Organic Chemistry
Chapter 20
What is organic chemistry?
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The name implies that it is the chemistry
of living things
That is partially true
Organic chemistry- the study of carbon
containing compounds (*with a few
exceptions-like CO2)
All living things are carbon based.
However, carbon is not only involved in
living things.
Why does carbon get its own
class of chemistry?
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Since carbon can form 4 covalent bonds
it has a large number of possibilities for
structures.
It also readily bonds with other carbon
atoms forming chains or rings, which
gives it billions of stable structures.
Also, living things continuously do
“experiments” making new carbon
compounds.
…because there are so many
useful carbon compounds
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Chemistry is basically split into organic
and inorganic.
Carbon chemistry and everything else, and
the everything else didn’t really become
important until recently.
Since living things naturally make all of
these carbon compounds, man found
several uses for them without having to
manufacture them.
Just a small sampling
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Some carbon compounds include
DNA, diamonds, natural gas, aspirin, octane,
polyester, freon, asphalt…
Caffeine, carbohydrates , plastics, rubber,
acrylic, vinyl, graphite, proteins, propane…
Vinegar, citric acid, leather, TNT, alcohol,
ibuprofen, soot, cellulose, butane etc.
There are more known compounds of carbon
than there are for all other elements
combined!
Allotropes of pure carbon
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Allotrope- Different molecular structure of
molecules containing the same atom
Diamonds- dense tetrahedral network
Graphite- layers laying on top of each other
Buckminsterfullerene or buckyball ~ found
in soot ( a sphere)
Simplest organic compounds
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Hydrocarbons- compounds containing
carbon and hydrogen
Alkanes- straight chain hydrocarbons
with all single bonds
Organic molecules follow their own
system of nomenclature (naming)
Alkanes get the suffix “-ane”
Naming and drawing organic
compounds
Root words
Meth
# of C
atoms
1
Hex
# of C
atoms
6
Eth
2
Hept
7
Prop
3
Oct
8
But
4
Non
9
Pent
5
Dec
10
So for example
H HHH
H-C-C-C-C-H
H HHH
butane
H HHHHHHH
H-C-C-C-C-C-C-C-C-H
H HHHHHHH
octane
H HH
H
H-C-C-C-H
H-C-H
H HH
H
propane
methane
Molecular Formulas
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Alkanes always have the molecular
formula of:
CxH2x+2
2 H on every C except the end, they get 3
HexaneC6H14 molecular formula
HHHHHH
Lewis Dot, or
H-C-C-C-C-C-C-H
Structural Formula
HHHHHH
Skeleton Formulas
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Drawing Lewis Dot structural formulas for
long organic compounds can get rather
tedious.
So organic has shortened it
They don’t write the C’s or the H’s
You draw a jagged line, at each corner
there is a Carbon
Assume all extra spaces are filled with H
For Example
Heptane, C7H16
HHHHHHH
H-C-C-C-C-C-C-C-H
HHHHHHH
=
Nonane, C9H20
HHHHHHHHH
H-C-C-C-C-C-C-C-C-C-H
HHHHHHHHH
=
Isomers
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Isomers- compounds with the same
molecular formula but different structural
formulas
Different structural formulas mean it has
different properties
Butane is the first alkane with a possible
isomer
HHHH
=
H-C-C-C-C-H
HHHH
H H H
or
H-C- C - C-H
H HCH H
Both are C4H10
H
Naming Isomers
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Name the longest chain possible.
As a prefix, name the chain attached
with –yl on the end and give the
number of the carbon atom it is
attached to 6
2
1
4
3
5
7
Longest Chain
3 ethyl heptane
•It could also be 5 ethyl heptane if you started numbering
from the other side, when given an option always go with the
Lower number!!!
