Introduction and Amino Acids and Proteins

Introduction To Medicine Module
Biochemistry and Molecular biology
By Eido (MSc)
1
Introduction…
What is biochemistry ?
INTRODUCTION…
Definition
Biochemistry is the study of the structure, composition, and chemical
reactions of substances in living systems.

Science concerned with chemical basis of life.
Biochemistry gives answer for the following questions:
how living things obtain energy from food?
what is the chemical basis of heredity? and
what fundamental changes occur in disease?

When the concept of biochemistry started?
 The discipline of biochemistry developed as chemists began to study the
molecules of cells, tissues, and body fluids and
 physicians began to look for the molecular basis of various diseases.
 Today, the practice of medicine depends on understanding the roles and

interactions of the huge number of different chemicals enabling our
bodies to function.
 From a biochemist’s point of view, most metabolic diseases are caused by

enzymes and other proteins malfunction and the pharmacological drugs
used to treat these diseases correct that malfunction.
Introduction(Cont’d) …
Biochemical basis of health and disease
WHO defines ‘health’ as a state of complete physical, mental

and social well-being not merely the absence of disease and
infirmity.
From a biochemical point of view, health may be considered
as a situation in which all of intra-and extra-cellular
reactions that occur in the body are proceeding at rates
adequate with the organism’s maximal survival in the
physiologic state.
5 By Eido, Biochemist 3/9/21
Introduction(Cont’d) …
A disease state, on the other hand, could be defined as the

condition in which the speed, direction and/or occurrence of the
reactions is altered to affect the physiological processes of the body.
These alterations could be caused by any one of the following:
i. Physical agents: Mechanical trauma, extremes of temperature,

sudden change in atmospheric pressure, radiation and electric shock.

Introduction… (Cont’d)
• These physical forces disrupt the structural organization of the cells or cellular
organelles; or they cause imbalance in the normal interplay of the
biomolecules.
• Ionizing radiations generate:
 Free radicals and
Reactive oxygen species
• that can break the bonds in molecules, even modify nitrogen bases in the DNA
and cause gene mutations.
• Antioxidants like Vitamins E, C and Beta carotene can prevent free radical
attacks.
ii. Chemical agents, including drugs: The toxic compounds and

therapeutic drugs can also trigger a disease process.
• The toxins could interact and, thus, inhibit the action of enzymes;
disturb a transport channel in the cell membrane; disrupt the
energy generation or its utilization.
iii. Biologic agents: Viruses, bacteria, fungi and higher forms of

parasites can infect/infest the human body and disturb the normal
homeostasis, leading to disease.

• Investigation into metabolic differences between these

microorganisms and human beings has led to the development of
antibiotics and other drugs to control and fight this kind of disease.
iv. Oxygen deficiency: This can lead to energy deficiency thereby

lead to cell death or necrosis of the tissue.
v. Nutritional imbalance: e.g diseases caused by vitamin

deficiency, and kwashiorkor and marasmus are caused due to
protein-energy malnutrition disorders.

• Today, thanks to biochemists, we know much more about the value of balanced
nutrition and the importance of various nutritional components of our diet so as
to eat the healthy food for the best upkeep of our health.
vi. Endocrine imbalance: Hormones maintain the homeostasis of metabolism in

our body.
• The metabolic disturbance due to the deficiency or excess of one or more

hormones can participate in a disease state.
• In biochemistry, we study the mechanisms by which hormones influence the

metabolism, the receptors and the signal transduction molecules that
mediate these actions.
vii. Autoimmunity: Immune system gets triggered against molecules that

are components of one’s own body.
• Therefore; health depends on a harmonious balance of biochemical
reactions occurring in the body, and disease reflects abnormalities in
biomolecules, biochemical reactions, or biochemical processes;
• This is the main concerns of medical biochemistry.

• Biochemistry is important in solving health problems such as:
metabolic disorders
nutritional problems
diagnostic problems
drug interactions and others

Role of Biochemistry:

The major objective of biochemistry is the complete understanding, at the

molecular level, of all of the chemical processes associated with living cells.
 To achieve this objective, biochemists have sought to:
Isolate the several molecules found in cells,
Determine their structures, and
Analyze how they function

Role of Biochemistry…
The biochemistry of the nucleic acids lies at the heart of genetics; in turn, the use
of genetic approaches has been critical for elucidating many areas of biochemistry.
Physiology, the study of body function, overlaps with biochemistry almost

completely.
 Immunology employs numerous biochemical techniques, and many immunologic

approaches have found wide use by biochemists.
Relation of Biochemistry with others
Pharmacology and pharmacy rest on a sound knowledge of biochemistry and
physiology; in particular, most drugs are metabolized by enzyme-catalyzed reactions.
Poisons act on biochemical reactions or processes; this is the subject matter of

toxicology.
Biochemical approaches are being used to study basic aspects of pathology (the study
of disease), such as
Inflammation,
Cell Injury, And
Cancer.
All diseases are manifestations of abnormalities of molecules, chemical reactions, or
biochemical processes.
Relation of Biochemistry with others…
Many workers in microbiology, zoology, and botany employ biochemical

approaches almost exclusively.
These relationships are not surprising, because life is depends on biochemical

reactions and processes.
The old barriers among the life sciences are breaking down, and biochemistry is
becoming their common language.
Relation of Biochemistry with medicine
CELL AND CELL ORGANELLES: CHEMISTRY AND FUNCTIONS
CELL AND CELL ORGANELLES…
All organisms are built from cells.
 All animal tissues including human are also organized from collections of cells.
Thus cell is the fundamental unit of life. If cell dies, tissue dies and it cannot
function.
Cell death is classified into two
Necrosis: Unprogrammed cell death cause inflammation
Example accidental injuries on cell
Apoptosis: programmed cell death which never cause inflammation
Example: RBC dies after 120 days
CELL AND CELL ORGANELLES…
Modern cell theory can be divided into the following fundamental statements:
Cells make up all living matter
All cells arise from other cells
The genetic information required during the maintenance of existing cells and the production of
new cells passes from one generation to the other next generation
The chemical reactions of an organism both anabolism and catabolism, takes place in the
cells.
Types of Cells
In general two types of cells exist in nature.

1. Prokaryotic cells
2. Eukaryotic cells
1. Prokaryotic Cells
 Typical prokaryotic cells (Greek: Pro-before and karyon nucleus) include
the bacteria and cyano bacteria.
 Most studied prokaryotic cell is Escherichia coli (E. coli).

Prokaryotic Cells…
Characteristics
• It has a minimum of internal organization and smaller in size
• It does not have any membrane bound organelles.
• Its genetic material is not enclosed by a nuclear membrane
• Its DNA is not complexed with Histones.
Histones are not found in prokaryotic cells

• Its respiratory system is closely associated with its plasma membrane and
• Its sexual reproduction does not involve mitosis or meiosis.
Prokaryotic Cells…
2. Eukaryotic Cells
The eukaryotic cells (Greek: Eu-true and karyon-nucleus) include the protists,
fungi, plants and animals including humans.
Cells are larger in size.
Characteristics
 It has considerable degree of internal structure with a large number of
distinctive membrane enclosed having specific functions
Nucleus is the site for informational components collectively called chromatin
Sexual reproduction involves both mitosis and meiosis
 The respiratory site is the mitochondria
Eukaryotic Cells…
DIFFERENCES OF PROKARYOTIC AND EUKARYOTIC CELLS
CELL ORGANELLES
ORGANELLES
• Organelles are structures inside a cell with some distinguishing
functions.
• These sub cellular structures have different biochemical activities and
play different roles within the cell.
• Compartmentalization of metabolic pathways inside organelles
increases the potential for controlling and also enhances its efficiency.

Cell Organelles…
1. Plasma Membrane
• It is also known as:
plasmalemma
cell membrane
cytoplasmic membrane
• It is the outermost boundary of a cell.
• It is not only regulates entry of the nutrients and exit of wastes, but also serves as a
communicator with the surrounding tissues.

Eukaryotic cells… (Cont’d)
• It is a thin, flexible, elastic structure 7.5-10nm thick

lipid bilayer membrane that surrounds the cytoplasm of
the cell.
• It is a fluid mosaic of membrane proteins floating in a
phospholipid bilayer.
• Lipid bilayer of the plasma membrane plays more of a
structural role (although membrane lipids give rise to
biologically active substances like second messengers);
whereas the proteins could be said to be the functional
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components of the membranes.
By Eido, Biochemist 3/9/21
Fluid Mosaic structure
Plasma Membrane … (Cont’d)
The membrane proteins are classified as:
 Integral proteins: span the lipid bilayer of the cell

membrane
 Peripheral proteins: attached to the membrane surface
lipids or integral proteins.
These proteins may be:
 Channels or transporters: Move molecules in one

direction.
 Receptors: Recognize certain chemicals (hormones, drugs,
and growth factors).
 Glycoproteins: Identify cell type.
Types of Membrane Proteins
Plasma Membrane … (Cont’d)
• Phospholipids bilayer is made from the fatty acids with

phosphate groups making two layers of the cell
membrane.
• Fatty acids are hydrophobic tails that face each other in
the membrane and the phosphate groups are hydrophilic
heads and faces to the polar surface.
• It is a semi-permeable membrane and restricts the entry

and exit of compounds by the aid of carrier proteins.

Amphipathic Property of membrane
Cell… (Cont’d)
• Proteins and lipids on the surface may contain bound

carbohydrate chains and termed as glycoproteins and
glycolipids respectively.
• This layer of carbohydrate is called the glycocalyx.
• The glycocalyx protects the cell against digestion and

restricts the uptake of hydrophobic compounds .
• These carbohydrate chains can also serve as cell
recognition molecules.

Direction of the component
TRANSPORT ACROSS MEMBRANE…
inside cell
lipid
NH3 salt
sugar aa H2 O
outside cell
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TRANSPORT ACROSS MEMBRANE…
Membrane becomes semi-permeable with protein channels
specific channels allow specific material across

cell membrane
inside cell H2 O aa sugar
outside
NH 3
cell salt
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Models & mechanisms of protein pumps
• Primary active transporters-generate energy themselves (e.g. ATP
hydrolysis)
• Secondary transporters-utilize energy stored in voltage and ion gradients
generated by a primary active transporter (e.g. Na +/K+-ATPase)
 Symporters (Co-transporters)
 Antiporters (Exchangers)
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antiport symport
2. The nucleus / nucleoid
All cells have it for at least some part of their

life.
Control center of the cell
Contains DNA
Surrounded by a double membrane
Usually the easiest organelle to see under a
microscope
Usually one per cell
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Nucleus…
The nucleus contains more than 95 per cent of the cell’s DNA and is the control
centre of the eukaryotic cell.
• Nuclear envelope: A double membrane structure called the nuclear envelope

separates the nucleus from the cytosol.
• Nuclear pore complexes: These are embedded in the nuclear envelope.
These complex structures control the movement of proteins and the nucleic acid
ribonucleic acids (RNAs) across the nuclear envelope.
Nucleus …
• Chromatin: DNA in the nucleus is coiled into a dense mass called chromatin, so
named because it is stained darkly with certain dyes
Nucleolus: A second dense mass closely associated with the inner nuclear
envelope is called nucleolus.
• Nucleoplasm: Nucleoplasm of nucleus contain various enzymes such as DNA

polymerases, and RNA polymerases, for m-RNA and t-RNA synthesis.
Nucleus…
Functions
 DNA replication and RNA transcription of DNA occur in the nucleus.
Transcription is the first step in the expression of genetic information and is the
major metabolic activity of the nucleus.
 The nucleolus is nonmembranous and contains RNA polymerase, RNAase, ATPase

and other enzymes but no DNA polymerase.
Nucleolus is the site of synthesis of ribosomal RNA (r-RNA).

 Nucleolus is also the major site where ribosome subunits are assembled.
Cell… (Cont’d)
3. Cytoplasm
• It is the internal volume (intracellular space other than the organelles) bounded
by the plasma membrane.
• It is composed of an aqueous solution, the cytosol and a variety of suspended

particles (organelles).
• Cytosol is the soluble part of cytoplasm.
• This soluble part of the cytoplasm contains many proteins including enzymes for:
glycolysis, pentose phosphate path way, and many other biosynthetic pathways.

Cytoplasm … (Cont’d)
• It contains:
enzymes and RNA molecules that encode them.
small organic molecules such as proteins, Carbohydrates, lipids…
intermediates of biosynthetic and degradative pathways.
coenzymes and inorganic ions.
• Proteins are synthesized in the cytosol of cytoplasm on the ribosomes.

Cytoplasm … (Cont’d)
• The cytoplasm also contains other non-membranous structure such as fat droplets
and glycogen.
• Cytoplasm is the site for metabolism of carbohydrates, lipids, proteins, and

nucleic acids through sequential reactions (pathways).
• Major pathways taking place in the cytosol include: glycolysis, glycogenesis,

glycogenolysis, hexose monophosphate shunt, gluconeogenesis, fatty acid
synthesis, synthesis of other lipids, metabolism of amino acids and nucleotides,
part of the urea cycle and metabolism of heme, etc.

