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Dr. Ali Ebneshahidi

A . Introduction

Chemistry – science that deals with the composition ofsubstances and the changes that take place in theircomposition.

Organic chemistry – chemistry that deals with organicsubstances (those that contain carbon and hydrogen).

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substances (those that contain carbon and hydrogen).

Biochemistry - chemistry of living organisms; essentialfor understanding physiology because body functionsinvolve chemical changes that occur within cells.

Matter – anything that has weight (or mass) and takes

up space. It can be solids, liquids, or gases.

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 ofmatters.

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Energy occurs in 4 forms in the human body:chemical, electrical, radiant, and mechanical energy.Chemical energy is the most important form interms of actually driving chemical reactions.

Models of the Atom

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Atomicnumber (AN)= number ofprotons =number ofelectrons.

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electrons.

Atomic weight(AW) = numberof protons +number ofneutrons.

IONS

In addition to neutrons, the electrons ofatoms tend to change also – atoms that haveeither lost or gained electrons are calledions. Atoms that have lost electrons (as aresult, now contain more p+ than e-) are

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result, now contain more p than e ) arecalled cations which carry positive charges,while atoms that have gained excessiveelectrons (as a result, now contain more e-

than p+) are called anions which carrynegative charges.

Chemically Reactive Elements

Reactive elementsdo not have their

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do not have theiroutermost energylevel fully occupiedby electrons.

Bonding of atoms

Ionic bonding = formed by attraction ofopposite 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 twoatoms (e.g. Cl + Cl →Cl2). The strongest typeof bonding.

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formed by weak attraction between H+ and nitrogen (N) or oxygen(O) [e.g. H of a water molecule attracting to O of another watermolecule]. The weakest type of bonding.

Hydrogen Bond

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Four Types of Chemical Reactions

Chemical reactions involve the formation, breaking, orrearrangement of chemical bonds. There are 4 general types:

Dehydration synthesis: A + B → AB + water

Decomposition (or hydrolysis): AB + water → A + B

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Decomposition (or hydrolysis): AB + water → A + B

Exchange: AB + CD → AD + CB

Reversible: A + B < - - - > AB

The rate of Chemical Reactions

size of reacting molecules: smaller molecules have greaterkinetic energy which produces faster reaction rate.

Temperature: higher temperature creates greater kineticenergy and faster reaction rate.

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Concentration of reactants: higher concentration producesfaster rate .

Presence of catalysts: inorganic catalysts or organiccatalysts (enzymes) increase reaction rate.

Electrolytes = compounds that release ions whendissolved in water (e.g. NaCl + water → Na+ + Cl- ).

Acids = electrolytes that release H+ (e.g. H2 CO3 → H+ +HCO3

- ).

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Bases = electrolytes that release anions that can combinewith H+ (e.g. NaOH → Na+ + OH- ).

Salts = substances formed by the reaction between anacid and a base (e.g. HCl + NaOH → H2O + NaCl ).

PH

measurement of H+ concentration in a solution

- More H+ = lower PH = more acidic

- Less H+ = higher pH = less acidic

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-Ph scale is form 0 to 14, where themidpoint (pH 7.0) is neutral. From pH 0to 6.9, it is acid; while from pH 7.1 to 14is base.

PH Scale

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Organic substances = chemicals that contain C andH (e.g. Carbohydrates, Protein, Fat, and nucleicacid).

Inorganic substances = chemicals that do notcontain C and H (e.g. table salt or NaCl, carbon

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contain C and H (e.g. table salt or NaCl, carbondioxides or CO2 , ammonia or NH3).

(Most inorganic substances are small, electrolytesand usually use ionic bonding, while most organicsubstances are large, non electrolytes, and usuallyuse covalent bonding ).

An Organic Compound(cholestrol)

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Protein

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Figure 2.3

Carbohydrate

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Nucleic Acid

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When a substance is dissolved in a liquid (ex. water), asolution is formed. The substance that is dissolved is the soluteand the liquid in which the dissolution occurred is the solvent.

Concentration: The measure of dissolution of a particularsolute in a given volume of solvent. it is measured in molarity.

Solution and concentration

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solute in a given volume of solvent. it is measured in molarity.

Molarity: The number of solute molecule per unit volume ofsolution.

Buffer: A substance that can react with an acid or a base andthus resist a change in PH.

Tonicity

the ability of a solution to change the tone or shape ofcells by changing their internal H2O volume.

- Hypertonic: solutions with higher osmotic pressure -cells in a Hypertonic solution lose H2O and shrink.

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- Hypotonic : solution with a lower osmotic pressure -cells in hyportonic solution gain H2O and swell.

- Isotonic : same tonicity - cell in isotonic solutionsneither gain, nor lose H2O.

The effect of solutions of varying tonicities onred blood cell

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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 areaction – resulting in a conservation of energy.

Enzymes

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4. Are usually reusable or recycled.

5. Are always very specific – using its active site, eachenzyme is designed to bind to only one specific substance, thesubstrate and rapidly transforms the substrate into aproduct.

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6. Many enzymes would not achieve their optimum efficiencyunless they are bound to a cofactor (i.e. ions, metals) or to acoenzyme (organic cofactors such as vitamins).

7. Most enzymes' names end with "ase“ (ex. DNAse,Sucrase).

Enzyme-substrate

complex (E–S)

1

Active site

Enzyme (E) Substrates (s)

Amino acids

H20

Mechanism of Enzyme Action

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2

3

Internal rearrangementsleading to catalysis

Free enzyme (E)

Peptide bond

Dipeptide product (P)

Many factors affect enzyme activity:

Since all enzymes are made of globular proteins,and proteins are made of amino acids linked bypeptide bonds, enzymes can be affected ordenatured very easily.

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denatured very easily.

Factors that could affect or denature enzymesinclude heat, radiation , electricity, certain chemicalsubstances, and extreme PH.

Synthesis and Hydrolysis of Sucrose :

Anabolic metabolism uses dehydration synthesis reaction to buildlarge molecules from small molecules.

Each reaction releases a water molecule and requires energy inputExample – monosaccharide + energy → polysaccharide + wateramino acids + energy → protein + water.

Metabolism

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Catabolic metabolism

Uses hydrolysis (or decomposition) reaction to breakup large molecules into smaller molecules.

Each reaction requires a water molecule and releases

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Each reaction requires a water molecule and releasesenergy.

Example -- triglyceride + water → fatty acids +energy.

Adenosine Triphosphate (ATP)

High- energy molecule that is derived from the nucleotide, adenine.

Contains 3 phosphate groups (PO4) and high-energy chemical bondsthat each time the bonds are broken, a large amount of energy isgenerated.

Energy is released by ATP is broken down by hydrolysis reaction:

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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]

ATP

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