BIOCHEMISTRY LC1

OVERVIEW ON BIOCHEMISTRY

➔ The study of chemical substances found compounds are studied in bio-organic chemistry.
in living organisms and the chemical This area of biochemistry integrates a sense of
interactions of these substances with each reaction mechanisms, organic synthesis,
other. analytical methods, and structural analysis, with
primary and secondary metabolic reactions, cell
BRANCHES OF BIOCHEMISTRY recognition, biosynthesis, and chemical diversity
• MOLECULAR BIOCHEMISTRY of organisms.
This branch of biochemistry deals with the study METABOLIC BIOCHEMISTRY
of structures and functions of proteins, This is an area of biochemistry that involves the
carbohydrates, DNA, and other biomolecules. study of different types of metabolic pathways
It covers a detailed study of how the different from an organic and cellular level.
biomolecules interact with one another and carry Bioenergetics, nutritional biochemistry and
out biochemical reactions. clinical biochemistry are the disciplines that arise
• CELLULAR BIOCHEMISTRY from metabolic biochemistry. The organic
This branch of biochemistry deals with the study biochemical indices, cellular biochemical
of chemical processes occurring within the reactions, the molecular basis of metabolic
cells of organisms. It covers a detailed study of diseases, or intermediate metabolic flows are
how energy is produced in the cells, how the studied in this branch of biochemistry.
structure of cells is maintained, how the nutrients
are synthesised, stored, and used in the cells, and BIOCHEMISTRY CAN BE USED IN:
other cellular chemical processes. • Medical Science
• BIOCHEMICAL GENETICS • Agriculture
This branch of biochemistry discusses the role of • Food Industry
genes in the biochemical processes of various
organisms. It provides a detailed study of how
genes play a role in synthesising biomolecules IMPORTANCE OF BIOCHEMISTRY
like proteins and how they function • Biochemistry can help you increase your
crop productivity.
MAJOR AREAS OF BIOCHEMISTRY • It is critical for enhancing land quality by
STRUCTURAL BIOCHEMISTRY preserving vegetables and flowers, as
Involves the study of macromolecules and their well as assisting in the preparation and
chemical architecture. Being a major area of preservation of food materials.
biochemistry, it also covers a detailed study of • It is necessary to understand the actions
DNA, RNA, and proteins. of numerous genes as well as their
ENZYMOLOGY interactions with enzymes.
• It is useful in determining the nutritional
The area of biochemistry that studies the requirements of animals. It aids in the
behaviour of enzymes. provision of adequate nutrition and the
XENOBIOTICS elimination of malnutrition.
• To understand heredity in plants and
This major area of biochemistry involves the animals, geneticists rely on metabolic
study of the metabolic behaviour of certain reactions.
compounds. The chemical structure of these • It aids in the discovery of new drugs in
compounds is improper in the usual metabolism the pharmaceutical industry.
for a particular organism. While entering the • It explains how to use medications
human body, these compounds are likely to be properly.
secondary metabolites of some other organisms, • It is beneficial in the treatment of sick
non-existent in nature, or infrequent compounds. people and animals.
BIO-ORGANIC CHEMISTRY • It aids in the improvement of beneficial
This area of biochemistry involves the study of animal breeds and nutrition, as well as
organic compounds derived from living the study of herbicide and pesticide
organisms. These compounds are identified by activity.
their carbon-hydrogen and carbon-carbon
covalent bonds. Most of the carbon biological
 APPLICATION OF BIOCHEMISTRY: 9. Kidney Function: A lot of Biochemistry tools