Name this molecule
And give its molecular formula
4 ethyl octane
C10H22
4 propyl decane
C13H28
Cyclic Hydrocarbons
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A hydrocarbon that is a ring instead of
a chain. To name it, give it the prefix
“cyclo-”
Molecular Formula
Subtract 2 H from CxH2x+2
CxH2X
cyclobutane
HH
H-C-C-H
H-C-C-H
HH
C4H8
Name the following compounds
and give their formula
cyclohexane
C6H12
cyclooctane
C8H16
cycloheptane
C7H14
cyclodecane
C10H20
Name and give the formula
Methyl cyclohexane
C7H14
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Alkenes
Contain a double bond
They get the suffix “-ene” and the
number of the carbon atom the double
bond is on (lowest number)
Molecular formula
Subtract 2 H for each double bond from
Skeleton fomula
CxH2x+2
1 butene
H
H H
H-C=C-C-C-H
H H H
C4H8
Alkynes
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Contain a triple bond
They get the suffix “-yne” and the
number of the carbon atom the triple
bond is on. Molecular formula
subtract 4 H for each triple bond from
CxH2x+2
Skeleton fomula
H
H H
H
H H
2 pentyne
H-C-C=C-C-C-H
C5H8
Name and give the formula for
these compounds
2 hexene C6H12
Cyclopentane
C5H10
3 methyl nonane C10H22
ethyne (commonly known as acetylene)
C2H2
3 methyl 1 pentene
C6H12
Name and give the formula for
these compounds
2 heptene C7H14
Cyclopentene
C5H8
cyclopropane
C3H6
1 butyne
C4H6
3 ethyl 1 hexene
C8H16
Doubles and triples
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If you have two of the same thing put
“di” in front of it
If you have three of the same thing put
“tri” in front of it
Examples
2,3 hexadiene
C6H10
3,4,4 trimethyl heptane
C10H22
Multiple groups on a chain
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Name each and put them in
alphabetical order
3, 4 diethyl 2 methyl
1 heptene
C12H24
Functional Groups
Things attached to carbon chains
Functional Groups
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Atoms other than hydrogen or carbon
covalently bonded to a carbon atom in
an organic molecule.
Most commonly oxygen, nitrogen, or
the halogens.
The presence of a functional group
drastically changes the chemical
properties of a molecule.
Different Functional groups
with a 2 carbon chain
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Ethane- gas (found in natural gas)
Ethanol- grain alcohol (drinkable)
Ethanoic acid- vinegar
Diethyl ether- starting fluid
Chloro fluoro ethane (CFC’s used as
refrigerants)
Ethanal- foul smelling liquid (similar to
formaldehyde)
Halogenated Hydrocarbons
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Hydrocarbons with halogens attached
Before the main chain name the halogen
as either fluoro, chloro, bromo or iodo
and give its number
For each halogen subtract 1 H
Cl
Cl
1,3-dichloro cycloctane
C8H14Cl2
Practice
F
2 fluoro 1 butene
C4H7F
Br
Br
2,5-dibromo 3-ethyl
4-methyl heptane
C10H20Br2
Alcohols
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Hydrocarbons with an –OH attached
To name it, give it the suffix –(an)ol and the
number the OH is attached to
Normally you subtract one H from the main
group and put an OH on the end (to signify it is
an alcohol)
Ethanol
C2H5OH
OH
C3H7OH
H
O
2 propanol
Commonly
Isopropanol or
Rubbing alcohol
Aldehydes
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Hydrocarbons with a =O on the outer
edge of the chain
(most have a foul stench, like
formaldehyde or methanal)
To name it add the suffix “–al”
For the formula subtract 2 H and add
=O
O
O=
hexanal
C6H12O
octanal
C8H16O
Ketones
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Hydrocarbons with a =O not on the
edge of the compound
To name it add the suffix “–one”
For the formula subtract 2 H and add O
O=
cyclopropanone
C3H4O
O=
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3-nonanone
C9H18O
Carboxylic Acid
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Hydrocarbons with a –COOH group
attached
To name it give it the suffix “–oic acid”,
the C in the group does count
Subtract one C one H and add COOH
This group looks like…
-C=O
O
H
Pentanoic acid
=O
O
H
C4H9COOH
Everything so far…
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Alkanes, alkenes, and alkynes
Isomers, halogenated and cyclic
-OH
*R means any carbon chain
Alcohols
Carboxylic Acids
R-OH
R-C=O
-ol
-oic acid
-al
Ketones
R-C-R
=O
Aldehydes
on the end
R=O
-one
2,4 dichloro 3 methyl
1 cyclobutanone
C5H6Cl2O
2, 3 dimethyl
hexanoic acid
C7H15COOH
3 bromo 2, 2 diethyl 1 hexanal
C10H19BrO
2, 2 dibromo 1 cyclohexanol
C6H9Br2OH
Large Molecule (ATP)
Petroleum Products
What is petroleum?
