General Chemistry Foundations: Atoms, Molecules, and Biological Macromolecules

Levels of Biological Organization

Atoms, Molecules, and Cells

Understanding the hierarchy of biological organization is essential for connecting chemistry to biology. Atoms are the fundamental building blocks of matter, which combine to form molecules. These molecules assemble into organelles, which are components of cells. Groups of similar cells form tissues, and collections of tissues make up organs.

• Atoms: The smallest units of matter, retaining the properties of an element.

• Molecules: Groups of atoms bonded together by chemical bonds (e.g., H2O, O2).

• Organelles: Specialized structures within cells, composed of molecules (e.g., mitochondria).

• Cells: Basic units of life, containing organelles and performing vital functions.

• Tissues: Groups of similar cells working together for a specific function.

• Organs: Structures composed of multiple tissue types, performing complex functions.

Example: The nervous system consists of the brain (an organ), which contains nerve tissue, made up of nerve cells, which in turn are composed of molecules and atoms.

Ecosystem Dynamics

Energy Flow and Nutrient Cycling

An ecosystem is a community of living organisms interacting with their physical environment. Two major processes govern ecosystem dynamics:

• Energy Flow: Energy from sunlight is captured by producers (plants) and transferred to consumers (animals) through food chains. Energy is lost as heat at each step.

• Nutrient Cycling: Elements and compounds are recycled within the ecosystem. Nutrients taken up by plants eventually return to the soil through decomposition.

Example: Carbon cycles from the atmosphere into plants via photosynthesis, moves through consumers, and returns to the environment through respiration and decomposition.

Introduction to Chemistry

Matter and Elements

Matter is anything that occupies space and has mass. It exists in three states: solid, liquid, and gas. All matter, living or nonliving, is composed of elements, which are substances that cannot be broken down into simpler substances by ordinary chemical means.

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

• Elements: Pure substances consisting of only one type of atom. There are 118 known elements, with 92 naturally occurring.

• Periodic Table: Organizes elements by increasing atomic number and similar properties into periods (rows) and groups (columns).

Example: Oxygen (O), Carbon (C), Hydrogen (H), Nitrogen (N), Phosphorus (P), and Sulfur (S) are the most abundant elements in living organisms.

Atomic Structure

Subatomic Particles and Atomic Number

Atoms are composed of three types of subatomic particles:

• Protons: Positively charged particles located in the nucleus.

• Neutrons: Uncharged particles also found in the nucleus.

• Electrons: Negatively charged particles that orbit the nucleus in energy levels (shells).

Atomic Number (Z): The number of protons in the nucleus, unique to each element.

Mass Number (A): The sum of protons and neutrons in the nucleus.

$\text{Atomic Number} = \text{Number of Protons}$ $\text{Mass Number} = \text{Number of Protons} + \text{Number of Neutrons}$

Example: Carbon-12 has 6 protons and 6 neutrons; its atomic number is 6, and its mass number is 12.

Isotopes and Radioactivity

Isotopes and Their Uses

Isotopes are atoms of the same element with different numbers of neutrons, resulting in different mass numbers. Some isotopes are unstable and radioactive (radioisotopes), emitting radiation as they decay.

• Stable Isotopes: Do not change over time (e.g., Carbon-12).

• Radioisotopes: Unstable, decay over time, and emit particles or energy (e.g., Carbon-14).

Half-life: The time required for half of a radioactive isotope to decay.

Applications:

• Medical imaging and cancer treatment

• Dating fossils (e.g., Carbon-14 dating)

• Sterilization of food and medical equipment

Electron Arrangement and Chemical Reactivity

Electron Shells and the Octet Rule

Electrons occupy energy levels (shells) around the nucleus. The arrangement of electrons determines an atom's chemical properties.

• The first shell holds up to 2 electrons; subsequent shells hold up to 8 electrons.

• Valence Electrons: Electrons in the outermost shell, responsible for chemical reactivity.

• Octet Rule: Atoms are most stable when their outer shell has 8 electrons (except for hydrogen and helium, which are stable with 2).

Atoms achieve stability by gaining, losing, or sharing electrons to fill their outer shell.

Chemical Bonds

Ionic, Covalent, and Hydrogen Bonds

Chemical bonds form when atoms interact to achieve stable electron configurations. The three main types are:

• Ionic Bonds: Formed when electrons are transferred from one atom to another, creating oppositely charged ions that attract each other. Example: Sodium (Na) donates an electron to chlorine (Cl), forming Na+ and Cl-, which combine to make NaCl.

• Covalent Bonds: Formed when atoms share pairs of electrons. Example: Two hydrogen atoms share electrons with one oxygen atom to form water (H2O).

• Hydrogen Bonds: Weak attractions between a slightly positive hydrogen atom in one molecule and a slightly negative atom (often oxygen or nitrogen) in another molecule. Example: Hydrogen bonds between water molecules give water its unique properties.

Polarity and Water

Polar and Nonpolar Molecules

Nonpolar Covalent Bonds: Electrons are shared equally between atoms (e.g., O2).

Polar Covalent Bonds: Electrons are shared unequally, resulting in partial charges (e.g., H2O).

Polar Molecules: Have regions of partial positive and negative charge due to unequal sharing of electrons.

