General Biology: Structure and Function of Biomolecules, Cell Theory, and Chemical Basis of Life

Chapter 3: Protein Structure and Function

Amino Acids: Structure and Properties

Amino acids are the building blocks of proteins, each consisting of a central carbon atom bonded to four different groups: an amino group, a carboxyl group, a hydrogen atom, and a unique side chain (R-group). The properties of amino acids determine the structure and function of proteins.

• Structure: Central carbon (α-carbon) bonded to amino group (NH2), carboxyl group (COOH), hydrogen, and R-group.

• R-group: Determines chemical reactivity and solubility.

• Classification: Amino acids can be nonpolar (hydrophobic), polar (hydrophilic), acidic (negatively charged), or basic (positively charged).

• Ionization: Amino and carboxyl groups can ionize, affecting the molecule's charge and reactivity.

• Polarity: Polar and electrically charged R-groups interact well with water; nonpolar R-groups do not.

Example: Glycine is the simplest amino acid, with a hydrogen as its R-group, making it nonpolar and small.

Peptide Bond Formation and Protein Structure

Amino acids link via peptide bonds, formed by a dehydration (condensation) reaction between the carboxyl group of one amino acid and the amino group of another. This process creates polypeptides, which fold into functional proteins.

• Peptide Bond: Covalent bond between C-N, formed by removal of water.

• Polypeptide: Chain of amino acids linked by peptide bonds.

• Directionality: Polypeptides have an N-terminus (amino end) and a C-terminus (carboxyl end).

• Residue: Term for individual amino acids within a polypeptide chain.

Levels of Protein Structure

Proteins have four levels of structure, each contributing to their final shape and function.

• Primary Structure: Unique sequence of amino acids in a polypeptide, stabilized by peptide bonds.

• Secondary Structure: Local folding into α-helices and β-pleated sheets, stabilized by hydrogen bonds between backbone groups.

• Tertiary Structure: Overall 3D shape, stabilized by interactions among R-groups (hydrogen bonds, hydrophobic interactions, van der Waals forces, covalent bonds, ionic bonds).

• Quaternary Structure: Association of multiple polypeptide chains (subunits), stabilized by the same types of interactions as tertiary structure.

Table: Types of R-group Interactions in Tertiary Structure

Interaction Type	Description
Hydrogen Bonding	Between polar side chains and partial charges
Hydrophobic Interactions	Nonpolar side chains cluster away from water
Van der Waals Forces	Weak attractions between hydrophobic side chains
Covalent Bonding	Disulfide bridges between cysteine residues
Ionic Bonding	Between oppositely charged side chains

Protein Folding and Function

Protein folding is crucial for function and is often spontaneous, driven by chemical interactions. Misfolded proteins can lose function or cause disease. Molecular chaperones (e.g., heat shock proteins) assist in proper folding.

• Denaturation: Loss of structure and function due to heat or chemicals.

• Chaperones: Proteins that help other proteins fold correctly.

Functions of Proteins:

• Catalysis (enzymes)

• Structural support

• Movement (motor proteins)

• Signaling (hormones, receptors)

• Transport (membrane channels, carriers)

• Defense (antibodies)

Chapter 5: Carbohydrates

Carbohydrate Structure and Classification

Carbohydrates are energy-rich molecules composed of carbon, hydrogen, and oxygen, typically with the formula (CH2O)n. They serve as energy sources, structural materials, and cell recognition molecules.

• Monosaccharides: Simple sugars (e.g., glucose), vary by carbon number, carbonyl group position, and spatial arrangement.

• Disaccharides: Two monosaccharides linked by a glycosidic bond (e.g., sucrose).

• Oligosaccharides: Short chains of monosaccharides.

• Polysaccharides: Long chains (e.g., starch, glycogen, cellulose, chitin).

Table: Major Polysaccharides and Their Functions

Polysaccharide	Organism	Function
Starch	Plants	Energy storage
Glycogen	Animals, fungi	Energy storage
Cellulose	Plants	Structural support (cell wall)
Chitin	Fungi, arthropods	Structural support (cell wall, exoskeleton)

Carbohydrate Function

• Provide chemical energy (e.g., glucose metabolism)

• Serve as structural components (e.g., cellulose in plants, chitin in fungi/arthropods)

• Cell recognition and signaling (glycoproteins, glycolipids)

Chapter 6: Lipids, Membranes, and the First Cells

Lipid Structure and Types

Lipids are hydrophobic, carbon-containing molecules that are insoluble in water due to their nonpolar C-H bonds. They serve as energy storage, structural components of membranes, and signaling molecules.

