TT_Building_a_Phenotype Flashcards

Question

What happens after membrane depolarisation occurs?

Answer 1

The fertilisation membrane forms.

Answer 2

Indicates calcium entry through the plasma membrane Ca2+ channels as a cause or consequence of membrane depolarisation.

Answer 3

Membrane depolarisation when Ca2+ ions influx into the egg.

Answer 4

… there is another Ca2+ wave.

Answer 5

Waves of Ca2+ in Medaka fish triggered by fertilisation. Jaffe et al., injected aequorin into an egg. Each of the photons is where Ca2+ has bound to aequorin, illustrating the wave of Ca2+ slowly spreading around the egg after fertilisation.

Answer 6

Bioluminescence is due to the interaction between aequorin and Ca2+, which gives off a flash of blue light. This blue light is absorbed then re-emitted by the jellyfish as green light, possibly because green light travels further in water.

Answer 7

The change in Ca2+ must match the timing of the process. Calcium is causal, if, when intrpduced into the system, it triggers downstream events. Inhibiting calcium should stop downstream events.

Answer 8

Add calcium ionophores that stick in the membrane, which allows Ca2+ entry into the cell.

Answer 9

Have different shapes, but calcium still plays a role in early fertilisation events in all of these systems.

Answer 10

The site of sperm entry as 'negative' to entry of additional sperm and all other points along the egg surface as initially 'positive'. He observed that the wave of 'negativity' preceded formation of the fertilisation envelope, so sperm could no longer enter even before the fertilisation envelope formed. He observed that the 'negativity' moved around the egg in a wave-like manner at a rate which varies with the rate at which teh sperm head disappaears into the cytoplasm.

Answer 11

A canonical signalling pathway.

Answer 12

Acyl chains linked to glycerol tehn there's a phosphate group linking it to an inositol head group.

Answer 13

Phosphatidyl inositol must be twice phosphorylated. PI -> PIP -> PIP2. First, it's phosphorylated on position 4 of inositol to form phosphatidyl inositol phosphate. This is phosphorylated agin to give phosphatidyl inositol bisphosphate.

Answer 14

This leaves diacylglycerol in the membarne, and release inositol triphosphate (IP3), which is small and hydrophilic, into the cytoplasm.

Answer 15

Acts as a signal in the membarne and a landing site for protein kinase C (PKC) among other things.

Answer 16

IP3 activates a receptor in the ER-- the IP3 receptor.

Answer 17

Calcium is released which activates protein kinase C (PKC, that's what the C stands for). The net result is [Ca2+] increases in the cytoplasm, and PKC is bound to the membarne and activated.

Answer 18

The activation of lots of membarne-localised processes such as vesicle fusion.

Answer 19

By calcium. This is calcium-induced calcium release: a little Ca2+ leads to more being released. This allows the calcium wave to spread around the egg.

Answer 20

Repetitive signals are required, so a mechanism to re-fill the Ca2+ store is required.

Answer 21

The store-operated calcium entry protein signals to the plasma membrane that the store is empty, which allows calcium in at ORA1. The calcium is pumped into the ER by a calcium pump, SERCA.

Answer 22

It was originally identified in the sarcoplasmic reticulum of muscle cells.

Answer 23

Egg-receptor mediated, or sperm oocyte-activating factor (SOAF).

Answer 24

Binding of a sperm-derived factor (fertilin) activates an egg receptor, possibly an integrin.

Answer 25

Mutations mean everything dies, so fertilisation doesn't occur.

Answer 26

Activation of PLC could be due to an activating factor from the sperm that is only released into the egg upon membrane fusion. Direct release of a second messenger (IP3 is the activating factor), teh sperm brings an activating factor that activates src-tyrosinase kinase that in turns activates egg PLC or introduction of sperm PLC zeta isoform.

Answer 27

The area of interaction between the egg and sperm can be as small as 100nm in diameter, which is ~0.025% of the egg's surface area of a 100µm egg. If the initial signalling cascade begins in a 1µm^3 volume, just ebneath the point of sperm-egg interaction, this represents 0.0002% of the egg's total volume.

Answer 28

The sperm introduces tyrosinase kinase, which activates the src-kinase that, in turn, activates PLC by phosphorylation.

Answer 29

PLC zeta from the sperm releases IP3 from PIP2 present in cytoplasmic oocyte vesicles. IP3 releases Ca2+ from the ER via IP3 receptor.

Answer 30

A cluster of Ca2+ channels giving a puff or spark of calcium. If the channels are close enough together, the Ca2+ is released into the cell, and diffuses away to start the wave by activating neraby chanels in an autocatalytic event. This produces calcium-induced calcium release.

Answer 31

The IP3 receptor channle and the ryanodine receptor.

Answer 32

A plant alkaloid. The ryanodine channel is also involved in muscle contraction.

Answer 33

The endogenous ligand fthat binds to the ryanodine receptor. IP3 is the endogenous ligand for the IP3 receptor.

Answer 34

Ca2+ channels are not discrete. There's enough buffering in the ER (due to calcium buffering proteins) that not all of the calcium is emitted at once.

Answer 35

Secondary mechanisms such as cortical granule fusion.

Answer 36

The contents of vesicles sitting just underneath the plasma membrane build an extracellular membrane around the embryo.

Answer 37

It secretes proteins and polysaccharides when forming the fertilisation membrane.

Answer 38

To trigger secretion of an extracellular matrix to prevent any more sperm entering and protect the embryo.

Answer 39

Rapid membrane polarisation from -170 mv to +20 mV from Na+ and Ca2+ influx. Could be a negative ion leaving the cell, or a positive ion entering the cell.

Answer 40

Calcium-induced calcium release Ca2+ wave via cortical granule fusion, which forms the fertilisation envelope.

Answer 41

Mucopolysaccharides, cross-linked vitelline and hyalin.

Answer 42

Activates the embryo.

Answer 43

Required to kickstart metabolism in the embryo.

Answer 44

Receptor with 4 binding sites for calcium. Acts as a universal sensor for other proteins that respond to its conformational change.

Answer 45

A massive conformational change from its linear to bent state. Such cooperative interactions confer a sigmoidal response.

Answer 46

There's no conformational change until [Ca2+] is over a certain threshold. Above the threshold, the response increases in a very small concentration range.

Answer 47

After the signalling cascade, [Ca2+] drops because Ca2+ is cytotoxic as it can bind to phosphate and precipitate, preventing ATP formation.

Answer 48

We only really have fluorescent molecules for Ca2+.

Answer 49

To the mitotic apparatus, often calcium-calmodulin binds to the developing spindle in the nucleus.

Answer 50

The signal is active until the phospahte is removed by a phosphatase. This turns a transient signal into a longer-term response.

Answer 51

Highly-charged, so are likely to cause a conformational change that activates or inhibits the protein.

Answer 52

Hardening of the zona pellucida following calcium-dependent exocytosis of cortical granules.

Answer 53

Calcium-CaM-kinase II inactivates the cytostatic factor (CSF), which stimulates centrosome duplication, and activates the anaphase promoting factor (APC).

Answer 54

8 cycles within 4 hours.

Answer 55

8 cycles in 6 hours.

Answer 56

13 nuclear divisions within 3 hours.

Answer 57

At metaphase-anaphase.

Answer 58

Follows the Jaffe guidelines. Microinject IP3 to activate a wave of calcium. When added, heparin inhibitors block IP3 receptors, so the cells are arrested in metaphase.

Answer 59

Flashes in light sheet microscopy could potentially indicate calcium regulation of embryonic cell division, but this is not yet known.

Answer 60

Can be used to image embryonic cell divisions.

Answer 61

It is highly conserved across eukaryotes.

Answer 62

Cyclin-Dependent Kinases.

Answer 63

They create lethal phenotypes.

Answer 64

Mammalian cell fusion, embryonic cells and yeast genetics.

Answer 65

In a 20-minute cycle.

Answer 66

Liquid-lipid phase separation.

Answer 67

The nculeus has a change in refractive index.

Answer 68

Polytene, or polyploid.

Answer 69

Lots of copies of the same, one chromosome.

Answer 70

Lots of copies of all the chromosomes.

Answer 71

More DNA is required to regulate more cytoplasm, which is required for elongation. Thus, DNA replication isn't always coupled to cell division.

Answer 72

All the chromosomes must be replicated once.

Answer 73

If there were no errors, the rate of evolution would decrease.

Answer 74

In order for daughter cells to be genetically idnetical to the parent cell-- especially crucial in multicellular organisms, e.g., humans have at least 10^14 cells.

Answer 75

… events occur in the correct sequence with the correct timing, cell proliferation is appropriate (e.g., in accordance with cell-signalling, and there are sufficient nutrients) and the cell cycle is coordinated with cell growth.

Answer 76

The mass of the cell usually doubles with every cell cycle, so the average mass of the cell stays the same over many generations. Cells must be physically large enough, so that daughter cell don't become increasingly smaller, and there's enough resources for DNA replication.

Answer 77

Cells divide until they fill the space, indicated by bumping into cells and cell-cell signalling, such as at the site of wounds.

Answer 78

By identifying proteins that can activate S phase or mitosi, or that increase in abundance in mitosis.

Answer 79

Mammalian cell fusions, embryonic cells (frogs and sea urchins), genetics (yeast and Drosophila) and complementation amd sequencing have been used to identify orthologous proteins in different species.

Answer 80

Take cells at different stages of the cell cycle, and fuse them. E,g,, take a G1 cell and an M phase cell, and see whether that is enough to drive the cell into division, even if it hasn't replicated its DNA yet.

Answer 81

If S phase is activated in the original G1 cell, this implies something present in S phase is capable of driving the cell through that checkpoint.

Answer 82

Normal controls are bypassed. There is a factor in the cytoplasm that is capable of driving the cell through the cell cycle checkpoints that you should be able to purify.

Answer 83

If fertilisation is synchronised, embryonic cell cycles are synchronised. You can stop them at a particular time, and observe which proteins are increasing or decreasing in abundance.

Answer 84

Mammalian cell fusion and embryonic cells are useful for identifying the relevant proteins, but genetics are required to identify the responsible genes.

Answer 85

To ensure the genome is not replicated until a zygote is formed.

Answer 86

Take cytoplasm from an egg cell at different stages, and inject it into an early-stage egg. There may be a factor present that is able to drive it into a mature cell. Try and purify that factor by separation on a gel or centrifugation. Eggs are useful as they're large.

Answer 87

Using synchronised cells.

Answer 88

Mitosis Promoting Factor as the same activity was present in all cell cycles, not just maturation.

Answer 89

It increases to metaphase then decreases disappears at anaphase due to calcium-induced cyclin degradation.

Answer 90

Extracts from mammalian and yeast cells both have MPF activity.

Answer 91

Hence, the egg cell starts out large to provide resources as the embryonic cell cycles are running on maternal resources. The zygotic genes are not being expressed.

Answer 92

… a blastula, which then inverts itself to form cell layers.

Answer 93

Gel electrophoresis at different times after fertilisation. One such protein, which appeared after fertilisation then whose concentration changed during the cell cycle, is cyclin.

Answer 94

S. pombe are rod-shaped, then elongate and finally split into two daughter cells.

Answer 95

The bud starts to enlarge at the start of S phase. By the end of M phase, the bud must be large enough to form the daughter cell.

