chapter 2

anything that takes up space and has mass

smallest chemical units of matter

• electrons: negatively charged subatomic particles circling a nucleus
• nucleus: structure containing neutrons and protons
• neutrons: uncharged particles
• Protons: positively charged particles

• Element: composed of a single type of atom
• Atomic Number: equal to the number of protons in the nucleus. change in number means change in element.
• Atomic mass: sum for the masses of protons, neutrons and electrons

• Carbon-13 and carbon-14
• Atoms of a given element that differ in the number of neutrons in their nuclei
• carbon-13 is stable
• carbon-14 is unstable; release energy during radioactive decay

• Electrons. only electrons of atoms interact
• electrons occupy electron shells

electrons in the outermost chell that interact

• combining capacity of an atom.
• -positive if it has electrons to give up
• -negative if it has electrons to give up
• -stable when outer electron shells contain eight electrons

atoms combine by sharing or transferring valence electrons

two or more atoms held together by chemical bonds

a molecule composed of more than one element

• attraction of atom for electrons
• -the more electronegative an atom the greater the pull it's nucleur exerts on electrons

• Nonpolar covalent: equal sharing, not electronegative
• Polar Covalent: electronegative, unequal sharing. angeled
• Ionic Bond: no sharing. electrons are given up making the element an ion, completely positive, cation or completely negative, anion
• Hydrogen Bond: weak bond of water.

• shared electrons spend equal amounts of time around each nucleus
• atoms with similiar electronegativities
• no poles exist
• carbon atoms form four non polar covalent bonds with other atoms
• organic compounds contain carbon and hydrogen atoms

• Unequal sharing of electrons due to signicantly different electronegativities
• Most important polar covalent bonds involve hydrogen -Allow for hydrogen bonding

• Occur when two atoms with vastly different electronegativities come together
• atoms have either positive (cation) or negative (anion) charges
• cations and anions attract eachother and form ionic bonds (no electrons shared)
• typically form crystalline ionic compounds known as salts

• Weak forces that combine with polar covalent bonds
• electrical attraction between partially charged H+ and full or partial negative charge on same or different molecule
• eaker than covalent bonds but essential for life
• many help to stabilize 3-D shapes or large molecules

• The breaking or making of chemical bonds
• involve reactants and products
• biochemistry involves chemical reactions of living things

atoms, ions or molecules that exist at the begining of a reaction.

• Involve the formation of larger, more complex molecules
• reactant + reactant = product
• require energy (endothermic)
•  Most common type is dehydration synthesis -water molecule is formed
• all the synthesis reactions in an organism are called anabolism

• Break bonds with larger molecules to form smaller atoms, ions, and molecules
• release energy(exothermic)
• Product = reactant + reactant 
• most common type is hydrolysis
• ionic components of water are added to products
• all the decomposition reactions in an organism are called catabolism

–Involve breaking and forming covalent bonds, and involve endothermic and exothermic steps

• –Involve atoms moving from one molecule to another
• Sum of all chemical reactions in an organism is called metabolism

• –Most abundant substance in organisms
• –Most of its special characteristics due to two polar covalent bonds
• –Cohesive molecules
• – surface tension
• –Excellent solvent
• –Remains liquid across wide range of temperatures
• –Can absorb significant amounts of energy without changing temperature
• –Participates in many chemical reactions

• –Dissociated by water into component cations and anions
• –Acid – dissociates into one or more H+ and one or more anions
• –Base – binds with H+ when dissolved into water; some dissociate into cations and OH
•  –Metabolism requires relatively constant balance of acids and bases
• –Concentration of H+ in solution expressed using the pH scale
• –Buffers prevent drastic changes in internal pH

• 0-6 is acidic increasing amts of H+
• 7 is neutral
• 8-14 is basic increasing amts of OH-
• change in # is an increase of base 10    

• –Compounds that dissociate in water into cations and anions other than H+ and OH–
• –Cations and anions of salts are electrolytes
• –Create electrical differences between inside and outside of cell
• –Transfer electrons from one location to another
• –Form important components of many enzymes