1. Increase Fertility: The fertility of the crop can are used for a simple urine test that checks the
be increased with the help of the study of pH and the colour of the urine that changes
Biochemistry. The agriculturist uses the during the kidney issues.
Biochemistry tools to find out the conditions of
the plants and experiment accordingly to 10. AFP Test: Alpha-fetoprotein is used as a
improve their fertility. marker to test the poor liver function of the
patient and to know whether the patient has liver
2. Increase Growth: The reaction between the dysfunction on liver cancer.
pesticides and the crops in the cell is analysed by
the biochemist and does it contribute to rising
plant growth. Carl Alexander Neuberg
3. Disease Control: The study of Biochemistry
because of its versatility provides a large number
(1877-1956)
of treatments to help control plant diseases. ➔ He was an early pioneer in
Exclusion and eradication of disease plants falls biochemistry, and often referred to as
under few of such techniques that are used in the "Father of Biochemistry".
Biochemistry.
4. Animal Husbandry: Appropriate cultivation DIFFERENCE BETWEEN BIOINORGANIC
and growth of domestic animals falls under the SUBSTANCE AND BIOORGANIC SUBSTANCE
animal husbandry. Various Biochemistry tools are
used by the experts to diagnose disease in such
animals and provide control accordingly.
5. Soil Conditions: The soil condition, its
composition and its deficiency is comprehended
with the help of Biochemistry tools. Therefore,
this focuses primarily on enhancing the soil
condition and work on it .
6. Blood Test: Blood test suggest serum test for
diagnosing hepatitis falls under few of the crucial
blood tests where Biochemistry plays a crucial SPONTANEOUS GENERATION
role. Biochemistry tools are mostly used for the ➔ For much of history, people believed that
qualitative and quantitative analysis of liver animals could come from non-living
functioning. Moreover, it also analyses the blood sources. They thought:
sugar level in human blood. It also helps in ⮚ Frogs developed from falling
performing the urine test to find out the kittens drops of rain
where the complete blood count indicates the
overall health of a patient. All these tests are ⮚ mice arose from sweaty
related to the study of Biochemistry. underwear
7. Liver Test: In order to understand and assist ⮚ and flies arose from decaying
the liver condition of a patient it is important to meat
know a few Biochemistry tools. For qualitative ➔ This is called abiogenesis
and quantitative analysis the same PCR test is ➔ Also known as spontaneous generation
used. Also the Biochemistry techniques are used THEORY OF SPONTANEOUS GENERATION
for diagnosis of HCC. ➔ Aristotle proposed that life arose from
nonliving material if the material
8. Pregnancy Test: Biochemistry test and contained pneuma (“vital heat”).
techniques are also used to find out about the ➔ nonliving matter + heat = living matter
pregnancy. Urine test is required to find out about ➔ Evidence: Appearance of fish in a new
the gonadotropin hormone that a body produces. puddle of water
A particular blood test which is also known as
HCG test is done to find out about the pregnancy.
It indicates the initial level of human
gonadotropin which rises during the pregnancy.
 ADDITIONAL EXPERIMENTATION ➔ He predicted that preventing flies from
• Proponents of the theory cited how frogs having direct contact with the meat would
simply seem to appear along the muddy also prevent the appearance of maggots.
banks of the Nile River in Egypt during the
annual flooding.
• Others observed that mice simply
appeared among grain stored in barns
with thatched roofs. When the roof leaked
and the grain molded, mice appeared.

