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Lecture Notes: Unit I: Organization of the Human Body
Chapter Two - The Chemical Level of Life
I. Introductory Concepts
A. Chemistry - the study of structure and interactions of matter
B. Matter- anything which occupies space (has volume) and possesses mass (has weight)
C. Mass - amount of matter of any object
D. All matter is composed of elements. Elements are the fundamental building blocks of chemistry.
Each element is a substance that cannot be split into a simpler substance (by ordinary means).
E. Elements are made up of atoms; atoms are the smallest whole units of matter that retain the
properties and characteristics of an element.
II. Atomic Structure (Note: All atoms are NEUTRAL in charge)
A. Subatomic particles are the components of atoms and they determine its binding characteristics
1. Protons (abbreviated p+)
a. found in the nucleus of the atom
b. carry a positive charge
c. have a mass of 1.007 daltons (or amu' s)
d. very large in comparison to electrons (approx. 2000x larger in mass than an electron)
2. Electrons (abbreviated e-)
a. located in electron shells around the nucleus (in a very strict distribution pattern):
(1) a maximum of 2 electrons can occupy the innermost electron shell
(2) a maximum of 8 electrons can be place in the second electron shell
(3) a maximum of 8 electrons temporarily; and then up to a total of 18 can be placed
in the third electron shell (some "retrofilling” occurs after a fourth shell is
established.
b. carry a negative charge
c. very small in comparison to protons or neutrons (mass of 0.0005 daltons)
3. Neutrons (abbreviated no)
a. found in the nucleus with the protons
b. neutral in charge
c. have a mass of 1.008 daltons (or amu' s)
d. serve to isolate the protons from each other (the proton's positive charges tend to cause
them to repel each other)
(1) isotopes are atoms of the same element that differ in their number of neutrons
(2) radioisotopes are unstable and give off gamma radiation during the decay (loss)
of neutrons from their nucleus. Used in Nuclear Medicine to treat diseases.
(3) Half-life refers to the amount of time it takes for one-half of the matter (element)
to become the stable form
B. The number of subatomic particles found in the atom can be determined from the atomic
number and the mass number
1. Atomic number represents the number of protons found in a given atom (also represents the
the number of electrons; since atoms are NEUTRAL, it stands to reason that for any given
atom, there will be equal number of protons (+ charges) as electrons (- charges).
2. Mass Number
a. Represents the number of protons and neutrons (e- are insignificant in mass when com-
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pared to protons or neutrons.)
b. Dalton (or atomic mass unit - amu) is the standard unit of measuring mass of atoms.
c. The mass number is determined by averaging the masses of all isotopes of a given element
C. Terminology
1. Ion - an atom that has lost or gained one or more electrons via ionization resulting in a particle with a charge. Cations are positive ions (resulting from atoms losing e-'s)
Anions are negative ions (resulting from atoms acquiring e-'s)
2. Molecule - result of a combination of atoms in which those atoms exchange or share
electrons to give a stable configuration. There are two types of molecules:
a. Elemental molecules: two or more atoms of the SAME ELEMENT in combination.
b. Compound molecules: two or more atoms of DIFFERENT ELEMENTS in combination.
3. Free radical - electrically charged atom or group of atoms with an unpaired electron in its
outermost shell
4. Compound - the same as compound molecules: substances which may be broken down into
two or more different elements by ordinary chemical means.
III. Chemical Bonding
A. Chemical bonding is determined by the number of e-'s in the outermost shell (valence electrons)
1. Elements with the same number of valence electrons (and thus binding characteristics) are
found within the same column on the Periodic Table.
2. Molecules are stable when they have the maximum number of electrons in the outermost electron shell (octet rule)
B. Types of chemical bonding
1. Ionic Bonding
a. Created due to the attraction between positively charged ions and negatively charged ions.
b. Cation - positively-charged ion resulting from the loss of one or more electrons (the
atom is positive now since there are more positively-charged protons than there are
negatively-charged electrons.)
c. Anion - negatively-charged ion resulting from the gain of one or more e-'s (atom is negative since there are now more negatively-charged e-'s than positively-charged p+'s)
d. Ions are also referred to as electrolytes.
