Physiological Principles and Cell Biology Notes

Module 1: Introduction to Physiological Principles

• Physiology is important for understanding how living organisms perform vital functions.
• The two central questions of physiology are:
  • Mechanism: How do living organisms perform their functions?
  • Origin: Why do living organisms perform their functions in a specific way?
• Levels of organization in organisms:
  • Atoms
  • Molecules
  • Organelles
  • Cells
  • Tissues
  • Organs
  • Organ Systems
  • Organism
  • Population
  • Species
  • Community
  • Ecosystem
  • Biosphere
• Basic mechanisms and enhancements in homeostasis.
• Positive and negative feedback mechanisms contribute to homeostasis.

Characteristics and Processes Shared by Organisms

• Organisms share common characteristics and processes:
  • Organization
  • Responsiveness (e.g., reaction to painful stimulus)
  • Regulation (e.g., body temperature homeostasis within a normal range)
  • Growth and Development
  • Reproduction (e.g., egg and sperm)
  • Metabolism: chemical reactions that occur in the body
    • $CD \rightarrow C + D + Energy$ (Catabolic chemical reaction example)

Anatomy and Physiology

• Anatomy: the study of structure
  • Derived from "a cutting open"
  • Study of internal and external structures and physical relationships among body parts
  • Gross anatomy (macroscopic)
  • Microscopic anatomy
  • Methods of study:
    • inspection
    • auscultation: listening to sounds
    • palpation: feeling for abnormalities
    • percussion: tapping to assess underlying structures
• Physiology: the study of function and how living organisms perform their vital functions
  • Example: Heartbeat coordinated by electrical events (detected by ECG)
  • Blood pressure in major arteries must be maintained within normal limits.
    • High pressures can cause vessel damage.
    • Low pressures can cause vessel collapse.
• Structure and function are interrelated
  • Example: Elbow joint (ulna, radius, humerus, ligaments)
    • The ulna has a broad, deep depression into which the end of the humerus fits.
    • Ligaments and surrounding muscles stabilize the joint.
    • Hinge-like movement is permitted.

Hierarchical Organization of Living Systems

• Living systems show hierarchical organization.
• Cellular Level
  • Atoms
  • Molecules
  • Macromolecules
  • Organelles
  • Cells (e.g., heart cell)
• Organismal Level
  • Tissues
  • Organ
  • Organ System
  • Organism
• Population Level
  • Population
  • Species
  • Community
  • Ecosystem
  • Biosphere

The Body's Structural Hierarchy

• Atom
• Molecule
• Macromolecule
• Organelle
• Cell
• Tissue
• Organ
• Organ System
• Organism

Cells

• Cells are the smallest units of life.
• Examples: Smooth muscle cells, blood cells, bone cells, fat cells
  • Smooth muscle cells: long and slender, contractions in the walls of organs.
  • Blood cells: flattened discs (red) or spherical (white); transport oxygen/CO2 or fight infection.
  • Bone cells: reside within cavities, maintain bone, and recycle calcium/phosphate.
  • Fat cells: spherical storage containers for excess energy.

Cellular Organization

• Cell division and growth
• Cell differentiation: specialized cell types
• Tissues: epithelial, connective, nervous, muscle
• Organ (e.g., kidney) - functional unit (nephron)
• Organ system (e.g., urinary system) - bladder, urethra, ureter

Organs and Organ Systems

• Organs are composed of tissues.
• Organ systems are made up of organs.

Anatomy and Physiology at Many Levels

• Atomic and molecular levels: membrane protein in neurons regulates the flow of ions.
• Cellular level: electrical signal travels down the length of a neuron.
• Tissue level: signals travel from cell to cell in nervous tissue.
• Organ level: nervous and connective tissue in the brain aid in sight, smell, memory, and thought.
• Organ system level: the brain and nerves send signals to control breathing, digestion, movement, etc.
• Organism level: the nervous system coordinates the functions of other systems to support life.

