BIO 328 Mammalian Physiology: Course Overview

BIO 328 Mammalian Physiology Course Information

• It is taught by Dr. Robert Watson, in the Department of Neurobiology & Behavior
• The course schedule for spring 2025 includes lecture and exam dates and topics.
• Lecture classes and recordings, as well as slides are available on Brightspace.
• Attendance is encouraged, and lectures will be live-streamed
• Office hours for instructors and TAs will occur via Zoom
• Textbooks for the course include: Medical Physiology (3rd edition), Boron and Boulpaep, 2016 and Open Online textbook: https://neurotext.library.stonybrook.edu

BIO 328 Mammalian Physiology Exam Information

• Exams will be administered in person with 30-35 multiple choice questions
• Students will have 75 minutes to complete each exam, with accommodations for approved students

BIO 328 Mammalian Physiology Grade Information

• The three exams are the only sources of possible points for the course, there are no extra credit opportunities
• Exam 1 covers the first eight lectures
• Exam 2 covers lectures 9-16
• Exam 3 covers lectures 17-24 and is given during the final exam period
• Exams are in Javits 110
• One excused absence from an exam is permitted
• To be excused, students must notify Ms. Pauciullo, the Course Administrator, within 24 hours of the exam. Students will be allowed to take one makeup exam for the entire course.
• Students who miss Exam 3 will receive an incomplete grade and will have to take a makeup test.
• Course grades are as follows:
  • A: ≥90
  • A-: ≥85
  • B+: ≥80
  • B: ≥75
  • B-: ≥70
  • C+: ≥65
  • C: ≥50
  • D: ≥45
  • F: <45

BIO 328 Mammalian Physiology Teaching Assistants

• Graduate TA: Christie Aprea
• Undergraduate TAs: Patrick Reynolds, Chun Auyeung, Karissa Lopez, Zarah Alam
• Office hours will be held via Zoom, and a schedule will be posted on Brightspace

Basic Principles of Life

• All life on Earth (short list):\
  • Is carbon-based\
  • Is compartmentalized; the cell is the fundamental unit of life\
  • Can tolerate a limited range of conditions

Levels of Organization in Biology

• Chemistry is at the base, including atoms and molecules
• The next level is cell biology, and includes molecular biology and cells
• Physiology includes Tissues -> Organs -> Organ systems
• Ecology includes Organisms -> populations of one species -> Ecosystem of different species -> Biosphere

All Life is Carbon-Based

• Living things are all carbon-based
• Key carbon structures include:
  • Lipids
  • Proteins
  • Carbohydrates
  • Nucleic acids
• The carbon atom is tetravalent
  • The outer electron shell contains four electrons that can form stable covalent bonds with up to four other atoms
• Carbon is relatively abundant
• The Miller-Urey experiment (1952)
  • Experiment included water (H2O), methane (CH4), ammonia (NH3), hydrogen (H2), a heat source, and an electric spark to simulate lightning
  • This type of experiment can generate >20 different amino acids.

Miller-Urey Experiment (1952)

• Simulated the conditions of early Earth to test the hypothesis that complex organic molecules could arise from inorganic substances
• Methane (CH4), water (H2O), ammonia (NH3), and hydrogen (H₂)
  • These were sealed in a 5-liter glass flask (upper chamber), connected to a 500 ml flask half-full of water (lower chamber).
• The water in the 500 ml flask was heated, and the water vapor entered the larger flask.
• An electrical spark simulated lightning in the upper chamber.
• A condenser cooled the water vapor, and liquid water was collected in a trap.
• After one week, Miller identified several amino acids present in the collection trap solution:\
  • Glycine\
  • Alpha-alanine\
  • Beta-alanine\
  • Paper chromatography used for assessment

Carbon-Based: Proteins

• Chains of amino acids
• Parts of an amino acid: Central carbon, Amino group (NH3+), Hydrogen, Carboxylic acid group (COO-), Side chain (R)
• All life depends on 20 standard amino acids that combine in various sequences to form peptides and proteins
• Peptide functions include catalyzing chemical reactions (enzymes), providing structural support, transporting molecules, and regulating metabolic processes
• These functions are possible due to the incredible diversity of structures from polymers of amino acids

Peptide Bonds

• Covalent bonds that form between amino acids
• Created through a condensation reaction, where the carboxyl group (-COOH) of one amino acid reacts with the amino group (-NH2) of another
• Releases water (dehydration synthesis)
• Peptide bonds are planar and rigid because of partial double-bond character from resonance
• Restricts rotation around the bond, rigidity is crucial for the three-dimensional structure and stability of proteins

