Fundamental Chemical and Cellular Principles in Biology

The Chemical Context of Life

Atoms and Their Valences

Cells are primarily composed of a few key elements, each with a characteristic valence that determines its bonding behavior.

• Predominant Atoms: Hydrogen (H), Oxygen (O), Nitrogen (N), Carbon (C) – "HONC"

• Valences: H (1), O (2), N (3), C (4)

• Phosphorus (P) and Sulfur (S): P (5), S (2)

Chemical Bonds

• Covalent Bonds: Atoms share pairs of electrons; strongest type of bond. Can be polar (unequal sharing, creates dipoles) or non-polar (equal sharing).

• Ionic Bonds: Electrons are transferred from one atom to another, typically between metals and nonmetals; second strongest bond.

• Hydrogen Bonds: Weak bonds formed between a hydrogen atom (bonded to O or N) and another electronegative atom; important for water and biological molecules.

• Van der Waals Interactions: Weakest; transient attractions due to temporary partial charges.

Water and Its Properties

• Polarity: Water is polar, allowing it to form hydrogen bonds.

• Solvent Abilities: Dissolves ionic compounds (e.g., NaCl) and polar molecules.

• Hydrophilic: Substances attracted to water.

• Hydrophobic: Substances that repel water; nonpolar molecules cluster together.

pH and Buffers

• pH Scale: Measures proton (H+) concentration. pH < 7 is acidic, pH > 7 is basic.

• Acid: Releases H+ in solution.

• Base: Reduces H+ concentration.

• Buffers: Weak acids/bases that minimize pH changes by accepting/donating protons.

Metric Prefixes and Units

• centi (c): $10^{-2}$

• micro (μ): $10^{-6}$

• nano: $10^{-9}$

• Angstrom (Å): $10^{-10}$ meters

Carbon and the Molecular Diversity of Life

Carbon's Versatility

Carbon can form four covalent bonds, allowing for diverse structures: chains, branches, and rings.

Functional Groups

• Hydroxyl: –OH

• Carbonyl: C=O (ketone if internal, aldehyde if terminal)

• Carboxyl: –COOH

• Amino: –NH2

• Sulfhydryl: –SH

• Phosphate: –PO42–

Macromolecules and Their Building Blocks

• Proteins: Amino acids

• Carbohydrates: Monosaccharides

• Nucleic Acids: Nucleotides

• Lipids: Fatty acids and glycerol

Polymerization and Depolymerization

• Dehydration Reaction: Joins monomers by removing water.

• Hydrolysis Reaction: Breaks polymers into monomers by adding water.

Proteins: Structure and Function

Amino Acids and Peptide Bonds

• Generic Structure: Central (alpha) carbon, amino group, carboxyl group, R group (side chain).

• Peptide Bond: Covalent bond between carboxyl of one amino acid and amino of another (via dehydration synthesis).

Classification of Amino Acids

Type	Examples	Properties
Nonpolar (Hydrophobic)	Glycine (G), Alanine (A), Valine (V), Leucine (L), Isoleucine (I), Methionine (M), Phenylalanine (F), Tryptophan (W), Proline (P)	Hydrophobic, avoid water
Polar (Uncharged)	Serine (S), Threonine (T), Cysteine (C), Asparagine (N), Glutamine (Q), Tyrosine (Y)	Hydrophilic, form H-bonds
Acidic (–, Charged)	Aspartate (D), Glutamate (E)	Negative charge, can form ionic bonds
Basic (+, Charged)	Lysine (K), Arginine (R), Histidine (H)	Positive charge, can form ionic bonds

Protein Structure Levels

• Primary: Sequence of amino acids (N to C terminus).

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

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

• Quaternary: Arrangement of multiple polypeptide chains.

Protein Denaturation and Renaturation

• Denaturation: Loss of structure (and function) due to heat, pH, or chemicals.

• Renaturation: Refolding into functional structure (sometimes possible).

Functions of Proteins

• Structure

• Regulation

• Signaling

• Movement

• Metabolism

• Transport

Carbohydrates

Monosaccharides, Disaccharides, and Polysaccharides

• Monosaccharide Formula: $C_nH_{2n}O_n$

• Properties: Simple sugars, high solubility, often ring-shaped.

• Disaccharides: Two monosaccharides joined by dehydration (e.g., sucrose = glucose + fructose).

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

Glycosidic Bonds

Covalent bonds linking monosaccharides in oligo- and polysaccharides.

Cellulose vs. Starch

Property	Cellulose	Starch
Structure	Linear chains	Branched chains
Function	Structural support (cell walls)	Energy storage
Solubility	Insoluble	Partially soluble

Nucleic Acids

DNA and RNA

• DNA: Double-stranded, deoxyribose sugar, bases G-C, A-T, antiparallel strands.

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

Nucleotides and Bonds

• Nucleotide: Sugar + phosphate + nitrogenous base.

• Phosphodiester Bond: Links 5' phosphate to 3' OH of adjacent nucleotide (dehydration reaction).

Nitrogenous Bases

Type	Bases
Purines	Adenine (A), Guanine (G)
Pyrimidines	Cytosine (C), Thymine (T, DNA), Uracil (U, RNA)

Lipids

Types and Functions

• Fatty Acids: Long hydrocarbon chains (16–18 C); saturated (no double bonds) or unsaturated (one or more double bonds).

• Triglycerides (Fats): Glycerol + 3 fatty acids.

• Phospholipids: Glycerol + 2 fatty acids + phosphate group; amphipathic (hydrophilic head, hydrophobic tails).