Answer 96

E.g., a mutation might cause all the cells to stop in S phase at which point all S. cerevisiae cells would have a small bud.

Answer 97

They used temperature sensitivity. A subtle mutation giving a slight change in structure allows the protein to function normally at low permissive temperatures. But at high temperatures, the mutation is expressed, and the protein falls apart. The cells with teh mutated protein then die. Next step: replica plating.

Answer 98

Put the membrane on top of the plate to transfer all the colonies in the same spatial orientation to another plate. Raise the temperature. Most of the colonies will then die, if they contain the mutated protein. Return to the master plate. Identify the colony containing the subtle yet lethal mutation, and grow it at a permissive temperature.

Answer 99

Cell Division Cycle Mutants

Answer 100

Use wildtype plasmids to transform the mutant bacteria. The majority of plasmids will make no difference. Some plasmids will have a owrking copy of the mutated gene, so the mutant will work when transformed-- complementation. Then sequence the plasmid to identify the gene.

Answer 101

You could use a wildtype Drosophila, plant or even mammalian gene as cell cycle regualtors are common across a range of organisms.

Answer 102

Cyclin-dependent kinase, catalytic. Discovered by gel electrophoresis. Conserved across all eukaryotes.

Answer 103

Regulatory. Identified by yeast genetics.

Answer 104

Cyclin and Cdk. The complex is only active when both components are present.

Answer 105

Increase in Cdk activity, partly due to an increase in cyclin B concentration.

Answer 106

… cyclin B, inactivating Cdk. All the cyclin is degraded as soon as the cell goes through anaphase.

Answer 107

Cdc2 binds to the G1 cyclin to form an active complex that drives the cell into S phase. As the cell enters S phase, the G1 cyclin is degraded to prevent the cell re-entering S phase, i.e., to prevent it going backwards. The Cdc2 then binds to mitotic cyclin to form a complex that drives the cell into mitosis.

Answer 108

Produces aequorin and GFP.

Answer 109

The fluorophore is tucked away in the middle of the beta barrel: it's designed to function within a biological system as the beta-barrel prevents damage due to radicals produced by the excited fluorophore. If cells were tagged with chemical probes, the damage would be much greater.

Answer 110

GFP can alter the structure of the protein, sometimes, affecting the protein's function.

Answer 111

By the position of the target protein. Proteins phosphorylated by the kinase move into the nucleus. De-phosphorylated proteins move out of the nucleus into the cytoplasm.

Answer 112

The Anaphase Promoting Complex (APC).

Answer 113

Single Cdk and multiple cyclins. The cyclins confer substrate specificity.

Answer 114

Multiple Cdks and multiple cyclins as there are different tissue types in which cells cycle at different rates.

Answer 115

Serine and threonine. Properties of the target protein are altered allosterically by phosphorylation.

Answer 116

To determine this, both phosphorylation by the kinase and de-phosphorylation by the phosphatase must be understood.

Answer 117

Osamu Shimomura identified GFP biochemically, Martin Chalfie sequenced the GFP gene and Roger Tsien used the GFP.

Answer 118

Proteins in nuclear transport, chromatin structure, DNA replication, cytokinesis and many more!

Answer 119

Cdk is partially activated by binding to cyclin as this allows a loop pf the Cdk protein to interact with the cyclin. To activate it fully, the Cdk activating kinase (CAK) phosphorylates the Cdk.

Answer 120

At some sites, phosphorylation causes activation. At other sites, phosphorylation inactivates the complex.

Answer 121

Phosphorylates Cdk at the inhibitory site to block activity. Discovered by Paul Nurse. If you mutate the kinase, you don't put the inhibitory phosphate on, so the cell proceeds into mitosis before it is large enough, and the daughter cells becme increasingly smaller.

Answer 122

Removes the inhibitory phosphate from Cdk to activate it.

Answer 123

Cdk inhibitor. It physically binds to the complex, so it can't work. This adds another layer of regulation.

Answer 124

Active p53 makes the CKI to ensure that cell division doesn't occur until the DNA damage has been repaired.

Answer 125

Means double-stranded breaks in the DNA are not detected, so cell are more likely to acquire more mutations. This is seen in some cancerous cells.

Answer 126

… both internally and with external signals.

Answer 127

Whether chromosomes know they are attached at both poles.

Answer 128

Can't be visualised using phase contrast imaging as they don't give phase-contrast, so they must be stained.

Answer 129

The centrosome.

Answer 130

Move vesicles around and are very long.

Answer 131

Prophase: microtubules get shorter. Metaphase: microtubules form spindle. Anaphase: microtubules pull apart. Telophase: microtubules start to grow longer, out towards the egde of the cell again.

Answer 132

Centrosomes.

Answer 133

Template-based duplication in S phase.

Answer 134

Contains two centrioles with microtubules in a 9 + 2 arrangement. Centrioles are at 90 degrees to each other.

Answer 135

They're self-replicating, but they don't have their own DNA or a membrane.

Answer 136

Microtubules associated between the centrioles after they are duplicated. The microtubules push apart, but the nucleus is still intact, so they push apart around the nucleus, so the centrioles are either side of the nucleus.

Answer 137

Subunits released from the microtubukes exchange their GDP for GTP, so re-join the microtubule.

Answer 138

Walk towards the - end.

Answer 139

Walk towards the + end.

Answer 140

The - end is usually embedded in the centrosome. The + end has the GTP cap.

Answer 141

Double-headed - end-directed motor proteins zip up/link adjacent microtubules, which creates a focussed pole at the end.

Answer 142

Dynein and Ncd. Evidence fron RNAi, mutants and immunolocalisation studies.

Answer 143

Non-claret disjunction, re-named kinesin 14. Walks towards the - end in Drosophila, and disrupts spindle formation.

Answer 144

Use RNAi to knockout candidate motor proteins, test with a mutant or an antibody tagged with GFP localises to the proteins. E.g., Ncd was visualised using GFP, which indicated that Ncd localises to the centrosomes then to the - end of the microtubules when forming spindle.

Answer 145

There are + end-directed motor proteins that are tethered to the centrosome to keep the microtubules as the motor proteins will try to walk towards the + end of the microtubule, but they can't as they are tethered to the centrosome.

Answer 146

Kin1 kinesin or EG5/kinesin-5.

Answer 147

The - ends are tethered to the centrsome. The + ends are overlapping, so a double-headed + end motor protein will push the chromosomes apart. Candidate motor protein: kinesin-5. Astral microtubules are orientated the other way, so interact with the plasma membrane. Dynein motor proteins in the plasma membrane pull the astral microtubules. Pulling from the outside; pushing from the inside.

Answer 148

Microtubules are good for pushing, pulling and withstanding lateral deformation, but are expensive as they have to span a lot of space using a ring of proteins. If you need something just to withstand tensio/pulling, use microfilaments as it's not a whole tube. If you need something static, use intermediate filaments as they are stable in the long-term.

Answer 149

Phosphorylation of the histones by Cdk, which changes how they pack together, and SMC proteins.

Answer 150

Stable Maintenance of Chromosomes. Condensin and cohesin. Form a ring around chromosomes to help keep them together. Many of the loops stabilise the structure, and pack up the DNA.

Answer 151

Helps the daughter chromosomes stay together.

Answer 152

Condenses the chromosomes.

Answer 153

Can be opened to allow chromosomes to separate or de-condense.

Answer 154

Intermediate filaments found in a meshwork just beneath the nuclear envelope that supports the nucleus.

Answer 155

Phosphorylation of nuclear lamins by Cdk, so the bonds between the lamins break. The nuclear envelope is vesiculated and no longer stable.

Answer 156

Add a reporter to the cytoplasm, which will become visible as it enters the nucleus upon disintegration of the nuclear envelope.

Answer 157

The kinetochores.

Answer 158

To search the nuclear space more efficiently. Otherwise, it's wasted energy.

Answer 159

Kinesin-Related Proteins. A + end motor protein zips along to the end of the microtubules, where it adds stress, causing catastrophe.

Answer 160

It's stabilised. Eventually, all of the chromosomes will have microtubules attached.

Answer 161

A layered structure that forms on a repetitive section of DNA at the centrosome.

Answer 162

The Ndc80 complex.

Answer 163

Every single microtubule in the cell.

Answer 164

Otherwise, all the chromosomes would just collapse in the middle.

Answer 165

A balance betweeen pulling (microtubules attached at the kinetochore are under tension) and oushing (polar ejection force) forces-- dynamic equilibrium

Answer 166

The + end-directed motor proteins (chromokinesin/kinesin-4) on the chromosome arms push the chromosomes away from the poles.

Answer 167

… the more microtubules push it away from the pole.

Answer 168

It decreases as the microtubules splay out.

Answer 169

The Ndc80 complex holds the microtubules at the kinetochores, so - end-directed motor proteins try to get to the - end of the microtubukes, but can't.

Answer 170

They are in dynamic equilibrium: subunits are added and removed at the same rate, so the net result is that the microtubules don't move, and the ends must be somewhat accessible.

Answer 171

Cut the chromosome with a high-powered laser. The cut section starts zipping away. Tension at the kinetochore an dpolar ejection force at the chromosome arms.

Answer 172

The + end-directed motor proteins, such as CENP-E (so-named because it is associated with the centromere) renamed to kinesin-7, that drive initial movement.

Answer 173

The - end-directed dynein motor proteins.

Answer 174

XKLP1 and Nod (kinesin-4) that generate polar ejection forces.

Answer 175

Only fluoresces when light is shone on it.

Answer 176

Light is shone in the middle of the spindle. This creates a green band that moves towards the pole gradually due to subunits being lost at the centrosome.

Answer 177

Added at the kinetochore then lost at the centrosome.

Answer 178

Motor proteins may hold onto microtubules.

Answer 179

Phosphorylates the Ndc80 proteins on the kinetochore complex.

Answer 180

If the chromosome is under tension, the kinetochore is pulled out of reach of the kinase, so phosphorylation doesn't occur. This means the system is stable, and the chromosomes are correctly attached.

Answer 181

A negative signal is better because, if it were a positive sognal, you'd have to distinguish between 22 and 23 signals when the last chromosome attaches. Any negative signal at all means the chromosomes are not correctly attached.

Answer 182

APC is activated by Cdk or other kinases. APC mediates securin degradation by ubiquitination. Degradation of securin leads to the degradation of cohesin that holds the chromosomes together.

Answer 183

Separase is no longer inhibited by securin, so it can degrade the cohesin.

Answer 184

… proteasome 26S.

Answer 185

When it is present, it prevents the activation of APC, thereby preventing mitosis when one or more of the chromosomes is not correctly attached. When all of the chromosomes are aligned on the metaphase plate, Mad2p is no longer present, so APC is unihibited, and mitosis can proceed.

Answer 186

It tags the mitotic cyclin with ubiquitin, and sends it off teo the 26S proteasome. This prevents re-entry into mitosis, as Cdk is no longer active, so the chromsomes can't be packaged up again.

Answer 187

76-amino acid protein.

Answer 188

When there is redundancy.

Answer 189

There are so many different mechanisms that could move the chromosomes apart during anaphase because the process must happen.

Answer 190

1. Subunit loss, so the motor proteins at the kinetochores keep holding the chromosome, and pulling it in. 2. Option 1 is passive, but if it were active, motor proteins could walk down the microtubules as soon as the tension is released. 3. Pulling by dynein at the kinetochore towards the poles. 4. + end-directed motor proteins reel in the microtubules. 5. Astral microtubules can pull chromosomes also. 6. In anaphase B, mid-zone motor proteins push the poles apart.

