copyright 2009, john wiley & sons, inc. chapter 2: the chemical level of organization 1/29/091

Copyright 2009, John Wiley & Sons, Inc.

Chapter 2: The Chemical

Level of Organization

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How Matter is Organized

Chemical Elements All forms of matter are composed of chemical

elements which are substances that cannot be split into simpler substances by ordinary chemical means.

Structure of Atoms Units of matter of all chemical elements are called

atoms. Nucleus + electrons

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2 Representations of the Structure of an Atom

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Atomic Number and Mass Number Atomic Mass

The atomic mass of an element is the average mass of all its naturally occurring isotopes

Isotopes – atoms of an element that have different numbers of neutrons and therefore different mass numbers, most isotopes are stable

Radioactive isotopes – some are unstable resulting in decay of the nucleus I131 for example used to detect and treat thyroid disease

and thyroid cancer

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Ions, Molecules, & Compounds

Ions an atom that gave up or gained an electron written with its chemical symbol and (+) or (-)

Molecule atoms share electrons written as molecular formula showing the

number of atoms of each element (H2O)

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Chemical Bonds

The atoms of a molecule are held together by forces of attraction called chemical bonds.

The likelihood that an atom will form a chemical bond with another atom depends on the number of electrons in its outermost shell, also called the valence shell.

Atoms of most biologically important elements do not have 8 electrons in their valence shells.

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Chemical Bonds

Two or more atoms can interact in ways that produce a chemically stable arrangement of 8 valence electrons for each.

Octet rule – One atom is more likely to interact with another if doing so will leave both with 8 valence electrons. Helps explain why atoms interact in a predictable way.

In order for this to happen an atom either empties its partially filled valence shell, fills it with donated electrons, or shares electrons with other atoms.

The way that valence electrons are distributed determines what type of bond is formed.

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Ionic Bonds

When an atom loses or gains a valence electron, ions are formed. Positively and negatively charged ions are

attracted to one another. Cations are positively charged ions that have

given up one or more electrons (they are electron donors).

Anions are negatively charged ions that have picked up one or more electrons that another atom has lost (they are electron acceptors).

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The Ionic Bond Formation

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Ionic Bonds

In general, ionic compounds exist as solids with an orderly repeating arrangement of ions.

In the body ionic bonds are found mainly in teeth and bones.

Electrolyte – An ionic compound that breaks apart into (+) and (-) ions in solution

In the body most ions are dissolved in body fluids as electrolytes; so named because their solutions can conduct electrical current.

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Covalent Bonds Covalent bonds are formed by the atoms of molecules

sharing one, two, or three pairs of their valence electrons. Covalent bonds are common and are the strongest

chemical bonds in the body. Single, double, or triple covalent bonds are formed by

sharing one, two, or three pairs of electrons, respectively.

Covalent bonds may be nonpolar or polar. In a nonpolar covalent bond, atoms share the

electrons equally; one atom does not attract the shared electrons more strongly than the other atom

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Polar Covalent Bonds

Unequal sharing of electrons between atoms. In a water molecule, oxygen (N & S) attracts the hydrogen electrons more strongly Oxygen has greater electronegativity as indicated

by the negative Greek delta sign.

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Hydrogen Bonds

weak intermolecular bonds; they serve as links between molecules

helps determine three-dimensional shape of many organic macromolecules

proteins DNA RNA

gives water cohesion which creates a very high surface tension

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Sons, Inc. 15

Hydrogen Bonds



Water Is the most important and abundant inorganic compound

in all living systems. Water’s most important property is polarity, the uneven

sharing of valence electrons Serves as lubricant universal solvent (the solvent dissolves the solute)

Hydrophilic – solutes which contain polar covalent bonds and dissolve in water

Hydrophobic – contain non-polar covalent bonds and water insoluble

Enables reactants to collide to form products Polarity of water and angled shape allow interaction with

several neighboring ions or molecules Dissolves waste products allowing removal via urine

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Polar Water Molecules

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Types of Chemical Reactions

Metabolism is “the sum of all the chemical reactions in the body.”

Synthesis reactions – Anabolism Endergonic – energy input to form bond Dehydration – release of water molecule when

covalent bond formed Decomposition reactions – Catabolism

Exergonic – energy released when bond broken Hydrolysis – input of water molecule to break

covalent bond

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Factors that Cause a Collision and Chemical Reaction

Concentration Temperature Catalysts are chemical compounds that speed up chemical reactions

by lowering the activation energy needed for a reaction to occur. A catalyst does not alter the difference in potential energy

between the reactants and products. It only lowers the amount of energy needed to get the reaction started. A catalyst helps to properly orient the colliding particles of matter

so that a reaction can occur at a lower collision speed. The catalyst itself is unchanged at the end of the reaction; it is

often re-used many times. See enzymes slides 40 & 41See enzymes slides 40 & 41

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Catalysts and chemical reactions

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Inorganic compounds usually lack carbon and are simple molecules (CO2, H2O)

organic compounds contain carbon and hydrogen, often oxygen and always have covalent bonds (CH4)

Also attached to the carbon skeleton are distinctive functional groups which are atoms or molecules bound to the hydrocarbon skeleton.

