Biochemistry

Biochemistry

• Defined as: • Also can be defined more

 The science concerned formally as
with – The science concerned with
– the chemical basis of
• studying various
life
molecules that occur in
• Because life depends on
living cells and organisms biochemical rxn’s,
• Biochemistry has
• their chemical rxn’s and become the basic
processes that they language of all biologic
sciences
undergo

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 Biochemistry…(Cont’d)
• It encompasses large areas of Biochemistry is concerned with
– Cell Biology the entire spectrum of life forms,
– Molecular Biology – From viruses & bacteria to
& complex human beings
– Molecular genetics • Essential to all life sciences; e.g.
• The scope of Biochemistry is – Genetics
– as wide as life itself – Immunology
Whenever there is life, – Pharmacology
– Chemical processes – Physiology
are occurring – Toxicology
– Pathology
– Microbiology, etc

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 Biochemistry…(Cont’d)
 The study of biochemistry is  How the body drive energy for
essential to the normal day to day work?
 understand basic function  How the various metabolic
of the body process is interrelated?
 Give information regarding  What is the function of genes ?
the function of the cell at  What is the molecular bases for
molecular level… immunological resistance
 How the food we eat against invading organisms ?
digested,absorbed and used  Answer for such basic
to make ingredients of the question - systematic study
body? of Biochemistry

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 Biochemistry…(Cont’d)

Biochemistry divided in three

areas of study
1. Conformational –
structural and 3D
arrangement of the
Biomolecules
2. Metabolism – energy
production and utilization
3. Informational - language
for communication inside
and b/n cells

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 The Aim of Biochemistry
• The major objective of Biochemistry • determine their
is: structures &
• the complete understanding, at
• analyze how they
the molecular level, of all of
function
the chemical processes
associated with living cells • Many techniques have
been used for these
• To achieve this objective,
purposes;
Biochemists have sought to:
–Chromatography
• isolate the numerous
–Electrophoresis
molecules found in cells
–Ultracentrifugation
–Specific
sequencing
methods 6
 The Value of Biochemistry

• Study of human Biochemistry – but also provides a foundation

for understanding
– will open your eyes to how
the body works as a chemical • how to improve its
system operation
– e.g. by appropriate
• From a Health professional’s nutrition and exercise
point of view,
• how to diagnose problems
– Biochemistry not only &,
describes how the system – where possible, how to
works, remedy them

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 The Value…(Cont’d)
• Knowing Biochemistry:
• Thiazolidinediones;
– helps to understand current
– used in type 2
therapies, which include
diabetes
• recombinant proteins, such
– w/c act through cell
as
signaling systems
– Human insulin or  In the future, therapies will
Erythropoietin
possibly involve
synthesized by bacteria
 Gene rather than organ
– It helps to understand the
transplants
action of new drugs, such as

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A Reciprocal Relationships b/n Biochemistry & Medicine
Biochemistry and medicine are  intimately related
Health depends on a harmonious balance of  biochemical rxn’s occurring in
the body
Disease reflects abnormalities in biomolecules, biochemical rxn’s, or
biochemical processes

Examples of the 2-way street connecting Biochemistry & Medicine

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 Most & Perhaps All Disease Has a Biochemical Basis

• Biochemical approaches are often A sound knowledge of

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fundamental in
• illuminating the causes of diseases – Biochemistry & of other
& related basic disciplines is
• designing appropriate therapies essential for:
• Use of various biochemical Lab tests is • The rational practice of
• an integral component of
– Medical & related
– Diagnosis & Health sciences
– Monitoring of treatment
 Significance of biochemistry in clinical medicine
• Physiology: Biochemistry helps one understand
• the biochemical changes and
• related physiological alteration in the body.
• Pathology of any disease is studied through biochemical changes
• Pathology :Based on the symptoms described by the patient,
physician can get clue on the biochemical change and the
associated disorder.
• Hormonal deficiency :The formation, role of hormones in the
normal body function is taught in biochemistry by which the
physician can understand the concerned problem during
treatment.
• Nutrition deficiency: In the present scenario, many people rely
in taking multivitamin & minerals for better health. The
function and role of vitamin in body is described by
biochemistry. 11
 Significance of biochemistry in (MLT)nursing
• Kidney function test: urine test help understand the
extent of excretion of drugs or other metabolites, the
change in pH, the colour of urine etc
• Blood test: Indiabetes biochemical test :
– the blood glucose level helps one understand the severity of
diabetes disorder.
– test for ketones bodies in urine also indicates the stage of
diabetes..
• Serum cholesterol test: Evaluation of blood cholesterol
level and other lipoproteins helps understand the
proneness of the patient to cardiovascular diseases.
• Liver function tests helps understand the type of disease
or damage to liver, the effect of any medication on liver
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.
Metabolic Processes Occur in a Variety of Spaces within Cells

