Fundamental Chemistry and Cellular Biology for Anatomy and Physiology

Fundamental Definitions of Chemistry and Biochemistry

• Chemistry is defined as the study of the structure of matter and the composition of substances, alongside their properties and the chemical reactions they undergo.

• Biochemistry is a specific branch of chemistry focused on the study of chemical reactions occurring in living things.

Nature of Matter and Energy

• Matter is defined as anything that possesses weight (mass) and occupies space.

• States of Matter: Matter exists in three primary forms:

  • Solid — Example: bone.

  • Liquid — Example: blood.

  • Gas — Example: oxygen.

• Law of Conservation: Matter is never created nor destroyed. However, it can change form through physical or chemical means. For example, chewing food is a physical change, whereas the digestion of food involves chemical changes.

• Energy is the ability to perform work or put matter into motion. In the human body, energy exists in two states:

  • Potential Energy: Energy stored within cells, waiting to be released.

  • Kinetic Energy: Energy resulting in work or actual motion.

Atomic Structure and Isotopes

• Atom: Derived from the term "atomos" meaning indivisible, it is the smallest piece of an element. A normal atom comprises subatomic particles:

  • Protons: Carry a positive charge ($+$).

  • Neutrons: Carry no electric charge.

  • Electrons: Carry a negative charge ($-$) and are arranged around the nucleus in orbital zones known as electron shells.

• Isotopes: These are atoms of a specific element that contain the same number of protons and electrons but a different number of neutrons.

• Radioactive Isotopes: These are unstable isotopes that decay (come apart) and emit energy in the form of radiation that can be detected.

• Nuclear Medicine: This medical branch utilizes radioactive isotopes for the prevention, diagnosis, and treatment of various diseases.

Stages of Matter: Elements, Compounds, and Molecules

• Elements: Formed by atoms that are alike, an element is a substance that cannot be created or destroyed by ordinary chemical means.

• Compounds: Formed when various elements combine in a definite proportion by weight. Every compound possesses unique characteristics.

  • Examples of compound formulas include: Water ($H_2O$), Sodium Chloride ($NaCl$), Hydrochloric Acid ($HCl$), Sodium Hydroxide ($NaOH$), Glucose ($C_6H_{12}O_6$), Carbon Monoxide ($CO$), Carbon Dioxide ($CO_2$), and Sucrose ($C_{12}H_{22}O_{11}$).

• Molecules: The smallest unit of a compound that retains all the properties of that compound and is capable of stable, independent existence.

  • Example: If water is broken down into the smallest possible unit that is still water, that unit is a molecule ($H_2O$).

Chemical Bonding and Ions

• Chemical Bonds: Atoms form bonds by sharing or combining electrons from their outermost shells with other atoms.

  • Ionic Bond: Formed when one atom gives up an electron to another. This creates an anion (negative charge) and a cation (positive charge). These bonds dissociate when immersed in water (e.g., $Na^+Cl^-$).

  • Covalent Bond: Formed when atoms share electrons to fill their outermost shells (e.g., $H-H$).

  • Hydrogen Bond: A weak intermolecular bond that helps hold molecules together, such as the bonds between individual water molecules.

Common Ions and Their Biological Significance

• Calcium ($Ca^{2+}$): Essential part of bones and teeth; vital for blood clotting, muscle contraction, and the release of neurotransmitters.

• Sodium ($Na^+$): Important for membrane potentials and maintaining water balance.

• Potassium ($K^+$): Critical for membrane potentials.

• Hydrogen ($H^+$): Vital for acid-base balance.

• Hydroxide ($OH^-$): Vital for acid-base balance.

• Chloride ($Cl^-$): Involved in water balance.

• Bicarbonate ($HCO_3^-$): Important for acid-base balance.

• Ammonium ($NH_4^+$): Involved in acid-base balance.

• Phosphate ($PO_4^{3-}$): Part of bones and teeth; functions in energy exchange and acid-base balance.

• Iron ($Fe^{2+}$): Necessary for red blood cell formation.

• Magnesium ($Mg^{2+}$): Necessary for enzyme function.

• Iodide ($I^-$): Present in thyroid hormones.

Electrolytes

• Electrolytes are minerals in the body carrying an electric charge.

• Functions:

  • Conduct electrical charges to generate impulses (e.g., in electrocardiograms).

  • Help maintain fluid balance.

  • Transmit nerve signals.

  • Facilitate muscle function.

