Download Dr. Ali Ebneshahidi

Dr. Ali Ebneshahidi
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A . Introduction
 Chemistry – science that deals with the composition of
substances and the changes that take place in their
composition.
 Organic chemistry – chemistry that deals with organic
substances (those that contain carbon and hydrogen).
 Biochemistry - chemistry of living organisms; essential
for understanding physiology because body functions
involve chemical changes that occur within cells.
 Matter – anything that has weight (or mass) and takes
up space. It can be solids, liquids, or gases.
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Energy
 Energy – the ability to do work . Potential energy
(PE) is stored energy in matters ; Kinetic energy
(KE) is working energy produced by the motion of
matters.
 Energy occurs in 4 forms in the human body:
chemical, electrical, radiant, and mechanical energy.
Chemical energy is the most important form in
terms of actually driving chemical reactions.
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Models of the Atom
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 Atomic
number (AN)
= number of
protons =
number of
electrons.
 Atomic weight
(AW) = number
of protons +
number of
neutrons.
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IONS
 In addition to neutrons, the electrons of
atoms tend to change also – atoms that have
either lost or gained electrons are called
ions. Atoms that have lost electrons (as a
result, now contain more p+ than e-) are
called cations which carry positive charges,
while atoms that have gained excessive
electrons (as a result, now contain more ethan p+) are called anions which carry
negative charges.
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Chemically Reactive Elements
 Reactive elements
do not have their
outermost energy
level fully occupied
by electrons.
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Bonding of atoms
 Ionic bonding = formed by attraction of
opposite charges of a cation and an anion.
(e.g. Na+ + Cl- →NaCl)
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Formation of an Ionic Bond
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Covalent bond
 formed by sharing of electrons between two
atoms (e.g. Cl + Cl →Cl2). The strongest type
of bonding.
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Hydrogen Bond
formed by weak attraction between H+ and nitrogen (N) or oxygen
(O) [e.g. H of a water molecule attracting to O of another water
molecule]. The weakest type of bonding.
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Four Types of Chemical Reactions
 Chemical reactions involve the formation, breaking, or
rearrangement of chemical bonds. There are 4 general types:
 Dehydration synthesis: A + B → AB + water
 Decomposition (or hydrolysis): AB + water → A + B
 Exchange: AB + CD → AD + CB
 Reversible: A + B < - - - > AB
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The rate of Chemical Reactions
 size of reacting molecules: smaller molecules have greater
kinetic energy which produces faster reaction rate.
 Temperature: higher temperature creates greater kinetic
energy and faster reaction rate.
 Concentration of reactants: higher concentration produces
faster rate .
 Presence of catalysts: inorganic catalysts or organic
catalysts (enzymes) increase reaction rate.
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 Electrolytes = compounds that release ions when
dissolved in water (e.g. NaCl + water → Na+ + Cl- ).
 Acids = electrolytes that release H+ (e.g. H2 CO3 → H+ +
HCO3- ).
 Bases = electrolytes that release anions that can combine
with H+ (e.g. NaOH → Na+ + OH- ).
 Salts = substances formed by the reaction between an
acid and a base (e.g. HCl + NaOH → H2O + NaCl ).
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PH
 measurement of H+ concentration in a solution
 - More H+ = lower PH = more acidic
 - Less H+ = higher pH = less acidic
 -Ph scale is form 0 to 14, where the
midpoint (pH 7.0) is neutral. From pH 0
to 6.9, it is acid; while from pH 7.1 to 14
is base.
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PH Scale
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 Organic substances = chemicals that contain C and
H (e.g. Carbohydrates, Protein, Fat, and nucleic
acid).
 Inorganic substances = chemicals that do not
contain C and H (e.g. table salt or NaCl, carbon
dioxides or CO2 , ammonia or NH3).
 (Most inorganic substances are small, electrolytes
and usually use ionic bonding, while most organic
substances are large, non electrolytes, and usually
use covalent bonding ).
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An Organic Compound
(cholestrol)
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Protein
Figure 2.3
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Carbohydrate
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Nucleic Acid
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Solution and concentration
When a substance is dissolved in a liquid (ex. water), a
solution is formed. The substance that is dissolved is the solute
and the liquid in which the dissolution occurred is the solvent.
Concentration: The measure of dissolution of a particular
solute in a given volume of solvent. it is measured in molarity.
Molarity: The number of solute molecule per unit volume of
solution.
Buffer: A substance that can react with an acid or a base and
thus resist a change in PH.
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Tonicity
 the ability of a solution to change the tone or shape of
cells by changing their internal H2O volume.
 - Hypertonic: solutions with higher osmotic pressure cells in a Hypertonic solution lose H2O and shrink.
 - Hypotonic : solution with a lower osmotic pressure cells in hyportonic solution gain H2O and swell.
 - Isotonic : same tonicity - cell in isotonic solutions
neither gain, nor lose H2O.
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The effect of solutions of varying tonicities on
red blood cell
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Enzymes
1. Are always made of globular proteins.
2. Can promote the rate of chemical reactions by billions of times.
3. Can lower the activation energy – energy necessary to start a
reaction – resulting in a conservation of energy.
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4. Are usually reusable or recycled.
5. Are always very specific – using its active site, each
enzyme is designed to bind to only one specific substance, the
substrate and rapidly transforms the substrate into a
product.
6. Many enzymes would not achieve their optimum efficiency
unless they are bound to a cofactor (i.e. ions, metals) or to a
coenzyme (organic cofactors such as vitamins).
7. Most enzymes' names end with "ase“ (ex. DNAse,
Sucrase).
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Mechanism of Enzyme Action
Active site
Amino acids
1
Enzyme (E)
Substrates (s)
H20
Enzymesubstrate
complex (E–S)
2
Free enzyme (E)
3
Peptide bond
Internal rearrangements
leading to catalysis
Dipeptide product (P)
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 Many factors affect enzyme activity:
 Since all enzymes are made of globular proteins,
and proteins are made of amino acids linked by
peptide bonds, enzymes can be affected or
denatured very easily.
 Factors that could affect or denature enzymes
include heat, radiation , electricity, certain chemical
substances, and extreme PH.
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Metabolism
Anabolic metabolism uses dehydration synthesis reaction to build
large molecules from small molecules.
Each reaction releases a water molecule and requires energy input
Example – monosaccharide + energy → polysaccharide + water
amino acids + energy → protein + water.
Synthesis and Hydrolysis of Sucrose :
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 Catabolic metabolism
 Uses hydrolysis (or decomposition) reaction to break
up large molecules into smaller molecules.
 Each reaction requires a water molecule and releases
energy.
 Example -energy.
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triglyceride + water → fatty acids +
Adenosine Triphosphate (ATP)
 High- energy molecule that is derived from the nucleotide, adenine.
 Contains 3 phosphate groups (PO4) and high-energy chemical bonds
that each time the bonds are broken, a large amount of energy is
generated.
 Energy is released by ATP is broken down by hydrolysis reaction:
ATP + water → ADP + PO4+ energy [ADP = adenosine diphosphate]
 ADP + water → AMP + PO4 + energy
 [AMP = adenosine monophosphate]
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ATP
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