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Chapter 1: An Introduction to Anatomy & Physiology

• Overview of Anatomy and Physiology:

  • Anatomy describes the structures of the body — what they are made of, where they are located, and what other structures they are associated with. It is the oldest medical science, with records dating to roughly 1600 B.C.

  • Physiology is the study of function — how anatomical structures work, individually and cooperatively.

  • The central principle of the course: structure determines function, and function reflects structure. All specific functions are performed by specific structures. If you can describe the shape of something, you can usually predict what it does.

• Subdivisions of Anatomy:

  • Gross (macroscopic) anatomy: Examines large, visible structures. It serves as the umbrella term for the five branches below.

  • Surface anatomy: Exterior features and landmarks visible or palpable on the body surface.

  • Regional anatomy: All structures within one body area studied together (e.g., everything in the neck).

  • Systemic anatomy: One organ system studied throughout the whole body (e.g., all bones).

  • Developmental anatomy: Structural changes across the life span, from conception to death.

  • Clinical anatomy: Anatomical features relevant to specific medical specialties.

  • Microscopic anatomy: Examines structures too small to see unaided.

  • Cytology: Study of cells and their internal structures (using the root prefix $cyt\text{-} = \text{cell}$).

  • Histology: Study of tissues and their structures (using the root prefix $histo\text{-} = \text{tissue}$).

• Subdivisions of Physiology:

  • Cell physiology: Processes within and between individual cells — the foundation of all other physiology.

  • Organ physiology: The functions of one specific organ (e.g., cardiac physiology).

  • Systemic physiology: The functions of an entire organ system (e.g., respiratory physiology).

  • Pathological physiology: How disease processes alter normal function.

• Standard Anatomical Terminology:

  • Terminologia Anatomica (International Anatomical Terminology) is the official global standard for anatomical names. It exists so that a structure has one accepted Latin/Greek-derived name worldwide — eliminating the ambiguity of eponyms and regional usage.

• Levels of Organization:

• The body is built in nested levels, each emerging from the one below it. Everything in anatomy and physiology lives at one of these levels, and problems at any level cascade upward.

• Chemical / molecular level: Atoms are the smallest chemical units; molecules are groups of atoms working together. Cardiac example: Atoms assemble into a complex protein molecule.

• Cellular level: Cells are groups of atoms, molecules, and organelles working together; the smallest living unit. Cardiac example: Protein filaments assemble into a heart muscle cell.

• Tissue level: A group of similar cells working together. Cardiac example: Cardiac muscle tissue.

• Organ level: A group of different tissues working together as a unit. Cardiac example: The heart.

• Organ system level: A group of organs working together; humans have 11 organ systems. Cardiac example: The cardiovascular system.

• Organism level: The total living individual. Cardiac example: A human being.

• Vertebrate Characteristics: Humans are vertebrates — animals characterized by a segmented vertebral column. Shared characteristics among vertebrates reflect a shared evolutionary path, which is why animal models are informative for human physiology.

  • The Eleven Organ Systems:

• Integumentary System:

  • Major Organs: Skin, hair, sweat glands, nails.

  • Functions: Protects against environmental hazards; helps regulate body temperature; provides sensory information.

• Skeletal System:

  • Major Organs: Bones, cartilages, associated ligaments, bone marrow.

  • Functions: Support and protection for other tissues; stores calcium and other minerals; forms blood cells.

• Muscular System:

  • Major Organs: Skeletal muscles and associated tendons.

  • Functions: Provides movement; protection and support for other tissues; generates heat that maintains body temperature.

• Nervous System:

  • Major Organs: Brain, spinal cord, peripheral nerves, sense organs.

  • Functions: Directs immediate responses to stimuli; coordinates or moderates other systems; provides and interprets sensory information.

• Endocrine System:

  • Major Organs: Pituitary gland, thyroid gland, adrenal glands, pancreas, gonads, endocrine tissues in other systems.

  • Functions: Directs long-term changes in other systems; adjusts metabolic activity and energy use; controls structural and functional changes during development.

• Cardiovascular System:

  • Major Organs: Heart, blood, blood vessels.

  • Functions: Distributes blood cells, water, nutrients, wastes, oxygen, and carbon dioxide; distributes heat and assists temperature control.

• Lymphatic System:

  • Major Organs: Spleen, thymus, lymphatic vessels, lymph nodes, tonsils.

  • Functions: Defends against infection and disease; returns tissue fluids to the bloodstream.

• Respiratory System:

  • Major Organs: Nasal cavities, sinuses, larynx, trachea, bronchi, lungs, alveoli.

