UNIVERSITY OF NORTH TEXAS

ANIMAL PHYSIOLOGY

(BIOL 3800)

CHAPTER OUTLINE

CH 1 and 3

CHAPTER 1: THE MEANING OF PHYSIOLOGY

Why Animal Physiology
Anatomy: structure
Physiology - function.
Anatomy & Physiology: obviously a combination but with less time devoted
to function
The human species is part of the animal kingdom.
Fundamental life processes are shared by all animals.
Physiology is the cornerstone of scientific medical practice
However: Medical practice is more than the application of physiology. In many
situations, the underlying mechanisms are not yet understood and the physician
must use personal observation, judgment, and population data.
The close relationship between Physiology and the practice of Medicine is
exemplified by the
Nobel Prize for "Physiology or Medicine".
Physiology and Philosophy (Human Experience)
Consciousness, awareness, thought, memory, learning, language, perception,
intellect result all from the function of the nervous system --i.e. from biological
processes
Scientific Method
Based on verifiable evidence!!!
Repeatability within small statistical fluctuations is essential
Verifiability is a PROCESS
Many laboratories (and different methods) participate in this process
News media often distort our view of this process
(i.e. results from ONE lab are reported as "definitive")
NOTE: The brain is emotional and inaccurate. The initial excitement of an idea
(hypothesis) must be followed by dispassionate, systematic investigation. The
scientific method keeps us from jumping to conclusions and helps us remain
honest. It is nothing special: police investigations follow the same principle.
Central Themes in Physiology

Function is linked to Structure: e.g. enzymes, neural circuitry

NOTE: the brain /mind dilemma is easily resolved:
Brain: cellular structure (100 billion neurons and their connections).
Mind: the electrophysiological dynamics generated by the cellular structure.
Chemical Composition
98% of body weight consists of
Hydrogen (63%); Oxygen (25.5%) and Carbon (9.5%)
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UNIVERSITY OF NORTH TEXAS

ANIMAL PHYSIOLOGY

(BIOL 3800)

CHAPTER OUTLINE

CH 1 and 3

It is the organization of these atoms that determines whether molecules are

organic or inorganic and whether a system is inanimate or animate (i.e. alive)

Genetics and Physiology

genomics >>>> proteomics >>>> dynamics
Evolution (basic mechanism: natural selection)
"blind process of evolution" : evolution has no specific target

NOTE: Evolution is sloppy. Structures and mechanisms are not optimized

unless there is specific competition between species where one is given a clear
advantage by a modified mechanism. Otherwise, even poor mechanisms are
carried along as long as they work.
During this course, you will see many examples of mechanisms that could be
improved.
1. The kidney filters all small molecules required to maintain life. It is only a
massive
re-absorption of necessary molecules (after filtration) that
keeps us from dying. Why not skip filtration and expel toxic metabolic
byproducts (such as urea) via transporters?
2. I am sure we could improve the menstrual cycle somewhat.
3. Why is the hypothalamus communicating with the anterior pituitary gland via a
capillary portal system? Why is the hypothalamus sending hormones in long
axons to the posterior pituitary to be released into capillaries? Could this be
done better???

Homeostasis Claude Bernard/Cannon 1926.

Organ systems integrated by automatic adjustments to keep
interior environment within narrow limits despite internal and external
changes.
General Mechanism: Feedback
negative: correction back to "center"
positive: amplification, away from center (ex. epilepsy)

UNIVERSITY OF NORTH TEXAS

ANIMAL PHYSIOLOGY

(BIOL 3800)

CHAPTER OUTLINE

CH 1 and 3

Negative
feedback
Uncorrected
trajectory

Fig. 1-2

Positive
feedback

NOTE: positive feedback is

temporary, and must be
controlled by negative
feedback

CHAPTER 2: EXPERIMENTAL METHODS

Use for reference when needed.

