Atoms, Chemical Bonds, and Biological Molecules: Study Notes for Anatomy & Physiology

Study Guide - Smart Notes

Tailored notes based on your materials, expanded with key definitions, examples, and context.

Section 2-1: Atoms and Subatomic Particles

Subatomic Particles of Atoms

Atoms are the basic units of matter, composed of three main subatomic particles. Each particle has distinct properties and locations within the atom.

Protons: Positively charged particles (+), located in the nucleus.
Neutrons: Neutral particles (no charge), also found in the nucleus.
Electrons: Negatively charged particles (–), found in electron shells/clouds surrounding the nucleus.

Electron Shell vs. Valence Shell

The arrangement of electrons around the nucleus is described by shells:

Electron Shell: A two-dimensional representation of the electron cloud, showing probable locations of electrons.
Valence Shell: The outermost electron shell; the number of electrons here determines the chemical properties and reactivity of the element.

Section 2-2: Chemical Bonds

Ions and Ionic Bonds

Chemical bonds are forces formed by interactions between atoms, often involving ions.

Cation: An ion with a positive charge (loss of electrons).
Anion: An ion with a negative charge (gain of electrons).

Ionic Bond: Formed by the attraction between oppositely charged ions (cations and anions). The process involves:

One atom loses electrons, becoming a cation.
Another atom gains electrons, becoming an anion.
Electrostatic attraction draws the ions together.
Results in an ionic compound.

Covalent Bonds

Covalent bonds are formed by sharing electrons between atoms.

Single Covalent Bond: Sharing one pair of electrons (e.g., H2 molecule).
Double Covalent Bond: Sharing two pairs of electrons.
Triple Covalent Bond: Sharing three pairs of electrons (e.g., N2 molecule).

Polar vs. Non-Polar Covalent Bonds

Polar Covalent Bond: Unequal sharing of electrons due to differences in electronegativity; results in partial charges.
Non-Polar Covalent Bond: Equal sharing of electrons, usually between atoms of the same type.

Hydrogen Bonds

Hydrogen bonds are weak bonds formed when a hydrogen atom (part of a polar covalent bond) carries a slight positive charge and is attracted to a nearby atom with a slight negative charge, often another polar covalent bond.

Section 2-3: Chemical Reactions in Physiology

Kinetic vs. Potential Energy

Kinetic Energy: Energy of motion; energy an object has due to its movement.
Potential Energy: Stored energy; energy due to structure or position.

Dehydration Synthesis vs. Hydrolysis Reactions

Dehydration Synthesis: Formation of complex molecules by removing water; anabolic process (builds larger molecules from smaller ones).
Hydrolysis: Breakdown of complex molecules into simpler ones by adding water; catabolic process (breaks down larger molecules into smaller ones).

Hint: Anabolic reactions build up molecules; catabolic reactions break them down.

Enzymes and Activation Energy

Enzymes: Proteins that act as catalysts, speeding up biochemical reactions by lowering the activation energy required.
Activation Energy: The energy needed to initiate a reaction.
Enzymes are not consumed or permanently altered in the process.

Section 2-5: Organic vs. Inorganic Compounds

Definitions and Examples

Organic Compounds: Mostly carbon and hydrogen atoms; form more complex molecules (e.g., carbohydrates, proteins, lipids).
Inorganic Compounds: Generally lack carbon or hydrogen; if carbon is present, it does not form carbon-hydrogen (C-H) bonds (e.g., water, salts, acids).

Note: Some exceptions exist, such as carbon dioxide (CO2).

Section 2-6: Water and Physiological Systems

Electrolytes

Electrolyte: Soluble inorganic substance that dissociates into ions in water, allowing conduction of electrical current; essential for physiological functions.

Hydrophobic vs. Hydrophilic Compounds

Hydrophobic Compounds: Do not interact with water; nonpolar; do not dissolve in water (e.g., fats and oils).
Hydrophilic Compounds: Readily interact with water; polar; dissolve in water (e.g., salts, sugars).

