Biochemistry by Lecture Biswanath.pdf

Biochemistry
INTRODUCTION
Biochemistry can be defined as the science concerned with the chemical basis
of life (Gk bios “life”). The cell is the structural unit of living systems. Thus,
biochemistry can also be described as the science concerned with the chemical
constituents of living cells and with the reactions and processes they undergo.
By this definition, biochemistry encompasses large areas of cell biology, of
molecular biology, and of molecular genetics.
BIOMOLECULES
More than 99% of the human body is composed of 6 elements, i.e. oxygen,
carbon, hydrogen, nitrogen, calcium and phosphorus. Human body is composed
of about 60% water, 15% proteins, 15% lipids, 2% carbohydrates and 8%
minerals. Molecular structures in organisms are built from 30 small precursors,
sometimes called the alphabets of biochemistry. These are 20 amino acids, 2
purines, 3 pyrimidines, sugars (glucose and ribose), palmitate, glycerol and
choline.
In living organisms, biomolecules are ordered into a hierarchy of increasing
molecular complexity. These biomolecules are covalently linked to each other
to form macromolecules of the cell, e.g. glucose to glycogen, amino acids to
proteins, etc. Major complex biomolecules are proteins, polysaccharides, lipids
and nucleic acids. The macromolecules associate with each other by non-
covalent forces to form supra molecular systems, e.g. ribosomes, lipoproteins.

STUDY OF METABOLIC PROCESSES
Our food contains carbohydrates, fats and proteins as principal ingredients.
These macromolecules are to be first broken down to small units; carbohydrates
to mono-saccharides and proteins to amino acids. This process is taking place in
the gastrointestinal tract and is called digestion or primary metabolism. After
absorption, the small molecules are further broken down and oxidized to carbon
dioxide. In this process, NADH or FADH2 are generated. This is named as
secondary or intermediary metabolism. Finally, these reducing equivalents
enter the electron transport chain in the mitochondria, where they are oxidized
to water; in this process energy is trapped as ATP. This is termed tertiary
metabolism. Metabolism is the sum of all chemical changes of a compound
inside the body, which includes synthesis (anabolism) and breakdown
(catabolism). (Greek word, kata = down; ballein = change).
Chemistry of Carbohydrates
Carbohydrates are the most abundant organic molecules in nature. They are
primarily composed of the elements carbon, hydrogen and oxygen. The name
carbohydrate literally means 'hydrates of carbon'. Some of the carbohydrates
possess the empirical formula (C.H2O)n where n >3, satisfying that these
carbohydrates are in fact carbon hydrates. However, there are several non-
carbohydrate compounds (e.g. acetic acid, C2H4O2; lactic acid, C3H6O3)
which also appear as hydrates of carbon. Further, some of the genuine
carbohydrates (e.g. rhamnohexose, C6H12O5; deoxyribose, C5H10O4) do not
satisfy the general formula. Hence carbohydrates cannot be always considered
as hydrates of carbon.
Carbohydrates may be defined as polyhydroxy aldehydes or ketones or
compounds which produce them on hydrolysis. The term 'sugar ' is applied to
carbohydrates soluble in water and sweet to taste.
Functions of Carbohydrates / Role of carbohydrates;
1. Carbohydrates are the main sources of energy in the body. Brain cells and
RBCs are almost wholly dependent on carbohydrates as the energy
source. Energy production from carbohydrates will be 4 kcal/g.
2. Storage form of energy (starch and glycogen).
3. Excess carbohydrate is converted to fat.
4. Glycoproteins and glycolipids are components of cell membranes and
receptors.

