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Introduction to Biochemistry

By
Zaheer uddin
(Pharm-D,M Phil (pharmacy
practice) MBA( MARKETING)
DEFINATION:
• Biochemistry is the application of chemistry to the
study of biological processes at the cellular and
molecular level.
• It emerged as a distinct discipline around the
beginning of the 20th century when scientists
combined chemistry, physiology and biology to
investigate the chemistry of living systems by:
A. Studying the structure and behavior of the complex
molecules found in biological material and

B. the ways these molecules interact to form cells, tissues


and whole organism
PRINCIPLE OF BIOCHEMISTRY
• Cells (basic structural units of living organisms) are highly
organized and constant source of energy is required to maintain
the ordered state.
• Living processes contains thousands of chemical reactions.
Precise regulation and integration of these reactions are
required to maintain life
• Certain important reactions E.g. Glycolysis is found in almost all
organisms.
• All organisms use the same type of molecules: CHO, proteins,
lipids & nucleic acids.
• Instructions for growth, reproduction and developments for
each organism is encoded in their DNA
Cells
• Basic building blocks of life
• Smallest living unit of an organism
• Grow, reproduce, use energy, adapt, respond to their
environment
• Many cannot be seen with the naked eye
• A cell may be an entire organism or it may be one of billions of
cells that make up the organism

• Basis Types of Cells


Cells May be Prokaryotic or
Eukaryotic

• Prokaryotes include bacteria & lack a nucleus or membrane-


bound structures called organelles

• Eukaryotes include most other cells & have a nucleus and


membrane-bound organelles (plants, fungi, & animals)
Nucleoid region contains the DNA Contain 3 basic cell structures:
•Cell membrane & cell wall • Nucleus
• Contain ribosomes (no membrane) • Cell Membrane
to make proteins in • Cytoplasm with organelles
their cytoplasm
Two Main Types of Eukaryotic Cells
Cell organelles

Plasma Membrane
A lipid/protein/carbohydrate complex, providing a barrier and
containing transport and signaling systems.

Nucleus
Double membrane surrounding the chromosomes and the nucleolus.
Pores allow specific communication with the cytoplasm. The
nucleolus is a site for synthesis of RNA making up the ribosome

Mitochondrion
Surrounded by a double membrane with a series of folds
called cristae. Functions in energy production through metabolism.
Contains its own DNA, and is believed to have originated as a
captured bacterium.

Chloroplasts (plastids)
Surrounded by a double membrane, containing stacked thylakoid
membranes. Responsible for photosynthesis, the trapping of light
energy for the synthesis of sugars. Contains DNA, and like
mitochondria is believed to have originated as a captured
bacterium.
.

Rough endoplasmic reticulum (RER)


A network of interconnected membranes forming channels within the
cell. Covered with ribosomes (causing the "rough" appearance) which
are in the process of synthesizing proteins for secretion or
localization in membranes.
Ribosomes
Protein and RNA complex responsible for protein synthesis

Smooth endoplasmic reticulum (SER)


A network of interconnected membranes forming channels within the
cell. A site for synthesis and metabolism of lipids. Also contains
enzymes for detoxifying chemicals including drugs and pesticides.

Golgi apparatus
A series of stacked membranes. Vesicles (small membrane
surrounded bags) carry materials from the RER to the Golgi
apparatus. Vesicles move between the stacks while the proteins are
"processed" to a mature form. Vesicles then carry newly formed
membrane and secreted proteins to their final destinations including
secretion or membrane localization.
Lysosymes
A membrane bound organelle that is responsible for degrading
proteins and membranes in the cell, and also helps degrade materials
ingested by the cell.
Vacuoles
Membrane surrounded "bags" that contain water and storage
materials in plants.

Peroxisomes or Microbodies
Produce and degrade hydrogen peroxide, a toxic
compound that can be produced during metabolism.

Cell wall
Plants have a rigid cell wall in addition to their cell membranes

Cytoplasm
enclosed by the plasma membrane, liquid portion called cytosol
and it houses the membranous organelles.

