CHAPTER 6--- CHEMISTRY IN BIOLOGY

Miss Queen

SECTION 6.1 Atoms, Elements, Compounds

COMPOSITION OF MATTER Matter - Everything in

universe is composed of matter Matter is anything that occupies

space or has massMass – quantity of matter an object has

Weight – pull of gravity on an object

Atom – the smallest unit of matter “indivisible”

Heliumatom

ATOMS

The simplest particle of an element that retains all the properties of that element

Properties of atoms determine the structure and properties of the matter they compose

Our understanding of the structure of atoms based on scientific models, not observation

STRUCTURE OF AN ATOM--THE NUCLEUS

Central coreConsists of

positive charged protons and neutral neutrons

Positively charged

Contains most of the mass of the atom

THE PROTONS

All atoms of a given element have the same number of protons

Number of protons called the atomic number

Number of protons balanced by an equal number of negatively charged electrons

THE NEUTRONSThe number varies slightly among

atoms of the same elementDifferent number of neutrons

produces isotopes of the same element

ELEMENTSPure substances that cannot be

broken down chemically into simpler kinds of matter

More than 100 elements (92 naturally occurring)

90% of the mass of an organism is composed of 4 elements (oxygen, carbon, hydrogen and nitrogen)

Each element unique chemical symbol Consists of 1-2 letters First letter is always capitalized

ATOMIC MASS

Protons & neutrons are found in the nucleus of an atom

Protons and neutrons each have a mass of 1 amu (atomic mass unit)

The atomic mass of an atom is found by adding the number of protons & neutrons in an atom

THE ELECTRONSNegatively charged high energy

particles with little or no massTravel at very high speeds at

various distances (energy levels) from the nucleus

ENERGY LEVELS Atoms have 7 energy levels The levels are K (closest to the

nucleus), L, M, N, O, P, Q (furthest from the nucleus)

The K level can only hold 2 electrons Levels L – Q can hold 8 electrons (octet

rule)

ATOMIC STRUCTURE

Electrons are arranged in Energy Levels

or Shells around the nucleus of an atom.

• first shell a maximum of 2 electrons

• second shell a maximum of 8

electrons

• third shell a maximum of 8

electrons

SUMMARY

1. The Atomic Number of an atom = number of

protons in the nucleus.

2. The Atomic Mass of an atom = number of

Protons + Neutrons in the nucleus.

3. The number of Protons = Number of Electrons.

4. Electrons orbit the nucleus in shells.

5. Each shell can only carry a set number of electrons.

PERIODIC TABLE Elements are arranged by their atomic

number on the Periodic Table The horizontal rows are called Periods &

tell the number of energy levels Vertical groups are called Families & tell

the outermost number of electrons

COMPOUNDSMost

elements do not exist by themselves

Readily combine with other elements in a predictable fashion

A compound is a pure substance made up of atoms of two or more elements The proportion of atoms

are always fixedChemical formula

shows the kind and proportion of atoms of each element that occurs in a particular compound

Molecules are the simplest part of a substance that retains all of the properties of the substance and exists in a free state

Some molecules are large and complex

CHEMICAL FORMULAS Subscript after a

symbol tell the number of atoms of each element

H20 has 2 atoms of hydrogen & 1 atom of oxygen

Coefficients before a formula tell the number of molecules

3O2 represents 3 molecules of oxygen or (3x2) or 6 atoms of oxygen

PROPERTIES

The physical and chemical properties of a compound differ from the physical and chemical properties of the individual elements that compose it

The tendency of elements to combine and form compounds depends on the number and arrangement of electrons in their outermost energy level

Atoms are most stable when their outer most energy level is filled

Most atoms are not stable in their natural state

Tend to react (combine) with other atoms in order to become more stable (undergo chemical reactions)

In chemical reactions bonds are broken; atoms rearranged and new chemical bonds are formed that store energy

COVALENT BONDSFormed when two atoms share

one or more pairs of electrons

IONIC BONDSSome atoms become stable by

losing or gaining electronsAtoms that lose electrons are

called positive ions

Atoms that gain electrons are called negative ions

Because positive and negative electrical charges attract each other ionic bonds form

SECTION 6.2Chemical Reactions, Enzymes

ENERGY AND CHEMICAL REACTIONS Living things undergo thousands of

chemical reactions as part of the life process

Chemical reaction is the process by which atoms or groups of atoms in substances are reorganized into different substances.

CHEMICAL EQUATIONS

represent chemical reactionsReactants are shown on the left side

of the equationProducts are shown on the right

side

The number of each kind of atom must be the same on either side of the arrow (equation must be balanced)

Bonds may be broken or made forming new compounds

Activation Energy is the minimum amount of energy needed to form products in a chemical reaction.

Enzymes are an important class of catalysts in living organisms

Catalyst is a substance that lowers the activation energy needed to start a chemical reaction. Mostly protein Thousands of different kinds Each specific for a different chemical reaction

ENZYME STRUCTURE

Enzymes work on substances called substrates

Substrates must fit into a place on an enzyme called the active site

Enzymes are reusable!

SECTION 6.3Water and Solutions

WATERA water molecule (H2O), is made up of three atoms --- one oxygen and two hydrogen.

H

HO

WATER: THE FACTS

Water is possibly the most important compound in living organisms.

