Chemical Basis for Life And Biochemistry

Chemistry of Life Chemistry is important to biologists because all of the life activities in our cells that keep us alive are the result of chemical reactions. Matter—anything that has mass and takes up space. Elements—found on Periodic Table. Cannot be broken down into simpler kinds of matter. HONC (Honk)—hydrogen, oxygen, nitrogen, carbon. These are the most important elements in living things.

Atoms Atom—simplest particle of an element that keeps all the properties of that element. Parts of an atom Protons—positive charge Neutrons—no charge Electrons—negative charge Inside Nucleus Orbit Nucleus

The atomic number is the number of protons in an atom The atomic mass is the number of protons plus the number of neutrons. The number of electrons in an atom is the same as the number or protons giving it a net charge of zero.

Isotopes Isotopes—atoms of the same element with different number of neutrons.

Compounds Compounds —atoms of two or more elements joined by chemical bonds. Examples: H2O NaCl C6H12O6 Three models below show a water molecule Electron Cloud model Stick model Bohr model http://www.lionden.com/graphics/AP/Water1.gif

Chemical Bonds Chemical bonds are attractive forces that hold atoms together. They form so that elements can become more stable by filling their outer energy levels.

Types of Chemical Bonds Covalent Bonds—two atoms SHARE electrons

Carbon has the ability to form multiple covalent bonds Carbon has 4 electrons in its outer shell. The shell can hold 8. Carbon needs 4 more electrons to become stable. This can result in big biological molecules based around chains of carbon atoms. http://t1.gstatic.com/images?q=tbn:ANd9GcTDsTGWMhdl6_3izM7K7RCw6b5ueLWXpacSg91FXY8Tt6PoObw&t=1&usg=__fkitOKpfQ768Lo6SF7eDzZ0qobs= http://www.chemistrydaily.com/chemistry/upload/d/d9/Covalent.png

Double —share 2 pair of electrons Triple —share 3 pair of electrons Many complex biological molecules will be formed using double and triple covalent bonds. Double —share 2 pair of electrons Triple —share 3 pair of electrons Ethane Ethylene Acetylene

Ionic Bonds—atoms LOSE or GAIN electrons creating charges that attract each other. SALTS!!!!

Energy and Chemical Reactions Chemical reactions occur when one or more substances change to produce one or more new substances. Chemical equations show what happens during the reaction Reactants on left Products on right 6CO2 + 6 H2O C6H12O6 + 6O2 +energy

Reaction Speed Most reactions need the addition of energy before they will begin. Activation Energy —energy required for a reaction to begin Catalyst —speed up chemical reactions by lowering the activation energy required. Enzymes are common catalysts in living things They remain unchanged throughout the reaction. http://xnet.rrc.mb.ca/davidb/photogallery/activationenergy1.gif

Endothermic and Exothermic Reactions Endothermic reactions result in a net absorption of energy Exothermic reactions results in the net release of energy

Oxidation Reduction Reactions Also called Redox Reactions Electrons are transferred between atoms Oxidation reaction —a reactant loses electrons resulting in a positive charge Example—Na loses an electron to become more stable creating a sodium ion (Na+) Reduction reaction —a reactant gains electrons resulting in a negative charge Example—Chlorine gains an electron to become more stable creating a chlorine ion (Cl-) The two always occur together. One reactant gives up what the other needs.

Water and Solutions Water’s chemical structure is important in its vital role in life. http://www.lenntech.com/images/Water%20molecule.jpg http://www.ci.rockford.il.us/uploadedImages/government/PublicWorks/Water/willing%20water%20color.jpg

Properties of Water Water is POLAR Electrons in the covalent bond are not shared equally. Results in a partial negative charge on the oxygen end and a partial positive charge on the hydrogen end.

Being polar allows water to: Dissolve many substances Form hydrogen bonds with other water molecules creating: Cohesion Surface Tension Adhesion Capillarity High heat capacity Less density when water freezes (ice floats!!)

