1.Chemical Foundation of Biochemistry

Chemical
Foundation of
Biochemistry
BY:
Dr. Anas Abed Darwish
LEARNING OBJECTIVES
• Define Biochemistry
• Distinguish between organic and inorganic chemistry
• Chemistry of Carbohydrates
• Chemistry of Protein
• Chemistry of Nucleotides
• Chemistry of Lipids
What is Biochemistry
• Biochemistry is the study the chemical processes within

living organisms (Chemistry of life).
• Biochemical molecules are based on carbon (organic

compounds).
• Biochemistry deal with the structures, functions, and

interaction of biological molecules ( e.g. carbohydrates,
protein, amino acid)
All matter, whether living or nonliving, is made of the
same type building blocks called atoms
An atom is the smallest basic unit of matter
All atoms have the same basic structure, composed of
three smaller particles
 Proton – a positively charged particle in an atom’s nucleus
 Neutron – a neutral (no charge) particle which has about the
same mass as a proton and is also in the nucleus
 Electron – a negatively charged particle found outside the
nucleus. Electrons are much, much smaller than proton and
neutrons
Elements…
• Different types of atoms are called elements,
• Only about 25 different elements are found in organisms
• However, atoms of different elements can “link” or bond together to form
compounds
The Foundations of Biochemistry
1. Cellular Foundations
2. Chemical Foundations
3. Physical Foundations
4. Genetic Foundations
5. Evolutionary Foundations
Cellular Foundations
• Cells are the structural and functional units of all living organisms.
• Study of the characteristics of micro-organisms (bacteria, fungi and
viruses) followed by the structure and function of human cells
Chemical Foundations
 Biomolecules are compounds of carbon with a
variety of functional groups.
 Cells contain a universal set of small molecules.
 Macromolecules are the major constituents of
cells.
 Interactions between biomolecules are
stereospecific.
Physical Foundations
 Organisms transform energy and matter from their

surroundings.
 The flow of electrons provides energy for organisms.
 Energy coupling links reactions in biology.
 Enzymes promote sequences of chemical reactions.
 Metabolism is regulated to achieve balance
Genetic Foundations
1. Genetic continuity is vested in single DNA molecules.

2. The structure of DNA allows for its replication and repair.
3. The linear sequence in DNA encodes proteins with three-
dimensional structures.
Evolutionary Foundations
1. Changes in the hereditary instructions allow evolution.
2. Biomolecules first arose by chemical evolution.
3. Chemical evolution can be simulated in the laboratory.
4. RNA or related precursors may have been the first genes and
catalysts.
Organic chemistry
• Organic chemistry is the study of compounds of carbon
and hydrogen and their derivatives.
• Inorganic Chemistry is compound is typically a

chemical compound that lacks carbon–hydrogen
bonds.
Carbon
• Life is based on compounds of carbon. This is the
subject matter of organic chemistry.
• The reactions of organic compounds are those of their
functional groups.
• which are specifically linked atoms that react in similar
ways under many different condition
• The group of atoms that responsible for characteristic
properties of a family of organic compounds is called
(functional group).
Polymers and Monomers
Each of these types of macromolecules ( carbohydrates, lipids,

proteins, and nucleic acid) are polymers that are assembled from
single units called monomers.
Polymers: are made up of many small, repeating molecular units

called monomers.
Polymers and Monomers
Macromolecule Monomer
- Carbohydrates -Monosaccharide
- Lipids
-Not always polymers;
Hydrocarbon chains
- Proteins
-Amino acids
- Nucleic acids
-Nucleotides
Chemistry of carbohydrates
ISOMERS:
• Isomers – Organic molecules with the same molecular formula but
differ in structure or arrangement of atoms.
STEREOISOMERS:
• Same molecular formula but different atomic
arrangement in space.
• Examples:
• C3H7O3
• CH2OHCH2OHCH(=O) CH2OHCH(=O)CH2OH
ISOMERS OF
MONOSACCHARIDES:
• 1) D- and L- isomers
• = mirror images
(enantiomers)
• naturally occurring:
D-monosaccharides
2)Aldoses and Ketoses:
H O
C CH2OH
H C OH C O
HO C H HO C H
H C OH H C OH
H C OH H C OH
CH2OH CH2OH
D-glucose D-fructose
3) pyranoses and furanoses
• Sugars Prefer To Be Cyclic in solutions
4)  and  anomers
• only cyclic molecules
5) epimers
EPIMERS: differ in
conformation around
ONE carbon
Glycosidic bonds:
Its covalent bond occur between CHO and other substance contain
OH ,or N.
Chemistry of nucleotides
Nucleotides are important cell metabolites which are

found primarily as the monomeric units comprising
the major nucleic acids of the cell, RNA, and DNA.
Nucleic acids are polymers of nucleotides.

