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.