Chapter 2: The Chemical Level of Organizationapedu.weebly.com/.../6/6/3/16632618/the_chemical_level_of_organization.pdf · Enzyme and substrate come together at active site of enzyme,

Copyright 2009, John Wiley & Sons, Inc.

Chapter 2: The Chemical Level of

Organization


Introduction

Since chemicals compose your body and all body activities are chemical in nature, it is important to become familiar with the language and fundamental concepts of chemistry.


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.

Elements are given letter abbreviations called chemical symbols.

Trace elements are present in tiny amounts


Structure of Atoms

Units of matter of all chemical elements are called atoms. An element is a quantity of matter composed of atoms of the same type.

Atoms contain: Nucleus: protons (p+) & neutrons (neutral

charge) Electrons (e-) surround the nucleus as a

cloud (electron shells are designated regions of the cloud)


2 Representations of the Structure of an Atom


Atomic Number and Mass Number

Atomic number is number of protons in the nucleus.

Mass number is the sum of its protons and neutrons.


Atomic Mass

Mass is measured as a dalton (atomic mass unit)

Neutron has mass of 1.008 daltons proton has mass of 1.007 daltons electron has mass of 0.0005 dalton

Atomic mass (atomic weight) is close to the mass number of its most abundant isotope.


Atomic Number and Mass Number

Atomic Mass The atomic mass, also called the atomic weight,

of an element is the average mass of all its naturally occurring isotopes and reflects the relative abundance of isotopes with different mass numbers.

The mass of a single atom is slightly less than the sum of the masses of its neutrons, protons, and electrons because some mass (less than1%) was lost when the atom’s components came together to form an atom.


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)


Free Radicals A free radical is an electrically charged atom or group

of atoms with an unpaired electron in its outermost shell

Unstable and highly reactive; can become stable by giving up an electron taking an electron from another molecule Antioxidants are substances that inactivate oxygen-derived

free radicals


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.


Ionic Bonds

When an atom loses or gains a valence electron, ions are formed (Figure 2.4a). 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).


The Ionic Bond Formation


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


Polar Covalent Bonds

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

the negative Greek delta sign.


Hydrogen Bonds

Approximately 5% as strong as covalent bonds

Useful in establishing links between molecules or between distant parts of a very large molecule

Large 3-D molecules areoften held together by a large number of hydrogen bonds.


Hydrogen Bonds

are weak intermolecular bonds; they serve as links between molecules.

help determine three-dimensional shape

give water considerable cohesion

which creates a very high surface tension


Chemical Reactions

New bonds form and/or old bonds are broken. Metabolism is “the sum of all the chemical

reactions in the body.” Law of conservation of energy

The total mass of reactants equals the total mass of the products.


Forms of Energy and Chemical Reactions Energy is the capacity to do work.

Kinetic energy is the energy associated with matter in motion.

Potential energy is energy stored by matter due to its position.


Energy Transfer in Chemical Reactions An exergonic reaction is one in which the bond being

broken has more energy than the one formed so that extra energy is released, usually as heat (occurs during catabolism of food molecules).

An endergonic reaction is just the opposite and thus requires that energy be added, usually from a molecule called ATP, to form a bond, as in bonding amino acid molecules together to form proteins.


Activation Energy


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.


Catalysts and chemical reactions


Types of Chemical Reactions

Synthesis reactions -- Anabolism Decomposition reactions-- Catabolism Exchange reactions Reversible reactions


Inorganic Compounds and Solutes

Inorganic compounds usually lack carbon and are simple molecules; whereas organic compounds always contain carbon and hydrogen, usually contain oxygen, and always have covalent 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

Enables reactants to collide to form products


Polar Water Molecules


Water as a Solvent In a solution the solvent dissolves the solute. Substances which contain polar covalent

bonds and dissolve in water are hydrophilic, while substances which contain non polar covalent bonds are hydrophobic.

The polarity of water and its bent shape allow it to interact with several neighboring ions or molecules.

Water’s role as a solvent makes it essential for health and survival.


High Heat Capacity of Water

Water has a high heat capacity. It can absorb or release a relatively large amount of heat

with only a modest change in its own temperature. This property is due to the large number of hydrogen

ions in water.

Heat of vaporization is also high amount of heat needed to change from liquid to gas evaporation of water from the skin removes large

amount of heat


3 Common MixturesA mixture is a combination of elements or compounds that arephysically blended together but are not bound by chemical bonds.

Solution: a substance called the solvent dissolves another substance called the solute. Usually there is more solvent than solute in a solution.

A colloid differs from a solution mainly on the basis of the size of its particles with the particles in the colloid being large enough to scatter light.

Suspension: the suspended material may mix with the liquid or suspending medium for some time, but it will eventually settle out.


Concentration

The concentration of a molecule is a way of stating the amount of that molecule dissolved in solution.

