Regulation and Signalling Flashcards
(150 cards)
1
Q
When was the first multicellular algae?
A
1.5 billion years ago
2
Q
How did multicellularity arise?
A
- Multiple times during eukaryotic evolution
- Evolved independentlu
- Last common ancestor was unicellular
- Good advantages to being multicellular
3
Q
What are the advantages to being multicellular?
A
- Bigger = better protection from predation
- More buffered from the environment → internal environment
- Allows development of different cell types with specialized functions within organisms
4
Q
What is the flagellar synthesis constraint hypothesis?
A
- Cells with flagella allow movement
- Micro-tubule (required for cell division)
- Cell with flagella is unable to divide
- Evolutionary pressure = need specialization
- Presence of both allows movement and division
5
Q
Why is the balance between differentaited cell types important?
A
- Don’t want one type vs another
- Need to coordinate
6
Q
Describe cell communication in multicellularity
A
Need to sense extracellular and intracellular environment
Recognition of self and non-self
7
Q
Describe cell adhesion in multicellular orgnaisms
A
Multicellular organisms need to stick together
Complex system
8
Q
Why does there need to be cell signalling?
A
- Homeostasis and maintanence
- Process of development
- Cells have to reach their 3D position
- Put in righ place at the righ time
- Make the decision to become specilaised
9
Q
What are choanoflagellates?
A
- Ancestral unicellular orgnaism
- Genome analysis indicates a close relationship with animals
- Have many genes found in animals including genes coding for parts of the signalling pathways
10
Q
Describe the yeast mating type.
A
Mating type factor = peptide → secretes
Cells from protrusions → for mating → produce haploid spores
Cell signalling → have to recognise the cells
11
Q
Describe development
A
- Highly conserved
- Hierarchical process
- Starts simple
12
Q
Describe regulative development.
A
- 2 cells are able to regulate
- Divides - ball of cells - mebryo
- If separate the two halves still form an embryo with the same genetic infomration (no loss)
- Experiment done with sea urchin
13
Q
What is gene constancy?
A
Somatic cells generally contain all the same genetic information
14
Q
What demonstrations that genetic informaiton is not lost during differentaiton?
A
Cloning by transfer of nuclei from differentiated somatic cells
15
Q
What is an example of cloning
A
Dolly the sheep
16
Q
What is differential gene expression?
A
- All cells are derived from the fertilised egg cell
- Cell lineage restriction is dependent upon differential gene expression
- Process of development generates different patterns of gene activity in the cells of the embryo
17
Q
What is gene expression?
A
Process by which a gene codes information converted into the structures present and operating in the cell
18
Q
Where are proteins regulated?
A
Splicing
Additions/modifications
Transcription
Translation
19
Q
Describe the eukaryotic gene
A
- Exon, intron structure (splicing)
- Cis regulatory elements
20
Q
What are the cis regulatory elements?
A
- Promoter → upstream → transcription begins
- Regulatory regions → can be distant, upstream or downstream → quite far
21
Q
What is the role of the cis regulatory elements?
A
key in regulating where and when a gene is transcribed
22
Q
What are trans-acting factors?
A
Transcription factor proteins - trans regulators - bind directly to DNA or associated with complexes of proteins bound to DNA
23
Q
Describe RNA polymerase II as a protein coding gene?
A
- Acts initially at promoter region
- Unable to transcribe DNA on its own
- Needs to be associated with proteins
- Need transcription factors
24
Q
What is the transcription initiation complex?
A
- Large complex of proteins
- Required for the transcription of all protein coding genes transcribe by RNA polymerase
- Assembly takes place at the TATA box
Specific sequences of DNA
In promoter region
25
What are the functions of the transcription initiation complex?
- Recognize sequence (TATA box binding proteins)
- Recruit RNA polymerase to promoter
- Help unwind DNA helix
26
What are specific transcription factors?
- Enhancers and silencers
- DNA binding - tissue specific
- Bind to extended regulatory regions
27
What are enhancers?
