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 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

elements in our

bodies, 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

(no)

Electrons (e-)

surround the

nucleus as a

cloud

Electrons are very small and light (mass about 1/2000th that of proton or neutron), often represented as a “planet” orbiting the “sun” (atomic nucleus). In reality, they are found in a “cloud” of probability. This concept, however, made even Einstein’s head hurt – we can use the planets-orbiting-the-sun model for this course!

Structure of Atoms

Mass is measured as a dalton (atomic mass unit).

– Masses of subatomic particles

Neutron - mass of 1.008 daltons

Proton - mass of

1.007 daltons

Electron has mass of

0.0005 dalton

Structure of Atoms

– Atomic number is the number of protons in an

atom.

– Mass number is the sum of protons and neutrons

in an atom and indicates how much the atoms

“weighs”—this is always a whole number.

– Atomic mass (atomic weight) is the average mass

of all naturally occurring isotopes—since this is an

average, it is not exactly a whole number.

Structure of Atoms

Structure of Atoms

Ions, Molecules, & Compounds Ions are atoms that have given up or gained

an electron in their outer electron shell (also called the valence shell).– Written with its chemical symbol and (+)

or (–)

Ions, Molecules, & Compounds Molecules are formed when atoms share electrons.

– Written as a molecular formula showing the number of atoms of each element (H2O)

– The oxygen gas in the atmosphere we breath is really not oxygen the atom, but a pair of oxygen atoms linked together into an oxygen molecule (O2) .

Compound

A free radical is an electrically charged atom or group of

atoms with an unpaired electron in its outermost shell.

Antioxidants are substances that inactivate oxygen-

derived free radicals.

Ions, Molecules, & Compounds

Chemical Bonds The atoms of a molecule are held together by

forces of attraction called chemical bonds.

Valence shell.

Ionic Bond

Formation

Chemical Bonds

Covalent bonds are formed by the atoms of molecules sharing one, two, or three pairs of their valence electrons.– Covalent bonds are the strongest chemical bonds.– Single, double, or triple covalent bonds are

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

Chemical Bonds

Hydrogen bonds are weak interactions (approximately 5% as

strong as covalent bonds) between hydrogen and adjacent

electronegative atoms like oxygen or sulfur.

Chemical Bonds

Hydrogen bonds are useful in establishing links between molecules or between distant parts of a very large molecule. Large 3-D molecules (like proteins) are often held together by a great many hydrogen bonds.In water, hydrogen bonding provides considerable cohesion which creates a very high surface tension (as this bug demonstrates).

Chemical Bonds

Chemical ReactionsChemical reactions occur when electrons in

the valence shell are shared or transferred. 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 .

Energy (the capacity to do work) is transferred in a chemical reaction.

Kinetic energy is the energy of matter in motion.

Potential energy is energy stored by matter - due to an object’s position in space, or stored in chemical bonds.

Chemical Reactions

Exergonic reactionsEndergonic reactions

Chemical Reactions

Activation Energy is the energy required to break chemical bonds in the reactant molecules so a reaction can start.

Chemical Reactions

Factors that cause a collision

- temperature

-concentration of the reactants,

-presence or absence of a catalyst.

Catalysts are chemical compounds that

speed up chemical reactions by lowering

the activation energy needed for a reaction

to occur.

Chemical Reactions

In a chemical reaction, a catalyst helps to properly orient the colliding particles

Chemical Reactions

Types of chemical reactions can be broadly classified as:

– Synthesis reactions – Anabolism

A + B ➙ AB

– Decomposition reactions – Catabolism

AB ➙ A + B

– Exchange reactions

AB + CD ➙ AD + CB– Reversible reactions

AC ↔ A + C

Chemical Reactions

Inorganic & Organic CompoundsInorganic compounds are structurally simple molecules that usually lack carbon - like the salt potassium chloride (KCl) depicted here:

Organic compounds always contain carbon and are usually large, complex molecules.

– Usually contain hydrogen

– 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 that enables reactants to collide to form products.

Inorganic Compounds

Inorganic CompoundsSodium and Chloride ions dissolve in the 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.

