General Biology Exam 1 Study Guide: Chemistry and Biological Molecules

General Information & Scientific Method

Characteristics of Living Organisms

• Living organisms share key characteristics such as organization, metabolism, homeostasis, growth, reproduction, response to stimuli, and adaptation through evolution.

Scientific Method

• Hypothesis: A testable statement or prediction about a natural phenomenon.

• Theory: A well-substantiated explanation of some aspect of the natural world, based on a body of evidence.

• Fact: An observation that has been repeatedly confirmed.

• Components of a well-designed experiment: Includes independent and dependent variables, controls, and replicates.

• Independent variable: The variable that is manipulated.

• Dependent variable: The variable that is measured.

• Scatter plot, line graph, bar graph: Types of data visualization used to represent experimental results.

• p values: Statistical measure indicating the probability that results are due to chance.

Basic Chemistry

Atoms and Elements

• Element: A substance that cannot be broken down into simpler substances by chemical means.

• Compound: A substance formed from two or more elements chemically bonded together.

• Essential elements: Elements required for life (e.g., C, H, O, N, P, S).

• Trace elements: Elements required in minute amounts (e.g., Fe, Zn, I).

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

• Atomic nucleus: The central core of an atom, containing protons and neutrons.

• Proton: Positively charged subatomic particle.

• Neutron: Neutrally charged subatomic particle.

• Electron: Negatively charged subatomic particle.

• Atomic number: Number of protons in an atom.

• Mass number: Sum of protons and neutrons in an atom.

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

Valence Electrons and Chemical Bonds

• Valence electrons: Electrons in the outermost shell, involved in chemical bonding.

• Electronegativity: The ability of an atom to attract electrons in a covalent bond.

• Covalent bond: A chemical bond formed by the sharing of electron pairs between atoms.

• Polar covalent bond: Electrons are shared unequally, resulting in partial charges.

• Non-polar covalent bond: Electrons are shared equally.

• Ionic bond: Transfer of electrons from one atom to another, resulting in oppositely charged ions.

Intermolecular Bonds/Interactions

• Hydrogen bond: Weak attraction between a hydrogen atom covalently bonded to an electronegative atom and another electronegative atom.

• Van der Waals interactions: Weak attractions due to transient local partial charges.

Properties of Water

• Cohesion and adhesion: Cohesion is the attraction between water molecules; adhesion is the attraction between water and other substances.

• Thermal regulation: Water has a high specific heat, helping to stabilize temperatures.

• Expansion and floating when frozen: Ice is less dense than liquid water, so it floats.

• Common solvent in nature: Water dissolves many substances, making it a universal solvent.

Solution Component	Description
Solute	Substance dissolved in a solution
Solvent	Substance that dissolves the solute (often water)

• Acid: Substance that increases H+ concentration in solution.

• Base: Substance that decreases H+ concentration.

• pH: Measure of hydrogen ion concentration; $pH = -\log[H^+]$

• Buffer: Substance that minimizes changes in pH.

Carbon Chemistry

Organic Molecules and Isomers

• Hydrocarbon: Molecule consisting only of carbon and hydrogen.

• Isomers: Compounds with the same molecular formula but different structures.

• Structural isomers: Differ in covalent arrangement of atoms.

• Geometric isomers: Differ in spatial arrangement around a double bond.

• Enantiomers: Mirror-image isomers due to asymmetric (chiral) carbon.

Functional Groups

• Hydroxyl group (-OH): Alcohols; polar, forms hydrogen bonds.

• Carbonyl group (C=O): Aldehydes and ketones; polar.

• Carboxyl group (-COOH): Acts as an acid.

• Amino group (-NH2): Acts as a base.

• Phosphate group (-PO4): Contributes negative charge.

• Methyl group (-CH3): Nonpolar, affects gene expression.

Polymers and Monomers

• Polymer: Large molecule made of repeating subunits (monomers).

• Monomer: Small building block molecule.

• Dehydration reaction: Joins monomers by removing water (condensation reaction).

• Hydrolysis: Breaks polymers by adding water.

