Biochem Chpt 12.1 General features of biosignalling

Question 1

What does signal transduction describe?

Answer 1

The signal represents information that is detected by specific receptors and converted to a cellular response, which always involves a chemical process. This conversion of information into a chemical change, signal transduction, is a universal proper§ty of living cells.

Question 2

Name 5 general features of signal transduction

Answer 2

Specificity
Amplification
Modularity
Desensitisation/ Adaptation
Integration

Question 3

What is meant by specificity?

Answer 3

Signal molecule fits binding site on its complementary receptor; other signals do not fit.

Question 4

What is meant by amplification?

Answer 4

When enzymes activate enzymes, the number of affected molecules increases geometrically in an enzyme cascade.

Question 5

What is meant by modularity?

Answer 5

Proteins with multivalent affinities form diverse signaling complexes from interchangeable parts. Phosphorylation provides reversible points of interaction.

Question 6

What is meant by desensitisation/ adaptation?

Answer 6

Receptor activation triggers
a feedback circuit that shuts
of the receptor or removes
it from the cell surface.

Question 7

What is meant by integration?

Answer 7

When two signals have opposite effects on a metabolic characteristic such as the concentration of a second messenger X, or the membrane potential Vm, the regulatory outcome results from the integrated input from both receptors.
i.e
if signal1-receptor1 = [X]
and Vm up
then signal2-Receptor2 = [X] and Vm down

Then the Net change in [X] or Vm determines the response

Question 8

Signal transductions are remarkably specific and exquisitely sensitive. How is specificity achieved?

Answer 8

Specificity is achieved by precise molecular complementarity between the signal and receptor molecules, mediated by the same kinds of weak (noncovalent) forces that mediate enzyme-substrate and antigen-antibody interactions.

Question 9

How do multicellular organisms have an additional level of specificity?

Answer 9

Multicellular organisms have an additional level of specificity, because the receptors for a given signal, or the intracellular targets of a given signal pathway, are present only in certain cell types.

Question 10

What features account for the sensitivity of signal transduction?

Answer 10

Three factors account for the extraordinary sensitivity of signal transduction:
The high affinity of receptors for signal molecules,

Cooperativity (often but not always) in the ligand-receptor interaction,

Amplification of the signal by enzyme cascades.

Question 11

How can the affinity be described numerically? Around what value is it usually?

Answer 11

The affinity between signal (ligand) and receptor can be expressed as the dissociation constant Kd, commonly 10^-10 M or less—meaning that the receptor detects picomolar concentrations of a signal molecule.

Question 12

How are receptor-ligand interactions quantified?

Answer 12

Scatchard analysis, which yields a quantitative measure of affinity (Kd) and the number of ligand-binding sites in a receptor sample

Question 13

What is meant by cooperativity in receptor-ligand interactions?

Answer 13

Cooperativity in receptor-ligand interactions results in large changes in receptor activation with small changes in ligand concentration

Question 14

When does amplification result?

Answer 14

Amplification results when an enzyme associated with a signal receptor is activated and, in turn, catalyses the activation of many molecules of a second enzyme, each of which activates many molecules of a third enzyme, and so on, in a so-called enzyme cascade

Question 15

What is the consequence of amplification?

Answer 15

Such cascades can produce amplifications of several orders of magnitude within milliseconds. The response to a signal must also be terminated such that the downstream effects are in proportion to the strength of the original stimulus.

Question 16

What does modularity of interacting signalling proteins allow for?

Answer 16

Modularity of interacting signalling proteins allows a cell to mix and match a set of signalling molecules to create complexes with different functions or cellular locations.

Question 17

What feature of signalling molecules allow for modularity to occur?

Answer 17

Many signalling proteins have multiple domains that recognise specific features in other proteins, or in the cytoskeleton or plasma membrane, and the result- ing multivalency of individual modules allows their assembly into a wide variety of multi-enzyme complexes.

Question 18

Describe a common theme in such interaction which allows regulation of these interactions

Answer 18

One common theme in such interactions is the binding of one modular signalling protein to phosphorylated residues in another protein; the resulting interaction can be regulated by phosphorylation or dephosphorylation of the protein partner

Question 19

How can scaffold proteins assist in these interactions?

Answer 19

Nonenzymatic scaffold proteins with affinity for several enzymes that interact in cascades bring those proteins together, ensuring their interaction at specific cellular locations and at specific times.

Question 20

Describe how the sensitivity of receptor systems are subject to modification and what function this may play

Answer 20

The sensitivity of receptor systems is subject to modification. When a signal is present continuously, desensitisation of the receptor system results; when the stimulus falls below a certain threshold, the system again becomes sensitive. (Think of what happens to your visual transduction system when you walk from bright sunlight into a darkened room or from darkness into the light.)

Question 21

What function may integration have in signal transduction?

Answer 21

A final noteworthy feature of signal-transducing systems is integration, the ability of the system to receive multiple signals and produce a unified response appropriate to the needs of the cell or organ- ism. Different signalling pathways converse with each other at several levels, generating complex cross talk that maintains homeostasis in the cell and the organism.

Question 22

Describe broadly the cellular actions of a hormone for the purpose of a scratchcard analysis

Answer 22

The cellular actions of a hormone begin when the hormone (ligand, L) binds specifically and tightly to its protein receptor (R) on or in the target cell.

Binding is mediated by noncovalent interactions (hydrogen- bonding, hydrophobic, and electrostatic) between the complementary surfaces of ligand and receptor.

