, Valine, Leucine, Isoleucine |
| Polar, Uncharged | Contains an -OH or -SH group (hydrophilic) | Serine, Threonine, Cysteine, Glutamine |
| Aromatic | Contains a ring structure (mostly hydrophobic) | Phenylalanine, Tyrosine, Tryptophan |
| Acidic (Negatively Charged) | Contains a second -COOH group (hydrophilic) | Aspartate (Aspartic Acid), Glutamate (Glutamic Acid) |
| Basic (Positively Charged) | Contains a second amino group (hydrophilic) | Lysine, Arginine, Histidine |
Exam Tip: You must know the essential amino acids. These are the ones the human body cannot synthesize and must be obtained from the diet.
Mnemonic: PVT TIM HALL (Phenylalanine, Valine, Threonine, Tryptophan, Isoleucine, Methionine, Histidine, Arginine*, Leucine, Lysine). *Arginine is semi-essential.
Mnemonic: PVT TIM HALL (Phenylalanine, Valine, Threonine, Tryptophan, Isoleucine, Methionine, Histidine, Arginine*, Leucine, Lysine). *Arginine is semi-essential.
Proteins: Structure and Function
Proteins are large, complex polymers of amino acids linked together. They perform almost all functions in a cell.
The Peptide Bond
- Formation: Amino acids are linked by a peptide bond.
- Reaction: This is a dehydration (condensation) reaction where the carboxyl group (-COOH) of one amino acid reacts with the amino group (-NH2) of the next, releasing a molecule of water (H2O).
- Chain: A chain of amino acids is called a polypeptide.
Levels of Protein Structure
A protein's function depends on its unique 3D shape, which is described in four levels:
- Primary (1°) Structure:
- Definition: The unique sequence (order) of amino acids in the polypeptide chain.
- Example: ...-Ala-Gly-Leu-Val-...
- Stabilized by: Peptide bonds (strong covalent bonds).
- Secondary (2°) Structure:
- Definition: Local, repeating folding patterns of the polypeptide backbone.
- Examples: The α-helix (a coil) and the β-pleated sheet (folded strands).
- Stabilized by: Hydrogen bonds between the C=O and N-H groups of the backbone (not the R-groups).
- Tertiary (3°) Structure:
- Definition: The overall 3D folding of a single polypeptide chain, bringing distant R-groups together.
- This is the final, functional shape for many proteins.
- Quaternary (4°) Structure:
- Definition: The assembly of two or more separate polypeptide chains (subunits) to form a larger, functional protein complex.
- Example: Hemoglobin is made of four subunits (two alpha, two beta).
Stabilizing Bonds in Protein Structure
The Tertiary (and Quaternary) structures are stabilized by several types of interactions, all involving the R-groups:
- Hydrogen Bonds: Between polar R-groups.
- Hydrophobic Interactions: Nonpolar R-groups cluster together in the protein's core, away from water.
- Ionic Bonds (Salt Bridges): Between acidic (-) and basic (+) R-groups.
- Disulfide Bridges: A strong covalent bond (S-S) that forms between the R-groups of two Cysteine amino acids.
Carbohydrates
Carbohydrates are biomolecules consisting of carbon, hydrogen, and oxygen, usually with a hydrogen-oxygen ratio of 2:1 (like water, Cn(H2O)n). They are the primary energy source for most organisms.
Structure, Properties, and Function of Monosaccharides
- Definition: The simplest carbohydrates ("simple sugars"). They are the monomers for larger carbohydrates.
- Structure: Can be classified by the number of carbons (e.g., Triose-3C, Pentose-5C, Hexose-6C) or by their functional group (Aldose = aldehyde, Ketose = ketone).
- Glucose: An aldohexose, the main energy fuel for cells.
- Fructose: A ketohexose, found in fruit.
- Galactose: An aldohexose, part of milk sugar.
- Properties: They are sweet, soluble in water, and can form ring structures in solution.
- Function:
- Primary energy source: Broken down in glycolysis.
- Building blocks: Used to build larger molecules.
Disaccharides and Polysaccharides
- Disaccharides: Two monosaccharides joined by a glycosidic bond.
- Sucrose (Table Sugar) = Glucose + Fructose
- Lactose (Milk Sugar) = Glucose + Galactose
- Maltose (Malt Sugar) = Glucose + Glucose
- Polysaccharides: Long chains (polymers) of monosaccharides.
- Starch: (Storage in Plants) A polymer of glucose.
- Glycogen: (Storage in Animals) A highly branched polymer of glucose, stored in the liver and muscles.
- Cellulose: (Structure in Plants) A polymer of glucose that forms plant cell walls. Humans cannot digest it (fiber).