Proteins

Page 1: Introduction to Proteins

• Title: Biology 189: Fundamentals for Life Sciences

• Focus: Introduction to proteins using humor with characters (e.g., a mean 'O' Acid).

Page 2: Learning Objectives

• Proteins Definition: Understand what proteins are and their six functions in living organisms:

  • Function Overview: Enzymes, structure, signaling, defense, transport, movement.

• Amino Acids Structure: Learn structure of amino acids as protein building blocks and variability in side chains (R-groups).

• Classification: Recognize three types of amino acids: nonpolar, polar, charged and how to identify them.

• Peptide Bonds: Mechanism of amino acids joining and defining peptide bonds.

• Protein Structures: Describe the four levels of protein structure: primary, secondary, tertiary, quaternary.

• Denaturation: Explain what protein denaturation is, its causes, and its effect on protein function.

Page 3: Proteins in the Real World

• Visual representation of proteins across various aspects of life (context of 'Brotein','ACD','Orogroughsketchz').

Page 4: Functions of Proteins

• Diverse Functions:

  • Enzymes: Catalyze reactions

  • Structural Support: Shape cells/bodies

  • Signaling: Intercellular communication

  • Defense: Antibodies against pathogens

  • Transport: Movement of materials within cells

  • Movement: Muscle contraction and cell mobility.

Page 5: Specific Protein Functions

• Types of Proteins:

  • Enzymes: Speed up chemical reactions.

  • Transport Proteins: E.g., Hemoglobin in red blood cells transports oxygen.

  • Structural Proteins:

    • Keratin: Forms hair, nails, feathers.

    • Collagen: Present in bones, tendons, cartilage.

  • Contractile Proteins: E.g., Actin and myosin in muscles.

Page 6: Amino Acid Basics

• Amino Acids as Polymers:

  • All amino acids share the same fundamental structure:

    • Central Alpha Carbon

    • Amino Group

    • Carboxyl Group

    • Side Chain (R group)

• Visual representation of amino acid structure.

Page 7: Carboxyl and Amino Groups

• Behavior in Water:

  • Carboxyl group can lose a proton (H+) and amino group can gain a proton.

Page 8: Diversity of Amino Acids

• 20 Common Amino Acids: Differentiated by side chains:

  • Nonpolar

  • Polar

  • Charged

• Hydrophobic (nonpolar) vs. Hydrophilic (polar) characteristics.

Page 9: Nonpolar Amino Acids

• Characteristics:

  • Hydrophobic side chains leading to nonpolar interactions.

• Examples: Glycine, Alanine, Valine, Leucine, Isoleucine, Methionine, Phenylalanine, Tryptophan, Proline.

Page 10: Polar Amino Acids

• Characteristics:

  • Hydrophilic side chains that interact well in aqueous environments.

• Examples: Serine, Threonine, Tyrosine, Asparagine, Cysteine, Glutamine.

Page 11: Charged Amino Acids

• Characteristics:

  • Electrically charged side chains.

  • Basic (positively charged): E.g., Lysine, Arginine, Histidine.

  • Acidic (negatively charged): E.g., Aspartic acid, Glutamic acid.

Page 12: Categorizing Amino Acids

• Rules for Classification:

  • Nonpolar: Abundant carbon and hydrogen.

  • Polar: Contain oxygen or nitrogen.

  • Charged: Exhibit a positive or negative charge.

Page 13: In-class question 2

• Question assessing classification skill of amino acids.

Page 14: Formation of Peptide Bonds

• Peptide Bond: Covalent bond formation between two amino acids via dehydration synthesis.

• Description of how polypeptides are formed by linking amino acids.

Page 15: Protein Shape and Function

• Shape Reflection: Protein function is dependent upon its structure.

• Structural Levels: Primary, secondary, tertiary, and quaternary structure.

Page 16: Primary Structure (1°)

• Definition: Exact sequence of amino acids in a chain determined by gene instructions.

Page 17: Secondary Structure (2°)

• Formation: Hydrogen bonding occurs along the polypeptides backbone.

  • Bonds between partially negative oxygens and partially positive hydrogens.

Page 18: Secondary Structure Types

• Major Types:

  • Alpha Helix

  • Beta-Pleated Sheet

• Visual representation of structures.

Page 19: Tertiary Structure (3°)

• Description: Interactions among various segments of a polypeptide shape its 3D structure.

• The role of amino acid side chains in determining structure.

Page 20: Bonds in Tertiary Structure

• Types of Bonds: Include Hydrogen bonds, Ionic bonds, Disulfide bridges, Van der Waals interactions.

Page 21: Protein 3D Shape Characteristics

• Structure in Aqueous Environment:

  • Hydrophobic (nonpolar) side chains positioned inward.

  • Hydrophilic (polar) side chains on the exterior.

Page 22: Quaternary Structure (4°)

• Definition: Assembly of multiple polypeptides into a single protein structure.

• Same bond types as tertiary structure present.

• Example: Hemoglobin consists of four polypeptides.

Page 23: Protein Diagram

• Visual Representation: Example of 'Myosin'—a motor protein with multi-colored polypeptide representation.

• Note: No test on this slide information.

Page 24: Protein Structure Summary

• Peptide Bonds in primary structure connect amino acids.

• Secondary Structures: Alpha-helix and Beta-pleated sheets formed by hydrogen bonding.

• Tertiary Structures: Stabilized through R group interactions.

• Quaternary Structures: Polypeptides arranged into functional proteins.

Page 25: Shape and Function Relationship

• Concept: Enzyme groove and active site configure to bind substrates effectively.

Page 26: Importance of Primary Structure

• Example: Change in hemoglobin structure (sickle-cell disease) by substitution of a single amino acid affecting protein function.

Page 27: Environmental Impact on Protein Folding

• Denaturation: Loss of normal shape due to environmental stressors (pH, salt concentration, temperature).

• Key Point: 1° structure remains intact despite denaturation.

Page 28: In-class question 3

• Question: Placement examination of leucine side chains within protein environments (exposed to water).

Page 29: Summary of Protein Structures

• Overview of four levels of protein structures including bonds maintaining each level and their definitions.

Page 30: Comparison of Macromolecules

• Visually summarize definitions and monomers of different macromolecules: Lipids, Carbohydrates, Nucleic Acids, and Proteins.

Page 31: Vocabulary Overview

• Key Terms:

  • Protein, Enzyme, Amino Acid, a-carbon, Side Chain (R Group), Ionized Amino Acid, Non-Ionized Amino Acid, Peptide Bond, Oligopeptide, Polypeptide, various protein structure levels, alpha-helix, beta-pleated sheet, disulfide bridge, denaturation, denatured protein.