– Water’s role as a solvent makes it essential for

health and survival.

Inorganic Compounds

Water has a high heat capacity, meaning 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 (amount of heat needed to

change from a liquid to a gas) is also high.

– Evaporation of water from the skin removes large

amounts of heat.

Inorganic Compounds

A mixture is a combination of elements or compounds

that are physically blended together but are not bound

by chemical bonds.

In a solution, a substance called the solvent dissolves

another substance called the solute. Usually there is

more solvent than solute in a solution.

– In our bodies, the most common solvent is water: We

are 65-80% water (depending on age - babies are very

“wet”… as anyone who has had one can attest.)

Three Common Mixtures

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 (milk).

In a suspension, the suspended material may mix with the liquid or suspending medium for some time, but it will eventually settle out (blood is a suspension.)

Three Common Mixtures

The convenience is that one mole of hydrogen atoms weighs 1.01 grams, the same in grams as the atomic mass of hydrogen in Daltons.– 1 mole of oxygen atoms = 15.999 grams– 1 mole of sodium atoms = 22.989 grams– 1 mole of any atom or molecule is found in the

atomic mass of that element, or the molecularmass of that compound.

Methods of Measurement

The concentration of a molecule is a way of

stating the amount of that molecule in solution.

Percent gives the relative mass of a solute found in

100 ml of solution (usually water).

A mole is just a convenient way of counting large numbers of small things (like atoms or molecules).– 1 mole is 6.02 x 1023 of something just like 1 dozen

is 12 of something.

Methods of Measurement The concentration of a molecule is a way of

stating the amount of that molecule in solution.

Percent gives the relative mass of a solute found in

100 ml of solution (usually water).

A mole is just a convenient way of counting large numbers of small things (like atoms or molecules).– 1 mole is 6.02 x 1023 of something just like 1 dozen

is 12 of something.

Methods of Measurement

Acid – Dissociates into one more hydrogen ions

Base – Dissociates into one or more hydroxide ions

Salt – Dissociates into cations and anions

Inorganic acids and bases

pH = –log[H+] (concentration of H+

in moles/l)

It is a scale that runs from 0 to 14

Acids, Bases and Buffers

pH < 7 is acidic

([H+] > [OH-]);

pH > 7 is alkaline

([H+] < [OH-])

A salt (like KCl) is

neutral

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.– Buffers convert strong acids and strong

bases into weak acids and weak bases. They do this by “hiding” excess H+ ions or excess OH– ions as other molecules (like HCO3

– ) .– The major buffer system in the body is

carbonic acid-bicarbonate buffer system.

Acids, Bases and Buffers

Functional groups are certain molecular configurations which are easy to recognize.

They are found attached to the carbon skeleton and impart certain properties to the organic molecule.

Some of the more common functional groups are:

– Esters, amino, carboxyl, phosphate groups – Others are found on the following chart

(next slide)

Organic Compounds

Organic Compounds

Organic Compounds

Organic Compounds

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 & galactoseare both C6H12O6).

Organic Compounds

Carbohydrates provide most of the energy

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 .

Organic Compounds

Monosaccharides (Carbohydrates)

are the simplest sugars:– 5 carbon sugars are used in

nucleic acids.

– 6 carbon sugars are the most

easily recognizable in our diet.

Organic Compounds

Disaccharides are made by combining 2

monosaccharides by removing a water

molecule (dehydration synthesis):

sucrose = glucose + fructose

lactose = glucose + galactose

Organic Compounds

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.

Organic Compounds

Lipids are another major group of organic molecules.

– Like carbohydrates, they contain carbon, hydrogen, and

oxygen; unlike carbohydrates, they do not have a 2:1 ratio

of hydrogen to oxygen.

Organic Compounds

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).– Triglyceride storage is virtually unlimited.– Excess dietary carbohydrates, proteins,

fats, and oils are deposited in adipose tissue as triglycerides.

Organic Compounds

Triglycerides provide more than twice as

much energy per gram as either

carbohydrates or proteins.

Organic Compounds

Phospholipids are important membrane components.

