Chemistry Comes Alive: Foundations for Anatomy & Physiology

Ch. 2 Chemistry Comes Alive

Concept: Atoms – The Smallest Unit of Matter

Atoms are the fundamental building blocks of all matter, including living and nonliving things. Understanding atomic structure is essential for grasping the chemical basis of life.

• Matter: Anything that takes up space and has mass (e.g., organisms, rocks, water).

• Chemical Element: A pure substance made of only one type of atom.

• Atom: The smallest unit of an element that retains its properties.

• Atoms make up both living and nonliving matter.

Atomic Structure

Atoms are composed of three subatomic particles, each with distinct properties:

• Protons: Positively charged particles found in the nucleus.

• Neutrons: Neutral particles (no charge) also located in the nucleus.

• Electrons: Negatively charged particles orbiting the nucleus in energy shells.

Particle	Electric Charge	Atomic Mass Unit (AMU)	Location
Proton	+1	1	Nucleus
Neutron	0	1	Nucleus
Electron	-1	0	Electron shell

Elements of Life

Only a small subset of elements are found in living organisms. The periodic table organizes these elements by their chemical properties.

• About 97% of the mass of most living things is composed of Carbon, Hydrogen, Nitrogen, Oxygen, Phosphorus, and Sulfur (CHNOPS).

• Trace Elements: Required for life in small amounts.

Atomic Properties

Each atom has unique properties that distinguish one element from another:

• Atomic Number: Number of protons in the nucleus (defines the element).

• Mass Number: Total number of protons and neutrons in the nucleus.

• Atomic Mass: The average total mass of all atoms of an element, accounting for isotopes.

Electron Orbitals & Energy Shells

Electrons occupy specific regions called orbitals, arranged in energy shells around the nucleus.

• Shells closer to the nucleus are lower in energy; distant shells are higher in energy.

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

• The first shell holds up to 2 electrons; the second shell up to 8 electrons.

Octet Rule

The octet rule states that atoms are most stable when their valence shell is full (usually 8 electrons).

• Atoms with incomplete valence shells are more reactive.

• Example: Neon (Ne) is unreactive because its valence shell is full.

Isotopes

Isotopes are atoms of the same element with different numbers of neutrons, resulting in different mass numbers.

• All isotopes of an element have the same atomic number (protons) but different mass numbers.

• Atomic Mass: The weighted average of all isotopes of an element.

Isotope	Protons	Neutrons	Electrons
Carbon-12	6	6	6
Carbon-13	6	7	6
Carbon-14	6	8	6

Introduction to Chemical Bonding

Chemical bonds are attractive forces that hold atoms together to form molecules and compounds.

• Molecule: Substance containing two or more chemically bound atoms (e.g., O2).

• Compound: Molecule composed of two or more different elements (e.g., H2O).

• Chemical Formula: Indicates the composition and number of atoms in a molecule (e.g., C6H12O6).

Intramolecular vs. Intermolecular Bonds

Bonds can be classified based on whether they occur within a molecule or between molecules:

• Intramolecular Bonds: Hold atoms together within a molecule (e.g., covalent bonds in H2O).

• Intermolecular Bonds: Occur between different molecules (e.g., hydrogen bonds between water molecules).

Ionic Bonding

Ionic bonds are formed by the electrical attraction between oppositely charged ions (cations and anions).

• Ions: Atoms or molecules with a net electrical charge due to the gain or loss of electrons.

• Anion: Negatively charged ion (gains electrons).

• Cation: Positively charged ion (loses electrons).

• Ionic bonds are common in salts, such as sodium chloride (NaCl).

Covalent Bonding

Covalent bonds involve the sharing of electron pairs between atoms. There are two main types:

• Nonpolar Covalent Bonds: Equal sharing of electrons (atoms have similar electronegativities).

• Polar Covalent Bonds: Unequal sharing of electrons (atoms have different electronegativities), resulting in partial charges (δ+ and δ−).

Noncovalent Bonds

Noncovalent bonds are interactions that do not involve sharing electrons. They include:

• Hydrogen Bonds: Weak attractions between a hydrogen atom and a highly electronegative atom (F, O, or N).

