reintroduction to Chemistry
Matter: Anything that has mass and volume
States of Matter
Physical Changes
Properties that do not change the chemical nature of matter
•Boiling point
•Melting point
•Freezing point
•Color
•Density
Chemical Changes
Changes that do change the chemical nature of matter



Oxidation
Rusting of iron =
Iron Oxide (FeO2)
pH
Flammability
Frying an egg
Physical & Chemical Changes
All Matter is composed of :
 Atoms
 The
– Means “unable to be cut”
smallest particle of an
element that still has the
characteristics of that element
Elements

Substances that can’t be broken down
into simpler substances
96% of human mass is
made up of C, H, O, N
Periodic Table of The Elements
Atoms are made up of smaller subatomic particles



Protons: positively charged (Located in the nucleus)
Neutrons: neutrally charged (Located in the nucleus)
Electrons: negatively charged (Located around the nucleus)
Discovered
by James
Chadwick in
1932
Discovered by Ernest
Rutherford in 1919
Discovered by
J.J. Thomson in
1897
Each atom has the same number of protons and electrons
Electrons located farther away from the nucleus have more energy
Electrons have less mass than protons. 1 proton= 1870 electrons
Atomic number = number of protons
Atomic mass = number of protons & neutrons
Electron # = Proton # in Neutral elements
2
He
4.003
Atomic number:
Atomic mass:
# of Protons
# of Electrons
# of Neutrons
Isotopes
Neutron #’s change
1
Hydrogen:
Deuterium:
H
1
1
H
2
1
Tritium
H
3
When elements combine to form substances with two or more
atoms…
Compounds are formed
Mixtures
When one or more atoms are physically combined
but NOT chemically combined (Individual atoms
retain their own properties)
Easily separated by non-chemical means
Solutions


Solute – Substance dissolved
Solvent – Dissolves substances
(Water is the universal solvent)

Colloids – light does not penetrate

Suspensions
Solubility of Solutions

The amount of solute a solvent can
dissolve
Solubility affected by:
 Temperature
 Concentration
Intramolecular Bonds



Forces of attraction that hold atoms together
within a molecule.
Stronger than intermolecular bonds
2 types
covalent
ionic
Ions
Ions are charged particles.
Atoms have either lost or gained one or
more electrons
Ionic bond
Cation
Anion
Redox Reactions
Important in ATP synthesis
Oxidation is a loss of electrons
Reduction is a gain of electrons
Redox Reactions
Covalent Bond
Occurs when atoms SHARE electrons
Special Note
Diatomic molecule
Molecules are
only formed
with covalent
bonds
Molecules
A
group of atoms held together
by covalent bonds

Water, hydrogen gas, oxygen, carbon dioxide
Intermolecular Bonds



Intermolecular bonds refers to the forces of
attraction that hold molecules together
Considerably weaker than intramolecular bonds
3 types of intermolecular bonds
Hydrogen bonds
Van der Waals forces
Molecule-ion attractions
Uneven distribution of electrons results in a polar molecule
––
+
H+
+
+
Figure 3.2
 ––
 ––
++
Hydrogen
bonds
H
+
+

–
–
Hydrogen Bond
A bond formed in polar molecules
Cohesion & Adhesion: Due to Hydrogen Bonding
Cohesion – The ability of
hydrogen bonds to attract like
molecules
Adhesion – The ability of
hydrogen bonds to attract
different types of molecules
Why can these animals walk on water?
Capillary Action is
Due to Adhesion
How does the crown get water?
Van der Waals forces are weak attractive forces that hold non-polar
molecules together
molecule-ion attraction
Hydration shell forms as water
surrounds the dissolved ions
H2O
The molecule that supports all of life
Molality vs Molarity


Molality – the # of moles solute which
can be dissolved in 1 kg of solvent
Molarity – the # of moles solute which
can be dissolved in 1 liter of soloution
Water
Important biological properties






Cohesion
Adhesion
High specific heat
Heat of vaporization
Solvent of life
Insulation of bodies of water (floating ice) in
winter
Heat & Temperature


Heat – measurement of the total amount of kinetic energy
in matter
Temperature – measurement of the average kinetic
energy of molecules
Measurement of heat
calorie (cal) = amount of heat required to raise the
temperature of 1 g of water by 1°C
- or –
the amount of heat that 1 g of water releases when cooled
by 1°C
Calorie (kcal) = 1000 cal = amount of heat required to raise
the temp of 1 kg of water by 1°C
Specific Heat


The amount of heat that must be
absorbed or lost for 1 g of that
substance to change its temperature
by 1°C
Important because water does not
change temperature quickly & large
bodies of water can store much heat
to warm the air.
Specific Heat of Water

