This document provides an overview of biochemistry for pre-clerkship students. It begins by outlining the learning outcomes, which include understanding the roles of biochemistry in medical education and defining life. It then discusses the chemical foundations of cells and lists the main components and reactions that occur within cells. The document describes the key organelles found in cells and their biochemical roles. It also covers the different types of cell signaling found in multicellular organisms. Finally, it provides definitions and scopes of biochemistry, organic chemistry, and discusses the major biomolecules and cellular foundations of life.

1. Institute of Health
Department of Biomedical Sciences
Biochemistry for Pre-clerkship –I
2020/2021 Entry
By:. Minale F.

2. Learning outcomes: By the end of these sessions, the students
will be able to:
 Appreciate the role Biochemistry for Medical & Health
Sciences educator
 Define clearly what is meant by "life" & "living organisms“
 Describe Chemical Foundations of cell and level of
organization
 list the main components of cells and the metabolic reactions
that occur in cells
 Identify key Membranous & non-membranous organelles
 Describe biochemical roles of Membranous & Non-
membranous organelles
 Describe types of cell signaling found in multicellular
organisms

3. What is life?
What is Life Made of?
 Physical and Chemical sciences alone may not
completely explain the nature of life, but they at least
provide the essential framework for such an
explanation
 All students of life must have a fundamental
understanding of organic chemistry &
biochemistry.

4. Organic chemistry
 Organic chemistry is the study of C- compounds
 Organic compounds are compounds composed
primarily of a C-skeleton.
 All living things are composed of organic
compounds
 All organic biomolecules contain carbon
 What makes Carbon Special? Why is Carbon so
different from all the other elements on the periodic
table?

5. Answers
 Its unparalleled versatility in forming stable covalent
bonds by electron-pair sharing.
 The ability of Carbon atoms to bond together to form
long chains and rings.
 Ability to accept four valence electrons, allowing
simultaneous association
of a carbon atom with four other atoms
 Highly exothermic oxidation reaction—oxidation of
reduced carbon releases much energy

6. Biochemistry
 Can be defined as the science concerned with the chemical basis
of life (Gk bios “life”).
 The cell is the structural unit of living systems.
 Thus, biochemistry can also be described as the science
concerned with the chemical constituents of living cells and with
the reactions and processes they undergo
Also can be defined more formally as
 The science concerned with the chemical basis of life
 Because life depends on biochemical rxn‟s,
 Biochemistry is concerned with the entire spectrum of life
forms, from relatively simple viruses and bacteria to complex
human beings.
 Biochemistry has become the basic language of all biologic
sciences

7. Scope of Biochemistry
 As wide as life itself
 Whenever there is life, Chemical processes are
occurring
 It concerned with the entire spectrum of life forms,
–from relatively simple viruses & bacteria to
complex human beings.

8. Biochemistry
 Biochemistry and medicine are intimately related.
 Health depends on a harmonious balance of
biochemical reactions occurring in the body, and
disease reflects abnormalities in biomolecules,
biochemical reactions, or biochemical processes
 Advances in biochemical knowledge have illuminated
many areas of medicine
 A sound knowledge of biochemistry and of other
related basic disciplines is essential for the rational
practice of medical and related health sciences.

9. Biochemistry
 As long as medical treatment is firmly grounded in a
knowledge of biochemistry and other basic sciences, the
practice of medicine will have a rational basis that can be
adapted to accommodate new knowledge.
 This contrasts with unorthodox health cults and at least some
“alternative medicine” practices, which are often founded on
little more than myth and wishful thinking and generally lack
any intellectual basis.

10. Biochemistry
 We believe that most if not all diseases are manifestations of
abnormalities of molecules, chemical reactions, or biochemical
processes.

11. Biochemistry is largely concerned with a limited
number of issues:.
 What are the chemical and 3D structures of biological
molecules?
 How do biological molecules interact with each other?
 How does the cell synthesize and degrade biological
molecules?
 How is energy conserved and used by the cell?
 What are the mechanisms for organizing biological
molecules and coordinating their activities?
 How is genetic information stored, transmitted, and
expressed?

