And Biochemistry

 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.
 Atom—simplest particle of
an element that keeps all
the properties of that
element.
 Parts of an atom
◦ Protons—positive charge Inside Nucleus
◦ Neutrons—no charge
◦ Electrons—negative charge 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—atoms of the same element with
different number of neutrons.
 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 are attractive forces that
hold atoms together. They form so that
elements can become more stable by filling
their outer energy levels.
 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_3izM7K7RCw6b5ueLWXpac
http://www.chemistrydaily.com/chemistry/upload/d/d9/
Sg91FXY8Tt6PoObw&t=1&usg=__fkitOKpfQ768Lo6SF7eDzZ0qobs=
Covalent.png
 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!!!!
 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
 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/activatione
nergy1.gif
 Endothermic reactions
result in a net absorption
of energy
 Exothermic reactions
results in the net release
of energy
 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’s chemical structure is important
in its vital role in life.

http://www.lenntech.com/images/Water%20mo
lecule.jpg
http://www.ci.rockford.il.us/uploadedImages/government/PublicWorks/Water/willing%20water
%20color.jpg
 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!!)
 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
 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

 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
 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.
 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
-OH
(Alcohols)
H
Carbonyl (on end)
(Aldehydes) - C=O
Carbonyl (in middle) O
(Ketone)
C
Carboxyl
COOH
(Organic Acids)

Amino
NH2
(Amino Acids)

Phosphate
PO43-
(Nucleic Acids)
 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/monome
r.jpg
 Polymers form during condensation reactions
 In these reactions; water is released
Example: Glucose and Fructose combine to form Sucrose
 Polymers break down by a hydrolysis reaction
 In these reactions; water is used

http://imcurious.wikispaces.com/file/view/hydrolysis_reaction.jpg/113609729/hydrolysis_reacti
on.jpg
 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
 Four main groups of organic compounds:
◦ Carbohydrates
◦ Proteins
◦ Lipids
◦ Nucleic Acids

http://ez002.k12.sd.us/Chapter%20One%20Science.htm
 Used for energy
 Three types:
◦ Monosaccharides
(glucose and fructose)
◦ Disaccharides (sucrose)
◦ Polysaccharides
(glycogen, starch and
cellulose)

Structure is too complex to show

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