Chemistry of nucleotides
A nucleotides is made of
three components:
1.Nitrogenous base-
2.Sugar-
3.Phosphate.
Chemistry of proteins
AMINO ACIDs are the basic building blocks of

PROTEINS
Each AMINO ACID has All are

An amino group, bonded to the
A carboxyl group,
α-carbon
A hydrogen atom
atom
A specific side chain (R group)
Asymmetric carbons of the amino acids
• Carbon atom attached to 4 different atoms or groups is said to be
asymmetric.
• All amino acids have asymmetric alfa carbon EXCEPT glycine
• Thus amino acids can exist in two forms; L and D.
• All amino acids in proteins are in L form.
Peptide bonds
 Peptide bond is an amide linkage between the
α-carboxyl group of one amino acid & the α-amino
group of another amino acid
Properties of peptide bond
• Strong bond: can only be broken by:
• Prolonged exposure to strong acid or alkali at high temperature
• Specific enzymes such as the digestive enzymes
• Has partial double bond characters:
• Shorter than single bond.
• Rigid with no rotation of groups around it.
• Has a trans-form to avoid steric interference of R groups
• Uncharged but polar;
• Peptide bonds contain polar hydrogen atoms (with partial
positive charge) & polar oxygen atoms (with partial negative
charge)
• This allows hydrogen bond formation between carbonyl oxygen
of one peptide bond and amino hydrogen of another peptide
bond as in α- helix and β- pleated sheet
Levels of protein Structure:
1. Primary structure
2. Secondary structure
3. Tertiary structure
4. Quaternary structure
Primary structure of protein
• It is the linear sequence of amino acids in the peptide chain.

• The only bond present in primary structure is the peptide bond
Secondary structure of protein

• This conformation is stabilized by hydrogen bonds between
peptide bonds in different parts of the chain
• The secondary structure includes:
• α- helix
• β- pleated sheet
Forces that stabilize tertiary
structure
•The tertiary structure is stabilized by interaction
between side chains of amino acid, these
interactions include:
•Hydrogen bonds between hydrogen and oxygen
of side chains
•Electrostatic interactions (ionic bonds) between
opposite charges on side chains
•Hydrophobic interactions between non polar
side chains.
•Disulfide bonds between SH groups of 2
cysteine side chains
Forces that stabilize protein tertiary
structure
Quaternary structure
 Many proteins are composed of 2 or more polypeptide chains which
are loosely held together by non-covalent interactions (hydrogen
bonds, ionic bonds and hydrophobic interactions) between the side
chains of amino acids
Chemistry of Lipids
Fatty Acids
(FA)
• Most fatty acids contain even number of carbon
atoms.
• Most fatty acids are straight chains (unbranched),
except few e.g. phytanic acid: a branched chain
fatty acid present in dairy products
• They are either short chain (2-10C, water soluble,

liquid at RT) or long chain (>10C, water
insoluble, solid at RT).
• They are either saturated (contain no double bonds,
solid at RT) or unsaturated (contain double bonds,
liquid at RT).
• They may be essential or non essential.
FA
Structure
• FA consists of a hydrophobic
hydrocarbon chain with a
terminal carboxyl group,
which is ionized at a
physiologic pH
• This ionic (anionic) group
gives FA its amphipathic
nature (hydrophobic +
hydrophilic region)
Saturated FA Unsaturated FA
• They contain no • They are either:
double bonds – Monounsaturated
• Their general formula (MUFA): one double
bond
is CH3–(CH2)n– – Polyunsaturated (PUFA) :
COOH where n: more than 1 double bond
CH (methylene)
number
2 of
groups • Double bonds are in the cis
• Examples: configuration and are spaced at
3 C interval if the fatty acid has
Palmitic acid: 16C > 1 double bond
(C15H31COOH), • Examples:
MUFA: Palmitoleic acid 16:1∆9,
PUFA: Arachidonic acid
20:4∆5,8,11,14.
Thank You

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Chemical

• Biochemistry is the study the chemical processes within

• Biochemical molecules are based on carbon (organic

• Biochemistry deal with the structures, functions, and

 Organisms transform energy and matter from their

1. Genetic continuity is vested in single DNA molecules.

• Inorganic Chemistry is compound is typically a

Each of these types of macromolecules ( carbohydrates, lipids,

Polymers: are made up of many small, repeating molecular units

Nucleotides are important cell metabolites which are

Nucleic acids are polymers of nucleotides.

AMINO ACIDs are the basic building blocks of

Each AMINO ACID has All are

• It is the linear sequence of amino acids in the peptide chain.

Secondary structure of protein

• They are either short chain (2-10C, water soluble,

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