CHAPTER 3: MOLECULES, ENERGY and BIOSYNTHESIS

Hypothesis: Life arose through processes of chance and natural selection.
Science is evidence driven
Evidence is based on verifiable and quantifiable observations
Example

destruction of "vitalism" theory by experimental observations

Theory of Vitalism": organic substances can be produced only by living

organisms
1828: Friedrich Whler
synthesized urea from inorganic compounds (mineral sources)
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UNIVERSITY OF NORTH TEXAS

ANIMAL PHYSIOLOGY

(BIOL 3800)

CHAPTER OUTLINE

CH 1 and 3

NH2-CO-NH2
These experiments destroyed the Vitalist Theory
CYTOSKELETON (3 major structures):
structure
microtubules
250
intermediate filaments
microfilaments
many other molecular

protein

cross-sect. diam
tubulins

three proteins
120
actin
70
components attach to cytoskeleton

Metric System
1 meter
=
100 centimeter (cm)
1 centimeter
=
10 millimeter (mm)
1 mm
=
1000 micrometer (m)
[macroscopic to microscopic
domains]
1m
= 10,000 Angstroms ()

lysosomes - (digestive enzymes in vesicles)

Note: they are not directly involved in NECROTIC cell death
(however, ion deregulation, especially Ca++ is involved in
NECROTIC cell death)
The other form of cell death is APOPTOSIS (genetically-controlled)
Apoptosis

Fragmentation of nucleus
and cytoplasm induced by
specific signaling pathways

In necrosis, the nucleus

stays intact longer than the
cytoplasmic structures.
Apoptosis: Programmed Cell Death
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UNIVERSITY OF NORTH TEXAS

ANIMAL PHYSIOLOGY

(BIOL 3800)

CHAPTER OUTLINE

CH 1 and 3

Apoptosis (or programmed cell death) is defined as a mechanism of cellular suicide.

It is characteristically different from cell necrosis in morphology and biochemistry.
The mechanism is used to reduce the number of cells that are overproduced during organ
development. It also occurs after internal cellular damage.
Plasma membrane damage usually results in necrosis: rapid Ca++ entry.
Slow Ca++ entry can trigger apoptotic pathways.
Apoptosis results in the
1. Cell shrinkage.
2. Condensation of the nucleus, and fragmentation
3. Chromosomal fragmentation due to the controlled digestion of DNA by apoptosis DNAses.
4. Cytoplasmic blebbing
The end result of apoptosis is cell death without inflammation of the surrounding tissue.

ATOMS, BONDS, MOLECULES (pg 42 - 44)

PHYSICAL CONCEPTS (please review)
Atoms: smallest particle of an element that still retains the properties of the element.
Elements: substance composed of atoms of one particular kind.
Compound: substance formed by chemical union of two or more elements.
Mixture: combination of compounds or elements not chemically combined.
Electrons, Neutrons, Protons
hydrogen: 1H atomic number=1, atomic mass 1.00797.
Ion:
Ionization:
Valence: (pg. 40) number of bonds an atom can form. Know H, C, O.
Solution: solvent + solute.
Electrolyte: any substance that ionizes in water. NaCl -> Na + + Cl-.
Radioisotopes: unstable isotopes.
Atomic Number: number of protons = number of electrons.
Each element has different atomic number.
Mass number - protons + neutrons
Atomic Weight: sum of protons and neutrons; weights are different for different isotopes
Ideally, the atomic weight of an element is a weighted average of the actual masses of its
naturally occurring isotopes (relative abundance considered).
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UNIVERSITY OF NORTH TEXAS

ANIMAL PHYSIOLOGY

(BIOL 3800)

CHAPTER OUTLINE

CH 1 and 3

Weighted average: 0.3(isotope 1) + 0.2 I(isotope 2) + 0.4 I(isotope 3) + 0.1(isotope 4)

That is difficult to attain in practice
Atomic Mass Unit:
Before 1960: based on oxygen-16
1960 to present: 1/12 of the mass of a neutral atom of the most abundant isotope of carbon.
Isotope - same atomic number, but different atomic weight (neutrons).
39

Ca20

40

Ca20

41

Ca20

42

Ca20

>>>>

47

Ca20

RELATIVE ATOMIC WEIGHT:

based on hydrogen being one or oxygen = 16 (arbitrary measure)
Units: "Daltons"

UNIVERSITY OF NORTH TEXAS

ANIMAL PHYSIOLOGY

(BIOL 3800)

CHAPTER OUTLINE

CH 1 and 3

Review Molecular Weights

Na+ = 22.99 daltons, Cl- = 35.45 daltons: NaCl =

Na+ + Cl- = 58.44 daltons.

