CellCommunicationMechanisms2022Nov.ppt

Molecular Biology of the Cell
Fifth Edition
Chapter 15
Mechanisms of Cell
Communication
Copyright © Garland Science 2008
Alberts • Johnson • Lewis • Raff • Roberts • Walter

Cell Signaling:
• Cell Surface Receptors;
• Second Messenger System;
• Map Kinase Pathways
• Signaling from Plasma Membrane To Nucleus

Unicellular
organisms
Multicellular
organisms
2.5 Billion years
Mechanisms evolved over this long period to
enable cells that share the same genome to
•Collaborate
•Coordinate behaviour
•Specializing in different ways
•Sacrifice self survival in the
interest of multicellular organism

• Collaborate
• Coordinate behaviour
• Specializing in
different ways
• Sacrifice self survival
in the interest of
multicellular organism

Figure 15-2 Molecular Biology of the Cell (© Garland Science 2008)
How do a group of
unicellular organisms
communicate
with each other?
Quorum sensing

Quorum sensing:
Unicellular organisms like bacteria,
yeast respond to molecules secreted by
other cells in terms of;
•motility,
•antibiotic production,
•spore formation,
•conjugation etc.

Quorum sensing: Unicellular model of communication e.g.
bacteria, yeast that respond to molecules secreted by other cells
in terms of motility, antibiotic production, spore formation,
conjugation etc.
A: Normally spherical cells respond to mating factor B: and stop
proliferation, produce projection towards the source of mating
factor in preparation of conjugation: Yeast example

A: Normally spherical cells respond to mating factor
B: & stop proliferation, produce projection towards the
source of mating factor in preparation of conjugation

A simple intracellular signalling
pathway activated by an
extracellular signal molecule:
Signal molecule
usually binds to a
receptor protein
embedded in plasma membrane
of the target cell &
activates one or more
intracellular signalling
pathways mediated by a series of
signalling proteins
One more the activity of
effector proteins
alters the behaviour of the cell

Figure 15-3a Molecular Biology of the Cell (© Garland Science 2008)

Which are the
signal molecules?
•Proteins
•Small peptides
•Amino acids
•Nucleotides
•Steroids
•Retinoids
•Fatty acid derivatives
•Dissolved gases viz., NO & CO

Extracellular signals
1.Exocytosis to release outside
2.Emitted by diffusion
3.Attached on plasma membrane
May act locally or
following proteolytic
cleavage to release and act
at a distance, target cell
responds by binding with
receptor

Signal / Receptor binding:
How much & How strong?
• Extracellular signal molecules act at
low concentration
• E.g. ~10-8M, Affinity Constant ‘Ka’
is >108 liters/mole
• Larger the Ka, tighter the binding
between the two

What about Hydrophobic signal?

Figure 15-3b Molecular Biology of the Cell (© Garland Science 2008)
Hydrophobic molecules
• Receptor proteins
inside the target cell
• Signal molecule enters
inside, binds, & elicits
response
• Signal molecules are
small and hydrophobic
as compared to the
extracellular receptor
signal molecules

How signal
molecules interact
with receptor on
target cell?

Examples:
* During
development,
* Immune response,
* Even through long
extensions,
* Secretion of signal
molecules that act on
distant cells

== Talking to people at a party
• Occurs between
different cells i.e.
signalling and
targeting
• Signals remain locally
confined
How local confinement
is achieved?

How local confinement is achieved
and far diffusion is avoided?
•Uptake by nearby cells
•Destruction by nearby cells
•Immobilized by extracellular
matrix e.g. Heparan Sulfate
Proteoglycans bind to signal
molecules with long side chains and
immobilize them
•Antagonists compete with receptor
binding and affect cellular decisions
at development and for therapy

== Locally confined
== Occurs between different cells i.e.
signalling and targeting
•To ensure local confinement, far diffusion
is avoided by various mechanisms viz.,
uptake by nearby cells, destruction by
nearby cells, immobilized by extracellular
matrix
•E.g. Heparan Sulfate Proteoglycans bind
to signal molecules with long side chains
and immobilize them
•Antagonists compete with receptor
binding and affect cellular decisions at
development and for therapy

Figure 15-4c Molecular Biology of the Cell (© Garland Science 2008)
==Telephone communication
== Private conversation
== one to one
== at some distance
≠≠ One way in synaptic, two way in telephone
• Large organisms need specialized cells
for long distance effect, e.g. neurons,
that form chemical synapse at the target
sites far away
• The electrical pulse released in
response to a stimuli triggers secretion
of a chemical ‘neurotransmitter’ that is
delivered at the receptor on post-
synaptic target cell

Figure 15-4d Molecular Biology of the Cell (© Garland Science 2008)
== Radio Announcement
== Sent out to almost whole body or big area
== Only target cells respond or are affected,
i.e. those with specific receptors etc.
• Endocrine cells secrete ‘hormone’ into
blood stream that act on far away target
cells on other parts of the body

Neuron Vs. Endocrine signalling
• Relies on electric impulse @
~100meters per second
• On release acts in less than
mili second to act at <100nm
distance
• Can achieve high local
concentrations  ON switch
• OFF switch Relatively low
affinity for ligand, can
dissociate rapidly from
receptor, may be pumped
back into nerve terminal or
neighbouring glial cells, or
degraded by hydrolytic
enzymes
• Relies on diffusion and
blood flow
• Slow
• Can act at very low
concentrations, <10-8M

Autocrine signalling
• == talking to oneself
• Signal is sent and received by same cell
• Mainly cancer cells adapt this mechanism to
stimulate their own survival and proliferation

Fastest mode of cell signalling is
A. Endocrine
B. Paracrine
C. Contact dependent
D. Synaptic

Fastest mode of cell signalling is
A. Endocrine
B. Paracrine
C. Contact dependent
D. Synaptic ☺

How fast the response can be?
• Milliseconds to seconds, many minutes
to hours
depending on;
• Electric potential,
• Protein phosphorylation
• Change in gene expression
• Synthesis of new proteins
required for response

How fast the response can be? Milliseconds to seconds, many minutes to hours – depending on –
electric potential, protein phosphorylation, change in gene expression, synthesis of new proteins
required for response
Increased growth
and cell proliferation
Change in cell
movement, secretion,
metabolism

Narrow water filled channels present in epithelial cells and others,
allow exchange of inorganic ions & small water soluble molecules
but not macromolecules, most intimate form of cell
communication, the only bidirectional mode, homogenize
conditions in concerned cells, useful in passing nerve signal to
non-innervated cells through Calcium, cyclic AMP etc.
E.g., Blood Glucose Norepinephrine release from nerve cells,
stimulate glycogen breakdown to release glucose by increased
intracellular cyclic AMP

• Cell behaviour can be affected by
various combinations of stimuli
• Cells respond in a variety of ways
• Cells receive survival signals as
per the cell type in the absence of
which they undergo programmed
cell death, e.g. basal lamina for
epithelial cells
• Total types of signals are limited,
their combinations are much more
diverse that drive diverse
responses

• Cells receive survival signals as per
the cell type in the absence of which
they undergo programmed cell
death, Example; basal lamina for
epithelial cells
• Cell behaviour can be affected by
various combinations of stimuli
• Cells respond in a variety of ways
• Total types of signals are limited,
their combinations are much more
diverse that drive diverse responses

Can one signal molecule
induce more than one
type of response??
A: Yes
B: No

Can one signal molecule
induce more than one
type of response??
A: Yes ☺
B: No

Same signal molecule: Different response as per the cell type

Same signal molecule: Different response as per the cell type
•Acetylcholine – on heart muscle / skeletal muscle / salivary gland
•Even with same receptor protein, response is different
•Effector molecules and intracellular machinery plays a role in
how a signal is interpreted

Which is the other
mechanism by which a
signal can have different
variety of responses?
CONCENTRATION

How the same signal affect differently on different cells?
Concentration of stimulus can have difference qualitatively
•Extracellular signal molecule secreted from a localized cellular
source is a morphogen – during embryonic development
•Cells near the source of morphogen activate more receptors,
leading to a pathway which is different in cells exposed to lower
concentration of morphogen, pattern of gene expression is
different as per the concentration
•Concentration is also decided by turn-over rate of effectors
•Presence of signal  duration of response / different during
development and in adult organism

• Regulation by rate of synthesis and degradation & its equilibrium
• Conversion from active to inactive form
• Phosphorylation or binding to GTP
• Rapidity, magnitude, and duration of response determined by
inactivation process that is reverse of above various mechanisms
• [Figure] After the molecule’s synthesis rate decrease (A) or
increase (B) abruptly, the time required to reach halfway of initial
concentration is its half life. The rapidly degrading molecules
change quickly, & slowly degrading molecules change linearly

General Principles of signalling via
cell surface receptor proteins
• Extracellular signals – 1st messengers
• Intracellular mediators – 2nd messengers
• Intracellular signalling proteins – large, relay signals by generating intracellular
MEDIATORS or by activating next signalling or effector proteins in the
pathway / may act as Scaffold to bring together 2 or more signalling proteins
for quick and efficient interaction
• May transduce signal in different form
• May amplify the signals it receives– by cascade sometimes
• COINCIDENCE DETECTOR –protein may require inputs from 2 or more
signalling pathways to integrate them before relaying signal onward
• May spread signal from one to another pathway, thus increasing branching and
complexity
• May anchor one or more proteins to a particular structure in cell
• May modulate activity of other signalling proteins to regulate strength of
signaling

Integration: Intracellular
coincidence detectors;
“ABC [and] PQR”

What are the following?
• Phosphorylation / Dephosphorylation
• GTP / GDP binding
• Cyclic-AMP
• Calcium
• Covalent modification [e.g. Ubiquitilation]

Molecular ON / OFF
switches of signalling
What are the following?
• Phosphorylation / Dephosphorylation
• GTP / GDP binding
• Cyclic-AMP
• Calcium
• Covalent modification [e.g. Ubiquitilation]

Cell surface receptors and down stream events –
Molecular players: Molecular switches
Phosphorylation / dephosphorylation:
• Protein Kinase / Protein phosphatase:
• ~30% proteins have covalently bound
Phosphate,
• human genome codes for ~ 520 Protein
kinases,
• ~150 Protein phosphatases
• Two types;
– Serine/Threonine &
– Tyrosine kinases

Intracellular Signalling
Proteins that act as molecular
switches:
SWITCH-1
•A Protein kinase covalently
adds P from ATP to the
signalling protein, & a protein
phosphatase removes the P.
•The same can be activating or
deactivating for some proteins
i.e. ON/OFF are
interchangeable mechanisms as
per the case

• GTP-binding proteins:
• ON state when GTP is bound & OFF state when GDP is bound
• Intrinsic GTPase activity to convert bound GTP to GDP and thus
shut itself off.
• Two types;
– Large trimeric GTP-binding proteins or G proteins (relay signals from
GPCR that activate them), &
– Small monomeric GTPases (relay signals from many classes of cell
surface receptors)
• GAPs and GEFs regulate the monomeric GTPases

Intracellular Signalling
Proteins that act as molecular
switches:
SWITCH-2
•A GTP-binding protein is
induced to exchange its bound
GDP for GTP, which activates
the protein;
•The protein inactivates itself
by hydrolysing its bound GTP
to GDP

Others switches are;
• Calcium ions,
• Cyclic AMP,
• Covalent modification like ubiquitylation, that make them
ON/OFF or also may modify to be used for some other pathway

Cell surface receptors & signalling:
Signal transduction, by 3 types of receptors, also some other;
bind to receptors on surface and do not enter inside the cytosol or nucleus,
alter the behaviour of cells by signal transduction i.e. convert extracellular
ligand-binding event into intracellular signals
• Rapid synaptic signalling in nerve and
muscle cells, by neurotransmitters
• Homologous multipass trans membrane
proteins
Ion channel
coupled
• An ion channel or enzyme, change
permeability or change mediator
concentration
• Trimeric GTP binding protein mediates
interaction between receptor and target
protein
G-protein
coupled
• Mainly protein kinases
• Single pass trans-membrane, ligand
binding site outside the cell, catalytic
binding site inside, heterogenous
structures
Enzyme
coupled

• Rapid synaptic
signalling in nerve
and muscle cells, by
neurotransmitters
• Homologous
multipass trans
membrane proteins
Ion
channel
coupled

• An ion channel or enzyme, change
permeability or change mediator
concentration
• Trimeric GTP binding protein mediates
interaction between receptor and target
protein
G-protein
coupled
Single pass trans-
membrane, ligand
binding site outside the
cell, catalytic binding
site inside, heterogenous
structures

Or….transmitter gated ion-channel coupled receptors

GPCR: G-protein coupled receptors
•Largest family of cell-surface receptors
•Human senses of SIGHT, SMELL,
TASTE (except sour),
•~700 in human / ~ 1000 in mice
regarding smell alone
•Same molecule different GPCR
members activated as per the cell type
•Adrenaline 9 distinct GPCRs
•Acetylcholine 5
•Serotonin 14

G-protein is a trimeric molecule, made up of Alpha, beta,
and gamma subunits;
Alpha & Gamma bind with plasma membrane with lipid
molecules,
Alpha subunit has a GDP bound to it, and has GTPase
activity that hydrolyzes bound GTP to GDP.

Activation of G protein by
activated GPCR:
Change in conformation due to
binding of signal to GPCR,
Alpha subunit exchange its
GDP for GTP,
Activates both Alpha & Beta-
Gamma complex,
Act on target protein to
regulate its activity

Signals: Proteins, small peptides,
derivatives of amino acids & fatty
acids, light photons, molecules that we
smell / taste
Receptor: GPCR / G protein
Mediators: cAMP, Ca2+
& also
Direct regulation:
Ion channels viz., Olfaction &
Vision

Examples of functions of G- Protein
• Regulation of Cyclic-AMP production:
Normal levels in cytoplasm are 10-7 M
increase 20 folds in seconds
in response to extracellular signal
Role in many hormone mediated cellular
responses {Table:15-1}

• Nerve cell in culture: Blue dye indicates low
levels of c-AMP, which turns Yellow when
increases to intermediate levels and Red i.e.
high levels within seconds in response to
Serotonin

Adenylyl Cyclase catalyzes
cyclization reaction that
removes two PO4
(Pyrophosphate) groups from
ATP /
Pyrophosphatase
hydrolyses it to PO4 / Cyclic
AMP is generated that is
short-lived because it is
hydrolysed by specific
Phosphodiesterases to
form 5’-AMP

c-AMP & c-AMP dependent Protein Kinase A
mediates effects of c-AMP
• Phosphorylates specific Ser / Thre on target proteins to
regulate their activities
Inactive state;
2catalytic + 2regulatory subunit tetramer
c-AMP binding  change in regulatory subunits and
dissociate them
Activated to phosphorylate target proteins A-kinase anchoring
proteins bind to them and help tethering of enzyme to target
proteins like cytoskeleton, organelle etc.
• Some A-kinase also bind with a phosphodiesterase that lowers
c-AMP concentration immediately enabling pulse response of
PKA

C-AMP dependent response:
Fast & Slow
• Concentration dependent: Affect
ion channels directly in olfactory
neurons
• Thru’ GEF activator: activates a
monomeric GTPase Rap1 leading
to increased adhesion thru
activation of integrins

C-AMP dependent response:
Fast & Slow
• Gene transcription dependent: Secretion of
peptide hormone Somatostatin, gene is
activated on binding of Cyclic-AMP
response Element (CRE) with CRE
binding protein  recruits CREB-binding
protein;
• Thus short cAMP signal leading to long
term change; role in brain learning &
memory

Assigned before Diwali vacation 2017
Describe any one response that is affected by
absence of c-AMP

Figure 15-36 (part 1 of 2) Molecular Biology of the Cell (© Garland Science 2008)

Figure 15-36 (part 2 of 2) Molecular Biology of the Cell (© Garland Science 2008)

G-Protein/GPCR
• Adenylate cyclase c-AMP as mediator
• Phospholipase-C Ca+2 as mediator
PLCB (plasma membrane bound enzyme Phospholipase C-β)
 acts on Phosphatidylinositol 4,5-bisphophate
present in small amount in inner plasma membrane
 cleaves it into two, IP3 & diacylglycerol
• IP3 bind on ER to IP3 gated Ca channels, release
Ca in cytosol quickly increasing its concentration

Table 15-2 Molecular Biology of the Cell (© Garland Science 2008)

Intrinsic enzyme activity OR Need associated enzymes

Second Messengers
(small intracellular mediators)
• Water soluble: Ca+2, cAMP – in cytoplasm
• Lipid soluble: Diacylglycerol – in plasma
membrane
Bind to selected signalling and effector
proteins, pass the signal on..

Large Intracellular Signalling Proteins: Functional
Network that work by various possible ways
1. Relay the signal to next signalling molecule
2. Act as a scaffold to bring 2 or more signalling proteins
together for quick and efficient interaction
3. Transform the signal in a different form suitable for next step
4. Amplify the signal by activating many copies downstream
5. Integrate signals received from 2 or more pathways
6. Spread signal from one pathway to another, branching
signalling streams
7. Anchor proteins in a pathway to a structure
8. Modulate the activity and regulate the strength of signalling

How the specificity to
many signalling
response is achieved and
cross talk is avoided?

• By binding
together groups
of interacting
signalling
proteins into
signalling
complexes
• Holds the
components in
close
proximity,
achieve high
local
concentration

• How the specificity to
many signalling
response is achieved
and cross talk is
avoided?
• Transiently
intracellular
proteins bind
around a receptor,
cytoplasmic tail get
phosphorylated and
serve as docking
site

• How the specificity to
many signalling
responses is achieved
and cross talk is
avoided?
• Receptor activation
lead to modified
phospholipid
molecules
‘phosphoinositides’ in
adjacent plasma
membrane and serve to
recruit specific
proteins where they get
activated
ASSEMBLY OF SIGNALLING COMPLEX

Assembly of Signalling Complex:
How Specific Proteins are recruited?
• Highly conserved, small interaction
domains bind to structural motifs like…
– short peptide sequence
– covalent modification
– phosphorylated /ubiquitinylated amino acids
• These are Modular Interaction Domains

What are Modular Interaction Domains?
• Can be inserted anywhere in protein without
affecting the folding or function

Pleckstrin
Homology
Domain
Src
Homology
Domain
Phospho-
tyrosine
binding
domain

Induced Proximity: Sufficient
to activate in many cases
Here a signal triggers assembly
of a signalling complex that is
used to relay signals from
protein to protein
Assembly depends on various
highly conserved, small
interaction domains that bind
to particular structural motifs
that protein interacts with;
Examples of motifs: short
peptide sequence, covalent
modification, phosphorylated
or ubiquitinylated AA,
These are Modular Interaction
Domains

Modular Interaction
Domains of proteins
• SH2 (Src Homology 2) domains &
• PTB (Phosphotyrosine binding domains)
bind to Phosphorylated Tyrosines in a peptide
sequence
• SH3 domain
bind to short proline-rich amino acid sequences
• Pleckstrin homology (PH) domains
bind to charged heads of phosphoinositides
• Some proteins act as ‘adaptors’ to link two
other proteins as they have two or more
interaction domains

Other ways for proximity of
Signals & Receptors
• Lipid rafts on plasma membrane
• Specific region of cell e.g., primary cilia
that projects like an antenna, made up of
microtubules, has many receptors and
signalling proteins concentrated

How Ca+2 response is terminated
• IP3IP2 by a lipid phosphatase
• IP3 IP4 by a lipid kinase
• Calcium is pumped out to cell exterior
{PIP2 IP3 + DA} What happens to diacylglycerol (DA)?
• Remains embedded in plasma membrane
• Signalling role in many functions
• DA activates PKC (calcium dependent ser/thre protein kinase)
that act on various target proteins in presence of Ca2+ and
diacylglycerol and negatively charged membrane phospholipid
phosphatidyl serine
• DA  cleaved to release arachidonic acid used in synthesis of
‘eicosanoids’ viz., prostaglandins that play a role in inflammatory
and pain responses

How Aspirin / Ibuprofen /
Cortisone work in pain relief ??
• These block the synthesis of prostaglandins
{DA  cleaved to release arachidonic acid
used in synthesis of ‘eicosanoids’ viz.,
prostaglandins that play a role in
inflammatory and pain responses}