• – large molecules used by all organisms
• Functional groups
• Lipids
• Carbohydrates
• Protiens
• nucleic acids
• –Monomers – basic building blocks of macromolecules

• –Contain carbon and hydrogen atoms
• –Atoms often appear in certain common arrangements – functional groups

• –Not composed of regular subunits, but are all hydrophobic because they are all carbon and hydrogen and all nonpolar.
• –Four groups: Fats, Phospholipids, Waxes, Steroids
• - Sterols maintain fluidity

• made by organisms via dehydraton synthesis that form esters between the 3 chains and an alcohol, glycerol.
• three fatty acid chains attached to a glycerol (triglycerides)
• saturated: each C molecule is bound to two H molecules
• unsaturate: one or more C atoms is attached to another C atom.
• Polyunsaturated: if several C atoms are bound.
• Abundant energy is stored in C-C covalent bonds.

• similiar to fats but two fatty acid chains and one phosphate.
• phosphate head is polar and hydrophilic.

• 1 long fatty acid chain and 1 long alcohol chain. completely water insoluable.
• mycobacterium tuberculosis surrounded by a waxy wall.

• 4 rings consisting of 5 or 6 C each, fused together and attached to various side chains.
• play many roles in human motabilism, some act as hormones.
• Fungi, plants and mycoplasm use sterol to mantain fluidity at low temperatures

• –Organic molecules composed of carbon, hydrogen, and oxygen (CH2O)n
• –Functions
• –Long-term storage of chemical energy
• –Ready energy source
•  –Part of backbones of nucleic acids
• –Converted to amino acids
• –Form cell wall
• Involved in intracellular interactions between animal cells

• –Monosaccharides: simple sugars 
• –Disaccharides: 2 monosaccharides are linked together via dehydration synthesis 
• –Polysaccharides: polymers of 10s-1,000s of monosaccharides that are covalently linked via dehydration synthesis

• Polymers composed of monomers called amino acids
•  –Mostly composed of carbon, hydrogen, oxygen, nitrogen, and sulfur
• –Functions: Structure, Enzymatic catalysis, Regulation, Transportation and Defense and offense
• Structures:primary, secondary, tertiary (3D shape), quanternary

• Structure: cell walls. membranes, hair, skin, nails, muscles, flagella, cilia etc
• Enzymatic Catalysis: enhace the speed or liklihood of  a chemical reaction
• Regulation: regulate cell function ie: hormones
• Transportation: channels and pumps
• Defense and offense: antibodies, complement, bacteriocins     

• Primary:sequence of amino acids in a polypeptide chain
• Secondary: interaction between regions of the polypeptide resulting in a helix or pleated sheet, hydrogen bonding
• Tertiary: continued hydrogen bonding and covalent bonding. 3D shape
• Quaternary: more than one polypeptide chain

• –The monomers that make up proteins
• –Most organisms use only 21 amino acids in the synthesis of proteins
• –Side groups affect how amino acids interact with one another and how a protein interacts with other molecules
• –A covalent bond (peptide bond) is formed between amino acids by dehydration synthesis reaction

molecules that are mirror images of eachother

• –DNA and RNA: the genetic material of organisms
• –RNA also acts as enzyme, binds amino acids, and helps form polypeptides

• –Monomers that make up nucleic acids (DNA/ RNA) 
• –Composed of three parts :
•             Phosphate,
•             Pentose sugar:deoxyribose or ribose
•             One of five cyclic nitrogenous bases
•                      Adenine
•                      Guanine
•                      cytosine
•                      thymine or Uracil

• –Three H bonds form between C and G
• –Two H bonds form between T and A in DNA or between U and A in RNA
• –DNA is double stranded in most cells and viruses
• –Two strands are complementary and antiparallel

• –DNA is genetic material of all organisms and of many viruses
• –Carries instructions for synthesis of RNA and proteins; controls synthesis of all molecules in an organism