O2 = 32 daltons
glucose: C6H12O6
# of atoms atomic wt.
sum
C = carbon 6
x 12
= 72
H = hydrogen 12
x1
= 12
O = oxygen
6
x 16 = 96
180 daltons
Is Carbon special to life in this universe???
carbon forms double bonds, providing for diversity of structure and chemical
reactivity.
silicone (carbon's closest rival) does not form double bonds except at very
high temperatures.
CHARGE DISTRIBUTIONS and their effects
Neutral:
Equal number
of charges

Charged:
Unequal
number of
charges

Dipole:
Equal number
of charges
BUT unequally
distributed

Example: WATER (pg 42)

dipole properties
partial charges produced by tendency of oxygen to pull valence electrons closer to
nucleus (Linus Pauling's "electronegativity principle")
forms an electric dipole

for

dipole/dipole interactions are responsible

"hydrogen bonds" ( ~ 4.5 kcal/mol)

UNIVERSITY OF NORTH TEXAS

ANIMAL PHYSIOLOGY

(BIOL 3800)

CHAPTER OUTLINE

CH 1 and 3

UNIVERSITY OF NORTH TEXAS

ANIMAL PHYSIOLOGY

(BIOL 3800)

CHAPTER OUTLINE

CH 1 and 3

Definitions
Hydration - water around ions or at dipoles (pg 42)
Hydrophilic able to form hydrogen bonds with water (ions, amino acids, ATP,
sugars)
Hydrophobic unable to form hydrogen bonds with water (fats, oil, hydrocarbons)

Figs. 3.2 and 3.4

ORGANIZATION and STRENGTH of ATOMIC and MOLECULAR BONDS

Bond

Physical Characteristics

Bond Strength

Covalent

overlapping electron orbitals

50 - 130 kcal/mole

Electrostatic
Ionic bonds

charge - charge

3 - 9 kcal/mole

H-bonds
kcal/mole

charge-dipole OR
Dipole-dipole

Vander Waals bonds charge - neutral OR

dipole - neutral
9

2- 5
0.5 - 2 kcal/mole

UNIVERSITY OF NORTH TEXAS

ANIMAL PHYSIOLOGY

(BIOL 3800)

CHAPTER OUTLINE

CH 1 and 3

London dispersion neutral - neutral

very weak
_____________________________________________________________________
Fig. 3-4

F= k 1
da

Coulombs law:

F = Q1 Q2
d2

for 2 charges

Fig. 3-5

Amphipathic molecule with both hydrophobic and hydrophilic regions (example pg. 44,
oleate). NOTE: self-assembly of unique structures (micelles and membranes)
Other amphipathic molecules: phospholipids, detergents.
Phospholipids play a vital role in the self-assembly of membranes.
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UNIVERSITY OF NORTH TEXAS

ANIMAL PHYSIOLOGY

(BIOL 3800)

CHAPTER OUTLINE

CH 1 and 3

SOLUTIONS and COLLIGATIVE PROPERTIES (pg 44)

Colligative Properties - Solute particles affect water.
1. Depress freezing point (salt water).
2. Elevate boiling point.
3. Depress water vapor pressure.
4. Osmotic pressure (membrane).
NOTE: colligative properties of a 10 mM NaCl solution are close to that of a 20 mM
sucrose solution.
Suggesting that the number of ions released in water is important !!

.
Activity: "effective" free
concentration
Think of it as a department store: You can
move faster and get more done when it is not
crowded. The more people the slower the
service.
Molecules interfere with each other more at
high concentrations, making the equations less
accurate. The "activity coefficient" tries to

The Concept of the MOLE (pg 44)

A Mole is defined as the Relative Molecular Weight in Grams
(gram molecular weight or gram equivalent weight)
[-nothing to do with Chemical Equivalents: ionic or formula weight divided by its valence]
Examples:
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UNIVERSITY OF NORTH TEXAS

ANIMAL PHYSIOLOGY

(BIOL 3800)

CHAPTER OUTLINE

CH 1 and 3

Oxygen: O2 has a relative molecular weight of 32 daltons. Hence: 1 Mole = 32g of

O2
NaCl: Rel. molecular weight = 58.4 daltons; hence 1 Mole = 58.4g
Molarity: moles/liter of solution (total final volume).
used in research labs and hospitals.
Molality: moles/1,000g solvent
Note: at 4C: 1 ml of H2O weighs 1g

Molarity: concentration 1 mole of compound

1 liter of solute + solvent
Problem:

= 1 Molar solution

make a 2 mM solution of sucrose.

