Exhaustive Mammalian Anatomy, Physiology, and Biological Systems Notes

Mammalian Respiratory System

• Pathway of Air: Air enters through the trachea, which branches into two bronchi. These continue to branch into smaller tubes called bronchioles.
• Alveoli: At the end of the bronchioles are alveolar sacs, which are grape-like clusters. This structure effectively increases the surface area for gas exchange ($CO_2$ and $O_2$).
• Gas Exchange and Cellular Respiration:     * Exchange occurs between the lungs, alveoli, and capillaries.     * Red blood cells containing hemoglobin transport oxygen to the mitochondria within cells.     * In the mitochondria, cellular respiration occurs, utilizing the electron transport chain (ETC).     * Oxygen acts as the final electron acceptor in the ETC to produce $ATP$.
• The Diaphragm:     * The diaphragm is a skeletal muscle that functions mostly involuntarily.     * Only mammals possess a diaphragm.     * When the diaphragm muscle contracts, it moves down, pulling air into the lungs. When it expands/relaxes, air is expelled.
• Evolutionary Context:     * Gills utilize countercurrent flow, where water and blood flow in opposite directions to maximize oxygen extraction. Oxygen ($O_2$) moves from high concentration (water) to low concentration (blood).     * Before the evolution of gills, most invertebrates relied on simple diffusion.
• Physiological Calculations (Heart Rate Examples):     * $19 \times 4 = 76\,bpm$     * $17 \times 4 = 68\,bpm$     * A heart rate of $72\,bpm$ is also noted as a standard.

The Circulatory System: Structure and Evolution

• Three Main Parts: The pump (heart), the blood vessels, and the blood itself.
• Circuits:     * Pulmonary Circuit: Blood travel between the heart and the lungs.     * Systemic Circuit: Blood travel between the heart and the rest of the body.
• Evolution of the Heart:     * Fish: $2$ chambers.     * Amphibians: $3$ chambers.     * Reptiles/Birds/Mammals: $4$ chambers (left and right atria and ventricles).
• Open vs. Closed Systems:     * Closed System: Blood is contained within vessels.     * Open System: No blood vessels; found in insects. Because it is not precise, insects cannot grow to very large sizes.     * Mollusks and annelids were among the first to develop circulatory systems; before this, materials moved via diffusion.
• Heart Dynamics:     * Triggered by electrical signals.     * The signal travels from the brain down to the pacemaker, known as the SA node (Sinoatrial node), located in the Right Atrium (RA).     * The heart is composed of muscle tissue. The left ventricle is the most muscular chamber because it must pump blood throughout the entire body (systemic circuit), whereas the right ventricle only pumps to the lungs.     * All muscles, including the heart, only contract under the direction of the nervous system.

Blood Vessels and Hemodynamics

• Arteries:     * Carry blood away from the heart ("A" for Away).     * Typically represented as red (oxygenated), with the exception of the pulmonary artery.     * Possess a smaller lumen diameter and thicker muscle layers to handle high pressure.     * Do not have valves.
• Veins:     * Carry blood toward the heart.     * Typically represented as blue (deoxygenated).     * Possess a larger lumen diameter and less muscle.     * Contain valves to ensure one-way blood flow.
• Capillaries:     * The site of nutrient and waste exchange.     * Smallest diameter, allowing erythrocytes (red blood cells) to squeeze through one at a time. This ensures every cell in an organ receives required oxygen and slows the flow to allow for the transfer of glucose and amino acids.     * They have the greatest total surface area.
• Vessel Hierarchy: Arteries $\rightarrow$ Arterioles $\rightarrow$ Capillaries $\rightarrow$ Venules $\rightarrow$ Veins.
• Velocity:     * The velocity of blood flow involves both direction and magnitude.     * Velocity is greatest in the aorta and least in the capillaries.

Composition of Blood

• Layers of Blood: Blood consists of three layers when separated.
• Erythrocytes (Red Blood Cells): Specialized cells for transporting oxygen via hemoglobin.
• Leukocytes (White Blood Cells): Larger cells involved in the immune response.
• Platelets: Fragments responsible for blood clotting. They plug tears in blood vessels, and a protein called fibrin forms a mesh to stabilize the clot.
• Plasma: The top liquid layer, mostly composed of water ($55\%$). It contains:     * Proteins, electrolytes, hormones, and waste products.     * Positive ions and negative ions.     * Bicarbonate ($HCO_3^-$): Important for maintaining blood pH.
• Blood Types: A, B, AB, and O. The body will recognize conflicting blood types as pathogens and attack them.