4. Mitochondrion:
Mitochondrion is the power house of cell
• Number: The number of mitochondria in a cell varies dramatically.
Some algae contain only one mitochondrion, whereas the protozoan contain half a
million.
 A mammalian liver cell contains from 800 to 2500 mitochondria.
• Size: They vary greatly in size. A typical mammalian mitochondrion has a
diameter of 0.2 to 0.8 and a length of 0.5 to 1.0μm
• Shape: The shape of mitochondrion is not static.
Mitochondria assume many different shapes under different metabolic conditions.
• Mitochondria occur in almost all higher animal cells, except in erythrocytes.

Mitochondrion…
Structure and Functions

The mitochondrion is bounded by two concentric membranes that have markedly
different properties and biological functions.
Mitochondrial Membranes
(a) Outer mitochondrial membrane
• The outer membrane forms smooth envelope and it is freely permeable to most
substances.
• Relatively few enzymes are associated with it.
• It is the lipid-rich membrane composed of phospholipids and cholesterol.

The outer membrane also contains many copies of the protein called Porin.
Mitochondrion…
Functions of Porin and other Proteins

(i) These proteins faorm channels that permit substances with molecular weights of
less than < 10,000 to diffuse freely across the outer mitochondrial membrane.
Mitochondrion…
(b) Inner mitochondrial membrane: The inner mitochondrial membrane is very rich in
proteins and the ratio of lipid to proteins is only 0.27:1 by weight.
In contrast to outer membrane, the inner membrane is virtually impermeable to polar
and ionic substances.
These substances enter the mitochondrion only through the mediation of specific
transport proteins.

• Cristae: The inner mitochondrial membrane is highly folded.
The tightly packed inward folds are called “cristae”.
Mitochondrion…
(c) Intermembrane space: The space between the outer and inner membranes is
known as the intermembrane space.
Since the outer membrane is freely permeable to small molecules, the
intermembrane space has about the same ionic composition as the cytosol.
(d) Mitochondrial matrix: The region enclosed by the inner membrane is known as the
mitochondrial matrix.
Composition of matrix: The enzymes responsible for citric acid cycle and fatty acid
oxidation are located in the matrix.
The matrix also contains several strands of circular DNA, ribosomes and enzymes
required for the biosynthesis of the proteins coded in the mitochondrial
genome.
The mitochondrion is not, however, genetically autonomous, and the genes
encoding most mitochondrial proteins are present in nuclear DNA.
Mitochondrion…
Functions
• Many enzymes associated with carbohydrates, fatty acids and nitrogen metabolism
are located within the mitochondrion.
Enzymes of electron transport and oxidative phosphorylation are also located in

different areas of this cell organelle.
The mitochondrion is specialized for the rapid oxidation of NADH (reduced NAD)
and FAD. H2 (reduced FAD) produced in the reactions of glycolysis, the citric acid
cycle and the oxidation of fatty acids.
The energy produced is trapped and stored as ATP, for future use of energy in the
body.
Cell… (Cont’d)
5. Ribosomes
• Not surrounded by a membrane.
• Composed of protein and ribosomal RNA.
• Made in the nucleolus.
• The site of protein synthesis in a cell.
• The most common in almost all cells.
54 By Eido, Biochemist
Ribosomes … (Cont’d)
• Exist in two sizes:
70s are found in all Prokaryotes, chloroplasts and mitochondria and

they are free-floating.
80s are found in all eukaryotic cells – attached to the rough endoplasmic
reticulum.

Ribosomes … (Cont’d)
• Most antibiotics work by blocking bacterial protein

synthesis by acting on one of the subunits (prevent
bacterial multiplication).
Fig: Ribosome structure

Cell… (Cont’d)
6. Endoplasmic reticulum (ER)
• Double membranous channels that are continuous with the

nuclear membrane.
• It traverses the cytosol of eukaryotic cells.
• Forms channels through the cytoplasm thereby helps in the

transport of various substances within the cell

Endoplasmic reticulum … (Cont’d)
• On the basis of its appearance as well as function, there are two
types of ER:
i. Smooth endoplasmic reticulum (SER)- lacks ribosomes.
ii. Rough endoplasmic reticulum (RER)- contains ribosomes

attached.

•The RER (ergastoplasm) involved in:
 Protein synthesis with help of ribosomes which are attached to the channels on
the surface: The protein is either secreted, sequestered within membrane-
enclosed organelles or embedded in the plasma membrane.
 Post-translational modifications of these proteins such as glycosylation.
• The RER is attached to the cell membrane and synthesizes secretory proteins, e.g,
digestive enzymes
• The internal structure of ER is called cisternae.

• The SER involved in the:
 Synthesis and transport of lipids, synthesis cholesterol and steroid

hormones.
 Detoxification of drugs and toxic chemicals such as ethanol.
 Storage of glycogen in regions of liver cells that are rich in SER.
 Storage of Ca2+ in muscle cells.
 It also carries enzymes for modification of the proteins

synthesized in RER.

Cell… (Cont’d)
7. Golgi complex (Golgi apparatus)
• Composed of a curved stack of membrane-bound flattened vesicles known as

cisternae (singular: cisterna) in the cytoplasm.
• It is derived from ER.
• Involved in sorting of cellular components and the post-translational

modification of proteins (secretion of proteins).

Golgi complex … (Cont’d)
• Often called the "shipping department" of the cell; it packages,
sorts and distributes them to lysosomes, secretory vesicles or the
plasma membrane.
• Also involves in the transport of lipids around the cell.

Cell… (Cont’d)
8. Lysosome
• Are large membrane vesicles that are formed from pieces of the Golgi
apparatus that break off.
• Its size varies from 0.1–1.2μm.
• Enclosed by a single membrane that prevents the release of the

digestive enzymes into the cytosol.
• Release of lysosomal enzymes has been implicated in the causation of a
number of allergic conditions, inflammation, and arthritis.

Lysosome … (Cont’d)
• Contains hydrolytic enzymes for the degradation of proteins, nucleic

acids, lipids, and carbohydrates.
• For instance: hydrolase enzymes such as nucleases, phosphatases,
glycosidases, esterases and proteases.
• pH inside the lysosome is maintained near 5.5 by vesicular ATPases
which actively pump protons into the lysosome.
• (This pH is optimal for these hydrolases).

• Lysosomes are ‘hydrolytic bodies of the cell’, involved in the

digestion or destruction of the foreign bodies, cellular debris or the
excess/waste biomolecules.
• It is cells' garbage disposal system - eliminates unwanted materials
and recycles its components.
 digestion of invading microbes and dying cells.
 digestion of excess, damaged or wornout organelles and abnormal proteins and

recycling them.
 endocytosis of receptor proteins and recycling.

Generally, lysosomes are responsible for the degradation of macromolecules taken into
the cell by endocytosis and for the degradation of unwanted intracellular
biomolecules, by the process known as autophagy, and for the complete destruction of
cellular structure after cell death by the process known as autolysis.
• It is the site of food digestion in the cell.

9. Peroxisome
• It is single membrane bounded organelle, similar in size

to lysosomes.
• Involves certain enzymes that carry out oxidation-
reduction reactions.
• Many of these oxidation reactions generate hyperactive
superoxide free radicals.
• Contain catalase that degrade the toxic chemical
hydrogen peroxide /H2O2 / produced by fatty acid
oxidative reaction.
Peroxisome … (Cont’d)

Peroxisome… (Cont’d)
• Peroxisomes function in:
 metabolic reactions like oxidative deamination of amino acids and

oxidative catabolism of long chain and branched chain fatty.
 Since these organelles do not have an associated electron transport chain
to harvest energy, no energy is harvested during these pathways.
 the conversion of cholesterol to bile acids.
 the synthesis of plasmalogens.

 the synthesis of cholesterol.
 the breakdown of excess purines to uric acid.
• They have no DNA but self replicate by fission.
• They are dependent on the import of proteins to make copies of

themselves.


Cell… (Cont’d)
Biochemical Composition of the Cell
• The different substances that make up the cell are

collectively called protoplasm.
• The protoplasm consists:
 Inorganic substances (H2O, mineral salts (ions) and gases like O2 and Co2), and
 Organic substances (proteins, carbohydrates, lipids and nucleic acids).

Water
• Water is the most abundant substance in living system

that makes up 70% or more of the total weight of most
organisms.
• It is polar covalent molecule with two lone pair electrons

on the oxygen.
• Due to the polar nature of water molecule, weak
intermolecular non covalent bonds known as hydrogen
bonds are formed in addition to the covalent bond between
74 oxygen and hydrogen.
Water… (Cont’d)
Functions (Importance) Water
Water is a solvent for many ionic and neutral compounds.
Water is involved in metabolism. E.g. digestion

/hydrolysis.
It solubilizes and modifies the properties of biomolecules
such as carbohydrates, proteins, and nucleic acids by
forming hydrogen bond.
Hydrogen bond plays an important role in stabilizing the
structure of macromolecules, particularly, proteins and
nucleic acids (DNA and RNA).
Functions of Water… (Cont’d)
Water is important to maintain the structure and

functions of macromolecules of cells. E.g. Proteins, lipids
etc.
Regulation of body temperature by evaporating the
moisture in the lung and from the skin.
 Water is the main constituent of all body fluids.

 Removal of waste materials from the body.
 It bathes our cells, dissolves and transports compounds

in the blood.
 It provides a medium for the movement of molecules

into and throughout cellular compartments.
 Due to its high degree of cohesiveness, it is used for

transporting dissolved nutrients from roots to leaves.
 It separates charged molecules.

 It acts as “heat buffer” because of the specific heat of

water to keep the temperature constant.
 It participates in chemical reactions.
• Total body water is distributed between two main

compartments.
i. Intracellular fluid: this is fluid within cell.
ii. Extracellular fluid: this is all the fluid outside the body
cell.

Water… (Cont’d)
Water balance
• It means that water intake is equal to water loss.
• Excessive water loss is due to:
 In kidney disease due to limited reabsorption.
 Diarrhea and vomiting.
 Fever due to excessive sweating.
 High environmental temperature.

Water… (Cont’d)
Table: Daily water balance

Water… (Cont’d)
Properties of water
 Water molecule is polar.
 It forms intermolecular hydrogen bond with each other.
 Hydrogen bonding favors the self-association of water

molecules into ordered arrays.
 It also forms hydrogen bond with other molecules.

Properties of water… (Cont’d)
 Water exists in three state (liquid, solid, and gas).
 It slightly dissociate at physiological conditions.
 Hydrogen bonding profoundly influences the physical

properties of water and accounts for its exceptionally high
surface tension and boiling point relative to other
solvents.

Acids and Bases
• According to Bronsted-Lowry definition, acids are defined

as proton donors and bases are proton acceptors.
• Acids and bases could be strong or weak acids and bases.

Medical and biological Importance
1. Proper pH is required for the optimal action of enzymes and for the transport of
molecules within the body and between cells and its surroundings.
2. Proper pH is required for the maintenance of structure of nucleic acids, proteins,

coenzymes and various metabolites.
3. Acidosis and alkalosis are two important disorders of acid base balance.

Concepts of Acid, Base and Buffer …
Buffers: are the solutions that resist the change in pH upon addition of
acid or base.
The buffers are:
 mixture of a weak acid and its conjugate base or its salt
 Buffers work best near their pKa (pH at which the protons dissociate from
the weak acid).
 It should be noted that around the pKa, the pH of a solution does not change
appreciably even when large amounts of acid or base are added
Concepts of Acid, Base and Buffer …
 The amount of protons or hydroxyl ions that can be neutralized by any buffer, without
change in pH, depends upon the concentration of the components of the buffer in
solution, known as its ‘buffering capacity’.
It is defined as ‘the number of grams of a strong acid or a strong base required to bring
about a change of one pH unit in one liter of a buffer solution’.
Henderson-Hasselbalch equation. An equation that defines the relationship between
pH, pKa and the concentrations of salt and acid in a buffer solution
Action of buffer
Example acetate buffer
The two components of acetate buffer are acetic acid (CH3COOH) and sodium
acetate (CH3COONa).
When acid like HCl is added the base component of buffer reacts as shown
below.
Since acetic acid is weak acid compared to HCl, the pH change is little on addition
of HCl to acetate buffer.
When alkali like NaOH is added acetic acid of buffer reacts and neutralizes change
in pH caused by addition of alkali.
NaOH+CH3COOH→CH3 COONa +H2O
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Thus buffer resist change in pH when acid or alkali is added.
Buffers of blood plasma
1. Bicarbonate and Carbonic acid (HCO3–/H2CO3) buffer.
 It is present in greater concentration and plays major role in regulating pH of
blood with in normal limits.
 Even though the pK of H2CO3 is 6.1, the HCO3–/H2CO3 function as major

buffer at pH 7.4 by maintaining ratio of 20 : 1 for conjugate base (H CO3 –) to
weak acid (H2CO3).

