Ch. 2 Chemistry Comes Alive – Study Notes for Anatomy & Physiology

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Atoms: The Smallest Unit of Matter

Definition and Structure of Atoms

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

Atom: The smallest unit of an element that retains the properties of that element.
Subatomic particles: Atoms are composed of protons (positive charge), neutrons (neutral), and electrons (negative charge).
Atomic number (Z): Number of protons in the nucleus; defines the element.
Mass number (A): Sum of protons and neutrons in the nucleus.

Example: A carbon atom has 6 protons, 6 neutrons, and 6 electrons.

Particle	Charge	Location	Mass (amu)
Proton	+1	Nucleus	1
Neutron	0	Nucleus	1
Electron	-1	Electron cloud	~0

Elements and the Periodic Table

Elements in Life

Elements are pure substances consisting of only one type of atom. Living organisms are primarily composed of a few key elements.

CHNOPS: Carbon, Hydrogen, Nitrogen, Oxygen, Phosphorus, and Sulfur make up most of the mass of living organisms.
Periodic Table organizes elements by atomic number and properties.

Example: Oxygen, carbon, hydrogen, and nitrogen account for over 96% of body mass.

Atomic Properties

Atomic Number, Mass Number, and Isotopes

Each atom is defined by its atomic number (number of protons). Isotopes are atoms of the same element with different numbers of neutrons.

Isotope: Atoms with the same number of protons but different numbers of neutrons.
Atomic mass: Weighted average of all isotopes of an element.

Example: Carbon-12, Carbon-13, and Carbon-14 are isotopes of carbon.

Radioactive Isotopes

Unstable isotopes that decay, emitting radiation.
Used in medical imaging and dating fossils.

Electron Orbitals and Energy Shells

Electron Arrangement

Electrons occupy energy levels (shells) around the nucleus. The arrangement of electrons determines chemical reactivity.

First shell: up to 2 electrons
Second shell: up to 8 electrons
Valence electrons: Electrons in the outermost shell; determine chemical properties.

Octet Rule: Atoms are most stable when their outermost shell is full (usually 8 electrons).

Chemical Bonds

Types of Chemical Bonds

Chemical bonds are forces that hold atoms together in molecules and compounds.

Ionic bonds: Transfer of electrons from one atom to another, forming ions (cations and anions).
Covalent bonds: Sharing of electron pairs between atoms.
Noncovalent bonds: Weaker interactions, such as hydrogen bonds and van der Waals forces.

Ionic Bonds

Formed between oppositely charged ions.
Example: Sodium chloride (NaCl) forms when sodium donates an electron to chlorine.

Covalent Bonds

Nonpolar covalent: Equal sharing of electrons (e.g., O2).
Polar covalent: Unequal sharing of electrons, leading to partial charges (e.g., H2O).
Electronegativity: The ability of an atom to attract electrons in a bond.

Hydrogen Bonds

Weak attractions between a hydrogen atom (bonded to O, N, or F) and another electronegative atom.
Important in stabilizing the structure of proteins and DNA.

Properties of Water

Structure and Hydrogen Bonding

Water is a polar molecule, with hydrogen bonds forming between molecules. This gives water unique properties essential for life.

Cohesion: Water molecules stick to each other.
Adhesion: Water molecules stick to other substances.
Surface tension: Difficulty of breaking the surface of a liquid.
High specific heat: Water resists temperature changes.
High heat of vaporization: Large amount of energy required to convert water from liquid to gas.
Density: Ice is less dense than liquid water, so it floats.
Universal solvent: Water dissolves many substances due to its polarity.

Emergent Properties of Water

Property	Description
Cohesion	Attraction between water molecules
Adhesion	Attraction between water and other substances
High Specific Heat	Resists temperature change
High Heat of Vaporization	Requires much energy to evaporate
Lower Density of Ice	Ice floats on water
Universal Solvent	Dissolves many polar substances

Solutions, Acids, and Bases

Solutions

Solvent: Substance that dissolves another (water is the universal solvent).
Solute: Substance dissolved in the solvent.
Homogeneous solution: Uniform composition throughout.
Heterogeneous solution: Non-uniform composition.

Acids and Bases

Acid: Substance that increases the concentration of H+ ions in solution.
Base: Substance that decreases the concentration of H+ ions (often by releasing OH-).
pH scale: Measures the concentration of H+ ions; ranges from 0 (acidic) to 14 (basic), with 7 being neutral.

Equation:

Buffers

Substances that minimize changes in pH by accepting or donating H+ ions.
Example: Bicarbonate buffer system in blood.

Carbon Chemistry and Biomolecules

Carbon as a Building Block

Carbon forms four covalent bonds, allowing for diverse molecular structures (chains, rings, branches).
Organic molecules contain carbon and hydrogen, often with oxygen, nitrogen, phosphorus, and sulfur.

Functional Groups

Groups of atoms that confer specific chemical properties to molecules.
Common functional groups: hydroxyl (-OH), carboxyl (-COOH), amino (-NH2), phosphate (-PO4), sulfhydryl (-SH).

Biomolecules: Monomers and Polymers

Classes of Biomolecules

Carbohydrates: Sugars and starches; energy storage and structural support.
Proteins: Polymers of amino acids; structure, enzymes, signaling.
Nucleic acids: DNA and RNA; genetic information.
Lipids: Fats, oils, and steroids; energy storage, membranes.

Monomers and Polymers

Monomer: Small building block molecule (e.g., glucose, amino acid, nucleotide).
Polymer: Large molecule made of repeating monomers (e.g., starch, protein, DNA).
Dehydration synthesis: Joins monomers by removing water.
Hydrolysis: Breaks polymers by adding water.

Carbohydrates

Structure and Function

Composed of carbon, hydrogen, and oxygen (typically C:H:O ratio of 1:2:1).
Monosaccharides: Simple sugars (e.g., glucose).
Disaccharides: Two monosaccharides joined (e.g., sucrose).
Polysaccharides: Long chains of monosaccharides (e.g., starch, glycogen, cellulose).
Functions: Energy storage (glycogen in animals, starch in plants), structural support (cellulose in plants, chitin in fungi and arthropods).

Proteins

Structure and Function

Polymers of amino acids linked by peptide bonds.
Amino acid structure: Central carbon, amino group (-NH2), carboxyl group (-COOH), hydrogen, and R group (side chain).
Functions: Enzymes, structural proteins, transport, signaling, immune response.

Summary Table: Key Chemical Concepts in Anatomy & Physiology

Concept	Definition	Example/Application
Atom	Smallest unit of matter	Carbon atom in glucose
Isotope	Atoms with same protons, different neutrons	Carbon-12 vs. Carbon-14
Ionic Bond	Transfer of electrons	NaCl (table salt)
Covalent Bond	Sharing of electrons	H2O molecule
Hydrogen Bond	Weak attraction between polar molecules	DNA double helix
Buffer	Minimizes pH changes	Bicarbonate in blood
Monomer	Single building block	Glucose, amino acid
Polymer	Chain of monomers	Starch, protein

Additional info: These notes expand on the provided study prep materials by including definitions, examples, and tables for clarity and completeness, suitable for college-level Anatomy & Physiology students.