Answer 191

The + end-directed, double-headed motor proteins in the mid-zone push the spindle poles. Astral microtubules pull the spindle poles apart.

Answer 192

It's dephosphorylated, and moves to the mid-zone. Dephosphorylation activates microtubule binding.

Answer 193

Spindle formation, chromosome condensation, nuclear envelope breakdown and motor protein localisation to initiate mitosis.

Answer 194

1. Specificity. 2. Coordination of multiple events. 3. Integration with other pathways. 4. Signal processing. 5. Sub-cellular localisation. 6. Speed. 7. Duration. 8. Tissue localisation. 9. Cost of machinery and metabolism.

Answer 195

When Cdk is activated then activates many downstream targets.

Answer 196

Required to produce a strong enough signal by creating a high enough concentration.

Answer 197

Can send the protein off in lots of different directions.

Answer 198

… have a low bidning affinity, so bind to a ligand at low concentration, but don't let go, thus necessitating endocytosis.

Answer 199

There's high sensitivity at the low concentration end, so molecualr noise could still initiate a response.

Answer 200

The fastest is 15 minutes, but can take hours, or even days.

Answer 201

They probably didn’t begin from a blank state: it may have begun from the duplication of a different signalling pathway.

Answer 202

1. Contact-dependent. 2. Paracrine. 3. Endocrine. 4. Synaptic.

Answer 203

Exposed plasma membranes can have membrane-bound receptors and signalling molecules. Often found in developmental pathways.

Answer 204

A cell secretes something locally into the extracellular matrix. The signal is diffusible. Spatially organised.

Answer 205

The bloodstream transports hormones. Some phytohormones can be transported in the vascular system. Steroid and peptide hormones.

Answer 206

Neuronal, long-distance; fast. Highly spatially-targeted and loaclised. Massive cost to build the nervous system. Plants have slow-acting action potentials.

Answer 207

Small, hydrophobicmolecules, so are cheap to make. Based on a cholesterol backbone, but small changes to the molecule can change the its category.

Answer 208

From gene duplication events as tehir modular structures are similar.

Answer 209

Thus, they can get anywhere, and the specificity comes from the receptor not the signalling molecule. Transported in the blood via a carrier protein.

Answer 210

They get diluted when travelling to different parts of the body.

Answer 211

The conserved receptor sequence has been identified in the genome, but the ligand is not known.

Answer 212

Cortisol, estradiol, testosterone, thyroxine, retinoic acid and vitamin D3.

Answer 213

Long-term , developmental processes as they persist for hours/days.

Answer 214

1. Enzyme-linked receptors. 2. G-protein-coupled receptors. 3. Ion channel receptors.

Answer 215

Catalytically active or associate with catalytic subunits. Most are single-pass membarne proteins.

Answer 216

Not catalytically active; they just undergo a conformational change. Usually the target protein is an enzyme that makes lots of secondary messengers.

Answer 217

Massive amplification as one ion channel can let in 1-10 million ions per second.

Answer 218

Development, activating cell division and growth.

Answer 219

Assemble as dimers on binding the target ligand, and autophosphorylate their cytoplasmic tails.

Answer 220

Serine/threonine kinases.

Answer 221

What proteins have been phosphorylated?

Answer 222

Which amino acids they phsophorylate.

Answer 223

Tend to have conserved tyrosinase kinase domains, but their homology diverges in the extracellular domains.

Answer 224

Could lock the GTPase into a constitutively active form, which keeps activating the developmental pathway.

Answer 225

Accessory factors that help to exchange GDP for GTP in the small GTPase.

Answer 226

It's activated in the membrane, so can activate membrane-localised events. The probability of bumping into its target is much higher in the membrane, a 2D plane, than in the 3D cytoplasmic volume. At some point, the GTP is hydrolysed spontaneously, so the pathway is turned off.

Answer 227

Mitogen-Activated Protein Kinase

Answer 228

3 kinases in the cascade. MAPKK is phosphorylated on 2 sites by MAPKK kinase. MAPKK phosphorylates MAPK on 2 sites. Phosphorylated MAPK phosphorylates and activates transcription factors.

Answer 229

>800. 4% of the human genome.

Answer 230

The N terminus and extracellular loops bind the ligand. There are 7-membrane spanning alpha helix domains. The large cytoplasmic loops interact with the G-proteins.

Answer 231

… sigmoidal binding kinetics.

Answer 232

The pathways are the same, but the input and output are different.

Answer 233

The pathway is the same as in fertilisation, but PLC is activated by a G-protein instead.

Answer 234

2 sensory components and 2 catalytic components.

Answer 235

Cyano-fluorescent and yellow-fluorescent (CFP and YFP) proteins are coupled to calmodulin and M13. When Ca2+ is added, calmodulin undergoes a conformational change, so wraps around M13, bringing the two proteins closer together. By Förster resonance energy transfer, it's yellow when there's Ca2+ present, but blue when there's not, as in taht case only teh blue is excited.

Answer 236

A fluorescent protein that can be used in all organisms.

Answer 237

A little peptide from the myosin light chain kinase that acts as the calmodulin binding domain.

Answer 238

Membrane scaffolds for other proteins, and skeletal elements can be stuck to it.

Answer 239

….networks, as there's cross-talk between pathways.

Answer 240

Acetylcholine receptors, GABA receptors, ionotropic glutamate receptors and metabotropic glutamate receptors.

Answer 241

Pentameric ion channel. The alpha binding sites for acetylcholine exhibit some cooperativity as it can bind two acetylcholines. Charges above and below the pore confers specificity for cations. Na+ is the main cation transported as it's furthest from equilibrium.

Answer 242

Pentameric channels permeable to Cl- ions. Inhibited by strychnine. Activated by benzodiazepines and barbiturates. Inhibit the generation of an action potential by maintaining me,brane hyperpolarisation.

Answer 243

Gamma-amino butyric acid.

Answer 244

E.g., the glutamate receptors is linked into the G-protein-coupled receptor pathway that ultimately phosphorylates a different channel.

Answer 245

Serotonin. Serotonin receptors actiavte channels directly or via the IP3 and cAMP pathways. The results can be inhibitory or excitatory.

Answer 246

The charge on the ion dictates whether hyperpolarisation or depolarisation occurs. E.g., NMDA receptors and AMPA receptors.

Answer 247

When glutamate binds, it displaces Mg^2+, so Ca2+ can pass through. Promotes depolarisation.

Answer 248

Permeable to Na+. Promote depolarisation.

Answer 249

Glutamate receptors initiate a G-protein cascade that actiavtes adenylate cyclase and PKA. PKA phosphorylates Na+ channels to activate them.

Answer 250

Genomic instability, telomere attrition, epigenetic alterations, loss of proteostasis, deregualted nutreint sensing, mitochondrial dysfunction, cellular senescence, stem cell exhaustion and altered intercellular communication.

Answer 251

… turnover at different rates. E.g., kidney cells turnover every 6-7 years.

Answer 252

Ageing and cancer.

Answer 253

To make (development) and maintain (regeneration/homeostasis) the cells, tissues and organs of multicellular organisms.

Answer 254

They aren't considered to be differentiated.

Answer 255

Their large nucleus:cytoplasm ratio.

Answer 256

A population of stem cells can be the source of some, amny or even all cell types of an organism.

Answer 257

Self-renewal, so they can maintained through rounds of cell division.

Answer 258

Gives rise to one stem cell and one committed cell.

Answer 259

With asymmetric population behaviour. Gives rise to either two stem cells, or two committed cells.

Answer 260

Not able to self-renew, so not technically a stem cell anymore.

Answer 261

Identifies early cells that give rise to later cells and tissues during development.

Answer 262

Microinject a fluorescent dye into the embryo, and follow 4-5 cells during development. This can be sued to map which cells make each germ layer, and to identify neural crest cells.

Answer 263

Arise during neural tube formation. They contribute to all 3 germ layers even though they are neuro-ectodermal, multipotent stem cells.

Answer 264

Zygote and morula. Makes everything, incl. extraembryonic tissue (placenta).

Answer 265

Blastocyst. Can make all the cells in eth embryo and the adult.

Answer 266

Blastocoel and gastrula. All cell types of a tissue or organ.

Answer 267

Can make several, related cell types.

Answer 268

Makes only one cell type. Involved in morphogenesis, organogenesis, growth, homeostasis and regeneration.

Answer 269

Become progressively more determined, and tehir potency decreases as the lineage progresses.

Answer 270

Maintained as adult stem cells.

Answer 271

Continue to maintain our tissues and organs in response to wear and tear, infection and dieases and other environmental factors, e.g., toxins.

Answer 272

Are carried through into the adult. Tehse are adult stem cells. Some stem cells that make tissues are set aside to continue making tissues throughout development.

Answer 273

It means they are easily studied, but they are also associated with some cancers.

Answer 274

A lineage of committed cells produced by stem cells later in development and adult stem cells. Neither differentiated nor self-renewing. They divide by mitosis quickly, several times to make a population of cells that eventually differentiates. This reduces the number of divisions the stem cells themselves must make.

Answer 275

Transcription factors, epigenetic modifications, such as chromatin modifiers, micro-RNAs, alternate splicing, etc.. All these layers of regulation provide opportunities to control and manipulate stem cells.

Answer 276

Maintain a stable, undifferentiated state by suppressing genes that drive differentiation.

Answer 277

Transcriptionally silence genes that would aid differentiation, but aid in allowing gene expression for the present state.

Answer 278

Finely balanced, so external signals can drive differentaion to the required fates.

Answer 279

Embryonic stem cells from the inner cell mass, and primordial germ cells.

Answer 280

Trophectoderm (TE), Inner Cell Mass (ICM) and Primitive Endoderm (PE).

Answer 281

By culturing cells from a mouse embryo, labelling them; then putting them back in mice to test their potency. This test the cells' (from the blastocyst) ability to contribute to the embryo.

Answer 282

On embryonic fibroblast cells that allowed them not only to survive in culture, but also to self-renew, as the fibroblast cells produced certain factors. Once the factors were identified, the fibroblast cells were no longer required, so a medium containing only the things required could be used.

Answer 283

Naïve> formative > primed. Naïve: pluripotent, but their gene regulation is locked down. Primed: dividing celsl that are pluripotent, but are ready to differentiate to make the germ layers.

Answer 284

Pluripotent, diploid cells that go on to make the germline. Indirectly totipotent. More difficult to work with. Distinct gene expression profile, associated with animal germlines, suggests a different mechanism.

Answer 285

If you inject them randomly, they form teratomas-- germlime tumours that contain parts of all three germ layers. Teratomas can occur naturally in animals.

Answer 286

… is very similar as in the primordial germ cells/germline to drive regeneration.

Answer 287

Using the signalling factors, e.g., BMP4, Wnt; activin, in the right amounts, in the right combinations and at the right times, cells can be pushed into different fates.

Answer 288

Can self-organise in response to an external stimulus.

Answer 289

Using permissive and restricted micropatterned cultures.

Answer 290

OCT4, NANOG, SOX2 and DAPI.

Answer 291

Marker of trophectoderm.

Answer 292

Marker of mesoderm.