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Also known as crude oil
It is a thick black sludge
It comes from ancient plant and animal
life long since buried and kept under
extreme pressure for millions of years.
It is composed of countless different
organic compounds.
What is made from petroleum
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Gasoline, kerosene, and rocket fuel
Most plastics and other polymers
(elastomers and fibers)
Synthetic rubbers and fabrics
Most pharmaceutical drugs
And several other things
If we run out of petroleum it would have
a devastating effect on us
Petroleum is separated in a
fractionating tower
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Fractionating Tower- structure where
crude oil is heated to boiling and
different structures are collected at
different temperatures
There are several
other things pulled
out that I didn’t include.
Fractionating Tower
Natural Gas (doesn’t
Condense)
Gasoline condenses
Kerosene condenses
Crude oil in
Heat
Asphalt never
vaporizes
One compound that comes
from petroleum
Benzene
Which changes to…
And back again
constantly
It also is drawn
as
Double bonds
Are a little shorter
Than single bonds
But in benzene all
Bonds are the
Same length.
Compounds that contain benzene are
called aromatic
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Aspirin (acetyl salicylic acid)
O-H
O
O=
O
Compounds that contain benzene are
called aromatic
Trinitro Toluene (TNT)
O2N-
- NO2
O2N-
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A few other aromatics
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Vinyl, napthalene (found in moth balls),
acetaminophen, penacillin
Benzene is an extremely common organic
compound
The fact that the double bonds flip back and
forth (called resonance) give it a very stable
structure
IUPAC vs. Common and
copyrighted names
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Several compounds have names similar
to what we went over but slightly
different.
Common names for several compounds
have been around for centuries and are
still used (acetic acid, formaldehyde)
Several other names were copyrighted
for sale (acetaminophen and
polypropylene)
To burn or to build?
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Burning hydrocarbons normally
produces carbon dioxide.
As our fossil fuels use has increased, so
have our CO2 levels.
Petroleum products are used to produce
several fuel sources as well as
polymers.
Polymerization
A functional group we did not
cover…
O=
the water came
from…
R-C-O-H
R-C-O-R
+
H-O-R
It is very similar to carboxylic acid
~In fact it is formed by a
carboxylic acid and an alcohol
R-C-O-R
O=
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Esters- a functional group in the middle
of a carbon chain; R-COO-R
It gets the suffix –oate (you won’t have
to name these!)