• Key examples include sodium, potassium, magnesium, calcium, chloride, and bicarbonate.

Inorganic and Organic Compounds

• Inorganic Compounds: Molecules that generally do not contain Carbon ($C$).

  • Examples include Salt ($NaCl$), Carbonate ($CaCO_3$), and Carbon Dioxide ($CO_2$).

  • Water ($H_2O$) is the most important inorganic compound for living organisms, constituting $55\text{--}65\%$ of body weight and acting as a universal solvent.

• Organic Compounds: Found in living things and their products.

  • Always contain Carbon ($C$) combined with Hydrogen ($H$) and other elements.

  • Molecules are typically large and complex.

  • The four main groups are Carbohydrates, Lipids, Proteins, and Nucleic Acids.

Carbohydrates: Composition and Classification

• All carbohydrates are comprised of Carbon ($C$), Hydrogen ($H$), and Oxygen ($O$).

• Monosaccharides: Simple sugars.

  • Examples: Glucose, fructose, galactose, ribose, and deoxyribose.

• Disaccharides: Double sugars formed by dehydration synthesis (Monosaccharide + Monosaccharide $-$ $H_2O$).

  • Glucose + Fructose $\rightarrow$ Sucrose.

  • Glucose + Glucose $\rightarrow$ Maltose.

  • Glucose + Galactose $\rightarrow$ Lactose.

  • These are broken down via hydrolysis (digestion).

• Polysaccharides: Large, complex molecules made of many glucose units.

  • Examples: Starch, cellulose, and glycogen (the storage form of glucose in animals).

Lipids: Energy and Structure

• Lipids are often referred to as fats or triglycerides.

• Functions: Stored energy, protection, insulation, regulation, vitamins, and cellular structure.

• Fats: Consist of glycerol and fatty acids; they make up $95\%$ of the fats in the human body.

• Phospholipids: Contain $C$, $H$, $O$, and $P$; found in cell membranes, brain tissue, and nervous tissue.

• Steroids: Lipids that contain cholesterol. Cholesterol is essential for Vitamin D production and hormones, though it can be problematic in excess.

  • Examples of steroids: Estrogen (estradiol), Testosterone, and Bile salt (glycocholate).

Proteins and Enzymes

• Proteins are the most diverse and essential organic compounds.

• Amino Acids: The small molecular units used to build proteins. There are 20 different amino acids.

  • Classification: Essential (must be obtained from diet) and Nonessential (can be synthesized by the body).

• Enzymes: Specialized protein molecules that control and catalyze chemical reactions.

Nucleic Acids: DNA and RNA

• Nucleic acids are the building blocks of genetic material and are the largest known organic molecules, made of repeating subunits called nucleotides.

• Deoxyribonucleic Acid (DNA):

  • Sugar: Deoxyribose.

  • Bases: Adenine ($A$), Thymine ($T$), Guanine ($G$), Cytosine ($C$).

  • Strands: 2 (Double-stranded).

  • Location: Cell nucleus and chromosomes.

• Ribonucleic Acid (RNA):

  • Sugar: Ribose.

  • Bases: Adenine ($A$), Uracil ($U$), Guanine ($G$), Cytosine ($C$).

  • Strands: 1 (Single-stranded).

  • Location: Cytoplasm, nucleoli, and ribosomes.

Acids, Bases, and pH

• Acids: Substances that yield Hydrogen ions ($H^+$) in solution. Characteristics include a sour taste.

  • Acetic Acid ($CH_3COOH$): Found in vinegar.

  • Boric Acid ($H_2BO_3$): Used as a weak eyewash.

  • Carbonic Acid ($H_2CO_3$): Found in carbonated beverages.

  • Hydrochloric Acid ($HCl$): Found in the stomach; pH of approximately $0.8$.

  • Nitric Acid ($HNO_3$): Industrial oxidizing acid.

  • Sulfuric Acid ($H_2SO_4$): Found in batteries.

• Bases (Alkali): Substances that ionize into negatively charged Hydroxide ions ($OH^-$) and positive metal ions when dissolved in water. Characteristics include a bitter taste and slippery feel.

  • Ammonium Hydroxide ($NH_4OH$): Household liquid cleaners.

  • Magnesium Hydroxide ($Mg(OH)_2$): Milk of magnesia.

  • Potassium Hydroxide ($KOH$): Caustic potash.

  • Sodium Hydroxide ($NaOH$): Lye.

• pH Scale: Measures acidity or alkalinity from $0$ to $14$.

