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Bio 5, Physiology
Physiological processes based upon properties and interactions of atoms, ions, and molecules.
Water is the major constituent (compound) of the body (65-75% of body weight). 2/3 water intracellular;
1/3 extracellular (lymph, blood plasma, interstitial fluid, urine, saliva, etc..).
I. Elements and Atoms:
A. Elements: Living and nonliving things are composed of elements which cannot be broken
down further into simpler substances. Every element has a name, a chemical symbol,
an atomic number. 99% human body composed of 6 elements: carbon, oxygen,
hydrogen, nitrogen, calcium, and phosphorus.
B. Atoms: General term for a structure composed of neutrons, protons, and electrons.
Smallest units of matter that undergo chemical change. The number of subatomic
particles varies from one element to the next (especially protons).
1. Definition: The smallest unit of an element that still retains the chemical and physical
properties of an element.
2. Outer energy shells:
a. Electrons (negative charge, almost no mass).
b. First shell filled with 2 electrons, second and third shells stable with 8 electrons.
c. Valance electrons: electrons in the outermost shell participate in chemical
3. Nucleus: Subatomic particles:
a. Protons (positive charge; one atomic mass unit).
b. Neutrons (no charge; one atomic mass unit).
4. Atomic number=number of protons in an atom. Determines the type of element the
atom is. For example: all carbon atoms will have 6 protons in their nucleus.
5. Atomic weight (mass):
a. number of protons plus the number of neutrons.
b. electrons so light that they are not figured into weight.
6. Isotopes=different number of neutrons in an element. Commonly radioactive
elements. The atomic number is the same but the atomic mass is different.
7. Ions:
a. charged atoms.
b. Anions=negatively charged atoms. Atom has more electrons than protons.
c. Cations=positively charged atoms. Atom has more protons than electrons.
II. Molecules and Compounds:
A. Molecules: Atoms bond with each other to form a chemical unit (possibly more than one
element, or the same element). Molecules are formed through reactions between
valence electrons. Electrons react to fill outer shells. The molecular formula indicates
proportion, number, and types atoms in a molecule.
1. Molecular formula:
a. Octet Rule: Atoms react to produce 8 electrons in outer shells
(Hydrogen and Helium exceptions because they have only 1 shell).
b. Ionic Bonds
- When one or more valence electrons are transferred from one atom to
another producing ions of opposite charge (opposite charges bring atoms
together and create bond). The atom losing the electron becomes
positively charged. The atom gaining the electron becomes negatively
-Ionic bonds are weaker than covalent bonds (ie: they dissociate easily).
- NaCl: salt dissolves in water to form ions.
c. Covalent Bonds: When atoms form a molecule by sharing a
pair of valence electrons. Both nuclei are attracting the electrons equally.
Polar covalent bonds result when electrons are shared unequally.
form and an
of one
d. Hydrogen Bonds: Important organic bonds. Relatively weak bonds.
-When a partially positive hydrogen atom is attracted to a partially
atom in another molecule (N, F, O). Polar molecules
attraction between positive and negative ends of
bind molecules together. Form bonds between
-Water is an important polar molecule that dissolves many substances. In
water, the hydrogen bond is between a Hydrogen atom
molecule and an oxygen atom of another molecule.
B. Chemical Reactions:
1. Anabolic reactions (synthesis reactions): reactions that formulate molecules and
require the input of energy. 2N +6H ---- 2NH3
2. Catabolic reactions (breakdown reactions): reactions that break molecules down and
liberate energy. Excess energy is stored in molecules of ATP. CH4 ----- C + 2H2
3. Exchange reactions: molecules exchange atoms (or groups of atoms) with one
another. NaOH + HCl ---- NaCl + H2O. This example is also an acid/base
C. Compounds: Molecules composed of different atoms: ie: Elements bonded are not the
same. eg: NaCl, H2O, CaCl2.
D. Properties of Water:
1. Liquid at room temperature rather than a gas (hydrogen bonding).
2. Universal solvent for polar molecules. A medium for chemical reactions.
3. Involved in many chemical reactions.
4. Excellent transport medium. Evenly distributes dissolved substances.
5. Resistant to temperature changes. Stabilizes body temperature.
6. Frozen water is less dense than the liquid. Ice floats on water.
7. Water is the most abundant compound in the body.
D. Acids, Bases, pH Scale:
1. Acids: Hydrogen donators: Molecules that release or donate hydrogen ions
(protons) to a solution. Acidic solutions have much H+, low pH.
eg: HCl (Hydrochloric acid)= H++ Cl-
2. Bases: Hydrogen Acceptors: Molecules that take up hydrogen ions
(protons) or dissociate in water to release OH- ions. Basic solutions have few H+.
high pH.
NaOH (Sodium hydroxide)= Na++ OH-
3. Neutral Solutions: pH=7 (Pure water); contain equal amounts of H+ and OH-.
a. pH Scale; 0-6.9 is acidic, 7 is neutral, 7.1-14 is basic (alkaline).
b. Living organisms need to carefully maintain pH homeostasis of body fluids.