MW = 342.3 daltons
1 Mol = 342.3 g
1 mMol = 0.34g OR 342.3 mg
AMOUNT
2 mMol = 0.34g x 2 = 0.68 g
2 mMolar = 0.68 g/Liter = 0.68 mg/ml

CONCENTRATION

any volume can now be calculated

for 10 ml = 0.68 mg x 10 ml = 6.8 mg/10 ml to give a 2
milliMolar solution
ml
Percent Solutions: ex. 10% solution of NaCl = 10g per 100g solution
Milligram Percent Solutions: 10 mg% = 10 mg per 100g solution
80mg of glucose in 100ml solution
= 80mg% = 0.08%
(80mg = 0.08g)
SOLUTIONS of ELECTROLYTES
electrolyte definition: see glossary
hydronium ion
hydroxyl ion
acids and bases
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UNIVERSITY OF NORTH TEXAS

ANIMAL PHYSIOLOGY

(BIOL 3800)

CHAPTER OUTLINE

CH 1 and 3

Simple definition
Acid - any substance which releases H+.
Base - any substance which captures H+.
S.P.L. Srenson: Biochemische Zeitschrift, 21, 1909, pp.131-200

pH = - log [H+] =

log
1
[H+]

a DEFINITION

NOTE:
Log a/b = - log b/a

A rapid method for estimating pH values

NOTE: a "log" is always the exponent
[H+]
concentration
in moles/liter

|exponential
|log [H+]
|notation |
|(base 10)

-log [H+]

--------------------------------------------------------------------------------------------

1.0
| 100
|
0
0
0.1 = 1/10
| 10-1
| -1
1
0.01
| 10-2
| -2
2
-3
0.001
| 10
| -3
3
0.0000001
| 10-7
| -7
7
________________________________________________
Blood pH
7.0 coma or death
7.4 normal (7.4 0.1)
change

(if maintained at that level for over 30 min)

at 7.5 alkalosis!

Brain already notices this small

7.8 convulsion and death (if maintained at that level for over 30 min)
NOTE: the time listed (30 min) is a rough estimate; individual responses can vary
greatly.
Buffer Systems
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UNIVERSITY OF NORTH TEXAS

ANIMAL PHYSIOLOGY

(BIOL 3800)

CHAPTER OUTLINE

CH 1 and 3

3 Major Mechanisms of Controlling Acid or Alkaline Load

1. pulmonary ventilation (CO2 removal) - fast reaction
2. kidney acid or alkaline urine (H + removal) - slow reaction
3. buffer system in blood
(a) proteins
(b) phosphate buffer
(c) bicarbonate buffer system
An acid-base buffer system is a solution of two or more chemical compounds
that react in a manner so as to prevent changes in the H + concentration.

CO2 + H2O <----> H2CO3 <----> H+ + HCO3Carbonic acid

bicarbonate ion

skip Henderson-Hasselbach Equation (pg 48)

14

(see Chapt 13)

UNIVERSITY OF NORTH TEXAS

ANIMAL PHYSIOLOGY

(BIOL 3800)

CHAPTER OUTLINE

CH 1 and 3

ELECTRIC CURRENTS IN AQUEOUS SOLUTIONS (pg 49 & 50)

Know definitions of: current, voltage, resistance and resistivity, conductance and
conductivity. Ohms law (V = IR), and capacitance (C = q/V)
Binding of Ions to Macromolecules (read lightly)
but know terminology and structures in Fig. 3-12 (pg 52)
Fig. 3-12:

common functional groups

indicates partial charges

BIOLOGICAL MOLECULES
Lipids (fats, phospholipids, sterols)
Characterized by:
1. Solubility in organic solvents (chloroform ether, benzene) (variable solubilities).
2. Insoluble in water (most of them).
Principal classes:
1. triglycerides (fats and oils)
glycerol + 3 fatty acids) (pg 52)