Cytoskeleton
Arrays of protein filaments in the cytosol. Gives the cell its
shape and provides basis for movement.
E.g. microtubules and microfilaments.
Plasma Membrane
• Boundary that separates the living cell from it’s
non-living surroundings.
• Provide shape
• Phospholipid bilayer
• Amphipathic - having both:
hydrophilic heads
hydrophobic tails
Phospholipid
• ~8 nm thick
• Is a dynamic structure
Membrane Functions
1. boundaries
6. Cell-cell
2. Localize adhesion
specific
functions

5. Cell-cell
communication
3. transport

4. Signal detection
Fluid Mosaic Model
Proteins embedded and floating in a sea of
phospholipids
Hydrophobic region
of protein

Hydrophobic region of protein


Fluid Mosaic Model
predicts:

A. Membranes are fluid: lipids & proteins move in


the plane of the bilayer

B. Proteins and lipids are asymmetrically distributed


in the bilayers
Fluid Mosaic Model:
fluid nature & asymmetric distribution of
components
2. Components:
•Lipids – phospholipids, sterols, glycolipids
•Fluidity

•Proteins – integral, peripheral, lipid-linked


•transport, receptors, enzymes, structural support,
electron transport, specialized functional domains

•Carbohydrates – as glycolipids & glycoproteins.


Fluid-Mosaic Model
Proteins—For Function
• Transport
• Receptors
• Enzymes
• Signal Transducers
• Support
Plasma Membrane Proteins

PROTEINS CAN
MOVE IN THE
MEMBRANE,
TOO!
Channel protein
Carrier protein
Cell recognition protein
Receptor protein
Enzymatic protein

Example of
Enzymatic
activity
associated
with a
membrane:
G-protein
cascade
Permeability of the Cell Membrane-
Differentially Permeable
Permeability of the Cell Membrane
DIFFUSION
• Diffusion
– the passive movement of molecules from a
higher to a lower concentration until
equilibrium is reached.
– How can we explain diffusion?
– Gases move through plasma membranes by
diffusion.
• Osmosis– A special case of diffusion
Process of diffusion
Gas exchange in lungs by diffusion
Osmosis
The diffusion of water across a
differentially permeable
membrane due to concentration
differences
Question:
What’s in a Solution?
Answer:

• solute + solvent  solution

• NaCl + H20  saltwater


TONICITY
• Refers to the concentration of SOLUTES
• Is a RELATIVE term, comparing two
different solutions
• Hypertonic
• Hypotonic
• Isotonic
Hypertonic
• A solution with a greater solute concentration
compared to another solution.

Which
way
will 3% NaCl solution
the 97% H2O 5% NaCl
water 95% H2O
move? Red Blood Cell
Hypotonic

• A solution with a lower solute concentration


compared to another solution.

Which
way
will 3% Na solution
the 97% H2O
1% Na
water 99% H2O
move? Red Blood Cell
Isotonic
• A solution with an equal solute concentration
compared to another solution.

Which
way
will 3% Na solution
the 97% H2O 3% Na
water 97% H2O
move? Red Blood Cell
ISOTONIC SOLUTION
HYPOTONIC SOLUTION
HYPERTONIC SOLUTION
Carrier Proteins
• Function—Transport. Are specific,
combine with only a certain type of
molecule.
• Types
–Facilitated transport--passive
–Active transport—requires energy
Facilitated Transport
Active Transport
The sodium-potassium pump
Exocytosis and Endocytosis
• Exocytosis---Cellular secretion
• Endocytosis—
–Phagocytosis— “Cell eating”
–Pinocytosis– “Cell drinking”
–Receptor-mediated endocytosis-
specific particles, recognition.
Exocytosis
Phagocytosis

Phagocytosis 1
Phagocytosis 2
Pinocytosis
Receptor-mediated Endocytosis
Receptors and signal molecules
• Cell-to-cell communication is essential for
multicellular organisms
• Biologists have discovered some universal
mechanisms of cellular regulation