Bicarbonate…
The ratio of conjugate base to weak acid required to keep the blood pH 7.4 is obtained by substituting pH and pK values in Henderson
- Hasselbalch equation as shown below :
The pH of blood remain 7.4 as long as this ratio is maintained.
Increase or decrease in pH due to entry of acids or bases into blood is met by

adjustment in this ratio.
Any alteration in the ratio for prolonged time leads to disturbances in acid base
balance.
Mechanism of action of bicarbonate buffer in controlling blood pH
Bicarbonate buffer acts against metabolic acids or nonvolatile acids produced.
Metabolic acids are aceto acetic acid, β-hydroxy butyric acid, lactic acid, pyruvic
acid and small amounts of phosphoric and sulphuric acids.
The bicarbonate neutralizes more than 50% of all the acids stronger than carbonic
acid.
The bicarbonate that remain in plasma after neutralization of all acids is referred as
alkali reserve.
In blood HCO–3 is in association with Na+.

bicarbonate buffer…
When acid enter blood Na+ HCO– 3 is used to convert strong acid to weak acid as
shown below :

Role of Lungs
Respiratory system (Lungs) serve as immediately available temporary mechanism for

maintenance of acid base balance.
 Lungs affect acid-base balance by altering carbonic acid component of bicarbonate
buffer.
The carbonic acid content of blood depends on partial pressure of CO2 (PCO2) in
plasma which is in turn controlled by lungs.
Further, in lungs carbonic acid formation from CO2 and H2O is catalyzed by carbonic
anhydrase.
92 By Eido, Biochemist
Role of Lungs…
When blood pH falls, the plasma HCO– 3 concentration decreases and the ratio of
HCO–3:H2 CO3 is decreased.
 In this acidotic state respiratory centre is stimulated and respiratory rate (Hyper
ventilation) is increased.
 So, more of CO2 is blown off.
 This results in decreased PCO2 and less carbonic acid formation.
 Now the ratio of HCO–3 : H2CO3 increases and blood pH returns to normal 7.4.

Role of Lungs…
 When the blood pH increases exactly reverse occurs.
 Due to decreased H+ concentration in blood, the H2 CO3 is less and the ratio of
HCO–3 : H2 CO3 is increased.
This acid base disturbance is compensated by decreasing respiratory rate

(Hypoventilation).
Hypoventilation raises the plasma PCO2 and hence H2 CO3 is increased. As a

result of this the ratio of HCO–3 : H2CO3 come back to normal and blood pH is
restored to pH
BIOCHEMISTRY OF AMINO ACIDS AND PROTEINS
95
General Objectives
At the end of this session, You will be able to:
 Discuss some important proteins
 Define the Amino acids and Enzyme
 Explain the proteins(AAs) and Enzyme composition
 Describe the functions of proteins ,Amino acid and Enzymes
 Identify the factors affecting Enzyme activities
96  Diagnostic values of Enzymes

Functions of Proteins
Proteins are physically & functionally complex macromolecules that
perform important roles:
Structural:
main structural component in bone, muscles, cytoskeleton
& cell membrane
Nutrition:
provide the body with essential AAs, N & S
Catalytic:
almost all metabolic enzymes are proteins in nature
Endocrine:
most of hormones and all receptors are protein in nature
Defence:
antibodies (Ig’s) & complement system are proteins in
nature
they play an important role in the body’s defensive
mechanisms
Osmotic Potential:
plasma proteins are responsible for most effective osmotic
pressure of the blood
this osmotic pressure plays a central role in many processes,
e.g., urine formation
Blood clotting factors are proteins e.g. Fibrinogen
Transport Role:
 Proteins carry lipids in the blood forming lipoprotein
complexes
 Proteins also carry:
hormones, e.g., thyroid hormones
minerals, e.g., calcium, iron & copper
 Hemoglobin (a chromo-protein)
carries O2 from the lung to tissues

Signal Transduction:
 Intercellular & Intracellular signal transduction
carried out largely by proteins
Membrane Transport:
 plasma membrane is lipoprotein & semipermeable in nature
 the proteins in the membranes act as channels or
transporters
 to allow selective molecules/ions to cross into or out
of the cells
Gene Regulation:
 control cellular activities through control of gene expression:
 most factors required for:
 DNA replication,
 Transcription  are protein in nature
 mRNA translation
Classification of Proteins
About 25,000 to 35,000 genes in human genome
coding for about 100,000 proteins.
Proteins may be:
simple monomeric or complex oligomeric
with or without a conjugated non-protein ligand
Different criteria for classification can be used; such as
Biological value
The composition of protein
Solubility and Physical properties
Function
Nutritional (Biological) value
Nutritional value of proteins depends upon their

digestibility & AA composition
High biological value:
when they are easily digestible
contain all the essential AAs in well balanced
proportions
Low biological value:
when they are deficient in one or more EAAs, or
containing very little amount of one of them, or
are indigestible
According to The Composition of Protein
Simple proteins:
proteins composed of AAs only Insulin, Myosin, Albumin
etc.
Conjugated proteins:
proteins that also carry certain non-AA prosthetic groups like;
heme, carbohydrates, lipids or nucleic acids etc.
conjugation with prosthetic groups is stabilized by:
covalent & non-covalent secondary bonds
one protein could contain more than one type of such groups
Derived Proteins: all the proteins derived from either of the above
two types partial hydrolysis products of proteins e.g.,
protein proteoses peptones polypeptide
peptides denatured proteins coagulated albumin or
globulin
Functional Properties
: Igs & complement proteins involved in neutralizing the ‘foreign’
substances in our body
Respiration:
 The proteins involved in the transport of oxygen i.e. Hb and
Mb & components of electron transport chain like
cytochromes
Contractile:
 Actin, myosin, troponins & other proteins involved in the
contraction or relaxation of muscles
Signal transduction:
 Hormones, their receptors and the proteins that mediate the
action of second messengers
Structural:
Proteins in the cartilaginous tissues, nails, skin & hair as well
as the proteins in plasma membranes
Enzymes:
 Proteins that mediate in the catalysis of different metabolic
rxn’s
AMINO ACIDS…
 Chemically, amino acids are organic acids that contain one or more amino (–NH2)
group(s).
They are the structural units of proteins and are obtained from them by hydrolysis.
 But they also attain important functions in their free form.
 Each amino acid has a carboxylic group (–COOH), an amine group (–NH2) and a
characteristic side chain, radical or R-group (–R).
Thus amino acids (proteins) are amphoteric electrolytes or ampholytes, i.e., react as
proton donor acid by –COOH and as proton accepting base by –NH2 to attain
negative or positive charges.
105 03/09/2021
Structure and properties contd.
Because of the tetrahedral arrangement of the bonding orbital around the - carbon
atom, the amino acids have two possible stereoisomers (D and L).
Figure 2. D- and L- stereoisomers of amino acids.
03/09/2021 Eido Shemeni(MSc) 106

AMINO ACIDS…
Functions of amino acids:

 Apart from being the constituents of proteins, amino acids serve a variety of
functions.
The non-protein amino acids along with polymerizable amino acid in their free
form carry vital biochemical functions:
they are urea cycle intermediates, and
precursors for neurotransmitters,
polyamines, thyroid and
adrenal medullary hormone synthesis.
107 03/09/2021
Functions of amino acids
They are polymerized to form proteins.

Presence of specific amino acids at the active site of enzymes is vital for their
catalytic activity
 Some amino acids (glucogenic) can be converted to carbohydrates.

Cysteine and methionine are sources of sulfur in the body.
The carbon skeleton and nitrogen of amino acids is used for the synthesis of purine
and pyrimidine bases for nucleotides and nucleic acids.
Certain amino acids give rise to biologically important derivatives:
108 03/09/2021
Structure and properties contd.
• The amino acid residue in protein molecules are exclusively L- stereoisomers
• D-Amino acids have been found only in some bacterial cell wall and certain peptide antibiotics
like gramicidin.
Classification of amino acids

According to side chain
• Amino acids are classified according to the properties of their side chain (polarity, size and
structural features) of the R group as

Classification contd.
1. Amino acids with non polar side chain (aliphatic)

 does not bind or give proton
 does not participate in hydrogen bond
 they promote hydrophobic interaction
 The aimino group of proline is held in a rigid conformation that
reduces flexibility of polypeptide regions containing proline.

Figure 2. Non-polar aliphatic amino acids

2. Amino acids with uncharged polar side chain (R)
• Can participate in hydrogen bond.
• The hydroxyl group of threonine and serine are site for protein
phosphorylation and glycosylation that is important to regulate a metabolic
pathway.
• The R group is more soluble in water (hydrophilic)

• Cysteine is readily oxidized to form a covalently linked dimeric amino acid
(disulfide bond) called cystine.
Figure 4. Uncharged, polar amino acids

3. Amino acids with aromatic R-group

• All can participate in hydrophobic interaction
• The hydroxyl group of tyrosine can form hydrogen bonds, and it is
an important functional group in some enzymes.

Figure 5. Aromatic side chain amino acids

4. Positively charged (basic) R group

• Have most hydrophilic R group
• In many enzyme-catalyzed reactions Histidine residue facilitate the

reaction by serving as a proton donor/ acceptor since it has an
ionizable side chain with a pKa near neutrality (pKa= 6).

Figure 6 Positively charged amino acids

Classification contd
5. Negatively charged (acidic) R group

• The amino acids aspartic and glutamic acids are proton donors
• They are negatively charged at physiologic pH.
• They form ionic or electrostatic bond with positively charged
molecules.

Figure 7. Negatively charged chain amino acids
Eido Shemeni(MSc)
03/09/2021 119
• Examples of amino acids that are not constituent of proteins are ornithine and
citrulline that are key metabolites in the biosynthesis of arginine and in urea
cycle.
There are also uncommon amino acids created by modification of common

residues.

Amino acids can act as bases and acids
• Every amino acid has two ionizable groups: - the

carboxyl and amino group capable of either donating
or accepting protons when the pH of the solution
altered.
• When amino acids dissolved in water, it exists in
solution as dipolar ion, or Zwitterion that is they bear
no net charge.
• The pH at which an amino acid is electrically neutral is

called isoelectric point (pI) and the molecule has
equal amount of positive and negative charge.

Figure 9. a zwitterion ion that acts as a base (proton
acceptor)

Examples :-
1. 4-hydroxy proline and 5-hydroxy lysine- both of them found in collagen.
2. 6-N-methyllysine- constituent of myosin
3.-carboxyglutamate – found in prothrombin
4. Desmosine- derivatives of four lysine residue- found in elastin
5. Selenocysteine- It occurs at the active site of several enzyme like thioredoxine
reductase, glutathione peroxidase and deiodinase.

Amino acids can act as bases and acids
• Every amino acid has two ionizable groups: - the carboxyl and amino group capable of either
donating or accepting protons when the pH of the solution altered.
• When amino acids dissolved in water, it exists in solution as dipolar ion, or Zwitterion that is
they bear no net charge.
• The pH at which an amino acid is electrically neutral is called isoelectric point (pI) and the
molecule has equal amount of positive and negative charge.

Classification of amino acids by synthesis
Essential and non-essential amino acids
• Essential amino acids cannot be synthesized by the body and must be supplied by diet.
• Non-essential amino acids can be synthesized in sufficient amount from the

intermediates of metabolism or as in the case of cysteine and tyrosine from essential
amino acids.
• Cysteine is synthesized from the essential amino acid methionine and tyrosine is
synthesized from phenylalanine

Figure 13. Synthesis of cysteine
The essential and non essential amino acids
Essential amino acids Non essential amino acids
Phenyl alanine Alanine
Valine Asparagine
Isoleucine Aspartate
Threonine Glutamate
Methinonine Serine
Arginine Glycine
Lysine Tyrosine
Histidine Proline
Tryptophan Cysteine
leucine Glutamine

Classification by catabolic fate of carbon skeleton
Catabolism of carbon skeleton of amino acids

• The catabolism of the carbon skeleton converges to form seven products
– Oxaloacetate - Pyruvate
– Acetyl CoA - Succinyl CoA
–  -ketoglutarate - Fumarate
– Acetoacetyl CoA
• These products enter into intermediary metabolism that can be converted into glucose or lipid or be
oxidized by citric acid cycle.

Figure 14.Summary of amino acids catabolism

Glucogenic and Ketogenic Amino acids
• Amino acids that are degraded to acetyl CoA or Acetoacetyl CoA are termed ketogenic amino acids.
• Amino acids that are degraded to pyruvate,  -ketoglutarate, succinyl CoA, fumarate, oxaloacetate
are termed as glucogenic amino acids.
• Leucine and lysine are purely ketogenic.
• Isoleucine, phenylalanine, tryptophan, threonine and tyrosine are both ketogenic and glucogenic
because they give both glucose and fatty acid precursors.
• The other 13 amino acids are termed as purely glucogenic.

Conversion of amino acids to specialized products
• In addition to serving as building blocks for proteins, amino acids are precursors of
many nitrogen containing compounds.
• Physiologically important products derived from amino acids includes
• Heme
• Purine
• Pyrimideine
• Hormones
• Nuerotransmitters and biologically active peptide.
131 Eido Shemeni(MSc) 03/09/2021

Creatine phosphate (CP)
Creatine phosphate is the phosphorylated derivative of creatine found in muscle.

