Chapter 3: Water in Biological Systems

Function and Structure of Water

Water is a vital molecule in biological systems, serving as a solvent, reactant, and temperature buffer. Its unique properties arise from its molecular structure and hydrogen bonding.

• Structure: Water (H2O) is a polar molecule with a bent shape due to the two hydrogen atoms bonded to oxygen at an angle of approximately 104.5°.

• Function: Water acts as a universal solvent, facilitates chemical reactions, and helps regulate temperature in cells.

• Hydrogen Bonding: The polarity of water allows for hydrogen bonds between molecules, contributing to cohesion, adhesion, and high specific heat.

• Polarity: Water's oxygen atom is more electronegative, creating a partial negative charge, while hydrogens are partially positive.

• pH and Buffers: Water participates in acid-base chemistry. Buffers help maintain stable pH in cells, crucial for enzyme function.

Example: Water's high heat capacity helps organisms maintain stable internal temperatures.

Chapter 4: Functional Groups in Organic Molecules

Seven Common Functional Groups

Functional groups are specific groups of atoms within molecules that confer distinct chemical properties. They are key to the structure and function of biomolecules.

• Hydroxyl (-OH): Found in alcohols; increases solubility in water.

• Carbonyl (C=O): Found in aldehydes and ketones; reactive in sugar chemistry.

• Amino (-NH2): Found in amino acids; acts as a base.

• Sulfhydryl (-SH): Found in cysteine; forms disulfide bonds in proteins.

• Phosphate (-PO4): Found in nucleotides; involved in energy transfer (e.g., ATP).

• Methyl (-CH3): Nonpolar; affects gene expression when added to DNA.

• Carboxyl (-COOH): Found in amino acids and fatty acids; acts as an acid.

Structural Isomers, Cis-Trans Isomers, and Enantiomers

• Structural Isomers: Molecules with the same molecular formula but different connectivity of atoms.

• Cis-Trans (Geometric) Isomers: Differ in spatial arrangement around a double bond or ring structure.

• Enantiomers: Mirror-image isomers; important in drug design and biochemistry.

Example: Glucose and fructose are structural isomers; cis- and trans-fatty acids differ in health effects.

Chapter 5: Macromolecules and Protein Structure

Structure and Function of Macromolecules

Biological macromolecules include carbohydrates, lipids, proteins, and nucleic acids. Each plays a unique role in cellular structure and function.

• Carbohydrates: Energy storage and structural support (e.g., glucose, cellulose).

• Lipids: Long-term energy storage, membrane structure (e.g., fats, phospholipids).

• Proteins: Catalysis, structure, transport, signaling (e.g., enzymes, hemoglobin).

• Nucleic Acids: Information storage and transfer (e.g., DNA, RNA).

Atoms in Macromolecules

• Carbohydrates: C, H, O

• Lipids: C, H, O (sometimes P)

• Proteins: C, H, O, N, S

• Nucleic Acids: C, H, O, N, P

Dehydration and Hydrolysis Reactions

• Dehydration Synthesis: Builds polymers by removing water.

• Hydrolysis: Breaks polymers into monomers by adding water.

Example: Formation of a peptide bond between amino acids via dehydration synthesis.

Monomers and Polymers

• Monomer: Small building block (e.g., glucose, amino acid, nucleotide).

• Polymer: Chain of monomers (e.g., starch, protein, DNA).

DNA, Protein, and Enzyme Relationships

• DNA encodes instructions for protein synthesis.

• Proteins (enzymes) catalyze biochemical reactions.

• Central Dogma: DNA → RNA → Protein

Mutation

• Mutation: A change in DNA sequence, which can affect protein structure and function.

Protein Structure Levels

• Primary Structure: Sequence of amino acids.

• Secondary Structure: Local folding (α-helix, β-sheet) via hydrogen bonds.

• Tertiary Structure: Overall 3D shape due to side chain interactions.

• Quaternary Structure: Association of multiple polypeptide chains.

Rules to Protein Folding

• Hydrophobic residues tend to be buried inside.

• Hydrogen bonds, ionic bonds, and disulfide bridges stabilize structure.

Amino Acid Structure and Classification

• Structure: Central carbon, amino group, carboxyl group, hydrogen, and variable R group.

• Classification: Based on R group properties: nonpolar, polar, acidic, basic.

Structure of DNA and RNA

• DNA: Double helix, deoxyribose sugar, bases A-T, G-C.

• RNA: Single strand, ribose sugar, bases A-U, G-C.

Example: Sickle cell anemia results from a single amino acid mutation in hemoglobin.

FRQ Preparation: Data Analysis and Protein Structure

Graphing Guidelines

Proper graphing is essential for presenting biological data.

• Label axes with units.

• Include a descriptive title.

• Use appropriate scales and legends.

SEMs and Statistical Differences

• SEM (Standard Error of the Mean): Measures precision of sample mean estimate.

• Statistical Differences: Use statistical tests (e.g., t-test) to determine significance between data sets.

Protein Structure and Function

• Protein function depends on its structure, which is determined by amino acid sequence and folding.

• Enzymes are proteins that catalyze reactions by lowering activation energy.

Additional info:

• Equations for pH:

• Central Dogma:

• Dehydration Synthesis: