cell signalling pathways Flashcards
(134 cards)
1
Q
what is the definition of cell signalling
A
The process by which a cell responds to substances outside the cell through signalling molecules found on the surface and inside the cell.
2
Q
Why is cell signalling important?
A
Cellular functions such as cell growth, proliferation, secretion, motility and metabolism must be integrated and regulated according to the needs and physiological status of the cell or organism.
3
Q
why is this key
A
- Cells respond in real time to cues from their neighbours and environment.
- All communication relies on secreted chemical messengers - are proteins or other molecules produced by a cell, they are often secreted from the cell and released into the extracellular space.
- Not all cells can respond to a particular chemical message– has to be the correct target cell with the right receptor for that signal.
4
Q
what is the process of cell signalling?
A
- When a signalling molecule (ligand) binds to its receptor, it alters the shape or activity of the receptor, triggering a change inside of the cell.
- The message carried by a ligand is often relayed through a chain of chemical messengers inside the cell.
- Leads to a change in the cell, such as alteration in the activity of a gene or even the induction of a whole process, such as cell division.
- The original intercellular (between-cells) signal is converted into an intracellular (within-cell) signal that triggers a response.
- The message carried by a ligand is often relayed through a chain of chemical messengers inside the cell.
5
Q
what is the main difference between the different categories of signalling
A
the distance that the signal travels through the organism to reach the target cell
6
Q
how many forms are there?
A
4
7
Q
what are the 4 basic categories of chemical signalling:
A
- paracrine signalling
- autocrine signalling
- endocrine signalling
- signalling through cell-cell contact
8
Q
what is paracrine signalling
A
Cells close to one another communicate through the release of chemical messengers. Over relatively short distances.
9
Q
example of paracrine signalling:
A
synaptic signalling
10
Q
what is synaptic signalling
A
- Nerve cells transmit signals through the synapse.
- When the neuron fires, an electrical impulse moves rapidly through the cell, traveling down the axon
- When the impulse reaches the synapse, it triggers the release of ligands called neurotransmitters.
- The neurotransmitter crosses the small gap between the nerve cells and binds to receptors on the receiving cell causing a chemical change inside of the cell.
11
Q
what is autocrine signalling:
A
- A cell signals to itself, releasing a ligand that binds to receptors on its own surface.
- Important during development, helping cells take on and reinforce their correct identities.
12
Q
what is endocrine signalling:
A
- Signals are produced by specialised cells and released into the bloodstream, which carries them to target cells in distant parts of the body e.g. hormones.
- Endocrine glands release hormones - thyroid, the hypothalamus, and the pituitary.
- It can affect many different types of cells throughout the body.
13
Q
example of endocrine signalling
A
E.g. the pituitary releases growth hormone which promotes growth - particularly of the skeleton and cartilage
14
Q
what is signalling through cell-cell contact:
A
- Gap junctions are tiny channels that directly connect neighbouring cells.
- Water-filled channels allow small signalling molecules, called intracellular mediators to diffuse between the two cells.
15
Q
in cell-cell contact, small molecules and ions are able to move between cells but what cannot?
A
large molecules like proteins and DNA cannot fit without special assistance.
16
Q
- what is another form of direct signalling?
A
two cells may bind to one another because they carry complementary proteins on their surfaces.
The proteins bind to one another causing a change in the shape of one or both proteins transmitting a signal.
E.g. Immune cells use cell-surface markers to recognise the body’s own cells and cells infected by pathogens.
17
Q
how many diff types of extracellular messengers are there
A
3
18
Q
what are the diff types of extracellular messengers
A
- hormones
- neurotransmitters
- local chemical mediators
19
Q
hormones are secreted by?
A
endocrine glands (e.g. insulin from the Islets of Langerhans in the pancreas)
20
Q
how are hormones carried?
A
in the blood to target tissues (e.g. insulin to white adipose tissue).
21
Q
how do hormones act
A
over long distances of cm to metres (ie all over body) and within minutes to days.
22
Q
neurotransmitters are secreted by?
A
Secreted by neurones to conduct nerve impulses across a synapse
23
Q
how do neurotransmitters work?
A
Work over the shortest distances -the synapse is only nanometers in width and over the shortest time intervals e.g. milliseconds.