Creatine phosphate is a high-energy compound that can reversibly donate a phosphate group to
ADP to form ATP.
It functions as store of high-energy phosphate in muscle.
Creatine is synthesized from glycine and Arginine, plus a methyl group from S-adenosyl
methionine (SAM).

Arginine + Glycine
Amidinotransferase
ornithine
Guanidinoacetate
SAM
Methyl transferase
S-adenosylhomo
cysteine
H2O
Creatine
ATP ATP
Creatine Kinase
Creatinine
ADP ADP
Creatine Phosphate
Pi
Figure 22. Synthesis of Creatine

CP contd…
Creatine is reversibly phosphorylated to creatine phosphate (phosphocreatine) by

creatine kinase (CK) using ATP.
Creatine and creatine phosphate spontaneously cyclize to form creatinine that is

excreted in the urine.

S-adenosyl methionine (SAM)
SAM is the major methyl group donor in one carbon

metabolism that is synthesized from methionine and
ATP by methionine adenosyl transferase.
SAM is unusual in that without having phosphate it is

a high-energy compound.

Figure 23. Synthesis of S-Adenosyl methionine

Histamine
Decarboxylation of histidine by histidine decarboxylase forms

histamine.
Histamine mediates wide range of cellular responses:-

 Including gastric acid secretion, and possibly neurotransmission in
parts of the brain.
 It is a powerful vasodilator.
 It is secreted by mast cells as a result of allergic reactions or
trauma.
Eido Shemeni(MSc)
Figure 24. Synthesis of Histamine
138 03/09/2021
Serotonin
Serotonin (5-hydroxytryptamine) is synthesized from

tryptophan. It has multiple physiological roles:-
 Stimulator of smooth muscle contraction

 Plays role in pain perception
 Normal and abnormal behavior, including affective
disorders.
 Regulation of sleep, temperature and blood pressure.

Serotonin Contd…
The largest amount of serotonin is found in cells of the intestinal

mucosa.
N-acetylation of serotonin, followed by O-methylation in the pineal
body, forms melatonin that is a neurohormone that function in
regulation of our circadian rhythm, and also function as
nonenzymatic free radical scavenger.
Eido Shemeni(MSc)
Structure of melatonin
140 03/09/2021
Figure 25. Synthesis of Serotonin

Melanin
Melanin is pigment that occurs in a number of tissues in the

body, particularly in the eye, hair and skin.
It is synthesized to protect underlying cells from the harmful
effects of sunlight.
There are two types of pigments pheomelanine and eumelanine.
Pheomelanine :– red to yellow pigment is found in red and
blond hair

Melanin contd….
• Eumelanin :– dark brown to black pigment predominates in

black.
Synthesis of melanin
Its formation from tyrosine is a hydroxylation that form
dihydroxyphenylalanine (Dopa), catalyzed by the copper
containing enzyme tyrosinase.

Figure 26. Synthesis of melanin
03/09/2021
144 Eido Shemeni(MSc)

Melanin contd….
Subsequent reactions leading to the formation of brown and black
pigments are thought to be catalyzed by tyrosinase or to occur
spontaneously.
Defective melanin biosynthesis results in albinism which includes

a spectrum of clinical syndromes characterized by hypo melanosis
due to heritable defects in eye and skin melanocyte.

Catecholamines
Dopamine, norepinephrine, and epinephrine are biologically

active amines that are collectively called catecholamines.
Catecholamines produced in the brain and in other neural tissues

function as neurotransmitters, but epinephrine and norepinephrine
are also hormones, synthesized and secreted by adrenal gland.

Catecholamines Contd…
They are synthesized from tyrosine

Tyrosine is first hydroxylated to form 3,4-DOPA.
3,4-DOPA is decarboxylated by hydroxylase enzyme to yield
norepinephrine.
Epinephrine is formed by a methylation using SAM as a methyl
donor.

Figure 27. Synthesis of catecholeamines

-aminobutyrate (GABA)
GABA is an inhibitory neurotransmitter found in the CNS,
principally on gray matter and also in the gut and lumen.
GABA is formed by decarboxylation of L-glutamate, a reaction

catalyzed by the PLP dependent enzyme L-glutamate decarboxylase.

Figure 28. Synthesis of -aminobutyrate

Glutathione
Glutathione (GSH) is derived from glycine, glutamate and cysteine.
The -carboxyl group of glutamate is activated by ATP which is then

attacked by the α- amino group of cysteine
A second condensation reaction follows, with the α-carboxyl group

of cysteine and glycine.
Glutathione helps to remove toxic peroxides formed during normal
151
metabolism.
Eido Shemeni(MSc) 03/09/2021
figure 29 synthesis of glutathione

Protein
Proteins are the most abundant biological macro molecules

occurring in all cells
Proteins are linear polymers of amino acids that are functionally

diverse.
The sequence of amino acids, determines the way a protein folds

into a unique three dimensional structure which is its native
conformation.
Protiens and Amino Acids
153 3/9/21
Structure of protein
The peptide bond
Proteins are polymers formed by linking the -carboxyl group
of one amino acid is to the – amino group of another amino acid
by a peptide bond

Figure 1. The peptide bond
154 3/9/21
Structure of protein Contd
Many amino acids are joined by peptide bonds to form a polypeptide chain
and each amino acid in a polypeptide is called residue.
By convention the amino end (N-terminal) is taken to be the beginning of a

polypeptide chain and the free carboxyl end to the right.
Eg. In the tripeptide Ala-Gly-Trp (AGW), alanine is the amino terminal

residue
The peptide bond is rigid and planar and have trans configuration.
155
3/9/21
Types of protein structure & their folding
The complexity of protein structure is best analyzed by
considering the molecule in terms of four organizational

levels namely
 Primary
 Secondary
 Tertiary
 Quaternary.
156 3/9/21
Protein structure contd
1. Primary
It is linear sequence of amino acid residue joined through peptide bond
to form a polypeptide chain.
Understanding the primary structure of proteins is important because

many genetic disease result in proteins with abnormal amino acids
sequences.
157 3/9/21
Figure 2. The primary structure of human globin protein
158 3/9/21
. Secondary
2
The polypeptide back bone form regular arrangement

of amino acids that are located near each other, this
arrangement is called secondary structure of the
polypeptide.
Examples of secondary structure:-
 The -helix
 The -sheet
159 3/9/21
-helix
It is a spiral structure, consisting of a tightly packed, coiled
polypeptide backbone core with side chains of component amino
acids
 Examples of proteins that contains -helix
 The - keratins – fibrous protein – nearly entirely -helical
 Hemoglobin – globular protein – 80% -helical
An -helix is stabilized by hydrogen bonds between the peptide
bond carboxyl oxygen and an amide hydrogen.
C = O ---------- H – N
160 3/9/21
Figure 3. The α-helix
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3/9/21 Protiens and Amino Acids
The -sheet
 -sheet another type of secondary structure where the peptide
bond components are involved in hydrogen bonding
 The surface of -sheet appear “pleated “ and therefore called “-
pleated sheets”
 Composed of two or more peptide chains (-strands) or segments
of polypeptide chain that is almost fully extended.
 Hydrogen bonds are perpendicular to the polypeptide backbone.
162 3/9/21
A -sheet can be formed from two or more polypeptide chains that

are arranged either parallel or antiparallel to each other.
If the polypeptide strands run in the same direction it is parallel if it is

in opposite direction anti parallel.
A -sheet can also be formed by a single polypeptide chain folding

back on itself in which the hydrogen bonds are intrachain bonds.
163 3/9/21
Figure 4. The β-conformation of polypeptide chain
164 3/9/21
3.Tertiary structure
It is the folding pattern of the secondary structural element into a three
dimensional conformation.
Tertiary refers both to the folding of domains and the final arrangement
of domains in a polypeptide.
165 3/9/21
The interaction of different domains is stabilized by :-
1. Disulfide bonds- is a covalent linkage formed from the sulfhydryl group

(- SH) of each of two cysteine residues.
2. Hydrogen bonds- amino acid side chain containing oxygen or nitrogen

bound hydrogen as in the alcohol group of serine or threonine.
166 3/9/21
3. hydrophobic interaction- amino acids with non polar side chain

tend to be located in the interior of a polypeptide molecules, in contrast
amino acids with polar or charged side chain tend to be located on the
surface of the molecule in contact with the polar solvent.
4. Ionic interaction- negatively charged groups such as the carboxyl
group (COO-) in the side chain of Aspartate or glutamate can interact
with positively charged groups such as the amino group (- NH3+) in the
side chain of lysine
167 3/9/21
4. Quaternary structure
Quaternary structure involves the association of two or more

polypeptides chains into a multi subunit structure.
Many proteins function in the cell as dimers, tetramers or oligomers
proteins in which two or more subunits have combined to make one
functional proteins.
168 3/9/21
Figure 9. Levels of Protein structure
169 3/9/21
Protein folding
There are proteins that help in folding of protein structure these are
chaperones.
They participate in folding of over half of mammalian protein.
Protein folds into stable three-dimensional structure known as

native conformation.
170 3/9/21
Protein folding contd
The three dimensional structure of a protein
 must have binding site for one specific molecule or group of
molecules
 must exhibit degrees of flexibility and rigidity appropriate to its
function.
 must have a structure that can be degraded when it is damaged
or no longer needed in the cell.
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Several neurologic disorders result from altered protein
conformation
Prion disease
 Prion disease or spongiform encephalopathy are fatal
neurodegenerative diseases.
 It is characterized by spongiform changes, astrocytic gliomas and
neuronal loss
 Result from the deposition of insoluble protein aggregates in
neural cells that are resistant to proteolytic degradation
172 3/9/21
Alzheimer’s disease
 Result from misfolding or refolding of the protein
endogenous to human brain tissues, -amyloid.
 This protein undergoes a conformational transformation from a
soluble α-helix rich state to a state rich in - sheet and prone to
self-aggregation.
 In Alzheimer’s disease patients level of -amyloid become
elevated.
173 3/9/21
Denaturation of protein
Definition: Denaturation may be defined as a disruption of the
secondary, tertiary, and quaternary organization of a protein molecule
due to cleavage covalent bonds.
Note: Primary structure of protein molecule, i.e. peptide bond is not

affected.
Agents that cause denaturation: Various agents which can disrupt

the conformation are:
174 3/9/21
Denaturation of protein contd
• Physical agents: Heat, UV light, ultrasound, and high pressure. Even
violent shaking can denature the protein.
• Chemical agents: Organic solvents, acids/alkalies, urea and various

detergents.
The disruption/disorganization of the protein molecules results in

alteration of the chemical, physical and biological characteristics of
the protein.
175 3/9/21
• It is in rare case reversible, (see figure 10) in which case the

protein refolds into its original native structure when the
denaturing agents is removed.
• However most protein, once denatured, remains permanently

disordered.
176 3/9/21
Figure 10. Denaturation of ribonuclease
177 3/9/21
Protein classification
Proteins are classified into two major groups according to overall
shapes.
1. Fibrous protein
 proteins that are insoluble in aqueous medium.
 strong and play a structural role for support or
protection.
 They have polypeptide chain arranged in long
strands or sheets
Examples:- -Keratin, collagen, elastin, etc.
178 3/9/21
Protein classification
Figure 11. The triple helix of collagen
2. Globular protein- having polypeptide chain folded into a spherical or

globular shape.
They usually soluble in aqueous medium.
Example:-. Hemoglobin, Immunoglobulin, enzymes, hormones, etc
179 3/9/21
Fibrous protein
Many of the cells in tissues are embedded in an extracellular matrix
(ECM).
ECM fills the space between cells and binds cells and tissue together
and helps organize cells into tissue.
Provide support and anchorage for cells
Coordinates their cellular function by activating intracellular signaling

pathway that control cell growth, proliferation and gene expression.
180 3/9/21
Fibrous protein contd
Basic components of the extracellular matrix include
 Structural proteins, collagen fiber
 Highly viscous proeteoglycans and
 multiadhesive matrix proteins.
The fibrous structural proteins such as collagen, elastin, laminin,

etc. are the principal structural proteins of connective tissues that
are composed of repeating elements that form linear structure.
181 3/9/21
Elastin is connective tissue protein with rubber like properties

It is found in
 Lungs
 Walls of large arteries, and
 Elastic ligaments.
They can be stretched to several times than their normal length, but
recoil to their original shape when the stretching force is relaxed.
182 Protiens and Amino Acids 3/9/21

Figure 12. An overview of connective tissue extracellular

matrix
183 3/9/21
Collagen
Collagen is major components of extracellular matrix in most tissues
produced by a variety of cells types but principally by
 Fibroblasts,
 Muscle cells and
 Epithelial cells.
All collagens are trimeric proteins made from three polypeptides
called collagen α–chains.
We have more than twenty types of collagen but each type is found
only in particular locations in the body.
184 3/9/21
Collagen contd
Figure 13. The collagen triple helix
185 3/9/21
Collagen contd
The various types of collagen can be classified as