12. What do biochemists do?
 Provide new ideas and experiments to
understand how life works
Support our understanding of health and
disease
 Contribute innovative information to the
technology revolution
 Work along side chemists, physicists,
healthcare professionals, policy makers,
engineers and many more professionals

13. The aim of Biochemistry
The major objective of biochemistry is:
 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 numerous molecules found in cells
Determine their structures,
Analyze how they function

14. Chemical Molecules of Life
 Life is composed of lifeless chemical molecules
 A single cell of the bacterium, Escherichia coli
contains about 6,000 different organic compounds
 It is believed that man may contain about 100,000
different types of molecules although only a few of
them have been characterized

15. The major complex biomolecules of the cell

17.  The basic information on the various biomolecules is essential
for a better understanding of the concepts of biochemistry

18. Cellular Foundations
 All organisms are built from cells
 All animal tissues including human are also
organized from collections of cells
 Functional and Structural unit of all living organisms
 If cell dies, tissue dies and it cannot functional
 First discovered by Robert Hooke in 1665
 What is organelles?

19. Fundamental Statements of Modern Cell Theory
 Cells make up all living matter
 All cells arise from other cells(pre- existing )
 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 that is its
metabolism, both anabolism and catabolism, takes
place in the cells.

20. Types of cells
The three-domain (Superkingdoms) of System

21. Eukaryotic cells (Animal cell)
 Three main components of Eukaryotic cells are
1- Cell membrane
2- Nucleus
3- Other various types of organelles
 Nucleus is the largest organelle
 Mitochondrion the second largest organelle in animals & the
3rd in plant cells.
 Mitochondria are unusual organelles in two ways:
 In the matrix they have their own unique DNA called
mitochondrial DNA.
 Mitochondria have the ability to replicate themselves even
when the cell to which they belong is not undergoing cell
division.

22. THE CELL MEMBRANE
 A cell cannot survive if it is totally isolated from its
environment. Plasma membrane ?
 The cell membrane is a complex barrier separating
every cell from its external environment.
 This "Selectively Permeable" membrane regulates what
passes into and out of the cell
 The cell membrane is a fluid mosaic of proteins
floating in a phospholipid bilayer
 It functions like a gate, controlling which molecules
can enter and leave the cell.
7/17/2021 22

23. Cell membrane/plasma membrane
 About 40% lipid and 50% protein 10% Carbohydrate , ~5 nm
thick
 Similar in structure and composition to the prokaryotic inner
membrane and highly selective pemeability barrier.
Pumps and channels
Enzymes
Reception of extracellular information
Acts as a semi-permeable barrier
Associated with several enzymes
Contain receptors for hormones
Contain recognition sites for antibodies

24. Chemical Composition of membranes(%)

25. Composition of different membranes
Content of various lipids as % of total Ls

26. Functions of Plasma Membrane
It is selectively permeable membrane
 Its principal role is to regulate the flow of materials in
and out of the cell;
 Carrier proteins in the membrane are involved in the
transport of certain materials across the plasma
membrane;
 In some cases it protects the inner cytoplasmic
inclusions;
 it perceives the chemical stimulus.

27. Formation of Lipid Bilayer
 Membrane is often referred to as the phospholipid bilayer b/s
made up of two layers of lipids
 Each contains a hydrophobic (water repelling) tail and a
hydrophilic (water attracting) head
 hydrophobic tails oriented inside the bilayer while hydrophilic
„polar‟ heads oriented exterior to wards water rich environments
 Not all lipids can form bilayers.
 A lipid bilayer can form only when the cross-sectional areas of
the hydrophobic tail and hydrophilic polar head are about equal
 The hydrophobic effect and the solvent entropy provide the
driving force for the formation of lipid bilayer

29. Fluid Mosaic Model of Cell Membranes
 The fluidity of the membrane are highly dependant upon the
lipid composition of the membrane.
 Membranes are fluid(viscous like vegetable oil).
 The molecules of the cell membrane are always
in motion, so the phospholipids are able to drift
across the membrane, changing places with their
neighbor.
 Proteins, both in and on the membrane, form a Mosaic.
 Because of this, scientists call the modern view of membrane
structure the „Fluid Mosaic Model‟.

30. Fluid Mosaic Model of Biomembrane

32. The Components and Functions of the Plasma Membrane

33. Prokaryotic cell labeled diagram

34. Essential differences between Pro & Eu cells

36. Organelle
 An organelle is a specialized subunit within a
cell that has a specific function .
 A specialized subunit within a cell that has a
specific function, and is usually separately
enclosed within its own membrane.
 Two types of organelles found in the cell.
1. Membranous Organelles
2. Nonmembranous Organelles

37. 1. Membranous Organelles
 Are organelles which are surrounded by a cell membrane in
order to separate out the organelles.
 comprise a defined boundary to the organelle
 comprise fluid-filled cavities inside the organelle.