24
Q
what produces local chemical mediators?
A
Produced by specialised or non-specialised cells and affect other cells in the local environment (e.g. histamine is secreted by mast cells and causes local swelling and inflammation)
25
local chemical mediators work how what distances / how long
Work over distances of mm to cm (in a local environment) and usually over time periods of seconds to minutes to hours.
26
how do local chemical mediators have diverse chemical structures?
* Insulin (H), enkephalin (NT) and nerve growth factor (LCM) are all peptides.
* Adrenaline (H), GABA (NT) and histamine (LCM) are small molecules from amino acids.
* Steroid hormones (H) from the lipid cholesterol.
* Prostaglandins (LCM) from fatty acids.
27
peptide vs prostaglandins
Peptide = short chain of amino acids, Prostaglandins = group of lipids with hormone-like actions
28
what are receptors?
a region of tissue, or a molecule in a cell membrane, which responds specifically to a particular neurotransmitter, hormone, antigen, or other substance.
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how receptors generally work:
- Receptors that are specific for a given extracellular messenger must be present in the target tissue in order for that tissue to respond to the messenger.
- The receptor may be on the cell surface, or may be intracellular depending on the type of extracellular messenger.
- A secreted chemical messenger will react specifically with a receptor protein.
30
process of receptors working and the bonds involved
- Receptors that are specific for a given extracellular messenger must be present in the target tissue in order for that tissue to respond to the messenger.
- The receptor may be on the cell surface, or may be intracellular depending on the type of extracellular messenger.
- A secreted chemical messenger will react specifically with a receptor protein.
- non cavalry bonds hold the ligand and protein binding site together
31
how many receptor superfamilies are there?
4
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what are the receptor super families
1. ligand gated ion channels (ionotropic receptors)
2. g protein coupled receptors (metabotropic)
3. kinase linked receptors
4. nuclear receptors
33
what decided what receptor superfamily it is?
they are one of these based on molecular structure and the transduction mechanism linking the ligand-receptor complex and the physiological response
34
table to compare the families
https://www.notion.so/cell-signalling-pathways-1a500bb3982d80f482c1e1758b8b6b46?pvs=4#1a600bb3982d8023aba2e09cbe59aa2c
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schematic of the four receptor superfamilies
https://www.notion.so/cell-signalling-pathways-1a500bb3982d80f482c1e1758b8b6b46?pvs=4
36
Ligand-gated ion channels/ionotropic receptors:
- what are these?
These are transmembrane ion-channel proteins that contain a pore that allows the regulated flow of ions (Na+, K+, Ca2+, and/or Cl−) through the membrane following the binding
of ligand e.g. a neurotransmitter
37
what do ionotropic receptors mediate
They mediate fast synaptic transmission - millisecond time-scale: at chemical synapses these receptors are found on the post-synaptic membrane and transduce the binding of a neurotransmitter into an electrical signal - they alter the membrane potential of the post-synaptic membrane.
38
what do ionotropic receptors contain multiple of?
subunits - The receptor consists of 5 protein subunits ( 17 types α1-10, β1-4, γ, δ and ε.)
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inotropic receptors: how often does each subunit span the membrane
4 times so that a single channel has 20 membrane spanning helices surrounding a central pore.
40
how are the subunits arranged in ionotropic receptors
so that they surround a central aqueous channel or pore.
41
One or more of the subunits in ionotropic receptors is responsible for the binding of ?
the neurotransmitter extracellularly
42
In the resting state the channel is closed but the binding of the ligand causes what?
a conformational change in shape of the protein that is transmitted to the other subunits → this causes the channel to open and allows passage of anions or cations that alters the electrical potential of the post-synaptic membrane.
43
what are the 2 types of ligand gated ion channels
- the muscle type
- the neuronal type
44
For example: The nicotinic acetylcholine receptors
- Nicotinic acetylcholine receptors (nAChRs) are cholinergic receptors.
- Ionotropic receptors - directly linked to ion channels.
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nicotinic acetylcholine receptors:
- details on it working
- The 5 M2 helices that form the pore are sharply kinked halfway through the membrane.
