General Biology: Foundations of Chemistry and Biological Molecules

Foundations of Chemistry in Biology

Matter, Elements, and Atoms

Understanding the basic chemical principles is essential for studying biological systems. Matter and its organization into elements and atoms form the basis of all living and non-living things.

• Matter: Anything that has mass and takes up space.

• Element: A pure substance consisting of only one type of atom; cannot be broken down by chemical means.

• Atom: The smallest unit of an element, retaining its chemical properties.

• Atomic #: Number of protons in an atom; determines the element and the number of electrons in a neutral atom.

• Subatomic particles:

  • Protons (P+): Positive charge, located in the nucleus.

  • Neutrons: Neutral charge, located in the nucleus.

  • Electrons (E-): Negative charge, orbit the nucleus in shells.

Elements in the Human Body

Elements are classified as essential or trace based on their abundance and biological roles.

Essential Elements (96%)	Trace Elements (3.7%)
Oxygen	Calcium
Carbon	Phosphorus
Hydrogen	Potassium
Nitrogen	Sulfur
	Sodium
	Chlorine
	Magnesium

Electron Shells and Energy

Electrons are arranged in shells around the nucleus, influencing chemical reactivity.

• Electrons in the inner shell have the least amount of energy.

• Valence Shell: The outermost electron shell; electrons here determine bonding behavior.

• Valence Electrons: Electrons in the valence shell; unpaired electrons can bond with others.

Molecules and Compounds

Molecules and compounds are formed by atoms bonding together in specific ratios.

• Molecule: Two or more atoms bonded together.

• Compound: Substance made of two or more different atoms bonded in a fixed ratio.

Chemical Bonds

Chemical bonds hold atoms together in molecules and compounds. There are several types:

• Covalent Bonds: Strongest; atoms share pairs of electrons.

  • Non-polar: Equal sharing of electrons (e.g., O2).

  • Polar: Unequal sharing, resulting in partial charges (e.g., H2O).

• Ionic Bonds: Middle strength; electrons are transferred, forming charged ions.

• Hydrogen Bonds: Weakest; form between polar molecules due to attraction between opposite charges.

Electronegativity

Electronegativity is the tendency of an atom to attract electrons in a bond.

• Non-polar Covalent Bonds: Atoms with equal electronegativity.

• Polar Covalent Bonds: Atoms with unequal electronegativity; shared electrons are pulled closer to the more electronegative atom.

Ions

• Cation: Positively charged ion.

• Anion: Negatively charged ion.

Chemical Reactions

Chemical reactions involve making or breaking chemical bonds.

• Reactants: Substances entering the reaction.

• Products: Substances produced by the reaction.

Water and Life

Properties of Water

Water's unique properties are essential for life, largely due to hydrogen bonding.

• Cohesion: Water molecules stick to each other via hydrogen bonds.

• Adhesion: Water molecules stick to other substances.

• Surface Tension: Resistance of a liquid's surface to breaking; water has high surface tension due to hydrogen bonding.

• Ability to Moderate Temperature: Water absorbs and releases heat slowly.

• Expansion Upon Freezing: Water expands as it freezes, making ice less dense than liquid water.

• Versatility as a Solvent: Water dissolves many substances, forming aqueous solutions.

Term	Definition
Solution	Even mixture of solute and solvent
Solvent	Liquid that dissolves the solute
Solute	Substance being dissolved
Aqueous Solution	Solution with water as the solvent

Hydrophilic and Hydrophobic Substances

• Hydrophobic: Substances that do not interact with water (e.g., oils).

• Hydrophilic: Substances that interact with and dissolve in water.

Acids, Bases, and pH

Acids and bases affect the concentration of hydrogen ions in solution.

• Acid: Substance with a lot of H+ ions.

• Base: Substance with a lot of OH- ions.

• Buffer: Substance that neutralizes acids and bases.

• pH Scale: Measures acidity/basicity; ranges from 0 (most acidic) to 14 (most basic), with 7 as neutral.

Formula:

$\text{pH} = -\log_{10}[\text{H}^+]$

Carbon and the Molecular Diversity of Life

Organic Chemistry

Organic chemistry studies carbon-containing compounds, which are the basis of biological molecules.

• Carbon skeletons can vary in:

  • Length

  • Branching

  • Double bond position

  • Presence of rings

• Hydrocarbons: Chains of carbon atoms with attached hydrogens.

• Functional Groups: Chemical groups attached to the carbon skeleton that determine molecular properties.

The Structure and Function of Large Biological Molecules

Macromolecules

Large biological molecules are essential for life and are built from smaller units.

• Monomers: Small molecules that bond together to form polymers.

• Polymers: Large molecules made of many monomers.

• Macromolecules: Giant polymers (e.g., proteins, nucleic acids).

Making and Breaking Down Molecules

• Enzymes: Special proteins that speed up chemical reactions.

• Dehydration Reaction: Joins monomers by removing a water molecule.

• Hydrolysis: Breaks polymers apart by adding a water molecule.

Types of Macromolecules

Type	Monomer	Function
Carbohydrates	Monosaccharides	Energy, structure
Lipids	Not true polymers	Energy storage, membranes, hormones
Proteins	Amino acids	Structure, enzymes, signaling
Nucleic Acids	Nucleotides	Genetic information

Lipids

Lipids are hydrophobic molecules important for energy storage and membrane structure.

• Not true polymers

• Mix poorly with water

• Consist mostly of hydrocarbon regions

Fats

• Major function: energy storage

• Constructed from glycerol and fatty acids

• Glycerol: Three-carbon alcohol with hydroxyl groups

• Fatty acid: Long hydrocarbon chain with carboxyl group

• Unsaturated fatty acids: Have double bonds, causing kinks (common in plants and fish)

• Saturated fatty acids: No double bonds, straight chains (common in animal fats)

Phospholipids

• Major component of cell membranes

• Made of phosphate head (hydrophilic) and two fatty acid tails (hydrophobic)

• Form bilayers in water, with heads facing outward and tails inward

Steroids

• Characterized by four fused carbon rings

• Function as hormones (e.g., cholesterol, testosterone)

Proteins

Proteins are polymers of amino acids and perform a wide variety of functions.

• Amino acids: Have an amino group, carboxyl group, and a variable side chain (R group)

• Polypeptides: Chains of amino acids

• Protein: One or more polypeptides folded into a specific shape

Structure and Function: Chemical and physical conditions (pH, salt, temperature) affect protein structure; denaturation is the loss of structure and function.

Nucleic Acids

Nucleic acids store and transmit genetic information.

• Functions:

  1. Store hereditary material

  2. Transmit hereditary information

  3. Help express hereditary information (instructions for protein synthesis)

• Types:

  • Deoxyribonucleic acid (DNA)

  • Ribonucleic acid (RNA)

• Nucleic acids are polymers of nucleotides.

Nitrogenous Bases

Base	Found in
Thymine (T)	DNA
Adenine (A)	DNA & RNA
Guanine (G)	DNA & RNA
Cytosine (C)	DNA & RNA
Uracil (U)	RNA

• Base Pairing (DNA): A-T, G-C

• Base Pairing (RNA): A-U, G-C

RNA Structure

• Single stranded

• Complementary pairing can occur between two RNA molecules or within the same molecule

DNA Structure

• DNA molecules consist of two polynucleotides spiraling around an imaginary axis, forming a double helix

Example: The double helix structure of DNA allows for complementary base pairing, which is essential for accurate replication and transmission of genetic information.

Additional info: This guide expands on the original notes by providing definitions, examples, and academic context for each topic, ensuring completeness and clarity for exam preparation.