Receptor-ligand interaction brings about a conformational change that alters the biological activity of the receptor, which may be an enzyme, an enzyme regulator, an ion channel, or a regulator of gene expression.

Question 23

How is receptor ligand binding described in an equation?

Answer 23

R + L <=> RL (complex)

This binding, like that of an enzyme to its substrate, depends on the concentrations of the interacting components and can be described by an equilibrium constant:

R + L <(k-1)=(k+1)> RL

Ka = [RL]/[R][L] = k+1/k-1 = 1/Kd

where Ka is the association constant and Kd is the dissociation constant.

Question 24

What does it mean to say that receptor-ligand binding is saturable?

Answer 24

Like enzyme-substrate binding, receptor-ligand binding is saturable. As more ligand is added to a fixed amount of receptor, an increasing fraction of receptor molecules is occupied by ligand

Question 25

What is a rough measure of receptor-ligand affinity?

Answer 25

A rough measure of receptor-ligand affinity is given by the concentration of ligand needed to give half-saturation of the receptor.

Question 26

How can we estimate the dissociation constant and the number of binding sites?

Answer 26

Using Scatchard analysis of receptor- ligand binding, we can estimate both the dissociation constant Kd and the number of receptor-binding sites in a given preparation.

Question 27

Describe the scratchcard analysis process

Answer 27

When binding has reached equilibrium, the total number of possible binding sites, Bmax, equals the number of unoccupied sites, represented by [R], plus the number of occupied or ligand-bound sites, [RL]; that is,

Bmax = [R] + [RL].

The number of unbound sites can be expressed in terms of total sites minus occupied sites:

[R] - Bmax - [RL].

The equilibrium expression can now be written:

Ka = [RL] / [L] (Bmax - [RL])

Rearranging to obtain the ratio of receptor-bound ligand to free (unbound) ligand, we get:

[bound] / [Free] = [RL] / [L] = Ka(Bmax - [RL])
=1/Kd(Bmax - [RL])

We can then plot this slope-intercept form of the equation

Question 28

How can you interpret this plotted slope from the scratchcard analysis?

Answer 28

Where the y axis is [RL]/[L]
Where the x axis is [RL]

should give a straight line with a slope of 2Ka (–1/Kd) and an intercept on the abscissa of Bmax,
the total number of binding sites

Question 29

Describe how to interpret a plot of [RL] versus [L] 􏰃 [RL] (total hormone added)

Answer 29

It is hyperbolic:
Total binding would show a sharp high rise before levelling off

Specific binding would show a more gradual but still steep rise before leveling off

Nonsepecific would show a low gradual increase

Question 30

Name however many signals you want to which cells bind

Answer 30

Antigens
Cell surface:
glycoproteins/ oligosaccharides
Developmental signals
Extracellular matrix components
Growth factors Hormones Hypoxia
Light
Mechanical touch
Microbial, insect pathogens
Neurotransmitters Nutrients Odorants
Pheromones
Tastants

Question 31

Comment on the numerocity of signals, responses and protein components of signals

Answer 31

Although the number of different biological signals is probably in the thousands, and the kinds of response elicited by these signals are comparably numerous, the machinery for transducing all of these signals is built from about 10 basic types of protein components.

Question 32

Name 6 basic receptor types

Answer 32

1. G protein–coupled receptors
2. Receptor tyrosine kinases
3. Receptor guanylyl cyclases
4. Gated ion channels
5. Adhesion receptors
6. Nuclear receptors

Question 33

Briefly describe GPCR signalling

Answer 33

G protein–coupled receptors that indirectly activate (through GTP-binding proteins, or G proteins) enzymes that generate intracellular second messengers. This type of receptor is illustrated by the B-adrenergic receptor system that detects epinephrine (adrenaline)

E.g: An external ligand binds to receptor activates an intracellular GTP- binding protein, which regulates an enzyme that generates an intracellular second messenger.

Question 34

Briefly describe tyrosine kinase signalling

Answer 34

Plasma membrane receptors that are also enzymes. When one of these receptors is activated by its extracellular ligand, it catalyses the phosphorylation of several cytosolic or plasma membrane proteins. The insulin receptor is one example; the receptor for epidermal growth factor (EGFR) is another.

E.g: Ligand binding activates tyrosine kinase activity by autophosphorylation leading to a kinase cascade.

Kinase activates transcription
factor, altering gene expression.

Question 35

Briefly describe guanylyl cyclase signalling

Answer 35

Also plasma membrane receptors with an enzymatic cytoplasmic domain. The intracellular second messenger for these receptors, cyclic guanosine monophosphate (cGMP), activates a cytosolic protein kinase that phosphorylates cellular proteins and thereby changes their activities

Question 36

Briefly describe gated ion channel signalling

Answer 36

Gated ion channels of the plasma membrane that open and close (hence the term “gated”) in response to the binding of chemical ligands or changes in transmembrane potential. These are the simplest signal transducers. The acetylcholine receptor ion channel is an example of this mechanism

Question 37

Briefly describe adhesion receptor signalling

Answer 37

Adhesion receptors that interact with macromolecular components of the extracellular matrix (such as collagen) and convey instructions to the cytoskeletal system about cell migration or adherence to the matrix. Integrins illustrate this general type of transduction mechanism

Question 38

Briefly describe nuclear receptor signalling

Answer 38

Nuclear receptors that bind specific ligands (such as the hormone estrogen) and alter the rate at which specific genes are transcribed and translated into cellular proteins.