Answer 293

Marker of ectoderm.

Answer 294

Cells repsond differently, depending on their position, and start expressing different genes. This can be used to recapitulate the pattern of gene expression in the embryo.

Answer 295

This could be for spatial/timing reasons (i.e., which cells receive it first), it could be due to different combinations, it could be a combination of both, or it could be due to internal signalling between the cells.

Answer 296

Transplant cells form the inner cell mass of one embryo into another embryo. This gives a chimeric mouse. Germ celsl derived from both embryos are seen in the next generation.

Answer 297

The generation of the donor genotype in the F2 generation.

Answer 298

The transplanted embryonic stem celsl can get into all germ layers, and the germline.

Answer 299

Provide DNA to the embryonic stem celsl atht is homologous to part of the genome. Insert the construct (DNA you want to add) in the middle of the homologous DNA. Also add a selective marker, so transformed stem cells acn be identified. Inject the DNA into the mouse to make a chimeric mouse. Breed that mouse to get an animal with teh construct in all of its cells. This construct undergoes homologous recombination with the host gene because embryonic stem celsl recombine well.

Answer 300

It's a long and laborious process. Now, gene editing using CRISPR-Cas9 can be used.

Answer 301

He took out the nuclei of frogs eggs, then injected the whole adult cells without their nuclei into the egg. The adult cell could be reprogrammed by the egg cytoplasm and yolk to remake everything.

Answer 302

They generated a line of embryonic stem cells in culture that had the regulatory elements of the Fbx15 gene (a marker, only expressed in pluripotent stem cells) to drive drug resistance genes, so if the drug resistance genes were expressed, they knew pluripotency had been achieved. They used retroviral infection to insert the cDNA of the transcription factors known to be involved in expression in embryonic stem cells. They used mouse embryonic fibroblasts that are not pluripotent. they removed transcription factors in a subtractive screen until they got down to 4.

Answer 303

They are destined to become fibroblasts.

Answer 304

Oct3/4, Sox2, Klf4 and c-Myc (an oncogene). These 4 factors switch on the Fbx15 locus, so the drug resistance genes are expressed.

Answer 305

That the modified cells can form teratomas.

Answer 306

By injecting the modified cells into the inner cell mass, they demonstrated that they were pluripotent as they contributed to all 3 germ layers and the germline in chimeric mice.

Answer 307

Their timing, capacity to regenearte and their epigenome.

Answer 308

The promoters of genes in primed cells are ready for transcription to start.

Answer 309

Yamanaka factors can be used to re-program cells back to this primed state.

Answer 310

Make the decision on which fate to become. This is not the same in all stem cells.

Answer 311

Essential for the maintenance of pluripotency. It is switched on after Yamanaksa factors are added to the cell.

Answer 312

Signals push that balance in a particular direction to make a fate decision.

Answer 313

Affect how much proliferation stem cells should do in order to self-renew.

Answer 314

BMP4 pushes cells with low OCT4 expression into the extraembryonic lineages.

Answer 315

Vary stochastically.

Answer 316

Adult stem cells. 50-200,000 of them produce 2.5 million erythrocytes per second, as well as immune cells.

Answer 317

Using Fluorescent Activated Cell Sorting (FACS) that involves using antibodies to identify the cell surface markers on the different cells.

Answer 318

Sickle cell anaemia, and autoimmune diseases.

Answer 319

They observed a 1:1 relationship between the number of cells transferred, and the number of colonies observed, demonstrating that each cell was able to give rise to a large population of cells.

Answer 320

CBC cells, fixed in the stem cell zone at the base of the crypt, that give rise to all the cells in the intestinal system.

Answer 321

The entire gut lining is replaced every few weeks.

Answer 322

Differentiation of adult intestinal cells down these pathways.

Answer 323

Mainatins self-renewal of adult intestinal stem cells.

Answer 324

Pulse chase approaches, and transgenic mouse experiments using inducible expression.

Answer 325

In vitro and in vivo experiments in embryonic stem cells.

Answer 326

Only very short-lived animals.

Answer 327

No cellular response to damage. --> Turnover of some tissues and organs. --> Regeneration of some tissues, and organ homeostaiss and repair. --> Regeneration of some tissues and organs. --> Regeneration of many tissues and organs. --> Whole Body Regeneration.

Answer 328

Involves regenerating all 3 germ layers, whereas organ regeneration does not.

Answer 329

Regenerating a particular cell type.

Answer 330

E.g., neuronal regeneration. Doesn't involve proliferation.

Answer 331

Fixed number of cells, and no cell division in the adult, e.g., C. elegans. Not good for a long life-history, but they reproduce rapidly, so are adapted for this.

Answer 332

Means no mitotic response to damage.

Answer 333

Like C. elegans, it's short-lived, and reproductively-explosive, but it encounters more pathogens, and consumes more toxins, so has stem cells in the gut.

Answer 334

It can regenerate more than other mammals.

Answer 335

Hydrazoans, Planaria, zebrafish, salamanders and newts, Xenopus, Acoels and mice (and relatives).

Answer 336

Annelids, sea cucumbers, Ascidians, insects and starfish. These either don't regenerate as well, or the tools aren't available to manipulate their genomes.

Answer 337

Good regenerators have life-histories that weren't accessible or convenient for classical genetics.

Answer 338

E.g., the gut lining, skin and blood regenerate better than the psinal cord, cardiac muscle and limbs, in humans.

Answer 339

Earlier in life-history stages such as druing embryonic development, neonatally or just after birth, some organsism can regenerate well, but then lose this ability.

Answer 340

Gives the same results. If above the elbow, they have to make an elbow, wrist and a hand, but an elbow doesn’t have to be made, if below the elbow is amputated.

Answer 341

Regeneration is different from development because, unlike development, you have to make something that is compatible with the existing organism, and there are different starting points to reach the final outcome.

Answer 342

Regnerate their gut, after ejecting it to escape predators.

Answer 343

Regenerate as an adaptation to being partially predated.

Answer 344

E.g., the gecko has regenerated two tails. Depending on the life-history, the costs/risk may mean regneration is not worth doing.

Answer 345

Oligochaetes make a whole new tail, body and head before it splits in order to reproduce.

Answer 346

… become obligate asexual, which means they amy accumulate mutations due to a lack of recombining.

Answer 347

Has skin that detaches easily to deposit spines in a predator's mouth. These rodents can regenearte the skin and pisnes, but they can also regenerate other tissues.

Answer 348

1. Stem cells that are self-renewing, and produce differentiated cells. 2. Differentiated cells that de-differentiate, then make cells of the same type (unipotency). 3. Cells go through trans-differentiation from one cell type to another. 4. Major populations of adult pluri- or multipotent stem cells that differentiate into different cell types. 5. Adult stem cells specified to a group of cell types within one germ layer, e.g., connective tissues, or nerve cells, so are lineage-restricted and resident in the tissue in which they act.

Answer 349

No mesoderm. Foot to attach to a substrate. Nematocytes in the tentacles. Regenerate well, when cut in half.

Answer 350

This can be imaged with RFG in the endoderm, and GFP in the ectoderm. The cells retain their identity, and find where they're meant to be. Not possible in Bilaterians.

Answer 351

Icells/interstitial stem cells in the body column.

Answer 352

To reproduce asexually by budding, but also for sexual reproduction by making the germ cells.

Answer 353

The first two populations are the endoderm and ectoderm cells that are made by their own stem cells; the third groups are the Icells that make everything else, e.g., neurones, secretory cells.

Answer 354

They don't make ectoderm or endoderm body column cells.

Answer 355

Then cluster cells by similarity: what they are expressing at a particular point in time. You can map trajectories of regeneration of stem cells as they differentiate into different cell types.

Answer 356

The transitions form different cell lineages into different cell types, and changes in gene expression tahtd emonstarte how this is mechanistically regulated.

Answer 357

Vertebrate, so it has more biomedical relevance because you can study regeneration in tissues homologous with those in humans.

Answer 358

Retina, brain, kidney, spinal cord, fin, skin, pancreas, liver and heart.

Answer 359

A hormone nuclear receptor connected to a recombinase enzyme. The rpomoter is only active in the heart, so the recombinase is only expressed in the heart. Throughout the body, there's also a construct that has promoters, meaning the gene is expressed in all muscle, so all muscle appaears red.

Answer 360

When a drug is added, the heart turns green due to activation of the the recombinase. All the other muscle-derived cells are still red. Damage the heart, and it regenerates all green. This is the same for bones in the fin.

Answer 361

They use lineage-restricted progenitors. Transplant GFP-labelled tissue from a GFP-labelled animal into the embryo you're working with. Label future bone, msucle and nerve cells. Bone makes bone, msucle makes muscle etc., so there's lineage specification early in tail regeneration.

Answer 362

They don’t cross the germ alyers.

Answer 363

Pigmented cells in the newt eye de-differentiate, undergo mitosis, then re-differentiate, and express crystallin.

Answer 364

Piwi proteins are found in these granules.

Answer 365

Regulate piRNAs that protect the germline by silencing selfish elements.

Answer 366

Neoblasts.

Answer 367

Add a radiation dose that is non-lethal. Raise the dose, so animals only have a few cells left, so they can still regenerate the whole organism. Or destroy all the stem cells, and transplant one stem cell from another individual to regenearte the irradiated organism.

Answer 368

Populations of stem cells.

Answer 369

Many have somatic stem cells that express germline stem cell genes.

Answer 370

… having body-wide adult stem celsl that express piwi.

Answer 371

We can't use mutagens, or CRISPR editing to break the genome, as we could when studying development, because when you break soemthing, you see the change in the earliest phenotype first.

Answer 372

When genes have an early and a late function.

Answer 373

Can do posterior, but not anterior regeneration. It can't regenerate the brain or CNS.

Answer 374

Base analogue that is incorporated in the S phase of the cell cycle.

Answer 375

By the presence of EDU that can be detected with antibodies. This indicates new cells.

Answer 376

Like piwi, it's a marker of adult stem cells that is found in granules. In Platynereis dumerilii, it works with piwi, and is present at the wound site.

Answer 377

adult stem cells in this Acoel have piwi. It sexually reproduces, so has unicellular zygotes that can eb edited, so it's a useful system.

Answer 378

Feeder polyps and lots of other types of polyp are all connected at the bottom. They communicate through their feet, probably.

Answer 379

These ones are pluripotent, and are highly migratory to move to replace the damaged tissue.

Answer 380

Either the ancestor of all tehse renerating animals had these somatic stem cells (then it was lost in vertebrates), or it evolved multiple times independently.

Answer 381

lineage-specific or pluripotent (Planarians), or lineage-restricted, multipotent cells (Hydras and vertebrates).

Answer 382

It's both throughout the animal kingdom.

Answer 383

E.g., Wnt for the AP axis.

Answer 384

The proteins axin, GSK-3β and APC inhibit the transcription factor β-catenin.

Answer 385

The inhibitory proteins are degraded, so the β-catenin can enter the nucleus, interact with other transcription factors and switch on target genes.

Answer 386

… animals using it to specificy/pattern their posterior ends.

Answer 387

Likely used Wnt signalling to pattern its posterior end.

Answer 388

The terminal effector in the Wnt signalling pathway.

Answer 389

Means Wnt signalling is effectively off, so heads develop everywhere.

