What is Biochemistry?

Biomolecules

l  Is also known as “ Biological Chemistry” -  Are present in the plant and animal cells.
à Composition of the cell:
l  It is defined as the investigation of molecular basis of life. -  50-95% - H2O
-  1% - Ions
l  It is the study of Chemistry of the living organisms. It deals -  Others are organic molecules
with biomolecules and biochemical reactions viewed in the
context of biological structures. What is an organic molecule?
-It is a carbon based molecule that is covalently bonded to itself
or other elements like H, O, N, S, P.

l  One important organic molecule is the Hydrocarbon.

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Biomolecules: Hydrocarbon Functional groups of Organic Biomolecules

Hydrocarbons (HC) Functional group - is a group of atoms that renders the chemical
-  Biomolecules are derived from the HC properties of an organic molecule or biomolecule.
-  are non-polar, therefore, they are __________in H2O
-  Hydrophobic
-  Biomolecules with HC group- have hydrophobic character.
(Cell membrane)

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Functional Groups 4 major classes of small biomolecules

Biomolecules- can have one or more functional groups l  4 families of small molecules which are found inside the cell:
Ex. l  1. Amino acids
1. Sugars l  2. Sugars (Monosaccharides)
a. Have Hydroxyl group and aldehyde – l  3. Fatty Acids
b. Have Hydroxyl group and Ketone – l  4. Nucleotides
2. Amino Acids- What are their functions?
-  are building blocks of proteins 1.  They are used to synthesize larger molecules like polymers
-  Have an amino group and carboxyl group (proteins, and nucleic acids)
-  Ex. Glycine Alanine Valine 2.  Some have special biological functions (ex. ATP- a
nucleotide)
3.  Involved in complex reaction pathways.

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Amino acids (AA) Amino acids

-  There are 20 common amino acids l  are being used to synthesize long chain polymer called
_______________.
POLYPEPTIDE CHAIN
O
H3N+ l  Short Polypeptide – AAs are less than 50 are called, PEPTIDE
residue
CH O-
R
R- side Chain
l  Longer Polypeptides are called __________
PROTEINS

l  Ex of polypeptides:
-  The chemical properties of the AA are determined largely by 1.  Transport protein
the R group. 2.  Structural Proteins
3.  Enzymes

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Peptide Bond Sugars

-  Is the bond connecting the amino acids in the polypeptide l  are called carbohydrates
residue. l  are the most abundant organic molecules in nature.
l  What are some functions?
-  it is also called as “ Amide Bond”
1.  Energy source
-  Illustration: 2.  Structural Component
Ex. Gly-Ala 3.  Intercellular communication

Basic unit of Sugar is ______________.

MONOSACCHARIDE It is also known as
simple sugar.
l  note: the R groups of the polypeptide determines its final 3-D
shape and therefore its biological functions. Monosaccharides can be described in terms of functional. Group.
1.  Polyhydroxy Aldehyde
2.  Polyhydroxy Ketone
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Sugars Polysaccharides

l  Sugar Containing an Aldehyde is called _________

ALDOSE l  are polymer containing large number of monosaccharides.
l  Sugar containing a ketone group is called ________
KETOSE

l  Examples
Examples of Sugars (Monosaccharides): 1.  Glycogen - an energy storage molecule for the animals.
2.  Starch - an energy storage molecule for the plants.
1.  Glucose 2. Fructose 3. Ribose 4. Deoxyribose 3.  Cellulose – a structural material/component of the plant cell
wall.

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FATTY ACID (FA) Fatty Acids

1. FA Unsaturated Fatty Acids

-  Is a monocarboxylic acid ex.
-  usually it contains an even number of carbon atoms. 1.  Oleic Acid (18:1)

-  2 Types of FA l  FAs are components of other classes of lipid molecules

1.  Saturated Fatty acid - all of its bonds are single in the HC
chain or tail.
2.  Unsaturated Fatty acid - contains one or more double bonds 2. Triacylglycerol (Fat or Oil) -
in its HC chain or tail. Is an ester containing glycerol and 3 FAs
H2C OH
Ex. of saturated FA Glycerol- is a three carbon-alcohol
HC OH
1.  Palmitic Acid - a hexadecanoic acid with 3 hydroxyl groups
H2C OH

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Other examples of Lipids

Triacylglycerol- O 1.  Steroids -

H2C O C R1
Ex. Cholesterol
O

R2 C O CH O

H2C O C R3 - A sex hormone

A lipid molecule that resembles like triacylglycerol is
Phosphoglycerides (A phospholipid).
3. Phospholipid
-  And an important part of animal cell membranes
2. Fat soluble Vitamins
Some examples : Vitamin E and Vitamin A
3.  Carotenoid
- a plant pigment molecule that plays a role in photosynthesis.

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Nucleotides Nitrogenous Base

l  the primary component of Nucleic Acids

l  3 Components of Nucleotides
1. 5 C sugar
2. Phosphate Group
3. Nitrogenous Base

2 classes of the Bases:

1.  Purine - A and G
2.  Pyrimidine - T, C and U

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Nucleic Acids Other role of Nucleotides

2 types of Nucleic Acids l  it involves in biosynthetic and energy generating reactions.

1.  Deoxyribonucleic Acid
2.  Ribonucleic Acid l  Ex. Formation of Phosphate bonds to make ATP

Function of DNA?
- Contains/Stores- Genetic Information

Function of RNA?
- Involves in expressing the information primarily in the protein
synthesis.

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Biochemical reactions Biochemical processes

l  There are five frequent chemical reactions:

l  The sum of all the enzyme-catalyzed reactions in a living
organism is called “ Metabolism. 1.  Nucleophilic Substitution
2.  Elimination
l  4 functions of Metabolism 3.  Addition
1. Acquisition and utilization of Energy 4.  Isomerization
2. Synthesis of molecules needed for cell structure and function 5.  Redox
3. Growth and development
4. Removal of waste products

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Nucleophilic Substitution Nucleophilic Substitution

l  Reaction of glucose with ATP

Nucleophile:
- is a nucleus-loving specie.
- usually it is an anion or an atom with a lone-pair.

Electrophile:
-  Is an electron-loving specie.
-  usually a cation, radical or a lewis acid

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Nucleophilic Substitution: Hydrolysis reaction Hydrolysis

l  Is the cleavage of a covalent bond by WATER. l  Hydrolysis of ATP - involves breaking of phosphate bonds
l  a kind of SN reaction and can be catalyzed by an acid, base or
enzymes.

l  Importance: digestion of food involves Hydrolysis reaction.

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Elimination Addition Reactions

l  A = bond forms when atoms are removed from the molecule. l  Two molecules combine to form a single product
l  Dehydration of 2-phosphoglycerate

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Isomerization Reactions REDOX

l  It involves intra-molecular shift of atoms.
l  Ex of biochemical isomerization
1. Aldose-Ketose pair
l  Involves transfer of electron from a donor (RA) to a electron
acceptor (OA)
l  Oxidation - Gain of Oxygen, loss of Hydrogen
l  Reduction - Loss of Oxygen, gain of Hydrogen

Ex.

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