Integrative Nature of Physiology

• Ecological and evolutionary levels:
  • For a pheasant escaping a predator is crucial.
  • Muscle cell structure/properties determine escape speed.
  • Failure to escape = death; Success = life and future reproduction.
• Biochemical level:
  • Krebs cycle helps make ATP for muscle contraction.
• Evolution
  • Genetic difference between populations.
  • $Thrust - Drag = Mass \times Acceleration$
  • $C<em>6H</em>{12}O<em>6 + 6O</em>2 \rightarrow 6CO<em>2 + 6H</em>2O + energy$

Other Integrative Aspects of Physiology

• Physiology depends on all levels of organization
  • Cell physiology: voltage across nerve cell membrane
  • Morphology: nerve cell
  • Biomechanics
  • Systems physiology: Nerves delivered through the nervous system activate swimming muscles
  • Biochemistry: ATP Fuel for muscles.
• Physiology acts within an ecological context.
  • Salmon modify ion-transport proteins in gills when moving from saltwater to freshwater.

Physiology's Two Central Questions

• Mechanism: How does it work?
  • Mechanism refers to the components of actual,living plants and animals and the interactions among those components that enable them to perform as they do.
• Origin: Why does it work that way?

Natural Selection

• Natural selection is a key process of evolutionary origin.
• Natural selection increases the frequency of genes that produce phenotypes that raise the likelihood that animals will survive and reproduce.

Homeostasis

• Claude Bernard's work on digestion (pancreas, gastric juices, intestines)
• Homeostasis: controlled stability of the internal milieu.
• fixity of the internal environment is the condition for free life

Walter Bradford Canon

• Coined the term "fight or flight."
• Expanded on Claude Bernard's concept of homeostasis
• Described the ceaseless balancing and rebalancing of physiological processes.
• Homeostasis.

Homeostasis – Environments

• External environment: everything outside the body
• Internal environment: cells, tissues, fluids, and organs

Changes in the Internal Environment

• Potential changes arise from:
  • Materials from the environment surrounding cells (oxygen, nutrients, salts).
  • Responses to the organism’s external environment.

Homeostatic Regulation

• Homeostatic regulation adjusts physicalogical systems to preserve homeostasis in environments that are often inconsistent, unpredictable, and potentially dangerous.

Thermoregulation

• Regulation of temperature in the human body
  • Sensors detect increases or decreases in body temperature.
  • Signals are sent to the hypothalamus.
  • The hypothalamus signals effectors to take corrective action.

Feedback Mechanisms

• Negative feedback
  • The response of the integrator is opposite to the input of the sensor, thus helps with maintaining stability.
    • Receptors (skin and brain) detect temperature changes.
    • The control center (hypothalamus) receives information and sends commands.
    • Effectors (smooth muscle in blood vessels, sweat glands) take corrective action (e.g., dilation of blood vessels, increased sweating).
  • At normal body temperature, the control center is relatively inactive.
• Positive feedback
  • Changes increase the deviation from the set point.
  • Conditions move away from the normal range; accelerates process to completion.
    • Example: Blood clotting
      • Damage to cells releases chemicals.
      • Chemicals start chain reactions to form a clot.
      • Clotting accelerates as each step releases more chemicals.
      • The process ends with the formation of a blood clot.

Cellular Physiology

• Cellular components
  • Nucleoid
  • Cytoplasm
  • Capsule
  • Cell wall
  • Ribosomes
  • Lysosome
  • Smooth endoplasmic reticulum
  • Mitochondria
• Cell wall
• Cell membrane
• Nucleus.
• Nucleolus
• Rough endoplasmic reticulum
• Cytoplasm
• Plasma
• Pili
• Flagellum
• Golgi
• apparatus
• Ribosomes
• Chloroplast
• Plasmo-
• desma
• Vacuole

Basics of Cells

• A cell is the smallest unit of life that can function independently

Cell Theory Components

• Components of early cell theory
  • All organisms are made of one or more cells.
  • The cell is the fundamental unit of life.
  • All cells come from preexisting cells.
• Additional ideas in modern cell theory
  • All cells have the same basic chemical composition.
  • All cells use energy.
  • All cells contain DNA that is duplicated and passed on as each cell divides.

