introduction to biochemistry

History and scope

Significance and application to medicine
Cells, organelles and their markers
 Introduction

• as the science of the chemical basis of life

• describes in molecular terms the structures, mechanisms, and chemical processes
shared by all organisms and provides organizing principles that underlie life in all
its diverse forms
• the molecular logic of life
• cell biology, molecular biology, and of molecular genetics
• Con….
• shows how the collections of inanimate molecules that constitute living organisms
interact to maintain and perpetuate life

• A high degree of chemical complexity and microscopic organization.

• Systems for extracting, transforming, and using energy from the environment
• A capacity for precise self-replication and self-assembly
• Mechanisms for sensing and responding to alterations in their surroundings
• Con…
• The interplay among the chemical components of a living organism is dynamic
• changes in one component cause coordinating or compensating changes in another
• Con..
• Hence biochemistry provides important insights and practical
applications in medicine, agriculture, nutrition, and industry, its
ultimate concern is with the wonder of life itself
 Aim of biochemistry
• to Describe & Explain, in Molecular Terms, All Chemical
Processes of Living Cells
• major objective is the complete understanding, at the molecular level,
of all of the chemical processes associated with living cells
• biochemists have sought to isolate the numerous molecules found in
cells, determine their structures, and analyze how they function
• Con…

• It answer the following questions.

a. What are the chemical compounds by which living things are composed of ? What
is the structure of macromolecules characterized of living organism?

b. HOW is the food which we eat digested, absorbed and used?

c. How are various metabolism functions interrelated?

d. How does the body derive its energy for work?

• Con…

e. How do enzyme accomplish their catalytic task.

f. What is the structure of a living cell.

g. What is the chemistry of inheritance? What is a gene and how does it function?
• The correlation of biological function and molecular structure is the main theme of
biochemistry
 Application of biochemistry to medicine
• understanding and maintenance of health and the understanding and effective
treatment of diseases
• Biochemical studies have illuminated many aspects of health and disease

• protein structure and function was necessary to elucidate the single biochemical
difference between normal hemoglobin and sickle cell hemoglobin.

• alkaptonuria, albinism, cystinuria, pentosuria, familial hypercholesterolemia

• Con….
• health may be considered as a situation in which all of the many thousands of intra-
and extracellular reactions that occur in the body are proceeding at rates
commensurate with the organism’s maximal survival in the physiologic state.

• Biochemist involve in research

• Biochemical Research Has Impact on Nutrition & Preventive Medicine
• nutritional approaches to—for example—the prevention of atherosclerosis and
cancer are receiving increased emphasis
• Most & Perhaps All Diseases Have a Biochemical Basis
• Con…
• of various biochemical laboratory tests is an integral component of diagnosis and
monitoring of treatment
• Liver function test, renal test, blood glucose test
 The major chemical constituents of cells

• All organisms are made of cells

• All cells are formed from previously existing cells.
• All cells have several basic features in common
▫ They are bounded by a plasma membrane
▫ They contain a semifluid substance called the cytosol
▫ They contain chromosomes
▫ They all have ribosomes
• Con..
• Cells Are the Structural and Functional Units of All Living Organisms
• Unicellular and multicellular
• On the basis of their biochemical characteristics, the diverse organisms of the
modern world can be divided into three fundamental groups called domains:
Eukarya (eukaryotes), Bacteria, and Archaea called Prokaryotic
 Chemical composition of life