2. Covalent Bonding
a. Stable molecules are formed due to the sharing of electron pairs
b. Types of covalent bonding
(1) single covalent bond - a single pair of electrons is shared between two atoms
(2) double covalent bond - two pairs of electrons are shared between two atoms
(3) triple covalent bond - three pairs of electrons are shared between two atoms
(4) non-polar covalent bond - one atom does not attract the shared electrons more
strongly than the other atom
(5) polar covalent bond
a. Sharing of e-' s between two atoms is unequal with the atom having the greater
number of p+'s (greater electronegativity) attracting the e-'s with greater force
b. Polar covalent bonded molecules are attracted to each other (Water is an example)
3. Hydrogen Bonding
a. A molecule having a polar covalent bond is attracted to another polar covalent bond
with the hydrogen atom directed toward the negative side of the second molecule.
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b. Hydrogen bonds are only 5% as strong as covalent bond
c. These are what give water its unique characteristics (adhesion + cohesion) and it is
also hydrogen bonds that hold two DNA strands together.
d. Hydrogen bonds DO NOT form molecules; however, they are responsible for holding
a molecule in a particular spatial arrangement or configuration. (ie: the secondary and
tertiary (and sometimes quaternary) structure of proteins.
IV. Chemical Reactions
A. Chemical reaction - new bonds form or old bonds break between two atoms
1. Reactants - the beginning compounds
2. Products - the ending compounds
3. Law of Conservation of Mass - total mass of the reactants must equal total mass of the products.
4. Metabolism - refers to all chemical reactions occurring within the body
B. Energy
1. Types of energy
a. Potential energy
(1) stored energy
(2) chemical energy is the potential energy found in the bonds of compounds
b. Kinetic energy - energy in motion (electrical, mechanical, thermal, etc.)
2. Law of Conservation of Energy - energy can be neither created nor destroyed, although it may be
interconverted between one form and another
3. Types of reactions based upon energy transfer
a. Exergonic reaction - releases more energy than it absorbs; chemical bonds are broken
b. Endergonic reaction - absorbs more energy than it releases; chemical bonds are formed.
c. Exergonic reactions are couples with endergonic reactions so that the energy released from the
exergonic reaction may drive the endergonic reaction.
4. Activation energy
a. Energy necessary for reactants to form products (energy needed for colliding molecules to react)
b. Factors which influence the rate of reaction (chance that molecules will collide and form products):
(1) Size of particles - larger particles will have a greater chance of colliding
(2) Concentration - increasing concentration of reactants will cause them to collide more often
(3) Temperature - increasing temperature will increase the speed and frequency of collisions
(4) Catalysts - presence of an appropriate catalyst (enzyme) will increase the rate of reaction
c. Catalysts are substances which speed up a chemical reaction by reducing the activation energy
C. Types of chemical reactions
1. Synthesis Reactions = Anabolism
a. Larger molecules are formed from smaller molecules, ions, or element.
b. Chemical bonds are formed (A + B +energy  AB)
c. Energy is used ( endergonic reactions)
2. Decomposition Reactions = Catabolism
a. Large molecules are broken down to form smaller molecules, ions, or elements.
b. Chemical bonds are broken (XYZ  X + Y + Z +energy)
c. Energy is released ( exergonic reactions)
3. Exchange Reactions
a. An exchange of chemical partners occurs
b. Chemical bonds are broken and then reformed
c. AB + CD  AD + BC
4. Reversible Reactions - reactants go to form products while products go to form reactants
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5. Oxidation - Reduction Reactions
a. Oxidation -loss of electrons from a molecule
b. Reduction - gain of electrons to a molecule
(A transition paragraph here, by way of introducing the topics of inorganic and organic chemistry. Most
chemicals in the body exist as compounds (substances which may be broken down into two or more
elemental substances by chemical means). Compounds are classified as (1) INORGANIC if they lack the
element Carbon, and (2) ORGANIC is they contain both the elements Carbon and Hydrogen in some
proportion. As a rule, inorganic compounds consist of small (low molecular weight), ionically-bonded
molecules; although there are some inorganic compound molecules that are covalently-bonded: H2O being the most fundamental of these, CO2 being another. Such compounds are vital to body functions; a few
examples of these are water, salts, acids, and bases. As a rule, organic compounds consist of molecules
that are entirely covalently-bonded and are large, straight or branched chains, or ring molecules. The
major examples are carbohydrates, lipids, proteins, nucleic acids, and ATP (Adenosine Triphosphate.)