The Digestive System: Process and Anatomy

• Stages of Digestion:     1. Ingestion: Eating, including mechanical chewing and chemical breakdown via salivary enzymes.     2. Propulsion: Swallowing (voluntary) and peristalsis (involuntary smooth muscle contraction).     3. Mechanical Breakdown: Increases surface area of food; involves smooth muscle after the food leaves the mouth.     4. Chemical Digestion: Enzymes from the liver, gallbladder, and pancreas break down polymers into monomers.     5. Absorption: Occurs primarily in the small and large intestines.     6. Defecation: Removal of waste.
• Mouth and Esophagus:     * Mechanical and chemical breakdown starts here.     * Food is called a "bolus" after being chewed.     * Salivary amylase breaks down carbohydrates (hydrolysis of starch).     * Peristalsis moves the bolus into the esophagus.
• Stomach:     * Protects itself with mucus.     * Contains parietal cells which secrete hydrochloric acid ($HCl$), killing pathogens and activating enzymes.     * Contains chief cells which secrete pepsinogen (an inactive enzyme). $HCl$ activates pepsinogen into pepsin, which breaks down proteins.     * Enteroendocrine cells release hormones to regulate digestion.
• Small Intestine:     * Has a smaller diameter than the large intestine but is much longer.     * Folds called villi and cellular extensions called microvilli increase surface area for absorption.     * Three Segments:         1. Duodenum: Site of most chemical digestion.         2. Jejunum: Site of most absorption.         3. Ileum: Acts as a "bacteria farm," absorbing water and vitamins.
• Large Intestine: Contains bacteria capable of breaking down lactose. Small amounts of acid that leak into the small intestine are neutralized by bicarbonate ($HCO_3^-$).

Accessory Organs of Digestion

• Liver:     * Produces bile to break down fat globules (lipid digestion).     * Involved in many systems and has the unique ability to regenerate via mitosis.     * Nutrients from the small intestine (except lipids) go to the liver first.
• Gallbladder: Stores bile produced by the liver and secretes it through the bile duct into the duodenum.
• Pancreas:     * Secretes bicarbonate ($HCO_3^-$) to neutralize stomach acid.     * Produces a suite of enzymes:         * Trypsin: Breaks down proteins.         * Lipase: Breaks down lipids.         * Amylase: Breaks down carbohydrates.         * Nuclease: Breaks down nucleic acids.

The Excretory System

• Primary Organs:     * Lungs: Remove carbon dioxide ($CO_2$) as waste.     * Kidneys: The main excretory organ. Filters blood (blood in, filtered, blood out) to form urine, which travels to the bladder.     * Liver: Considered an accessory excretory organ.     * Skin: Secretes sweat to get rid of salt.     * Bladder: Holds urine; does not produce anything.
• Kidney Functions:     1. Remove small wastes.     2. Regulate hydration.     3. Regulate blood pressure.
• Nephrons: The functional filtering units of the kidneys. There are many nephrons in each kidney.
• Nitrogenous Waste:     * Amino acids contain nitrogen. Waste products of amino acid metabolism differ by species.     * Ammonia ($NH_3$): Produced by fish; very toxic, must be excreted immediately.     * Urea: Produced by the liver in mammals as a less toxic waste product of protein metabolism.
• Medical/Anatomical Terminology:     * Renal: Refers to the Kidneys.     * Hepatic: Refers to the Liver.     * Pulmonary: Refers to the Lungs.

Tissues and Biological Macromolecules

• Four Types of Tissue:     1. Epithelial: Includes stratified squamous (mouth, esophagus, anus) and columnar (inner digestive tract).     2. Muscle: Categorized as Skeletal (voluntary), Cardiac, and Smooth (involuntary).     3. Connective: Includes bone, blood, and fat (adipose).     4. Nervous: Transmits electrical signals; involves the brain, hypothalamus (homeostasis), and neurons (axon transmitting signals).
• Macromolecules and Digestion:     * Carbohydrates: Polymers called polysaccharides (e.g., starch). Monomers are monosaccharides (e.g., glucose). Dimers like sucrose (table sugar) are also common. Dextrose is an old name for glucose.     * Lipids: Triglycerides composed of fatty acids. Used for energy, hormones (cholesterol is the foundation for testosterone and estrogen), and cell membranes (phospholipids).     * Proteins: Polypeptides composed of $20$ different amino acids. Sequence is determined by genetics. Structural examples include actin and myosin filaments in muscle fibers.     * Nucleic Acids: Polymers made of nucleotides (A, C, G, T, U).

Metabolism and Nutrition

• Body Composition: Approximately $64\%$ water, $16\%$ protein, $16\%$ fat, $4\%$ minerals, and $1\%$ carbohydrates.
• Metabolism Definitions:     * Catabolism: Breaking down molecules (e.g., hydrolysis); releases energy (combustion of glucose).     * Anabolism: Synthesis of polymers from monomers (e.g., dehydration); requires energy.     * Modification: Rearranging molecules (e.g., converting fructose to glucose).
• Water Properties:     * Constitutes over $50\%$ of cells and blood.     * Polar molecule with hydrogen bonds.     * High cohesion, heats up slowly, and evaporates slowly. Excellent solvent.
• Lactose Digestion:     * Lactose is a dimer made of glucose and galactose.     * Lactase is the enzyme that breaks it down. Lactose intolerance is caused by a lack of this enzyme outside the intestinal cells.
• Vitamins and Minerals:     * Vitamin B: Vital for cellular respiration.     * Coenzymes: Vitamins that assist enzymes.     * Minerals: Essential ions such as Calcium ($Ca^{2+}$), Magnesium ($Mg^{2+}$), Iron ($Fe^{2+}$), Sodium ($Na^+$), and Potassium ($K^+$).