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 mass  Mass – quantity of matter an object has

 Weight – pull of gravity on an object

Atom – the smallest unit of matter “indivisible”

Helium atom

 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

 Central core  Consists of positive charged protons and neutral neutrons

 Positively charged  Contains most of the mass of the atom

 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 number varies slightly among atoms of the same element

 Different number of neutrons produces isotopes of the same element

 Pure 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

 Negatively charged high energy particles with little or no mass

 Travel at very high speeds at various distances (energy levels) from the nucleus

 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)

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

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.

5.  Electrons orbit the nucleus in shells.

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

 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

 Most 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 fixed  Chemical 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

  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 BONDS  Formed when two atoms share one or more pairs of electrons

IONIC BONDS  Some atoms become stable by losing or gaining electrons

 Atoms 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 6.2 Chemical 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 reactions  Reactants are shown on the left side of the equation

 Products 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 6.3 Water and Solutions

H

H O

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.

 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

 One of the most important aspects of a living system is the degree of acidity or alkalinity

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

 HCl H+ + Cl-

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

 NaOH Na+ + OH-

 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

 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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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

=

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

=

O C-CH2-CH2-CH2-CH

=

unsaturated

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PRIMARY STRUCTURE

aa1 aa2 aa3 aa4 aa5 aa6

Peptide Bonds

Amino Acids (aa)

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O O=P-O O

N

CH2

O

C1 C4

C3 C2

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