V. Inorganic Compounds and Solutions
A. Inorganic acids, bases and salts
1. Acids dissociate to release hydrogen ions (H+)
2. Bases dissociate to release hydroxide ions (OH-); proton acceptor
3. Salts dissociate into charged particles other than H+ or OH- ions when dissolved in water
4. pH Scale - measure of acidity or alkalinity of a substance/solution
a. pH of 7 is neutral
b. pH of less than 7 is acidic
c. pH greater than 7 is basic
d. pH is expressed on a scale running from 0 - 14. The scale is based on the number of hydrogen
ions in a solution measured in the chemical unit "moles per liter". pH scale numbers convert the
negative exponent of 10 to a positive number; each change in one whole number on the scale
represents a 10x decrease from the previous concentration. (0 is the most acidic pH with a concentration of H+ ions at one full mole per liter. 1 is the next most acidic with a concentration of
H+ ions at 0.1 moles per liter. 2 indicates a concentration of H+ ions at 0.01 moles per liter, etc.
e. pH may be maintained by buffer systems which react with strong acids and strong bases
and replace them with weak acids and weak bases.
5. Buffer system - two chemical compounds which work together to prevent drastic pH changes
(An acid and its conjugate base; or a base and its conjugate acid)
a. Most ubiquitous buffer system in the body is the carbonic acid - bicarbonate system
Carbonic acid (H2CO3) is the acid; Bicarbonate (HC03-) is its conjugate base.
b. Other buffering systems in the body include: Phosphate, hemoglobin-oxyhemoglobin, and
certain protein systems.
B. Mixtures
1. Combinations of elements or compounds that are physically blended but not bound by chemical bonds.
a. The compound with the greatest quantity in a mixture is called the solvent.
b. The compound(s) with lesser quantity in a mixture is/are called the solutes.
c. Mixtures may be gaseous (ie: air); liquid (ie: beer); or solids (ie: rubber in tires)
2. There are three types of mixtures based upon compound size and behavior:
a. True solutions - consist of a solvent which has a solute dissolved within
These are clear, homogeneous mixtures and have very small solute size
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(ie: Air: N2 is the solvent, O2, CO2, H2O are the solutes)
b. Colloids - these are translucent, heterogeneous mixtures and have larger solute size, yet
the solutes will not "settle out". (ie: the cytosol within a cell; or Jello gelatin)
c. Suspensions - these are opaque, heterogeneous mixtures and have very large solute size
(can be entire cells as solutes!) than definitely will settle out with gravity.
(ie: Blood (solvent is water, solutes are proteins, electrolytes, gases, nutrients and cells: red blood cells, white blood cells, and platelets.)
3. Concentration of a solution may be measured in several ways:
a. Percent - parts per hundred parts; the percentage designation always refers to the solute,
and unless otherwise noted, the solvent is assumed to be water.
b. Molarity (M) - moles per liter. (ie: a one-molar solution of glucose has 180.156 g (one gram
molecular weight, of glucose added to enough water to make 1 liter of solution.)
4. Water
a. Most important and abundant molecule in the human body
b. ,Polarity of the water molecules determines the unique behavior and characteristics
c. Functions of water in the body: as a solvent (it is the universal solvent)
as a suspending medium
heat absorber (high heat capacity)
cooling mechanism (high heat of vaporization)
as a lubricant (high surface tension)
as a participant in chemical reactions
VI. Organic Compounds - Introduction
Contain C and H with O, N, S, P being the other most frequently occurring elements.
Carbon atoms form 1 covalent bond with H,
2 covalent bonds with O,
(These bonds are easily made and easily broken,
3 covalent bonds with N,
therefore, such compounds are useful as sources
2 covalent bonds with S
of energy.)
5 covalent bonds with P
The five classes of Organic Compounds you will need to be very familiar with are:
(1) Carbohydrates, (2) Lipids, (3) Proteins, (4) Nucleic Acids, and (5) ATP.
A. Carbohydrates
1. Known as "the sugars and starches"; include glycogen (in animals) and cellulose (in plants)
2. Are the body's preferred and most immediate source of energy.
3. Comprised of the basic formula: (CH2O)n (Ratio of C:H:O is 1:2:1)
4. May be divided into 3 main sub-groups:
a. Monosaccharides (3 -7 C's) These are the "simple sugars"; 3C = triose, 4C = tetrose,
5C = pentose, 6C = hexose, 7C = heptose.
Pentoses (ribose and deoxyribose) and Hexoses (glucose, fructose, and others) are
extremely important to humans.
b. Disaccarharides (exactly two monosaccharides joined by dehydration synthesis)
These are also known as simple sugars; and behave like monosaccharides in that they are
Sweet to the taste, very soluble in water, and form a white granular/powdery substance.