Answer 390

Also gives anterior structures everywhere, in this case tentacles.

Answer 391

It's active everywhere, e.g., it's also used to make anterior brain structures.

Answer 392

Negatively regualtes Wnt, so when APC is absent, β-catenin can enter the nucleus, and Wnt signalling becomes constitutive.

Answer 393

Suppresses anterior identity by producing two tails and two pharynxes.

Answer 394

Has independent signalling pathways, so is still formed when APC is knocked out in Planarians.

Answer 395

A negative regulator of the Hedgehog signalling pathway that temporarily makes Wnt high.

Answer 396

Gives temporarily high wnt, so two tails and two pharynxes again, but its' temporary as APC is still present. Thus, when Wnt decreases, the animal decides the most anterior end is between the two pharynxes, so a head is made in the middle.

Answer 397

Wnt dominates, irrespective of the Patched genotype, so two tails and two tails form.

Answer 398

Wnt comes from other cells to the gut lining. Secreted Wnt is highest at the bottom of the crypt. If you remove Wnt, the mesenchymal cells stop renewing, and the gut fades.

Answer 399

52% of colon cancers have this gene mutated.

Answer 400

Gives constitutive Wnt signalling in the gut, which means stem cells are over-produced, and cancer may occur.

Answer 401

The zygote makes more and more differentiated cells. Germ stem cells are made at different points in different animals.

Answer 402

The germplasm can be set aside at the first stage in development to make germ stem cells (this is stem cells coming directly from the zygote), or they can be induced at any stage in development by signalling.

Answer 403

By adult pluripotent stem cells.

Answer 404

In development, as C. elegans is highly reproductive, but has no intermediates, just post-mitotic differentiated cells. The opposite extreme to planarians.

Answer 405

Remove all the stem cells from Hydroactinia by radiation. Terminally differentiated cells in Hydroactinia can recognise that no stem celsl are present, and naturally de-differentiate to regenerate the whole Hydroactinia.

Answer 406

Mild disease, cowpox (vaccinia, conferred resistance to smallpox (vaccination).

Answer 407

Infectious diseases are caused by microorganisms. Hypersensitivity reactions: allergic reactions.

Answer 408

Developed vaccines for fowl cholera and rabies.

Answer 409

It recognises, and responds to problems, e.g., invasion, inefction and altered self. It's trained on normal self, so recognises when something has changed. Recognition, response, effect and integration.

Answer 410

Detects and differentiates problems, e.g., between different types and subtypes of pathogen, e.g., bacteria vs. viruses.

Answer 411

Intra- and extracellular signalling cascades, and cellular events (differentiation, movement or proliferation by cell division).

Answer 412

Effector molecules directly kill pathogens, e.g., by lysis, or by binding to the surface of the pathogens (block, opsonise and/or agglutinate).

Answer 413

The ability to communicate, cross-activate or regulate different parts of the immune system.

Answer 414

The surface of the pathogen is tagged, so immune cells can recognise it.

Answer 415

It prevents invasion or colonisation, limits early proliferation and dissemination, restricts growth (post-spread), kills or controlds that pathogen, effects clearance and offers enhances short-term or long-term resistance to rechallenges.

Answer 416

Restriction enzymes, and CRISPR-Cas systems.

Answer 417

Target specific, non-self nucleic acid sequences, can be induced and may confer resistance to bacteriophages.

Answer 418

Uses RNA guides to target foreign, typically DNA, sequences.

Answer 419

Induction of intracellular antiviral/antibacterial mechanisms. The ability to kill vacuolar organsims by producing reactive oxygen species, or reactive nitrogen species. Protists have more similar immune functions to humans than bacteria; our immune systems are not unique.

Answer 420

As diverse as animal phylogeny. Specialised cells.

Answer 421

New sites for the pathogen to exploit, e.g., the extracellular matrix. There are new surfaces and body fluids to protect.

Answer 422

Highly conserved mechanisms. Detection, response and outcome of the response.

Answer 423

Detecting and differentiating the problem. Pattern recognition: the process of detection in the innate immune system.

Answer 424

Innate and adaptive.

Answer 425

Pathogen removal/killing, control without removal (persistence) and pathology (most is self-induced).

Answer 426

Innate is faster; it can take 10-14 days for a strong antibody response to the primary infection. Different mechanisms: molecules, cascades and cell types. The adaptive immune system has more specificity.

Answer 427

E.g., antibodies.

Answer 428

Pattern recognition receptors, e.g., the Toll-like receptors.

Answer 429

Develop from myeloid progenitor cells. All innate.

Answer 430

All adaptive, except one that's innate. Develop from lymphoid progenitor cells.

Answer 431

… the adaptive immune system emerged in vertebrates.

Answer 432

The innate triggers the adaptive response. Long-term memory in the adaptive immune system, means it is faster the 2nd time round. The inante immune system is the same speed the 2nd time round, and has a lower magnitude as there's less pathogen to kickstart it.

Answer 433

Barriers, tissue fluid systems and cellular systems.

Answer 434

Mechanical (epithelila cell layers), chemical (pH, oils, antimicrobial peptides enzymes, and mucus, whose composition changes upon infection), and microbiological (enteric microbiota, the commensal bacteria compete with pathogenic bacteria

Answer 435

Complement cascades, coagulation cascades and iron-binding molecules.

Answer 436

Lytic cells (natural killer cells) and phagocytic cells (macrophgaes and neutrophils).

Answer 437

The blood-clotting enzyme csacade. It not only stops the bleeding, but initiates wound repiar, creating a barrier, and captures pathogens.

Answer 438

Lactoferrin and transferrin. Compete with bacteria for iron molecules to slow bacterial growth.

Answer 439

A plasma-based enzyme cascade. Formation of deposits on microbial surfaces. Some of the deposits are lytic, so form the lytic attack complex. Marking the surface assists interactions with immune cells by opsinisation. Elements have chemotactic ability (calling in cells). An effector for both adaptive and innate pathways.

Answer 440

They all go through the central capability (C3 convertase). The classical pathway (initiated by antibodies in the adaptive response), the lectin pathway and the alternative (a spontaneous) pathway.

Answer 441

Proteins that bind sugars. Pattern recognition receptors.

Answer 442

Chemotactic.

Answer 443

an opsin that sticks to the surafce of invading bacteria, so cells can recognise it. It also initiates a cascade that culminates with C9.

Answer 444

A membrane-attack complex that punches holes in the pathogen's cell surface.

Answer 445

Microbial lysis, and enhanced phagocytosis.

Answer 446

Encoded in an effective configuration in the genome. Soluble, trans-membrane and cytoplasmic locations. Most animals have 100-200 different receptors, each expressed at a high frequency.

Answer 447

Lectins, Toll-like recptors and NOD-like receptors.

Answer 448

Antibodies, B cell receptors and T cell receptors. Huge repertoire: >10^8 different specificities per person. Soluble or cell surface receptors. Each receptors is clonally expressed on very few cells, unless stimulated.

Answer 449

~100 million T and B cells.

Answer 450

Thus, these receptors are made by re-arrangement: moving genomic segements together, and actually mutating.

Answer 451

They are present on only a few cells, so must divide in resposne to the pathoge, hence the adaptive immune response takes time.

Answer 452

Drosophila has a mutation in Toll.

Answer 453

Charles Janeway.

Answer 454

Conserved elements of eth pathogen that they can't change very easily, but are different to ours. These are recognised by pattern recognition receptors,

Answer 455

Mannose-binding lectin (tissue fluid), Toll-like receptors (transmembrane), NOD1 and NOD2 (cytoplasmic) and cell-associated pattern recognition receptors are strong inducers of the translocation of NfkB to the nucleus.

Answer 456

Use a common pathway for signal transduction. They trigger a wide array of pro-inflammatory effects.

Answer 457

Recognises LPS of gram negative bacteria, then initiates a cascade. This highlights the specificity of the innate immune system, albeit not as specific as the adaptive immune response.

Answer 458

Recognises DNA with unmethylated CpG motifs in bacteria.

Answer 459

Recognises dsRNA in RNA viruses.

Answer 460

Recognises flagellin on gram-negative bacteria.

Answer 461

Agonists: ssRNA and imidazoquinolines.

Answer 462

Agonists include bacterial lipoprotein, peptidoglycan, porins and glycophosphatidyl inositol anchors. It recognises gram-positive bacteria, yeast, mycobacteria, Neisseria and Trypanosomes.

Answer 463

There isn't one receptor for each pathogen. A set of receptors are used, then the system integrates the signals to be specific about the invading pathogen.

Answer 464

TLR3 (dsRNA), TLR4 (RSV surafce glycoprotiens), TLR7/8 (ssRNA) and RIG-I (dsRNA, cytoplasmic).

Answer 465

TLR1/6 with 2 (cell wall components), TLR4 (LPS), TLR9 (Cpg motifs in DNA), NODs (cytoplasmic cell wall components) and mannose receptors.

Answer 466

TLR2 (GPI anchors), TLR4, TLR( (Plasmodium hemozoin).

Answer 467

T cell, B cell and plasma cell (adaptive). NK cell (innate).

Answer 468

Platelets, erythrocytes, monocytes that develop into macrophages, eosinophiles, neutrophils, basophils, mast cells and dendritic cells. All innate.

Answer 469

Cell with differently-shaped nuclei, such as dendritic cells that have long dendrites to stimulate the adaptive immune system.

Answer 470

… lymphoid progenitor and myeloid progenitor cells.

Answer 471

Phagocytosis and intracellular killing, release of pro-inflammatory cytokines, antigen presentation and tissue repair.

Answer 472

Antigen uptake in peripheral sites. Antigen presentation in lymph nodes. They have long dendrites with a large surface area. They travel to activate the adaptive immune system.

Answer 473

… gives different responses.

Answer 474

Neutrophils. 40-75% of leukocytes.

Answer 475

They have granules that stain with a neutral dye.

Answer 476

Phagocytosis once then dies. Called in by the macrophage. Intracellular killing. Inflammation and tissue damage.

Answer 477

Killing of antibody-coated parasites. Have granules containing different chemicals to spew out onto the surface of pathogens. Tissue damage in allergic reactions.

Answer 478

Release lytic granules that kill some virus-infected cells.

Answer 479

Many numbers of neutrophils in the tissue.

Answer 480

Has at least one form of macrophage.

Answer 481

Macrophages induce the walling off of pathogens that the immune system cannot remove.

Answer 482

They use many of the same agents to kill the pathogen, e.g., antimicrobila peptides that punch holes in the pathogens.

Answer 483

Acidification, toxic oxygen-derived products, toxic nitrogen oxides, antimicrobial peptides, enzymes and competitors.

Answer 484

pH ~3.5-4.0, bacteriostatic or bacteriocidal.

Answer 485

Superoxide, hydrogen peroxide, singlet oxygen, hydroxide radical and hypohalite (OCl).

Answer 486

Nitric oxide (NO).

Answer 487

Defensins and cationic proteins.

Answer 488

NADPH-dependent oxidases: generate toxic oxygen derivatives. Lysozyme: dissolves the cell walls of some gram-positive bacteria. Acid hydrolases: further digest bacteria.

Answer 489

Lactoferrin (binds iron) and vitamin B12-binding protein.

Answer 490

Communication, organisation and anti-pathogen effects.

Answer 491

Soluble mediator produced by cells, such as macrophages.