5. Structural basis of many organisms: Cellulose of plants; exoskeleton of
insects, cell wall of microorganisms, mucopolysaccharides as ground
substance in higher organisms.
6. Fiber is a carbohydrate that aids in digestion, helps you feel full, and
keeps blood cholesterol levels in check
Your body can store extra carbohydrates in your muscles and liver for use when
you're not getting enough carbohydrates in your diet.
Classification of carbohydrates
(1) Monosaccharides are those carbohydrates that cannot be hydrolyzed into
simpler carbohydrates: They may be classified as trioses, tetroses,
pentoses, hexoses, or heptoses, depending upon the number of carbon
atoms; and as aldoses or ketoses depending upon whether they have an
aldehyde or ketone group.
(2) Disaccharides are condensation products of two monosaccharide units.
Examples are maltose and sucrose.
(3) Oligosaccharides are condensation products of two to ten
monosaccharides; maltotriose* is an example.
(4) Polysaccharides are condensation products of more than ten
monosaccharide units; examples are the starches and dextrins, which may
be linear or branched polymers. Polysaccharides are sometimes classified
as hexosans or pentosans, depending upon the identity of the constituent
monosaccharides.
Molecules having only one actual or potential sugar group are called
monosaccharides (Greek, mono = one; saccharide = sugar). They cannot be
further hydrolysed into smaller units. When two monosaccharides are combined
together with elimination of a water molecule, it is called a disaccharide (e.g.
C12H22O11). Trisaccharides contain three sugar groups. Further addition of
sugar groups will correspondingly produce tetrasaccharides, pentasaccharides
and so on, commonly known as oligosaccharides (Greek, oligo = a few). When
more than 10 sugar units are combined, they are generally named as
polysaccharides (Greek, poly = many). Polysaccharides having only one type of
monosaccharide units are called homopolysaccharides and those having
different monosaccharide units are heteropolysaccharides.
Lipids
BIOMEDICAL IMPORTANCE
The lipids (Greek: lipos-fat) are a heterogeneous group of compounds,
including fats, oils, steroids, waxes, and related compounds, which are related

more by their physical than by their chemical properties. They have the
common property of being (1) relatively insoluble in water and (2) soluble in
nonpolar solvents such as ether and chloroform. They are important dietary
constituents not only because of their high energy value but also because of the
fat-soluble vitamins and the essential fatty acids contained in the fat of natural
foods. Fat is stored in adipose tissue, where it also serves as a thermal insulator
in the subcutaneous tissues and around certain organs.
Definition - Lipids may be defined as compounds which are relatively insoluble
in water, but freely soluble in non-polar organic solvents, such as benzene,
chloroform, ether, hot alcohol, acetone, etc.
CLASSIFICATION OF LIPIDS;
1. Simple lipids: Esters of fatty acids with various alcohols.
a. Fats: Esters of fatty acids with glycerol. Oils are fats in the liquid state. The difference
between fat and oil is only physical. Thus, oil is a liquid while fat is a solid at room
temperature.
b. Waxes: Esters of fatty acids with higher molecular weight monohydric alcohols.
2. Complex lipids: Esters of fatty acids containing groups in addition to an
alcohol and a fatty acid.
a. Phospholipids: Lipids containing, in addition to fatty acids and an alcohol, a
phosphoric acid residue. They frequently have nitrogen containing bases and other
substituents, Eg, in glycerophospholipids the alcohol is glycerol and in
sphingophospholipids the alcohol is sphingosine.
b. Glycolipids (glycosphingolipids): Lipids containing a fatty acid, sphingosine, and
carbohydrate.
c. Other complex lipids: Lipids such as sulfolipids and aminolipids. Lipoproteins may
also be placed in this category.
3. Precursor and derived lipids: These include fatty acids, glycerol, steroids,
other alcohols, fatty aldehydes, and ketone bodies hydrocarbons, lipid-
soluble vitamins, and hormones.
4. NEUTRAT LIPIDS: The lipids which are uncharged are referred to as
neutral lipids. These are mono-, di-, and triacylglycerols, cholesterol and
cholesteryl esters.
Function of Lipids;
1. Storage form of energy (triacylglycerol)
2. Structural components of bio membranes (phospholipids and
cholesterol)