Jan Baptist
➔
Van Helmont
He is a 17th century Flemish scientist, who ➔ Francesco Redi’s experimental setup
consisted of an open container, a
proposed that mice could arise from rags container sealed with a cork top, and a
and wheat kernels left in an open container covered in mesh that let in air
container for 3 weeks. but not flies. Maggots only appeared on
the meat in the open container. However,
maggots were also found on the gauze of
the gauze-covered container.
Lazzaro Spallanzani
(1729–1799)
➔He performed hundreds of carefully
executed experiments using heated broth.
□In reality, such habitats provided ideal food ➔As in Needham’s experiment, broth in sealed
sources and shelter for mouse populations to jars and unsealed jars was infused with plant
flourish. and animal matter. Spallanzani’s results
contradicted the findings of Needham:
John Needham Heated but sealed flasks remained clear,
without any signs of spontaneous growth,
(1713–1781)
In 1745, published a report of his own
unless the flasks were subsequently opened
to the air.
➔This suggested that microbes were
➔
experiments, in which he briefly boiled introduced into these flasks from the air. In
broth infused with plant or animal matter, response to Spallanzani’s findings, Needham
hoping to kill all preexisting microbes. argued that life originates from a “life force”
that was destroyed during Spallanzani’s
He then sealed the flasks. After a few extended boiling.
➔Any subsequent sealing of the flasks then
➔
days, Needham observed that the broth prevented new life force from entering and
had become cloudy and a single drop causing spontaneous generation
contained numerous microscopic
creatures.
Louis Pasteur
➔ He argued that the new microbes must
have arisen spontaneously. In reality,
however, he likely did not boil the broth
enough to kill all preexisting microbes.
(1822-1895)
In 1858, Pasteur filtered air through a
➔
gun-cotton filter and, upon microscopic
Francesco Redi examination of the cotton, found it full of
microorganisms, suggesting that the
(1626–1697)
An Italian physicist who performed an
➔
exposure of a broth to air was not
introducing a “life force” to the broth but
rather airborne microorganisms.
experiment in 1668 that was one of the Later, Pasteur made a series of flasks with
first to refute the idea that maggots (the ➔
long, twisted necks (“swan-neck” flasks),
larvae of flies) spontaneously generate on in which he boiled broth to sterilize it.
meat left out in the open air.
 ➔ Pasteur’s experiment consisted of two parts.
In the first part, the broth in the flask was
boiled to sterilize it. When this broth was
cooled, it remained free of contamination. In
the second part of the experiment, the flask
was boiled and then the neck was broken
off. The broth in this flask became
contaminated.
➔ In a subsequent lecture in 1864, Pasteur
articulated “Omne vivum ex vivo” (“Life
only comes from life”). In this lecture,
Pasteur recounted his famous swan-neck
flask experiment, stating that “life is a
germ and a germ is life.”
JohnIn Tyndall
➔
(1820-1893)
1876, an English physicist John
conducted an experiment to support the
Pasteur’s experiment.
➔ He designed an apparatus to prove that air
carries particulate matter.
➔ From his experiment, he proved that pure
air is free of microorganisms. When this
pure air is introduced into life-supporting
media no microorganism was formed.
BIOCHEMISTRY LC2
CARBOHYDRATES
➔ Carbohydrate, as the name implies, CLASSIFICATION OF CARBOHYDRATES
consist of carbon, hydrogen, and
oxygen.
➔ Hydrate=(water) hydrogen and oxygen.
➔ General formula : Cx(H2O)y
➔ Basic formula : CH2O
➔ All have C=O and -OH functional groups.
➔ Classified based on
● Size of base carbon chain
● Number of sugar units
● Location of C=O MIRROR IMAGE
● Stereochemistry is the reflection of an object in a mirror.
SUPERIMPOSABLE
FUNCTIONS OF CARBOHYDRATES
Provide Energy mirror images are images that coincide at all
●
Structural components cellulose in plants points when the images are laid upon each
●
and chitin in arthropods. other.
● Transfer to other life molecules such as
lipids and protein NONSUPERIMPOSABLE
mirror images are images not all points
coincide when the images are laid upon each
other.

