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Organic biochemistry
Chem. 360
Chapter 1
Introduction
M.F
Organic Chemistry
It is the science that studies the properties of the construction, installation and
interactions of chemical compounds containing the element carbon as an essential element
in addition to the other elements . It is rare for the existence of a composite of organic
compounds free of hydrogen component , and can contain any number of other elements ,
such as nitrogen , oxygen, halogens , and sometimes a few phosphorus , or sulfur .
The original definition of organic chemistry was wrongly chosen depending on the
vehicle that this was always going to belong more or less to the vital processes in living
organisms. And subsequently been treated with these compounds which belong to the vital
processes in the branch of organic chemistry called biochemistry
Organic compounds are compounds composed primarily of a
carbon skeleton.
Organic VS. inorganic compounds
Organic compounds
Inorganic compounds
Contain carbon (C) and hydrogen ( H ).
Rarely contain carbon.
Typically larger molecules due to carbons
bonding capabilities.
Usually smaller than organic compounds.
Some dissolve in water, most dissolve in
organic liquids
Usually dissociate in water
Nonelectrolytes
Electrolytes.
What makes Carbon Special? Why is Carbon so different from all the other
elements on the periodic table?
The answer derives from the ability of Carbon atoms to bond
together to form long chains and rings.
Carbon can covalently bond with up to four
other atoms.
Carbon can form diverse compounds, from simple to
complex.
Methane with 1 Carbon
atom
DNA with tens of Billions of
Carbon atoms
What is Life Made of?
Physical and Chemical sciences alone may not completely explain the
nature of life, but they at least provide the essential framework for
such an explanation.
All living things are composed of organic
compounds.
Biochemistry
- Biochemistry is a special branch of organic chemistry that deals
with matter inside the living cell called protoplasm.
- Protoplasm is the living content of a cell that is surrounded by
a plasma membrane. It is acomplex mixture of organic
compounds where high levels of chemical activity occur.
-
.
1- You need to know the structure of organic molecules
important to major biological processes.
2- You will be expected to learn the basic biochemical
processes of major cell functions, such as photosynthesis,
respiration, and protein synthesis.
Primary Organic Compounds
You will learn the structure and functions of these organic
compounds:
1. Carbohydrates
2. Lipids
3. Proteins
4. Nucleic Acids
Polymers and Monomers
 Each of these types of molecules are polymers that are
assembled from single units called monomers.
 Each type of macromolecule is an assemblage of a different
type of monomer.
Monomers
Carbohydrates
Monosaccharide
Lipids
Hydrocarbon chains
Proteins
Amino acids
Nucleic acids
Nucleotides
How do monomers form polymers?
In condensation reactions (also called dehydration
synthesis), a molecule of water is removed from two
monomers as they are connected together.
Dehydration synthesis of polymers
Hydrolysis
In a reaction opposite to condensation, a water
molecule can be added (along with the use of an
enzyme) to split a polymer in two.
Hydrolysis
Carbohydrates
 Carbohydrates are made of carbon, hydrogen, and oxygen
atoms, always in a ratio of 1:2:1.
 Carbohydrates are the key source of energy used by living
things.
 The building blocks of carbohydrates are sugars, such as
glucose and fructose.
Carbohydrates
What do the roots mono-, di-, oligo-,
and poly mean?
Each of these roots can be added to the
word saccharide to describe the type of
carbohydrate you have.

How do two monosaccharides combine to make a disaccharide?
Polysaccharides
Lipids
Lipids are molecules that consist of long hydrocarbon chains.
Attaching the three chains together is usually a glycerol
molecule. Lipids are non polar.
Saturated and Unsaturated Fat
Proteins
 Proteins are building blocks of structures called amino acids.
Proteins are what your DNA codes to make .
 A peptide bond forms between amino acids by dehydration
synthesis.
Levels of Protein Structure
Protein Structure
Level
Primary
Secondary
Tertiary
Quaternary
Description
The amino acid sequence
Helices and Sheets
Disulfide bridges
Multiple polypeptides connect
Cellular Metabolism
Cellular metabolism refers to all of the chemical processes that
occur inside living cells.
In general, we can classify metabolic reactions into two broad
groups:
(1) those in which molecules are broken down to provide the energy
needed by cells (Catabolism)
(2) those that synthesize the compounds needed by cells both simple
and complex (anabolism).
Comparison of catabolic and anabolic pathways
A biochemical pathway is a series of consecutive
biochemical reactions.
The food we eat consists of many types of compounds,
carbohydrates, lipids, and proteins. All of them can serve as
fuel, and we derive our energy from them.
To convert those compounds to energy, the body uses a
different pathway for each type of compound. All of these
diverse pathways converge to one common catabolic
pathway
The purpose of catabolic pathways is to convert the
chemical energy in foods to molecules of ATP.
Energy
Energy can exist in two states:
1- Kinetic energy – energy of motion.
2- Potential energy – stored energy.
Chemical energy – potential energy stored in bonds, released
when bonds are broken.
Energy can be transformed form one state to another.
The ultimate source of energy for most
living things is the sun.
Importance of ATP
- ATP consists of adenosine
(adenine + ribose) and a
triphosphate group.
- The bonds between the phosphate
groups are high energy bonds.
A-P~P~P
- The energy gained in the oxidation
of food is stored in the form of ATP.
AMP (adenosine monophosphate)
ADP (adenosine diphosphate)
The mitochondria, which possess two membranes, are the organelles in
which the common catabolic pathway takes place in higher organisms.
The matrix is the inner nonmembranous portion of a mitochondrion.
The inner membrane is highly corrugated and folded.
The enzymes that catalyze the
common pathway are all located in
these organelles
- These enzymes are synthesized in the cytosol therfore, they
must be imported through the two membranes.
- The enzymes are located inside the inner membrane of
mitochondria so, the starting materials of the reactions in the
common pathway must pass through the two membranes to enter
the mitochondria. Products must leave the same way
- We will discuss in detail how the specific sequence of these
enzymes causes the chain of events in the common catabolic
pathway.
Regulating Cellular Respiration
 Rate of cellular respiration slows down when your cells
have enough ATP.
 Enzymes that are important early in the process have an
allosteric (regulating) site that will bind to ATP.
 When lots of ATP is present, it will bind to this site,
changing the shape of the enzyme, halting cellular
respiration.