Functional or R groups have a specific arrangement of atoms that confer characteristic repeatable chemical properties on the organic molecule to which it is attached (see table 2.5)

Very large molecules are called macromolecules (or polymers if all the monomer subunits are similar)

Isomers have the same molecular formulas but different structures (glucose & fructose are both C6H12O6)

Carbon and Its Functional Groups

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02_table_05


Carbohydrates

Carbohydrates provide most of the energy needed for life and include sugars, starches, glycogen, and cellulose.

basic formula of all carbohydrates – (CH2O)n

used to build structures and to generate ATP. Other carbohydrates function as food reserves. Carbohydrates are divided into three major groups

based on their size: monosaccharides, disaccharides, and polysaccharides

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Disaccharides Combining 2 monosaccharides by dehydration synthesis releases a water

molecule. sucrose = glucose & fructose maltose = glucose & glucose lactose = glucose & galactose (lactose intolerance)

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02_table_06


Lipids Lipids, like carbohydrates, contain carbon, hydrogen, and oxygen; but unlike

carbohydrates, they do not have a 2:1 ratio of hydrogen to oxygen. They have few or no polar covalent bonds

hydrophobic mostly insoluble in polar solvents such as water combines with proteins (lipoproteins) for transport in blood

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Triglycerides Triglycerides are the most plentiful lipids in

the body and provide protection, insulation, and energy (both immediate and stored). At room temperature, triglycerides may be either

solid (fats) or liquid (oils). Triglycerides provide more than twice as much

energy per gram as either carbohydrates or proteins.

Triglyceride storage is virtually unlimited. Excess dietary carbohydrates, proteins, fats, and

oils will be deposited in adipose tissue as triglycerides.

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Triglycerides

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Saturated Fats

triglycerides containing only single covalent bonds

each carbon saturated with hydrogens solid at room temperature found mostly in red

meats and dairy products associated with atherosclerosis, heart

disease and colorectal cancer

January 6, 2009Copyright 2009, John Wiley &

Sons, Inc. 30

Unsaturated Fats

monounsaturated – one double covalent bond forms kink in fatty acid olive, peanut, and canola oil thought to decrease risk of CVD

polyunsaturated – more than one double covalent bond linoleic acid – fish fats corn, safflower, sunflower and soybean oils protect against CVD

January 6, 2009Copyright 2009, John Wiley &

Sons, Inc. 31


Phospholipids

Phospholipids are important membrane components.

They are amphipathic, with both polar and nonpolar regions a polar head

a phosphate group (PO4-3) & glycerol molecule forms hydrogen bonds with water

2 nonpolar fatty acid tails interact only with lipids

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Steroids

Steroids have four rings of carbon atoms Steroids include sex hormone bile salts some vitamins cholesterol serving as an important component

of cell membranes and as starting material for synthesizing other steroids.

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Proteins Constructed from combinations of 20 amino acids.

dipeptides formed from 2 amino acids joined by a covalent bond called a peptide bond

polypeptides chains formed from 10 to 2000 amino acids.

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02_table_08


Formation of a Dipeptide Bond Dipeptides formed from 2 amino acids joined by a

covalent bond called a peptide bond dehydration synthesis

Polypeptides chains contain 10 to 2000 amino acids.

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Levels of Structural Organization Levels of structural organization include

primary secondary tertiary quaternary

The resulting shape of the protein greatly influences its ability to recognize and bind to other molecules.

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Levels of Structural Organization Denaturation of a protein by a hostile environment

causes loss of its characteristic shape and function breaks down to primary structure causes:

extremes of pH high temperature abnormal salt concentrations heavy metals alcohols

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Enzymes Biologic catalysts in living cells are called

enzymes. Enzymes are highly specific in terms of the

substrate with which they react. Enzymes are subject to variety of cellular

controls. Enzymes speed up chemical reactions by:

increasing frequency of collisions lowering the activation energy properly orienting the colliding molecules.

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How and Enzyme Works

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DNA and RNA Nucleic acids are huge organic molecules that contain

carbon, hydrogen, oxygen, nitrogen, and phosphorus. Deoxyribonucleic acid (DNA) forms the genetic code

inside each cell and thereby regulates most of the activities that take place in our cells throughout a lifetime.

Ribonucleic acid (RNA) relays instructions from the genes in the cell’s nucleus to guide each cell’s assembly of amino acids into proteins by the ribosomes.

The basic units of nucleic acids are nucleotides, composed of a nitrogenous base, a pentose, sugar, and a phosphate group.

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RNA Structure

Differs from DNA single stranded ribose sugar not deoxyribose sugar uracil nitrogenous base replaces thymine

Types of RNA within the cell, each with a specific function messenger RNA ribosomal RNA transfer RNA

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Adenosine Triphosphate (ATP)

Temporarymolecular storage ofenergy as it is beingtransferred fromexergonic catabolicreactions to cellularactivities

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Formation & Usage of ATP

Hydrolysis of ATP (removal of terminal phosphate group by enzyme - ATPase) releases energy leaves ADP (adenosine diphosphate)

Synthesis of ATP enzyme ATP synthase catalyzes the addition

of the terminal phosphate group to ADP energy from 1 glucose molecule is used during

cellular respiration to create 36 to 38 molecules of ATP

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End of Chapter 2

Copyright 2009 John Wiley & Sons, Inc.All rights reserved. Reproduction or translation of this work beyond that permitted in section 117 of the 1976 United States Copyright Act without express permission of the copyright owner is unlawful. Request for further information should be addressed to the Permission Department, John Wiley & Sons, Inc. The purchaser may make back-up copies for his/her own use only and not for distribution or resale. The Publishers assumes no responsibility for errors, omissions, or damages caused by the use of theses programs or from the use of the information herein.

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copyright 2009, john wiley & sons, inc. chapter 2: the chemical level of organization 1/29/091

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valence electrons

chemical bonds

number of electrons

number of atoms

chemical elements

nucleus electrons

isotopes isotopes atoms