Biological Macromolecules

Carbohydrates

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

• Disaccharide: Two monosaccharides joined by a glycosidic linkage (e.g., sucrose).

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

• Glycosidic linkage: Covalent bond joining monosaccharides.

• Structure of starch vs. glycogen: Both are storage polysaccharides; starch in plants, glycogen in animals.

• Cellulose: Insoluble fiber, structural polysaccharide in plant cell walls.

Lipids

• Hydrophobic: Repels water; nonpolar molecules.

• Hydrophilic: Attracts water; polar molecules.

• Fats: Composed of glycerol and fatty acids; energy storage.

• Unsaturated vs. saturated fats: Unsaturated fats have double bonds; saturated fats do not.

• Phospholipid: Glycerol, two fatty acids, and a phosphate group; forms cell membranes.

• Phospholipid bilayer: Double layer of phospholipids in cell membranes; amphipathic (hydrophilic head, hydrophobic tails).

• Steroids: Lipids with four fused rings (e.g., cholesterol).

Proteins

• Polypeptide: Polymer of amino acids.

• Amino acids: Building blocks of proteins; 20 types with different side chains (R groups).

• Non-polar side chains: Hydrophobic.

• Polar side chains: Hydrophilic.

• Acidic/basic side chains: Charged, hydrophilic.

• Peptide bond: Covalent bond between amino acids.

• N-terminus: End with free amino group.

• C-terminus: End with free carboxyl group.

• Primary structure: Sequence of amino acids.

• Secondary structure: Local folding (alpha helix, beta pleated sheet) stabilized by hydrogen bonds.

• Tertiary structure: 3D shape formed by interactions among R groups.

• Quaternary structure: Association of multiple polypeptides.

• Denaturation: Loss of protein structure and function due to environmental changes.

Nucleic Acids

• DNA (deoxyribonucleic acid): Stores genetic information.

• RNA (ribonucleic acid): Involved in protein synthesis and gene regulation.

• Sugar-phosphate backbone: Alternating sugars and phosphates in nucleic acid chains.

• Phosphodiester bond: Covalent bond linking nucleotides.

• Nucleotide: Monomer of nucleic acids; consists of a sugar, nitrogenous base, and phosphate group.

Summary Table: Biological Macromolecules

Macromolecule	Monomer	Bond Type	Main Functions
Carbohydrates	Monosaccharide	Glycosidic linkage	Energy storage, structure
Lipids	Glycerol & fatty acids	Ester linkage	Energy storage, insulation, membranes
Proteins	Amino acid	Peptide bond	Enzymes, structure, transport, signaling
Nucleic acids	Nucleotide	Phosphodiester bond	Genetic information storage & transfer

Practice Questions and Key Concepts

• Covalent vs. hydrogen bond: Covalent bonds are strong, involve sharing electrons; hydrogen bonds are weak, involve attraction between partial charges.

• Hydrogen bonding: Involves partial charges, polar covalent bonds, and electronegativity differences.

• Properties of water: Cohesion, adhesion, high specific heat, expansion upon freezing, solvent abilities.

• Buffer systems: Bicarbonate buffer maintains blood pH by reversible reactions: $H_2CO_3 \rightleftharpoons HCO_3^- + H^+$

• Valence electrons: Dictate the number of covalent bonds an atom can form.

• Carbon's versatility: Can form four covalent bonds, allowing for diverse organic molecules.

• Macromolecule functions: Carbohydrates (energy, structure), lipids (energy, membranes), proteins (many functions), nucleic acids (genetic information).

• Polymerization: Dehydration (condensation) reactions join monomers; hydrolysis splits them.

• Bond types: Glycosidic (carbohydrates), ester (lipids), peptide (proteins), phosphodiester (nucleic acids).

• Functional groups in adrenaline: Alcohol (-OH), amine (-NH2 or similar).

Additional info:

• For exam preparation, focus on understanding definitions, functions, and relationships between terms.

• Be able to apply concepts to biological systems and interpret data from graphs and tables.