Maltose is a disaccharide formed from 2 glucoses
Sucrose is a disaccharide formed from 1 glucose and one fructose
Lactose is a disaccharide formed from 1 glucose and one galactose
(Note: the formula for sucrose is C12H22O11, since one H2O molecule is lost.)
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c. Polysaccharides (many monos joined together through dehydration synthesis.) These
are known as the complex sugars and starches. Polysaccharides have the generalized
formula: (C6H10O5)n
1. Like di's, poly's may be broken down into their constituent sugars through
hydrolysis
2. Poly's lack the sweetness of “simple sugars” (mono’s + di’s)
3. They are NOT soluble in water
4. The chief polysaccharide of animals is glycogen. (Storage molecule in the liver)
B. Lipids
1. Known as the "fats and oils"; most are hydrophobic and do not mix with water.
2. Contain C, H, and 0 but not in a 1: 1 ratio of C:O (O is always less than C) nor in a 2: 1 ratio
of H to O.
3. Function in protection, insulation, storage, vitamin + hormone formation.
4. Basic monomer consists of one glycerol group and three fatty acid groups.
5. Fats are the body's most concentrated source of energy: more than twice the energy yield per
weight as compared to carbohydrates or proteins; however, they are 10-12% less efficient
than carbohydrates due to non-availability to the body.
6. Subclasses of lipids include: fats, phospholipids, steroids, carotenes, vitamins E & K, and the
eicosanoids (prostaglandins and leukotrienes which are derived from arachidonic acid, a 20-C
fatty acid found in the fatty acid tails of many plasmalemma phospholipids molecules)
a. Triglycerides (or more appropriately, triacylglycerates) have the most fundamental makeup
of 1 glycerol and 3 fatty acids. These can be saturated (all fatty acid C's have single covalent
bonds) or unsaturated (monounsaturated if there is one double bonded C present, or
polyunsaturated if there are two or more double bonded C's present in the fatty acids)
b. Phospholipids
(1) Fundamental monomer is altered by one of the fatty acids being replaced with a phosphate group
(2) These are amphipathic - the phosphate portion is able to deal with polar molecules
(therefore it is hydrophilic) while the fatty acids interact with non-polar molecules and
is hydrophobic.
c. Steroids
(1) Fundamental monomer is totally altered, in that steroids have a four-ringed structure
(three 6-C rings and one 5-C ring)
(2) Cholesterol is the precursor molecule for all steroids
d. Eicosanoids - valuable local hormones (paracrines and autocrines) whose effects are very short-lived
(1) Derived ftom arachidonic acid, a 20-C fatty acid found extensively in membrane phospolipid molecules (Eicos is Greek for 20)
(2) Prostaglandins - regulate a wide variety of body functions including inflammation, fever,
pain intensity, smooth muscle contraction (therefore blood flow), glandular secre-
tion, reproductive processes, lipid metabolism, and immune responses)
(3) Leukotrienes - participate in allergic activities and inflammatory responses
c. Proteins
1. The new element is Nitrogen. Consist of C, H, O, N (and some contain Sulfur and Phosphorus)
2. Monomers are amino acids linked together by a specific type of covalent bond called a peptide bond, that
is a bond between the amine end of one amino acid and the acid end of the adjacent amino acid.
3. Functionally, this is the most diverse class of organic compound. Proteins are used extensively
throughout the body to build tissues (structural proteins); to hasten biochemical rxns (enzymatic
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proteins); for muscle and glandular contraction (contractile proteins); to recognize and defend against
invaders (immunological proteins, chiefly antigens and antibodies); to regulate body functions (regulatory proteins); and to transport substances from place to place (transport proteins).
4. All proteins have at least three levels (some proteins have four levels) of structural organization. Protein
structure is much more complex than that of carbohydrates or lipids, and is dynamic.
a. Primary structure - pertains to the particular sequence of amino acids (aa's)
b. Secondary structure - pertains to the coiling (ie: alpha helix = clockwise spiraling) or to the
folding (pleating) of neighboring aa's in the polypeptide chain stabilized at
regular intervals by hydrogen-bonds
c.Tertiary structure - creates a three-dimensional structure with interaction of distant sites of aa's due
to a variety of bonds: disulfide (S-S), Hydrogen, ionic, or hydrophobic interactions
d.Quaternary structure - found only in complex proteins composed of two or more polypeptide
chains and pertains to the particular arrangements of one chain to another. Bonds similar to those in tertiary structure are responsible for this.