Cell Architecture

*Overview diagram of cellular architecture

Types of Cells

• There are two types of cells: prokaryotes and eukaryotes *Bacterial cell
  • DNA and RNA
• Ribosomes (produce proteins)
• Cytoplasm
• Cell membrane
  *Eukaryotic cell

Bacterial Cell Anatomy

• Lacks membrane-bounded organelles.
• Their ribosomes and DNA are free in the cytoplasm.

Animal Cell Anatomy

*Centrosome Centriole
*Peroxisome
*Nucleus
*Nuclear Nuclear DNA Nucleolus
*pore
*envelope
*Microtubule Intermediate Microfilament
*filament
*Cytoskeleton
*Rough endoplasmic reticulum
*Cell membrane
*Lysosome
*Cytosol
*Mitochondrion
*Smooth endoplasmic reticulum
*Golgi apparatus
*Cytoplasm
*(all cell contents
*except nucleus)

Plant Cell Anatomy

*Nucleus
*Ribosomes
*Nuclear
*pore
*Nuclear
*envelope
*Nucleolus
*DNA
*Rough
*endoplasmic
*reticulum
*Chloroplast
*Golgi
*Nucleus
*Chloroplast-
*Cell wall
*Vacuole
*apparatus Mitochondrion
*Smooth
*endoplasmic
*reticulum
*Peroxisome
*Cell wall
*Cell
*membrane
*Plasmodesma
*Cytoplasm (all
*cell contents
*except nucleus)
*Cytosol
*Central
*vacuole
*Intermediate Microfilament Microtubule
*filament
*Cytoskeleton

Microscopy and Magnification

• Microscopes and magnifications
  • Light microscope (LM): 200 nm - 10 mm
  • Scanning electron microscope (SEM): 10 nm - 1 mm
  • Transmission electron microscope (TEM): 10 pm - 100 μm
  • Atomic force microscope (AFM): 0.1 nm - 10 nm
  • Unaided eye: ≥ 200 μm

Cell Size

• Range of electron microscope
  10^10 Å = 10^9 nm = 10^6 μm
• Range of light microscope
• Range of human eye

Light Microscopy

• Image examples

TEM Microscopy

• Image examples

SEM Microscopy

• Image examples

Nucleus

• The nucleus stores and transmits information.
• Genetic information is encoded in DNA (chromosomes).
• Nucleolus - RNA molecules in ribosomes are manufactured and the large and small ribosomal subunits are assembled.

Ribosomes

• Sites of protein synthesis
• Eukaryotic ribosomes are scattered free in the cytosol and are also associated with the endoplasmic reticulum
• Proteins manufactured by free ribosomes either remain in the cytosol or are imported into other organelles, such as the nucleus

Endoplasmic Reticulum

• Site of synthesis processing, and storage.
• ER is continuous with the nuclear envelope and possesses two distinct regions:
  • system of membrane-bound sacs and tubules with ribosomes attached
  • system of membrane- bound sacs and tubules that lacks ribosomes

Golgi Apparatus

• Site of protein processing, sorting, and shipping
• A collection of flattened sacs called cisternae

Lysosomes

• Recycling centers
• Oval or globular organelles that contain enzymes to digest macromolecules.
• Contain about 40 different enzymes, each specialized for hydrolyzing different types of macromolecules - proteins, nucleic acids, lipids, or carbohydrates

Vacuoles

• Storage centers in plant and fungal cells.
• Vary in size and function
• Some contain digestive enzymes and serve as recycling centers
• Most are large storage containers

Peroxisomes

• Site of oxidation reactions
• Globular organelles that contain enzymes involved in detoxifying reactive molecules, such as hydrogen peroxide.
• Centers for reduction - oxidation (redox) reactions.