Heat is absorbed when hydrogen bonds break

Heat is released when hydrogen bonds form
Evaporative Cooling

Due to the high specific heat, when water
evaporated it removes much heat from the
system, thereby cooling the organism
Latent Heat
Latent Heat is the heat
given up or absorbed by a
substance as it changes
state. It is called latent
because
it
is
not
associated with a change
in temperature
Heat of Vaporization
The quantity of heat a liquid must absorb for 1 g of it to
be converted from the liquid to the gaseous state
The hydrogen bonds in ice
Are more “ordered” than in liquid
water, making ice less dense
Hydrogen
bond
Figure 3.5
Ice
Liquid water
Hydrogen bonds are stable
Hydrogen bonds
constantly break and re-form
The different regions of the polar water
molecule can interact with ionic compounds
called solutes and dissolve them
Negative
oxygen regions
of polar water molecules
are attracted to sodium
cations (Na+).
Positive
hydrogen regions
of water molecules
cling to chloride anions
(Cl–).
–
Na+
+
–
–
Na+
Cl–
+
Cl –
–
+
+
–
Figure 3.6
–
+
+
–
–
+
+
–
–
Acids & Bases
Acids are formed by
hydrogen cations
Bases are formed
by hydroxide anions
Acids

Donate protons (Hydrogen Ions) to water to
form hydronium ions

pH 0-6.99

Taste Sour

Turn litmus paper red

Strong acids completely dissociate to form ions
Dissociation of Water
–
+
H
H
H
H
Figure on p. 53 of water
dissociating
H
H
H
Hydronium
ion (H3O+)
+
H
Hydroxide
ion (OH–)
Bases

Donate hydroxide

pH 7.01-14

Accept protons

Taste bitter

Feel slimy

Turn litmus paper blue

Strong bases completely dissociate to form ions
pH
pH Scale
Buffers

Compounds that tend to neutralize the
pH of a solution by combining with
either H+ ions or OH- ions to keep the
solution neutral
Chemical Reactions








Synthesis (A+BC)
Decomposition (CA+B)
Single Replacement (AB+C AC+B)
Double Replacement (AB+CDAC+BD)
Reactants are to the left of the arrow (Elements
reacting)
Products are to the right of the arrow (Stuff made)
Subscripts CANNOT be changed
Coefficients can be changed to balance an equation)
Chemical Reactions


Endothermic rxn’s absorb heat
Exothermic rxn’s give off heat
Organic Chemistry




Organic molecules are any molecules that contain atoms from three
elements: carbon, hydrogen, and oxygen.
For example, glucose is organic, since its molecular formula is
C6H12O6
Carbon dioxide (CO2) is inorganic since it does not contain hydrogen.
Covalent bonds link carbon atoms together in long chains that form
the skeletal framework for organic molecules. These carbon
skeletons may vary in:
• Length
• Shape (straight chain, branched, ring)
• Number and location of double bonds
• Other elements covalently bonded to available sites
All organic molecules have two parts:
The carbon backbone & the functional group
Tetravalence of carbon allows for complex arrangement of
carbon compounds
Carbon atoms can form single, double, or triple covalent
bonds
Name and
Comments
(a) Methane
Molecular Structural
Formula
Formula
Ball-andStick Model
SpaceFilling
Model
H
CH4
H C
H
H
(b) Ethane
H H
C2H
H C C H
6
(c) Ethene
(ethylene)
H H
H
C2H4
H
C C
H
H
Hydrocarbons
–Are molecules consisting of only carbon and hydrogen
–Hydrocarbon chains are hydrophobic because the C—C
and C—H bonds are nonpolar
Hydrocarbons
Found in fossil fuels and makes up the “tails” of lipids
Fat droplets (stained red)
Figure 4.6 A, B
(a) A fat molecule
100 µm
(b) Mammalian adipose cells
Functional Groups
groups of atoms acting as a unit, that give organic molecules their physical
properties,their chemical reactivity, & solubility in aqueous solutions.
most possess electronegative atoms (N, P, O, S... EASILY ATTRACT PROTONS)
key bonds are : ester (C-O-C) & amide (O=C-N-)
are ionizable at physiological pH
-NH2 AMINE=
amino acid
-C=Ox CARBONYL=
-COOHx CARBOXYL=
-OHx HYDROXYL =
-PO4 PHOSPHORYL=
-SH SULFHYDRYL=
-CH3 METHYL=
aldehyde/ketone
acid
alcohol
organic phosphate
disulfide
hydrocarbon
hydroxyl group



Polar group; the bond between the oxygen and
hydrogen is a polar covalent bond.
Makes the molecule to which it is attached
water soluble. Polar water molecules are
attracted to the polar hydroxyl group which
can form hydrogen bonds.
Organic compounds with hydroxyl groups are
called alcohols.
Carbonyl Group


Functional group that consists of a carbon atom doublebonded to oxygen (-C=O)
Is a polar group. The oxygen can be involved in hydrogen
bonding, and molecules with his functional group are water
soluble.