• The chemical composition of living matter is strikingly different from that of the
inanimate world
• The former composed of compounds rich in the elements carbon, oxygen, nitrogen,
and phosphorus
• Molecules are lifeless. Yet, in appropriate complexity and number, molecules
compose living things
• cells possess sub cellular structures, called organelles, which are complex
assemblies of very large polymeric molecules, called macromolecules
• Con…
• Only about 30 of the more than 90 naturally occurring chemical elements are
essential to organisms.
• Most of the elements in living matter have relatively low atomic numbers.
• The four most abundant elements in living organisms, in terms of percentage are
hydrogen, oxygen, nitrogen, and carbon,
• which together make up more than 99% of the mass of most cells
• capable of forming one, two, three, and four bonds, respectively
• Con..
• Con…
• The trace elements represent a miniscule fraction of the weight of the human body,
• but all are essential to life, usually because they are essential to the function of
specific proteins, including enzymes
• The chemistry of living organisms is organized around carbon, which accounts for
more than half the dry weight of cells
• Of greatest significance in biology is the ability of carbon atoms to form very stable
carbon–carbon single bonds
• Con….
• The major precursors for the formation of bio molecules are water, carbon dioxide,
and three inorganic nitrogen compounds—ammonium (NH4), nitrate (NO3), and
dinitrogen (N2).
• Metabolic processes assimilate and transform these inorganic precursors
• precursors are converted to metabolites, simple organic compounds that are
intermediates in cellular energy transformation and in the biosynthesis of various
sets of building blocks: amino acids, sugars, nucleotides, fatty acids, and
glycerol
• Con…
• Through covalent linkage of these building blocks, the macromolecules are
constructed: proteins, polysaccharides, polynucleotides (DNA and RNA), and
lipids
• Interactions among macromolecules lead to the next level of structural
organization,supramolecular complexes. Here, various members of one or more
of the classes of macromolecules come together to form specific assemblies that
serve important sub cellular functions
• Con…
• Forces like hydrogen bonds, ionic attractions, van der Waals forces, and
hydrophobic interactions between macromolecules maintain supramolecular
assemblies in a highly ordered functional state
• Organelles Represent a Higher Order in Biomolecular Organization

Inorganic molecules
Metabolites
Building blocks
Macromolecules
Super molecular
Organelle
cells
• Con….
• Features of bio molecules
• Biological Macromolecules and Their Building Blocks Have a “Sense” or
Directionality
• Biological Macromolecules Are Informational
• Biomolecules Have Characteristic Three-Dimensional Architecture
• Molecular Recognition Through Structural Complementarity
• hydrogen bonds, van der Waals forces, ionic interactions, and hydrophobic
interactions Weak Forces Maintain Biological Structure and Determine
Biomolecular Interactions
• Eukaryote
• membrane-enclosed organelles that best characterizes eukaryotic cells
• In addition to a nucleus, eukaryotes have an endoplasmic reticulum, Golgi
apparatus, mitochondria in almost, lysosomes and peroxisome

• The various organelles that compartmentalize eukaryotic cells represent a level of

complexity that is largely lacking in prokaryotic cells
• Organelles
• Sub cellular structures (organelles) are present in the cell
• Each organelles has its own characteristic activities and properties that work
together to maintain the cell and its functions
• each having a characteristic protein and lipid composition tailored to the organelle’s
function
• Plasma membrane
• Every cell possesses a plasma (or cell) membrane
• which isolates its contents from its surroundings

• define the boundaries of cells and organelles

• they are complexes of proteins and phospho lipid bi layer maintained by non
covalent forces
• Hydrophobic interactions are particularly important in maintaining membrane
structure.
• Hydrophobic interactions arise because water molecules prefer to interact with
each other rather than with non polar substances
• Con…
• proteins facilitate the transport of molecules and ions through the membrane, while
others are receptors
• short chains of sugars, which are attached to both phospholipids and proteins.
• They form glycocalyx.
• protection for the membrane, a site for attachment of proteins and an identity for
the cell, enabling it to be identified as ‘self’ and not foreign by the immune system
 Mitochondria

• have an outer membrane, which is permeable to small molecules, and

• an inner membrane, which is much less permeable and extensively folded
• The main function is the generation of adenosine triphosphate (ATP)
• Some cells (e.g. hepatocytes) contain several thousand mitochondria, whereas
others, such as erythrocytes, lack them entirely
 endoplasmic reticulum
• intricate system of membranes that spreads throughout the cytosol.
• Part of it is studded with ribosomes and is called the rough endoplasmic reticulum
• It has four main function
Synthesis of proteins
Synthesis of phospholipids and steroids
Hydroxylation (addition of an –OH group) of compounds
Storage of Ca2+ ions
• Con…
 The smooth ER: is where polypeptides are converted into functional proteins and
where proteins are prepared for secretion.
• site of lipid and steroid synthesis, and is associated with the Golgi apparatus.
• Smooth ER has no ribosomes and is also involved in the regulation of calcium
levels in muscle cells, and the breakdown of toxins by liver cells