 Fibril forming (type I, II, III, and XI)
 Network forming (Type IV, VIII and X).
 Those that associate with fibril surfaces (Types IX,
XII, and XIV).
 Those that are transmembrane proteins (Type XIII
and VII)
 Endostatin-forming (Type XV and XVIII)
 Those that form periodic beaded filaments (Type
VI).
186 3/9/21
Collagen contd
For example Type I collagen.
 the most abundant protein in mammals, which is found in
extracellular matrix of loose connective tissue, bone, tendon, skin,
blood vessel, and the cornea of the eye.
 contains approximately 33% glycine and 21% proline and
hydroxyproline.
 Hydroxyl proline is an amino acid produced by post translation
modification of peptidyl proline residues
187 3/9/21
Collagen contd
Procollagen (I), the precursor for collage (I), is a triple helix
composed of three polypeptide (pro- α ) chains that are twisted
around each other, forming a rope like structure.
Polymerization of collagen (I) molecule forms collagen fibrils,

which provide great tensile strength to connective tissue.
The three polypeptide chains of the triple helix are linked by

intrachain hydrogen bonds.
188 3/9/21
Collagen contd
These reactions occur after the protein has been synthesized and require
vitamin C as coenzyme.
The Hydroxy proline residues are involved in hydrogen bond

formation that helps to stabilize the triple helix where as the
hydroxylysine residues are the site of attachment of disaccharides.
All collagen contain three polypeptide chains with at least one stretch
of triple helix.
The non triple helical domain can be short (as in fibril forming
collagen).
190
Figure 14. Hydroxylation of proline and lysine residue in collagen 3/9/21
Figure 15. Type IV collagen contains a globular carboxy- terminal domain
191 3/9/21
Collagen contd
Synthesis and secretion of collagen
 It is synthesized in the endoplasmic reticulum (ER) as a
precursor collagen preprocollagen.
 Preprocollagen is cleaved from mRNA]) forming procollagen in

ER and transported to the golgi apparatus.
 Three procollagen molecules associate through formation of intra

strand disulfide bonds at the carboxy-terminal; and align properly
to initiate formation of the triple helix.
192 3/9/21
Collagen contd
The triple helix forms from the carboxy end toward the amino
terminal, forming tropocollagen.
The tropocollagen contains a triple helical segment between two

globular ends, the amino and carboxy-terminal extension.

The tropocollagen secreted from the cell, the extensions are removed
using extracellular protesase, and the mature collagen takes its place
within the ECM.
The individual fibrils of collagen line in a highly ordered fashion to
193
form the collagen fiber. 3/9/21
Collagen contd
Degradation of collagen
Normal collagen is highly stable molecules, having half-lives as
long as several months.
Connective tissue is a dynamic and is constantly being remodeled,

often in response to growth or injury of the tissue.
The enzymes are collagenases that are part of large family of

matrix metaloproteinases.
194 3/9/21
Collagen contd
Disorders associated with collagen
Without the structural support of collagen blood vessel, tendon and
skin become fragile. Collagen containing mutant chains is not secreted,
and is either degraded or accumulated to high level in intracellular
compartments.
 Alport’s syndrome - Mutation in the
C-terminal globular domain of certain type IV chains (found in the
glomerular basement membrane of kidney) are associated with
progressive renal failure and also sensor neural hearing loss and
ocular abnormalities.
195 3/9/21
Collagen contd
Goodpasture’s syndrome – A relatively rare autoimmune disease,

where the auto antibodies bind to type IV collagen that is found in
glomerular basement membrane and lungs, result in renal failure
and pulmonary hemorrhage.
Osteogenesis Imperfecta (brittle bone disease) – Autosomal
dominant disorder result from certain mutations in the gene encoding
collagen I chains.
For example mutation of Glycine to almost any other amino acid is
deleterious, that disrupt the whole molecule’s triple-helical structure
and function.
196 3/9/21
Collagen contd
Ehlers-Danlos syndrome - mutation in the amino acid sequence of
collagen type I, III and V. Clinically important mutation are found in
Type III. Marked by extremely loose joints, and hyperelastic skin that
bruises easily, and easily damaged blood vessels.
Figure 16. Stretchy skin of Ehlers-Danlos syndrome
197 3/9/21
Oxygen Transport
INTRODUCTION
 Humans are aerobic organisms
 Our lungs extract O2 from air & deliver CO2 in exhaled gases
the inspired O2 leads to a more efficient utilization of;

• metabolic fuels, such as glucose & fatty acids
expired CO2 is a major product of cellular metabolism
 Living systems contain proteins that interact with O 2 & consequently,
increase its solubility in water & sequester it for transport

 In mammals, these proteins are;
• Myoglobin (Mb) &

• Hemoglobin (Hb)
199
Oxygen Transport
Hemoglobin and Myoglobin

Hemoglobin and myoglobin are two oxygen binding proteins with
very similar primary structure.

In hemoglobin and myoglobin, the two most abundant heme
proteins in humans, the heme group serves to bind oxygen reversibly.
200 3/9/21
Oxygen Transport cont’d..
Ligands that are tightly bind to a protein is called prosthetic group.

In case of hemoglobin, heme is the prosthetic group.
A protein with its attached prosthetic group is called holoproteins

and without the prosthetic group it is called apoprotein.
Heme is a complex of protoporphyrin IX and ferrous iron (Fe2+).
201 3/9/21
Figure 19. Heme
202 3/9/21
Structure and function of Myoglobin
Myoglobin, a heme protein present in heart and skeletal muscle.
It functions as a reservoir of oxygen and as oxygen carrier within the

muscle cell.
It consists of single polypeptide chain of 153 amino acids residues

with one molecule of heme
It has 8 -helical segments connected by bonds and labeled A to H
203 3/9/21
Structure and function of Myoglobin contd…
There are two Histidine residues termed as
 proximal and
 distal Histidine.
The proximal binds directly to the iron of heme
the distal does not directly interact with heme group but helps to
stabilize the binding of oxygen to the ferrous iron.
204 3/9/21
205
Fig-1. Structure of Heme. S-23
Figure 20. Three dimensional structure of Myoglobin
206 3/9/21
Structure and function of hemoglobin
Hemoglobin (Hb) is a red blood cell protein that transports oxygen from
the lungs to the tissue and it carries carbon dioxide from the tissues back
to the lungs.
Nearly all the oxygen carried by whole blood in animals is bound and
transported by hemoglobin in red blood cells.
Hemoglobin is roughly spherical, with a diameter of 5.5nm.

It is a tetrameric protein containing four heme prosthetic groups
207 3/9/21
Hemoglobin contd
Adult Hb (2 2) contains four polypeptide chain, two - (with

141 amino acids each) and two - chains (with 146 amino acids
each).
It has 8 -helical segments labeled from A to H except that the
- subunit lacks the short D-helix.
The four-polypeptide chain held together by non-covalent
interactions like hydrophobic interaction, hydrogen bonds and
ionic bonds.
Two major conformation of Hb exist:- the R (relaxed) and T
208
(tensed) state. 3/9/21
209
Figure 21. Structure of Hemoglobin 3/9/21
Hemoglobin contd
The binding of O2 to a hemoglobin subunit in the T
state triggers a change in conformation to the R state.
T- state
It is deoxy form of Hb
It is the low oxygen affinity form of Hb.
R- state
It is the high oxygen affinity form of Hb.
Oxygen binding stabilizes the R state
The T  R transition is triggered by changes in the
position of key amino acids side chain surrounding the
heme.
210 3/9/21
Hemoglobin contd
Table 2. Forms of Hemoglobin
Forms Chain composition Fraction of total Hb
HbA 2 2 96%
HbF 2 2 <2%
HbA2  2 2 2.5%
HbA1c 2 2-glucose 3-9%
211 3/9/21
Hemoglobin contd
Binding of oxygen to Hb
Hb can bind oxygen molecule (O2) at each of its four heme groups
Myoglobin can bind only one oxygen molecule because it contains
one heme group.
The binding of the first O2 molecule to deoxy Hb shifts the heme
Fe2+ towards the plane of the heme ring and this motion is
transmitted to the proximal Histidine (F8).
His F8 and its associated residue are pulled along with the iron
atom.
212 3/9/21
Hemoglobin contd
The binding of an oxygen molecule at one heme group increases the

oxygen affinity of the remaining heme groups and it is referred to as
heme-heme interaction or co-operative binding.
The cooperativity in oxygen binding in Hb comes from conformational

change in the tertiary structure.
When the amount of oxygen bound to hemoglobin or myoglobin is

plotted against the partial pressure of oxygen, a sigmoid or hyperbolic
curve is obtained respectively.
213 3/9/21
Hemoglobinopathies
Methemoglobin
In methemoglobin the heme iron is ferric (Fe3+) rather than ferrous
(Fe2+), it can neither bind nor transport oxygen.
Reactive oxygen species can oxidize the iron to ferric state and it
can also induced by inherited HbM.
Methemoglobin can be regenerated by the enzyme NADH-

cytochrome b5 methemoglobin reductase.
214 3/9/21
Hemoglobinopathies contd
Hemoglobin M (HbM)
In Histidine F8 has been replaced by tyrosine and the iron of HbM forms a
tight ionic complex with the phenolate anion of tyrosine that stabilizes HbM
the Fe3+ form.
Sickle cell anemia
A molecule of HbS contain two normal  -globin chain and two mutatnt -
globin chain (s) in which glutamate at position six has been replaced with
valine.
It generates a hydrophobic sticky patch which at low PO 2 deoxy HbS can
polymerize to form long insoluble fiber.
 These twisted helical fiber distort the erythrocyte into a characteristic
sickle shape.
215 3/9/21
It generates sticky membranes that are abnormally adhere to the
endothelium of small capillaries that result in vasooclussion of

capillaries and premature destruction of RBC.
Result in ischemic pain, hemoltytic anemia, abnormal red cell
morphology, etc
216 3/9/21
a. b.
a. b.
Figure 24. a) Normal red blood cell and b) variable shaped erythrocyte in sickle cell anemia
217 3/9/21
Hemoglobin C disease
Hemoglobin variants having a single substitution in the sixth
position of β-globin chain. i.e lysine is substituted for glutamate.
Thalassemias
are heterogenous group of inherited anemia characterized by
defects in the synthesis of one or more of the globin chain.
Caused by mutation that decreases or abolish the synthesis of α-
or - chains.
Thus in o thalassemia, the superscript o denotes none of the -
chains is present; where as in + thalassemia, the + denoted a
partial reduction in the synthesis of the chain.
218 3/9/21
BIOCHEMISTRY OF ENZYMES
219
ENZYMES
General Properties:
Enzymes are protein catalysts for chemical reaction in biological

systems.
They increase the rate of chemical reactions taking place within

living cells with out changing themselves.
220
Nature of Enzymes
Most enzymes are protein in nature.
Depending on the presence and absence of a non protein component with the
enzyme, enzymes can exist as, simple enzyme or holoenzyme
1. Simple enzyme: It is made up of only protein molecules not bound to any non
proteins.
Example: Pancreatic Ribonuclease.
Pepsin
2. Holo enzyme is made up of protein groups and non-protein component.
 The protein component of this Holo enzymes is called apoenzyme

 The non-protein component of the Holo enzyme is called a cofactor.
221
Nature of Enzymes…
If this cofactor is an organic compound it is called a coenzyme and if
it is an inorganic groups it is called cofactor. (Fe 2+, Mn 2+, or Zn
2+ ions).
If the cofactor is bound so tightly to the apoenzyme and is difficult to

remove without damaging the enzyme it is sometimes called a
prosthetic group
222
COENZYMES:
Coenzymes are derivatives of vitamins without which the enzyme cannot exhibit
any reaction.
 One molecule of coenzyme is able to convert a large number of substrate

molecules with the help of enzyme.
 Coenzyme accepts a particular group removed from the substrate or donates a

particular group to the substrate
 Coenzymes are called co substrate because the changes that take place in
substrates are complimentary to the changes in coenzymes.
The coenzyme may participate in forming an intermediate enzyme-substrate
complex
223
Example: NAD, FAD, Coenzyme A
Activators of enzymes
 Agents increase the activity of enzyme or make the inactive form
become active form
 They are mostly metal ions(Mg2+,K+,Mn2+),also some anion(Cl-) and

organic compounds.
 Most anions are necessary to enzyme activity, they are called essential
activators.
 Of course there are non-essential activators, Cl- is so to Ptyalin.

