Chemistry of Life - Summary Notes

Introduction to the Chemistry of Life

Living organisms have a hierarchical arrangement of chemical components.
Organization maintains homeostasis and enables biological functions.

Matter and Elements

Matter: Fundamental substance of living and nonliving things.
Elements: Pure substances with one type of atom.
Atoms: Smallest unit of an element with chemical properties (protons, neutrons, electrons).
Molecules: Two or more atoms chemically bonded.
Compounds: Atoms of different elements bonded in specific proportions.

Key Elements in Living Organisms

Primary Elements (96%): Carbon (C), Hydrogen (H), Oxygen (O), Nitrogen (N).
Secondary Elements (4%): Calcium (Ca), Phosphorus (P), Potassium (K), Sodium (Na), Sulfur (S), Magnesium (Mg).
Trace Elements (<0.1%): Iodine (I), Iron (Fe).

Atomic Structure

Atoms consist of protons (+), neutrons (neutral), and electrons (-).
Nucleus: Protons and neutrons, determining mass and stability.
Electron Orbitals: Electrons move around the nucleus, influencing chemical behavior.
Atomic Number: Number of protons, determines element.
Mass Number: Protons + neutrons, affecting isotopic nature.

Isotopes and Atomic Variations

Isotopes: Atoms of the same element with different neutrons.
Examples: Carbon-12, Carbon-13, Carbon-14 (radioactive).

Radioisotopes and Radioactive Decay

Radioisotopes: Unstable isotopes that decay, releasing radiation.
Decay Process: Carbon-14 decays into Nitrogen-14 (beta decay).
Biological/Medical Uses: Cancer treatment, medical imaging, sterilization.
Potential Risks: DNA damage, mutations, cancer.

Electron Arrangement and Energy Levels

Quantum Energy Levels: Electrons occupy energy levels (shells).
Shell Capacities: First shell (2 electrons), second (8), third (18).
Excitation and Stability: Atoms absorb energy, electrons jump to higher shells, emitting energy as light when returning to lower levels.

Valence Electrons and Chemical Reactivity

Valence Electrons: Outermost shell electrons determine chemical properties.
Octet Rule: Atoms gain/lose/share electrons for a stable outer shell (8 electrons).
Reactivity Trends: Incomplete valence shells are more reactive.

Chemical Bonds in Biological Molecules

Ionic Bonds: Electrostatic attraction between ions (e.g., Na+ and Cl-).
Covalent Bonds: Atoms share electrons (e.g., H2O, CO2, CH4).
Hydrogen Bonds: Weak interactions between polar molecules (e.g., DNA).
Van der Waals Forces: Weak intermolecular forces.

Polar Molecules and Electronegativity

Electronegativity: Atom's ability to attract electrons in a bond.
Polar Covalent Bonds: Unequal sharing of electrons (e.g., water).
Biological Importance: Water's polarity enables hydrogen bonding and solvent properties.

Dehydration Reactions

Removal of -OH and -H from two reactants.
Forms a water molecule and joins reactants.
Used to build larger polymers.

Hydrolysis Reactions

Reverse of dehydration reactions.
Water breaks down large molecules.
-OH and -H from water are added to products.
Essential for digestion and metabolism.

Redox Reactions

Involve electron transfer between atoms.
Oxidation: Loss of electrons.
Reduction: Gain of electrons.
Always occur together.
Essential in cellular respiration.

Neutralization Reactions

Occur between acids and bases.
Produce salts and often water.
Important for pH balance in biological systems.

Water - Essential Molecule for Life

60% of the human body is water.
Facilitates cellular processes, acts as a transport medium, regulates temperature, provides structural support.

Unique Properties of Water

"Universal solvent".
Hydrogen bonding properties (cohesion, adhesion).
High specific heat.
Density differences between liquid and ice.

Hydrophilic vs. Hydrophobic

Hydrophilic: "Water-loving", polar, dissolves in water (e.g., salt, sugar).
Hydrophobic: "Water-fearing", non-polar, repels water (e.g., oils, fats).

The pH Scale

Acids: pH below 7, presence of H+ ions.
Bases: pH above 7, presence of OH- ions.
pH affects chemical reactivity and solubility.