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

Properties of Water

Water is a small, polar molecule with unique properties essential for life:

• Cohesion: Water molecules stick to each other due to hydrogen bonding.

• Adhesion: Water molecules stick to other substances.

• Surface Tension: Difficulty in breaking the surface of water.

• High Specific Heat: Water resists temperature changes, helping maintain homeostasis.

• High Heat of Vaporization: Large amount of energy required to convert water from liquid to gas.

• Density: Ice is less dense than liquid water, allowing it to float and insulate aquatic life.

• Universal Solvent: Water dissolves many substances due to its polarity.

Acids, Bases, and pH

The concentration of hydrogen ions (H+) in solution determines acidity or basicity, measured by the pH scale.

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

• Base: Substance that decreases H+ concentration (often by releasing OH−).

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

• Buffers: Substances that minimize changes in pH by accepting or donating H+.

Carbon and Organic Molecules

Carbon is the backbone of organic molecules, which include carbohydrates, proteins, nucleic acids, and lipids.

• Organic Molecules: Contain covalently linked carbon and hydrogen atoms.

• Hydrocarbons: Molecules made only of carbon and hydrogen.

• Carbon can form four bonds, allowing for diverse molecular structures (chains, rings, branches).

Functional Groups

Functional groups are specific groups of atoms that confer characteristic chemical properties to organic molecules.

• Common functional groups include hydroxyl, carboxyl, amino, phosphate, and methyl groups.

Biomolecules: Monomers and Polymers

Biomolecules are essential organic molecules in living organisms, classified into four main types:

• Carbohydrates

• Proteins

• Nucleic Acids

• Lipids

Most biomolecules (except lipids) are polymers made from repeating monomer units.

• Dehydration Synthesis: Links monomers by removing water to form polymers.

• Hydrolysis: Breaks polymers into monomers by adding water.

Carbohydrates

Carbohydrates are hydrated carbon molecules, often called sugars. They serve as energy sources and structural materials.

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

• Disaccharides: Two monosaccharides linked together.

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

• Glycosidic Bonds: Covalent bonds linking monosaccharides in polysaccharides.

Lipids

Lipids are hydrophobic molecules that include fats, oils, phospholipids, steroids, and waxes. They do not form true polymers.

• Fatty Acids: Hydrocarbon chains with a carboxylic acid group.

• Saturated Fatty Acids: No double bonds; solid at room temperature.

• Unsaturated Fatty Acids: One or more double bonds; liquid at room temperature.

• Triglycerides: Three fatty acids linked to glycerol.

• Phospholipids: Major component of cell membranes; amphipathic (hydrophilic head, hydrophobic tails).

• Steroids: Four fused carbon rings (e.g., cholesterol).

Proteins

Proteins are polymers of amino acids linked by peptide bonds. They perform a vast array of functions in cells.

• Amino Acids: Building blocks of proteins; 20 different types in living organisms.

• Peptide Bonds: Covalent bonds between amino acids.

• Protein Structure: Organized into four levels: primary, secondary, tertiary, and quaternary.

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

• Chaperone Proteins: Assist in proper protein folding.

Nucleic Acids

Nucleic acids (DNA and RNA) store and transmit genetic information. They are polymers of nucleotide monomers.

• Nucleotide: Composed of a phosphate group, a pentose sugar, and a nitrogenous base.

• DNA: Double helix, stores hereditary information.

• RNA: Single-stranded, involved in protein synthesis and other functions.

• Phosphodiester Bonds: Link nucleotides in a chain.

Adenosine Triphosphate (ATP)

ATP is the primary energy currency of the cell, providing energy for cellular processes through hydrolysis of its phosphate bonds.

• Composed of three phosphate groups, a ribose sugar, and an adenine base.

• ATP hydrolysis releases energy and forms ADP (adenosine diphosphate).

• ATP is regenerated by cellular respiration and used in energy coupling reactions.

Key Equations

• Atomic Mass Calculation: $\text{Atomic Mass} = \sum (\text{Isotope Abundance} \times \text{Isotope Mass})$

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