  • Functions: Delivers air to alveoli; provides oxygen to bloodstream; removes carbon dioxide; produces sounds for communication.

• Digestive System:

  • Major Organs: Teeth, tongue, pharynx, esophagus, stomach, small and large intestine, liver, gallbladder, pancreas.

  • Functions: Processes and digests food; absorbs and conserves water; absorbs nutrients; stores energy reserves.

• Urinary System:

  • Major Organs: Kidneys, ureters, urinary bladder, urethra.

  • Functions: Excretes waste products from blood; controls water balance by regulating urine volume; stores urine; regulates blood ion concentrations and pH.

• Male Reproductive System:

  • Major Organs: Testes, epididymides, ductus deferentia, seminal vesicles, prostate gland, penis, scrotum.

  • Functions: Produces sperm, suspending fluids, and hormones; sexual intercourse.

• Female Reproductive System:

  • Major Organs: Ovaries, uterine tubes, uterus, vagina, labia, clitoris, mammary glands.

  • Functions: Produces oocytes and hormones; supports the developing offspring; provides milk to nourish the newborn; sexual intercourse.

• Study Tip: Notice how many systems have a secondary role in temperature control: integumentary, muscular, and cardiovascular. Homeostasis is almost never one system's job.

  • Homeostasis and Mechanisms of Regulation:

• Homeostasis is the existence of a stable internal environment — all body systems working together to keep conditions such as temperature, pH, and fluid balance within a normal range despite external and internal changes. It is the goal of physiological regulation and the key to survival.

• Autoregulation (intrinsic): A cell, tissue, or organ automatically adjusts its own activity in response to an environmental change. Scope: Local — the affected tissue handles it itself.

• Extrinsic regulation: The nervous and endocrine systems control the response. Scope: Body-wide — can coordinate several systems at once.

• Three Parts of Every Control System:

  • Receptor: Receives the stimulus — detects the change (Room-temperature analogy: The thermometer).

  • Control center: Processes the signal, compares it to a set point, and sends instructions (Room-temperature analogy: The thermostat).

  • Effector: Carries out the instructions and produces the response (Room-temperature analogy: The air conditioner or heater).

• Dynamic Equilibrium: Homeostasis is a dynamic equilibrium, not a fixed value. Conditions fluctuate continually around a set point within an acceptable range; opposing forces are in balance and the body adapts continuously. Failure to maintain homeostasis results in disease or death.

  • Negative Feedback Mechanisms:

• Definition: In negative feedback, the response of the effector negates or opposes the stimulus. The variable is driven back toward the set point, the normal range is restored, and the loop shuts itself down. This is the mechanism behind the vast majority of homeostatic regulation in the body.

• Thermoregulation Worked Example:

  1. Stimulus: Body temperature rises above about $37.2^\text{o}\text{C}$.

  2. Receptors: Temperature sensors in the skin and hypothalamus detect the rise.

  3. Control center: The thermoregulatory center in the hypothalamus acts as a thermostat with a set point near $37^\text{o}\text{C}$.

  4. Effectors: Sweat glands in the skin increase secretion; blood vessels in the skin dilate.

  5. Response: Heat loss increases and body temperature drops — back into the $36.7\text{--}37.2^\text{o}\text{C}$ range.

  6. Once normal temperature is restored, the receptors stop signalling and the response turns off.

• Study Tip: On an exam, the giveaway phrase for negative feedback is that the response is in the opposite direction from the stimulus: temperature rises $\rightarrow$ body cools itself; blood glucose rises $\rightarrow$ insulin lowers it.

  • Positive Feedback Mechanisms:

• Definition: In positive feedback, the response of the effector increases or exaggerates the change caused by the stimulus. The body is moved away from the starting condition and the normal range is temporarily lost. This is not a malfunction — it is used deliberately to speed up processes that need to run to completion quickly.

• Blood Clotting Worked Example:

  1. Damage to cells in the blood vessel wall releases chemicals that begin the clotting process.

  2. Those chemicals start chain reactions in which cells, cell fragments, and soluble proteins begin to form a clot.

  3. As clotting continues, each step releases chemicals that further accelerate the process.

  4. The escalating loop ends with formation of a blood clot, which patches the vessel wall and stops the bleeding.

• Comparison of Negative vs. Positive Feedback:

  • Effect of response: Negative feedback opposes / cancels stimulus; Positive feedback reinforces / amplifies stimulus.

  • Direction relative to set point: Negative feedback moves back toward normal; Positive feedback moves further away from normal.

  • How loop ends: Negative feedback ends when variable returns to set point; Positive feedback ends when goal event is completed.