Is a functional group found in sugars.

Aldehyde = carbonyl group on end carbon of chain

Ketone =- carbonyl group attached to internal carbon
Carbonyl Group
Carboxyl Group



Functional group that consists of a carbon atom which is both doublebonded to an oxygen and single-bonded to the oxygen of a hydroxyl
group (-COOH).
Carboxyl group
Is a polar group and water soluble. The covalent bond between oxygen
and hydrogen is so polar, that the hydrogen reversibly dissociates as
H+. This polarity results from the combined effect of the two
electronegative oxygen atoms bonded to the same carbon.
Since it donates protons, this group has acidic properties. Compounds
with this functional group are called carboxylic acids.
amino group




Functional group that consists of a nitrogen atom bonded
to two hydrogen atoms & to the carbon skeleton (—NH2).
Is a polar group and soluble in water.
Acts as a weak base. The unshared pair of electrons on
the nitrogen can accept a proton, giving the amino group a
+1 charge.
Organic compounds with this
function group are called amines.
Sulfhydryl group



Functional group which consists of an atom of sulfur bonded
to an atom of hydrogen (—SH).
Stabilize the structure of proteins. (Disulfide bridges of
proteins)
Organic compounds with this functional group are called
thiols.
Phosphate group


Functional group which is the dissociated form of phosphoric
acid (H3PO4).
Loss of two protons by dissociation leaves the phosphate group
with a negative charge.

Has acid properties since it loses protons.

Polar group and soluble in water.

Organic phosphates are important in cellular energy storage and
transfer
methyl group

methyl group (—CH3)

Non-polar hydrophobic functional group
Polymerization




Organic compounds are formed by polymerization
Large carbon compounds are built up from
smaller simpler molecules called MONOMERS
Monomers can bind to one another to form
complex molecules known as POLYMERS
Macromolecules are very large polymers
Polymerization
Building and Breaking Polymers




Monomers link to form polymers through a chemical reaction
called a CONDENSATION REACTION or Dehydration
Synthesis
Water is released during the formation of polymers
The BREAKDOWN of some complex molecules, such as
polymers, occurs through a process known as HYDROLYSIS
Hydrolysis is the reversal of a condensation reaction
Dehydration Synthesis
Hydrolysis
4 Groups of Organic Compounds Found in Living Things

Carbohydrates (C-H-O 1:2:1 ratio)

Lipids (C-H-O)

Proteins (C-H-O-N)…sometimes S

Nucleic Acids (C-H-O-N-P)
Carbohydrates

MONOSACCHARIDES are simple sugars in a 1:2:1
ratio

GLUCOSE

GALACTOSE = sugar found in milk

FRUCTOSE = fruit sugar

Chemical composition (C6 H12 O6)
Important Monosaccharides
Glucose
ISOMERS
Isomers
Are molecules with the same molecular
formula but different structures and
properties
3 types
 Structural
 Geometric
 Enantiomers
Structural isomers

Isomers that differ in the covalent
arrangement of their atoms.
• Number of possible isomers increases as the carbon
skeleton size increases.
• May also differ in the location of double bonds.
Geometric isomers



Isomers which share the same covalent partnerships,
but differ in their spatial arrangements.
Result from the fact that double bonds will not allow
the atoms they join to rotate freely about the axis of
the bonds.
Subtle differences between isomers affects their
biological activity.
Cis – H
on same
side
Trans –
H on
opposite
sides
Cis vs Trans
Enantiomers
(aka Chiral molecules)




Isomers that are mirror images of each other.
Can occur when four different atoms or groups of atoms
are bonded to the same carbon (asymmetric carbon).
There are two different spatial arrangements of the four
groups around the asymmetric carbon. These arrangements
are mirror images.
Usually one form is biologically active and its mirror image
is not.
Enantiomers
L isomer
D isomer
L & D are used to describe left & right isomers
From the latin “Levo & dextro”
Enantiomers cannot be superimposed on each other
Structure determines function
(L-Dopa works, D-Dopa doesn’t)
Carbohydrates

DISACCHARIDES consist of two single
sugars(monosaccharides) linked together
by glycosidic linkage (Dehydration
synthesis)

Lactose = Milk sugar

Sucrose = Table sugar
Carbohydrates
Carbohydrates





POLYSACCHARIDE is a carbohydrate made of long chains of
sugars (3 or more monosaccharides)
Starch - Plants convert excess sugars into starches for long-term
storage (Alpha linkage)
Glycogen -Animals store glucose in the form of polysaccharide
glycogen in the liver and muscles to be used as quick energy
Cellulose -a structural polysaccharide contained in the cell walls
of plants (ß linkage)
Chitin – a polysaccharide found in the cell walls of fungi and the
exoskeletons of insects and arthropods
Starch
Glucose
Lipids