Metal ions in enzymes
Many enzymes require metal ions like ca2+, K+, Mg2+, Fe2+, Cu2+,
Zn2+, Mn2+ and Co2+ for their activity.
Metal-activated enzymes-form only loose and easily dissociable

complexes with the metal and can easily release the metal without
denaturation.
Metalloenzymes hold the metal tightly on the molecule and do not

release it even during extensive purification.
225
Metal ions in enzymes
Metal ions promote enzyme action by:
a. Maintaining or producing the active structural conformation
of the enzyme.
b. Promoting the formation of the enzyme-substrate complex
c. Acting as electron donors or acceptors
d. Causing distortions in the substrate or the enzyme
226
Properties of Enzyme
A. Active site
Enzyme molecules contain a special pocket or cleft called the active site.
The active site contains amino acid chains that create a three-dimensional surface
complementary to the substrate.
The active site binds the substrate, forming an enzyme-substrate (ES) complex.
ES is converted to enzyme-product (EP); which subsequently dissociates to
enzyme and product.
For the combination with substrate, each enzyme is said to possess one or more
active sites where the substrate can be taken up.
227
Active site….
The active site of the enzyme may contain

free hydroxyl group of serine,
 phenolic (hydroxyl) group of tyrosine,
SH- thiol (Sulfhydryl) group of cysteine or
 imindazolle group of histidine to interact with the substrates.
It is also possible that the active site (Catalytic site) is different from the binding
site in which case they are situated closely together in the enzyme molecule.
228
Properties …
B. Zymogen: inactive precursors of active enzymes

Example; Trypsinogen, Pepsinogen…
C. Isoenzymes: similar function but different physical and chemical
properties
Examples; CK (CK 1, CK2, CK3), Phosphatse (ALP,ACP)…
229
Mechanism of enzyme action
Occurrence of a reaction depends on the following factors:

Collision of reactants i.e frequency of collision (Z)
Availability of proper orientation between reacting species (P)
Temperature of the medium (T)
 Availability of Activation energy (E)
230
231
B. Catalytic efficiency/ Enzyme turnover number
Most enzyme- catalyzed reactions are highly efficient proceeding

from 1000 to 100000000 times faster than uncatalyzed reactions.
 Typically each enzyme molecule is capable of transforming 100 to

1000 substrate molecule in to product each second.
Enzyme turn over number refers to the amount of substrate

converted per unit time (carbonic anhydrase is the fastest enzyme).
232
ENZYME SPECIFICITY
Enzymes are highly specific compared to other catalyst.
An enzyme catalyzes only specific reaction.

1. Substrate Specificity
Enzymes are specific towards their substrates.
 For example, glucokinase catalyzes the transfer of phosphate from
ATP to glucose.
Galactokinase catalyzes transfer of phosphate from ATP to galactose.
233
Substrate Specificity…
Though both enzymes catalyzes transfer of phosphate from

ATP they act only on specific substrate.
234
Substrate Specificity…
Transaminase
In the Similar way catalyze transfer of amino group
are specific to substrate.
Aspartate transaminase catalyzes the transfer of amino

group from Aspartate and alanin transaminase
catalyzes transfer of amino group from Alanine only.
 So, they are specific towards substrate.
235
Transaminase
236
These interactions are two types.
1. Template or Lock-and-Key Model
This model was originally proposed by Fischer which states that the active site
already exists in proper conformation even in absence of substrate.
Thus the active site by itself provides a rigid, pre-shaped template fitting with
the size and shape of the substrate molecule.
Substrate fits into active site of an enzyme as the key fits into the lock and
hence it is called the lock-and-key model.
This model proposes that substrate binds with rigid pre-existing template of the
active site, provides additional groups for binding other ligands.
But this cannot explain change in enzymatic activity in presence of allosteric
modulators

MODELS OF ENZYME-SUBSTRATE COMPLEX…
2. Induced-Fit or Koshland Model

Because of the restrictive nature of lock-and-key model, another model was
proposed by Koshland in 1963 which is known as induced-fit model.
The important feature of this model is the flexibility of the region of active
site.
According to this, active site does not possess a rigid, preformed structure on
enzyme to fit the substrate.
 On the contrary, the substrate during its binding induces conformational
changes in the active site to attain the final catalytic shape and form

Lock and key model
Induced fit model
239
2. Reaction Specificity
A given enzyme catalyze only one specific reaction.

For example
Lipases only hydrolyze lipids

Urease hydrolyzes urea.
They do not catalyze any other type of reaction.
 Likewise amino acid oxidase catalyze oxidation of amino acid and

Decarboxylase catalyze only Decarboxylation of amino acids.
240
Reaction Specificity…
241
3. Group Specificity
Some lytic (hydrolases) enzymes act on specific groups.
Proteases are specific for peptide groups, glycosidase are specific to

glycosidic bonds.
242
243
244
FACTORS AFFECTING ENZYME ACTION
Rates of enzyme catalyzed reactions are affected by:
1. Enzyme concentration
2. Temperature
3. Hydrogen ion concentration or pH
4. Substrate concentration
5. Inhibitors and cofactors
245
FACTORS AFFECTING ENZYME ACTION…
1. Enzyme concentration
The rate of enzyme catalyzed reaction is directly proportional to the
concentration of enzyme.
The plot of rate of catalysis versus enzyme concentrations a straight line
2. Temperature
Like any chemical reaction, enzyme activity increases with increase in
temperature initially.
After a critical temperature, the enzyme activity decreases with increase in the
temperature.
When the effect of temperature on enzyme activity is plotted, cone-shaped

246
curve is obtained
247
Effect of PH
Extreme pH can also lead to denaturation of the enzyme, because

the structure of the catalytically active protein molecule depends on
the ionic character of the AA chains.
The pH at which maximum enzyme activity is achieved is different

for different enzymes, and after reflects the pH+ at which the
enzyme functions in the body.
For example, pepsin, a digestive enzyme in the stomach, has

maximum action at pH 2-2.5, where as other enzymes, designed to
work at neutral pH, are denatured by such an acidic environment.
248
Effect of Ph…
249
PH
250
4. Effect of substrate concentration

If the concentration of the substrate (S) is increased while other
conditions are kept constant, the initial velocity v0 (velocity measured
when little substrate is reacted) increases proportionately in the
beginning.
As the substrate concentration continues to increase, theincrease in v0

slows down and reaches maximum Vmax and no Further increment.
251
Concentration of substrate…
252
Enzyme Inhibition
Any substance that can diminish the velocity of an enzyme-catalyzed

reaction is called an inhibitor and the process is known as inhibition.
There are two major types of enzyme inhibition, Irreversible and

Reversible.
253
Irreversible Inhibition
The type of inhibition that can not be reversed by increasing
substrate concentration or removing the remaining free
inhibitor is called Irreversible inhibition
Eg. Diisopropyl & luorophosphate Inhibits the enzyme

acetyl cholinesterase, important in the transmission of nerve
impulses.
Acetyl cholinesterase catalyzes the hydrolysis of

Acetylcholin (to acetic acid and choline) aneurotransmitter
substance functioning in certain portions of the nervous
system 254
INHIBITORS
Competitive Inhibition:
This type of inhibition occurs when the inhibitor binds reversibly to
the same site that the substrate would normally occupy, therefore,
competes with the substrate for that site.
In competitive inhibition the inhibitor and substrate compete for the
same active site on the enzyme as a result of similarity in structure.
The enzyme substrate complex will be broken dawn to products (E+S

ES E+P) where as enzyme inhibitor complex;(EI) will not
be broken down to products.
255
Competitive Inhibitors as Chemotherapeutic Agents
When used in clinical situations, the competitive inhibitors
are called as antagonists or antimetabolites of the substrate
with which they compete.
 The use of anti-metabolites in the treatment of diseases is

called as chemotherapy.
Therefore, competitive inhibitors are useful chemotherapeutic

agents.
They are used as:
1. Antibiotics
2. Anti-cancer drugs
256
3. In the treatment of metabolic diseases like gout, atherosclerosis and
hypertension
Competitive Inhibitors as Chemotherapeutic Agents…
1. Competitive inhibiter as Antibiotics:
Sulfonamide antibiotics are used in the treatment of
bacterial infections.
 Bacteria synthesize folic acid from p-aminobenzoic acid
(PABA).
 Since these sulfonamide drugs contain sulfonilamide a

structural analog of PABA when used as chemotherapetic
agent, it blocks the synthesis of folic acid in bacteria.
257
The lack of folic acid leads to death of bacteria.
Sulfonamide act as competitive inhibitor for the enzyme

involved in the formation of folic acid using PABA as
substrate
258
2. Competitive inhibitors used in the treatment of cancer

These are aminopterin and amethopterin (methotrexate).
They are structural analog of folic acid.
They are competitive inhibitors for the enzyme dihydrofolate
reductase.
They are used in the treatment of leukaemia,a type of cancer.
259
Competitive inhibitors used in the treatment of cancer…
When used these drugs block formation of nucleic acids.
For cell proliferation, nucleic acid are needed.
So, lack of nucleic acids lead to arrest of tumour growth and advancement
of cancer is prevented.
260
Competitive inhibitors used in the treatment of gout
Allopurinol is a drug used in the treatment of gout.
Gout is due to excessive production of uric acid.
 Xanthine oxidase is an enzyme involved in the formation of uric acid from

hypoxanthine.
Allopurinol is a structural analog of hypoxanthine and hence it is an

antimetabolite of hypoxanthine.
When it is used it blocks formation of uric acid by inhibiting the enzyme

261
xanthine oxidase
262
4. Competitive inhibitors used in the treatment of
atherosclerosis
Lovastatin is a competitive inhibitor of enzyme HMG-CoA

reductase, when used it blocks production of cholesterol.
In atherosclerosis, cholesterol is more.
Lovastatin reduces cholesterol formation thus arrest the

advancement of atherosclerosis.
263
Biosynthesis of Cholesterol…
264
Competitive inhibitors used in the treatment of hypertension
captopril, lisinopril and enalapril.
They competitively inhibit angiotensin converting enzyme, which is

involved in regulation of blood pressure.
When used they lower blood pressure by reducing activity of angiotensin

converting enzyme.
265
Non-Competitive Inhibition
In non-competitive inhibition the inhibitor binds at different site rather
than the substrate-binding site.
When the inhibitor binds at this site there will be a change in

conformation of the enzyme molecules, which leads to the reversible
inactivation of the catalytic site.
Non-competitive inhibitors bind reversibly either to the free-enzyme or

the ES complex to form the inactive complexes EI and ESI (Enzyme
substrate Inhibition)
266
Noncompetitive inhibition
267
Non-Competitive Inhibition…
The most important non-competitive inhibitors are naturally occurring metabolic

intermediates that can combine reversibly with specific sites on certain regulatory
enzymes, that changes the activity of their catalytic sites.
*Such type of Enzyme is called Allosteric Enzyme, which has a specific sites or
allosteric site other than the substrate-binding site.
268
Uncompetitive Inhibition
Uncompetitive Inhibitor binds only to ES complex at locations other than the catalytic
site.
Substrate binding modifies enzyme structure, making inhibitor-binding site available.
Inhibition cannot be reversed by substrate.
269
Regulation of enzyme activity
There are several means by which the activity of a particular enzyme is specifically
regulated.
1. Irreversible covalent Activation / Zymogen activation
Some enzymes are secreted in an inactive form called Proenzymes or zymogens.
At the site of action specific peptide bonds are hydrolysed either enzymatically or by
PH changes to convert it into active form, e.g. Pepsinogen pepsin, Trypsinogen
trypsin, plasminogen plasmin.
After hydrolysis when it is activated, it cannot be reconverted into proenzyme form.
270
Regulation of enzyme activity…
Reversible Covalent Modification

2.
By addition of or removal of phosphate or adenylate, certain enzymes are reversibly
activated and inactivated as per the requirement.
Protein kinase of muscle phosphorylate phosphorylase kinase, glycogen synthetase

by making use of ATP.
271
3. Allosteric Modulation
In addition to simple enzymes that interact only with substrates and
inhibitors, there is a class of enzymes that bind small, physiologically
important molecules and modulate activity in ways other than those
described above.
These are known as allosteric enzymes; the small regulatory
molecules to which they bind are known as effectors.
Allosteric effectors bring about catalytic modification by binding to
the enzyme at distinct allosteric sites, well removed from the catalytic
site, and causing conformational changes that are transmitted through
the bulk of the protein to the catalytically active site(s).
272
Feedback inhibition
4.
In allosteric regulation in which end products inhibit the activity
of the enzyme is called” feedback inhibition”.
A high conc. D typically inhibits conversion of A B.

The kinetics of feedback inhibition cay be competitive, mixed, etc.
273
ENZYMES IN CLINICAL DIAGNOSIS
 enzymes measured in clinical chemistry laboratory are:
1. Transaminases
Aspartate aminoa transferase (AST) and alanine amino
Transferase (ALT) are two transaminases most frequently
measured.
 Normal levels are 3-20 U/L for AST and 4-20 U/L for ALT .
The former enzyme is also referred as GOT (Glutamate

oxalo acetate transaminase) and latter is referred as GPT
(Glutamate Pyruvate Transaminase).
274
275
ENZYMES IN CLINICAL DIAGNOSIS…
These two enzymes differ in distribution.
 Heart is rich in AST where as liver contains both of them in equal

amounts.
Hence, AST estimation is most commonly done in diseases that affect

heart.
 AST level increases in plasma following heart attack or myocardial

infarction.
276
Plasma ALT level is more in liver diseases like
alcoholic cirrhosis,
biliary obstruction,
cancer and
 toxic hepatitis.
Both the enzymes are elevated in acute infective hepatitis

because liver contains both of them in significant amount.
 After the onset of viral hepatitis, the levels of these

enzymes reaches peak rapidly and come back to normal
reference level within a week.
277
Since the skeletal muscle contains appreciate amounts of ALT, its level
is increased in muscle damage as in severe trauma and in muscular
dystrophy.
Serum transaminases are also elevated in lung disease
278
2. Alkaline phosphatase
This enzyme catalyzes the hydrolysis of organic esters at alkaline pH
9.0, hence the name alkaline phosphatase.
The normal level is 20-90 units/L.