Mitochondria

• Power-generating stations
• Vary in size and shape but all have two membranes with sac-like cristae formed from the inner membrane that are involved in producing ATP
• copies of a small, circular or, in some species, linear chromosome called mitochondrial DNA (mtDNA) that is independent of the nuclear chromosomes

Chloroplast

• Sugar-manufacturing centers in plants and algae
• Many enzymes and other molecules are located in membranes inside the chloroplast
• Membranes form thylakoids that consist of discs stacked into grana

Chemical Foundations of Life

*Examples of chemicals: Sodium, Water ,Oleic acid, D-serine, L-glucos

Chemical Level of Organization

• Atoms, ions, and molecules: the building blocks of chemical evolution

Atoms

• Atoms are the basic particle of matter
• Protons ($p^+$) have a positive electrical charge.
• Neutrons ($n$ or $n^0$) are electrically neutral, which means they are uncharged.
• Electrons ($e^-$) are much smaller and about 1/1836th the mass of either protons or neutrons. They have a negative electrical charge.

Chemical Reactions

• Three basic types of chemical reactions are important for understanding physiology
  • Synthesis of a biomolecule - occurs when subunits bond during a dehydration reaction (removal of $H_2O$)

Degradation by Hydrolysis

• Occurs when the subunits separate during a hydrolysis reaction (addition of $H_2O$)

Water and Carbon

*Water and carbon: the chemical basis of life

Carbon and Life

• a) lipids that store energy in the canola plant b) carbohydrates that provide structure for the tree c) proteins that form the hemoglobin of red blood cells d) genetic material that the lioness has passed on to her offspring.

Water as Solvent

*Water - the solvent of life

Properties of Water

• Partial charges on water molecules can form up to four hydrogen bonds
• The oxygen can form two - each hydrogen can form one
• Polar covalent bonds in water give the oxygen a partial negative charge and each hydrogen atom a partial positive charge

Forms of Water

*(a) Steam becoming water vapor (gas)
*(b) Water (liquid)
*(c) Ice (solid)
*32°F, 0°C, 212°F, 100°C, 50°C

Regulation of Body Fluid pH

*Regulation of body fluid pH is vital for homeostasis

• The $[H_3O^+]$, PH values are given in diagram of lyre to stomach acid.

PH Range

*Diagram of PH range from extremely acid (0) to extremely basic (14) - stomach acid to Oven cleaner

Water Properties

• Hydrogen bonds give water its emergent properties

Water: Cohesion

• Cohesion is the tendency of water molecules to stick to one another
• Cohesion between molecules on the surface of liquid water give it high surface tension
• Water is cohesive

Water: Adhesion

• Water molecules also form hydrogen bonds with other molecules - adhesion
  Water evaporates through pores in leaves.
  2 Evaporating molecules pull water up stem.
  3 Water molecules are pulled into roots.

Water as a Solvent

• The polarity of water molecules helps water dissolve most biologically important molecules, since many of them are hydrophilic
• Water is an excellent solvent

Water: Temperature Regulation

• Hydrogen bonds make water resist changes in temperature.

Water and Freezing

• Hydrogen bonds make water molecules spread out as the water freezes into ice.
• Water expands when it freezes

Organic Molecules

• Organic molecules are biologically important
• The organic molecules needed for life’s processes are categorized into four main types:
  • Carbohydrates
  • Proteins
  • Nucleic acids
  • Lipids

Carbohydrates Overview

*Carbohydrates

Monosaccharides

• Monosaccharides are simple sugars and the monomers that make up larger carbohydrates.
  • Examples: Ribose ($C<em>5H</em>{10}O<em>5$), Glucose ($C</em>6H<em>{12}O</em>6$), Fructose ($C<em>6H</em>{12}O_6$)

Carbohydrates: Synthesis and Breakdown

• Dehydration synthesis binds two monosaccharides together, forming a disaccharide
• Hydrolysis separates disaccharides into monosaccharides