Protein Structures

• A protein's conformation is its three-dimensional shape
  • Critical for its function in physiological processes
  • Determined by the sequence of amino acids, allowing the protein to interact with other molecules like ligands, substrates, receptors, or DNA
• Conformational changes are changes in the protein's 3-D shape
  • Play a critical role in regulatory mechanisms, enabling proteins to respond dynamically to cellular signals and maintain homeostasis
• Misfolded proteins can lead to diseases like Alzheimer's, cystic fibrosis, prion diseases, and sickle cell anemia

Carbon-based: Carbohydrates and Nucleic Acids

• Carbohydrates (glucose, galactose, and fructose): hexoses (6-carbon sugars)
• Structural isomers that have the same chemical formula (C6H12O6) but different atom arrangement.
• In its various polymeric forms (starch, glycogen, chitin), glucose is probably the most abundant organic molecule in the biosphere.
• Double stranded DNA molecule, in which adenine forms hydrogen bonds with thymine, and guanine with cytosine. The two hydrogen-bonded strands strands run antiparallel to each other. The sugar-phosphate backbone is located on the outside, and the bases are in the middle.

Carbon-based: Lipids

• Saturated fatty acids
  • Have no double bonds between carbons, they are “saturated” with hydrogens
  • The more saturated a fatty acid is, the more likely it is to be solid at room temperature.
• Monounsaturated fatty acids
  • Have one double bond between two of the carbons in the chain.
  • For each double bond, the molecule has two fewer hydrogen atoms attached to the carbon chain.

Triacylglycerols and Phospholipids

• Triacylglycerol
  • Ester linkage joins fatty acids
• Phospholipid
  • Linked to phosphate
• Note: Triacylglycerols are sometimes referred to as 'triglycerides'; triacylglycerol is the preferred term

Phospholipids

• Polar head group is hydrophilic, and interacts with water molecules
• Phosphate group (PO4³⁻) included in the head. Additional molecules attached to the phosphate is a possibility
• Hydrophobic tails are interactive with other hydrophobic molecules, so they do not react with water
• Glycerol as a scaffold
  • Two the carbon atoms engage in ester linkages with fatty acids, the third carbon is bound to phosphate

Phospholipids

• Have polar head groups and nonpolar tails
• Amphipathic molecules that are the building blocks of lipid bilayers
• Even distribution of electrons and no positive or negative poles, nonpolar molecules such as fatty acids are hydrophobic and repel water molecules
• Amphipathic = polar and nonpolar regions, and they play important roles in biological systems and the formation of biological membranes
• Molecules form bilayers for biological membranes
• Separate compartments

Fluid mosaic model of biological membranes with integral & peripheral proteins

• A structure which is a dynamic lipid bilayer composed of phospholipids interspersed with proteins, carbohydrates, and cholesterol.
• Key features are lateral mobility of proteins/lipids
• Allows the membrane to remain fluid and adaptable
• An asymmetrical distribution of components gives distinct inner and outer surfaces
• Versatile membrane functions: transport, signaling, and maintaining cellular integrity.
• Peripheral membrane proteins bind non-covalently with lipid head groups or with integral membrane proteins
• Peripheral membrane proteins be dissociated if pH or salt concentration levels change
• Integral membrane proteins
  • Embedded within the lipid bilayer often span the membrane with one or more ~20 hydrophobic amino acid segments, and can't be extracted by changing pH or salt.

Life is Compartmentalized

• Cellular compartmentalization is critical for the efficiency and specificity of biochemical processes within cells.
• Segregating cellular components into membrane-bound organelles (nucleus, mitochondria, and lysosomes) can create diverse microenvironments
• This enhances the regulation of cellular activities preventing harmful interactions enhancing metabolic efficiency overall.

Compartmentalization in Animals

• Cellular Level
• Tissue Level: groups of cells with common structure and function.
  • Four types of tissue: epithelial, connective, nervous, muscle
• Organ Level: organization of different tissues to perform specific functions (heart, lungs, brain, liver, kidneys, etc.)
• System Level: several organs organized to carry out major body functions (cardiovascular, nervous, endocrine, respiratory, reproductive, digestive, urinary, immune, etc.)

Animal Body Tissue Types

• Connective tissue is dispersed in extracellular matrix supporting the cells. Ex: blood, bone, and adipose tissue
• Epithelial tissue tightly packed with minimal extracellular matrix forming sheets controlling body surfaces, cavities, secretion, and absorption
• Muscle tissue has specialized proteins (actin and myosin) that contract and generate force Three muscle types are skeletal, cardiac, and smooth
• Nervous tissue electrically excitable with neurons and supportive glial cells

Body Tissue Components

• Histology: The study of the structure and function of tissues
• Extracellular matrix (ECM): material present outside cells
• ECM synthesized & secreted by cells
• The amount and precise composition of ECM varies from tissue to tissue, but is composed largely of proteins
• Cells within tissues stick together through cell junctions

Cell Junctions

• Communicating junctions (gap junctions): allow direct cell to cell communication
• Occluding (tight) junctions block substance movement between cells
• Anchoring junctions (desmosomes): hold cells to one another and the extracellular matrix

Epithelial Tissue

• Epithelial tissue (= epithelia):
  • Several types.
  • Exchange epithelia: the gas change that occurs by diffusion of fluid
  • Transport epithelia: transporting a larger molecules across cell concentrations

Epithelial tissue

• Exchange epithelia:
  • Thin, typically composed of simple, flattened (squamous) cells specializing in diffusion of gases and small molecules Ex: Lung alveoli and capillaries
• Transport epithelia:
  • Columnar or cuboidal cells with tight junctions and specialized proteins
• Movement regulation based on the selective movement of ions, nutrients, and large molecules across gradients.
• In kidney tubules & intestinal lining.