  • pH < 7: Acidic.

  • $pH = 7$: Neutral (Distilled water).

  • pH > 7: Basic (Alkaline).

  • Qualitative method: Litmus paper. Acid turns blue paper red; bases turn red paper blue.

Acid-Base Homeostasis

• Normal human blood pH range is $7.35$ to $7.45$.

• Human tears have a pH of $7.4$.

• Maintenance of pH balance is achieved through buffers, such as sodium bicarbonate ($NaHCO_3$).

• Organisms must maintain a balance between extracellular fluid (interstitial fluid) and intracellular fluid.

Cell Theory and Functional Characteristics

• The cell was discovered by Robert Hooke and is the basic structural and functional unit of all living things.

• Three Tenets of Cell Theory:

  1. All living things are made of cells.

  2. Cells are the basic unit of life.

  3. All cells come from pre-existing cells.

• Cellular Functions:

  1. Cell Metabolism and Energy Use: All chemical reactions in a cell. Energy released by one reaction (e.g., digestion) is used for others (e.g., muscle contraction).

  2. Synthesis of Molecules: Cells produce proteins, nucleic acids, and lipids specific to their structural and functional needs.

  3. Communication: Cells use chemical and electrical signals (e.g., nerve cells signaling muscle cells to contract).

  4. Reproduction and Inheritance: Cells contain genetic info passed to future generations via gametes.

Cellular Structure: Protoplasm and Plasma Membrane

• Protoplasm: The entire living content of a cell, including nucleoplasm (inside the nucleus) and cytoplasm (outside the nucleus).

• Plasma Membrane: A selective semipermeable membrane that separates the cell from the external environment.

  • Composition: Primarily lipids (phospholipid bilayer) and proteins, with minor carbohydrates.

  • Structure: Phospholipids have hydrophilic (polar) heads and hydrophobic (nonpolar) tails.

• Membrane Proteins:

  • Integral Membrane Proteins: Penetrate the lipid bilayer; act as transport channels, carriers, and receptors.

  • Peripheral Membrane Proteins: Attached temporarily to the inner or outer surface; function in signaling, structural support, and enzymatic activity.

  • Marker Molecules: Allow cells to recognize each other (e.g., sperm recognizing an oocyte, immune system identifying foreign cells).

  • Attachment Proteins: Cadherins (attach cell to cell) and Integrins (attach cell to extracellular molecules).

Membrane Transport Systems

• Transport Protein Characteristics:

  • Specificity: Binds only to a certain type of molecule.

  • Competition: Similar shapes compete for the same protein.

  • Saturation: Rate is limited by the number of available transport proteins.

• Channel Proteins:

  • Leak Channels: Always open.

  • Gated Channels: Open/close in response to chemical signals like Acetylcholine.

• Carrier Protein Classifications:

  • Uniport: Moves one specific ion/molecule in one direction.

  • Symport (Cotransport): Moves two different molecules in the same direction.

  • Antiport (Countertransport): Moves two different molecules in opposite directions.

• G-Protein Signaling: A chemical signal binds to a receptor, causing the receptor to associate with a G-protein complex. GDP is released from the alpha subunit, and GTP is attached. The activated alpha subunit then separates to stimulate a cellular response.

Intracellular Organelles

• Nucleus: Contains genetic material (DNA/RNA). Surrounded by a nuclear envelope with nuclear pores.

• Nucleolus: Round body within the nucleus containing rRNA and ribosomes.

• Cytoplasm: Material outside the nucleus, consisting of cytosol (fluid) and cytoplasmic inclusions (e.g., glycogen granules, melanin).

• Ribosomes: Sites of protein synthesis; can be free or attached to the ER.

• Endoplasmic Reticulum (ER):

  • Rough ER: Studded with ribosomes; site of protein synthesis.

  • Smooth ER: No ribosomes; site of lipid synthesis, detoxification, and (in skeletal muscle) calcium storage.

• Golgi Apparatus: Stack of flattened membranes; collects, modifies, packages, and distributes proteins and lipids into secretory vesicles.

• Mitochondria: Powerhouse of the cell; site of aerobic respiration and ATP production. Contains its own DNA.

• Lysosomes: Contain enzymes for digesting worn-out organelles (autophagy), bacteria, and foreign matter.

• Peroxisomes: Contain oxidase for fat digestion and detoxification. Catalase within peroxisomes breaks down toxic hydrogen peroxide into water and oxygen.

