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Chemistry Hand Out
Dr. Stewart
i. Anatomy- the study of the form and structure of the body parts and their
interrelationships, i.e. what the body is made of and how all the parts fit together.
ii. Physiology- the study of the normal functioning of the body, i.e. how do the various
parts of the body work.
Principle of Complementarity of Structure and Function: Structure determines
function and function reflects structure; what a structure can do depends of its form. In
the class you should continually ask, "how does the structure of X relate to its function Y.
Ascending hierarchy of structural organization of the human body:
atoms----molecules---organelles----cells----tissues----organs---organ systems----organism.
Definitions:
we will start our study of the body at the chemical level of organization
1) matter is defined as anything that takes up space and has mass
for our purpose mass and weight will be equal
2) chemistry is the science that deals with the structure of matter
4) elements All matter is composed of elements, elements are unique substances
that cannot be broken down into simpler substances by ordinary chemical means.
There is 116 known elements. 92 of with occur in nature the rest are produced
artificially. (look at periodic table of elements)
the elements Carbon, Nitrogen, oxygen, and hydrogen make up 96% of
the bodies weight, 20 other elements are present in trace amounts. The
periodic table is a complete listing of the known elements.
Each element is composed of similar particles or building
blocks called atoms.
More on atoms later
The elements differ in the nature of the atoms they are made of. Atoms of
the element gold are different from the atoms that make up the element
silver. It is the differences in the atoms that make gold unique from silver.
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4) molecule Atoms of the same or different elements combine to produce
molecules
Molecules are the simplest combination of atoms held together by
chemical bonds that are chemically pure:
Includes Oxygen or O2; water or H2O and large complicated structures
like DNA.
atoms and molecules
Atomic Structure:
Atoms consist of dozens of different subatomic particles
only three are important for understanding chemical properties
1. protons with a positive charge
2. neutrons which have no charge
Protons and neutrons have almost identical wieght
3. electrons negative charge very low mass
nucleus contains protons and neutrons and accounts for
99.9% of the mass.
A complete atom has equal numbers of protons and electrons and thus are
electrically neutral
All protons are alike and all electrons are alike.
what makes the atoms of each element different or unique is the different number
of protons, neutrons, and electrons. The number of electrons is particularly
important in determining how reactive a compound is.
Atomic Number; is equal to the number of protons in the nucleus. Since atoms are
normally electrically neutral, the number of protons are always balanced by an equal
number of electrons
Mass Number; Equal to the sum of protons and neutrons. This number tells you the
number of subatomic particles in the nuclei of an atom. Helium has 2 protons and 2
neutrons so it as a mass of 4.
Helium has an atomic number of 2
Isotopes: atoms which have the same number of electrons and protons but vary in
number of neutrons. Example is Carbon 12, 13, 14- each has 6 electrons and 6
protons but 6,7,8 neutrons receptively
carbon has an atomic number of 6
carbon 12 has a mass number of 12
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carbon 13 has a mass number of 13
carbon 14 has a mass number of 14
atomic weight: is the average mass number of an element that reflex the
proportions of the different isotopes and includes the small mass the
electrons add to the atom
carbon’s = 12.01
thus in nature most carbon is carbon 12
Remember that isotopes of an atom have the some number of electrons
and protons (which determines how atoms interact with each other) and
thus typically have the same function in metabolic reactions.
Exposure to isotopes results in there incorporation into your body
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Radioisotopes: The heavier isotopes of many elements are unstable and their
atoms decompose spontaneously into more stable forms. The disintegration of
nucleus releases energy in the form of
alpha particles packets of 2 protons and 2 neutrons. Has lest penetration
power,
beta particles electron-like particles
gamma rays are electromagnetic energy similar to X-rays andhas the
highest energy form, thus most penetration power
Very dangerous
weak radioisotopes are useful in medicine because they can be added to then
followed through the body
stronger radioisotopes are useful because the energy can be used to destroy
cancerous cells (cobalt 60).
the dense cancer cells absorb the energy and their DNA is destroyed
How Matter (atoms) is Combined:
Atoms of a particular element rarely exist alone in a free state, they are combined
with other atoms to produce molecules. The atoms in a molecule are held
together by chemical bonds.
To understand how matter is combined it is necessary to discuses the electrons
that surround an atom.
It is ultimately these electrons that determine the reactivity or desire of an atom to
combined with other atoms.
Electron Shells:
Electrons circle the nucleus in electron shells also called energy shells. Each
electron shell represents an energy level (electron shell = energy level).
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Therefore the further out the electron shell is (further from nucleus) the more
reactive that type of atom is.