3. Metabolic regulators (steroid hormones and prostaglandins)
4. Act as surfactants, detergents and emulsifying agents (amphipathic
lipids)
5. Act as electric insulators in neurons
6. Provide insulation against changes in external temperature
(subcutaneous fat)
7. Give shape and contour to the body
8. Protect internal organs by providing a cushioning effect (pads of fat)
9. Help in absorption of fat soluble vitamins (A, D, E and K)
10.Improve taste and palatability of food.
Nucleic acid
There are two types of nucleic acids, namely deoxyribonucleic acid (DNA) and
ribonucleic acid (RNA). Primarily, nucleic acids serve as repositories and
transmitters of genetic information.
Brief history
DNA was discovered in 1869 by Johann Friedrich Miescher, a Swiss researcher.
The demonstration that DNA contained genetic information was first made in
1944, by Avery, Macleod and MacCarv.
It is sometimes useful to describe nucleic acid structure in terms of hierarchical
levels of complexity (primary, secondary, tertiary). The primary structure of a
nucleic acid is its covalent structure and nucleotide sequence. Any regular,
stable structure taken up by some or all of the nucleotides in a nucleic acid can
be referred to as secondary structure
Components of nucleic acids
Nucleic acids are the polymers of nucleotides (polynucleotides) held by 3' and
5' phosphate bridges. In other words, nucleic acids are built up by the
monomeric units-nucleotides (it may be recalled that protein is a polymer of
amino acids).
Nucleotide
Nucleotides are precursors of the nucleic acids, deoxyribonucleic acid (DNA)
and ribonucleic acid (RNA). The nucleic acids are concerned with the storage
and transfer of genetic information.

Composition of Nucleotides
A nucleotide is made up of 3 components:
a. Nitrogenous base (a purine or a pyrimidine)
b. Pentose sugar, either ribose or deoxyribose
c. Phosphate groups esterified to the sugar
When a base combines with a pentose sugar, a nucleoside is formed. When the
nucleoside is esterified to a phosphate group, it is called a nucleotide or
nucleoside monophosphate. When a second phosphate gets esterified to the
existing phosphate group, a nucleoside diphosphate is generated. The
attachment of a 3rd phosphate group results in the formation of a nucleoside
triphosphate. The nucleic acids (DNA and RNA) are polymers of nucleoside
monophosphates.
Bases Present in the Nucleic Acids
Two types of nitrogenous bases; the purines and pyrimidines are present in
nucleic acids.
Purine Bases
The purine bases present in RNA and DNA are the same; adenine and guanine.
Adenine is 6-amino purine and guanine is 2-amino, 6-oxopurine. The
numbering of the purine ring with the structure of adenine and guanine are
shown in Figure 01
Fig. 01: Structure of purines
Minor Purine Bases
These bases may be found in small amounts in nucleic acids and hence called
minor bases. These are hypoxanthine (6-oxopurine) and xanthine (2, 6-di-
oxopurine) (Fig. 02). Uric acid (2,6,8-tri-oxopurine) is formed as the end

product of the catabolism of other purine bases. It can exist in the "enol" as well
as "keto" forms (tautomeric forms) (Fig. 02). Keto form is by far the
predominant type under physiological conditions.
Fig. 02: Minor bases seen in nucleic acids
Pyrimidine Bases
The pyrimidine bases present in nucleic acids are cytosine, thymine and uracil.
Cytosine is present in both DNA and RNA. Thymine is present in DNA and
uracil in RNA. Structures are shown in Figure 03.
Fig. 03: Common pyrimidines

Nucleosides
i. Nucleosides are formed when bases are attached to the pentose sugar, D-
ribose or 2-deoxy-D-ribose (Fig. 04).
ii. All the bases are attached to the corresponding pentose sugar by a beta-N
glycosidic bond between the 1st carbon of the pentose sugar and N9 of a purine
or N1 of a pyrimidine.
iii. The deoxy nucleosides are denoted by adding the prefix d- before the
nucleoside.
iv. The carbon atoms of the pentose sugar are denoted by using a prime number
to avoid confusion with the carbon atoms of the purine or pyrimidine ring (Fig.
05).
The names of the different nucleosides are given in Table 43.1
.v. Nucleosides with purine bases have the suffix -sine, while pyrimidine
nucleosides end with -dine.
vi. Uracil combines with ribose only; and thymine with deoxyribose only.
Fig. 04: Sugar groups in nucleic acids