  • Frequency in body: Negative feedback is the rule — most control systems; Positive feedback is the exception — a few specific processes.

  • Examples: Negative feedback includes body temperature, blood glucose, blood pressure, blood pH; Positive feedback includes blood clotting, labor contractions, action potentials.

  • Anatomical Posture and Orientation:

• Anatomical position: Standing upright, face forward, hands at sides, palms forward. Every directional term assumes this standard position. Without this convention, "anterior" would change meaning as the body moved.

• Supine: Lying down, face up.

• Prone: Lying down, face down.

• Study Tip Memory Hook: Supine $\rightarrow$ you could hold soup on your belly. Prone $\rightarrow$ you are prone (face down) on the floor.

  • Anatomical Landmarks — Regional Terms:

• Anterior View — Head and Neck:

  • Cephalic: Head

  • Cranial: Skull

  • Frontal: Forehead

  • Facial: Face

  • Ocular / orbital: Eye

  • Nasal: Nose

  • Otic: Ear

  • Buccal: Cheek

  • Oral: Mouth

  • Mental: Chin

  • Cervical: Neck

• Anterior View — Trunk and Upper Limb:

  • Thoracic: Thorax, chest

  • Mammary: Breast

  • Abdominal: Abdomen

  • Umbilical: Navel

  • Pelvic: Pelvis

  • Pubic: Pubis

  • Inguinal: Groin

  • Axillary: Armpit

  • Brachial: Arm (shoulder to elbow)

  • Antecubital: Front of elbow

  • Antebrachial: Forearm

  • Carpal: Wrist

  • Manual: Hand

  • Palmar: Palm

  • Pollex: Thumb

  • Digital / phalangeal: Fingers or toes

• Anterior View — Lower Limb:

  • Femoral: Thigh

  • Patellar: Kneecap

  • Crural: Leg (knee to ankle)

  • Tarsal: Ankle

  • Pedal: Foot

  • Hallux: Great toe

• Posterior View:

  • Acromial: Shoulder

  • Dorsal: Back

  • Olecranal: Back of elbow

  • Lumbar: Loin (lower back)

  • Gluteal: Buttock

  • Popliteal: Back of knee

  • Sural: Calf

  • Calcaneal: Heel of foot

  • Plantar: Sole of foot

• Study Tip: Watch the pairs that flip front-to-back: antecubital (front of elbow) vs. olecranal (back of elbow); patellar (kneecap) vs. popliteal (back of knee).

  • Abdominopelvic Quadrants and Regions:

• Four Quadrants (formed by two perpendicular lines intersecting at the navel — clinical shorthand):

  • Right Upper Quadrant (RUQ): Liver (most of it), gallbladder, right kidney, parts of stomach and large intestine.

  • Left Upper Quadrant (LUQ): Stomach, spleen, left lobe of liver, pancreas, left kidney.

  • Right Lower Quadrant (RLQ): Appendix, cecum, right ureter, portions of small intestine.

  • Left Lower Quadrant (LLQ): Descending and sigmoid colon, left ureter, portions of small intestine.

• Nine Regions (precise anatomical description):

  • Superior Row: Right hypochondriac region | Epigastric region | Left hypochondriac region.

  • Middle Row: Right lumbar region | Umbilical region | Left lumbar region.

  • Inferior Row: Right inguinal (iliac) region | Hypogastric (pubic) region | Left inguinal (iliac) region.

• Clinical Rule: Right and left always mean the patient's right and left, not yours as you face them.

  • Directional Terms:

• Anterior (ventral): Front; toward the front surface (Example: The sternum is anterior to the heart).

• Posterior (dorsal): Back; toward the back surface (Example: The spine is posterior to the heart).

• Superior: Above; toward the head (Example: The heart is superior to the stomach).

• Inferior: Below; toward the feet (Example: The stomach is inferior to the heart).

• Cranial (cephalic): Toward the head (Example: The cranial end of the spinal cord).

• Caudal: Toward the tail / coccyx (Example: The caudal end of the vertebral column).

• Medial: Toward the midline of the body (Example: The heart is medial to the lungs).

• Lateral: Away from the midline; toward the side (Example: The lungs are lateral to the heart).

• Proximal: Toward the point of attachment of a limb to the trunk (Example: The elbow is proximal to the wrist).

• Distal: Away from the point of attachment of a limb to the trunk (Example: The fingers are distal to the elbow).

• Superficial: At or near the body surface (Example: The skin is superficial to the muscles).

• Deep: Farther from the body surface (Example: The bones are deep to the muscles).