Epithelial Tissue: Exchange Epithelia

• Thin, flat cells of exchange epithelia allow movement through and between cells.
  • In alveoli of the lungs, gas exchange occurs by diffusion.
• The epithelial cells that line blood vessels are called endothelial cells. Together, endothelial cells make the endothelium In capillaries, the fluid and solute moves across the walls by bulk flow (moves in pressure gradient).
• Endothelial cells line the blood vessels

Epithelial Tissue: Transport Epithelia

• Tight junctions in transport epithelia prevent movement between adjacent cells as substances pass through the epithelial cell.
• The substances must cross two phospholipid cell membranes in the process

Renal tubule cells

• These line nephron, the functional & control selective unit of kidney for ion transport, water & solute transport
• The epithelial sodium channel (ENaC) is an example expressed at surface of nephron tubule
• ENaC regulates Na+ diffusion down a concentration gradient towards inside cells = The Na+/K+-ATPase pump regulates the basolateral surfaces
• The pump transports ATP out of the cell using the energy of ATP

Fluid Compartments

• Body fluids of all animals have the same general composition
• H2O and salts
• Water is the major component which takes up ~65% of body weight
• 99% of all molecules are H₂O.
• Salts = ~.75% Biochemical substances = ~.25%.

Body Fluid Classification

• Intracellular fluid (ICF) in cells
• Extracellular fluid (ECF) is outside cells. Ex: Plasma & Interstitial fluid
  • Plasma is fluid portion of blood; plasma is an ECF.
  • Interstitial fluid (IF) is fluid outside of blood vessels and between cells in a tissue
• The body fluid compartments exist in a state of chemical disequilibrium. Their asymmetric distribution must maintain energy.

ATP in energy consumption

• Human body consumes entire weight in ATP each day
• Consumed by average adult; (produces and uses) 50 to 75 (110 to 165 pounds) of ATP per day.
• At point of turnover body contains 50 grams
• ATP not stored, and recycled instead

Cost of Endothermy

• a 65 kg ectotherm (small crocodile) consumes 5–10 kg (11-22 pounds) of ATP per day with some variability

Cellular Respiration

• Aerobic production of ATP is more efficient than anaerobic respiration.
• The estimated max is 38, however actual is 30-32 ATP per glucose.

Aerobic Respiration

• 95-98% is produced aerobically in mitochondria
• 2-5% produced anaerobically through glycolysis in the cytoplasm
• ATP and glucose are produced within high-intensity, short-duration tasks, such as type IIb skeletal muscle.

Metabolic Rate (MR)

• Definition: Energy rate an animal uses in time
• Calculated with O2 consumption in kilocalories for metabolic chamber data. MR requires:
  • Anabolic pathways
  • Catabolic pathways
  • Sustaining muscle contraction Basal Metabolic Rate (BMR): at rest for 12 hours Maintaining asymmetric ion distributions using Na+/K+-ATPase pump makes up 20-40% of the brain’s energy.

Asymmetry maintenance

• Maintaining requires constant maintenance
• Sustaining these functions, energetically is expensive
• Cell uses transport machines to generate their mechanisms

Na+/K+-ATPase pump

• Is an example of cellular transport machines that uses ATP to transport Na+ and K+ ions. Low Na+ and High K+ in the cell, the inverse is true for outside the cells to keep the consumer for cellular energy for equal charge maintenance in the membrane

Energy Conversion

Macromolecules are metabolizable energy: Carbohydrates (glucose), proteins (amino acids), fats

• ATP is involved in biosynthesis, cellular work, and mechanical work
• Nitrogenous wastes are an output

Nitrogenous Wastes

• Breakdown releases ammonia
• Toxic, requires CO2
• Waste is salvaged, excreted (ammonia is lethal)

Ammonia, urea & uric acid

• Ammonia is very water soluble and toxic, like in fish
• Urea is water soluble and is less so, like in mammals
• Uric acid is not water soluble, and not toxic, like in birds

Course information for BIO 328 Mammalian Physiology taught by Dr. Robert Watson. Spring 2025 schedule details lecture and exam dates and topics. Resources include live-streamed lectures, recordings, slides on Brightspace, and online office hours.