Solutions Solution —mixture in which one or more substances are uniformly distributed in another substance. Solute —dissolved substance Solvent —substance in which the solute is dissolved Concentration —amount of solute dissolved in a fixed amount of solution Saturated Solution —no more solute can be dissolved

Ionization of Water Water molecules can collide and break each other apart H2O H+ + OH- OH- is known as the hydroxide ion Free H+ ions react with water molecules: H+ + H2O H3O+ H3O+ is known as the hydronium ion

Acids and Bases Acid —solution in which the number of hydronium ions is greater than the number of hydroxide ions They have a value BELOW 7 on the pH scale. Base —solution in which the number of hydroxide ions is greater than the number of hydronium ions (Alkaline) They have a value ABOVE 7 on the pH scale

Biochemistry Carbon—element of life Organic compounds—contain carbon (and hydrogen) Can form 4 covalent bonds with other elements so it is the backbone of all organic compounds.

Functional Groups Various functional groups can be attached to these carbon backbones. These groups determine how these molecules will react with other molecules. Functional groups can be seen on the following chart:

Functional Group Structural Formula Example Hydroxyl (Alcohols) -OH H Carbonyl (on end) (Aldehydes) - C=O Carbonyl (in middle) (Ketone) O C Carboxyl (Organic Acids) COOH Amino (Amino Acids) NH2 Phosphate (Nucleic Acids) PO43-

Large Carbon Molecules The building of large molecules occurs as follows: Monomers —small, simple carbon molecules Polymers —consists of repeated, linked monomers Macromolecules —large polymers: (Carbohydrates, lipids, proteins, nucleic acids) http://kenpitts.net/bio/human_anat/monomer.jpg

Condensation Reactions Polymers form during condensation reactions In these reactions; water is released

Example: Glucose and Fructose combine to form Sucrose

Hydrolysis Polymers break down by a hydrolysis reaction In these reactions; water is used http://imcurious.wikispaces.com/file/view/hydrolysis_reaction.jpg/113609729/hydrolysis_reaction.jpg

The Energy Molecule: ATP Adenosine Triphosphate (ATP ) —the most important energy currency molecule of cells. Made of Adenine; Ribose (a sugar) and 3 phosphate groups

The Hydrolysis of ATP is used by the cell to provide the energy needed to drive chemical reactions. http://kentsimmons.uwinnipeg.ca/cm1504/atp.htm -ATP can lose its end phosphate which releases the energy stored in it. and makes adenosine diphosphate (ADP). -This energy is used to do work in the cell. -Adding the phosphate back to make ATP requires that we add energy

The Molecules of Life Four main groups of organic compounds: Carbohydrates Proteins Lipids Nucleic Acids http://ez002.k12.sd.us/Chapter%20One%20Science.htm

Carbohydrates Used for energy Three types: Monosaccharides (glucose and fructose) Disaccharides (sucrose) Polysaccharides (glycogen, starch and cellulose) Structure is too complex to show

Proteins Made of chains of amino acids held together by peptide bonds. Dipeptides (two amino acids) Polypeptides (long chains of amino acids) that fold and bend into proteins. Typical amino acid

Form by condensation reactions.

Enzymes —special types of proteins that act as catalysts

Lipids Lipids are fats. Used for energy Nonpolar Fatty acids bonded to other molecules

Saturated Fatty Acids —each carbon is covalently bonded to four atoms (NO DOUBLE BONDS) Unsaturated Fatty Acids —not all carbons are bonded to four other atoms (HAS DOUBLE BONDS) http://www.biology.lsu.edu/introbio/Link2/fatty%20acids.gif

Classes of Lipids Triglycerides (fats) —three molecules of fatty acid joined to one molecule of glycerol. Saturated triglycerides —the 3 fatty acids are saturated: hard at room temp: found in butter and red meat: “bad fats” Unsaturated triglycerides —the 3 fatty acids are unsaturated: soft at room temp: found in plant seeds: “good fats” Phospholipids —two fatty acids joined to glycerol. They also have a phosphate group. Important part of all cell membranes Waxes —fatty acid chain joined to an alcohol chain: waterproof: form protective layers in plants and animals Steroids —four fused carbon rings with a functional group: include many hormones and cholesterol

Nucleic Acids Include DNA and RNA Information molecules Made of repeating monomers called nucleotides. Phosphate, pentose sugar, nitrogenous base.