- When two molecules of acetylcholine bind to the extracellular binding sites of the two α subunits a conformational change.
- This is transmitted to the other subunits and the channel opens.
- The M2 helices are rich in negatively charged amino acids which facilitates the passage and influx of sodium ions that depolarises the cell and generates an action potential and an excitatory response.
46
GABA receptors:
- found where?
GABAa (gamma-aminobutyric acid) receptor found on neurons in the amygdala and hypothalamus in
the brain.
47
GABA receptors: - how many protein subunits
five protein subunits α2, β2, and γ.
48
how does gaba work e.g. what it binds to etc
- Binds to the receptor the M2 helices of each subunit
- Change shape and opens the channel for negative chloride ions to pass into the neuron.
- The primary structure of the M2 helix is rich in positive amino acids (arginine and lysine) to attract the Cl- ions into the channel. This hyperpolarises the postsynaptic neuron and makes it less likely to fire thus producing and inhibitory (sedative) effect.
49
The inhibitory neurotransmitter molecule =
GABA
50
. G-protein coupled receptors (7TM receptors)
- Examples:
muscarinic acetylcholine receptors, adrenoceptors, dopamine receptors etc.
51
G-protein coupled receptors (7TM receptors): what are the 3 classes
Gs, Gi, Gq
52
G-protein coupled receptors (7TM receptors) these receptors comprise what
a single polypeptide chain with both extracellular and intracellular domains and seven membrane spanning segments (transmembrane alpha helices).
53
G-protein coupled receptors (7TM receptors): where does ligand binding occur
in a pocket in the membrane on one or more of the alpha helical segments.
54
G-protein coupled receptors (7TM receptors): the binding of the ligand alters what?
the conformation of the receptor protein such that the largest of its intracellular loops in the C terminus binds to, and activates a G-protein.
55
There are several types of G-protein that interact with different receptors and different target proteins. what diff things can they do?
Some G-proteins activate (or inhibit) membrane associated enzymes that result in the increased (or decreased) synthesis of second messengers. Other G-proteins regulate ion channels.
56
G-protein consists of what three subunits:
α,β,γ
57
which subunit possesses the GTPase activity
α subunit
58
β-adrenergic receptor
- where is it found?
embedded in the plasma membrane
59
what sites do β-adrenergic receptor have near the N-TERMINUS
two N-linked glycosylation sites
60
two (…) are covalently linked bound to asparagine amino acids at these sites but their function is unclear
oligosaccharides
61
it contains (…) stretches of (…) amino-acids that represent membrane spanning regions.
7
20-28
62
what do these amino acids do?
These form a pocket that is the specific binding site for the ligand.
63
which specific amino acids have been identified as crucial to ligand binding.
in the M3, M5 and M6 transmembrane domains
64
what is the natural ligand
adrenaline
65
M3 =
Adrenaline has a charged amine NH3+ that forms an ionic bond with a COO- group of aspartate (D)
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M6 =
OH on its alkyl chain that forms a H-bond with an asparagine (N), Benzene ring that forms a hydrophobic bond with phenylalanine (F).
67
M5 =
Two OHs that form H-bonds with serines (S).
68
- The α-subunit of the G-protein binds to this loop and changes its shape so that?
GDP dissociates away and GTP binds in its place = α-subunit is active.
69
- The active Gα-GTP dissociates from the βγ-subunits which remain as a
dimer.
70
- The active Gα-GTP then binds to, and activates the enzyme adenylate cyclase that results in?
the increased synthesis of the second messenger called cyclic AMP (cAMP) from ATP.
71
- The cAMP binds to the regulatory subunits of inactive cAMP- dependent protein kinase (PKA) and causes what change?
a change in their conformation that releases the active catalytic subunits of the protein kinase.
72
- These active protein kinase catalytic subunits can now phosphorylate what?
target proteins to lead to a physiological response.
73
- The Gα is rapidly hydrolysed to GDP during the interaction with adenylate cyclase and then what happens to the Gα
it then reassociates with the βγ -subunits to return to the resting inactive state.
74
what acts as a second messenger
Cyclic AMP (cAMP) is a nucleotide that acts as a second messenger.
75
how do second messengers work
Second messengers bind to intracellular proteins and change their biological activity.
