IB Bio Proteins & Enzymes

PROTEINS

Essential Idea

  • Proteins have a wide range of functions in living organisms.

Overview of Proteins

  • Proteins can form many structures, resulting in diverse functions.

  • Proteins perform most of the work in cells and act as enzymes.

  • Proteins are made of monomers called amino acids.

Key Definitions

  • Monomer: An individual building block of proteins; specifically, amino acids.

  • Polypeptide: A polymer formed from amino acids linking together as a chain.

  • Proteins can consist of one or more polypeptide chains that are folded and bonded together.

  • Proteins are large and complex molecules characterized by their unique 3-D shapes.

Examples of Proteins

  • Rubisco: An enzyme involved in carbon fixation.

  • Hemoglobin: A transport protein that carries oxygen in the blood.

  • Growth Hormones: Hormones that regulate growth in organisms.

Amino Acids

  • There are 20 different amino acids that can link together in any sequence, allowing for a vast range of potential polypeptides.

  • Each amino acid consists of:

    1. Central carbon (C)

    2. Amino group (NH2)

    3. Carboxyl group (−COOH)

    4. Variable R group (side chain) – gives unique chemical properties to each amino acid.

  • Comparison: The 20 amino acids are like letters in an alphabet that can form various words (proteins).

Types of Amino Acids

  • 20 Common Amino Acids

    • Alanine (Ala, A)

    • Arginine (Arg, R)

    • Asparagine (Asn, N)

    • Aspartic Acid (Asp, D)

    • Cysteine (Cys, C)

    • Glutamine (Gln, Q)

    • Glutamic Acid (Glu, E)

    • Glycine (Gly, G)

    • Histidine (His, H)

    • Isoleucine (Ile, I)

    • Leucine (Leu, L)

    • Lysine (Lys, K)

    • Methionine (Met, M)

    • Phenylalanine (Phe, F)

    • Proline (Pro, P)

    • Serine (Ser, S)

    • Threonine (Thr, T)

    • Tryptophan (Trp, W)

    • Tyrosine (Tyr, Y)

    • Valine (Val, V)

  • Essential Amino Acids: Those that must be ingested in the diet, as the body cannot synthesize them.

Linking Amino Acids

  • The linking of amino acids occurs in any sequence, leading to extremely high variability in polypeptides.

  • Possible combinations for polypeptides:

    • 1 amino acid = 20 possibilities

    • 2 amino acids = 400 possibilities

    • 3 amino acids = 8,000 possibilities

    • 4 amino acids = 160,000 possibilities

    • 5 amino acids = 3,200,000 possibilities

    • 6 amino acids = 64,000,000 possibilities

    • Example: A polypeptide composed of 7 amino acids can yield 1,280,000,000 possible combinations.

  • Polypeptides can range from 20 amino acids to tens of thousands (e.g., Titin).

Peptide Bonds

  • Amino acids are linked by peptide bonds, which are covalent bonds formed between the amine group of one amino acid and the carboxyl group of another.

  • This process involves condensation reactions, forming polypeptides during translation at the ribosomes.

Protein Structure

  • Proteins fold into unique shapes essential for their functions. There are four levels of protein structure:

1. Primary Structure

  • Sequence of amino acid subunits connected by peptide bonds.

2. Secondary Structure

  • Folding or coiling of the polypeptide chain into repeating configurations (e.g., α helix, β pleated sheet).

3. Tertiary Structure

  • Overall 3-D shape of the polypeptide, determined by interactions among R groups (side chains), including:

    • Disulfide bonds

    • Hydrogen bonds

    • Hydrophobic interactions

    • Ionic bonds

4. Quaternary Structure

  • Assembly of multiple polypeptide chains into a functional protein (e.g., hemoglobin consists of four subunits).

Techniques for Analyzing Protein Structure

  • X-ray Crystallography: Used to determine the 3-D structure of proteins through X-ray diffraction patterns.

Types of Proteins

  • Proteins are classified as either fibrous or globular:

    • Fibrous Proteins: Structural roles, highly resistant to digestion (e.g., collagen).

    • Globular Proteins: Functional roles active in cell metabolism, soluble in water (e.g., hemoglobin).

Functions of Proteins

  • Classification of some proteins based on functions includes:

    • Structural: e.g., collagen, keratin (provide structure).

    • Contractile: e.g., myosin, actin (facilitate muscle movement).

    • Transport: e.g., hemoglobin, lipoprotein (carry substances).

    • Storage: e.g., casein, ferritin (store nutrients).

    • Hormonal: e.g., insulin (regulate metabolism).

    • Enzymatic: e.g., sucrase, trypsin (catalyze reactions).

    • Protective: e.g., immunoglobulins (defense against pathogens).

Important Examples of Proteins

  • Rubisco: Enzyme that fixes carbon dioxide from the atmosphere.

  • Insulin: A hormone that regulates blood glucose levels by signaling cells to absorb glucose.

  • Immunoglobulins: Antibodies that protect against pathogens.

  • Rhodopsin: A light-absorbing pigment found in the retina.

  • Collagen: A structural protein that contributes to tissue strength.

  • Spider Silk: A versatile protein with remarkable strength and flexibility.

Protein Problems

  • Sickle-Cell Disease: An inherited disorder caused by a mutation in the hemoglobin gene, leading to misshaped red blood cells and reduced oxygen-carrying capacity.

  • Characterized by a single amino acid substitution that affects the protein's structure and function.

Denaturation of Proteins

  • Denaturation involves disruption of both secondary and tertiary structures, leading to loss of functionality.

  • Conditions that can cause denaturation include:

    • Temperature changes

    • pH deviations

    • Salinity variations

  • Denaturation is typically irreversible, meaning the protein cannot regain its original functional shape.

Metabolism Overview

  • Metabolism refers to all chemical reactions in a cell, often organized into specific pathways controlled by enzymes.

  • Enzymes: Globular proteins that act as biological catalysts, speeding up reactions by lowering activation energy.

    • Enzymatic action can be affected by substrate concentration, temperature, pH, and the presence of inhibitors.

    • The process is influenced by molecular motions and the collision of substrates with the enzyme’s active site.

Enzyme Inhibition

  • Competitive Inhibition: Inhibitor competes with substrate for binding to the enzyme's active site.

    • Example: Relenza as a competitive inhibitor to neuraminidase in influenza.

  • Non-Competitive Inhibition: Inhibitor binds to a site other than the active site, causing a conformational change that prevents substrate binding.

    • Example: Cyanide as a non-competitive inhibitor of ATP production in mitochondrial chains.

End-Product Inhibition

  • Feedback inhibition occurs when the final product of a metabolic pathway inhibits an enzyme involved in its synthesis, preventing overproduction.

  • Example: Isoleucine inhibiting threonine deaminase in its production pathway.

Proteomics and Genomics

  • Genome: All genes of an organism, determining protein production capabilities.

  • Proteome: All proteins expressed by a cell or organism at any given time, reflecting the interaction between genetics and environment.

  • Gel electrophoresis is a technique used to analyze and separate proteins from cellular extracts for study.

Conclusion

  • Proteins are vital biomolecules with diverse structures and functions, playing crucial roles in every biological process in an organism's life. Understanding protein structure and function is essential for insights into biological mechanisms and the development of medical and biotechnological applications.