The Structure of Atoms

          Chemistry is the study of interactions between atoms and molecules

          The atom is the smallest unit of matter that enters into chemical reactions

          Atoms interact to form molecules

          Atoms are composed of

          Electrons: Negatively charged particles

          Protons: Positively charged particles

          Neutrons: Uncharged particles

          Protons and neutrons are in the nucleus

          Electrons move around the nucleus


Chemical Elements

          Each chemical element has a different number of protons

          Isotopes of an element are atoms with different numbers of neutrons. Isotopes of oxygen:


Electronic Configurations

          Electrons are arranged in electron shells corresponding to different energy levels


How Atoms Form Molecules

          Atoms combine to complete the outermost shell

          The number of missing or extra electrons in this shell is known as the valence

          Molecules hold together because the valence electrons of the combining atoms form attractive forces, called chemical bonds, between the atomic nuclei


Chemical Bonds

          A compound contains different kinds of atoms      

Ionic Bonds

          The number of protons and electrons is equal in
an atom

          Ions are charged atoms that have gained or lost electrons

          Ionic bonds are attractions between ions of opposite charge. One atom loses electrons, and another gains electrons.


Covalent Bonds

          Covalent bonds form when two atoms share one or more pairs of electrons


Hydrogen Bonds

          Hydrogen bonds form when a hydrogen atom that is covalently bonded to an O or N atom is attracted to another N or O   atom in another molecule


Molecular Weight and Moles

          The sum of the atomic weights in a molecule is the molecular weight

          One mole of a substance is its molecular weight in grams


Chemical Reactions

          Chemical reactions involve the making or breaking of bonds between atoms

          A change in chemical energy occurs during a chemical reaction

          Endergonic reactions absorb energy

          Exergonic reactions release energy


Synthesis Reactions

          Occur when atoms, ions, or molecules combine
to form new, larger molecules

          Anabolism is the synthesis of molecules in a cell


Decomposition Reactions

          Occur when a molecule is split into smaller molecules, ions, or atoms

          Catabolism is the decomposition reactions in a cell


Exchange Reactions

          Are part synthesis and part decomposition


Reversible Reactions

          Can readily go in either direction

          Each direction may need special conditions


Important Biological Molecules

          Organic compounds always contain carbon and hydrogen

          Inorganic compounds typically lack carbon




          Polar molecule


          Polar substances dissociate,forming solutes

          H+ and OH- participate in chemical reactions

          H bonds absorb heat

          Makes water a temperature buffer



          Substances that dissociate into one or more H+
H+ + Cl-



          Substances that dissociate into one or more OH-
Na+ + OH-



          Substances that dissociate into cations and anions, neither of which is H+ or OH-
Na+ + Cl-


Acid-Base Balance

          The amount of H+ in a solution is expressed as pH

          pH = -log[H+]

          Increasing [H+], increases acidity

          Increasing [OH-] increases alkalinity

          Most organisms grow best between pH 6.5 and 8.5


Structure and Chemistry

          The chain of carbon atoms in an organic molecule is the carbon skeleton

          Functional groups are responsible for most of the chemical properties of a particular organic compound.


Functional Groups

          Identify the functional groups in an amino acid:


Organic Compounds

          Small organic molecules can combine into large macromolecules

          Macromolecules are polymers consisting of many small repeating molecules

          The smaller molecules are called monomers



          Monomers join by dehydration synthesis or condensation reactions



          Cell structures and energy sources

          Consist of C, H, and O with the formula (CH2O)n

          Monosaccharides are simple sugars with 3 to 7 carbon atoms

          Disaccharides are formed when 2 monosaccharides are joined in a dehydration synthesis

          Disaccharides can be broken down by hydrolysis

          Oligosaccharides consist of 2 to 20 monosaccharides

          Polysaccharides consist of tens or hundreds of monosaccharides joined through dehydration synthesis

          Starch, glycogen, dextran, and cellulose are polymers of glucose that are covalently bonded differently

          Chitin is a polymer of 2 sugars repeating many times



          Primary components of cell membranes

          Consist of C, H, and O

          Are nonpolar and insoluble in water


Simple Lipids

          Fats or triglycerides

          Contain glycerol and fatty acids; formed by dehydration synthesis

          Saturated fat: No double bonds

          Unsaturated fat: One or more double bonds in the fatty acids

          cis: H atoms on the same side of the double bond

          trans: H atoms on opposite sides of the double bond


Complex Lipids

          Contain C, H, and O + P, N, or S

          Membranes are made of phospholipids



          4 carbon rings with an –OH group attached to one ring

          Part of membranes



          Are essential in cell structure and function

          Enzymes are proteins that speed chemical reactions

          Transporter proteins move chemicals across membranes

          Flagella are made of proteins

          Some bacterial toxins are proteins


Amino Acids

          Proteins consist of subunits called amino acids

          Exist in either of two stereoisomers:
D or L.

          L-forms are most often found in nature.


Peptide Bonds

          Peptide bonds between amino acids are formed by dehydration synthesis


Levels of Protein Structure

          The primary structure is a polypeptide chain

          The secondary structure occurs when the amino acid chain folds and coils in a regular helix or pleats

          The tertiary structure occurs when the helix folds irregularly, forming disulfide bonds, hydrogen bonds, and ionic bonds between amino acids in the chain

          The quaternary structure consists of 2 or more polypeptides.

          Conjugated proteins consist of amino acids and other organic molecules





Nucleic Acids

          Consist of nucleotides

          Nucleotides consist of a     


          Phosphate group

          Nitrogen-containing (purine or pyrimidine) base

          Nucleosides consist of a


          Nitrogen-containing base



          Deoxyribonucleic acid

          Has deoxyribose

          Exists as a double helix

          A hydrogen bonds with T

          C hydrogen bonds with G



          Ribonucleic acid

          Has ribose

          Is single-stranded

          A hydrogen bonds with U

          C hydrogen bonds with G



          Adenosine triphosphate

          Has ribose, adenine, and 3 phosphate groups.

          Is made by dehydration synthesis

          Is broken by hydrolysis to liberate useful energy
for the cell