• The rough ER: is studded with ribosomes and is the site of protein synthesis. It is an
extension of the outer membrane of the nuclear envelope, so allowing mRNA to be
transported to the 80s ribosomes, where they are translated in protein synthesis
 Golgi complex
• directs’ proteins that have been synthesized on the ribosomes and have then entered
the endoplasmic reticulum to various parts of the cell
• Cis and trans face
• proteins can be modified
• Vesicles, containing these modified proteins, bud from the trans-face of the Golgi
and are then transported to other parts of the cell to form another organelle
• Lysosomes
• are membrane-bound organelles that contain hydrolytic enzymes to break down
macromolecules and other organelles taken up by the lysosomes
• The enzymes degrade a number of compounds Proteins ,bacteria, Damaged or
senescent organelles
• Any indigestible material within the lysosome is normally expelled through the
plasma membrane
 Peroxisomes
• spherical vesicles bounded by a single membrane.
• They contain enzymes that catalyse oxidation that produce hydrogen peroxide
• which is degraded by the enzyme catalase.
• For example, very long or unusual fatty acids that are present in the diet but have
no function are completely degraded in the peroxisomes
 Ribosomes

• Unlike the organelles described above, ribosomes have no membrane but are
aggregates of ribonucleic acid (RNA) and protein.
• Each ribosome consists of two subunits: a large and a smaller one
• Most of the protein synthesis in a cell takes place within or upon the ribosomes
 nucleus
• All eukaryotic cells begin their existence with a nucleus and its loss or removal
normally leads to death of the cell.
• The exception to this is the reticulocyte which, while within the bone marrow,
extrudes its nucleus to form an erythrocyte
• Material within the nucleus (nucleo plasm) is separated from the cytoplasm by the
nuclear membrane (also known as an envelope), a double membrane
• The membrane is punctuated by a large number of nuclear pores, which are
composed of proteins that permit diffusion of small molecules and limited diffusion
of larger molecules
• Very large molecules also diffuse across if they possess the correct ‘identifying
signal
• Con…
• messenger RNA and ribosomal subunits can leave, and proteins and
enzymes that are involved in DNA replication and in mRNA
processing can enter the nucleus
• Within the nucleus resides DNA, which possesses the information
required for the synthesis of almost all the proteins in the cell
 cytoplasm
• the internal volume bounded by the plasma membrane, is composed of an
• aqueous solution, the cytosol, and a variety of suspended particles with specific
functions
• a highly concentrated solution containing enzymes and the RNA molecules that
encode them amino acids and nucleotides
 cytoskeleton

• several types of protein filaments crisscrossing the eukaryotic cell, forming an

interlocking three-dimensional meshwork.
• three general types of cytoplasmic filaments—actin filaments, microtubules, and
intermediate filaments
• differing in width composition, and specific function.
• All types provide structure and organization to the cytoplasm and shape to the cell.
• Actin filaments and microtubules also help to produce the motion of organelles or
of the whole cell
 water
 is a major chemical component of the earth’s surface. It is
indispensable to life
 provided conditions for the origin, evolution, and flourishing of life;
water is the medium of life
 organisms are 70% to 90% water
 Water constitutes 45-73% of total human body weight
• Con…
• Water Has Unusual Properties
• Hydrogen Bonding in Water Is Key to Its Properties
• The geometry of the water molecule and
• The Solvent Properties of Water Derive from Its Polar Nature
• its properties as a solvent play major roles in determining the
properties of living systems
• As the biological solvent, water plays a major role in
all aspects of metabolism:
• Absorption, transport, digestion, excretion as well as maintenance of
body temperature
• Con..
• water is central to biochemistry
 Nearly all biological molecules assume their shapes in response to
the physical and chemical properties of the surrounding water
 The medium for the majority of biochemical reactions is water
 Water itself actively participates in many chemical reactions that
support life
• All organisms require water
• Living organisms can be found wherever there is liquid water
• PHYSICAL PROPERTIES OF WATER
• colorless, odorless, and tasteless nature
• Water Is a Polar Molecule
• Water Molecules Form Hydrogen Bonds. The angular geometry of the
water molecule has enormous implications for living systems
• Electrostatic attractions between the dipoles of water molecules are
crucial to the properties of water itself and to its role as a biochemical
solvent