Calcium as Intracellular signalling mediator
• Egg cells: Rise lead to embryonic development
• Muscle cells: Contraction
• Nerve & other secretory cells: Triggers secretion
Concentration gradient of Calcium:
Extracellular ~10-3M < Cytoplasm ~10-7M ~= ER
Rushing of Ca+2 from membranes to cytosol ~10-20
fold increase, activation of Ca+2-responsive proteins
• Calcium release itself can lead to negative and
positive feedback mechanism causing oscillations
or spikes which are sensed by target proteins

Calcium/Calmodulin-dependent protein kinases
(CaM-Kinases) mediate many responses to Ca2+
signals

• 15.1 Calcium Signaling <CGTC>
• In this experiment, glial cells from the rat brain are
grown in cell culture.
• Calcium concentrations are visualized with a
fluorescent dye that becomes brighter when
calcium ions are present. In the presence of small
amounts of a neurotransmitter, individual cells
light up randomly as ion channels open up and
allow calcium ions to enter the cell.
• Occasionally, calcium waves are transmitted to
adjacent cells through gap junctions at regions
where the cells contact each other.

• 15.2 Chemo taxis of Neutrophils <GTCG>
These human neutrophils, taken from the blood of a
graduate student, are mobile cells that will quickly
migrate to sites of injury to help fight infection.
They are attracted there by chemical signals that are
released by other cells of the immune system or by
invading microbes.
In this experiment tiny amounts of chemo-attractant are
released from a micropipette. When neutrophils sense
these compounds they polarize and move towards the
source. When the source of the chemoattractant is
moved, the neutrophil immediately sends out a new
protrusion, and its cell body reorients towards the new
location.

Intracellular receptors: Small
signal molecules
• NO [nitric oxide]
• CO [carbon monoxide]
• Hormones

Example of signalling molecules that activate
intracellular receptors –NO & steroid hormones
•NO – relaxes smooth muscles by acting on
blood vessel walls (Nitro glycerine to treat
angina pain)
•NO is released by deamination of Arginine by
NOS, released outside, half life in seconds, O2
converts it to Nitrate & Nitrite
•eNOS and nNOS in endothelial cells /nerve and
muscle cells respectively, & iNOS (inducible) in
macrophages in response to infection

NO: Nitric Oxide, an intracellular signal
• Signals cells through Cyclic GMP, binding to
iron (Fe) binding site of enzyme Guanylyl
cyclase
• Can also signal independent of cGMP, by
covalently nitrosylating –SH group on specific
cysteine in protein
CO: Carbon Monoxide – also stimulates
Guanylyl cyclase and passes intracellularly

Which are the other hydrophobic
diffusible small signal molecules
passing intracellularly?
Molecule Bind with
•Vitamin D3 – Vitamin D3 receptor
•Cortisol
•Estradiol
•Retinoic acid
•Thyroxine
•Testosterone

• All receptors have a
small DNA binding domain
in case of The Nuclear Receptor
Superfamily – either as homodimers
or heterodimers

3-D structure of a ligand-binding domain
without -- with ligand binding

• The inactive receptor
protein is bound to
inhibitory proteins; all three
domains can act as
interchangeable modules

What activates the receptor?
•Ligand binding to the
receptor causes;
shutting up of the same /
dissociation of inhibitory
protein / binding of
coactivating proteins to
receptor’s transcription-
activating domain, thus
increasing gene transcription

Which are the other hydrophobic diffusible small
signal molecules passing intracellularly?
• All are nuclear receptor superfamily that control transcription of
specific genes, thus are both intracellular receptors and effectors
• Many are orphan nuclear receptors as ligands are not yet known
• Only certain type of cells have receptors for these & specific
combination of gene regulatory proteins decide the final outcome
thus leading to cellular response by these signals

G-Proteins also directly regulate ion channels
• G12 alpha subunit type directly activates a GEF
that activates a monomeric GTPase of Rho family
regulating actin cytoskeleton
• Directly activate or inactivate ion channels thus
alter ion permeability & hence excitability
• Stimulating channel-phosphorylation or affecting
production or destruction of cyclic nucleotides
that act on ion channels viz., cyclic nucleotide
gated channels in olfaction and vision