4. Buffers
a. a system of molecules and ions that act to prevent (resist) changes in H+
concentration of solutions.
b. Blood buffer:
-blood pH ranges from 7.35-7.45. Above 7.45 is alkalosis. Below 7.35
is acidosis.
-bicarbonate ion (HCO3-): base that buffers acidic metabolic wastes.
- carbonic acid (H2CO3): acid that buffers loss of body acids (vomiting).
HCO3- + H+ = H2CO3
E. Organic Molecules:
1. Traits:
a. Usually contain Carbon and Hydrogen.
b. Frequently formed with covalent bonds.
c. Found in living organisms.
d. Usually larger than inorganic molecules (eg: proteins, carbohydrates, lipids,
nucleic acids, ATP).
e. Many organic molecules are formed by dehydration synthesis
(ie: remove H+ from one molecule and OH- from another to form H2O).
2. Carbon:
a. An important organic element. Often forms carbon chains and rings.
b. 4 electrons in outer shell. Tends to bond with oneself.
c. Hydrocarbon chains make up backbones of many organic molecules
(starch, glycogen, cellulose, fatty acids, DNA, RNA). Reactive groups
(functional groups) are attached and responsible for chemical
properties of molecule.
d. Functional groups:
-carbonyl: C=O (ketones)
-hydroxyl: - OH (alcohols)
-amino: - NH2 (amino acids)
-carboxyl:- C=O (organic acids)
-phosphate: - O-P- OH (H2PO4)
3. Proteins: a very diverse set of molecules composed of amino acids (20). Enzymes,
antibodies, cell receptors, membrane carriers, hormones, structural molecules.
a. Mainly a structural function in living organisms:
Collagen-- connective tissue protein
Keratin-- hair, nails, skin
Elastin-- connective tissue protein
Actin & Myosin-- muscle proteins
Hemoglobin--red pigment molecule in RBCs
b. Enzymes: Initiate (catalyze) and accelerate chemical reactions. Act as
to speed up chemical reactions. Enzymes are not destroyed in the
reaction and are used repeatedly. Enzymes act upon specific substrates.
c. Hormones: Stimulate functions in various parts of body. Produced in
endocrine glands and transported through the blood to target tissues.
d. Structure of Proteins: Amino acids (subunits of proteins; building block
molecules joined by peptide bonds).
-Dipeptide= 2 amino acids bonded together covalently.
-Polypeptide= many amino acids covalently bonded.
COOH (carboxyl group)
H--C--NH2 (amine group)
R (functional group)
e. Denaturation: the breaking of hydrogen bonds that maintain tertiary structure.
Enzyme loses proper functional, molecular shape for its substrate.
4. Carbohydrates: Organic molecules that contain carbon, hydrogen, and oxygen
(sugars and starches).
a. Structure; H-C-OH, 2:1 ratio H to C (CH2O).
b. Monosaccharides (simple sugars)-- 1 single-unit sugar molecule comprises
molecule of the compound (glucose, fructose, galactose, deoxyribose).
Monosaccharides are the building blocks of carbohydrates.
c. Disaccharides-- 2 monosaccharide molecules covalently bonded
(glucose+glucose=maltose: glucose + fructose=sucrose:
glucose + galactose= lactose).
d. Polysaccharide-- many monosaccharides covalently bonded.
-Glycogen, animal sugar (storage of glucose). Stored in liver and
-Starch, plant sugar (storage of glucose).
-glucose is stored as a large molecule rather than individual molecules.
Prevents osmotic damage to the cell.
5. Lipids: All nonpolar molecules insoluble in water.
a. In animals, fats function as energy storage molecules that provide
protection, insulation, padding, support.
b. Fats & Oils (triglycerides)
-Glycerol + 3 fatty acids (long carbon chains).
-Saturated fatty acids (only single covalent bonds between carbons).
Beef, pork, lard, butter, whole milk, eggs, cheese, palm oil.
-Unsaturated fatty acids (1 or more double covalent bond between
-Polyunsaturated: corn, safflower, sunflower, cottonseed, sesame,
Soybean oils.
-Monounsaturated: olive, canola, and peanut oils.
-Ketone bodies: catabolism of triglycerides yields fatty acids; liver
converts into ketone bodies (acidic molecules). Diabetes
mellitus: rapid catabolism of triglycerides-- serum ketones-ketosis --decreased blood pH-- ketoacidosis-- possible coma.
c. Other important lipids:
-Steroids: Cholesterol (structural and precursor molecule to the sex
hormones and adrenal cortex hormones.
- Phospholipids: components of membranes. Phosphate end of
molecule is polar (hydrophilic). Hydrocarbon chain is nonpolar
(hydrophobic). Form micelles, surfactant.
- Prostaglandins: blood molecules with many functions
-Vitamins E, A, D, K (fat soluble vitamins).