Complex Carbohydrates

• Complex carbohydrates
  • Cellulose
  • Starch
  • Glycogen

Major Groups of Carbohydrates

• Based on structures
• Simple sugars
  • Monosaccharides: glucose, galactose, mannose
  • Disaccharides: sucrose, maltose, lactose
  • Oligosaccharides: milk oligosaccharides, raffinose
• Polysaccharides
  • Glucose homopolymers: cellulose, starch, glycogen (
  • Disaccharide heteropolymers: chitin, keratan sulfate (-
• Glycoconjugates
  • Glycoproteins: antibodies, viral coat proteins
  • Proteoglycans: aggrecan, syndecan, glypican
  • Glycolipids: blood antigens, membrane anchors

Amino Acids, Peptides and Proteins

Amino acids, peptides and proteins

Proteins

• Proteins are at the center of action in most biological processes.
• Nearly all the molecular transformations that define cellular metabolism are mediated by protein catalysts.

Protein Associations with Membranes

• Phospholipid bilayer
  • Outer leaflet
  • Inner leaflet
  • Exterior environment
• Alpha-helical protein
• Ion channel
• Transmembrane protein
• Cytosol
• Lipid anchored protein
• Peripheral membrane proteins

General Amino Acid structure

• General structure of amino acids
• Amino group
• Carboxyl group

Amino Acid Properties

• The 20 different amino acids have 20 different R-groups
• Each amino acid has its own chemical and physical properties

Protein Synthesis

• Proteins: synthesis and breakdown
• Dehydration synthesis binds two amino acids together, forming a dipeptide
• Hydrolysis separates dipeptides and polypeptides into individual amino acids

Protein Folding

• Polypeptides fold up into proteins
• A chain of amino acids folds into a unique 3-D shape to become a protein
• The function of a protein depends on its shape, or tertiary structure.
  • Protein is functional
  • Protein is not functional

Protein Structures

• Primary structure (sequence):
• Amino acid sequence of a polypeptide
• Secondary structure (“substructure”):
• Localized areas of coils, sheets, and loops within a polypeptide
• Tertiary structure (polypeptide shape):
• Overall shape of one polypeptide
• Quaternary structure (protein shape):
• Overall protein shape, arising from interaction between the multiple polypeptides that make up the functional protein.

Nucleic acids

*Nucleic acids carry
the genetic
information

Nucleic Acids

• Nucleic acids include DNA and RNA.
• The primary structure of each protein in a cell is determined by the nucleic acids.

Nucleotide

• The monomers of nucleic acids are nucleotides
  The three parts of a nucleotide are a phosphate group, a 5-carbon sugar and a nitrogenous base.

Nitrogenous bases

• Different nitrogenous bases are found in nucleotides
  DNA and RNA both incorporate adenine, cytosine, and guanine. Only DNA uses thymine. Only RNA uses uracil.

Synthesis of Nucleic Acid

• Nucleic acids– synthesis and breakdown
  • Dehydration synthesis binds two nucleotides together
  • Hydrolysis separates nucleic acids into individual nucleotides

Lipids

• Roles: energy storage, hydrophobic barriers, endocrine system & signaling

1. energy storage molecules and are either obtained directly from the diet or synthesized from carbohydrates 2. form the hydrophobic barriers of cell membranes 3. function in the endocrine system and activate a variety of signaling pathways

Hydrophobic Nature of Lipids

• Lipids are a collection of different hydrophobic molecules
  Unlike carbohydrates, proteins, and nucleic acids, lipids are NOT built from chains of monomers.

Triglycerides

• Classes of lipids – Triglycerides
• Triglycerides are formed by covalently attaching three fatty acid molecules to a glycerol molecule.

Waxes

• Waxes are the second class of lipids
  Waxes are composed of fatty acids combined with alcohols. This class of lipid is particularly hydrophobic.

Steroids

• Steroids are the third class of lipids
  Cholesterol regulates the fluidity of animal cell membranes It is also used to synthesize many sex hormones.