Acids and Bases in Chemical Reactions

Acids donate hydrogen ions.
Bases accept hydrogen ions or release hydroxide ions.
Strong acid/base completely dissociates in water; weak acid/base partially dissociates.
Buffers regulate pH by absorbing excess H+ or OH- ions.

Carbon and Functional Groups

Carbon atoms form long chains, rings, or branched structures.
Hydrocarbons: Molecules of carbon and hydrogen.
Carbon skeleton: Chain of carbon atoms.

Functional Groups

Functional groups affect molecule function via chemical reactions.
Usually ionic or strongly polar.
Polar functional groups allow molecules to dissolve in water.
Examples: Carboxyl, amino, phosphate.

Nutrients - Carbohydrates

Body’s main source of energy.
Consist of carbon, oxygen, and hydrogen.
Simple Sugars (Monosaccharides): Triose, pentose, hexose backbones.

Disaccharides

Two monosaccharides bond together, forming H2O.
Bond between the sugars is a glycosidic linkage.

Complex Carbohydrates - Polysaccharides

Chains of monosaccharides joined by glycosidic linkages.
Function as storage (glycogen, starch) or structural (cellulose, chitin) carbs.

Lipids

Store energy, insulate the body, protect organs.
Categories: Fatty acids, fats, phospholipids, steroids, waxes.

Fatty Acids

Hydrocarbon chain with a carboxyl group (-COOH).
Saturated: Firmer, lack double bonds.
Unsaturated: Contain double bonds.

Fats

One glycerol molecule with one to three fatty acids.
Triglycerides: well-known fats.
Trans Fats
- Increase LDL cholesterol and decrease HDL cholesterol. These are generally not found in nature.

Phospholipids

Main components of cell membranes.
Phosphate group and two fatty acids attached to glycerol.

Steroids

Four fused carbon rings.
Differ by side groups attached to the rings.

Waxes

Hydrophobic, non-polar.
Example: Wax coating on fruits.

Proteins

*Composed of amino acid monomers.

Polypeptides have more than 50 amino acids linked together.
A protein is one or more polypeptides folded into a 3D shape.

Protein Structure

Primary Structure: The amino acid sequence.
Secondary Structure: Folding or spiraling due to hydrogen bonding.
Tertiary Structure: Further folding.
Quaternary Structure: Two or more polypeptides come together

Nucleic Acids

Polymers of nucleotides.
Linked by phosphodiester bonds.
Bases: Purines (double ring) and pyrimidines (single ring).

Enzymes

Biological catalysts that speed up chemical reactions.
Essential for metabolism, digestion, and cellular processes.

Enzyme Structure

Active Site: Region where substrate binds.
Substrate: Reactant molecule.
Product: Resulting molecule.

Enzyme Function

Lower Activation Energy.
Provide an Alternative Reaction Pathway.

Activation Energy and Enzymes

Activation energy is the minimum energy required for a reaction.
Stabilize transition state. Reduce energy needed.

Induced Fit Hypothesis

This demonstrates that enzyme is flexible and adapts its shape when the substrate binds.

Unfavorable Reactions and Enzymes

Endergonic reactions absorb energy rather than release it.

Cofactors and Coenzymes

Non-protein molecules aiding enzyme function.
Types: Metal Ions, Organic Cofactors (Coenzymes).

Enzymes and Substrate Concentration

Higher enzyme concentration increases reaction rate if substrate is available.
Higher substrate concentration increases rate until saturation.

pH and Temperature Effects on Enzymes

Each enzyme has an optimal pH; extreme pH denatures enzymes.
High temperature increases kinetic energy but too high denatures enzymes.

Enzyme Inhibitors

Molecules reducing enzyme activity.
Types: Competitive (binds active site), Noncompetitive (alters shape).

Allosteric Regulation

Regulation by molecules binding to an allosteric site.
Activator enhances function; Inhibitor decreases activity.

Allosteric Site

Sites where regulatory molecules bind.
Can increase or decrease enzyme activity.

Feedback Inhibition

Final product of a pathway inhibits an earlier enzyme.
Prevents overproduction and maintains balance.