Molecular Interactions and Biomolecules: Study Notes for Anatomy & Physiology

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Molecular Interactions

Physiology and Pathology

Physiology is the study of the normal functioning of a living organism and its component parts, focusing on how the body works. Pathology occurs when normal function is disrupted, leading to disease or a condition that forces the internal environment out of balance.

Atoms, Ions, and Molecules

Ion: An atom that gains or loses one or more electrons, acquiring an electrical charge. A positively charged ion is called a cation; a negatively charged ion is called an anion.
Ligand: A molecule or ion that binds to another molecule.

Polarity of Molecules

Polar molecules: Have regions of partial positive and negative charge (e.g., water).
Nonpolar molecules: Have electrons distributed so evenly that there are no regions of partial positive or negative charge (e.g., carbon).

Water and Its Properties

Water (H2O): Universal solvent, can dissolve many substances.
Hydrophilic: Water loving (dissolves in water).
Hydrophobic: Water fearing (does not dissolve in water).

Mixtures and Solutions

Mixture: Two or more compounds combined but not chemically bound.
Solution: Homogeneous mixture where molecules are evenly distributed and will not separate upon standing.
Solvent: The dissolving substance (usually water).
Solute: The substance being dissolved (e.g., sugar, salt).
Suspension: Heterogeneous mixture where particles will separate upon standing (e.g., blood cells in plasma).
Colloid: Heterogeneous mixture where particles remain suspended, but do not separate upon standing (e.g., plasma proteins in blood).

Acids, Bases, and Buffers

Acid: Can donate a hydrogen ion (H+) to a solution.
Base: Can accept hydrogen ions from a solution.
pH scale: Measures the acidity or alkalinity of a solution. Lower pH = more acidic (higher H+ concentration); higher pH = more basic (lower H+ concentration).
Buffers: Resist pH change and help prevent sharp changes in H+ concentration.

Cellular Fluid Compartments

Intracellular – within cells
Extracellular – outside cells
Interstitial – between circulatory and cells (in tissue), e.g., plasma

Biomolecules

Carbohydrates

Composed of carbon (C), hydrogen (H), and oxygen (O). When combined in various combinations, they are referred to as saccharides. Carbohydrates are the most abundant biomolecules.

Simple Carbohydrates

Monosaccharides: Single sugar molecules (e.g., glucose, fructose, galactose).
Disaccharides: Two sugars joined together (e.g., sucrose, lactose, maltose).

Complex Carbohydrates

Polysaccharides: Many sugar molecules joined together (e.g., starch, glycogen, dietary fiber).
Starch: Found in grains, legumes, beans; main storage form in plants.
Glycogen: Storage form in animal muscle tissue; important for metabolism and energy balance.
Dietary Fiber: Indigestible polysaccharides.

Lipids

Organic substances that are mostly nonpolar and insoluble in water. Includes fats, oils, waxes, and other fat-related compounds.

Fatty acids: Building blocks of triglycerides (glycerol + 3 fatty acids).
Glycerides: Formed from glycerol with one, two, or three fatty acids attached.

Types of Fatty Acids

Essential Fatty Acids: Must be obtained from the diet; the body cannot synthesize them.
Saturated Fatty Acids: No double bonds; solid at room temperature (e.g., animal fats, coconut oil).
Unsaturated Fatty Acids: One or more double bonds; liquid at room temperature (e.g., olive oil, canola oil).
Monounsaturated Fatty Acids: One double bond (e.g., olive oil, peanut oil).
Polyunsaturated Fatty Acids: Two or more double bonds (e.g., fish oil, flaxseed oil).
Omega-3 Fatty Acids: A type of polyunsaturated fat important for heart and brain health (e.g., walnuts, flaxseed, fish).

Eat Types

Cholesterol: Found in animal products; important for cell membrane structure and hormone synthesis.
Lipoproteins: Transport lipids in the blood (see table below).

Table: Types of Lipoproteins

Lipoprotein	Function
Low-density lipoprotein (LDL)	Carries cholesterol to cells; high levels associated with increased risk of atherosclerosis.
High-density lipoprotein (HDL)	Carries cholesterol from tissues to liver for breakdown and excretion; high levels are protective.

Proteins

Composed of chains of amino acids (primary structure). Proteins are essential for structure, function, and regulation of the body's tissues and organs.

Peptides: Short chains of amino acids.
Polypeptides: Longer chains of amino acids.

Protein Structure

Primary: Sequence of amino acids.
Secondary: Local folding (e.g., alpha helix, beta sheet) stabilized by hydrogen bonds.
Tertiary: 3D shape of a single polypeptide chain.
Quaternary: Association of multiple polypeptide chains (e.g., hemoglobin).

Classes of Amino Acids

Indispensable (Essential) Amino Acids: Must be obtained from the diet; the body cannot synthesize them in sufficient quantities.

Essential Amino Acids
Histidine
Isoleucine
Leucine
Lysine
Methionine
Phenylalanine
Threonine
Tryptophan
Valine

Conjugated Proteins

Proteins combined with another kind of biomolecule (e.g., glycoproteins, lipoproteins).

Nucleotides and Nucleic Acids

Nucleotide: Composed of a phosphate group, a 5-carbon sugar (ribose or deoxyribose), and a nitrogenous base (adenine, guanine, cytosine, thymine, or uracil).
DNA (deoxyribonucleic acid): Double helix; stores genetic information; bases: A, T, G, C.
RNA (ribonucleic acid): Single strand; involved in protein synthesis; bases: A, U, G, C.

Table: Nitrogenous Bases in DNA and RNA

Base	DNA	RNA
Adenine (A)	Yes	Yes
Guanine (G)	Yes	Yes
Cytosine (C)	Yes	Yes
Thymine (T)	Yes	No
Uracil (U)	No	Yes

Protein Synthesis

Transcription: DNA is used as a template to synthesize messenger RNA (mRNA).
Translation: mRNA attaches to a ribosome, and transfer RNA (tRNA) brings amino acids to build the protein according to the mRNA code.

Steps of Information Delivery (Protein Synthesis)

Transcription: DNA → mRNA
Translation: mRNA → Protein

Factors Affecting Protein Synthesis

Factor or Condition	Effect on Synthesis
Decreased protein intake	Decrease
Increased protein intake	Increase
Decreased cellular hydration	Decrease
Increased cellular hydration	Increase
Increased intake of Leucine	Increase
Muscle stretch or exercise	Increase
Overtraining	Decrease
Normal thyroid hormone	Increase
Glucocorticoids	Decrease

Enzyme Activity

Competitive inhibitor: Competes with ligand by binding to the active site of the enzyme, preventing substrate binding.

Key Equations

pH calculation:
General formula for carbohydrates:

Additional info:

Some context and examples were expanded for clarity and completeness.
Tables were recreated and summarized for key comparisons.