38. Example of Membranous Organelles
 Nucleus
 endoplasmic reticulum
 mitochondria
 Golgi apparatus
 plastids, and
 lysosomes

39. 2. Nonmembranous Organelles
 Are organelles which do not contain surrounding cell
membranes, separating the organelle from the cytoplasm.
 do not comprise fluid-filled cavities inside the organelles.
 are continuous with the cytoplasm

40. Example of Nonmembranous Organelles
 Ribosomes,
 Nucleoid
 centrioles
 Cilia
 flagella, and
 components of the cytoskeleton (MT,MF& IF)
 NB: Prokaryotic organelles are nonmembranous organelles

42. Introduction
 At the cellular level, Sensing of environments & cell
communication for coordination relies on signal transduction;
modeling signal transduction systems as self-organizing allows
one to explain how equilibria are maintained.
 Cell-to-cell communication is absolutely essential for
multicellular organisms and is also important for many
unicellular organisms.
 Cells must communicate to coordinate their activities.
 Cells may receive a variety of signals, chemical signals,
electromagnetic signals, and mechanical signals.
 Any process occurring within cells that convert one kind of
signal/stimulus into another type is called Cell
signaling/Signal Transduction

43. General Principles of Cell Signaling
 Cell communication occurs at various distances
 Numerous signaling molecules (ligands) and receptors but
limited signaling pathways
 Ligand-receptor interactions are specific
 Formation of signaling complex
 Some intracellular signaling proteins function as molecular
switches

44. Cell signaling Cont.….
 Single cellular organisms need to detect nutrients in their
environment, and
 cells in multicellular organisms are involved in a complex
system of communication with each other.
 They need cell signalling to regulate different functions.
 Signalling in multicellular organisms is a complex process, in
which many millions of highly specialized cells may need to
act in a coordinated fashion

45. Cell signaling Cont.….
 Multicellular organisms can also release signaling molecules
that target other cells.
• Some transmitting cells release local regulators that
influence cells in the local vicinity.
• In synaptic signaling, a nerve cell produces a
neurotransmitter that diffuses to a single cell that is
almost touching the sender.
• Plants and animals use hormones to signal at greater
distances.
• Cells may communicate by direct contact.

46. Cell signaling pathways regulate:
 cell cycle- proliferation
 cytoskeleton- migration
 transcription- differentiation
 membrane traffic- exocytosis
 cell survival and death- apoptosis
 Development- body plan

47. Cell signaling Cont.….
 Cell signalling can be intercellular as well as
intracellular.
 Intracellular signals are produced by the same
cells that receive the signal.
Signaling chains within the cell, responding to
extracellular and intracellular stimuli
 Intercellular signals travel throughout the body

48. Different Types of intercellular Signalling
 Cell Signalling can be categorized based the distance over
which the signalling occurs.
1. Autocrine signals: Affect the same cell that releases them.
E.g. many tumor cells reproduce uncontrollably because they
self-stimulate cell division by making their own division
signals.
2. Paracrine signals: Diffuse to and affect nearby cells.
E.g. is a neurotransmitter made by a nerve cell that diffuses to
an adjacent cell and stimulates it.

49. D/t Types of intercellular Signalling
Cont…
3. Juxtacrine signaling (Direct Contact ):Requires direct contact
between the signaling and the responding cell, and usually
involves interaction between signaling molecules bound to
the surfaces of the two cells.
4. Endocrine signals: That travel through the circulatory systems
of animals or the vascular systems of plants to reach
receptors on distant cells are generally called hormones.
5. Synaptic signalling: Is performed by neurons that transmit
signals electrically along their axons and release
neurotransmitters at synapses, which are often located far
away from the cell body

51. Signal Transduction Pathways
 Allow the cell to sense and respond to signals in the
environment.
1. Signal
2. Receptor
3. Transducer
4. Effectors
5. Response(upstream/ downstream)

52. Stages Cell Signaling Pathway
 Cell Signaling Pathway can be divided into 3 stages:
1. Reception:
 A cell detects a signaling molecule from the outside of the cell.
 A signal is detected when the ligand binds to a receptor protein
on the surface of the cell or inside the cell.
2. Transduction:
 When the signaling molecule binds to the receptor, it changes
the receptor protein.
 This change initiates the process of transduction.
 Each relay molecule in the signal transduction pathway
changes the next molecule in the pathway.
3. Response:
 Finally, the signal triggers a specific cellular response
 The response is observed

53. Steps in Cell-to-cell Communication
1. synthesis of the signaling molecule by the signaling cell
2. release of the signaling molecule by the signaling cell
3. transport of the signal molecule to the target cell
4. detection of the signal by a specific receptor protein
5. initiation of intracellular signal-transduction pathways
6. a change in cellular metabolism, function, or
development of the target cell
7. removal of the signal, which usually terminates the
cellular response