CHIRALITY
CHIRAL CENTER
is an atom in a molecule that has four different
groups bonded to it in a tetrahedral orientation.
CHIRAL MOLECULE
is a molecule whose mirror images are not
superimposable. Chiral molecules have
handedness.
ACHIRAL MOLECULE
is a molecule whose mirror images are
superimposable. Achiral molecule do not
possess handedness.
IDENTIFYING CHIRAL CENTER
1. A carbon atom involved in a multiple bond
(double or triple bond) cannot be a chiral
center since it has fewer than four groups
bonded to it. To have four groups present, all
bonds about the chiral center must be single
bonds.
2. A carbon atom that has two like groups bonded
to it cannot be a chiral center since it does not
meet the requirement of four different groups.
The commonly encountered entities -CH3 and
-CH2- in a structural formula never involve
chiral centers because of the presence of two or
more like hydrogen atoms.
3. Carbon atoms in a ring system, if not involved
in multiple bonding, can be chiral centers. Such
carbon atoms have four bonds—two to
neighboring atoms in the ring and two to
substituents on the ring. Chirality occurs when
both (1) the two substituents are different and
(2) the two “halves” of the ring emanating
from the chiral center are different.
EXAMPLE #1 (2-Butanol)

EXAMPLE #2 (Lactic Acid)

STEREOISOMERISM
➔ Stereoisomers are isomers that have the
same molecular and structural formulas
but differ in the orientation of atoms in
space.
TWO MAJOR STRUCTURAL FEATURES
(1) the presence of a chiral center in a
molecule
IDENTIFYING CHIRAL CARBON (2) the presence of “structural rigidity” in a
molecule.
★ Structural rigidity is caused by
restricted rotation about chemical
bonds. It is the basis for cis–trans
isomerism, a phenomenon found in
some substituted cycloalkanes.
TYPES OF STEREOISOMERS
ENANTIOMERS
➔ are stereoisomers whose molecules are
nonsuperimposable mirror images of each
other.

MONOSACCHARIDES
➔ also called sugars.
➔ The word sugar is associated with
“sweetness” and most (but not all)
monosaccharides have a sweet taste.
➔ The designation sugar is also applied to
disaccharides, many of which also have a
sweet taste. Thus sugar is a general
DIASTEREOMERS designation for either a monosaccharide
➔ are stereoisomers whose molecules are
or a disaccharide.
not mirror images of each other. CLASSIFICATION OF MONOSACCHARIDES

ALDOSE
➔ monosaccharide that contains an
HERMANN
EMILTheFISCHER
aldehyde group.
➔ polyhydroxy aldehydes.

➔ German chemist, the developer of the KETOSE

two-dimensional system for specifying
chirality, was one of the early greats in ➔ monosaccharide that contains a ketone
organic chemistry. functional group.
➔ polyhydroxy ketones.
FISCHER PROJECTION FORMULA
➔ a two-dimensional structural notation
for showing the spatial arrangement of
groups
➔ a chiral center is represented as the
intersection of vertical and horizontal lines
HANDEDNESS(D-L)
★ The handedness (right-handed or
left-handed) of the two enantiomers is
specified by using the designation of D
and L.
 Pyranose and Furanose
➔ A cyclic monosaccharide containing a
six-atom ring is called a pyranose, and one
containing a five-atom ring is called
furanose because their ring structures
resemble the ring structures in the cyclic
ethers pyran and furan, respectively.
THE THREE IMPORTANT DIETARY ➔ In a Haworth projection, the hemiacetal
MONOSACCHARIDES : ring system is viewed “edge on” with the
● Glucose, which is produced in plants oxygen ring atom at the upper right
during photosynthesis. (six-membered ring) or at the top
● Fructose, which is also produced in plants (five-membered ring)
during photosynthesis and found in fruit
juices and honey.
● Galactose, which is found in milk.

D-Glyceraldehyde and
Dihydroxyacetone
➔The simplest of the monosaccharides
➔ Important intermediates in the process of
glycolysis D and L Configuration
◦Glycolysis is a series of reactions whereby
glucose is converted into two molecules
of pyruvate.
◦D-Glyceraldehyde is a chiral molecule,
but dihydroxyacetone is not.
D- Glucose
➔ The most abundant in nature and the
most important from a human nutritional
standpoint.
➔ Ripe fruits, particularly ripe grapes
(20%-30% glucose by mass), are a good
source of glucose, which is often referred
to as grape sugar.
➔ Two other names for D-glucose are
dextrose and blood sugar.
➔ Cells use glucose as a primary source of
energy

HAWORTH PROJECTION FORMULA

➔ A two-dimensional structural notation that
specifies the three-dimensional structure
for a cyclic form of a monosaccharide