- Bound by transcription factor proteins
| - Promote transcription
28
What are silencers?
- Repressor proteins
| - Inhibit transcription
29
What are DNA binding transcription factors?
Recognize and bind to specific sequence of DNA in cis regulatory elements
30
How big are the binding sites for DNA binding transcription factors?
6 -12 bases
31
What is a protein interaction domain?
Binding association with other proteins
32
What is meant by integration of regulatory information?
- Multiple transcription factors will influence the expression of a gene
- Cause DNA to loop → bending of DNA structure
- Allows them to interact with the transcription initiation complex
- Can contact and alter activity of RNA polymerase II
- Have multiple
- Binding of Txn factor 1 to enhancer of gene x activates transcription
- Factor 2 to enhancer gene y activates transcription factor
33
What is differential gene expression?
- Combination of cis regulatory element in each gene is different
- Genes regulated by different transcription factors bound at cis-regulatory element
- Combinants → which genes expressed
34
What do RNA polymerase and TF do?
Unwind small region of DNA helix at promoter. Use on strand as template
35
What do TF regulate?
Expression of multiple downstreams targets.
| Cascade of gene transcription
36
What can a combination of TF achieve?
Regulate multiple - initiate one - cascade - rapidly gene complex patterns
37
How do cells generate different patterns of gene activity?
- Cells developing communicate with each other
- Cell signalling
- Process of development
38
What happens during the formation of the embryo?
- Cells communicate
| - The 2 cells msut be aware of each other
39
What is the organiser graft experiment?
- Early frog embryos
- Cells move during development
- Gastrulation
- CNS
- Blastopore
- Cut and paste in the emrbyo
- Too the dorsal blastopore lip
- Put in another embryo which resulted in 2 dorsal blastopore lips
- You get a double headed frog
40
What happens during gastrulation?
Cells form the gut. They are outside the embryo so have to move inside the embryo
41
How is the CNS formed in an embryo?
Start on the outside of the embryo. Flat sheet of cells which roll up into a tube - move inside the embryo
42
Describe what happened when they repeated the organiser graft experiment.
1. Dyed the dorsal blastopsore which had been transplanted
2. Determine which cells in the second body are derived from the host and the donor
3. Most cells in secondary axis are host derived
3. Graft produces signals that recruit/organise the host tissue
43
What can cell signalling do?
Regulate gene transcription and expression
44
What is meant by development?
Cell cycle control. Cell movement. Differentiation. Patterning
45
What is an example of signalling going wrong?
A cyclopic lamb - had been eating corn lily. Cyclopamine which inhibits a signalling pathway of development of cells along the midline
46
What are the different components of a signalling pathway?
- Extracellular signal molecules
- Receptor protein
- Intracellular signalling
- Target proteins
47
What is the role of the receptor protein in the signalling pathway?
allows the cell to perceive that signal
48
What is the role of the intracellular signalling proteins in the signalling pathway?
chain of proteins which pass that signal onn operating within the cell. can be very complicated
49
What is the role of the target protein in the signalling pathway?
Effectors of the signalling pathway.
50
What kind of signalling molecules transmit over large distances through the extracellular enviornment?
Hormones
51
When is short distance signalling very important?
During the developmental process.
| Specialisation happens when the embryo is very small
52
What are some classes of singalling molecules?
Peptides. Small molecules eg nitrous oxide. Metabolic products. Lipids
53
How do receptor proteins work?
- Signals bind to specific receptor proteins
- High affinity for receptor - binds
- Signalling molecules present at very low concentrations
- Cell can only respond to a signal if it has the right receptor
- Typically present at the cell surface but also within the cell
54
Describe the signal transduction pathway
- Pass the signal from receptor to targets
- Can be very complex
- Contains a series of proteins
55
What are the main functions of the signal transduction pathway
1. Amplification of the signal
2. Integration of multiple signalling pathways
3. Allows levels regulation
56
How could a signal be amplified?
If the receptor proteins have an enzymatic property they can act as a catalyst
57
How could a signal be integrated?