Answer 492

Soluble mediator produced by leukocytes. A subset of cytokines.

Answer 493

Soluble mediator that can induce a state that interferes with viral replication. They instruct cells to create a refractory state against pathogens. A type of cytokines.

Answer 494

Induce apoptosis in cells.

Answer 495

Regulatory cytokines that tell cells to calm down, but too many of them turns everything off.

Answer 496

Small, chemotactic molecules.

Answer 497

Small, antimicrobial molecule.

Answer 498

Always produced by a part of the body.

Answer 499

Massively upregulated in response to a pathogen.

Answer 500

For organisation/homeostasis, and movement towards sites of infection by chemotaxis.

Answer 501

Some cells near the site of infection create a gradient of chemokines, which act as a molecular map, and modify the surface of the endothelia in this patch of blood vessel. Diapedesis: polymorphonuclear cells flatten, and move across the endothelia into the tissues. They then follow the chemokine gradient to the site of infection.

Answer 502

Immune cells exiting the blood vessels.

Answer 503

A pathogen invades, trigerring a cascade of local events, including tissue damage. Cells are called in by macrophages and chemotactic gradients created by complement cascades.

Answer 504

By a chemokine gradinet as the lymph node produces its own unique chemokine.

Answer 505

They can detect it themselves, or this can be indicated by the dendritic cells.

Answer 506

7-14 days.

Answer 507

Takes 7-14 days.

Answer 508

Takes 3-5 days.

Answer 509

Alteration of three genomic sequences to create an anticpatory repertoire: lots of receptors to be able to recognise a pathogen, made prior to the infection. Lterations in the repertoire occur according to circumstance. TCR, BCR and VLR. Memory!

Answer 510

T Cell Receptor.

Answer 511

B Cell Receptor. Only in jawed vertebrates.

Answer 512

Variable Lymphocyte Receptors. In jawless fish.

Answer 513

Antibodies and T cell receptors.

Answer 514

Duplicated heterodimer: two heavy chains, and two light chains.

Answer 515

Secreted by B cells. Membrane-bound (B cell receptors).

Answer 516

E.g., lipids, proteins or carbohydrates etc..

Answer 517

… as long as it's non-self, though occasionally when it's self.

Answer 518

Antibodies can be raised against any part of the structure, be it linear, e.g., linear amino acid chains, or against a conformational epitope (a non-linear shape).

Answer 519

Also recognise shape, but are more restricted. Always a membrane-bound heterodimer.

Answer 520

Linear peptides on antigen-presenting MHC complexes.

Answer 521

Alpha-beta (classical) and gamma-delta (non-classical).

Answer 522

A moelcule seen be the adaptive immune system. Doesn't apply to the innate. Antigen= antibody-generating.

Answer 523

The specific part of the antigen involved in recognition.

Answer 524

A molecule capable of stimulating a specific adaptive response.

Answer 525

Antibodies see shape directly, whereas alpha-beta T cell receptors recognise peptides on MHC molecules.

Answer 526

Generated by rearrangement with junctional modifications. All of the receptors are made in heterodimeric pairs.

Answer 527

…are very structurally similar-- conserved organisation.

Answer 528

Up to 10^15 different TCRVbeta rearrangements in humans, yet we only express 10^8 different TCR at any time.

Answer 529

Sequences encoded in an array in the germline. Variable, diversity and juncyional. Then c: the constant region.

Answer 530

Complementary Determining Region 3. The tip that detects the epitope. It can be v and j, or v, d and j.

Answer 531

One of the vs is brought with one of the js and one of the ds to create this diversity by recombination.

Answer 532

The recombination process is semi-random.

Answer 533

One of the vs and one of the js are stitched randomly together, after breaking the DNA.

Answer 534

There are open junctions where random deletions and additions of nucleotides occurs, which creates junctional diversity. This creates the immense divserity of the repertoire as the junction is what recognises the peptide. The same process occurs for antibodies.

Answer 535

Recombination Activation Gene

Answer 536

Recombination Signal Sequence

Answer 537

RAG genes scan part of the genome, then recognise and attach to the RSS. The RAG complex bends the DNA, then cuts it. That leads to broken DNA within the chromosome and a loop.

Answer 538

The Signal Joint. (The loop is essentially discarded.)

Answer 539

It is protected by repair molecules Ku70 and Ku80, which bind to the loop.

Answer 540

Artemis and DNA-PK that bind to the junction.

Answer 541

Terminal deoxynucleotidyl transferase. Enzyme that dives into the junction at the same time as Artemis and DNA-PK bind to the junction, just ebfore the junction closes.

Answer 542

Randomly adds and deletes nucleotides at the junction.

Answer 543

closes the junction, forming the receptor.

Answer 544

Receptors that recognise self too strongly will be made as theis re-arrangement is random.

Answer 545

Each receptor is only found on 1-10 cells.

Answer 546

During development, each cell (which each have a different receptor) is tested, so if the receptor responds too much to self, the cell is killed.

Answer 547

Autoimmune diseases could occur.

Answer 548

Lymphocyte cells are capable of self-renewal, and can replicate rapidly.

Answer 549

At top speed, they can divide once every 6 hours. They can't maintain this rate, but they can maintain dividing every 10-12 hours.

Answer 550

B Cells= Bone Marrow. T Cells= Thymus.

Answer 551

All of the self-antigens are presented to the cells. If they fail to detect anything, they die by neglect. If they detect the self antigens too well, they are killed.

Answer 552

RAG turns on in late DN2. RAG turns off in DN4. RAG turns on in early DP. RAG turns off in SP.

Answer 553

Cluster of Differentiation. A term for cell surface molecules.

Answer 554

Refer to the status of CD4 and CD8. DN= double-negative. DP= double-positive. SP= single-positive. This indicates the type of receptors present on the cell, i.e., double-positive means both CD4 and CD8.

Answer 555

Die by neglect as they don't receive the survival signal.

Answer 556

Are activated in the thymus, so are killed by activation-induced cell death.

Answer 557

Cells with different receptors on theme with an intermediate affinity for MHC self-peptides. They see the self-peptides, but they don't actually respond. These cells are exported from the thymus to become our naïve repertoire.

Answer 558

They recognise the pathogenic antigens, are dragged across the activation threshold and divide.

Answer 559

Most of the cells die, some survive, and this group of surviving cells represents the memory population. They drop below the activation threshold.

Answer 560

You start with more cells, so the number of divisions required to reach the same number of cells is lower. memory cells are also closer to the activation threshold than naïve T cells due to their changed transciption profile and biochemistry, so are more easily activated and divide faster. a similar process applies to B cells.

Answer 561

… multiple antigen binding sites.

Answer 562

Have different numbers of units in the mature structure.

Answer 563

Go into the gut where they interact with good and bad microbes, and 2g are flushed out daily.

Answer 564

Some are good at activating complement, whilst others are good at beig recognised by cells as receptors bind to their Fc tails, for example. Different Fc regions determine the different classes.

Answer 565

1. The antigen-binding Fab fragment (2 in each unit). 2. The Fc region recruits other molecules (complement), or is bound by cells expressing the Fc fragment.

Answer 566

Block, agglutinate, opsonise and activate complement.

Answer 567

Bind to important molecules on the pathogen, e.g., receptors on a virus.

Answer 568

Fc is recognised by Fc receptors on cells.

Answer 569

The mechanism by which innate cells gain specificity. Innste cells covered in Fc receptors bind to antibodies. This helps them target a specific type of cell, e.g., an infected or a pathogenic cell.

Answer 570

Categories of alpha-beta T cells, both communicate and kill, but have primary functions: either helper or cytotoxic.

Answer 571

Not restricted to MHCs. Their functions are still being elucidated, but they appear to be performing all the functions of alpha-beta T cells under different circumstances.

Answer 572

T helper cells (Th). Restricted to MHC class II.

Answer 573

T cytotoxic cells (Tc). Restricted to MHC class I.

Answer 574

They multiply to give 8: CD8 x MHC class I = 8, and CD4 x MHC class II = 8.

Answer 575

CD8 produces mostly Tc1, but also some Tc2. CD4 produces Th1, Th2, Th3, Th17 and T-reg.

Answer 576

B cells make natibodies (Th2 via IL4), and help macrophages to become activated (Th1 via interferon gamma).

Answer 577

Undifferentiated T cells. They produce IL2 and IL4, which are both cytokines and autocrine growth factors that support proliferation.

Answer 578

… different T cell subtypes/stable differentiation points. They also give the function of T cells.

Answer 579

T-regulatory cells that calm everything down, and switch everything off by producing IL10. Without them, serious pathology would occur.

Answer 580

Loaded with peptides from the cytosol-- the endogenous pathway. Peptides from the cytoplasm are pumped into the ER, and are presented on MHC Class Is. CD8s bind to the outside of the MHCs, which helps stabilise them.

Answer 581

Brings peptides from outside the cell-- the exogenous pathway.

Answer 582

Peptides bind on the groove of the MHC. The upward-facing part of the MHC that recognises the peptide is in a similar location in both MHC classes.

Answer 583

… MHCs must be matched, when grafting.

Answer 584

The most polymorphic of all the loci in all jawed vertebrates, which prevents pathogens escaping all MHCs through mutation. The locu is in such a variable state due to the selective pressure from pathogens.

Answer 585

MHC Class I is loaded in the ER. Peptides are produced by the proteasome. The TAP pump passes proteins into the lumen of the ER, where they bind to the MHC Class I. MHC Class I is then put onto the surface for the CD8 cells to recognise.

Answer 586

MHC Class II is made, then put into an endomembrane unit/vacuole. The pathogen is engulfed by phagocytosis into a phagosome. This fuses with a lysosome to form a phagolysosome. This fuses with the compartment with the MHC Class II in it. The proteins from the pathogen are chopped up, and loaded onto the MHC Class II.

Answer 587

Antigen-Presenting Cells.

Answer 588

They generally use soluble mediators/cytokines to change the environment, whereas killer cellshave to touch the target they're going to kill.

Answer 589

MHC Class I peptides are constitutively expressed on most cells in the body as you could ebcome infected in any cell in the body, so you need T cells to be able to recognise it.

Answer 590

MHC Class II peptides are constitutively expressed on a restructed set of cells (professional APCs).

Answer 591

Constitutively express MHC Class I and II. Dendritic cells, macrophages and B cells.

Answer 592

The only cell able to stimulate naïve T cells (when they're mature), hence they have very high levels of MHC Class I and II peptides. The innate cells that stimulate the adaptive immune response.

Answer 593

Active scavengers. Their activity is increased by interacting with CD4 T cells.

Answer 594

Can help macrophages revert to wound-healing cells.

Answer 595

In most tissues. Take up and process antigens.

Answer 596

Do not take up microbes. Migration to lymphoid organs. Present the antigen to naïve T cells.

Answer 597

Apoptosis.

Answer 598

A cytokine differentiation signal produced by T cells and other cells in the environment.

Answer 599

Signal 1 (MHCs), signal 2 (co-stimulatory molecules) and signal 3 (cytokines for differentiation).

Answer 600

… a lower threshold for further activation.

Answer 601

A feature of B and T cells. The population of specific cells is larger, easier to activate and migration patterns differ.

Answer 602

They no longer go to the lymph nodes, but migrate through the tissues because they have changed their chemokine receptors to respond to chemokines produced by particular tissues. They also produce more adhesion molecules.