Fig. 06: Numbering in base and sugar groups. Atoms in sugar is denoted with
primed numbers
Nucleotides
i. These are phosphate esters of nucleosides. Base plus pentose sugar plus
phosphoric acid is a nucleotide.
ii. The esterification occurs at the 5th or 3rd hydroxyl group of the pentose
sugar. Most of the nucleoside phosphates involved in biological function are 5'
phosphates (Table 43.2).
iii. Since 5'-nucleotides are more often seen, they are simply written without any
prefix. For example, 5'- AMP is abbreviated as AMP; but 3' variety is always
written as 3'-AMP.
iv. Moreover, a base can combine with either ribose or deoxy ribose, which in
turn can be phosphorylated at 3' or 5' positions. One purine and one pyrimidine
derivative are given as examples in Table 43.3.
v. Many co-enzymes are derivatives of adenosine monophosphate. Examples
are NAD+, NADP, FAD and Co-enzyme A.
vi. Nucleotides and nucleic acids absorb light at a wavelength of 260 nm; this
aspect is used to quantitate them. As nucleic acids absorb ultraviolet light,
chemical modifications are produced leading to mutation and carcinogenesis.

Proteins & Amino Acid
Proteins are of paramount importance in biological systems. All the major
structural and functional aspects of the body are carried out by protein
molecules. All proteins are polymers of amino acids. Proteins are composed of a
number of amino acids linked by peptide bonds.
Although about 300 amino acids occur in nature, only 20 of them are seen in
human body. Most of the amino acids (except proline) are alpha amino acid,

which means that the amino group is attached to the same carbon atom to which
the carboxyl group is attached.
Origin of the word 'protein'
The term protein is derived from a Greek word proteios meaning holding the
first place. Berzelius (Swedish chemist) suggested the name proteins to the
group of organic compounds that are utmost important to life. Mulder (Dutch
chemist) in 1838 used the term proteins for the high molecular weight nitrogen-
rich and most abundant substances present in animals and plants.
Function of protein’s
Proteins perform a great variety of specialized and essential function in the
living cells .These functions may be broadly grouped as static (structural) and
dynamic.
Structural functions: Certain proteins perform brick and mortar roles and are
primarily responsible for structure and strength of body. These include collagen
and elastin found in bone matrix, vascular system and other organs and α-
keratin present in epidermal tissues.
Dynamic functions: The dynamic functions of proteins are more diversified in
nature. These include proteins acting as enzyme, hormones, blood clotting
factors, immunoglobulin’s, membrane receptors, storage proteins, besides their
function in genetic control, muscle contraction, respiration etc. Proteins
performing dynamic functions are appropriately regarded as the working horses
of cell.
Elementary composition of protein’s
Proteins are predominantly constituted of five major elements in the following
proportion.
Carbon: 50 - 55%
Hydrogen: 6 - 7.3%
Oxygen: 19 - 24%
Nitrogen: 13 - 19%
Sulfur: 0 – 4%
Besides the above, proteins may also contain other elements such as P, Fe, Cu,
l, Mg, Mn, Zn etc. The content of nitrogen, an essential component of proteins,
on an average is l6%. Estimation of nitrogen in the laboratory (mostly by