• A signal transduction pathway is a series of steps by


which a signal on a cell’s surface is converted into a
specific cellular response

• Signal transduction pathways convert signals on a


cell’s surface into cellular responses
Types of Chemical
Signaling

Chemical signaling
between cells is one of the
most important ways that
activities of tissues and
organs are coordinated.
The nervous system is the
other major coordinating
system in animals, but even
here chemical signaling is
used between adjacent
neurons.
Modes of cell-cell signaling
1. Direct cell-cell or cell-matrix
2. Indirect: Secreted molecules.
signaling. The signaling molecules are hormones secreted by
endocrine cells and carried through the circulation system to act on
target cells at distant body sites.
signaling. The signaling molecules released by one cell act on
neighboring target cells (neurotransmitters).

signaling. Cells respond to signaling molecules that they


themselves produce (response of the immune system to foreign
antigens, and cancer cells).
Three Stages of Cell Signaling:
• Sutherland suggested that cells receiving signals
went through three processes:
– Reception
– Transduction
– Response
Three Steps in Cell Signaling
Target organ specificity is the result of specific receptor molecules for
the hormone, either on the plasma membrane surface, or in some cases
in the cytoplasm, of cells in the target organ.

1) Reception 2) Transduction 3) Response


Receptors in the Plasma Membrane
• Most water-soluble signal molecules bind to
specific sites on receptor proteins in the plasma
membrane
• There are three main types of membrane
receptors:
– G-protein-linked receptors
– Receptor tyrosine kinases
– Ion channel receptors
• 1- A G-protein-linked receptor
It is a plasma membrane receptor that works with the
help of a G protein
• The G-protein acts as an on/off switch: If GDP is
bound to the G protein, the G protein is inactive
Signal-binding site

Segment that
interacts with
G proteins

G-protein-linked receptor
• 2- Receptor tyrosine kinases are membrane
receptors that attach phosphates to tyrosines
• A receptor tyrosine kinase can trigger multiple
signal transduction pathways at once
Signal Signal-binding site
molecule
a Helix in the Signal
membrane molecule

Tyr Tyr
Tyrosines Tyr Tyr Tyr Tyr
Tyr Tyr
Tyr Tyr Tyr Tyr
Tyr Tyr
Tyr Tyr Tyr Tyr

Receptor tyrosine
kinase proteins Dimer
CYTOPLASM (inactive monomers)

Activated relay
proteins

Cellular
Tyr Tyr P Tyr Tyr P P Tyr Tyr P response 1
Tyr Tyr P Tyr Tyr P Tyr Tyr P
P
Tyr Tyr P Tyr Tyr P P Tyr Tyr P Cellular
6 ATP 6 ADP response 2

Activated tyrosine- Fully activated receptor


kinase regions tyrosine-kinase
(unphosphorylated (phosphorylated Inactive
dimer) dimer) relay proteins
• 3- An ion channel receptor acts as a gate when
the receptor changes shape
• When a signal molecule binds as a ligand to the
receptor, the gate allows specific ions, such as
Na+ or Ca2+, through a channel in the receptor
Signal Gate
molecule closed Ions
(ligand)

Plasma
Ligand-gated
membrane
ion channel receptor

Gate open

Cellular
response

Gate closed
The Specificity of Cell Signaling
• Different kinds of cells have different collections
of proteins
• These differences in proteins give each kind of
cell specificity in detecting and responding to
signals
• The response of a cell to a signal depends on
the cell’s particular collection of proteins
• Pathway branching and “cross-talk” further help
the cell coordinate incoming signals
Signal
molecule

Receptor

Relay
molecules

Response 1 Response 2 Response 3

Cell A. Pathway leads Cell B. Pathway branches,


to a single response leading to two responses

Activation
or inhibition

Response 4 Response 5

Cell C. Cross-talk occurs Cell D. Different receptor


between two pathways leads to a different response
Termination of the Signal
• Inactivation mechanisms are an essential aspect
of cell signaling
• When signal molecules leave the receptor, the
receptor reverts to its inactive state