Answer 603

Their transcriptional profile, signalling status and surface molecules have changed. There's an earlier commitment to effector status.

Answer 604

The Faroe islands in 1846 had their first measles outbreak since 1781. Ludwig Panum found that no one infected in 1781 was infected again in 1846.

Answer 605

Antigens from the pathogen stimulate B and T cells, and induce immunological memory. There is also the adjuvant.

Answer 606

A carrier, often oil-based, that contains immunstimulatory components to stimulate TLRs and other pattern recognition receptors.

Answer 607

They must carry material, present antigens and stimulate the innate immune system.

Answer 608

Attenuated pathogens (e.g., Sabin polio). Related pathogens.

Answer 609

Bacillus Calmette-Guerin. An attenuated form of Mycobacterium bovis to protect against M. bovis and M. tuberculosis.

Answer 610

Require an adjuvant. Whole dead pathogen (e.g., Salk polio, influenza). Subunit (e.g. tetanus toxoid).

Answer 611

Subunit delivery using a live carrier or DNA.

Answer 612

1963 Nobel Prize in medicine for examining a squid giant axon.

Answer 613

Mantle axons from a stellate ganglion. This is required for the speed of propulsion.

Answer 614

It's large, so electrodes can be stuck in it. It's a weak signal, so an amplifier is required. This is depicted on an oscilloscope. The system sits inside a Faraday cage to prevent disruption to the measurement.

Answer 615

1 A is 1 C of charge moving per second.

Answer 616

A 1 ohm resistor allows a current of 1 A to flow in response to a potential difference of 1 V.

Answer 617

g is the symbol for conductance. Conductance is the reciprocal of of resistance, units= Siemens, S.

Answer 618

Paint phospholipids over a hole between the two chambers to form a single lipid bilayer. You can put different solutions in each chamber and use electrodes to measure the voltage between them. The charge difference builds up until the potential difference across the membrane matches the potential difference at the battery.

Answer 619

Capacitance C = Q/V.

Answer 620

1 µF cm^-2.

Answer 621

Only 6,000 ions need to be moved to change the membrane potential by 100mV. The electrical system can respond quickly.

Answer 622

You can measure their conductance.

Answer 623

Act like a battery by creating a net charge movement. They establish an electrical membrane potential.

Answer 624

The amount of current that flows for a given membrane potential.

Answer 625

Positive charge flowing out of the cytoplasm is a positive current. Negative ions moving into the cell give a negative membrane potential.

Answer 626

Due to the Na+/K+ pump.

Answer 627

… sets up a membrane potential.

Answer 628

When the electrochemical potential is the same on both sides of the membrane. The concentration gradient driving diffusion is exactly balanced by the diffusion gradient attracting ions back into the cytoplasm.

Answer 629

The equilibrium for sodium has a positive internal membrane potential.

Answer 630

It's -70 mV.

Answer 631

It's -90 mV.

Answer 632

It's +60 mV.

Answer 633

It's +130 mV.

Answer 634

It just switches between the membrane potentials of Na+ and K+. A constant amplitude is reached when equilibrium is reached.

Answer 635

The system would short-circuit, so the timing of the channels and when they open must be controlled.

Answer 636

[Ca2+] is very far from equilibrium, so membrane potential changes quickly, when channels are opened.

Answer 637

Measuring the activity of a single ion channel.

Answer 638

A cell is held on the end of a pipette. A blunt electrode is used to trap a patch of the membrane on the cell. Gentle suction is applied to give whole cell- attched mode. To get more control, pull the electrode out to extract a membrane patch-- inside-out patch. Then the ion compositions of the solutions on both sides can be controlled. if you continue to pull with suction, and the membrane re-seals itself, you have an outside-out patch.

Answer 639

The channels are open for half the time on average. The frequency of changing between open and closed gives the intermeditae range for an I/V plot.

Answer 640

Current and the probability that the channels is open.

Answer 641

4 subunits, each with two membrane helices and a pore loop, surrounding a central pore.

Answer 642

It has more transmembrane domains, but the core structure is the same.

Answer 643

The energy required to remove water from the hydration shell.

Answer 644

Ionic radius and hydration energy. K+ has a greater ionic radius, but a less exothermic hydration energy than Na+.

Answer 645

K+ is too large to fit through the Na+ pore, but not vice versa. Na+ can't pass through K+ channels because not enough energy is obtained from interactions with the amino acid residues to overcome the hydration energy.

Answer 646

The selectivity filter, so amny ions can pass through per second.

Answer 647

Water-filled, to regain hydration, and to allow ions to pass through the selectivity filter quickly.

Answer 648

Juxtaposition of 4 P loop chains.

Answer 649

Has positively charged arginine or lysine residues every 3rd amino acid. If you apply a voltage, those charges will also try to move in that voltage gradient. If they start to move, that translates into a conformational change in that channel, which affects whether it is open or closed. The helix moves in response to membrane potential.

Answer 650

Have 4 subunits, each with 6 membrane-spanning domains.

Answer 651

Each have 4 domains, which each have 6 membrane-spanning alpha helices, incl. 4 copies of the S4 voltage sensor.

Answer 652

It responds to voltage.

Answer 653

It also responds to time. It takes time to reach full activation/to be fully open.

Answer 654

Pore-occlusion: a bit of protein is flapping around, so physically swings up and blocks the pore.

Answer 655

voltage-dependent kinetics, time-dependent kinetics and ion selectivity.

Answer 656

Part of the membrane can't respond, so this gives unidirectional, spatial propagation of the nerve impulse as the membrane can only respond further down, and the impulse can't go backwards.

Answer 657

Found in the spine or brain.

Answer 658

Spatial summation and temporal summation to reach the threshold depolarisation for an action potential. Increase the likelihood of a post-synaptic action potential occurring. Typically mediated by glutamate receptors, allowing an influx of Na+ or Ca^2+.

Answer 659

Decrease the likelihood of a post-synaptic action potential. Typically mediated by GABA receptors allowing an influx of Cl- ions, preventing depolarisation by Na+. Spatial or temporal inhibition.

Answer 660

Neuromuscular junction, neuroglandular junction or a synapse between two neurones.

Answer 661

The transverse tubules (T-tubules).

Answer 662

When the membrane is depolarised, dihydropyridine receptors (DHPs) let Ca2+ in. This triggers ryanodine receptors (RyRs) on the sarcoplasmic reticulum release Ca2+. Calcium-induced calcium release: enough RyRs releasing Ca2+, and there is a wave of Ca2+. Ca2+ binds to troponin C, causing a shift that moves tropomyosin out of the way to allow the myosin head to interact with the actin. Myosin heads pulling on the actin is required for contraction in the catalytic cycle.

Answer 663

The contraction process is the same, but slower.

Answer 664

An action potential can be activated by turning on the light via light-activated channels and pumps.

Answer 665

E.g., the nematode stops moving when the light is turned on. Optogenetics was used to map every single one of the 302 neurones in C. elegans.

Answer 666

Channel Rhodopsin 2.

Answer 667

Halorhodopsin chloride pumping.

Answer 668

You can control aggression in the hypothalamus by turning on the light. Activating circuits can be added to the amygdala to de-tune its fear response when the light is turned on, so the mouse moves more.

Answer 669

Allows you to study parts of the brain in intact organisms. Previously, the effects of lesions were studied.

Answer 670

Plants are composed of repeated units, plants develop throughout their lives and plant hormones coordinate plant development.

Answer 671

Modified leaves.

Answer 672

Reproductive shoots.

Answer 673

Apical growth, branching and radial growth.

Answer 674

Along the vertical axis. Above and below ground, directed by the shoot and root respectively.

Answer 675

The root and shoot need to explore by lateral growth.

Answer 676

To support apical growth.

Answer 677

1. The epidermal system protects 2) and 3). 2. The ground tissue system, supports and surrounds 3). 3. The vascular tissue system.

Answer 678

The permanent tissue. They are produced by the meristem.

Answer 679

Simple, complex and secretory.

Answer 680

Categorised into the parenchyma, schlerenchyma, collenchyma and epidermis.

Answer 681

The meristem.

Answer 682

By the thickness and complexity of the cell wall, e.g., does it have lignin? Or does it contain cellulose?

Answer 683

1. The Shoot Apical Meristem (SAM). 2. Cambia. 3. The Root Apical Meristem (RAM).

Answer 684

Contained in the terminal bud. Responsible for the production of shoot organs.

Answer 685

For radial growth and secondary tissues, e.g., cork and secondary xyelm and phloem. Found both the shoots and roots.

Answer 686

Production of organs occurs mostly post-embryonically in plants, unlike in animals that have more or less all the organs of the adult. SAM and RAM are found in plant embryos, early in development.

Answer 687

Adventitious roots form from inactiev meristem, or because tissues have de-differentiated to form meristem that forms roots.

Answer 688

To compensate for sessility, which is essntial when facing the grazing activity of herbivores. Meristem regnerates from differentiated tissue.

Answer 689

Produce new shoot and root meristems, so can generate new palnts.

Answer 690

Can re-activate silent meristems to restore growth, such as after wildfire.

Answer 691

Only 50-100 cells. Very small, and early on the new cells differentiate.

Answer 692

Reporter proteins able to produce a signal.

Answer 693

Fluorescent (e.g., GFP and RFP), chromogenic (e.g., GUS, enzymes in the presence of a substarte produce a colourful product) and luminescent (e.g., luciferase).

Answer 694

Reporter genes can be used with a set of specific promoters that define when and where genes are expressed in plants. Alternatively, the reporter gene can be fused with the coding gene sequence itself as well as promoters, so only in certain cell types can this gene be translated.

Answer 695

Cell identity is not always determined just at the transciptional level, but also at the translational level.

Answer 696

1. The division zone where meristematic cells are actively dividing beneath the root cap for protection. 2. The elongation zone where cells don't differentiate, they just expand. 3. The differentiation zone where adult cells acquire tehir final function.

Answer 697

4 cells in the root that don't divide, but specify what cell types the surrounding cells (initials) should be.

Answer 698

Certain stem cells that can divide into one type of cell, or can divide into intermediates that tehn divide into two different cell types, e.g., endodermis and cortex.

Answer 699

Distal part of the RAM. Cells differentiate by changing their shape and/or metabolism to acquire specific functions.

Answer 700

If the epidermal cells is in contact with two cortex cells beneath it, the epidermal cell elongates into a root hair with a high surface area: volume ratio to maximise exchange of water and minerals from the soil.

Answer 701

… to maximise absorption of nutrients.

Answer 702

Cells go through progressive wall thcikening and disappearance of cytoplasm to generate lignified conduits. Lignification provides strong mechanical support for xylem under tension, but it also kills off the eclls.

Answer 703

They originate by losing their cytoplasmic components, and are connected by perforations in the transverse cell wall.

Answer 704

Due to the production of lateral roots, which occurs early on in development.

Answer 705

At intervals, cells from the external part of the stele (pericycle) located in close proximity to xylem vessels (xylem pole cells) divide to generate a new root meristem (lateral root primordium) that self-organises to produce a lateral root. The dome-shaped structure perforates teh cortex and epidermis to emerge from the root.

Answer 706

Secondary reserves.

Answer 707

After divisions, the organiser tends to differentiate into a new xylem cell. The stem cells divide asymmetrically to produce a new stem cell and a new organiser.