Shared components of different signalling pathways
58
How could a signal be regulated?
Inhibiting, modulating or fine tuning
59
What happens when the target protein is reached?
Changes in the activity of the target proteins which will affect cell behvaiour
60
Give some examples of altered cellular function
1. Metbabolic = insulin and glucoagon
2. Cell division = growth factors
3. Cytoskeleton - axon guidance chemotropic factors (cell movement and cell shape)
4. Gene expression = growth factors
61
Describe slime mould as an example of signalling and cell behaviour.
Normally = free living unicellular amoebae. Can for coordinated slug like colonies
Regulated by cAMP - move towards and join together
62
Describe how cell signalling affects gene transcription
- Receives the signalling
- Activated receptor complex
- Signal transduction pathway
- Passes signal on to the nucleus
- Changes the activity of transcription factor proteins in the nucleus
63
Describe how cell signalling affects cell fate.
- Group of cells in the developing embryo
- produces a signal
- acts on adjacent cells
- changes the pattern of gene transcription in those cells
- some will be encoding addition signalling molecules
- those signalling molecules can act back or can act on to other cells to change the gene expression
64
Where are hydrophillic molecules found?
On the surface membrane
65
Describe the process of hydrophillic signalling moelcules
- Unable to cross plasma membrane
- Bind to cell surface receptors
- Activates an intracellular signal transduction pathway
- Passes signal onto intracellular target proteins
66
What are intracellular receptors?
Hydrophobic signalling molecules
67
Describe the process of hydrophobic molecules
- Carried through carrier proteins
- Pass through plasma membranes
- Binds with receptor protein in the cytoplasm or nucleus
68
What are the different types of intracellular signalling?
1. Contact dependent/juxtacrine signalling
2. Endocrine signalling
3. Paracrine and autocrine signalling
69
What is Contact dependent/juxtacrine signalling?
- Signal may be membrane bound or tightly associated with the extracellular matrix
- Signal requires direct contact between signalling and responding cell
70
What is Endocrine signalling?
- Hormone signalling eg insulin
- Produce by an endocrine cell
- Systemic transport of the signaling molecules to distant cells
71
What is Paracrine and autocrine signalling?
- Signalling that occurs during development
- Signalling molecules are secreted into the extracellular space
- Paracrine signal acts on cells neighboring the signalling cell
- Autocrine signal acts back on the signalling cell → signalling to itself
72
What are molecule switches?
proteins involved in the signal transduction pathway
73
Describe protein phosphorylation as a switch.
- Activities of many proteins in signalling pathways are regulated by the removal or addition of phosphate groups
- Addition or removal of phosphate groups changes the conformation of the proteins
- Phosphorylation can either activate or inhibit protein function
- One third of eukaryotic proteins are phosphorylated
74
How do protein kinases work?
- Transfer the terminal phosphate group from ATP to the hydroxyl group of tyrosine, serine or threonine in protein chains
75
Describe protein kinases
- Each cell may contain hundreds of different protein kinases
- The amino acid sequence of each kinase determines its target specificity
- Each kinase has many different protein targets
- Recognize and bind specific target proteins
76
How much of the human genes encode kinases?
2%
77
How do protein phosphatases work?
Phosphatases catalyse the reverse reaction of removing phosphates groups from tyrosine, serine or threonine residues in phosphorylated proteins
78
What are GTP binding proteins?
Guanosine triphosphate binding proteins - class of molecular switch
79
What are the 2 states of GTP binding proteins?
1. Inactive GDP bound form
| 2. Active GTP bound form
80
What processes are small monomeric GTP binding proteins involved in?
Relaying growth factor signalling and regulation
1. Cytoskeletal behaviour
2. Growth and cell division
3. Differentiation
81
What do small monemeric GTP binding proteins do?
Active state are able to hydrlyse bound GTP to GDP
82
Describe the intrinsic enzymatic activity of the small monomeric GTP binding proteins.
