Download Organic Chemistry for Biology

Organic/BioChemistry
Inorganic
vs.
Organic
Inorganic chemistry:
• compound which usually
does not contain carbon
AND hydrogen
–Ex. O3, NaCl, H2O, CO2
Inorganic Chemistry:
• Compounds that do not
need to contain:
–Carbon: C
AND
–Hydrogen: H
Biochemical Compounds
A.K.A Organic chemistry:
• compounds usually found in Living
or once living organisms
• contains both Carbon and Hydrogen
• other elements found in living things
are: C, H, O, N, Phosphorous
• Carbon = “element of LIFE”
Carbon: The element of LIFE
Biochemical Compounds
Types of Organic Compounds
found in all living things include:
1. Carbohydrates
KNOW
2. Lipids
THESE!!!
3. ProteiNs
4. Nucleic Acids
Organic Chemistry:
• Organic Compounds (Carbs,
lipids, Nucleic Acids, and
Proteins) are chemically bonded
together or broken down by:
– Dehydration Synthesis:
– Hydrolysis:
Dehydration Synthesis:
• process of joining (bonding)
molecules to form large molecules
called: MACROMOLECULES
• macromolecules are formed by
REMOVING WATER!!
– Hence the name dehydration…
as in dehydrate 
Hydrolysis:
• process of breaking down
macromolecules into smaller
molecules called MONOMERS
• smaller molecules are formed
by ADDING WATER!
PROCESS
STARTS
WITH ...
dehydration
synthesis
small molecules
(monomers)
hydrolysis
water &
macromolecules
ENDS
WITH ...
large
molecules &
water
(macromolecules)
small
molecules
(monomers)
Ex.
growth
digestion
• dehydration synthesis and hydrolysis
Macromolecules
• Smaller organic molecules join together
to form larger molecules
– macromolecules
• 4 major classes of
macromolecules:
– carbohydrates
– lipids
– proteins
– nucleic acids
Polymers
• Long molecules built by linking repeating
building blocks in a chain
– monomers
• building blocks
• repeated small units
H 2O
– covalent bonds
HO
H
HO
H
Dehydration synthesis
HO
H
How to build a polymer
• Synthesis
– joins monomers by “taking” H2O out
• one monomer donates OH–
• other monomer donates H+
• together these form H2O
– requires energy & enzymes
HO
H 2O
H
Dehydration synthesis
HO
H
enzyme
Condensation reaction
HO
H
How to break down a polymer
• Digestion
– use H2O to breakdown polymers
• reverse of dehydration synthesis
• cleave off one monomer at a time
• H2O is split into H+ and OH–
– H+ & OH– attach to ends
– requires enzymes
– releases energy
H2O
HO
enzyme
H
Hydrolysis
Digestion
HO
H
HO
H
Carbon Compounds - Concept Map
Building blocks of all life
Carbon
Compounds
include
Macromolecules
Carbohydrates
Lipids
Nucleic acids
that consist of
Sugars and
starches
Proteins
Building Blocks
Fats and oils
Nucleotides
Amino Acids
which contain
Elements
Carbon,
hydrogen,
oxygen
Carbon,
hydrogen,
oxygen
Carbon,hydrogen,
oxygen, nitrogen,
phosphorus
Carbon,
hydrogen,oxygen,
nitrogen,
Macromolecules ID lab
Organic Compounds Cont…
Carbohydrates:
• Made of the elements Carbon,
Hydrogen & Oxygen
• Usually the Carbon, Hydrogen
and Oxygen have a 1:2:1 ratio
• Used in organisms for quick
energy
Carbohydrate:
a. Monosaccharide:
–simple sugar (1- ring)
– “ose” ending = sugar
–ex. Fructose, glucose:
CarbohydrateMonosaccharide:
Carbohydrates:
b. Disaccharide
• 2 simple sugars are
chemically bonded together
• ex. Sucrose, lactose
Carbohydrate- Disaccharide:
Carbohydrates:
C. Polysaccharide:
• many sugars chemically bonded
together
• form long chains = polymers
• are macromolecules (lg molecules)
• ex. Starches, Chitin, and cellulose
(found in fruits and veggies)
CarbohydratePolysaccharide
4
1
2
3
Elements Present
Used by
organisms
for ...
carbon
hydrogen Quick
oxygen energy
C:H:O = 1:2:1
always!
Building
Blocks
(Monomers)
Related Terms &
Info
Disaccharide:
2 connected
monosacchar
monosaccharide
ide
(ex: maltose)
(simple
sugars)
ex: glucose
Polysaccharide
3 or more
connected
monosaccharide
(ex: starch,
glycogen,
chitin,
cellulose)
Organic Compounds cont.