• Cytoskeleton: Supports the cell and holds organelles in place.

  • Microtubules: Used in cell division, centrioles, cilia, and flagella.

  • Microfilaments (Actin): Support cytoplasm and define cell shape.

  • Intermediate filaments: Provide mechanical strength.

• Microvilli: Finger-like projections that increase surface area for absorption (e.g., in small intestine).

• Cilia and Flagella: Protrusions for movement. Cilia are numerous and short; flagella are long (e.g., sperm tail).

• Centrosome and Centrioles: Centers for microtubule organization; functional during cell division.

Tay-Sachs Disease

• A rare genetic disorder caused by the inability of lysosomal enzymes to break down gangliosides (membrane lipids of neurons).

• The resulting accumulation damages cells, leading to paralysis, blindness, and death typically before age 5.

• There is no known cure.

Movement of Materials across Membranes

• Passive Transport (No ATP required):

  • Diffusion: Solutes move from high to low concentration. Affected by temperature.

  • Osmosis: Diffusion of water across a semipermeable membrane. Aquaporins are specific water channels.

  • Facilitated Diffusion: Uses carrier/channel proteins to move substances (e.g., glucose) down a concentration gradient.

  • Filtration: Movement resulting from mechanical force (e.g., blood pressure in the kidney glomerulus).

• Active Transport (Requires ATP):

  • Uses energy to move molecules against a concentration gradient (low to high).

  • Example: Sodium-potassium pump ($Na^+\text{--}K^+$ pump) moves three $Na^+$ out and two $K^+$ into the cell.

• Vesicular Transport:

  • Endocytosis: Material taken into the cell. Includes Phagocytosis (cell-eating of solids), Pinocytosis (cell-drinking of liquids), and Receptor-mediated endocytosis (specific uptake, e.g., cholesterol).

  • Hypercholesterolemia: A genetic disorder where a lack of LDL receptors causes cholesterol to accumulate in the blood.

  • Exocytosis: Release of materials from the cell via vesicles (e.g., secretion of digestive enzymes or mucus).

Tonicity and Osmotic Pressure

• Osmolarity: Concentration of solute particles.

• Osmotic Pressure: The force required to prevent water movement via osmosis.

• Isotonic: Equal solute concentration; cell size remains constant.

• Hypertonic: Higher solute concentration outside the cell; water leaves the cell, causing it to shrink (crenation).

• Hypotonic: Higher solute concentration inside the cell; water enters, causing the cell to swell and potentially burst (lysis).

The Cell Life Cycle

• The life cycle consists of Interphase and Cell Division.

• Interphase Stages:

  • $G_1$ Phase: Routine metabolic activities.

  • $S$ Phase: DNA replication.

  • $G_2$ Phase: Preparation for division.

  • $G_0$ Phase: A resting state for cells that do not divide for long periods.

• Checkpoints: Surveillance mechanisms ($G_1$, $G_2$, and $M$ checkpoints) ensure safe division. Failure leads to mutations and cancer.

• Mitosis (Nuclear Division):

  1. Prophase: Chromatin condenses into chromosomes; centrioles migrate, and spindle fibers form; nucleolus/nuclear envelope disappear.

  2. Metaphase: Chromosomes align at the equator (metaphase plate).

  3. Anaphase: Chromatids separate and move toward poles; cytokinesis begins.

  4. Telophase: Nuclear envelopes reform; chromosomes uncoil.

• Cytokinesis: Division of cytoplasm; marked by a cleavage furrow.

Comparison: Mitosis vs. Meiosis

• Mitosis:

  • Occurs in somatic cells.

  • One division resulting in two diploid daughter cells.

  • Produces 46 chromosomes in humans.

  • No crossing over.

• Meiosis:

  • Occurs in germ cells to form gametes.

  • Two divisions resulting in four haploid daughter cells.

  • Produces 23 chromosomes in humans.

  • Involves crossing over for genetic variation.

Protein Synthesis and Facts

• Central Dogma: Flow of information from DNA $\rightarrow$ RNA $\rightarrow$ Protein.

• Transcription: Process of moving from DNA to mRNA in the nucleus.

• Translation: Process of moving from mRNA to protein at the ribosome in the cytoplasm.

• Cell Stats:

  • Adult body contains $30\text{--}40$ trillion cells.

  • Stomach lining is replaced every $2\text{--}4$ days.

  • Apoptosis: Programmed cell death/self-destruction of damaged or infected cells.