76
how do these intracellular proteins produce the response we need
These proteins are often protein kinases that can then phosphorylate and alter the activity of a target regulatory enzymes or proteins to produce the physiological response required.
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there is normally a cascade of (…) between the second messenger and the target regulatory enzyme.
protein kinases
78
what happens in a cascade
one protein kinase phosphorylates and activates the next protein kinase which in turn phosphorylates the target protein or perhaps even a further protein kinase.
79
- what other kinases similarly activate a protein kinase cascade?
tyrosine
80
whats good about cascades?
amplification of response
81
what does cAMP activate
cAMP-dependent protein kinase and this phosphorylates more than one molecule of phosphorylase kinase.
82
how does the cascade also achieves diversity
it phosphorylates other targets
83
to get subsequent stimulation of the signalling pathway - […] must be removed.
the second messenger
84
cAMP is converted to AMP by what enzymes
phosphodiesterase enzymes
85
how are tyrosine kinase receptors are quite different in structure.
- Cell surface receptors for certain hormones such as insulin and for many growth factors such as epidermal growth factor.
- The C-terminal intracellular domain has a protein kinase active site that can phosphorylate the amino acid tyrosine (hence “tyrosine kinase receptor”).
- Most growth factor receptors have a very large N- terminal extracellular ligand-binding domain and a single alpha helical transmembrane segment.
- It binds the protein substrate to be phosphorylated and the ATP from which the phosphate is transferred.
86
the hormone or growth factor binds to the large extracellular domain of the receptor, causing a conformational change in the receptor protein that activates
the tyrosine kinase in the C terminus inside the cell.
87
what happens after the tyrosine kinase is activated
Receptors then dimerise and “autophosphorylate” each other on tyrosine amino acid residues.
88
This phosphorylation on tyrosine amino acids causes a further shape change in what?
the C-terminal protein kinase domain that increases the tyrosine kinase activity of each receptor.
89
The receptor tyrosine kinase then phosphorylates tyrosine residues where?
on the C-terminus of its partner or on substrate proteins.
90
These phosphotyrosines form binding sites for what
target proteins
91
Once bound what happens to the target proteins
they become activated - there are a large number of different target proteins depending on the receptor and these produce a physiological response by activating intracellular protein kinases that phosphorylate and change the activity of intracellular target proteins.
91
The target proteins have regions of protein structure known as SH2-domains and these do what?
bind the phosphotyrosines that project from the surface of the receptor.
92
insulin receptors:
- how many subunits?
have 4 subunits.
93
what are the 4 insulin subunits
- Two α subunits are extracellular, linked by a disulphide bridge and form the insulin binding site.
- They are joined by disulphide bridges to two β subunits that cross the membrane and each has tyrosine kinase activity in the cell.
94
epidermal growth factor: EGF
- what does this do?
activates its receptor and the binding of Grb2 via its SH2 domain activates a GTP-binding protein called Ras.
95
what does Ras activate?
a protein kinase called Raf and this initiates a cascade of protein kinases.
96
what does the Raf protein kinase do
Raf phosphorylates and activates another protein kinase called MEK.
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what does MEK do?
it phosphorylates and activates another protein kinase called MAP kinase and this phosphorylates and activates target proteins that are transcription factors.
98
these MAP phosphorylations are mostly on what?
serine amino acids
99
These phosphorylated and activated transcription factors act like steroid- hormone receptor complexes - how?
as they migrate to the nucleus, bind to response elements in DNA and form complexes of coactivators and RNA polymerase on the TATA box to initiate the transcription of specific genes.
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Growth factors signal an increase in the synthesis of?
new proteins for cell growth
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4. nuclear receptors (DNA-binding): these include what receptors
the receptors for steroid hormones, thyroid hormone, vitamin D, retinoic acid.
102
are nuclear receptors intracellular or extracellular
The receptors are intracellular (cytosolic or nuclear) so that the ligand must first enter the cell.
103
what does the ligand-receptor complex for nuclear receptors bind to, to stimulates the transcription of specific target genes.
DNA in the nucleus
104
The mRNA produced is then translated by the ribosomes and the result is?