O=
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+ H-O-H
Now if you have a few
compounds that have both a
Carboxylic acid end
H-O- R-C-O- R-C-O-H
They could form an ester that looks like…
But the compound still has a…
And an alcohol end
Carboxylic acid end
O=
O=
+
H-O- R-C-O-H
O=
O=
+an alcohol end
H-O- R-C-O-H
+ H-O-H
So it could repeat this process thousands even millions of
times and make a whole bunch of…
esters
poly
Of course the scientific prefix for “whole bunch of” is
This is the basis for a polymer
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Polymer-A large chain-like molecule
composed of smaller molecules linked
together
The smaller units it is made up of are called
monomers
monomers need to have ends that can join
together (or stack on top of one another)
Like an extension cord or markers
So you could (infinitely) join them together
to make a large polymer
Polymers can get very large
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common polymers have a molecular
mass of around 50,000 g/mol
The first molecules seen under a
microscope were polymer chains
Common polymers include things like…
Nylon, Kevlar©, latex, PVC, rubber,
acrylic, vinyl, Deoxyribonucleic acid
(DNA) and carbohydrates
Piece of DNA
Polymers are put into three
classes
Elastomers-
Fibers
Plastics
Polymers that can be
stretched to 10x their
normal size and
return to their
original shape
Polymers that
cannot stretch
or be reshaped
once formed
Polymers that can
stretch and flex
more than fibers
but less than
elastomers
Elastic
Nylon and
Acrylic
Polypropylene
polystyrene
and PVC
(polyvinyl chloride)
Biochemistry
Chapter 21
Elements in the body
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About 96% of the mass of the human
body is made up of 4 elements
Oxygen 65%
carbon 18%
hydrogen 10%
nitrogen 3%
The only other elements that make up
a significant portion are:
Calcium 1.5%
Phosphorus 1.2%
Water
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Of course, the vast majority of the oxygen is
found in water.
Water is essential for life.
It is what all chemical reactions in the body
occur in.
However, water is not considered a
biochemical or organic compound.
Organisms are not bonded to water, instead
water is contained within the organism.
If we remove water…
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Then the human body is made up of
37% carbon
30% oxygen
18% hydrogen
6.2% nitrogen
3.1% calcium
2.5% Phosphorus
Elements Essential to Life
The green elements are
called “trace” elements
because they make up
less than .05%.
Uses of elements
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Carbon is a requirement for all
biochemical compounds
Nitrogen is needed for proteins
Iron is needed for using oxygen
http://www.mii.org/periodic/LifeElemen
t.html
Biochemical Compounds
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These elements are bonded together to
form different biochemical compounds.
Biochemical compounds include:
Proteins
Carbohydrates
Nucleic acids
Lipids
Proteins
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Proteins are polymers made up of
monomers called amino acids.
Amino acids have a carboxylic acid end
and an amine (NH2) end.
Bonding an amine group and carboxylic
acid is called a peptide bond.
Amino acid to protein
+
O=
H-N-R-C-O-H
H-
H-N-R-C-O-H
O=
Amino acid
H-
Amino acid
Protein
Peptide bond
Amine Carboxylic
Group Acid
O=
O=
H-
R is any carbon
chain
H-
H-N-R-C- N-R-C-O-H
This has to repeat at
+ H-O-H
least 50x for it to be a protein
Otherwise it is just a polypeptide.
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Amino
acids
Proteins
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A protein is at least 50 amino acids
linked together.
This makes proteins very large
molecules.
Most have a molar mass between 60001,000,000 g/mol.
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Protein Structure
Proteins naturally fold into distinct 3-D
structures.
It is based off of a few different aspects.
Primary structure of proteins is the amino
acid sequence.
3 letter or one letter abbreviations are used
for each amino acid.
gly-cys-met-aspGlycine-cytoseine-methionine-aspartic acid-
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Secondary structures
The secondary structure is local structures
formed throughout the molecule.
Alpha helix, beta pleated sheet, and turns
are common formations.
Alpha helix is when the molecules start to
spiral around.
Beta pleated sheet is when the molecules
take a jagged back and forth formation.
Turns are when the chain flips directions.
Triose Phosphate Isomerase
Alpha helix
Turns
Beta pleated sheet
Tertiary Structure of proteins
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Tertiary structure- the overall structure of
the protein.
This greatly effects the function of
the protein.
Enzymes are proteins that catalyze certain
reactions.
Enzymes work at specific spots on an
molecule.
Other functions of proteins
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Structure- Tendons, bones, skin,
cartilage, hair, are mainly protein
Movement- Muscles are mainly protein
Transport- hemoglobin, a protein,
carries oxygen to cells from the lungs
Protection- antibodies that fight off
foreign substances are proteins
Control- many hormones such as
insulin are proteins.