Both polar and nonpolar regions make them soluble in both water and fats (this is called amphipathic—they are both hydrophilic and lipophilic.)– They have a polar head formed from a

phosphate group (PO4-3) & a glycerol

molecule (forms H-bonds with water), and 2 nonpolar fatty acid tails that interact only with lipids.

Organic Compounds

Phospholipids have a polar head and 2 non-

polar tails:

Organic Compounds

Steroids are lipids molecules that have four rings of carbon atoms. They include: – Sex hormones– Bile salts– Some vitamins– Cholesterol, which serves as an important

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

Organic Compounds

Steroids are based on the lipid cholesterol molecule.– They include the molecules used as sex hormones,

as well as other hormones used in coping with stress (cortisol).

Organic Compounds

Proteins are large molecules that contain

carbon, hydrogen, oxygen, and nitrogen.

This graphic is a model of an

enzyme protein.

Organic Compounds

Proteins are constructed from combinations of different amino acids.

The structures of 6 of the 20 human amino acids are depicted below:– All amino acids (a.a.)have the same basic structure– only the “R” group changes.

Proteins

Dipeptides are formed from 2 amino acids joined by a covalent bond called a peptide bond.– This process involves dehydration

synthesis.Polypeptide chains contain 10 to 2000

amino acids.

Proteins

There are 4 levels at which proteins are structurally organized :– Primary– Secondary– Tertiary– Quaternary

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

Proteins

The 4 levels of protein structural organization are depicted:

– Denaturation (loss of protein structure) by a hostile

environment causes loss of

its characteristic shape

and function.

– An egg white turning

solid white when exposed

to high temperatures is an

example of protein

denaturation.

Proteins

Enzymes are special proteins that catalyze (speed up) metabolic reaction in all living cells.

The substrate is the substance upon which an enzyme has its effect. In this regard, enzymes are highly specific.

Enzymes are subject to a variety of cellular controls.

Enzymes speed up chemical reactions by increasing frequency of collisions, lowering activation energy, and properly orienting colliding molecules.

Proteins

Nucleic acids are huge organic molecules composed of monomeric nucleotides (like the one shown below):– They contain carbon, hydrogen, oxygen, nitrogen,

and phosphorus, and form the principle molecules that contain our genetic code – DNA and RNA.

Organic Compounds

Nucleic acids are universal in living things.

These molecules carry genetic information

as deoxyribonucleic acid (DNA) and

ribonucleic acid (RNA).

– By controlling the formation of

proteins, the genetic code

regulates most of the activities

that take place in our cells

throughout a lifetime.

Nucleic Acids

Nucleic AcidsDNA molecules remain inside the nucleus of

cells and are the “master” template of our genetic code.

RNA is a slightly different nucleic acid macromolecule that relays instructions from the nucleus to guide assembly of amino acids into proteins in the cytoplasm.

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

The nucleotides of DNA and RNA are joined to a “sugar-phosphate” backbone to make a long chain.

There are 2 sugar-phosphate strands of DNA, joined in the middle by hydrogen bonds from one nucleotide to another.

Nucleic Acids

RNA structure differs from DNA in that it is single

stranded (instead of double stranded), ribose

replaces the sugar deoxyribose, and uracil is the

nitrogenous base that replaces thymine.

There are 3 types of RNA within the cell,

each with a specific function:

– Messenger RNA

– Ribosomal RNA

– Transfer RNA

Nucleic Acids

ATP is often called the “molecular unit of currency”

of intracellular energy transfer.

Synthesis of ATP is catalyzed by the ATP synthase

enzyme which adds the terminal high energy

phosphate bond (often depicted as ~P as opposed to

a regular –P bond) to ADP.

– Energy from 1 glucose molecule is used during

both anaerobic and aerobic respiration to create 36

to 38 molecules of ATP.

Nucleic Acids

Nucleic Acids

When needed, the high energy phosphate is hydrolyzed by the enzyme ATPase to release the stored energy, leaving ADP (adenosine diphosphate).

A human will use up his/her body weight of ATP over the course of the day. This means that each ATP molecule is recycled 1500 times during a single day.

Nucleic Acids