Chapter 1
Introduction in Biochemistry
What is Biochemistry
 Biochemistry: Greek : Bios =life
 It is branch of science deals with study of
chemical basis of life
 That means chemistry of living matters at cellular
and molecular level in living beings
Biochemistry
 Biochemistry is a special branch of organic
chemistry that deals with matter inside the living
cell called Protoplasm.
 Protoplasm is an enormously complex mixture of
organic compounds where high levels of chemical
activity occur.
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 students of life must have a fundamental
understanding of organic chemistry and
biochemistry.
Organic Chemistry
 Organic chemistry is the study of Carbon
compounds.
 Organic compounds are compounds
composed primarily of a Carbon skeleton.
 All living things are composed of organic
compounds.
Organic VS. inorganic compounds
 Organic compound : contain carbon (C)
and hydrogen ( H ).
 Inorganic compounds: rarely contain
carbon.
Organic VS. inorganic
 Organic compound: typically larger
molecules due to carbons bonding
capabilities.
 Inorganic compound: usually smaller than
organic compounds.
Organic VS. inorganic
 Organic compound: some dissolve in water.
 nonelectrolytes
 Most dissolve in organic liquids
 Inorganic : usually dissociate in water
 electrolytes.
Organic VS. inorganic
 Organic compound:
 carbohydrate
 Proteins
 Lipids
 Nucleic acids
Organic Chemistry
 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.
Organic Chemistry
Organic Chemistry
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
Biochemistry
 How much biochemistry
do you need to know for
this course?
 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 are expected to
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
Nucleic acids
Amino 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.
.
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.
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 polysaccharide?
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 vs. 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
Description
The amino acid sequence
Helices and Sheets
Tertiary
Quaternary
Disulfide bridges
Multiple polypeptides
connect
Cellular Metabolism
Cellular metabolism refers to all of the chemical processes that
occur inside living cells.
Pathway: a series of biochemical reactions.
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).
Catabolism:the biochemical pathways that are involved in
generating energy by breaking down large nutrient
molecules into smaller molecules with the concurrent
production of energy
Anabolism: the pathways by which biomolecules are
synthsized (use ATP energy to build larger molecules from
smaller building blocks).
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 cytosoltherfore, 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.