Chapter 2: The Chemistry of Life – Study Notes

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Chapter 2: The Chemistry of Life

2.1 Overview of Molecules and Atoms

Understanding the chemical basis of life is essential for studying biology. All living and nonliving things are composed of matter, which exists in three physical states: solid, liquid, and gas.

Matter: Anything that occupies space and has mass.
Atoms: The smallest units retaining the properties of their type of matter. Atoms bond to form molecules.
Elements: Basic substances that cannot be broken down by chemical means. Each element consists of one type of atom.
Compounds: Substances formed by the chemical combination of two or more elements (e.g., NaCl – table salt).

Example: Table salt (NaCl) is formed from sodium (Na) and chlorine (Cl) atoms.

2.2 Matter is Composed of Elements

The periodic table organizes all known elements by atomic number. Elements are essential to life, with only a few making up most of living cells.

Elements are listed by atomic number (number of protons).
Four elements (oxygen, carbon, hydrogen, nitrogen) make up 96.3% of living cells.
Other elements are required in smaller or trace amounts.

Table: Major Elements in Living Cells

Element	Approximate % in Cells
Oxygen (O)	65%
Carbon (C)	18.5%
Hydrogen (H)	9.5%
Nitrogen (N)	3.3%

2.3 Atom Composition

Atoms are made of three subatomic particles: protons, neutrons, and electrons.

Protons: Positive charge, located in the nucleus, determine the element.
Neutrons: No charge, located in the nucleus, determine the isotope.
Electrons: Negative charge, orbit the nucleus, determine ion state and chemical reactivity.

Isotopes are atoms of the same element with different numbers of neutrons. Ions are atoms that have gained or lost electrons, becoming charged.

2.4 Chemical Bonds

Atoms are held together by chemical bonds, which are crucial for forming molecules.

Ionic Bonds: Transfer of electrons from one atom to another, resulting in oppositely charged ions that attract each other.
Covalent Bonds: Sharing of one or more pairs of electrons between atoms. Covalent bonds can be single, double, or triple and are the strongest type of bond.
Nonpolar Covalent Bonds: Equal sharing of electrons.
Polar Covalent Bonds: Unequal sharing of electrons, leading to partial charges (e.g., in water molecules).
Hydrogen Bonds: Weak bonds between polar molecules, important in water and biological molecules.

Example: Water (H2O) contains polar covalent bonds and forms hydrogen bonds with other water molecules.

2.5 The Properties of Water

Water's unique properties are essential for life and are due to its polar nature and ability to form hydrogen bonds.

Ice floats because stable hydrogen bonds hold water molecules apart, making ice less dense than liquid water.
Water is an excellent solvent, dissolving many substances necessary for life.
Water resists temperature changes, helping regulate climate and body temperature.
Cohesion and adhesion: Water molecules stick together and to other surfaces, creating surface tension.

Example: Surface tension allows small insects to walk on water.

2.6 pH

The pH scale measures the acidity or basicity of a solution, which is critical for biological processes.

Acids: Release H+ ions in solution (pH < 7).
Bases: Remove H+ ions from solution (pH > 7).
Buffers: Substances that minimize changes in pH by accepting or donating H+ ions.

Equation:

Changes in pH can affect organism health and ecosystem stability, such as ocean acidification impacting marine life.

2.7 Life is Based on Carbon

Carbon's ability to form four covalent bonds makes it the backbone of organic molecules.

Carbon forms large, branched, and diverse molecules.
Organic compounds contain carbon bonded to other elements.
Functional groups attached to carbon skeletons determine molecular properties and reactions.

2.8 Polymers

Most biological macromolecules are polymers, made by joining smaller units called monomers.

Dehydration Synthesis: Links monomers by removing water.
Hydrolysis: Breaks polymers into monomers by adding water.

Example: Digestion breaks down food polymers into monomers for absorption.

2.9 Carbohydrates

Carbohydrates are a major energy source and structural component in living organisms.

Monosaccharides: Simple sugars (e.g., glucose, fructose).
Disaccharides: Two monosaccharides joined together (e.g., sucrose).
Polysaccharides: Long chains of monosaccharides (e.g., starch, cellulose, glycogen, chitin).

2.10 Lipids

Lipids are hydrophobic molecules that include fats, oils, and steroids. They serve as energy storage, insulation, and are key components of cell membranes.

Triglycerides: Main form of stored fat in animals.
Phospholipids: Form the bilayer of cell membranes.
Steroids: Include cholesterol and hormones like estrogen and testosterone.

2.11 Dietary Fats

Fats are classified based on their chemical structure and health effects.

Type	Structure	State at Room Temp	Source	Health Impact
Saturated	No double bonds	Solid	Animal products	Less healthy
Unsaturated	One or more double bonds	Liquid	Plant products	Healthier
Trans fat	Unusual double bond (hydrogenated)	Solid	Processed foods	Unhealthy
Omega-3	Double bond at third carbon	Liquid	Fish, some plants	Beneficial

2.12 Proteins

Proteins are polymers of amino acids and perform a vast array of functions in living organisms.

Each protein has a unique sequence and shape, determining its function.
Proteins are made by linking amino acids via peptide bonds to form polypeptides.
Protein function depends on its three-dimensional structure.

2.13 Enzymes

Enzymes are proteins that catalyze (speed up) chemical reactions by lowering activation energy.

Each enzyme is specific to its substrate.
Enzyme activity can be inhibited by competitive or noncompetitive inhibitors.
Enzyme function depends on its shape; changes (mutations) can lead to loss of function (e.g., lactose intolerance).

Equation: