Proteins (Biomolecules)

Cheatsheet Content

### Introduction to Proteins - **Definition:** Proteins are complex macromolecules composed of amino acids linked by peptide bonds. They are essential for virtually every process within living organisms. - **Abundance:** Most abundant organic molecules in living systems. - **Functions:** Enzymes, hormones, structural components, transport, immunity, etc. ### Amino Acids: Building Blocks of Proteins - **General Structure:** An amino acid has a central carbon atom (alpha-carbon) bonded to: 1. An amino group (-NH₂) 2. A carboxyl group (-COOH) 3. A hydrogen atom (-H) 4. A variable side chain (R-group) - **Zwitterionic Form:** At physiological pH, amino acids exist as zwitterions, where the amino group is protonated (-NH₃⁺) and the carboxyl group is deprotonated (-COO⁻). - **Classification:** Based on the nature of their R-group: - **Nonpolar/Hydrophobic:** Glycine (Gly), Alanine (Ala), Valine (Val), Leucine (Leu), Isoleucine (Ile), Methionine (Met), Proline (Pro), Phenylalanine (Phe), Tryptophan (Trp). - **Polar/Uncharged:** Serine (Ser), Threonine (Thr), Cysteine (Cys), Asparagine (Asn), Glutamine (Gln), Tyrosine (Tyr). - **Acidic (Negatively charged):** Aspartic acid (Asp), Glutamic acid (Glu). - **Basic (Positively charged):** Lysine (Lys), Arginine (Arg), Histidine (His). - **Essential Amino Acids:** Cannot be synthesized by the body and must be obtained from the diet (e.g., Valine, Leucine, Isoleucine, Lysine, Methionine, Phenylalanine, Threonine, Tryptophan, Histidine). ### Peptide Bond Formation - **Definition:** A covalent bond formed between the carboxyl group of one amino acid and the amino group of another amino acid with the elimination of a water molecule. This is a dehydration reaction. - **Characteristics:** - Rigid and planar. - Has partial double-bond character due to resonance, restricting rotation around the C-N bond. - Uncharged but polar. - **Polypeptide Chain:** A sequence of amino acids linked by peptide bonds. Has an N-terminus (free amino group) and a C-terminus (free carboxyl group). ### Levels of Protein Structure Proteins exhibit four levels of structural organization: #### Primary Structure - **Definition:** The unique linear sequence of amino acids in a polypeptide chain. - **Importance:** Determined by genetic information, it dictates all higher levels of protein structure and function. - **Bonding:** Peptide bonds. #### Secondary Structure - **Definition:** Regular, recurring arrangements of amino acids stabilized by hydrogen bonds between the backbone atoms (not R-groups). - **Types:** - **α-Helix:** Right-handed coiled structure. Hydrogen bonds form between the C=O of one amino acid and the N-H of an amino acid four residues away. - **β-Pleated Sheet:** Polypeptide chains lie side-by-side, connected by hydrogen bonds between backbone atoms. Can be parallel or antiparallel. - **Random Coil/Loops:** Irregular structures that connect α-helices and β-sheets. #### Tertiary Structure - **Definition:** The overall three-dimensional folding of a single polypeptide chain, including all secondary structures and R-group interactions. - **Stabilizing Forces:** - **Hydrophobic interactions:** Nonpolar R-groups cluster in the interior, away from water. - **Ionic bonds:** Attractions between oppositely charged R-groups. - **Hydrogen bonds:** Between polar R-groups. - **Disulfide bonds:** Covalent bonds formed between two cysteine residues (-S-S-), a strong bond. - **Van der Waals forces:** Weak, short-range attractions. - **Importance:** Gives the protein its specific biological function. #### Quaternary Structure - **Definition:** The arrangement of multiple polypeptide chains (subunits) to form a functional protein complex. - **Stabilizing Forces:** Same as tertiary structure (hydrophobic interactions, ionic bonds, hydrogen bonds, disulfide bonds). - **Examples:** Hemoglobin (four subunits), antibodies. ### Denaturation of Proteins - **Definition:** The process by which a protein loses its native three-dimensional structure (secondary, tertiary, and quaternary, but not primary) due to disruption of non-covalent interactions and disulfide bonds. - **Causes:** - **Heat:** Increases kinetic energy, breaking weak bonds. - **Extreme pH:** Alters charge distribution, disrupting ionic bonds and hydrogen bonds. - **Organic solvents:** Interfere with hydrophobic interactions. - **Heavy metals:** Bind to sulfhydryl groups. - **Detergents:** Disrupt hydrophobic interactions. - **Consequences:** Loss of biological activity, often irreversible (e.g., cooking an egg). - **Renaturation:** In some cases, if the denaturing agent is removed, a protein can refold into its native structure. ### Classification of Proteins - **Based on Shape:** - **Fibrous Proteins:** Elongated, insoluble in water, structural roles (e.g., collagen, keratin). - **Globular Proteins:** Compact, spherical, soluble in water, functional roles (e.g., enzymes, hormones, antibodies). - **Based on Composition:** - **Simple Proteins:** Composed only of amino acids (e.g., albumin, globulin). - **Conjugated Proteins:** Composed of amino acids and a non-protein part (prosthetic group). - **Glycoproteins:** Protein + carbohydrate (e.g., antibodies). - **Lipoproteins:** Protein + lipid (e.g., HDL, LDL). - **Nucleoproteins:** Protein + nucleic acid (e.g., histones). - **Metalloproteins:** Protein + metal ion (e.g., hemoglobin - iron, carbonic anhydrase - zinc). - **Phosphoproteins:** Protein + phosphate group (e.g., casein).