The level of the enzyme is elevated in : rickets, obstructive jaundice,
hyper para thyroidism, metastatic cancer, bone cancer and osteomalacia.
 In obstructive jaundice, its level is 10 times the normal level because its
secretion is blocked due to obstruction.
Its level also increases in some non-specific diseases like leukemia, lung
and kidney damages and congestive heart failure, and intestinal
279 disorders.
3. Acid phosphatase
This enzyme catalyzes the hydrolysis of organic esters at
acidic pH (5.0) hence the name acid phosphatase.
The normal level of the enzyme is 2.5-12.0 units/L.
It is increased in prostrate cancer.
Small increase are seen in bone disease and breast cancer.
280
4. γ-glutamyl trans peptidase (GGT)

It is involved in the degradation of glutathione.
Its level is increased in alcoholic cirrhosis.
The normal plasma level of GGT is less than 30 units/L.
Since this enzyme is secreted into bile by liver, like alkaline

phosphatase γ-glutamyl trans peptidase level increases in
cholestatic or obstructive jaundice.
It is also elevated in brain lesions.

281
`
5. Lactate dehydrogenase (LDH)

The LDH normal level is 70-90 units/L.
LDH levels are elevated in myocardial infraction.
The serum LDH level raises within 24 hours after infraction, reaches
peak level around 2-3 days and returns to normal in a week.
Serum LDH level is also elevated in pernicious anemia, megaloblastic
anemia, acute hepatitis, blood cancer and in progressive muscular
dystrophy.
282
6. Amylase
The normal range of this enzyme in plasma is 800-1800
Units/L.
This enzyme is secreted by pancreas and salivary glands.

So, its level is elevated mainly in acute pancreatitis.
Its level raised in other conditions like intestinal obstruction

and in mumps.
283
7. Lipase
It is an enzyme produced by pancreas.
 It is secreted into duodenum through pancreatic duct.
The normal level of this enzyme is up to 150 Units/L.
 It is mainly elevated in acute pancreatitis and pancreas

cancer.
It is also elevated in patients with, intestinal obstruction.

284
8. Creatine kinase (CK) or ceratin phosphokinase (CPK)
The normal level of this enzyme in plasma is 12-60 U/l.’
CK (CPK) is found in heart muscle, brain and skeletal

muscle.
 Measurement of serum creatine phosphokinase activity is of

value in the diagnosis of disorders affecting skeletal and
cardiac muscle.
The level of CPK in plasma highly increased in myocardial

285
infarction.
Protein[Nitrogen Metabolism]
Overall Nitrogen Metabolism
 Nitrogen enters the body in a variety

of compounds present in food, the
most important being amino acids
contained in dietary protein.
 Nitrogen leaves the body as urea,

ammonia, and other products derived
from amino acid metabolism.
 The role of body proteins in these

transformations involves two
important concepts: the amino acid
pool and protein turnover.
A. Amino Acid Pool (90-100 g of A.A)
 Free amino acids are present throughout the body, for example,
in cells, blood, and the extracellular fluids (Amino Acid Pool).
 Supplied by three sources:
1) Amino acids provided by the degradation of body proteins,

2) Amino acids derived from dietary protein, and
3) Nonessential amino acids from simple intermediates of
metabolism.
 Conversely, depleted by three routes:
1) Synthesis of body protein

2) Consumed as precursors of essential nitrogen-containing small
molecules, and
3) Conversion of amino acids to glucose, glycogen, fatty acids,
ketone bodies, or CO2 + H2O
B. Protein Turnover
 Most proteins in the body are constantly being synthesized
and then degraded (permitting the removal of abnormal or
unneeded proteins).
 The total amount of protein in the body remains constant,

because the rate of protein synthesis is just sufficient to
replace the protein that is degraded and this is called
protein turnover.
 leads to the hydrolysis and resynthesis of 300-400 g of

body protein each day.
Rate of Protein Turnover:
 Varies widely for individual proteins.
1. Short-lived proteins (regulatory proteins and
misfolded proteins) are rapidly degraded, having half-
lives measured in minutes or hours.
2. Long-lived proteins (days to weeks)- majority of

proteins
3. Structural proteins (collagen), are metabolically

stable (months or years).
Protein Degradation:
 There are two major enzyme systems responsible for
degrading damaged or unneeded proteins:
1. The ATP-dependent ubiquitin-proteasome system of the

cytosol (degrade endogenous proteins)
2. The ATP-independent degradative enzyme system of the

lysosomes (degrade primarily extracellular proteins,
such as plasma proteins that are taken into the cell by
endocytosis, and cell-surface membrane proteins)
Ubiquitin-Proteasome Proteolytic Pathway
 are first covalently attached to ubiquitin (a small, globular,
non-enzymic protein).
 Ubiquitination occurs by linkage of the carboxyl group of

the C-terminal glycine of ubiquitin to the amino group of a
lysine on the protein substrate.
 The consecutive addition of ubiquitin moieties generates a

polyubiquitin chain.
 Proteins tagged with ubiquitin
are then recognized by a large, `
barrel-shaped, macromolecular,
proteolytic complex called a
proteasome, which functions like
a garbage disposal.

 The proteasome unfolds,
deubiquitinates, and cuts the
target protein into fragments that
are then further degraded to
amino acids, which enter the
amino acid pool.
Chemical Signals For Protein Degradation
 Proteins have different half-lives, so it is clear that protein

degradation cannot be random, but rather is influenced by:
1. Structural aspect of the protein.
 For example, some proteins that have been chemically

altered by oxidation or tagged with ubiquitin are
preferentially degraded.
2. The half-life of a protein is influenced by the nature of the

N-terminal residue.
Cont…
 For example, proteins that have serine as the N-terminal
amino acid are long-lived, with a half-life of more than 20
hours.
 In contrast, proteins with aspartate as the N-terminal

amino acid have a half-life of only 3 minutes.
 Additionally, proteins rich in sequences containing

proline, glutamate, serine, and threonine (called PEST)
are rapidly degraded and, therefore, exhibit short
intracellular half-lives
REMOVAL OF NITROGEN FROM AMINO ACIDS
Removal of Nitrogen From Amino Acids
 The presence of amino group keeps amino acids safely
locked away from oxidative breakdown.
 Removing the amino group is essential for producing

energy from any amino acid, and is an obligatory step in
the catabolism of all amino acids.
 Once removed, this nitrogen can be incorporated into

other compounds or excreted, with the carbon skeletons
being metabolized.
A. Transamination: The Funneling of Amino Groups to
Glutamate
 The first step in the catabolism of most amino acids is the
transfer of their amino group to α-ketoglutarate.
 The products are an α-keto acid and glutamate.
 α-Ketoglutarate plays a pivotal role in amino acid

metabolism by accepting the amino groups from most
amino acids, thus becoming glutamate.
 Glutamate produced by transamination can be oxidatively

deaminated , or used as an amino group donor in the
synthesis of nonessential amino acids.
Cont…
 This transfer of amino groups from one carbon skeleton to

another is catalyzed by a family of enzymes called
aminotransferases (transaminases).
 These enzymes are found in the cytosol and mitochondria of

cells throughout the body-especially those of the liver, kidney,
intestine, and muscle.
 All amino acids, with the exception of lysine and threonine,

participate in transamination at some point in their catabolism.
 Note: These two amino acids lose their α-amino groups by

deamination.
1. Substrate Specificity of Aminotransferases:
 Each aminotransferase is specific for one or, at most, a few
amino group donors.
 Aminotransferases are named after the specific amino group
donor, because the acceptor of the amino group is almost
always α-ketoglutarate.
 The two most important aminotransferase reactions are
catalyzed by alanine aminotransferase (ALT) and aspartate
aminotransferase(AST)
 ALT is present in many tissues. The enzyme catalyzes the
transfer of the amino group of alanine to α-ketoglutarate,
resulting in the formation of pyruvate and glutamate.
 AST is an exception to the rule that during amino acid
catabolism, AST transfers amino groups from glutamate to
oxaloacetate, forming aspartate, which is used as a source of
nitrogen in the urea cycle.
2. Mechanism of Action of Aminotransferases:
 All aminotransferases require the
coenzyme pyridoxal phosphate (a
derivative of vitamin B6, which is
covalently linked to the amino group of
a specific lysine residue at the active
site of the enzyme.
 Aminotransferases act by transferring
the amino group of an amino acid to the
pyridoxal part of the coenzyme to
generate pyridoxamine phosphate.
 The pyridoxamine form of the
coenzyme then reacts with an α-keto
acid to form an amino acid, at the same
time regenerating the original aldehyde
form of the coenzyme
3. Equilibrium of Transamination Reactions:
1. Amino acid degradation through removal of α-amino

groups (after consumption of a protein-rich meal) and
2. Amino acid biosynthesis through addition of amino

groups to the carbon skeletons of α-keto acids (when the
supply of amino acids from the diet is not adequate to
meet the synthetic needs of cells).
4. Diagnostic Value of Plasma Aminotransferases:
 Aminotransferases are normally intracellular enzymes, with
the low levels found in the plasma representing the release
of cellular contents during normal cell turnover.
 The presence of elevated plasma levels of aminotransferases

indicates damage to cells rich in these enzymes.
 For example, physical trauma or a disease process can cause

cell lysis, resulting in release of intracellular enzymes into
the blood.
 Two aminotransferases AST and ALT are of particular

diagnostic value when they are found in the plasma.
a. Liver Disease
 Plasma AST and ALT are elevated in nearly all liver
diseases, but are particularly high in conditions that cause
extensive cell necrosis, such as severe viral hepatitis,
toxic injury, and prolonged circulatory collapse.
 ALT is more specific than AST for liver disease, but the
latter is more sensitive because the liver contains larger
amounts of AST.
b. Nonhepatic Disease:
 Aminotransferases may be elevated in nonhepatic disease,
such as myocardial infarction and muscle disorders.
B. Glutamate Dehydrogenase: Oxidative Deamination
 Oxidative deamination by
glutamate dehydrogenase
results in the liberation of the
amino group as free ammonia
(NH3).
 Occur primarily in the liver and
kidney.
 They provide α-keto acids that

can enter the central pathway of
energy metabolism, and
ammonia, which is a source of
nitrogen in urea synthesis.
1. Glutamate Dehydrogenase
 Glutamate is unique in that it is the only amino acid that
undergoes rapid oxidative deamination.
a. Coenzymes:
 Glutamate dehydrogenase is unusual in that it can use
either NAD+ or NADP+ as a coenzyme.
 NAD+ is used primarily in oxidative deamination.
 NADPH is used in reductive amination (the simultaneous

gain of ammonia coupled with the reduction of the carbon
skeleton).
b. Direction of Reactions
 The direction of the reaction depends on
the relative concentrations of glutamate,
α-ketoglutarate and ammonia, and the
ratio of oxidized to reduced coenzymes.
 After ingestion of a meal containing

protein glutamate levels in the liver are
elevated and the reaction proceeds in the
direction of amino acid degradation and
the formation of ammonia.
 The reaction can also be used to

synthesize amino acids from the
corresponding α-keto acids.
c. Allosteric Regulators
 Guanosine triphosphate (GTP) is an allosteric
inhibitor of glutamate dehydrogenase,
 Where as adenosine diphosphate (ADP) is an

activator.
 Thus, when energy levels are low in the cell, amino

acid degradation by glutamate dehydrogenase is
high, facilitating energy production from the carbon
skeletons derived from amino acids
TRANSPORT OF AMMONIA TO THE LIVER
Transport of Ammonia…
 Two mechanisms are available in humans for the

transport of ammonia from the peripheral tissues to the
liver for its ultimate conversion to urea.
 1.Found in most tissues, uses glutamine synthetase to

combine ammonia (NH3) with glutamate to form
glutamine (a nontoxic transport form of ammonia) .
 The glutamine is transported in the blood to the liver

where it is cleaved by glutaminase to produce
glutamate and free ammonia.
 2. used primarily by muscle,
involves transamination of Cont…
pyruvate (the end product of
aerobic glycolysis) to form
alanine.
 Alanine is transported by the

blood to the liver, where it is
converted to pyruvate, again by
transamination.
 In the liver, the pathway of

gluconeogenesis can use the
pyruvate to synthesize glucose,
which can enter the blood and be
used by muscle (a pathway called
the glucose-alanine cycle).
Urea Cycle (Krebs-Henseleit Cycle)
 Elucidated by Krebs and Henseleit (1932).
 A five-reaction cyclic cascade that utilizes two amino groups and a
CO2 to synthesize urea, the nitrogenous waste of our body.
 Urea is the major disposal form of amino groups derived from
amino acids, and accounts for about 90% of the nitrogen-containing
components of urine.
 One nitrogen of the urea molecule is supplied by free ammonia, and