Cells respond to signals in
various ways
• On / Off i.e. ALL or NONE
• Gradual / linear

Topics for short-note
• Various modes of cell signalling & comparison
• Second messengers: cAMP, cGMP, Calcium
• GPCR and cell signalling
• cAMP and smelling
• cGMP and vision
• MAP kinase pathway
• JAK-STAT pathway
• ON-OFF mechanisms of cell signalling

Enzyme-coupled cell surface receptors
• One trans-membrane segment
• Has intrinsic enzyme activity or associates with an
enzyme
• Both activate some of the same signalling pathways
• 6 main classes;
– Receptor Tyrosine kinases
– Tyrosine-kinase-associated receptors
– Receptor serine/threonine kinases
– Histidine kinase associated receptors
– Receptor guanylyl cyclase
– Receptor like tyrosine phosphatases

RAS superfamily of monomeric GTPases
• Ras & Rho relay signals from surface receptors, can
coordinate various intracellular pathways – signalling
hub
• RTKs Signal to nucleus to stimulate cell proliferation
and differentiation are passed by RAS
• RAS function as a molecular switch
• RAS + GAP <---inactive RAS + GEF-- Active
GDP Inactive GTP Active
• RTKs could either
activate a Ras-GEF or inhibit a Ras-GAP

MAP Kinase signalling module
• RAS activation triggered by activated RTKs &
Tyrosine phosphorylation are short-lived
• To sustain the response and relay to nucleus for
gene expression mechanism is required
• Mitogen-Activated protein kinase module serves
the purpose, made up of three components that
form a module that is highly conserved

MAP - kinase serine / threonine phosphorylation:
Activating Signal from RAS is received by &
•MAP kinase kinase kinase (Raf) is recruited
which phosphorylates & activates 
•MAP kinase kinase (Mek) which
phosphorylates & activates 
•MAP kinase (Erk)  Activates expression of
immediate early genes within minutes  genes
that stimulate cell proliferation, viz.,G1 cyclins
MAP kinase Ser/Threo phosphorylation module
activated by RAS  Ras recruits Raf to plasma
membrane & helps activate it  Raf activates
Mek  activates Erk  Phosphorylates various
downstream proteins like other protein kinases &
gene regulatory proteins 

MAP kinase: in Proliferation &
Differentiation
• Response also depends on time for which
activation sustains
• Epidermal Growth Factor  5 mins, neural
precursor cells go on to divide
• Neural Growth Factor  For hours, cells
stop proliferation & go on for differentiation
• -Ve & +Ve feedback loops decide length of
signal response

MAP kinase: +ve & -ve feedback loops
• Can participate in both, making it On/Off as well as
Graded, long lasting or brief
• +ve feedback loop: Frog oocytes stimulated by
Progesterone to mature
• -ve feedback loop: By increasing concentration of a
Dual Specificity Protein Phosphatase gene that
removes Phosphate from tyr and thre on MAPK and
inactivates it
• Increase can be due to both; transcription of
phosphatase gene & stabilization of enzyme against
degradation
• Erk also phosphorylates & inactivates Raf, providing
another negative feedback loop

Budding yeast example: Same module, act differently with
different scaffold and signal, 6 MAP kinase modules in yeast

The intracellular signalling pathways from
cell surface to nucleus to alter gene expression
• JAK-STAT: Janus Kinase-
Signal transducers & activators of transcription,
cytokine receptor associated cytoplasmic tyrosine
kinases
• Janus kinase phosphorylates and activates
STATs in cytoplasm – latent gene regulatory
proteins that migrate into nucleus and regulate
gene expression after they are activated

Signalling pathways dependent on
regulated proteolysis of
latent gene regulatory proteins
• In response to a signal, regulated
proteolysis is used to control the
activity & location of latent gene
regulatory proteins

regulatory proteolysis of
• Direct linear pathway by which
extracellular signal control gene
expression

regulatory proteolysis of
• Widely functional during
development and later during new
cell formation

Signal Transduction Regulation
2nd Nov 2022
• Explain positive and negative feedback loops
• What is the mechanism of adaptation or
desensitization to a signal?
• How cell signaling response is modulated in
the absence of signaling molecule?