Water consists of 1 atom of oxygen combined with 2 atoms of hydrogen.

Water makes up 70 to 95 percent of most organisms.

- water is a polar molecule because oxygen is more electronegative than hydrogen, and therefore electrons are pulled closer to oxygen.

SOLUTIONS

A solution is a mixture in which 2 or more substances are uniformly distributed in another substance

Solute is the substance dissolved in the solution Particles may be

ions, atoms, or molecules

Solvent is the substance in which the solute is dissolved

Water is the universal solvent

SOLUTIONS Solutions can be

composed of varying proportions of a given solute in a given solvent --- vary in concentration (measurement of the amount of solute)

A saturated solution is one in which no more solute can be dissolved

Aqueous solution (water) are universally important to living things

ACIDS AND BASESOne of the most important aspects

of a living system is the degree of acidity or alkalinity

ACIDS

Number of hydronium ions in solutions is greater than the number of hydroxide ions

HCl H+ + Cl-

BASESNumber of hydroxide ions in

solution is greater than the number of hydronium ions

NaOH Na+ + OH-

PH SCALE logarithmic scale

for comparing the relative concentrations of hydronium ions and hydroxide ions in a solution

ranges from 0 to 14

Each pH is 10X stronger than next

e.g. ph 1 is 10 times stronger than ph 2

the lower the pH the stronger the acid

the higher the pH the stronger the base

pH 7.0 is neutral

BUFFERS

Control of pH is very important

Most enzymes function only within a very narrow pH

Control is accomplished with buffers made by the body

Buffers keep a neutral pH (pH 7)

Buffers neutralize small amounts of either an acid or base added to a solution

Complex buffering systems maintain the pH values of your body’s many fluids at normal and safe levels

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ORGANIC COMPOUNDS

Compounds that contain CARBON are called organic.

Macromolecules are large organic molecules.

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MACROMOLECULES

Large organic molecules.Also called POLYMERS.Made up of smaller “building

blocks” called MONOMERS.Examples:

1. Carbohydrates2. Lipids3. Proteins4. Nucleic acids (DNA and RNA)

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CARBOHYDRATES

Small sugar molecules to large sugar molecules.

Examples:A. monosaccharideB. disaccharideC. polysaccharide

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CARBOHYDRATES

Monosaccharide: one sugar unit

Examples: glucose (C6H12O6)

deoxyriboseriboseFructoseGalactose

glucose

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CARBOHYDRATES

Disaccharide: two sugar unit

Examples: Sucrose (glucose+fructose)

Lactose (glucose+galactose)

Maltose (glucose+glucose)glucoseglucose

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CARBOHYDRATES

Polysaccharide: many sugar units

Examples: starch (bread, potatoes)

glycogen (beef muscle)

cellulose (lettuce, corn)

glucoseglucose

glucoseglucose

glucoseglucose

glucoseglucose

cellulose

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LIPIDSGeneral term for compounds which are

not soluble in water.Lipids are soluble in hydrophobic solvents.Remember: “stores the most energy”Examples: 1. Fats

2. Phospholipids3. Oils4. Waxes5. Steroid hormones6. Triglycerides

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LIPIDS

Six functions of lipids:1. Long term energy storage2. Protection against heat loss (insulation)3. Protection against physical shock4. Protection against water loss5. Chemical messengers (hormones)6. Major component of membranes (phospholipids)

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LIPIDS

Triglycerides:composed of 1 glycerol and 3 fatty acids.

H

H-C----O

H-C----O

H-C----O

H

glycerol

O

C-CH2-CH2-CH2-CH2-CH2-CH2-CH2-CH2-CH2-CH3

=

fatty acids

O

C-CH2-CH2-CH2-CH2-CH2-CH2-CH2-CH2-CH2-CH3

=

O

C-CH2-CH2-CH2-CH =CH-CH2 -CH

2 -CH2 -CH

2 -CH3

=

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FATTY ACIDSThere are two kinds of fatty acids you may see these on

food labels:

1. Saturated fatty acids: no double bonds (bad)

2. Unsaturated fatty acids: double bonds (good)O

C-CH2-CH2-CH2-CH2-CH2-CH2-CH2-CH2-CH2-CH3

=

saturated

O

C-CH2-CH2-CH2-CH=CH-CH2 -CH

2-CH2 -CH

2 -CH3

=

unsaturated

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PROTEINS (POLYPEPTIDES) Amino acids (20 different kinds of aa) bonded

together by peptide bonds (polypeptides).

Six functions of proteins:1. Storage: albumin (egg white)2. Transport: hemoglobin3. Regulatory: hormones4. Movement: muscles5. Structural: membranes, hair, nails6. Enzymes: cellular reactions

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PRIMARY STRUCTURE

Amino acids bonded together by peptide bonds (straight chains)

aa1 aa2 aa3 aa4 aa5 aa6

Peptide Bonds

Amino Acids (aa)

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NUCLEIC ACIDSNucleotides include:

phosphate grouppentose sugar (5-carbon)nitrogenous bases:

adenine (A)thymine (T) DNA onlyuracil (U) RNA onlycytosine (C)guanine (G)

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NUCLEOTIDE

OO=P-O O

Phosphate Group

NNitrogenous base (A, G, C, or T)

CH2

O

C1C4

C3 C2

5

Sugar(deoxyribose)