• Steroids: Four-ring structure (e.g., cholesterol).

Membrane Structure

• Bilayer: Phospholipids form bilayers in water (basis of cell membranes).

• Micelle: Spherical arrangement of phospholipids (heads out, tails in).

Metabolism and Thermodynamics

Catabolism vs. Anabolism

• Catabolic Pathways: Break down molecules, release energy.

• Anabolic Pathways: Build molecules, require energy.

Thermodynamic Laws

• First Law: Energy is conserved.

• Second Law: Entropy (disorder) increases in energy transformations.

Key Terms

• Free Energy (G): Determines spontaneity of reactions.

• Enthalpy (H): Heat content.

• Entropy (S): Disorder.

• Spontaneous Reaction: $\Delta G < 0$

• Endergonic: $\Delta G > 0$ (requires energy)

• Exergonic: $\Delta G < 0$ (releases energy)

• Equation: $\Delta G = \Delta H - T\Delta S$

ATP and Chemical Coupling

• ATP Cycle: ATP ↔ ADP + Pi; energy currency of the cell.

• Chemical Coupling: Endergonic reactions are driven by coupling to exergonic reactions (e.g., ATP hydrolysis).

Enzymes

• Function: Biological catalysts; lower activation energy (EA), do not change $\Delta G$.

• Active Site: Region where substrate binds.

• Specificity: Each enzyme catalyzes a specific reaction.

• Inhibition: Competitive (binds active site), noncompetitive/allosteric (binds elsewhere).

• Regulation: Phosphorylation (on S/T/Y residues).

Cell Structure and Function

Cell Types

Feature	Prokaryotic Cells	Eukaryotic Cells
Examples	Bacteria, Archaea	Protists, Fungi, Plants, Animals
Nucleus	Absent	Present
Organelles	Absent	Present
Size	~1 μm	10–100 μm

Major Organelles and Structures

• Nucleus: Contains DNA; site of replication and gene expression.

• Cytoplasm: Everything outside the nucleus.

• Mitochondria: ATP synthesis.

• Chloroplasts: Photosynthesis (plants only).

• Lysosomes: Digestion of macromolecules.

• Vacuoles: Storage of nutrients and waste.

• Endoplasmic Reticulum (ER): Protein and lipid synthesis; rough ER (with ribosomes), smooth ER (no ribosomes).

• Golgi Apparatus: Protein/lipid processing and sorting.

• Cytoskeleton: Structure, movement, division (microtubules, microfilaments, intermediate filaments).

Membrane Structure and Transport

• Plasma Membrane: Phospholipid bilayer with embedded proteins.

• Integral Proteins: Span the membrane.

• Peripheral Proteins: Attached to membrane surface.

Transport Mechanisms

• Passive Diffusion: No energy or protein required.

• Facilitated Diffusion: No energy, but requires protein (carrier or channel).

• Active Transport: Requires energy (ATP), moves substances against gradient (e.g., sodium-potassium ATPase).

• Osmosis: Diffusion of water across membrane.

• Aquaporins: Water channel proteins.

Tonicity Effects

Solution	Effect on Animal Cell	Effect on Plant Cell
Hypotonic	Burst	Turgid
Isotonic	Normal	Flaccid
Hypertonic	Shrink	Plasmolyzed

Bulk Transport

• Exocytosis: Secretion of materials via vesicle fusion with membrane.

• Endocytosis: Uptake of materials via vesicle formation (includes phagocytosis, pinocytosis, receptor-mediated endocytosis).

Cytoskeleton and Cell Movement

Components

Type	Protein	Diameter	Function
Microtubules	Tubulin	25 nm	Cell shape, movement, division
Microfilaments	Actin	7 nm	Cell shape, muscle contraction
Intermediate Filaments	Various	10 nm	Structural integrity

Motor Proteins and Movement

• Kinesin: Moves cargo toward cell periphery (anterograde).

• Dynein: Moves cargo toward cell center (retrograde).

• Cilia and Flagella: Movement via organized microtubules (9+2 arrangement, axoneme).

Cell Division and the Cell Cycle

Prokaryotic vs. Eukaryotic Division

• Binary Fission: Prokaryotic cell division; simple process.

• Cell Cycle: Eukaryotic; includes G1, S, G2 (interphase), mitosis (M), and cytokinesis.

Chromosome Structure

• Chromosome: DNA + proteins; humans have 46 (23 pairs).

• Chromatid: Single DNA molecule; sister chromatids are identical copies.

• Centromere: Region where chromatids are joined.

• Kinetochore: Protein complex at centromere; attaches to spindle fibers.

• Telomere: Chromosome ends.

• Histones: Proteins organizing DNA into nucleosomes and higher-order structures.

Phases of Mitosis

• Prophase: Chromosomes condense, nucleolus disappears.

• Prometaphase: Nuclear envelope breaks down, spindle attaches to kinetochores.

• Metaphase: Chromosomes align at metaphase plate.

• Anaphase: Sister chromatids separate.

• Telophase: Chromosomes decondense, nuclear envelope reforms.

• Cytokinesis: Cytoplasm divides (contractile ring in animals, cell plate in plants).

Chromatin Structure

• Nucleosome: DNA wrapped around histone octamer.

• 30 nm Fiber: Higher-order chromatin structure.

Special Topics

• Henrietta Lacks: First "immortalized" human cell line (HeLa cells), important for research.

• Robert Hooke: Coined "cell" after observing cork.

• Anton van Leeuwenhoek: First to observe living cells ("animalcules").

Additional info: Where original notes were brief, standard academic definitions and explanations were added for clarity and completeness.