The outer most shell is called the valence shell
Each electron shell can hold a finite number of electrons.
First shell (shell closest to the nucleus) can hold only 2
Second shell can hold 8
Third can hold 8
Note: the third shell of elements with atomic numbers greater then
18 can hold 18 electrons
There is seven shells in the large atoms of the elements of berkelium,
einsteinium ect
Two important concepts are;
first, shells fill consecutively and
second only elements with partially full shells are reactive (hydrogen vs.
helium)
Atoms that have full outer energy shells (called valence shell) or outer shells
with eight (8) electrons tend to be stable (rule of eight’s or octet rule). If this is
not meet, the atom wants to loose or gain electrons to achieve a full outer shell or
8 outer electrons.
1. helium 2 electrons
2. neon 10 electrons; 2 in first shell and 8 electrons in second shell
both have full outer shells and are inert or noble gases (very low reactivity)
Atoms normal do not exist in a free state but are chemically combined with other
atoms forming molecules (2 hydrogens and one oxygen yields a molecule of
water).
remember: a Molecule is the simplest combination of atoms held
together by chemical bonds.
The object of chemical bonds is to achieve a stable number of electrons in the
valance shell (outer) or to gain electro neutrality
3 types of chemical bonds: 1. ionic 2 covalent 3 hydrogen
1. Ionic Bonds
Atoms are electrically neutral. However electrons can be
transferred from one atom to another which forms anions (-) the
electron acceptor, and cations (+) the electron donator .These
charge atoms (ions) will now be attracted to each other resulting in
an ionic bond. This functions to maintain electro neutrality.
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shell for
2. Covalent Bonds
Covalent bonds occur when electrons are shared instead of
transferred. This allows each atom to fill its outer electron
at least part of the time. H2 and CH4
single covalent bond= atoms share only one pair
of electrons
Double or triple share 2 or 3 pairs of electrons.
(O=O)
NonPolar molecules occur if the electrons
are shared equally between the atoms
(Carbon dioxide CO2 is a linear).
Polar molecules (dipole) occur in the
electrons are shared unequally, that is the
electrons spend more time at one end of the
molecule. (water H2O). This is due to oxygen
having a stronger attraction for electrons than
hydrogen (oxygen is electronegative) and
the triangular shape of the molecule.
3. Hydrogen bonds (see figure 2-6) are very weak and don’t bind atoms
together to form molecules. First must have a polar covalent bond. Polar
covalent bonds form when hydrogen bonds to strong electronegative
atoms like oxygen and nitrogen (remember electro negative atoms are
electron greedy), resulting in a weak (+) charge to the H (electron spends
less time on the hydrogen side of the molecule) and a weak (-) charge on
the oxygen or nitrogen (electron spends more time on the oxygen or
nitrogen side of the molecule).
The (-) end of the molecule will be
attached to the (+) end of nearest neighboring molecule. This attraction is
a hydrogen bond
Chemical reactions
the existence of a cell depends on the ability to control chemical reactions
chemical reactions involve the formation of new bonds between atoms or
the braking of existing chemical bonds between atoms
the formation of new bonds and the braking of existing bonds both involve the transfer of
energy so a basic understanding of energy is necessary
General back ground on energy
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Energy has no mass and does not occupy space. It can be measured only by its
effects on matter. Energy is defined as the capacity to do work or in other words
to put matter into motion.
Energy exists in two forms or work capacities
1. Kinetic is energy in action
2 Potential is stored or inactive energy
Biologically relevant forms of energy:
1. Chemical- energy stored in the bonds of
chemical
2. Electrical- movement of charged particles
3. Mechanical- energy directly involved in moving
matter
4. Radiant or electromagnetic- energy that
travels in waves or the electromagnetic spectrum.
This includes visible light, radio waves, ultraviolet
waves, and X-rays
* Energy can be converted from one form to another but it can not be destroyed*
the conversation of potential energy to kinetic energy is never 100 percent and
some energy is released in the form of heat
types of chemical reactions
1) decomposition reactions
breaking down of a molecule into smaller fragments
AB ⇒ A + B
energy is released
digestion involves the breakdown of complex carbohydrates to
sugars et.
