Chemistry of Biology & Biological Molecules: Study Notes

Chemistry of Biology & Biological Molecules

Understanding the chemistry underlying biological molecules is essential for studying biology. This section covers the structure and function of atoms, ions, molecules, and the major classes of biological macromolecules, as well as the importance of water and chemical bonds in biological systems.

Part 1: BioSkill 2 – Graphing

Graphs are fundamental tools for analyzing and communicating data in biology.

• Dependent Variable: The variable that is measured or observed in response to changes in the independent variable.

• Independent Variable: The variable that is manipulated or changed to observe its effect on the dependent variable.

• Steps to Reading a Graph:

  1. Read the axes to understand what is being measured.

  2. Look at the data points or bars to interpret the results.

  3. Determine the main point or trend shown by the graph.

• Scatterplots vs. Bar Graphs: Use a scatterplot when the independent variable is continuous (e.g., time, temperature). Use a bar graph when the independent variable is categorical or represents ranges.

Atoms, Ions, and Molecules

Subatomic Particles

Atoms are composed of smaller particles called subatomic particles, each with distinct properties.

Subatomic Particle Name	Charge	Property
Electron	Negative	Interacts with other atoms to form bonds
Proton	Positive	Determines the identity of the atom
Neutron	Neutral	The number can cause an atom to be radioactive

• Atomic Number: The number of protons in an atom, which identifies the element.

Common Elements in Living Organisms

The most common elements in living organisms are carbon (C), hydrogen (H), nitrogen (N), and oxygen (O). Their ability to form covalent bonds and their electronegativity are key to their biological roles.

Atom Name (Symbol)	Number of Covalent Bonds	Rank Electronegativity
Carbon (C)	4	2
Hydrogen (H)	1	4
Nitrogen (N)	3	3
Oxygen (O)	2	1

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

Covalent Bonds

Type of Covalent Bond	Definition	Example
Nonpolar Covalent Bonds	A bond that has equally shared electrons	Hydrogen molecule (H2)
Polar Covalent Bonds	Nonequal amount of electrons	Water molecule (H2O)
Ionic Bonds	A bond formed when an electron is transferred from one atom to another	Sodium chloride (NaCl)

Life Depends on Water

Water is essential for life due to its unique chemical and physical properties, which arise from its polar covalent bonds and ability to form hydrogen bonds.

• Electrostatic Interactions: Interactions dependent on opposite charges, such as hydrogen bonding.

• Hydrophilic Substances: Interact with water molecules and dissolve easily (e.g., salts, sugars).

• Hydrophobic Substances: Do not interact with water and tend to aggregate (e.g., oils, fats).

Carbon and Functional Groups

Importance of Carbon

• Carbon can form four covalent bonds, allowing for a variety of stable structures (chains, rings, branches).

• Its versatility enables the formation of complex organic molecules essential for life.

Functional Groups

Functional groups are specific groups of atoms within molecules that determine the chemical properties and reactions of those molecules.

Functional Group	Structure
Amino	-NH2
Carboxyl	-COOH
Hydroxyl	-OH
Phosphate	-PO4

Macromolecules and Polymers

• Polymer: A large molecule made by joining many smaller molecules (monomers) together.

• Condensation Reaction (Dehydration Synthesis): Monomers are joined together, releasing water.

• Hydrolysis: Polymers are broken down into monomers by the addition of water.

Nucleic Acids

Nucleic acids are polymers of nucleotides and are essential for storing and transmitting genetic information.

• Nucleotide Structure: Each nucleotide consists of a phosphate group, a five-carbon sugar, and a nitrogenous base.

• Nitrogenous Bases:

  • DNA: Adenine (A), Guanine (G), Cytosine (C), Thymine (T)

  • RNA: Adenine (A), Guanine (G), Cytosine (C), Uracil (U)

• Sugar in Nucleic Acids: DNA contains deoxyribose; RNA contains ribose.

Carbohydrates

Carbohydrates are organic molecules composed of carbon, hydrogen, and oxygen. They serve as energy sources and structural components in cells.

Type	Description	Example
Monosaccharide	Single monomer with a carbon backbone, carbonyl group, and hydroxyl groups	Glucose
Disaccharide	Formed when two simple sugars link together	Lactose
Polysaccharide	Formed by the polymerization of monosaccharides through glycosidic linkages	Starch

• Hydrophilicity: Simple sugars are hydrophilic due to their polar hydroxyl groups, which form hydrogen bonds with water.

• Enzymatic Breakdown: Enzymes in saliva break down starches into simple sugars, making foods taste sweet after chewing.

Lipids

Lipids are a diverse group of hydrophobic molecules that include fats, oils, waxes, and steroids. They are important for energy storage, membrane structure, and signaling.

• Definition: A lipid is a carbon-containing compound that is insoluble in water.

• Examples: Butter, beeswax, safflower oil, Crisco.

• Fatty Acids: A fatty acid is a hydrocarbon chain with a carboxyl group. Saturated fatty acids have straight chains (no double bonds), while unsaturated fatty acids have one or more double bonds, causing kinks in the chain.