GTPases → able to hydrolyses and remove phosphate group and recycling the molecules back to GDP its inactive form
83
Describe changing GDP to GTP
exchanges GDP for GTP → becomes active → in active state is able to pass signal on → intrinsic GTPase activity is stimulated → hydrolysis → phosphate group removed
84
What is required when turning GDP to GTP
- GEF - guanine nucleotide exchange factor → exchanges GDP to GTP
- GAP protein to stimulate the GTPase
85
What is FGF?
Fibroblast growth factor
86
Describe FGF
- Large family of peptide ligands
- Common structure
- 22 identified in the human genome
87
WHat are the biological activities of FGF?
1. Regulation of cell growth and survival - don't act just upon the fibroblast
2. Regulation of cell differentiation
3. Regulation of embryonic development
88
What happens if you block FGF in a developing frog embryo?
Lose development of all the structures in the posterior
89
What human diseases are FGFs involved in?
Skeletal abnormalities (eg dwarfism). Cancer.
90
What type of signal are FGFs?
Paracrine or autocrine
91
What do FGFs bind to?
Transmembrane receptors
92
Describe FGF being passed into the cell
- Intracellular domain has tyrosine kinase activity (can phosphorylate)
- Form a complex with extracellular proteoglycans
- Binding of ligand to receptor causes dimerisation and activation of receptor kinase activity
- Ligand bind to receptor in extracellular space
- Brings together 2 receptor molecules
- Activated receptors phosphorylated tyrosines on various target proteins and autophosphorylate tyrosine residues
- Signal has now entered the cell
93
Describe the transmembrane protein
passes through the plasma membrane → able to insert itself due to the hydrophobic domain
94
Describe receptor activation
Immuoglobulin like domains required for ligand binding specificity → extracellular membrane
Intracellular tyrosine kinase domain in the cytoplasm
Bind to cell surface → dimerization → activation of intracellular kinase activity
95
describe passing the signal on adaptor proteins.
- Phosphorylated tyrosine residues on the intracellular domain → act as docking points for addition proteins
Brings in a whole group of other protein → adaptor proteins → bind to activated receptor complex
Builds up a complex structure of proteins
Docking site for adaptor proteins
Grb2 adaptor protein → binds → acts as a docking site for a GEF aka recruits the GEF to the receptor complex
A GEF stimulates Ras to cycle to active GTP bound form
GAP stimulates the GTPase activity of Ras and it cycles back to inactive GDP bound form
96
describe passing the signal on Ras GTPase
Activated Ras can pass the signal onto a number of downstream signalling pathways
Ras is a critical regulator of signalling by many growth factors
97
describe mutations in Ras
lock into the active GTP bound form are oncogenic and are very common in human cancer → when activated it becomes permanent
98
describe amplification: the MAP cascade
The signal is passed on by a cascade of 3 protein kinases
Raf (MAP kinase kinase kinase) is recruited to the inside of the cell membrane by activated Ras
Raf phosphorylates and activates MEK (MAP kinase kinase)
MEK phosphorylates Mitogen Activated Protein Kinase (MAP KInase) also known as Erk (extracellular signal Regulated Kinase)
99
how is Raf recruited?
Ras recruited Raf to the inside of the cell membrane
This isn't a phosphorylation event as Ras is not a kinase simply recruits it
Raf becomes active
100
what happens at the end of the cascade?
alters the activity of the proteins for changes in cell behaviour
101
describe MAP kinase as a mediator of FGF signalling
Erk (MAP kinase) is phosphorylated and activated within minutes of stimulating a cell with an FGF ligand
Very rapid response
Erk phosphorylates and regulates the activity of multiple proteins including other kinases and regulatory proteins
Erk translocates to the nucleus where it phosphorylates and modulates the activity of multiple transcription factors
Stimulation of this pathway can rapidly lead to changes in gene transcription
102
what experimental data is there looking at FGF signalling
Treatment of embryonic cells with FGF rapidly elevates levels of phosphorylated ERK
Treatment with MAP kinase phosphatase inhibits this phosphorylation
Levels of total ERK are unchanged
103
what leads to gene transcription?
phosphorylation, activation and translocation
104
what problem does secretion present?