- E.g. Mineralocorticoids act on the kidney where they promote transcription of the genes encoding for the various transport proteins involved in renal tubular function.
- Oestradiol is secreted by the ovaries and binds to the oestrogen receptor of the uterus. Here it stimulates transcription of the genes encoding the proteins important in endometrial thickening, increased vascularity and mucus secretion.
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Steroid hormones eg oestradiol, progesterone, cortisone are lipid-derived molecules (from cholesterol), and so are carried where?
-
in the blood bound to plasma proteins but easily traverse the plasma membrane of the target cell.
106
Each steroid hormone binds with high affinity to the steroid hormone binding domain of an intracellular receptor protein that is specific for the steroid hormone in question. E.g. Oestradiol binds to
oestrogen receptors
107
The steroid hormone-receptor complex migrates to the …
nucleus and binds to specific sites on DNA.
108
These sites on DNA are upstream of the gene that is to be expressed, they are palindromic sequences of DNA and are known as ?
“Hormone Response Elements” (HRE).
109
The binding of the steroid hormone-receptor complex to the DNA allows the formation of
a stable complex of proteins.
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a stable complex of proteins includes coactivators that acetylate the histone proteins and change the shape of the chromatin structure so that?
the gene is exposed, and RNA polymerase that transcribes the DNA to mRNA.
111
This stimulates the transcription of the gene(s) and therefore increases the production of its
mRNA.
112
what explains the relatively slow response to steroid hormones that is more likely to take minutes-hours-days to increase the activity of an enzyme or protein in a cell via an increase in its concentration.
The increased production of mRNA results in increased translation into protein.
113
Antibodies are a special type of receptor. Their role is not linked to a cell signalling pathway but forms what response instead?
one half of the immune response that destroys invading foreign organisms and molecules such as bacteria, viruses and toxins.
114
The cells of the immune system originate from where?
the haematopoetic stem cells of bone marrow.
115
bone marrow cells include what 2 types?
the T cells that carry out the cell-mediated (eg cyotoxic) immune response to invasion, and the B cells that carry out the humoral immune response – this latter is the production and release of antibodies.
116
how do antibodies start life?
as receptors on the surface of B cells waiting to bind and be activated by a ‘foreign’ protein called antigens.
117
antibody structure: how many polypeptides and what types
Antibody or immunoglobulin consists of four polypeptides– two heavy chains (~50kDa each) and two light chains (25kDa each) joined to form a "Y" shaped molecule.
118
antibody amino acid sequence?
The amino acid sequence in the tips of the "Y" varies greatly among different antibodies.
119
- what is the antibody variable region made of
This variable region, composed of 110-130 amino acids, give the antibody its specificity for binding antigen.
120
how can we cleave the variable region
Treating the antibody with a protease can cleave this region, producing Fab or fragment antigen binding that include the variable ends of an antibody.
121
what does the constant region do?
The constant region determines the function and mechanism used to destroy antigen.
122
antibody types:
- how many major classes?
5, based on their constant region structure and immune function.
123
names of the major antibody classes?
IgM, IgG, IgA, IgD, and IgE
124
IgA
prevents the colonisation of mucosal areas by pathogens.
125
IgD
functions mainly as an antigen receptor on B cells.
126
IgE
binds to allergens and triggers histamine release from mast cells.
127
IgG (in its four forms)
provides the majority of antibody-based immunity against invading pathogens.
128
IgM
is found in the blood and lymph fluid and is the first antibody made when the body fights a new infection.
129
antibody specificity:
- what is called the epitope?
This antigen region is called an epitope and is likely to be on the surface.
- Antibodies can recognise even very small molecules.
- Importance of the 3-dimensional shape of proteins is clear
130
- the variable region that is complementary to
some region of the 3D shape (secondary and tertiary protein structure) of the antigen.
131
VDJ recombination:
- when are DNA segments for both heavy (VDJ) and light (VJ) chains are randomly combined.
when the stem cell changes to become a B cell
132
Each B cell ends up with functional genes for making what chains?
one light and one heavy chain coding for an antibody as a membrane-bound receptor.
133
Antibody specificity depends on
the gene fragments used.
over 15,000,000 combinations of variable, diversity and joining gene segments are possible.