54. Cell Signaling Mechanism

55. Stages Cell Signaling Pathway cont..

56. Signal molecules and Receptor Proteins
 A cell targeted by a particular chemical signal has a receptor
protein that recognizes the signal molecule.
• Recognition occurs when the signal binds to a specific site on
the receptor because it is complementary in shape.
• When ligands (small molecules that bind specifically to a
larger molecule) attach to the receptor protein, the receptor
typically undergoes a change in shape.
• This may activate the receptor so that it can interact with other
molecules.
• For other receptors this leads to the collection of receptors.

57. Different types of signaling molecules
 A cell can communicate signals to other cells in various
molecules ways.
 Intracrine ligands: These are produced by the target cell and
bind to the receptor within the cell.
 Autocrine ligands: They function internally and on other
target cells. For eg., immune cells.
 Juxtacrine ligand: These target the adjacent cells.
 Paracrine ligands: These target the cells in the vicinity of the
original cells. For eg., neurotransmitters
 Endocrine ligands: These produce hormones.

58. Examples of signalling Molecules

59. Forms of signaling molecules
 Gasses
– NO
– CO
 Steroid Hormones
– Testosterone
– Estradiol
– Progesterone
– Glucocorticoids
• Cortisol
– Mineralocorticoids
• Aldosterone
 Peptide Hormones & GF

60. Receptors
• Receptors :recognize a signal molecule and
transmit the signal by activating a downstream
signaling pathway.
• Receptors recognize the signal first.
 Receptors can be roughly divided into two
major classes:
 Intracellular receptors and
 Extracellular receptors

62. Extracellular receptors
 Extracellular receptors are integral transmembrane
proteins and make up most receptors.
 They span the plasma membrane of the cell, with one part of
the receptor on the outside of the cell and the other on the
inside.
 Signal transduction occurs as a result of a ligand binding to the
outside region of the receptor (the ligand does not pass through
the membrane).
 which bind hydrophilic messengers (water souble) .
• Are integral transmembrane proteins and make up most
receptors
• Large or polar ligands cannot cross the lipid bilayer
• These receptors span the membrane.

63. Classes of ligand-triggered cell-surface receptors.
 G protein-coupled receptors.
 Receptors with Kinase activity.
 Integrin receptors.
 Toll gate receptors.
 Ligand-gated ion channel receptors.

65. Extracellular Receptors cont..
• The G protein is
an intermediary
between the
receptor and an
effector protein.

66. Extracellular Receptors
 The mammalian
hormone insulin
binds to a protein
kinase receptor on
the outside surface
of the cell and
initiates a
response

67. Intracellular receptors
 Intracellular receptors are receptors located inside
the cell rather than on its cell membrane.
 Bind hydrophobic messengers (insoluble)
 Small or nonpolar ligands can diffuse across the phospholipid
bilayer
 E.g.
• steroid hormones,
• retinoic acid,
• thyroid hormone, and
• vitamin D.
 All hormones that act by regulation of gene expression have
two consequences in their mechanism of action;

69. Intracellular receptors
 Human growth
factor fits into its
membrane-
bound receptor
(a protein with
two subunits)
and binds to it
noncovalently.

70. Singnalsome
Signaling molecules interact with each other to
form large complexes, and most of those
complexes do not diffuse in the cytoplasm, but
rather are attached to cell membranes
The complex is called signalsome or
transducisome.
Among components of a signalsome, a protein
that binds to more than one protein and has no
enzymatic activity is defined as a scaffold protein,
because the primary function of such a molecule
is to provide other components with a framework
on which they efficiently work.

71. R/ship b/n stimulus
strength and
signalling responses
for normal and
remodelled
signalosome .

72. Importance of cell communication
 During development , cells differentiate to adopt
specialized roles.
 It helps in determination odd cell fate ( i.e. live, die or
divide).
 Help in neurotransmission.
 Regulation of metabolism.
 Contraction and expansion of muscle.
 Regulation of development of secondary sexual
characteristics.

73. Cell signaling Cont.….
 Intercellular signaling: Processes sensory information
Controls.
 Metabolic fluxes
 Cell division
 Growth
 Differentiation
 Development.

74. Cell signaling Cont.….
 The intracellular signaling paths control all functions of the
cell such as
 Intermediary Metabolism,
 Cell Division Activity,
 Morphology And
 The Transcription Program.