Lipids:
• Fats, cholesterol, waxes, oils
• Lipids + H2O3 fatty acids +glycerol
• H to O ratio is much greater than
2:1
• Do not EMULSIFY - break apart in
H2O
• Used as Stored energy in
organisms
3 Fatty Acids and a Glycerol:
G
L
1
Y
C
E
2
R
O
L
3
Lipids
• 2 classifications of fats:
1.Saturated fats
2.Unsaturated fats (which
includes polyunsaturated fats)
Lipids:
• Saturated fats:
• solid at room temperature
• linked to cardiovascular
disease
• have many H-C bonds
Lipids:
Unsaturated fats:
• not solids at room temp
• not associated with cardiovascular
disease
• have 1 or more double C-C bonds
• polyunsaturated fats have more
than 1 double or triple C-C bond
Used by
Elements
Organisms for
Present
...
Carbon
Hydrogen
Oxygen
ONLY !
There is
no
specific
H:O ratio.
Stored Energy
Structure
(important part
of cell
membranes)
Building
Blocks
of
Lipids
3 Fatty Acids
1 glycerol
Related Terms & Info
saturated fat = C-C bonds
are all single bonds
unsaturated fat = contain at
least one double or triple CC bond
STOP!!!
CK POINT
Topic: “chemistry of life”:
1. What elements are found in
carbohydrates and lipids?
2. Explain 2 differences between
carbohydrates and lipids.
3. Describe the function for each?
4. How are monomers bonded together?
Broken apart?
Organic Compounds:
NUCLEIC ACIDS: DNA & RNA
We will save the nitty, gritty
details of DNA & RNA for later in
the year (Genetics). But for
now, you should know there
functions & basic structure, and
how DNA compares to RNA.
DNA & RNA
DNA & RNA are polymers (many units)
--- long chains of smaller repeating
units.
The repeating unit (monomers) in
nucleic acids is called a nucleotide.
nucleotide remember this !
nucleotide
1. A phosphate
group
2. The
carbohydrate…
(see the “ring”?)
3. A nitrogen base:
Adenine
Thymine
Guanine
Cytosine
What elements make
up a nucleotide?
Repeating Units of Nucleotides
Nucleotide
Nucleotide
How many nucleotides are
in the nucleic acid above?
Nucleic Acid: DNA
Nucleic
Acid:
RNA
Nucleic Acids:
DNA
RNA
FULL NAME
Deoxyribonucleic acid
Ribonucleic acid
BASIC STRUCTURE
2 long twisting strands
of nucleotides in the
form of a "double
helix"
1 single strand of
nucleotides
NUCLEOTIDE SUGAR
Deoxyribose
Ribose
NITROGENOUS BASES
guanine (G)
cytosine (C)
adenine (A)
thymine (T)
LOCATION IN A CELL
nucleus
(the chromosomes)
FUNCTION
the hereditary
material
of a cell, directs &
controls cell
guanine (G)
cytosine (C)
adenine (A)
uracil (U)
nucleus, in the
cytoplasm, & at the
ribosomes
involved in protein
synthesis
Organic Compounds:
ProteiNs'
• Contain the elements: Carbon,
Hydrogen, Oxygen and Nitrogen
• take the shape of coils, helixes and
globules
• ex. Collagen, hormones, muscle
tissue, enzymes, Hemoglobin
Structure
of
ProteiNs:
ProteiNs:
Made up of basic building
blocks MONOMERS
called:
AMINO ACIDS!!!!
Amino Acids:
• are the structural units
(monomers) of protein
• bond together to form proteins
• The bond between amino
acids are called
Peptide bonds
Amino Acids:
• The order/sequence and size of
amino acid determines the
protein made
• 2 amino acids bonded together =
dipeptide
• amino acids form long chains
called a polypeptide chains
Elements Present
carbon
hydrogen
oxygen &
NITROGEN
(sometimes
Sulfur)
monomers
of Proteins:
Used by
organisms for
...
muscles
enzymes
antibodies
hormones
Pigments
Hemoglobin
AMINO ACIDS!!!
Related Terms &
Info
peptide bond =
the bond that
holds amino
acids together
in protein
molecules
dipeptide =
2 connected
amino acids
polypeptide =
3 or more
connected
amino acids
STOP!!!
CK POINT
Topic: “NA and ProteiNs”:
1. What are 2 types of Nucleic Acids?
2. What is the “monomer” of a nucleic
acid?
3. Describe the primary functions of
nucleic acids.
4. Identify elements found in ProteiNs.
5. What is the monomer for ProteiNs?
Group Activity:
• Group leaders to get a marker
• As a group, and when instructed, you
will go to a poster in a designated area
in the room
• When the timer begins WRITE 1
ACCURATE FACT
• Wait until instructed, move to the next
poster.
• As you move to each poster, read each
statement then add an additional fact
Enzymes:
• Are forms of protein!!!!!!!!!!!!!