- eukaryotic cell has a compartmentalised structure
| - complex system of internal membranes
105
what is the endomembrane system?
- complex system of internal membranes and membrane bound vesicles
- allows lots of different compartments with complex micro-environments
106
describe the functions of the vesicle transport system?
1. protein secretion and transport
2. protein processing and degredation
3. nutrient acquisition
107
what is endocytosis?
uptake of extracellular material into membrane bound vesicles
108
what is exocytosis?
release of material from membrane bound vesicles to the extracellular space
109
what is protein targeting/sorting?
- specific proteins are required in different compartments
| - proteins have peptide motifs
110
what are peptide motifs?
enables recognition by cellular machinery and target the proteins to different compartment
111
ehat is the Nuclear Localisation Signal (NLS) ?
a sequence of amino acids that targets proteins to be transported from the cytoplasm to the nucleus
112
what typically contain NLS?
transcription factors
113
where do proteins for the RER go?
either secreted from the cell or to be in the plasma membrane
114
what do secreted proteins usually contain?
amino terminal secretory signal sequence
115
what is the amino terminal secretory signal sequence?
- sequence of 20-30
- have an overall charactersitc
- contains a core of hydrophobic amino acid
- allows the protein as its being transported to be inserted into the ER membrane
116
where does translation occur from?
a pool of ribosmal subunits
117
how does translation happen?
- individual mRNA is simultaneously being translated by multiple ribosomes
- forms a polyribosome structure
- polyribosome floats freely in the cytoplasm
- if targeted for secretion the polyribosome becomes tethered to the RER
118
describe the mechanism of protein secretion
- Signal peptide recognised by signal recognition particle (SRP)
- SRP binds to SRP receptor on the external surface of an ER vesicle
- Protein translocates into the internal lumen via the protein translocator
- Signal peptide is cleaved by a signal peptidase
- Protein is trafficked through the ER
119
describe how protein being made gets from the cytoplasm side into the ER lumen
- first thing translated is the amino terminal signal peptide
- Emerges and is recognised by the signal recognition particle
- Binds to the signal peptide
- This halts the translation process
- Receptor protein present on the outside of the membrane surrounding the ER vesicle → signal recognition particle receptor
- Binds to the receptor
- The signal recognition particle is removed
- Translation of the protein commences again
- As the protein is made it moves into the lumen of the ER → through the protein translocation → signal peptide is inserted into the membrane → fed into the inside of the vesicle
- The signal peptide is ultimately removed from the protein chain by signal peptidase
- In the secreted protein that passes through the ER and the golgi → it is processed
120
what is the golgi apparatus?
- membrane associated with secretory proteins
121
what does the golgi apparatus do?
post translational modification
122
describe the role of vesicles in transporting a secretory protein
- fed into the golgi apparatus
- trafficked to the cell membrane
- fuse with the cell membrane
- release their contents
- either become part of the cell membrane or into the extracellular matrix
123
what are some examples of post translational modification?
- glycolysation
- protein folding (formation of intra and inter molecule disulphide bonds)
- attachment of lipid modifications to membrane bound proteins
124
describe glycolysation.
- occurs in RER and golgi
- enzymes
- addition of sugar residues to protein chains
- glycolysiation f secreted proteins is very common
- glycolysation can stabilise proteins and allow them to fold correctly
125
what are intracellular receptors?
hydrophobic signalling molecules
126
describe intracellular receptors
- tend to be products of metabolic pathways
- have a chain of enzymes which catalyse the formation of these signalling molecules
- small ad hydrophobic so can pass through the plasma membrane- can move around in solution via carrier proteins
- at the cell the signal is released and diffuses across the plasma membrane to bind with a receptor protein in the cytoplasm or nucleus
- to fulfill their function they need to move to the nucleus
127
what are nuclear hormone receptor signal?
