LESSON 3

Biochemistry
Biochemistry is the study of the structure and
function of biological molecules. It studies the
chemical processes that take place in living
organisms.
BIOMOLECULES

Biomolecules are carbon containing compounds and

is produced by living organisms.

These molecules are the building block of every

living organism, thus the presence and right
concentrations of these molecules are vital for the
structure and function of any living cells.
BIOLOGICAL MACROMOLECULES
CARBOHYDRATES
1. Carbohydrates
2. Proteins The name carbohydrate came from the basic
3. Lipids molecular formula (CH2O)n , where n = 3 or more.
4. Nucleic Acids These substances are hydrates of carbon (carbon +
water).
 Macromolecules are polymers.
 Polymers consist of subunits, called CLASSIFICATION OF CARBOHYDRATES
monomers, that are covalently linked to
form larger structures.

SYNTHESIS AND BREAKDOWN OF POLYMERS
Dehydration reaction – is a type of condensation
reaction where two compounds chemically
combined and water molecule is produced.
Hydrolysis – is a chemical reaction in which water
is used to break down the bonds of a particular
substance.
 Monosaccharides
- Monosaccharides are also called as “simple
sugars” and have the formula of
- These are the monomers from which more
complex carbohydrates are built.
Typically monosaccharides can be classified by the
location of the carbonyl group (C=O) as aldoses
(aldose sugar) and ketoses (ketone sugar).
It can also be classified based on the number of
carbons in the carbon skeleton of the sugar namely:
triose (3-carbon sugar), tetrose (4-carbon sugar),
pentose (5-carbon sugar), hexose (6-carbon
sugar) and so forth.
Thus monosaccharides are often given a more
detailed generic names to described both the
functional group and the total number of carbon
atoms.
Thus one can refer to aldotriose (3- carbon
aldehyde sugar), ketotriose (3-carbon ketone
sugar), aldopentose (5- carbon aldehyde sugar),
ketopentose (5- carbon ketone sugar), aldohexose
(6- carbon aldehyde sugar), ketohexose (6- carbon
ketone sugar), and so forth.
Glyceraldehyde is an aldose sugar and contains
 Oligosaccharides
three carbon in the carbon skeleton of the sugar.
Therefore glyceraldehyde is a aldotriose. Oligosaccharides derive their name from the Greek
word oligo, meaning “few,” and consist of from two
Dihydroxyacetone is a ketone sugar and contains
to ten simple sugar residues.
three carbon in the carbon skeleton of the sugar.
Therefore dihydroxyacetone is a ketotriose. The simplest oligosaccharides are the
disaccharides, which consist of two
monosaccharide units linked by a glycosidic
bond.
Glycosidic bond is form as a result of removing or
eliminating a water molecule between two
monosaccharides thru dehydration/ condensation
reaction.
Disaccharides are all commonly found in nature, but
among all of them, sucrose, lactose, and maltose
are the most common.
 Disaccharides
Sucrose is known as the common sugar or table
sugar. It is formed when a monomer of glucose and
fructose are joined in a dehydration reaction.