5. Denaturation is a disruption of the secondary, tertiary or quaternary structure of a protein and may
occur due to pH, temperature, and electrolyte concentration. A denatured protein is no
longer a functional protein.
6. Some specific terminology about catalytic proteins, aka: Enzymes
a. Holoenzyme - active, functioning enzyme
b. Apoenzyme - protein portion of the enzyme produced by the cell
c. Cofactor - non-protein portion of the enzyme which is obtained via the diet (essential minerals and
vitamins )
d. Substrate - reactant molecule to which the enzyme binds and which is changed by that enzyme.
e. Active site - place on the enzyme where the substrate binds forming the enzyme-substrate complex
f. Three very important properties of all enzymes:
(1) Highly specific
(2) Very efficient (rxn rates 100 million - 10 billion times more rapid than non-catalytic; and per second, a single enzyme may convert up to 600,000 molecules of substrate to product)
(3) Subject to a variety of cellular controls - especially, chemical environment of the cell determining
whether the enzyme takes on its active or its inactive form.
D. Nucleic Acids: DNA and RNA (Deoxyribonucleic Acid and Ribonucleic Acid)
1. DNA controls the activities of cells and stores hereditary information
2. RNA, together with DNA, assume major roles in protein synthesis
3. The monomers of nucleic acids are called nucleotides. Each nucleotide consists of three parts:
a. A pentose sugar (5-carbon monosaccharide)
b. A phosphate group (PO4- )
c. A nitrogen base
(Note: a "nucleoside" is a nucleotide minus its phosphate group)
4. More specifically, each DNA nucleotide consists of:
a. The pentose sugar deoxyribose
b. A phosphate group
c. One of four possible nitrogen bases: A = Adenine; T = Thymine; C= Cytosine; G= Guanine
A and G are called purines and are larger, double-ringed molecules; while T and C are called
pyrimidines and are smaller, single-ringed molecules. In a fashion called complementary
base pairing, A and T always bond together with two hydrogen bonds; and C and G always
bond together with three hydrogen bonds.
5. More specifically, each RNA nucleotide consists of:
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a. The pentose sugar ribose
b. A phosphate group
c. One of four possible nitrogen bases: A = Adenine; U = Uracil; C = Cytosine; G = Guanine
Note: three of the four RNA N-bases are identical to DNA N-bases; it is only Uracil that
replaces Thymine. THERE IS NO THYMINE IN RNA; U substitutes for T.
The rule of complementary base pairing for RNA is A with U; C with G.
6. The chemical differences between DNA and RNA may seem very minor (a slightly different
pentose sugar, and one different N-base), but these chemical differences result in huge structural
and behavioral differences between these two nucleic acids:
a. DNA is always double-stranded (a double helix); it is confined to the nucleus of the cell; it
acts as the hereditary information storage molecule arranged in genes. (Also, there are no
codons on DNA). There are only two forms of DNA: chromatin - the spread-out, threadlike
mass found in the nucleus of interphase (non-dividing) cells; and chromosomes - the
compact, rod-like structures (46 of them in human cells) visible during cell division.
b. RNA is always single-stranded; it is formed in the nucleus of the cell but leaves the nucleus
and functions out in the cytoplasm. There are three types of RNA: messenger RNA (mRNA)
ribosomal RNA (rRNA) (aka: ribosomes), and transfer RNA (tRNA). The three types of
RNA all play important roles in protein synthesis.
7. By counting repetitive nitrogenous base sequences on DNA molecules from tissue samples,
scientists have a powerful tool to more precisely identify suspected criminals by "DNA fmgerprinting" .
E. ATP (Adenosine Triphosphate)
1. The energy storage molecule in cells; referred to as the "energy currency" of the cell.
2. It is found universally in living systems and is indispensable to the life of a cell.
3. Consists of two major parts:
a. An adenosine unit (an Adenine-containing RNA nucleoside)
b. Plus three, high-energy Phosphate groups
4. ATP reacts with water in hydrolysis reactions to give: ATP  ADP + P + E; this energy
released can be used to drive anabolic reactions. A further breakdown with more energy
yielded is: ADP  AMP + P + E
5. Cyclic AMP (cAMP)
a. Adenosine-3,5-monophosphate
b. Formed by hydrolysis reaction (as above) from ATP, via action of the enzyme adenylate
cyclase in the cell membrane.
c.Has an important function as a second-messenger in the mechanism of action of water
soluble hormones.
d. See reference sheet entitled: “ATP Talking Points”