• Most metabolism • Such compartmentalization is

important for several reasons:
occurs;
– within the complex ecosystem – to protect from autodigestion
of the cell, in subcellular – to concentrate pathways &
organelles such as:
metabolites in space
• nucleus, cell membrane,
• rough and smooth ER, – to enable different pathways,
• GA, such as;
• mitochondrion, – synthesis & degradation
• lysosomes, or of proteins,
• peroxisomes.
• to operate at the same time

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 Cell and an organelles
 Is the fundamental unit of life Types of cells
 Cell theory 1. Prokaryotic
 Cell make up all living 2. Eukaryotic
matter
Prokaryotic include
 All cell arise from other
 Bacteria and cyanobacteria
cells
Characteristics
 The genetic information
 Has a minimum of internal
pass from one generation to
the other next generation organization and small in size
 The chemical rxn of an  Doesn't have any membrane
organism takes place in bounded organelles
cells

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 Cell and an organelles cont…

 Its genetic material is not Characteristics

enclosed in nuclear  Considerable degree of internal
membrane structure with a large number of
 Its DNA is not complexes distinctive membrane enclosed
with histones having specific function
2.Eukaryotic  The genetic material is enclosed
Include by nuclear membrane
 Protista ,fungi, plants &  Contain many membrane
animals bounded organelles that carry
out secullar processes

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Chemical composition of the living cell
 H,C,O and N make 99+% of  These elements are the back
atoms in the human body bone of Biomolecules
 Element percentage  Carbohydrate
 Oxygen - 63  Protein
 Hydrogen - 25.2  Lipids
 Carbon - 9.5  Nucleic acids
 Nitrogen - 1.4 b/c of they are forming
strong covalent bonds

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Biomolecular Hierarchy

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Water
 2.2. water
•Major component of a cell is Water and accounts for the high
percentage (by weight) of oxygen.
•All living cells are depend on water for their existence
• In cells it accounts for 60% to 90% of the mass of the cell.
• An understanding of water and its properties is important to the study
of biochemistry.
• The macromolecular components of cells like proteins,
polysaccharides, nucleic acids, and lipids—assume their characteristic
shapes in response to water.

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For example, some types of molecules interact with water
and, as a result, are very soluble.

While other molecules do not dissolve easily in water and

tend to associate with each other in order to avoid water.
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• Most of metabolic machinery of cells has to
operate in an aqueous environment because
water is an essential solvent.
• The physical properties of water allow to act as a
solvent for ionic and other polar substances.
• The chemical properties of water allow to form
weak bonds with other compounds, including
other water molecules.
• Structurally, water molecule (H2O) has V-shaped
polar structure and the angle between the two
covalent (O—H) bonds is 104.5°.

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 3. Proteins
• Proteins are the most abundant class of organic
compounds in the healthy, lean human body, constituting
more than half of its cellular dry weight.
• Proteins are polymers of amino acids and have molecular
weights ranging from approximately 10,000 to more than
one million.
• Biochemical functions of proteins include catalysis,
transport, contraction, protection, structure, and
metabolic regulation.
• The properties of proteins depend on the characteristic
sequence of component amino acids, each of which has
distinctive side chains.
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 3.1. Amino acids
 Amino Acids are the monomers of proteins.
 When linked together with peptide bond they form proteins.
 There are about 300 amino acids occur in nature.
 How ever, there are only 20 of standard L-alpha amino acids occur in proteins of
the living organism.
 But later scientists found other 3AA in the proteins of an organism.
• Proteinogenic amino acids:-
 are the L-alpha-amino acids and are incorporated into polypeptides and
proteins.
 are encoded by the Genetic Code (the nucleotide sequence of the gene and
of mRNA).
 Of the 23 proteinogenic amino acids, 20 are “standard” L-alpha amino
acids.
 The other three, "specialized" proteinogenic amino acids are:
• selenocysteine (Sec, U)
• pyrrolysine (Pyl, O) 24
• N-formylmethionine
The 20 standard L-ά amino acids encoded by genetic code