• Study Tip: Proximal/distal are limb terms. Do not use them for trunk structures — use superior/inferior instead. In humans (upright, bipedal), anterior = ventral and posterior = dorsal; in four-legged animals they are not equivalent.

  • Sectional Planes:

• Sagittal plane: Vertical, front-to-back axis; divides the body into left and right portions.

  • Midsagittal: Vertical along the exact midline; produces equal left and right halves.

  • Parasagittal: Vertical, offset from the midline; produces unequal left and right portions.

• Frontal (coronal) plane: Vertical, side-to-side axis; divides the body into anterior and posterior portions.

• Transverse (horizontal / cross) plane: Horizontal axis; divides the body into superior and inferior portions.

  • Body Cavities and Subdivisions:

• Internal organs (viscera) are suspended in fluid-filled body cavities.

• Essential functions of cavities: Protect organs from accidental shocks and permit changes in size and shape of internal organs (lungs, stomach, urinary bladder).

• Ventral Body Cavity (Coelom): Divided by the muscular diaphragm into thoracic cavity above and abdominopelvic cavity below.

• Thoracic Cavity Subdivisions:

  • Right and left pleural cavities: Each surrounds one lung.

  • Mediastinum: Tissue mass between pleural cavities containing great blood vessels, trachea, esophagus, and thymus.

  • Pericardial cavity: Sits within lower mediastinum and surrounds the heart.

• Abdominopelvic Cavity Subdivisions:

  • Peritoneal cavity: Chamber extending throughout abdominal cavity into superior pelvic cavity.

  • Abdominal cavity: Superior portion (diaphragm to top of pelvic bones); contains digestive organs.

  • Pelvic cavity: Inferior portion (within pelvic bones); contains urinary bladder, reproductive organs, last portion of digestive tract.

  • Retroperitoneal space: Posterior to peritoneum and anterior to muscular body wall; contains pancreas, kidneys, ureters, parts of digestive tract.

  • Serous Membranes:

• Parietal layer: Lines the wall of the cavity ($Pariet\text{-} = \text{wall}$).

• Visceral layer: Covers the surface of the organ ($Viscera = \text{internal organs}$).

• Balloon Analogy: Push fist into a partly inflated balloon: fist is organ, inner layer touching fist is visceral layer, outer layer is parietal layer, air space is cavity. Organ is surrounded by cavity, not inside it.

• Membrane Types:

  • Pleura: Parietal layer lines pleural cavity; Visceral layer covers lungs.

  • Pericardium: Parietal layer lines pericardial cavity; Visceral layer covers heart.

  • Peritoneum: Parietal layer lines internal abdominopelvic wall; Visceral layer covers abdominal organs.

• Function of Serous Fluid: Prevents friction as organs move, expand, and contract.

  • Chapter 1 Checkpoint Questions & Answers:

• Question: A structure is described as being distal to the elbow and lateral to the ulna. Which bone is being described, and why can't you use "inferior" here instead of "distal"?

  • Answer: The radius. "Distal" is required because proximal/distal are reserved for describing position along a limb relative to its point of attachment to the trunk; superior/inferior are used for the trunk and head.

• Question: A patient reports pain in the RLQ. Name the structure most often implicated, and give the nine-region name for that same area.

  • Answer: The appendix. The corresponding nine-region name is the right inguinal (iliac) region.

• Question: Why is blood clotting classified as positive feedback when its overall purpose is to restore homeostasis?

  • Answer: Feedback classification describes the mechanism of the loop, not its ultimate purpose. During clotting each step releases chemicals that accelerate the next step, driving the process further from the starting condition until the clot forms. The restoration of homeostasis happens after the loop terminates.

• Question: The kidneys are described as retroperitoneal. Explain precisely what that means in terms of the peritoneum and the body wall.

  • Answer: They lie posterior to the parietal peritoneum and anterior to the muscular body wall, so they are outside the peritoneal cavity rather than suspended within it.

• Question: A section through the body separates the anterior half from the posterior half. Name the plane, and name the plane that would instead produce superior and inferior portions.

  • Answer: Frontal (coronal) plane; transverse (horizontal) plane.

• Question: Identify the receptor, control center, and effector in the regulation of body temperature when a person becomes overheated.

  • Answer: Receptors: Temperature sensors in the skin and hypothalamus. Control center: The thermoregulatory center of the hypothalamus (set point $\thicksim 37^\text{o}\text{C}$). Effectors: Sweat glands (increased secretion) and skin blood vessels (dilation).

• Question: Arrange from simplest to most complex: cardiac muscle tissue, the heart, a protein filament, a heart muscle cell, the cardiovascular system.