• Usually end in “ASE”
• Are not changed during a
chemical rxn (a substance
affects a reaction w/o being
changed is called a
CATALYST)
Enzymes:
• Are organic catalysts :
–Control the rate of rxn within cells
–Catalysts allow rxns to occur at a
faster rate
• Are used over and over
• For each chem. rxn, there is a
specific enzyme to initiate the rxn
HOW ENZYMES WORK:
• Substrate– the substance the enzyme acts upon
• Enzyme Active– the region on the enzyme
• Substrate and Enzyme active site are
specific to each other.
• The substrate fits the enzyme active
site like a puzzle called: enzymesubstrate complex
HOW ENZYMES WORK:
• When the enzyme and
substrate come together:
• The enzyme:
–may cause 2 molecules to
join together
–may cause bonds to break
Enzyme-Substrate Complex
Enzyme-Substrate Complex
Factors Affecting Enzyme Action:
1. Concentration and surface area
2. Temperature
3. pH
4. Co-enzymes
Factors Affecting Enzyme Action:
• Concentration – determine rxn rates.
Sometimes adding more concentration has little
or no effect
Temperature– slowly raising the temp.
increases rate. However, at higher temps.,
the enzyme can breakdown called
Denaturation
•temp and enzymes
• pH level – specific to the enzyme
stomach acidic, intestines slightly
basic
• Presence of coenzymes (vitamins)
allows an enzyme to perform
Carbon Compounds
4 groups of carbon compounds found in living things are
carbohydrates, lipids, nucleic acids, and protein.
Living things use carbohydrates as their main source of
energy. Plants and some animals also use carbohydrates
for structural purposes.
Lipids can be used to store energy. Some lipids are
important parts of cell membranes and waterproofing.
Nucleic acids store and transmit hereditary, or genetic,
information.
Proteins:
• control the rate of reactions and regulate cell processes.
• build tissues such as bone and muscle. Others transport
materials or help to fight disease.
Chemical Reactions and Enzymes
Chemical rxns always involve the
breaking of bonds in reactants and
the formation of new bonds in
products.
Cells use enzymes to speed up
chemical reactions that take place
in cells.
Enzymes:
“Helper” Protein
molecules
2009-2010
Flow of energy through life
• Life is built on chemical reactions
Chemical reactions of life
• Processes of life
– building molecules
• synthesis
+
– breaking down molecules
• digestion
+
Nothing works without enzymes!
• How important are enzymes?
– all chemical reactions in living organisms
require enzymes to work
enzyme
• building molecules
– synthesis enzymes
+
• breaking down molecules
We can’t live
without enzymes!
– digestive enzymes
– enzymes speed up reactions
• “catalysts”
enzyme
+
Examples
 synthesis
+
enzyme
 digestion
enzyme
+
Enzymes are proteins
• Each enzyme is the specific helper to
a specific reaction
– each enzyme needs to be the right shape for
the job
– enzymes are named for the reaction
they help
Oh, I get it!
They end
in -ase
•
•
•
•
sucrase breaks down sucrose
proteases breakdown proteins
lipases breakdown lipids
DNA polymerase builds DNA
Enzymes aren’t used up
• Enzymes are not changed by the reaction
– used only temporarily
– re-used again for the same reaction with other
molecules
– very little enzyme needed to help in many
reactions
substrate
active site
product
enzyme
It’s shape that matters!
• Lock & Key model
– shape of protein
allows enzyme &
substrate to fit
– specific enzyme
for each specific
reaction
2
1
3
Enzyme vocabulary
• Enzyme
– helper protein molecule
• Substrate
– molecule that enzymes work on
• Products
– what the enzyme helps produce from the
reaction
• Active site
– part of enzyme
that substrate
molecule fits into
What affects enzyme action
• Correct protein structure
– correct order of amino acids
– why? enzyme has to be right shape
• Temperature
– why? enzyme has to be right shape
• pH (acids & bases)
– why? enzyme has to be right shape
Order of amino acids
• Wrong order = wrong shape = can’t do its job!
chain of
amino acids
DNA
folded
protein
right shape!
folded
protein
chain of
amino acids
DNA
wrong shape!
Temperature
• Effect on rates of enzyme activity
– Optimum temperature
• greatest number of collisions between
enzyme & substrate
• human enzymes
– 35°- 40°C (body temp = 37°C)
– Raise temperature (boiling)
• denature protein = unfold = lose shape
– Lower temperature T°
• molecules move slower
• fewer collisions between enzyme &
substrate
Temperature
reaction rate
human
enzymes
37°
temperature
What’s
happening
here?!
pH
• Effect on rates of enzyme activity
– changes in pH changes protein shape
– most human enzymes = pH 6-8
• depends on where in body
• pepsin (stomach) = pH 3
• trypsin (small intestines) = pH 8
pH
intestines
trypsin
What’s
happening
here?!
reaction rate
stomach
pepsin
0
1
2
3
4
5
6
pH
7
8
9
10 11
12 13 14
For enzymes…
What matters?
SHAPE!
2009-2010