Lipids are large, NONPOLAR organic
molecules that DO NOT dissolve in water
Oils, fats, waxes, and steroids are lipid based
Lipid molecules use less OXYGEN than
carbohydrates to store energy efficiently
Used in biological membranes and as chemical
messengers
Monomers – Fatty acids & Glycerol
Lipids


UNSATURATED FATS are a liquid at
room temperature (OILS).
Double bonds can have hydrogen added
SATURATED FATS are solid at room
temperature NO double bonds
Saturated or Unsaturated Fatty Acids
Stearic acid
Oleic acid
Liquid at room temp
Solid at room temp
Lipids - Saturated and unsaturated
Triacylglycerol
Phospholipids – Make up the cell membrane
Hydrophilic vs Hydrophobic
Hydrophilic = Water loving
Hydrophobic = Water fearing
Proteins



Chemical composition C-H-O-N-S
Proteins are made up of smaller monomers called AMINO ACIDS
Amino Acids differ ONLY in the type of R group they carry
Amino acids composed of 3 parts
1.
Amino Group
2.
Carboxylic group
3.
R-group (Makes 20 different amino acids)
Peptide Bonds –
link amino acids
20 Amino Acids
Proteins





Each protein has a specific, and complex shape
Different shapes allow proteins to perform different
functions
Two Amino Acids bond to form a DIPEPTIDE during a
condensation reaction (2 Amino Acids form a covalent
bond, called a PEPTIDE BOND)
Amino Acids can bond to each other one at a time,
forming a long chain called a POLYPEPTIDE.
Proteins are composed of one or more polypeptides.
Protein Conformation
Primary Structure – sequence of amino acids
Secondary structure – Folding and coiling due
to H bond formation between carboxyl and
amino groups of non-adjacent amino acid. R
groups are NOT involved.
Tertiary structure – disulfide bridges, ionic
bonding, or h-bonding of R-groups
Quaternary structure – 2+ amino acid chains
R- group interactions, H bonds, ionic
interactions
Primary Structure
Secondary Structure
Tertiary
Structure
Quaternary
Structure
Chaperonins
Amino Acids

Amino acid structure: NH3 - C - COOH

Amino acids differ due to the R group

The structure of the R-group determines the
chemical properties of the amino acid
Amino Acids
The polar uncharged amino acids are
hydrophilic & can form h-bonds
 Serine
 Threonine
 Glutamine
 Asparagine
 Tyrosine
 Cysteine
Amino Acids
The nonpolar amino acids are hydrophobic and are
usually found in the center of the protein. They also
found in proteins which are associated with cell
membranes.









Glycine
Alanine
Valine
Leucine
Isoleucine
Methionine
Phenylalanine
Tryptophan
Proline)
Amino Acids
The electrically charged amino acids have
electrical properties that can change depending
on the pH.
Aspartic Acid
 Glutamic Acid
 Lysine
 Arginine
 Histidine

Amino Acids
The electrically charged amino acids (Aspartic
Acid, Glutamic Acid, Lysine, Arginine, and
Histidine) have electrical properties that can
change depending on the pH.
 Cysteine can form covalent disulfide bonds
 Proline had a unique structure and causes kinks in
the protein chain
When two amino acids are joined together, the bond
formed is called a peptide bond


Denaturing of Protein
Denaturing of Protein


Transfer protein from aqueous solution to an
organic solvent (chloroform)
Any chemical that disrupts h-bonds, ionic
bonds, & disulfide bridges

Excessive heat

Changes in pH
Enzymes
Act as CATALYSTS that can speed up some reactions
by more than a billion times!
Enzymes work by a physical fit (Lock and Key) between
the enzyme molecule and its SUBSTRATE, the reactant
being catalyzed.
Enzymes reduces the activation energy for the chemical
reaction to occur.
After the reaction, the enzyme is released and is
unchanged, so it can be used many times
Enzyme names end in -ase
Enzyme & Substrate fit like
a lock & key (Shape specific)
pH or temperature can
change the active site
shape on any enzyme
Active site is where the
reactants bind to the enzyme
Activation Energy
The energy require to start a reaction is called Activation Energy
Nucleic Acids
Nucleic Acids
•RNA and DNA made of nucleic acids
•C-H-O-N-P atoms
•Polymers of nucleotides
•Nucleotides consist of a 5-carbon sugar, a
phosphate group, and a nitrogenous base.
•Store and transmit genetic information
Nucleic Acids