Kjeldahl's method is also used to find out the amount of protein in biological
fluids and foods.
All proteins are polymers of amino acids.
CLASSIFICATION OF AMINO ACIDS
Based on Structure
A. Aliphatic amino acids
a. Monoamino monocarboxylic acids:
• Simple amino acids: Glycine, Alanine
• Branched chain amino acids: Valine, Leucine, Isoleucine
• Hydroxyamino acids: Serine, Threonine
• Sulfur-containing amino acids: Cysteine, Methionine
• Amino acids with amide group: Asparagine, Glutamine
b. Monoamino dicarboxylic acids: Aspartic acid, Glutamic acid.
c. Dibasic monocarboxylic acids: Lysine, Arginine.
B. Aromatic amino acids: Phenylalanine, Tyrosine.
C. Heterocyclic amino acids: Tryptophan, Histidine
D. Imino acid: Proline.
E. Derived amino acids:
i. Derived amino acids found in proteins: After the synthesis of proteins, some
of the amino acids are modified, e.g. hydroxy proline and hydroxy lysine are
important components of collagen. Gamma carboxylation of glutamic acid
residues of proteins is important for clotting process . In ribosomal proteins and
in histones, amino acids are extensively methylated and acetylated.
ii. Derived amino acids not seen in proteins (Nonprotein amino acids): Some
derived amino acids are seen free in cells, e.g. Ornithine, Citrulline,
Homocysteine. These are produced during the metabolism of amino acids.
Thyroxine may be considered as derived from tyrosine.
iii. Non-alpha amino acids: Gamma amino butyric acid (GABA) is derived from
glutamic acid. Beta alanine, where amino group is in beta position, is a
constituent of pantothenic acid (vitamin) and coenzyme A.

Based on Nutritional Requirements
A. Essential or indispensable: The amino acids may further be classified
according to their essential nature for growth. Thus, Isoleucine, Leucine,
Threonine, Lysine, Methionine, Phenylalanine, Tryptophan, and Valine are
essential amino acids. Their carbon skeleton cannot be synthesized by human
beings and so preformed amino acids are to be taken in food for normal growth.
Normal growth and optimal health will not occur, if one such amino acid is
deficient in the diet.
B. Partially essential or Semi essential: Histidine and Arginine are semi-
indispensable amino acids Growing children require them in food. But they are
not essential for the adult individual.
C. Non-essential or Dispensable: The remaining 10 amino acids are non-
essential, because their carbon skeleton can be synthesized by the body. So we
need not have to ingest these amino acids as such. However, they are also
required for normal protein synthesis. The non-essential amino acids are
Alanine, Asparagine, and Aspartic acid, Cysteine, Glutamine, Glutamic Acid,
Glycine, Proline, Serine and Tyrosine. All body proteins do contain all the non-
essential amino acids.
D. Conditionally essential amino acids: When a person is suffering from a
moderate to severe chronic illness, person may lose the ability to manufacture
enough non-essential amino acids and thus require supplementation. Problems
with digestion will also necessitate supplementation of “non-essential” amino
acids. These amino acids are normally non-essential, but become essential
during times of physiological stress. Then these amino acids have to be taken in
food or through supplements. These conditionally essential amino acids are
Arginine, Glycine, Cysteine, Tyrosine, Proline, Glutamine and Taurine.
Based on Metabolism
A. Purely ketogenic: Leucine is purely ketogenic because it is converted to
ketone bodies.
B. Ketogenic and glucogenic: Lysine, Isoleucine, Phenylalanine, Tyrosine and
Tryptophan are partially ketogenic and partially glucogenic. During
metabolism, part of the carbon skeleton of these amino acids will enter the
ketogenic pathway and the other part to glucogenic pathway.
C. Purely glucogenic: All the remaining 14 amino acids are purely glucogenic
as they enter only into the glucogenic pathway.

Biochemistry by Lecture Biswanath.pdf

Ala- Alanine, Arg- Arginine, Asn- Aspargine, Asp- Aspartic acid, Cys-cysteine,
Glu- Glutamic acid, Gln- Glutamine, Gly- Glycine, His- histadine, Leu-leucine,
Ile- isoleucine

Biochemistry by Lecture Biswanath.pdf

More Related Content

What's hot (20)

Similar to Biochemistry by Lecture Biswanath.pdf (20)

More from College of pharmaceutical sciences (20)

Recently uploaded (20)

Biochemistry by Lecture Biswanath.pdf