  • Answer: Protein filament (chemical) $\rightarrow$ heart muscle cell (cellular) $\rightarrow$ cardiac muscle tissue (tissue) $\rightarrow$ the heart (organ) $\rightarrow$ cardiovascular system (organ system).

• Question: Distinguish autoregulation from extrinsic regulation, and give the two systems responsible for the latter.

  • Answer: Autoregulation is an automatic local response by a cell, tissue, or organ to a change in its own environment. Extrinsic regulation is controlled from outside the tissue by the nervous and endocrine systems.

Chapter 2: The Chemical Level of Organization

• Atomic Structure:

• Matter is made of atoms. Chemical characteristics determine molecular and cellular physiology.

• Subatomic Particles:

  • Proton ($p^+$): Charge = $+1$; Mass = $1\text{ mass unit}$; Location = Nucleus.

  • Neutron ($n^0$): Charge = $0$ (neutral); Mass = $1\text{ mass unit}$; Location = Nucleus.

  • Electron ($e^-$): Charge = $-1$; Mass = Negligible; Location = Electron cloud.

• Key Atomic Numbers:

  • Atomic number: Number of protons. Determines element identity.

  • Mass number: Protons + neutrons. Determines isotope.

  • Atomic weight: Weighted average of mass numbers of naturally occurring isotopes, measured in moles.

• Isotopes: Versions of same element differing only in neutron count. Behave identically in chemical reactions, making radioactive isotopes ideal physiological tracers.

  • Electron Shells and Chemical Reactivity:

• Valence shell: Outermost occupied electron shell; determines chemical bonding behavior.

• Shell Filling Capacities: First energy level holds max $2\text{ e}^-$; Second and third energy levels hold max $8\text{ e}^-$ each.

• Chemical Reactivity Rules: Full valence shell = chemically inert (e.g., helium, neon). Incomplete valence shell = reactive; gains, loses, or shares electrons to fill valence shell.

• Study Tip: Number of electrons per shell corresponds to elements in periodic table rows (row 1 has 2 elements, rows 2 and 3 have 8 each).

  • Principal Elements in the Human Body:

• Four major elements make up $\thicksim 96$% of body weight:

  • Oxygen (O): $\thicksim 65$% body weight. Water component, organic molecules, required for aerobic metabolism.

  • Carbon (C): $\thicksim 18.6$% body weight. Backbone of organic molecules.

  • Hydrogen (H): $\thicksim 9.7$% body weight. Water component, organic molecules, $H^+$ sets pH.

  • Nitrogen (N): $\thicksim 3.2$% body weight. Proteins and nucleic acids.

• Lesser and Trace Elements:

  • Calcium (Ca): $\thicksim 1.8$%. Bones/teeth, muscle contraction, nerve signals, clotting.

  • Phosphorus (P): $\thicksim 1.0$%. Bone matrix, nucleic acids, ATP, phospholipids.

  • Potassium (K): $\thicksim 0.4$%. Principal intracellular cation, membrane potential.

  • Sodium (Na): $\thicksim 0.2$%. Principal extracellular cation, fluid balance, membrane potential.

  • Chlorine (Cl): $\thicksim 0.2$%. Principal extracellular anion.

  • Trace Elements: Magnesium (Mg), Sulfur (S), Iron (Fe), Iodine (I) act as enzyme cofactors, protein structures, oxygen transport, thyroid hormones.

• Mnemonic for Big Four: CHON (Carbon, Hydrogen, Oxygen, Nitrogen).

  • Chemical Bonds:

• Ionic Bonds: Electron transfer occurs. Donor loses electron(s) $\rightarrow$ cation ($+$); Acceptor gains electron(s) $\rightarrow$ anion ($-$). Opposite charges attract (e.g., $\text{Na}^+$ and $\text{Cl}^-$ form $\text{NaCl}$). Strong when dry, weak in aqueous solution.

• Covalent Bonds: Electron sharing occurs. 1 pair = single bond; 2 pairs = double bond; 3 pairs = triple bond. Strongest of all three bond types.

  • Nonpolar covalent: Equal sharing of electrons ($\text{H}_2, \text{O}_2, \text{CO}_2$).

  • Polar covalent: Unequal sharing; creates partial charges and polar molecules ($\text{H}_2\text{O}$).

• Hydrogen Bonds: Weak attraction between molecules ($$ ext{i.e., } ext{between } ext{a } egin{matrix} egin{matrix} egin{matrix} egin{matrix} egin{matrix} egin{matrix} egin{matrix} egin{matrix} egin{matrix} egin{matrix} egin{matrix} egin{matrix} egin{matrix} egin