Amplification in the
light-induced
catalytic cascade in
vertebrate rods
The extent of
amplification is
shown in thickness
of arrows

Receptors for sour taste?
Nature, 2006 paper
• Allosteric protein
Has multiple binding sites, an effector protein
binds to a site that affects the active site for
binding the main ligand

Mechanism
for tasting
sour taste?
PKD2L1:
Polycystic
Kidney
Disease like
Ion Channel

Transduction mechanisms &
Cell Surface Receptor Proteins

A:Early primary response &
B:Delayed secondary response – induced by
the activation of a nuclear hormone receptor

Signalling pathways include ‘Feedback loops’
What are Feedback loops?
…the output of a process
acts back to regulate the same process,
can take mili-seconds to hours
Which are the two types?
• Positive Feedback loop:
• Negative Feedback loop:

“A” stimulus
Activates protein A,
which in turn,
activates protein B
Protein B then acts back
to either increase or
decrease
the activity of A

• Output inhibits own production
• Limits the level of response, thus system
becomes less sensitive to perturbations
• Delayed negative feedback can produce
oscillatory response
• Short delay leads to high response and rapid
decay
Signalling pathways: Negative Feedback loops

Signalling pathways: Positive Feedback loops
• Output stimulates own production
• Once activated does not depend on the signal
strength
• Long-term changes in cells and their progeny
persist for life time of organism, e.g. during
development mainly in response to a morphogen
• Makes it possible to have lasting change in
character without change in DNA sequence, also
passed to daughter cells (Epigenetic)

Positive Feedback Loop

The cellular response to a signal with increasing
concentration can be of two types;
Smoothly graded
OR
Switch like i.e. sudden change after accumulation of
some concentration

• Progesterone activates MAP
kinase by phosphorylation.
• The dose dependent increase in
MAP kinase activation in a
group of immature oocytes.
• The net increase is due to all the
cells getting activated MAP
Kinase?
OR
• A mix of cells with
no response < +ve response?
• All-or-None OR Linear
increase?
• Experiment to measure cell to
cell activation of MAP kinase
activity done

Figure 15-24b, c Molecular Biology of the Cell (© Garland Science 2008)
Observation of experiment reported in Science:280:895-898, 1998
Supported “C” model i.e.
All OR None response in an increasing number of cells

What is the molecular mechanism?
We enjoy a fragrance
or
don’t like foul smell initially,
then after sometime do not notice it!

Adaptation
or
Short delay leads to high response
and rapid decay
We enjoy a fragrance
or
don’t like foul smell initially,
then after sometime do not notice it!

Adaptation or
Desensitization to a signal
• Prolonged exposure to a stimulus
decreases the cells’ response to that
level of stimulus
• Reversible process
• Can sense the changes in concentration
and respond (Adaptation)

Various Mechanisms of Desensitization

MAP Kinase signalling module
• RAS activation triggered by activated Receptor
Tyrosine Kinase & Tyrosine phosphorylation are
short-lived
• To sustain the response and relay to nucleus for
gene expression mechanism is required
• Mitogen-Activated Protein kinase module serves
the purpose, made up of three components that
form a module that is highly conserved

Signalling pathways dependent on regulated
proteolysis of latent gene regulatory proteins
• In response to a signal, regulated proteolysis is
used to control the activity & location of latent
gene regulatory proteins
• Direct linear pathway by which extracellular
signal control gene expression
• Widely functional during development and later
during new cell formation

Signalling pathways dependent on regulatory
• In response to a signal, regulated proteolysis is
used to control the activity & location of latent
gene regulatory proteins
• Direct linear pathway by which extracellular
signal control gene expression
• Widely functional during development and later
during new cell formation

Signalling pathways dependent on regulatory
1. Mediated by receptor protein Notch
2. Activated by secreted protein WNT
3. Activated by secreted proteins Hedgehog
4. Activating pathways latent gene regulatory
protein NFkB

What
happens
when
WNT
signal is
absent?

• Explain the
mechanism of
SMELL & VISION
with role of G-
protein Coupled
Receptors in
regulation of
Cyclin-Nucleotide
gated Ion Channels
related to smell and
sight pathways

CellCommunicationMechanisms2022Nov.ppt

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