catabolism is a decomposition reaction that occurs in the cell
covalent bonds (potential energy) is broken down to release
kinetic energy that can perform cellular work like muscle
contraction
2) synthesis reactions
larger molecules are produces from smaller fragments
A + B ⇒ AB
involves the formation of new bonds
energy must be added
anabolism is a synthesis reaction occurring in the cell resulting in
the synthesis of new compounds
3) exchange reactions
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involves the shuffling around of molecules
AB + CD ⇒ AD + CB
is a combination of a decomposition reaction followed by a
synthesis reaction
may release or require energy
if released energy is exergonic reaction
if absorbs energy is endergonic reaction
chemical reactions are reversible
A + B ⇒ AB thus AB ⇒ A + B
sense reactions are reversible they establish an equilibrium where the rate
of synthesis is equal to the rate of decomposition
A + B ⇔ AB
for a reaction to occur there must be enough energy available for the reaction
this is called the activation energy
most chemical reactions occur to slow (require high activation energy) to be
useful for living cells.
to lower the activation energy cells produce enzymes with promote
chemical reactions.
enzymes are catalysts: they accelerate chemical reactions without
themselves being permanently changed or consumed.
Basic Biochemistry
Two major classes of compounds that contribute to body structure and function
1. Organic compounds; they contain carbon and all atoms are covalently bonded
in the molecule.
2. Inorganic compounds; no carbon and atoms are not always covalently bond.
Major types for us are water, salts, and inorganic acids and bases. Exceptions:
Carbon dioxide, carbon monoxide, and carbides all have carbon atoms but are not
considered organic but inorganic.
Major biologically important inorganic compounds
WATER (60-80% of volume of living cells) Is the single most important
constituent of the body.
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important properties of water in biological systems?
a. high heat capacity; absorbs and releases large
quantities of heat before changing temperature much.
important in temp regulation.
once a temperature is reached it changes temperature only slowly
(thermal inertia)
b. high heat of vaporization; requires a large amount of heat to
transform from a liquid to a gas (due to hydrogen bonds). Important in
sweating or body cooling.
c. Polarity; (see above) makes water a great solvent for chemical
reactions; stuff can dissolve in it.
polarity important in dissolving ionic compounds,
by
forming hydration (water) layers around large charged molecules
that shield them. For example sodium chloride will dissolve in
water. the slight positive charge of the hydrogen side of the water
molecule will surround the negatively charged chloride ion and the
slightly negatively charged oxygen side of the water
molecule will surround the positively charged sodium ion
this hydration layer will allow the sodium and the chloride
to separate from each other thus sodium chloride (table
salt) dissolves into the water
d. reactivity; important part of many types of
reactions. decomposition reaction called hydrolysis is
important part of metabolism.
e. lubricant; there is little friction between water molecules.
aqueous solutions (water solutions)
the polarity of water makes it an unusually effective solvent
because water is slightly negative on one side and slightly positive
on the other water can slip between ionic bonds or other polar
molecules allowing the atoms to separate or to undergo ionization
or dissociation causing the molecule to dissolve
water will form hydration spheres
any molecule that contains ionic bonds or is polar attracts water and thus
dissolves or goes into solution easy
this molecules are called hydrophilic
nonpolar molecules do not readily interact with water and are called
hydrophobic
when exposed to water they do not form hydration spheres and
don’t dissolve
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Acid and base concentrations
Acids and bases are extremely reactive and thus the concentration is
closely regulated
An acid is any compound the liberates hydrogen ions [H+]
A base is any compound that accepts hydrogen ions. In an aqueous
solution it results in the formation OHHydrogen ions concentrations can be measured in grams of ion per
liter of solution
Stomach juice has .01 grams of H+/liter
Ammonia has .00000000001 grams of H+/liter
The pH scale is a shorthand system to more easily tract the decimal
place of the H+ concentration
H+ concentration of .1 grams/liter = pH of 1
H+ concentration of .01 grams/liter = pH of 2
H+ concentration of .001 grams/liter = pH of 3
in pure water a small amount of water dissociated to yield hydrogen ions
(H) and hydroxide ions (OH)
(H2O ⇒ H + OH)
pure water contains .0000001 grams/liter (mols) of hydrogen ion
can be written [H] = 1 X 10-7 or pH = 7
thus the pH = negative logarithm of the hydrogen
ion concentration
pH scale
ranges from 0 to 14
a change by 1 along this scale is a difference in hydrogen
ion concentration of 10 times
pH 7 has 10 times less hydrogen ion then pH 6
(remember is a negative log scale, less is
more!)