- used in signalling by a large group of small of hydrophobic molecules
128
what uses nuclear hormone signalling?
steroid hormones, thyroid hormones, retinoic acid and vitamin D
129
what are the benefits of hydrophilic signals?
rapidly turned over and degraded in the bloodstream and cellular environment and are used for rapid signalling processes
130
what are the benefits of hydrophobic signals?
persist in the body much longer and are involved in long term signalling
- also transcription factors
131
what are some examples of steroid hormones?
sex hormones and cortisol
132
describe the features of sex hormones and cortisol.
sex hromones = by gonads
cortisol = by adrenal glands
steroid hormones are usually synthesized from cholesterol
act as endocrine hormones
transported systematically in the bloodstream
133
what are the functions of receptor proteins for hydrophobic signalling?
- not only receptors also transcription factors
| - means there is no need for molecular switches and changes in gene transcription
134
what happens when the receptor proteins are activated by binding?
- act to regulate directly the transcription of target genes by binding to the cis regulatory elements
135
what happens in the absence of a ligand?
receptor is held in an inactive protein complex
136
what does ligand binding lead to?
a conformational change in the receptor allowing it to become active and act as a transcription factor
- can go to the nucleus
- recognise specific sequences of DNA
- regulate transcription
137
describe cortisol in signalling
In the absence of ligand the receptor is held in an inactive complex in the cytoplasm
In the presence of the ligand the receptor is released from the complex and translocates to the nucleus
Receptor binds signaling molecule → conformational changed
You get dimerisation of the receptor → get 2 active receptors coming together to get a dimer
138
describe retinoic acid in signalling
Derivative of vitamin A → involved in multiple processes in animal development eg limb development
In the absence of ligand the receptor is bound to regulatory regions of target genes in the nucleus in association with negative regulators of transcription → co-repressor complex
In the presence of the ligand the receptor dissociates from the inhibitors and associates with activators → co-activator complex
139
what does nuclear hormone signalling elicit?
cascades of transcriptional regulation
140
what is the mosaic theory of animal development?
cell lineage
restriction is dependent on unequal division of nuclear determinants
during cell division and differentiation
141
what is the principle of nuclear equivalence?
during development all cells inherit
| the same genetic information
142
what evidence supports the nuclear equivalence during animal development?
- animal cloning experiments
- nuclear transfer from differentiated somatic cells
- frog cloning
- dolly the sheep
143
how do ras protein function as a self regulating molecular switch?
- activated ras, cycles from its inactive GDP bound form to its
active GTP bound form
- GTP bound form ras has a
GTPase activity which rapidly hydrolyses the bound GTP to GDP
- ras is able to self-regulate its own activity
144
what is Erk?
MAP kinase
| - can go to the nucleus and phosphorylate transcription factors which then alter gene transcription
145
describe cotisol signalling
absence of the
ligand the receptor is held in an inactive complex in the cytoplasm
presence of cortisol the receptor is released from the complex and translocates to the nucleus where it can bind to
DNA and regulate the expression of target genes
146
what are cortisol and RA?
not
| transcription factors but the ligands that bind to nuclear hormone receptors
147
What are the three main classes of cis-regulatory elements?
Promoters, enhancers and silencers
148
what is the function of transcription factors and binding to cis-regulatory regions?
- General transcription factors are components of the transcription initiation
complex
- containing RNA pol II
- RNA polymerase II is unable to transcribe a
gene on its own
149
how do general transcription factors enable RNA polymerase II to function?
TATA box recognition, recruiting RNA pol II and helicase activity
150
describe how trans-acting
| factors are able to regulate cell lineage
- egulation of the skeletal
muscle lineage by myogenic regulatory factors, such as MyoD
- bHLH transcription factors expressed exclusively in the cells that
will develop as skeletal muscle
- activate transcription of
genes coding for proteins required for muscle development
- binding as a dimer with
the E12 protein to E-box sequences in the cis-regulatory of these genes