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 Properties and features of L-alpha amino acids:
1. Amphoteric:-
 have both acidic and basic groups and properties,
 due to the presence of an alpha-carboxyl group and an
alpha-amino group.
[Note: Glut, asp, hist, arg, and lysine have additional
potentially charged groups in their side chains.]
Substances, such as amino acids, that can act either as
an acid or a base are defined as amphoteric, and are
referred to as ampholytes (amphoteric electrolytes).
2. The side-chain (R):-
 is important in determining the overall chemical properties
and function of an amino acid. 26
3. zwitterions:-
 They can exist as (neutral molecules containing both positive and
negative charges) in the same molecule.
 The amino acids usually exist as zwitterions at physiological pH.
 At low pH they exist as positively charged ions and at high pH they
exist as negatively charged ions.
 The pH at which an amino acid has an overall neutral charge is
called its isoelectric point (pI). The molecule below is alanine and
its isoelectric point occurs at pH 6.0

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 3.1.1. Structure of amino acids.
• The L-alpha amino acids of proteins consist of an alpha-
carbon atom covalently joined to four groups:-
 hydrogen atom (H)
 carboxyl (-COOH) group,
 an amino (-NH3) group, and
 a side-chain(R).
Basic structure of
an or-amino acid.
This structure is common to
all except for Proline, (a cyclic
amino acid)

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 3.1.2. Classification of amino acids
• The side-chains (R-group) determine the properties and
functions of amino acids in proteins.
• Therefore a useful classification of the amino acids is based on
the nature of the side chains (R groups).
• so, according to their R group AAs are classified as follows;
 Aliphatic (hydrophobic) side-chain: Gly, Ala, Val, Leu, Ile
 Hydroxyl (-OH) side-chain: Ser, Thr, Tyr
 Aromatic side-chain: Phe, Tyr, Trp
 Negatively charged(Acidic) side-chain: Asp, Glu
 Acid amide side-chain: Asn, Gln
 positively charged(Basic) side-chain: Arg, Lys, His
 Sulphur-containing side-chain: Met, Cys
 Cyclic (imino acid): Pro
 Polar/ uncharged side-chains: (Ser, Thr, Gln, Asn)
 Hydrophobic: (Ala, Val, Leu, Ile, Met, Phe, Tyr, Trp) 29
 Glycine (Gly, G),
• differs from the other amino acids because its
side-chain is a hydrogen atom and it lacks an
asymmetric alpha-carbon atom
• The glycine side-chain (H) is small and so it can fit
into small pockets of protein structure and also
create flexible ( moveable) areas of polypeptide
chains.

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 Alanine (Ala, A),
• has a methyl group side-chain and
• is hydrophobic, aliphatic.
• It can occur either within or on the outside of
proteins.

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 The branched-chain amino acids
• leucine(Leu, L), isoleucine (Ile, I) and valine (Val, V) are
– aliphatic,
– hydrophobic amino acids and
– tend to occur within the interiors of proteins.

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 Acidic amino acids
1) aspartic acid (Asp, D) and
2) glutamic acid (Glu, E).
– These have negatively charged side-chains and
– are usually on the surface of proteins,
– often involved in catalysis and binding of positively
charged structures.

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 Amide-containing amino acids
1. asparagine (Asn, N) and
2. glutamine (Gln, Q).
– They have polar, uncharged amino acid side-chains

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 The basic amino acids
1. arginine (Arg, R),
2. lysine (Lys, K) and
3. histidine (H).
• They have positively charged side-chains.
• Histidine is frequently involved in catalysis or
• binding to heavy metal ions.