pH of 7 is neutral
equal amounts of H and OH
pH less than 7 is acidic
greater concentration of H than OH
pH greater than 7 is basic or alkaline
greater concentration of OH than H
blood pH is 7.35 to 7.45
acidosis is abnormally low blood pH
alkalosis is abnormally high blood pH
inorganic acids
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an acid is any solute that dissociates in solution and releases
hydrogen ions thus lowering the pH
because hydrogen ion has no electron it is just a proton and
acids are called proton donors
strong acids dissociate completely in solution
HCL ⇒ H +Cl
weak acids fail to dissociate completely so establish an equilibrium
H2CO3 ⇔H + HCO3
inorganic bases
a base is a solute that removes hydrogen ions from a solution
they are proton acceptors
NaOH ⇒Na + OH
the OH will accept H to form water
(OH + H ⇒ H2O)
strong bases dissociate completely in solution
weak bases fail to dissociate completely
buffers
Are chemicals both inorganic and organic that resist changes in the
pH of a solution. The can release a H+ when pH rises to curve the
rise in pH and can accept a H+ when pH drops (becomes more
acidic). Buffers are actually weak acids or weak bases.
they can act as proton acceptors or donators depending on the
concentrations that are present
(bicarbonate buffer system)
H2CO3 ⇔H + HCO3
if H levels are low then more H2CO3 will
break down to yield H + HCO3
if H levels are high more HCO3 will bind
with H to yield H2CO3
so act to hold H concentrations at a steady level
Salts; a salt is an compound that dissolves in water to produce ionic or charged
particles.
The positive charges particles are called cations
The negative particles are called anions
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exception: the anion cannot be H+ and the cannot be the
hydroxyl ion OH_
ions are called electrolytes.
1. importance; carry electrical charges in the body
(nerve impulses, muscle contraction)
2. contribute to the hardness of bones and teeth
(Calcium phosphates
3. ionic iron is part of hemoglobin
biologically important salts:
1. NaCl
2. KCl
3. Ca2CO3
4. Ca2PO4
Major biologically important organic compounds
Proteins, carbohydrates, lipids and nucleic acids
1. Carbohydrates molecules include sugars and starches and are made of
carbon hydrogen, and oxygen
a. functions of carbohydrates
i. cellular fuel to produce ATP
ii. Structural purposes
iii. Signaling molecules (androgens)
Major types of carbohydrates:
1 monosaccharides; a single-chain or single ring structure are simplest
form and linked together to form larger polysaccharide molecules
glucose, galactose, fructose and deoxyribose (part of DNA)
2 Disaccharides = two monosaccharides joined together
sucrose = glucose + fructose
3 polysaccharides = a long chain of simple sugars linked together
resulting from a dehydration synthesis or removal of a water molecule
the longer the polysaccharide the less soluble in
water
starch is a digestible polysaccharide
cellulose is a nondigestible polysaccharide
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glycogen is a storage carbohydrate (polysaccharide)
used by animals
2. Lipids; organic compounds that are insoluble in water but
dissolve readily in other lipids and in organic solvents such as alcohol,
chloroform and ether.
Major types are neutral fats, phospholipids, steroids, and eicosanoids
1 Neutral fats; commonly known as fats when solid or oils when liquid.
made from fatty acids and glycerol (see figure 2-14)
three fatty acids on a glycerol backbone
function is to supply energy and insulation for the body
2 Phospholipids; are modified triglycerides with a phosphorus
containing group and two not three fatty acid chains.
the hydrocarbon portion (fatty acids) of the molecule is nonpolar
and interacts only with nonpolar compounds the phosphoruscontaining head is polar and attracts other polar particles such as
water.
function: major part of the cell membrane other functions
3 Steroids; are flat molecules formed of four interlocking hydrocarbon
rings
most abundant is cholesterol
important precursors of other molecules like steroid
hormones and bile salts
function: important for cell membrane rigidity
4 Eicosanoids: derived from a 20 carbon fatty acid called arachidonic
acid found in cell membranes.
most important are prostaglandins and leukotrienes
function: is blood clotting inflammation labor
contractions and intracellular signaling
3. Proteins; 10-30% of cell mass. Is both structural and non structural.
composed of carbon, oxygen, hydrogen, and nitrogen, and sum have sulfur and
phosphorus.
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are most abundant organic components of the human body
100000 different proteins in the body
Amino acids are the building blocks of proteins there
are 20 different types of amino acids. Each amino acids
has unique properties
all amino acids have an amine group -NH2 and a
organic acid group -COOH. because of the acid
group amino acids can act as proton acceptors or
release protons thus proteins are a very important
pH buffer in the body.
Amino Acids are joined by peptide bonds
is a bond between the carboxylic acid of one amino acid and the
amine group of a second amino acid
Two amino acids form a dipeptide three = a tripeptide, 10 or
more = polypeptide, 50 or more = a protein.