Example: In water, oxygen is more electronegative than hydrogen, so the shared electrons spend more time near oxygen, making it slightly negative and hydrogen slightly positive.

Water as the Solvent of Life

Properties of Water

Water's polarity allows it to dissolve many substances, making it an excellent solvent. Solutions consist of a solvent (the dissolving agent) and a solute (the dissolved substance).

• Hydrophilic: "Water-loving" substances that dissolve easily in water (e.g., salts, sugars).

• Hydrophobic: "Water-fearing" substances that do not dissolve in water (e.g., oils, fats).

Hydrogen bonds between water molecules contribute to its high specific heat, surface tension, and ability to moderate temperature.

Acids, Bases, and pH

pH Scale and Buffers

Water can dissociate into hydrogen ions (H+) and hydroxide ions (OH-):

$\mathrm{H_2O} \rightleftharpoons \mathrm{H^+} + \mathrm{OH^-}$

• Acid: Substance that increases H+ concentration in solution (pH < 7).

• Base: Substance that decreases H+ concentration (pH > 7).

• pH Scale: Ranges from 0 (most acidic) to 14 (most basic), with 7 being neutral.

Buffers: Chemicals that minimize changes in pH by accepting or donating H+ ions. For example, the bicarbonate buffer system in blood:

$\mathrm{H^+} + \mathrm{HCO_3^-} \rightarrow \mathrm{H_2CO_3}$ $\mathrm{OH^-} + \mathrm{H_2CO_3} \rightarrow \mathrm{HCO_3^-} + \mathrm{H_2O}$

Organic Molecules and Macromolecules

Carbon Chemistry and Macromolecule Structure

Organic molecules always contain carbon and hydrogen. Carbon atoms can form four covalent bonds, allowing for a variety of structures: chains, branched molecules, and rings.

• Monomers: Small, repeating subunits (e.g., glucose, amino acids, nucleotides).

• Polymers: Large molecules formed by joining monomers (e.g., starch, proteins, DNA).

Dehydration Synthesis: Joins monomers by removing a water molecule.

Hydrolysis: Breaks polymers into monomers by adding water.

Carbohydrates

Structure and Function

Carbohydrates are composed of carbon, hydrogen, and oxygen (C:H:O ratio of 1:2:1). They serve as energy sources and structural materials.

• Monosaccharides: Simple sugars (e.g., glucose, fructose, ribose, deoxyribose).

• Disaccharides: Two monosaccharides joined by dehydration synthesis (e.g., sucrose).

• Polysaccharides: Long chains of monosaccharides (e.g., starch, glycogen, cellulose, chitin).

Example: Starch is the storage form of glucose in plants; glycogen in animals; cellulose provides structural support in plants.

Lipids

Types and Functions

Lipids are hydrophobic macromolecules composed mainly of carbon, hydrogen, and oxygen. They function in energy storage, insulation, and as components of cell membranes.

• Fats and Oils: Triglycerides made of one glycerol and three fatty acids. Fats are solid at room temperature (saturated), oils are liquid (unsaturated).

• Phospholipids: Major components of cell membranes, with a hydrophilic head and hydrophobic tails, forming bilayers.

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

Emulsifiers: Molecules with both polar and nonpolar regions that help disperse fats in water (e.g., soap micelles).

Proteins

Structure, Function, and Organization

Proteins are polymers of amino acids linked by peptide bonds. They perform a wide range of functions, including structural support, catalysis (enzymes), transport, signaling, and defense.

• Primary Structure: Sequence of amino acids.

• Secondary Structure: Coiling (alpha helix) or folding (beta sheet) stabilized by hydrogen bonds.

• Tertiary Structure: Three-dimensional shape stabilized by covalent, ionic, disulfide, and hydrogen bonds.

• Quaternary Structure: Association of two or more polypeptide chains.

Denaturation: Loss of protein structure (and function) due to changes in temperature or pH.

Nucleic Acids

DNA, RNA, and Nucleotides

Nucleic acids store and transmit genetic information. They are polymers of nucleotides, each consisting of a 5-carbon sugar, a phosphate group, and a nitrogenous base.

• DNA (Deoxyribonucleic Acid): Double-stranded, contains deoxyribose, bases are adenine (A), guanine (G), cytosine (C), and thymine (T).

• RNA (Ribonucleic Acid): Single-stranded, contains ribose, bases are adenine (A), guanine (G), cytosine (C), and uracil (U).

Base Pairing Rules (in DNA):

• Adenine pairs with Thymine (A = T) via 2 hydrogen bonds.

• Guanine pairs with Cytosine (G = C) via 3 hydrogen bonds.

ATP (Adenosine Triphosphate): A nucleotide that serves as the energy currency of the cell. Hydrolysis of ATP releases energy:

$\mathrm{ATP} + \mathrm{H_2O} \rightarrow \mathrm{ADP} + \mathrm{P_i} + \text{energy}$

Summary Table: DNA vs. RNA

Feature	DNA	RNA
Sugar	Deoxyribose	Ribose
Nitrogenous Bases	A, T, G, C	A, U, G, C
Strands	Double-stranded	Single-stranded
Base Pairing	A = T, G = C	A = U, G = C