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 The aromatic amino acids

1. phenylalanine (F),
2. tyrosine (Y) and
3. tryptophan (W).

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 The hydroxyl group-containing amino acids
1. serine and
2. threonine.
3. tyrosine (Tyr, Y) – an aromatic amino acid,
– They contain –OH group

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 proline (Pro, P).
• Is an imino acid
• is not really an amino acid but an imino acid.
• Has a rigid structure that allows proline to
have an important role in protein structure, by
causing rigid “turns” in polypeptides.

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 Essential & non-essential AAs
a) Essential AAs :- cannot be synthesized in our
body
E.g. Val, Ile, Thr, Trp, Arg, Leu, Lys, Met, Phe, His
b) Non-essential AAs:- can be synthesized in our
body from other AAs or metabolites
• E.g. Glu, Gln, Asp, Asn, Gly, Ala, Pro, Tyr, Ser, Cys.

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 3.2. Classification of Proteins
• Proteins are the high molecular weight polymers
composed of a-amino acids united to one
another by peptide linkage (-CO-NH-).
• Proteins are the major constituents of all living
organisms.
• They contain carbon, hydrogen, nitrogen, oxygen
and sulphur.
• Proteins are classified into 3 main groups.
1. Simple protein
2. Conjugated protein
3. Derived proteins 40
1. Simple protein : These proteins on hydrolysis
yield only ά-amino acids. (eg).
 Albumin,
 Globulin
2. Conjugated protein
• simple proteins + non-protein part called as
prosthetic groups.
• They are further subdivided into:
a. Nucleo protein
b. Phosphoprotein
c. Glycoprotein
d. Chromoprotein
e. Lipoproteins
f. Metalloproteins 41
 a. Nucleo protein: b. Phosphoprotein :
present along with nucleic acids
contains phosphoric acid.
– (eg) Histones and  (eg) casein of milk.
– Protamines
c. Glycoprotein :
d. Chromoprotein :
contains carbohydrate moiety as contains heterocyclic compounds
prosthetic group. (eg.) Like Porphyrins as the prosthetic
– Gonadotropic hormone, group. (eg)
– mucous glycoprotein mucin Hemoglobin and
(saliva) and Myoglobin
– osseomucoid(bone)
f. Metalloproteins :
e. Lipoproteins :
contain metal as prosthetic group.
These are proteins conjugated with
(eg)
lipids. (eg)
– chlyomicron,
• Siderophilin (Fe) and
– very low density lipoprotein
• Ceruloplasmin (Cu).
(VLDL),
– low density lipoprotein (LDL)
and 42
–
3. Derived proteins :
derived from the simple and conjugated proteins by
the action of acids, alkalies or enzymes.
Simple protein + conjugated protein
•Acids
•Alkalies or
•enzymes

Drived protein
• They are the products resulting from partial to
complete hydrolysis of proteins. (eg.)
– proteoses,
– peptones and
– peptides. 43
 Functions of proteins.
1. Proteins are the essence of life processes.
2. They are the fundamental constituents of all protoplasm and are involved in the
structure of a living cell and in its functions.
3. Catalytic proteins
Enzymes are proteins which act as biocatalysts. (eg.)
– amylase,
– carbonic anhydrase etc.
4. Proteins serve as components of the tissues holding the skeletal elements together.
5. Nucleoproteins
Are found in association with nucleic acids and serve as carrier of genetic characters
and hence govern inheritance of traits. Eg:
 Histones
6. Transport proteins
• They are capable of binding and transporting specific types of molecules via blood.
(eg)
– hemoglobin and
– albumin.
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7. Hormonal proteins
– Some hormones are proteins which regulate numerous physiological
functions.eg.
 growth hormone,
 insulin and
 glucagon
8. They function in the homeostatic control of the volume of the circulating
blood.
9. Defensive or protective proteins.
• Some proteins have protective or defensive functions. Eg:
– thrombin and fibrinogen participate in blood clotting.
– Antibodies or immunoglobulin's are protective proteins against infections
10. Contractile proteins
 actin  
• Some Proteins function as essential elements in contractile and motile
systems in skeletal muscle. eg: myosin
– actin and   actin 
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– myosin
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