The different types of amino acids assembled yield proteins that have very
different properties.
protein shape
Primary, secondary, tertiary, quaternary structure
1. primary; linear sequence of amino acids in
a protein
2. secondary structure; twisting and or
folding of the chain upon itself to form a more
complex structure. is primarily the result of
hydrogen bonding between neighboring amino acids
alpha helix; coiled
beta pleated sheet; side-by-side
3. tertiary structure; this results from the helix or plated
sheet folding upon itself to produce a more compact
structure.
4. quaternary structure; when two or more separate
polypeptide chains interact to produce a complex
protein.
Proteins are found in two major forms
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fibrous- long filamentous proteins like collagen, elastin, et. are
structural proteins.
globular rounded or tightly compacted proteins-crucial in
virtually all biological processes. important in immunity,
hormones, enzymes, et.
Protein Denaturation; change in protein shape that occurs in high temp,
and acidic or basic pH. Results from breaking hydrogen bonds (first) this
may be reversible. If conditions to extreme may brake peptide bonds now
denaturation is irreversible.because the structure of a protein produces is
active site denaturing will inactive these active sites so protein can
perform its function. (hemoglobin cant transport oxygen if pH to high or
to low)
Enzymes are globular proteins that act as biological catalysts to greatly
speed up chemical reactions (by a factor of 1 million). Enzymes are
not used up in the reaction (see figure 2-19)
enzymes are very sensitive to denaturation
enzyme characteristics
1. specificity
each enzyme will catalyze only one type of reaction
2. saturation limits
an enzyme will catalyze the reaction faster as the
concentration of substrate (starting material) increases up
to a point when all enzymes are working at their maximally
rate (the enzymes are saturated)
3. regulation
a variety of factors can turn enzymes on or off to control
reaction rates
this allows the cell careful control over when a
reaction will occur
parts of an enzyme:
holoenzyme:
a complete and functioning enzyme is called a holoenzyme
some enzymes require a non protein portion.
apoenzyme: the protein part of the holoenzyme is
called the apoenzyme
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cofactor: the non protein part of a holoenzyme is
the cofactor
cofactor can be an ion of a metal element
like cooper or zinc.
if the cofactor is organic, derived from a
vitamin it is called a coenzyme
4. Nucleic Acids (DNA and RNA)
are composed of carbon oxygen, hydrogen, nitrogen, and phosphorous. These are
the largest molecules in the body.
DNA and RNA composed of the structural unit nucleotides.
Nucleotides are made of a
1. nitrogen-containing base: there is five types
of bases
1. adenine, 2 guanine 3 cytosine, 4 thymine,
5 uracil
adenine and guanine are constructed of two
large ring bases and are called purines
(see figure 2-20)
cytosine, thymine, and uracil are constructed
of a single ring base and are called pyrimidines
(see figure 2-20)
DNA has adenine, guanine cytosine thymine
RNA has adenine guanine cytosine uracil
2 pentose sugar: five carbon sugar
the pentose sugar of DNA has one less oxygen
molecule so is called deoxyribose
thus the name for DNA deoxyribonucleic acid.
RNA has one more oxygen molecule so is called
ribose
thus the name ribonucleic acid.
3. phosphate group: which is attached to the sugar
DNA A molecule of DNA is a double stranded chain of nucleotides.
The strains are attached by hydrogen bonds.
Because of hydrogen bonding
the chain of nucleotides are coiled so the structure is a double helix
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each nucleotide in the strand is attracted by the phosphate group to the
sugar group of the next nucleotide.
The bases on opposite strands are held together by the hydrogen
bonds between then
adenosine binds to thymine and cytosine binds to
guanine.
(see figure 2-20)
thus these base pairs are called complementary bases.
function of DNA- found in the nucleus and is the storage molecule for
the genetic code or information. heredity.
RNA
to
A molecule of RNA is a single stranded chain of nucleotides that
is made using the DNA as a template. The RNA will be complementary
the DNA template.
function of RNA- DNA is "read" producing RNA. this RNA is then
translated to produce a protein molecule.
RNA contains the directions for how to assemble a protein
Adenosine Triphosphate (ATP)
ATP is a molecule that is based on the adenosine molecule like that used in DNA
and RNA but it as to more phosphate groups attached to the end for a total of
three. The last two phosphate groups are held on by a unique chemical bond that
contains a high amount of energy that can be easily used by the body.
These bonds can be ruptured by hydrolysis liberating the energy. Normally only
the last bond is uses to yield ADP and P + energy, but the last two can by broken
to give AMP (adenosine monophosphate) and 2P + energy
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