the other nitrogen by aspartate.
 The carbon and oxygen of urea are derived from CO2.
 Urea is produced by the liver, and then is transported in the blood to

the kidneys for excretion in the urine.
Sites of urea synthesis
1. Liver is the only tissue that synthesizes urea from NH3 and CO2.
2. The cycle operates partly in mitochondria and partly in the cytoplasm of liver
cells.
3. Other tissues that have activity of part of the urea cycle enzymes include kidney
and brain.
4. Kidneys operate urea cycle up to the formation of arg but enzyme arginase is
absent, so urea is not synthesized but the cycle provides a source of arg in the
kidneys.
5. Brain tissue lack the enzyme ornithine transcarbamoylase, i.e., can not form
citrulline.
6. Rest of the enzymes are present, hence brain tissue can synthesize urea if
citrulline is provided.
314
Steps of urea cycle
1. Synthesis of carbamoyl-phosphate:
 Condensation of one mole of NH3, one mole of HCO-3 and one mole of phosphate
(derived from ATP) leads to the formation of carbamoyl phosphate.
 Enzyme :carbamoyl phosphate synthetase I, an enzyme present in the liver
mitochondria of ureotellic organisms ( man and higher primates).
 Cofactors: Mg2+ or Mn2+ ;
 Allosteric activator : N-acetyl glutamate (NAG) .
 NAG increases the affinity of carbamoyl phosphate synthetase I for ATP.
 The second type of this enzyme – the cytosolar liver carbamoyl phosphate synthetase II
is utilized in pyrimidine biosynthesis and does not require NAG as an allosteric
regulator.
315
Steps of urea cycle-contd.
2. Synthesis of citrulline:
 Transfer of the carbamoyl residue from carbamoyl phosphate into ornithine to form
citrulline with liberation of phosphate.
 Enzyme: Mitochondrial ornithine carbamoyl transferase (ornithine
transcarbamoylase).
 Citrulline goes to cytosol (facilitated by a specific transporter) to complete the
cytosolar component of the urea cycle, where, the rest of the reactions take place.
 Ornithine carbamoyl transferase is clinically utilized to check for liver function.
 The level of this enzyme in blood is increased in many diseases, e.g., liver metastasis
from breast cancer and malignant lymphomas.
316
3. Synthesis of argininosuccinate:
 Citrulline is condensed into the amino group of asp to form argininosuccinate with
liberation of H2O.
 Enzyme : argininosuccinate synthetase
 Cofactors: ATP and Mg2+.
 Citrullyl-AMP is an active intermediate formed during the reaction.
317
4. Cleavage of Argininosuccinate:
 Enzyme: Argininosuccinase found in liver and kidney tissues.
 Fumarate formed by this cleavage joins Krebs' cycle to replenish its intermediates.
 Fumarate is also converted into oxaloacetate that could be transaminated into asp to
return the N into the urea cycle, thus, closing a fumarate-aspartate loop.
318
5.Cleavage of arginine into urea and ornithine:
 Liberation of urea is brought about by cleavage of arg catalyzed by arginase.
 The ornithine returns to mitochondria (facilitated by a specific transporter).
 Arginase present mainly in the liver of all ureotellic organisms.
 Smaller quantities also occur in testes, skin and mammary gland.
319
Fate of Urea:
 1.Urea diffuses from the liver, and is transported in the blood
to the kidneys, where it is filtered and excreted in the urine.
 2. A portion of the urea diffuses from the blood into the
intestine, and is cleaved to CO2 and NH3 by bacterial Urease.
 This ammonia is partly lost in the feces, and is partly
reabsorbed into the blood.
 In patients with kidney failure, plasma urea levels are elevated,
promoting a greater transfer of urea from blood into the gut.
 The intestinal action of urease on this urea becomes a clinically
important source of ammonia, contributing to the
hyperammonemia often seen in these patients.
 Oral administration of neomycin reduces the number of
intestinal bacteria responsible for this NH3 production.
Regulation of the Urea Cycle
 N-Acetylglutamate is an essential activator

for carbamoyl phosphate synthetase I-the
rate-limiting step in the urea cycle .
 N-Acetylglutamate is synthesized from
acetyl coenzyme A and glutamate by N-
acetylglutamate synthase, in a reaction for
which arginine is an activator.
 Therefore, the intrahepatic concentration
of N-acetylglutamate increases after
ingestion of a protein-rich meal, which
provides both a substrate (glutamate) and
the regulator of N-acetylglutamate
synthesis(arginine)
 This leads to an increased rate of urea
synthesis.
Metabolism of Ammonia
 Ammonia is produced by all tissues during the metabolism
of a variety of compounds, and it is disposed primarily by
formation of urea in the liver.
 However, the level of ammonia in the blood must be kept

very low, because even slightly elevated concentrations
(hyperammonemia) are toxic to the central nervous system
(CNS).
 There must, therefore, be a metabolic mechanism by

which nitrogen is moved from peripheral tissues to the
liver for ultimate disposal as urea, while at the same time
maintaining low levels of circulating ammonia.
Hyperammonemia (Ammonia intoxication)
 The presence of NH3 in conc. > 80 g/dL in blood :
hyperammonemia.
 The reasons for the toxic symptoms of hyperammonemia
include:
1. Depletion of -KGA of Krebs' cycle in brain leading to
energy failure.
2. Depletion of brain glu leading to deficiency of GABA (an
inhibitory neurotransmitter) that is a decarboxylation product
of glu.
3. Increased entrance of trp to the brain (in exchange with gln)

leading to increased level of serotonin ( stimulatory
neurotransmitter) synthesized from trp.
4. Increased synthesis of the toxic -ketoglutaramate.
324
A. Sources of Ammonia
 Amino acids are quantitatively the most important source

of ammonia, because most diets high in protein provide
excess amino acids, which travel to the liver and undergo
transdeamination-producing ammonia.
 However, substantial amounts of ammonia can be

obtained from other sources.
1. From glutamine:
 The kidneys generate ammonia from glutamine by the
actions of renal glutaminase and glutamate dehydrogenase.
 Most of this ammonia is excreted into the urine as NH4+,
which provides an important mechanism for maintaining
the body’s acid-base balance through the excretion of
protons.
 Ammonia is also obtained from the hydrolysis of
glutamine by intestinal glutaminase.
 The intestinal mucosal cells obtain glutamine either from
the blood or from digestion of dietary protein.
 Note: Intestinal glutamine metabolism produces citrulline,
which travels to the kidney and is used to synthesize
arginine.
Hydrolysis of Glutamine To Form Ammonia
2. From Bacterial Action In The Intestine:
 Ammonia is formed from urea by the action of bacterial
urease in the lumen of the intestine.
 This ammonia is absorbed from the intestine by way of the
portal vein and is almost quantitatively removed by the
liver via conversion to urea.
3. From amines:
 Amines obtained from the diet, and monoamines that
serve as hormones or neurotransmitters, give rise to
ammonia by the action of amine oxidase.
4. From Purines And Pyrimidines:
 In the catabolism of purines and pyrimidines, amino
groups attached to the rings are released as ammonia.
B. Transport of Ammonia in The Circulation
 Although ammonia is constantly produced in the tissues,

it is present at very low levels in blood.
 This is due both to the rapid removal of blood ammonia
by the liver, and the fact that many tissues, particularly
muscle, release amino acid nitrogen in the form of
glutamine or alanine, rather than as free ammonia
1. Urea:
 Formation of urea in the liver is quantitatively the most
important disposal route for ammonia.
 Urea travels in the blood from the liver to the kidneys,
where it passes into the glomerular filtrate.
2. Glutamine:
 provides a nontoxic storage and transport form of ammonia.

 The ATP requiring formation of glutamine from glutamate
and ammonia by glutamine synthetase occurs primarily in
the muscle and liver, but is also important in the CNS where
it is the major mechanism for the removal of ammonia in
the brain.
 Glutamine is found in plasma at concentrations higher than
other amino acids-a finding consistent with its transport
function.
 Circulating glutamine is removed by the liver and the
kidneys and deaminated by glutaminase.
 In the liver, the NH3 produced is detoxified through
conversion to urea, and in the kidney it can be used in the
excretion of protons.
C. Hyperammonemia
 The capacity of the hepatic urea cycle exceeds the normal
rates of ammonia generation, and the levels of serum
ammonia are normally low (5-35 μmol/L).
 However, when liver function is compromised, due either

to genetic defects of the urea cycle or liver disease, blood
levels can rise above 1,000 μmol/L.
 Such hyperammonemia is a medical emergency, because

ammonia has a direct neurotoxic effect on the CNS.
1. Acquired Hyperammonemia:
 Liver disease is a common cause of hyperammonemia in
adults, and may be due, for example, to viral hepatitis or to
hepatotoxins such as alcohol.
 Cirrhosis of the liver may result in formation of collateral

circulation around the liver.
 As a result, portal blood is shunted directly into the systemic

circulation and does not have access to the liver.
 The conversion of ammonia to urea is, therefore, severely

impaired, leading to elevated levels of ammonia.
2. Congenital Hyperammonemia:
 Genetic deficiencies of each of the five enzymes of the

urea cycle have been described.
 Ornithine transcarbamoylase deficiency, which is X-
linked, is the most common of these disorders,
predominantly affecting males, although female carriers
may become symptomatic.
 All of the other urea cycle disorders follow an autosomal
recessive inheritance pattern.
 In each case, the failure to synthesize urea leads to
hyperammonemia during the first weeks following birth.
 The hyperammonemia seen with arginase deficiency is
less severe because arginine contains two waste nitrogens
and can be excreted in the urine.
Cont…
 Urea cycle defects had high morbidity
(neurological manifestations) and
mortality.
 Treatment included restriction of dietary
protein in the presence of sufficient
calories to prevent catabolism.
 Administration of compounds that bind
covalently to amino acids, producing
nitrogen-containing molecules that are
excreted in the urine, has improved
survival.
 For example, phenylbutyrate given
orally is converted to phenylacetate.
This condenses with glutamine to form
phenylacetylglutamine, which is
excreted.
336

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Introduction and Amino Acids and Proteins

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Introduction To Medicine Module

Biochemistry and Molecular biology

reactions of substances in living systems.

Biochemistry gives answer for the following questions:

how living things obtain energy from food?

what is the chemical basis of heredity? and

what fundamental changes occur in disease?

 physicians began to look for the molecular basis of various diseases.

 Today, the practice of medicine depends on understanding the roles and

 From a biochemist’s point of view, most metabolic diseases are caused by

Biochemical basis of health and disease

WHO defines ‘health’ as a state of complete physical, mental

A disease state, on the other hand, could be defined as the

i. Physical agents: Mechanical trauma, extremes of temperature,

6 By Eido, Biochemist 3/9/21

• Ionizing radiations generate:

 Free radicals and

Reactive oxygen species

ii. Chemical agents, including drugs: The toxic compounds and

iii. Biologic agents: Viruses, bacteria, fungi and higher forms of

8 By Eido, Biochemist 3/9/21

• Investigation into metabolic differences between these

iv. Oxygen deficiency: This can lead to energy deficiency thereby

v. Nutritional imbalance: e.g diseases caused by vitamin

9 By Eido, Biochemist 3/9/21

vi. Endocrine imbalance: Hormones maintain the homeostasis of metabolism in

• The metabolic disturbance due to the deficiency or excess of one or more

• In biochemistry, we study the mechanisms by which hormones influence the

vii. Autoimmunity: Immune system gets triggered against molecules that

11 By Eido, Biochemist 3/9/21

• Biochemistry is important in solving health problems such as:

drug interactions and others

12 By Eido, Biochemist 3/9/21

The major objective of biochemistry is the complete understanding, at the

 To achieve this objective, biochemists have sought to:

Isolate the several molecules found in cells,

Determine their structures, and

Analyze how they function

Physiology, the study of body function, overlaps with biochemistry almost

 Immunology employs numerous biochemical techniques, and many immunologic

Poisons act on biochemical reactions or processes; this is the subject matter of

Many workers in microbiology, zoology, and botany employ biochemical

These relationships are not surprising, because life is depends on biochemical

In general two types of cells exist in nature.

 Most studied prokaryotic cell is Escherichia coli (E. coli).

Histones are not found in prokaryotic cells

28 By Eido, Biochemist 3/9/21

• It is also known as:

• It is the outermost boundary of a cell.

29 By Eido, Biochemist 3/9/21

• It is a thin, flexible, elastic structure 7.5-10nm thick

The membrane proteins are classified as:

 Integral proteins: span the lipid bilayer of the cell

 Channels or transporters: Move molecules in one

• Phospholipids bilayer is made from the fatty acids with

• It is a semi-permeable membrane and restricts the entry

34 By Eido, Biochemist 3/9/21

• Proteins and lipids on the surface may contain bound

• The glycocalyx protects the cell against digestion and

36 By Eido, Biochemist 3/9/21

specific channels allow specific material across

inside cell H2 O aa sugar

All cells have it for at least some part of their

• Nuclear envelope: A double membrane structure called the nuclear envelope