Lactose known as the milk sugar. Like sucrose, it is
formed via dehydration reaction but the monomers
that are involved are different, glucose and
galactose.
Maltose is also known as malt sugar. It is formed
when a 2 monomer of glucose are joined in a
dehydration reaction.
 Polysaccharides
Polysaccharides, also called glycans, are assembled
from monosaccharides and their derivatives.
If a polysaccharide contains only one kind of
monosaccharide molecule, it is a
homopolysaccharide, or homoglycan, whereas
those containing more than one kind of
monosaccharide are heteropolysaccharides.
Polysaccharides function as storage materials,
structural components, or protective substances.
 STORAGE POLYSACCHARIDES
Starch is the most common storage polysaccharide
in plants.
It exists in two forms: α-amylose and amylopectin.
Most forms of starch in nature are 10% to 30% α-
amylose and 70% to 90% amylopectin.
 STORAGE POLYSACCHARIDES: α-
AMYLASE
α-Amylose is composed of linear chains of glucose
in (1 4) linkages.
 STORAGE POLYSACCHARIDES:
AMYLOPECTIN
Amylopectin is a highly branched chain of glucose
units.
The linear linkages in amylopectin are α
whereas the branch linkages are α
In animals, digestion and use of plant starches begin
in the mouth with salivary α-amylase, the major
enzyme secreted by the salivary glands.
 STORAGE POLYSACCHARIDES:
GLYCOGEN
Glycogen is the most common storage
polysaccharide in animals. It is found mainly in the
liver (where it may amount to as much as 10% of
liver mass).
Liver glycogen consists of granules containing
highly branched molecules, with α branches
occurring every 8 to 12 glucose units.
 STRUCTURAL POLYSACCHARIDE:
CELLULOSE
Cellulose is the most abundant natural polymer in
the word.
It is found in the cell wall of mostly all plants and is
one of the principal components for providing
physical structure and strength.
It is a homopolymer of D-glucose units, like α-
amylose, but the difference is, the glucose
molecules are linked by β whereas in α-
amylose, the bond is α
 STRUCTURAL POLYSACCHARIDE:
CHITIN
Chitin is a polysaccharide that is similar to
cellulose, both in its biological function and its
primary, secondary, and tertiary structure.
Chitin is present in the cell walls of fungi and is the
fundamental material in the exoskeletons of
crustaceans, insects, and spiders.
The structure of chitin is identical to that of
cellulose, except that the -OH group on each C-2 is
replaced by so the repeating units are N-
acetyl-D-glucosamines in β ) linkage.
PROTEINS
Proteins comes from the Greek work “proteios”
which means primary or first.
Proteins They are abundant and diverse class of
biomolecules. Their diversity and abundance reflect
the central role of proteins in virtually all aspects of
cell structure and function.
 Amino Acids
Amino acids are the monomer (building blocks) of
proteins. It is an organic molecule that contains both
an amino and carboxyl group.
The central asymmetric carbon is called alpha (α)  POLAR
carbon.
It has 4 attachments namely:
an amino group, a carboxyl group, a hydrogen
atom, and side chains represented by R
The side chain of each amino acid differs with
other amino acid.
There are 20 amino acids which are divided into 4
groups.

 NON-POLAR

ESSENTIAL VS. NON-ESSENTIAL AMINO

ACIDS

Amino acids are the building blocks of proteins in

living organisms, there are over 500 amino acids
found in nature – however, the human genetic code
only directly encodes 20. ‘Essential’ Amino acids
must be obtained from the diet, whilst Non-
Essential Amino acids can be synthesized in the
body.
CHART KEY:
Aliphatic
Aromatic
Acidic
Basic
Hydroxylic
Sulfur-Containing
Amidic
Non-Essential
Essential

NOTE: This chart only shows those amino acids

for which the human genetic code directly codes
for. Selenocysteine is often referred to as the 21 st

amino acid but is encoded in a special manner.

In some cases, distinguishing between
asparagine/aspartic acid and glutamine/glutamic
acid is difficult. In these cases, the codes asx (B)
ang glx (Z) are respectively used.
 Peptide Bond and Polypeptides
Peptide bond is a covalent bond form when the
carboxyl group of one amino acid is adjacent to the
amino group of another amino acid and are joined
via dehydration reaction.
When this process repeats many times, polypeptide
is formed. Polypeptide is a polymer of many amino
acids connected by peptide bonds.
  Primary Structure
it is the amino acid sequence of a particular protein.

 Secondary Structure
it is the folding of the amino acid backbone into a
repeating pattern caused by the hydrogen bonding
of the peptide backbone.
STRUCTURE OF PROTEINS

All proteins have three level structure namely:

primary, secondary, and tertiary. When a certain
protein has two or more polypeptide chains, it is
said to have a quaternary structure.

 Tertiary Structure
it is the three-dimensional folding pattern of a
protein due to side chains interaction.
  Fibrous Proteins
Fibrous proteins tend to have relatively simple,
regular linear structures.
These proteins often serve structural roles in cells.
Typically, they are insoluble in water or in dilute
salt solutions.
Examples of fibrous proteins are: collagen, elastin,
actin, myosin, fibrin, keratin, etc.

 Quaternary Structure
it is a protein that consist of two or more
polypeptide chain.

 Globular Proteins
Globular proteins are roughly spherical in shape.
The polypeptide chain is compactly folded so that
hydrophobic amino acid side chains are in the
interior of the molecule and the hydrophilic side
chains are on the outside exposed to the solvent,
water.
Globular proteins are usually very soluble in
aqueous solutions.
Examples of globular proteins are: enzymes,
hormones, hemoglobin, immunoglobulin,
ovalbumin, etc.
 LIPIDS

Lipids are a class of biological molecules defined

by low solubility in water and high solubility in
nonpolar solvents Lipids.
Lipids are thus the molecules of choice for
metabolic energy storage.
The lipids found in biological systems are either
hydrophobic (containing only nonpolar groups) or
amphipathic (possessing both polar and nonpolar
groups).
 Fatty Acids
A fatty acid is composed of a long hydrocarbon
chain (“tail”) and a terminal carboxyl group (or
“head”). Fatty acids occur in large amounts in
biological systems but only rarely in the free.