Note: error in book

-

HO or O; oxygen is divalent

Fig. 3-13

Saturated
Unsaturated

(no double bonds);

(some double bonds between carbons).
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UNIVERSITY OF NORTH TEXAS

ANIMAL PHYSIOLOGY

(BIOL 3800)

CHAPTER OUTLINE

CH 1 and 3

The degree of saturation and the length of the carbon chain determine the
physical properties of the molecule.
oil)

Fats with unsaturated fatty acid chains have low melting points

(olive

Fats with saturated fatty acid chains form solids at room temperature
(margarine)
(example: hydrogenation converts vegetable oil into shortening)
triglycerides accumulate in fat vacuoles in adipose tissue cells.
Significance: Can be stored in high concentrations without water !!!
2. PHOSPHOLIPIDS : phosphate group and two fatty acid chains.
Very important for membrane formation
3. STEROLS - (ex. cholesterol). Membrane components, precursors for steroid
hormones
4. OTHER
Sphingolipids Glycolipids:
Waxes

contain: fatty acid + the amino alcohol sphingosine

lipids with one or more sugar molecules
esters of higher fatty acids

General Functions of Lipids:

1. Structural components of membranes - self assembly.
2. Storage depots of metabolic fuel (intracellular).
3. Protective component of skin (exoskeleton of insects and oils).
Carbohydrates (pg. 54)
(Hydrates of carbon: C + H2O = CH2O
C H O
1:2:1
Three Categories:
1. Monosaccharides
2. Oligosaccharides - linked monosaccharides
3. Polysaccharides glycogen
glycogen: (large, covalently-linked macromolecule consisting of glucose
subunits)

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UNIVERSITY OF NORTH TEXAS

ANIMAL PHYSIOLOGY

Proteins (pg. 54)

Protein = chain of amino acids.
Primary structure Secondary structure -

(BIOL 3800)

CHAPTER OUTLINE

CH 1 and 3

Recommend writing formula as below:

R
R O
|
|
||
amino acid sequence.
NH
-C2
regional structure conformation: NH2--C-- C-COOH
ex. helix
; sheet; random
coil.
0H
|
|
detailed folding of entire molecule (S-S
bonds).

Tertiary structure Quarternary structure- non-covalently linked protein complexes (ex: hemoglobin).

or

For 22 amino acids, we can make 22! (factorial) different H

linear sequences.
R O 2O
R O
| ||
| ||
>>>> 1.1240007277776077e+21
NH2--C-- C-- NH2--C-- C-0H
0H
|
|
Nucleic Acids
nucleotide monomer: phosphoric acid-pentose sugar-pyrimidine (or purine base)
R O
R O
|
||
| ||
DNA
|
RNA
NH2--C-- C-NH--C-- C-- 0H
--------------------------------------------------------------------------------------------------|
guanine....cytosine
| | guanine....cytosine
H
adenine....thymine
| H adenine....uracil
|
purines
pyrimidines
|
ribosomal RNA (forms much of ribosome)
messenger RNA (information for protein

assembly)
transfer RNA (attach to amino acid
__________________________________________________________
Replication Transcription Translation -

DNA old -> DNA new

DNA ->
mRNA
mRNA -> protein

ENERGETICS OF LIVING CELLS

Animals are fueled by organic molecules and the release of chemical energy.
Please review:
potential energy
kinetic energy
1st Law of Thermodynamics:
energy is neither created nor destroyed in the universe
(but it can be transformed, i.e. chemical energy conversion to heat)
2nd Law
The entropy (randomness) of a closed system will always increase with time.
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UNIVERSITY OF NORTH TEXAS

ANIMAL PHYSIOLOGY

(BIOL 3800)

CHAPTER OUTLINE

CH 1 and 3

Biological organization requires a constant input of energy

Free Energy: useful chemical energy
Living systems can live only within a narrow range of temperature and pressure.
Therefore: biological systems can utilize only that component of the total
available energy capable of doing work under isothermal conditions.
skip for now (pg. 61-76)
______________________
NOTE: Copyright laws prevent the extensive use of figures from a textbook in
summary notes.
The course outlines in Aniphys will contain a minimum of figures, but Figure
Numbers will be prominently displayed. Those figures must be given special
attention during your studies.

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