Carbohydrates
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Carbohydrates are second class of
biochemical compounds.
They are commonly polymers made up
of monomer units called simple sugars
or monosaccharides.
Simple sugars are ketones or aldehydes
with several –OH (hydroxyl) groups
attached.
D Glucose
Bonding
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These sugars normally bend around to
form rings.
Then they link together.
Two sugars bonded together are called
a disaccharide.
Sucrose (common table sugar) is a
disaccharide of glucose and fructose.
Sucrose
Polysaccharides
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Polysaccharides are large molecules made
of many simple sugars.
Starch is the main fuel reservoir in plants.
Cellulose is the main structural component
for plants.
Both are polysaccharides, but because of
different types of bonds, humans are only
capable of digesting starch not cellulose.
Glycogen
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Animals, and humans, store
carbohydrates as glycogen.
These are large polysaccharide
molecules that are broken down into
simple sugars as you need them.
Carbohydrates Uses
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In animals, carbohydrates are used as
fuel sources.
Plants uses carbohydrates as both a
fuel source and structural support.
Nucleic Acids
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The biochemical polymer that stores and
transmits genetic information in a cell is a
polymer called deoxyribonucleic acid,
DNA.
DNA carries the instructions for making a
specific protein.
Ribonucleic Acid, RNA is needed to
translate and copy DNA.
Nucleic
acids
 Nucleic acids are polymers made up of
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nucleotides.
A nucleotide consists of a nitrogen
containing base, a 5 carbon sugar, and a
phosphate group.
In DNA, the sugar is deoxyribose. In RNA
the sugar is ribose.
Phosphate is PO42The bases are one of 5 organic compounds
Deoxyribose
Ribose
Nitrogen Bases
DNA Structure
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DNA forms a double helix structure.
That is two complementary strands wrapped around
one another is a spiral fashion.
The sugar and phosphate form the backbone, while
the bases from the rungs.
The strands are complimentary because the bases
must always be matched up.
Adenine and thymine will form a stable hydrogen
bond.
Guanine and cytosine will also form a stable
hydrogen bond.
These bases must always be matched up.
DNA Structure
DNA replication

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When DNA replicates it unwinds and
complimentary bases
Adenine – Thymine
Guanine- Cytosine
Are added to a new daughter strand.
Protein synthesis

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DNA is instructions for building a
protein.
The DNA is decoded by messenger
RNA, mRNA.
mRNA then carries the information to
the ribosome of a cell.
Transfer RNA, tRNA, then adds specific
amino acids in order to build the
protein.
Lipids
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Lipids are biochemical compounds
defined by being insoluble in water.
There are 4 classes of Lipids:
Fatty Acids
Waxes
Phospholipids
Steroids
Fatty Acids
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Fatty acids are carboxylic acid chains.
Vegetable oil and animal fats are
triglycerides.
Triglycerides- esters of glycerol bound to 3
fatty acids
The primary function of triglycerides is
storage of energy.
These fats can be saturated (with hydrogen)
They can also be unsaturated, meaning they
have double bonds decreasing the amount
of hydrogen.
Triglycerides
Phospholipids

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Phospholipids are similar to triglycerides
but only have 2 fatty acids instead of 3.
They also have a phosphate group
attached to the glycerol.
Phospholipids are needed in cell
membranes.
Waxes

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
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Waxes are long carbon chain esters.
They are solids at room temperature.
They provide water proof coatings on
leaves.
They are used in crayons, lip stick,
candles, and a variety of other things.
Steroids

Steroids are a class of lipids that have a
characteristic 4 carbon rings linked together.
Common Steroids

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Cholesterol- starting material for many
steroid molecules. A build up of
cholesterol in the arteries has been linked
to heart attacks
Testosterone- male sex hormone
Progesterone/Estrogen- female sex
hormones
Cortisone- reduces inflammation pain and
swelling