Fats & Oils

Types of lipids; hydrophobic; usually insoluble in water.
Serve as energy reserves.

Section 2-7: pH and Acid-Base Balance

pH Scale and Water

pH of pure water: 7 (neutral); equal number of hydrogen ions (H+) and hydroxide ions (OH–).

Acidic and Basic pH Ranges

Acidic: pH below 7; more H+ than OH– (e.g., stomach acid, vinegar).
Basic (Alkaline): pH above 7; more OH– than H+ (e.g., bleach, ammonia).

Blood pH

Normal blood pH: 7.35–7.45; slightly basic.

Section 2-8: Acids, Bases, and Buffers

Acids and Bases

Acids: Compounds that donate H+ ions when dissolved in water.
Bases: Compounds that absorb H+ ions or release OH– ions.

Buffers

Compounds that help stabilize pH by removing or releasing H+ ions.
Interact with acids and bases to prevent significant changes in pH.

Section 2-9: Organic Molecules—Monomers and Polymers

Monomers vs. Polymers

Monomers: Small, single molecules; building blocks for larger molecules.
Polymers: Large, complex molecules made of chains of monomers linked together (e.g., carbohydrates, lipids, proteins, nucleic acids).

Dehydration Synthesis

Forms polymers by joining monomers and removing water.

Section 2-10: Carbohydrates

Types of Carbohydrates

Monosaccharides: Simple sugars with 3–7 carbon atoms (e.g., glucose).
Disaccharides: Two monosaccharides joined together (e.g., sucrose, lactose, maltose).
Polysaccharides: Complex carbohydrates made of many monosaccharides (e.g., glycogen for energy storage in animals).

Glucose

Hexose sugar; primary energy source for cells.

Chemical Reactions Involving Carbohydrates

Dehydration Synthesis: Forms disaccharides/polysaccharides by removing water; anabolic reaction.
Hydrolysis: Breaks down disaccharides/polysaccharides into monosaccharides by adding water; catabolic reaction.

Glycogen

Polysaccharide; composed of glucose monomers; main storage form of glucose in animals.

Section 2-11: Lipids

Building Blocks of Lipids

Fatty Acids and Glycerol are the building blocks of monoglycerides, diglycerides, and triglycerides.

Phospholipids and Glycolipids

Named for their chemical groups: Phospholipids contain phosphate groups; Glycolipids contain carbohydrate groups.

Section 2-12: Proteins

Amino Acids and Protein Structure

Amino Acids: Building blocks of proteins; linked by peptide bonds.
Primary Structure: Linear sequence of amino acids.
Secondary Structure: Alpha helices and beta sheets formed by hydrogen bonding.
Tertiary Structure: Three-dimensional folding due to interactions among side chains.
Quaternary Structure: Multiple polypeptide chains forming a functional protein complex.

Enzymes

Most enzymes are proteins; they catalyze chemical reactions without being consumed.
Cofactors: Non-protein molecules required for enzyme function.
Enzyme activity depends on substrate concentration and protein structure.

Section 2-13: Nucleic Acids

Nucleotides

Building blocks of nucleic acids; consist of a nitrogenous base, a simple sugar, and a phosphate group.

DNA and RNA

DNA: Stores genetic information; bases are adenine (A), guanine (G), cytosine (C), and thymine (T).
RNA: Involved in protein synthesis; bases are adenine (A), guanine (G), cytosine (C), and uracil (U).

Complementary Base Pairing

DNA: A pairs with T, G pairs with C.
RNA: A pairs with U, G pairs with C.

Section 2-14: ATP and Energy Transfer

ATP and Phosphorylation

ATP (Adenosine Triphosphate): The primary energy carrier in cells.
Phosphorylation: The addition of a phosphate group to ADP to form ATP.
Energy is released when ATP is broken down to ADP and a phosphate group.

Equation:

Example: Muscle contraction and active transport use ATP as an energy source.