Unit 2: Biochemistry – General Biology Study Notes

Unit 2: Biochemistry

Overview & Purpose

This unit introduces the atoms and molecules that form the basis of living organisms. Students will learn fundamental chemistry concepts relevant to biology, including atomic structure, chemical bonds, chemical equations, and the properties of water. The unit also covers macromolecules such as lipids, nucleic acids, proteins, and carbohydrates, their structure, function, and synthesis. Understanding these concepts is essential for grasping the molecular foundations of life and for success in subsequent biology topics.

Matter and Chemical Elements

2.1 Pure Elements and Compounds

Matter consists of chemical elements in pure form and in combinations called compounds.

• Element: A substance that cannot be broken down into other substances by chemical means (e.g., Oxygen, Carbon).

• Compound: A substance formed when two or more elements are chemically bonded in fixed ratios (e.g., Water - H2O).

• Comparison: Elements are pure, while compounds are combinations of elements.

2.2 Atomic Structure and Isotopes

The properties of elements depend on the structure of their atoms.

• Atom: The smallest unit of an element, composed of protons, neutrons, and electrons.

• Electron Shells: Electrons are arranged in shells around the nucleus; the arrangement affects chemical reactivity.

• Isotope: Atoms of the same element with different numbers of neutrons.

Example: Carbon-12 and Carbon-14 are isotopes of carbon.

Chemical Bonding and Molecule Formation

2.3 Chemical Bonds

Molecules are formed by chemical bonds between atoms.

• Covalent Bond: Atoms share electrons (e.g., H2O).

• Ionic Bond: Atoms transfer electrons, forming ions (e.g., NaCl).

• Hydrogen Bond: Weak attraction between a hydrogen atom and an electronegative atom (important in water and DNA).

• Van der Waals Interactions: Weak attractions due to transient charge differences.

Example: Water molecules are held together by hydrogen bonds.

2.4 Chemical Reactions

Chemical reactions make and break chemical bonds, transforming reactants into products.

• Reactant: Starting substance in a chemical reaction.

• Product: Substance formed as a result of a chemical reaction.

• Equation Example: $2H_2 + O_2 \rightarrow 2H_2O$

Properties of Water

2.5 Water’s Structure and Function

Water’s unique properties are essential for life.

• Polarity: Water is a polar molecule, with partial positive and negative charges.

• Hydrogen Bonding: Water molecules form hydrogen bonds, leading to cohesion, adhesion, and surface tension.

• High Specific Heat: Water resists temperature changes, stabilizing environments.

• Solvent Properties: Water dissolves many substances, facilitating chemical reactions.

• pH Scale: Measures hydrogen ion concentration; water is neutral at pH 7.

• Buffer Systems: Help maintain stable pH in biological systems.

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

Example: Blood uses bicarbonate buffer to maintain pH.

Carbon Chemistry

3.1 Carbon Bonding

Carbon can form diverse molecules by bonding to four other atoms.

• Electron Configuration: Carbon’s four valence electrons allow it to form single, double, or triple bonds.

• Structural Diversity: Carbon skeletons can be straight, branched, or ring-shaped.

• Functional Groups: Groups of atoms that confer specific properties (e.g., hydroxyl, carboxyl).

Example: Glucose and fatty acids have different carbon skeletons and functional groups.

Macromolecules

3.2 Polymers and Monomers

Macromolecules are large polymers built from monomers.

• Polymer: Long molecule made of repeating units (monomers).

• Dehydration Synthesis: Joins monomers by removing water.

• Hydrolysis: Breaks polymers into monomers by adding water.

Example: Proteins are polymers of amino acids.

3.3 Carbohydrates

Carbohydrates serve as fuel and building material.

• Monosaccharide: Simple sugar (e.g., glucose).

• Disaccharide: Two monosaccharides joined (e.g., sucrose).

• Polysaccharide: Many monosaccharides (e.g., starch, glycogen, cellulose).

Example: Starch stores energy in plants; cellulose forms plant cell walls.

3.4 Lipids

Lipids are diverse group of hydrophobic molecules.

• Triglyceride: Composed of glycerol and three fatty acids.

• Phospholipid: Major component of cell membranes; forms bilayers.

• Steroid: Lipid with four fused rings (e.g., cholesterol).

Example: Phospholipids form the bilayer of cell membranes.

3.5 Proteins

Proteins are polymers of amino acids with diverse functions.

• Amino Acid: Contains central carbon, amino group, carboxyl group, and R group.

• Primary Structure: Sequence of amino acids.

• Secondary Structure: Alpha helix and beta sheet formed by hydrogen bonding.

• Tertiary Structure: 3D folding due to interactions among R groups.

• Quaternary Structure: Multiple polypeptides assembled together.

Example: Hemoglobin is a protein with quaternary structure.

3.6 Nucleic Acids

Nucleic acids store, transmit, and help express hereditary information.

• Nucleotide: Monomer with a five-carbon sugar, phosphate group, and nitrogenous base.

• DNA: Deoxyribonucleic acid; stores genetic information.

• RNA: Ribonucleic acid; involved in protein synthesis and gene regulation.

• Purines vs. Pyrimidines: Two types of nitrogenous bases; purines (adenine, guanine), pyrimidines (cytosine, thymine, uracil).

Example: DNA double helix is formed by complementary base pairing.

Additional info: The difference in function between DNA, mRNA, tRNA, and rRNA will be covered in more detail in later units.

Key Terms Table

The following table summarizes key terms from Chapters 2 and 3, organized by topic:

Chapter 2

Chapter 3

Matter Element Compound Essential elements Atom Neutron Proton Electron Atomic nucleus Mass number Atomic mass Isotope Radioactive isotope Energy Potential energy Electron shell Valence electron Valence shell Chemical bonds Covalent bond Molecule Single bond Double bond Valence Polar covalent bond Ion Cation Anion Ionic bond Ionic compounds Salts Hydrogen bonds Van der Waals interactions Reactant Product Chemical equilibrium Polar molecule Cohesion Adhesion Surface tension Kinetic energy Thermal energy Temperature Heat Calorie Kilocalorie Specific heat Heat of vaporization Evaporative cooling Solution Solvent Solute Aqueous solution Hydration shell Hydrophilic Hydrophobic Mole Molarity Hydrogen ion Hydroxide ion Acid Base pH Buffer Ocean acidification

Organic compound Macromolecules Valence Isomers Structural isomers Cis-trans isomers Enantiomers Functional groups ATP Polymer Monomer Enzyme Dehydration reaction Hydrolysis Carbohydrates Monosaccharide Disaccharide Polysaccharide Glycogen Cellulose Chitin Lipid Fat Triacylglycerol Saturated fatty acid Unsaturated fatty acid Trans fat Phospholipid Steroid Cholesterol Catalyst Polypeptide Amino acid Peptide bond Primary structure Secondary structure Alpha helix Beta pleated sheet Tertiary structure Hydrophobic interaction Disulfide bridge Quaternary structure Denaturation Sickle-cell disease Chaperonin X-ray crystallography Gene Nucleic acid DNA RNA Gene expression Polynucleotide Pyrimidine Purine Nucleotide Deoxyribose Ribose Double helix Antiparallel skip

Recommended Resources

• Campbell Biology in Focus, AP Edition, 3rd Edition – Chapters 2 & 3

• Bozeman Science Videos: Chemical Bonding, Properties of Water, Molecules of Life, Polymers, Carbohydrates, Lipids, Proteins, Nucleic Acids

• JOVE Chemistry of Life Videos