 Fats
Fats are composed of three fatty acids and glycerol.

 Membrane Proteins
Membrane proteins are found in association with
the various membrane systems of cells.
For interaction with the nonpolar phase within
membranes, membrane proteins have hydrophobic
amino acid side chains oriented outward.

Unsaturated vs. Saturated Fats

  Phospholipids
Phospholipids are the major components of cell
membrane.
It is similar to a triacylglyceride but the difference
is phospholipid has only two fatty acids attached to
glycerol.
The hydroxyl group on the third carbon is
connected to a phosphate group. The “head” of a
phospholipid is hydrophilic while the “tail” is
hydrophobic.

CIS AND TRANS FAT

 Steroids
Steroids are lipids that have four fused rings on the
carbon skeleton.
They are distinguished by specific group attached to
the rings of the steroid.
Cholesterol is the most common steroid in animals
and the precursor for all other animal steroids.
It is a principal component of animal cell plasma
membranes, and smaller amounts of cholesterol are
found in the membranes of intracellular organelles.
  STEROIDS: CHOLESTEROL
Steroids derived from cholesterol in animals include
five families of hormones (the androgens, estrogens,
progestins, glucocorticoids, and mineralocorticoids)
and bile acids.

NUCLEIC ACIDS

Nucleic acids are the elements of heredity and the

agents of genetic information transfer. Nucleic
Acids
There are two basic types of nucleic acids which are
DNA (deoxyribonucleic acid) and RNA
(ribonucleic acid).
DNA is the repository of genetic information in
cells.
RNA serves in the expression of this information
through the processes of transcription and
translation.
 STRUCTURE AND CHEMISTRY OF
NUCLEIC ACIDS
Nucleic acid is a polymer also called as
polynucleotides, and each polynucleotide consists
of monomer of nucleotides.
In general, nucleotides are composed of three parts:
a pentose (five-carbon sugar), a nitrogenous base
(nitrogen containing) and a phosphate group.  Pentose Sugar
Deoxyribose is the pentose sugar found in DNA and
lacks an oxygen atom on the second carbon in the
ring. On the other hand, ribose is the sugar found in
the RNA.

 Nitrogenous Bases
The bases of nucleotides and nucleic acids are
derivatives of either pyrimidine or purine.
Pyrimidines are six-membered heterocyclic  Nucleoside: Nitrogenous Base + Sugar
aromatic rings containing two nitrogen atoms.
Nucleoside is the part of nucleotide without any
Purine ring system consists of two rings of atoms. phosphate group.

 NITROGENOUS BASES: PYRIMIDINE

The common naturally occurring pyrimidines are
cytosine, uracil, and thymine.
Cytosine and thymine are the pyrimidines
typically found in DNA, whereas cytosine and
uracil are common in RNA.
 NITROGENOUS BASES: PURINES
Adenine and guanine, the two common purines,
are found in both DNA and RNA.
The link between the nitrogenous base and the sugar
(nucleoside) is called a glycosidic bond.
 Chargaff’s Rule
Erwin Chargaff noted that certain pairs of bases,
namely, adenine and thymine, and guanine and
cytosine, are always found in a 1:1 ratio.
The number of pyrimidine residues always equals
the number of purine residues.
These findings are known as Chargaff’s rules: [A] =
[T]; [C] = [G]; [pyrimidines] = [purines]
Note that in RNA, adenine (A) pairs with uracil (U);
thymine (T) is not present in RNA.
  Nucleotide Polymer
The linkage of nucleotides into a polynucleotide
involves a dehydration reaction.
The nucleotides are link by phosphodiester bonds
that connects the sugar of two nucleotides.
This bonding results in a repeating pattern of sugar-
phosphate units called the sugar-phosphate
backbone.

 DNA and RNA Structure

The DNA is consists of two polynucleotide strands
wound together to form a long, slender, helical
molecule, the DNA double helix.
The strands run in opposite directions; that is, they
are antiparallel.
The two strands are held together in the double
helical structure through interchain hydrogen
bonds.
These H bonds pair the bases of nucleotides in one
chain to complementary bases in the other, a
phenomenon called base pairing.
On contrast, RNA does only have one
polynucleotide strand.