• Fats (Triglycerides): Glycerol linked to three fatty acids via ester bonds; used for energy storage.

• Phospholipids: Glycerol, two fatty acids, and a phosphate group; form cell membranes.

• Steroids: Four fused carbon rings with functional groups; include cholesterol and hormones.

Saturated vs. Unsaturated Fatty Acids:

• Saturated: No double bonds, straight chains, solid at room temperature.

• Unsaturated: One or more double bonds, kinked chains, liquid at room temperature.

Membrane Structure and Function

Phospholipids form bilayers in water, creating selectively permeable membranes. The amphipathic nature (hydrophilic head, hydrophobic tail) drives bilayer formation.

• Micelles: Spherical aggregates of phospholipids.

• Lipid Bilayer: Double layer with hydrophobic tails inside, hydrophilic heads outside.

• Membrane Fluidity: Influenced by fatty acid saturation, tail length, cholesterol content, and temperature.

Table: Membrane Permeability

Molecule Type	Permeability
Small nonpolar molecules (O2, CO2)	High
Small uncharged polar molecules (H2O)	Moderate
Large uncharged polar molecules (glucose)	Low
Ions (Na+, K+)	Very low

Transport Across Membranes

• Diffusion: Passive movement of molecules from high to low concentration.

• Osmosis: Diffusion of water across a selectively permeable membrane.

• Facilitated Diffusion: Passive transport via channel or carrier proteins.

• Active Transport: Movement against concentration gradient, requires energy (e.g., sodium-potassium pump).

Chapter 1: The Study of Life

Characteristics of Life

Living organisms share several key characteristics:

• Composed of cells (cell theory)

• Process hereditary/genetic information (chromosome theory of inheritance)

• Acquire and use energy

• Capable of evolution by natural selection

Cell Theory: All organisms are made of cells; all cells come from preexisting cells.

Chromosome Theory of Inheritance: Genes are located on chromosomes, composed of DNA.

Central Dogma: Information flows from DNA → RNA → Protein.

Evolution: Populations change over time due to natural selection, leading to adaptation and speciation.

Chapter 2: Chemical Basis of Life

Atoms, Bonds, and Molecules

Atoms are the fundamental units of matter, composed of protons, neutrons, and electrons. Chemical bonds form when atoms share or transfer electrons.

• Covalent Bonds: Atoms share electron pairs.

• Ionic Bonds: Electrons are transferred, creating charged ions.

• Hydrogen Bonds: Weak attractions between partially charged regions of molecules (e.g., between water molecules).

• Van der Waals Interactions: Weak attractions due to transient dipoles.

Table: Bond Strength (Strongest to Weakest)

Bond Type	Relative Strength
Ionic	Strong
Covalent	Strong
Hydrogen	Weak
Van der Waals	Very Weak

Properties of Water

Water's unique properties are essential for life:

• High cohesion and adhesion

• High specific heat and heat of vaporization

• Excellent solvent for polar and ionic substances

• Expands upon freezing (ice is less dense than liquid water)

• Regulates temperature and pH in organisms

pH Scale: Measures acidity/alkalinity; 7 is neutral, <7 acidic, >7 basic.

Buffer Systems: Maintain stable pH in organisms (e.g., carbonic acid-bicarbonate buffer in blood).

Chemical Reactions and Energy

• Potential Energy: Stored energy due to position or structure.

• Kinetic Energy: Energy of motion.

• First Law of Thermodynamics: Energy is conserved.

• Second Law of Thermodynamics: Entropy (disorder) increases in isolated systems.

Endothermic Reaction: Absorbs energy.

Exothermic Reaction: Releases energy.

Organic Molecules and Functional Groups

• Organic molecules are carbon-based and versatile due to carbon's four valence electrons.

• Functional groups (e.g., hydroxyl, carboxyl, amino, phosphate) confer specific chemical properties.

• Monomers join to form polymers via condensation reactions (water out); hydrolysis breaks polymers (water in).

Additional info: Some explanations and tables were expanded for clarity and completeness based on standard biology curriculum.