Percent gives the relative mass of a solute found in a given volume of solution.

A mole is the name for the number of atoms in an atomic weight of that element, or the number of molecules in a molecular weight of that type of molecule, with the molecular weight being the sum of all the atomic weights of the atoms that make up the molecule.


Dissociation of Acids, Bases, and Salts


Concept of pH pH scale runs from 0 to 14 (concentration of H+

in moles/liter) pH of 7 is neutral

(distilled water -- concentration of OH- and H+ are equal)

pH below 7 is acidic ([H+] > [OH-]). pH above 7 is alkaline ([H+] < [OH-]). pH is a logarithmic scale

Example: a change of two or three pH unitspH of 1 contains 10x10=100 more H+ than pH of 3pH of 8 contains 10x10x10=1000 more H+ than pH of 11


The pH Scale


Maintaining pH: Buffer Systems

The pH values of different parts of the body are maintained fairly constant by buffer systems, which usually consist of a weak acid and a weak base. convert strong acids or bases into weak acids or

bases.


Many functional groups can attach to carbon skeleton esters, amino, carboxyl, phosphate groups 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


Carbohydrates

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

Some carbohydrates are converted to other substances which are 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


Monosaccharides


Disaccharides Combining 2 monosaccharides by dehydration

synthesis releases a water molecule. sucrose = glucose & fructose maltose = glucose & glucose lactose = glucose & galactose (lactose intolerance)


Polysaccharides

Polysaccharides are the largest carbohydrates and may contain hundreds of monosaccharides.

The principal polysaccharide in the human body is glycogen, which is stored in the liver or skeletal muscles.

When blood sugar level drops, the liver hydrolyzes glycogen to yield glucose which is released from the liver into the blood


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


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.


Triglycerides


Phospholipids

Phospholipids are important membrane components.

They are amphipathic, with both polar and nonpolar regions (Figure 2.18). a polar head

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

2 nonpolar fatty acid tails interact only with lipids


Steroids

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

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


Four Ring Structure of Steroids


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.


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.


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.

Denaturation of a protein by a hostile environment causes loss of its characteristic shape and function.


Enzymes

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 and properly orienting the colliding molecules.


How an Enzyme Works

Enzyme and substratecome together at activesite of enzyme, forming anenzyme–substrate complex

EnzymeSucraseActive site

of enzyme

SubstratesSucrose andWater

H2O

Mechanism of enzyme action

1

Enzyme catalyzesreaction and transformssubstrate into products

Enzyme and substratecome together at activesite of enzyme, forming anenzyme–substrate complex Glucose

Fructose


of enzyme


Products

H2O


1

2When reaction is complete,enzyme is unchanged andfree to catalyze same reactionagain on a new substrate

Enzyme catalyzesreaction and transformssubstrate into products

Enzyme and substratecome together at activesite of enzyme, forming anenzyme–substrate complex Glucose

Fructose


of enzyme


Products

H2O


1

3 2


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.


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


Adenosine Triphosphate (ATP)

Temporarymolecular storage ofenergy as it is beingtransferred fromexergonic catabolicreactions to cellularactivities


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

both anaerobic and aerobic respiration to create 36 to 38 molecules of ATP


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.

Chapter 2: �The Chemical Level of OrganizationIntroductionHow Matter is OrganizedStructure of Atoms2 Representations of the Structure of an AtomAtomic Number and Mass NumberSlide Number 7Atomic MassAtomic Number and Mass NumberIons, Molecules, & CompoundsFree RadicalsChemical BondsIonic BondsThe Ionic Bond FormationCovalent BondsSlide Number 16Polar Covalent BondsHydrogen BondsHydrogen BondsChemical ReactionsForms of Energy and Chemical ReactionsEnergy Transfer in Chemical ReactionsActivation EnergyFactors that Cause a Collision and Chemical ReactionCatalysts and chemical reactionsTypes of Chemical ReactionsInorganic Compounds and SolutesWaterPolar Water MoleculesWater as a SolventHigh Heat Capacity of Water3 Common MixturesConcentrationDissociation of Acids, Bases, and SaltsConcept of pHThe pH ScaleMaintaining pH: Buffer SystemsCarbon and Its Functional GroupsCarbohydratesMonosaccharidesDisaccharidesPolysaccharidesLipidsTriglyceridesTriglyceridesPhospholipidsSlide Number 47SteroidsFour Ring Structure of Steroids ProteinsFormation of a Dipeptide BondLevels of Structural OrganizationSlide Number 53EnzymesHow an Enzyme WorksSlide Number 56DNA and RNASlide Number 58RNA StructureAdenosine Triphosphate (ATP)Formation & Usage of ATPEnd of Chapter 2

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Chapter 2: The Chemical Level of Organizationapedu.weebly.com/.../6/6/3/16632618/the_chemical_level_of_organization.pdf · Enzyme and substrate come together at active site of enzyme,