Answer 708

In the vascular cambium, it's not static.

Answer 709

A lot of leaf primordia are protecting the small area of the SAM.

Answer 710

Both are dome-shaped structures. The SAM still has an Organising Centre beneath the 3 cell layers.

Answer 711

Layer 1: epidermis-like tissue. Layer 2: true meristamtic tissue. Layer 3: several cell layers.

Answer 712

The central zone: most of the division occurs here, but little differentiation. The peripheral zone: lateral organs are produced here.

Answer 713

WUSCHEL and CLAVATA1 and 3. It doesn't divide, but does dictate to the surrounding cells when to divide, amd what cell types to become.

Answer 714

Expressed in the 3rd cell layer.

Answer 715

Expressed in the 1st and partially in the 2nd cell layers.

Answer 716

… it also produces lateral, dome-shaped structures that develop into leaves at specific intervals.

Answer 717

Consists of a leaf, an axillary meristem and an internode. It is formed by a protrusion produced by the proliferation of the SAM.

Answer 718

…the apical meristem is inactivated.

Answer 719

Different plant species can have different lengths of internode. Even within the same plant, there can be internodes of different lengths at different stages of its development.

Answer 720

Describes the position of a new leaf/phytomer along the stem as compared to the previous one, e.g., 180°.

Answer 721

The time interval in-between the production of two consecutive phytomers.

Answer 722

Avoiding overlap of leaves to optimise light capture.

Answer 723

Layer 1 generates the epidermis. Layer 2 produces the mesophyll parenchyma. Layer 3 gives rise to the vasculature (leaf veins).

Answer 724

This means plants with different plastochrons may have the same phyllotaxis, or vice versa.

Answer 725

Protects and assists the vascular structure.

Answer 726

A leaf blade (distal and proximal areas) supported by a petiole, which contains a midvein.

Answer 727

Gradients of growth, which are generated by rate of cell division (initially) and direction of expansion (subsequently).

Answer 728

Hoe cells divide and in which direction they expand.

Answer 729

Found between different species as well as within individuals (i.e., simple leaves progress into more complex leaves with age).

Answer 730

Subunits are separated by a bladeless region.

Answer 731

Single, undivided blade.

Answer 732

Leaflets, lobes and serrations.

Answer 733

Persistence of the meristematic tissue (initiation) during primordium morphogenesis and differentiation creates outgrowths that develop into serrations or even leaflets, depending on how long the outgrowths remain active.

Answer 734

An adaxial and an abaxial side.

Answer 735

Upper side. Thick cuticle and organised mesophyll, optimised for light capture, chloroplast alignment and to reduce water loss. Sometimes it also has trichomes.

Answer 736

Lower side. Suited for gas exchange.

Answer 737

… adaxial side.

Answer 738

…abaxial side.

Answer 739

It is defined by proximity to the SAM very early in the primordium.

Answer 740

Generate fully abaxialised or adaxialised leaves. Study which genes are mutated to reveal the mechanism for these developmental pathways.

Answer 741

It turns into an inflorescence meristem (IM) that produces Flower Meristems (FMs). Depending on the species, the flower meristems develop into flowers, or the central region remains undifferentiated to turn into an IM.

Answer 742

Each meristem produces whorls of new organs.

Answer 743

Instead of a single organ emerging at a time, now there's the production of multiple organs at the same time by the IM.

Answer 744

1. Sepals that together form the calyx, and protect petals and internal organs during their development. 2. Petals that together form the corolla. 3. Stamens for pollen production. 4. Carpels that contain the ovaries, and become fruit post-fertilisation.

Answer 745

When vegetative meristems terminate and become reproductive, if this occurs at the apex or at lateral ones, and if the meristems terminate with a flower meristem, or continue producing meristems. If the floral meristem retains somatic activity for slightly longer, the number of structures that are produced varies, e.g., small florets inside the inflorescence, or large flowers.

Answer 746

A, B, C and E. Mutations in these genes alter organ identity, but not number (except for agamous).

Answer 747

A combination of two (se, ca) to three (pe, sta) gene classes. A combination of 2 or 3 of the class A, B, C or E genes being expressed in the same primordium.

Answer 748

8, 2-4 of which are shorter.

Answer 749

Don't produce petals or sepals. These organs are substituted for stamens and carpels.

Answer 750

Carpels and sepals. The stamens and petals are lost.

Answer 751

Only sepals and petals are produced. They are produced continuously to form several whorls. These are sterile as they don't have carpels or stamens.

Answer 752

The flower that is produced contains only leaf-like structures.

Answer 753

This means that, if A is mutated, C takes over, and is expressed where it is not normally expressed, and vice versa.

Answer 754

Gene redundancy.

Answer 755

Sufficient to confer hybrid identity to petals.

Answer 756

Produce fruits with ovules that resemble carpels.

Answer 757

The seedstick gene belonged to the same gene class as A, B, C and E-- MADS transcription factors (with one exception, the apetala-2 gene). Overexpressing the seedstick gene led to the production of carpel-like structures.

Answer 758

… within the fruit, you have carpels instead of seeds.

Answer 759

The identity of the carpel within the ovary.

Answer 760

The activity of the RAM and lateral root primordia (LRPs).

Answer 761

The activity of the SAM (phyllotaxis) and its branching.

Answer 762

Ethylene, abscisic acid, auxins, cytokinins and gibberellins.

Answer 763

Brassinosteroids, strigolactones, jasmonates, salicylates and peptides.

Answer 764

Molecules devoid of metabolic and catalytic function, they acts exclusively as signals. In plants, they are typically metabolites. Except for peptides, they are NOT encoded by genes.

Answer 765

Very low. In the nanomolar range in cells.

Answer 766

A cell targets itself.

Answer 767

A cell targets a nearby cell.

Answer 768

A cell targets a distant cell through the bloodstream.

Answer 769

They are not secreted by a specific cell type. Unlike in animals, most cell types can produce most hormones as plant cells can de-differentiate.

Answer 770

Growth (cell division, expansion and differentiation), development and responses to exogenous stimuli (biotic and abiotic). They have pleiotropic effects throughout the plant's life cycle.

Answer 771

Active hormones can be transported either a short or long distance, until they reach their targets. Here, they are perceived by dedicated receptors, triggering a signalling cascade by which they affect the state of the effector, typically activating it.

Answer 772

Mainly at the level of transcription, but there can also be faster responses such as the activation of transporters, for nutrient uptake, or the delivery of secondary signalling molecules, e.g., Ca2+.

Answer 773

Short-term inactivation by conjugation with another molecule, or long-term inactivation by degradation.

Answer 774

Primary and secondary metabolites as precursors, so compete for their consumption.

Answer 775

By hormone signalling.

Answer 776

… auxins/indole-acetic acid.

Answer 777

… ethylene.

Answer 778

Produces cytokinins, gibberellins, brassinosteroids, abscisic acid and strigol.

Answer 779

Lipid precursor to jasmonic acid. Lipids are typically produced in the chloroplast.

Answer 780

Hormone mutants can be complemented by exogenous addition of the hormone. Mutants often have a dwarfism phenotype. If they can't synthesise it, the phenotype can be alleviated by adding exogenous hormone.

Answer 781

By adding precursors, and observing when the wildtype phenotype is restored.

Answer 782

By supplementing it with intermediates from the hormone biosynthesis pathway. The pathway is intact up to teasterone because intermediates before that did not rescue the phenotype, but subsequent intermediates did.

Answer 783

Synthetic auxins still interact with the auxin receptors due to their structural similarity, but differ from the native auxins.

Answer 784

They persist for longer as plants haven't evolved to inactivate them.

Answer 785

2,4-dichlorophenoxyacetic acid. A potent synthetic auxin that is haloganted, so difficult to break down. This is agent orange that was sprayed on forests to defoliate them during the Vietnam war.

Answer 786

Amino acids and sugars. Not just to inactivate them by degradation, but to transport them in an inactive form.

Answer 787

E.g., jasmonates and salicylates. Methylated to make them volatile to serve as aerial messengers between individuals. They can be used to signal to a neighbouring plant that they are under attack by a pathogen.

Answer 788

Via plasmodesmata.

Answer 789

Unidirectional in the xylem, or source to sink in the phloem.

Answer 790

Complementation of biosynthetic mutants by grafting to the wildtype. Gibberellin biosynthesis mutants can be rescued by grafting the wildtype roots onto it, which indicates that gibberellins can be transported from the roots to the shoots.

Answer 791

As weak acids, they normally dissociate, but the low pH of the apoplast means they are protonated and uncharged, so can pass through the plasma membrane.

Answer 792

In the cytoplasm, the pH is higher, closer to neutral, so the auxins are deprotonated. Auxins are thence charged, so are trapped inside the cell.

Answer 793

Polar. They are enriched on specific sides of the plasma membrane in a cell-type-dependent manner.

Answer 794

By the continuous vesicle cycling of PIN proteins, which are moved towards the side of the membrane where they are needed.

Answer 795

PIN-mediated polar auxin transport.

Answer 796

Required for plant development.

Answer 797

In the Quiescent Centre (QC). This is created by inverse pumping: most of the auxins in the shoot are channeled to the QC, and auxins are also recycled upwards to the QC.

Answer 798

Sufficient to produce patterning. Cell identity can affect morphogen distribution and perception-- a feedback mechanism.

Answer 799

Specifically meant to report auxin activity.

Answer 800

Auxin gradients are disrupted, which abolishes QC identity, and disrupts root growth. This alters root shape by blocking the meristem, so it tends to expand instead of growing downwards.

Answer 801

Cells have different concentrations of signalling molecules, which creates a more linear response.

Answer 802

This gives different responses in different cell types, which dictate the identity and morphology of the cell.

Answer 803

Bind the hormone ligand and are in/activated mainly by the intra- or extracellular transfer of phosphates in signalling cascades. They typically sense hormones coming from the apoplast or ER of other cells.

Answer 804

Exploit the hormone as molecular glue for transient protein interactions that lead to effector modification, usually activation.

Answer 805

Ethylene, cytokinins and brassinosteroids.

Answer 806

ABA, jasmonates, gibberellins and auxins.

Answer 807

In the absence of the hormone, ranscriptional regualtors are bound to co-repressors. When hormone levels increase, the co-repressor is marked for proteasomal degradation by polyubiquitination.

Answer 808

Co-repressors.

Answer 809

Transcription factors that form a complex with the auxin co-repressors, keeping the trasncription factors inactive when auxin is absent, or at low concentration.

Answer 810

Aux/IAA proteins bind and repress the activity of ARFs via domains III and IV. When auxin binds to its receptor TIR1, TIR1 undergoes a conformational change, and connects the Aux/IAAs to a ubiquitin E3 ligase complex to be polyubiquinated. Polyubiquitinated Aux/IAAs are degraded via teh proteasome, thereby setting ARFs to recruit RNA polymerase II on target genes.

Answer 811

Dimer or multimeter receptors in the membrane in which one monomer phosphorylates the other one in a receptor that triggers a phosphorylation cascade that phosphorylates a shuttle protein to allow it to enter the nucleus to activate gene expression.

Answer 812

The phosphorylation of the shuttle protein also destabilises it.

Answer 813

Phosphotransfer between a membrane-bound receptor and a soluble shuttle (His to Asp residues).

Answer 814

Histidine kinases phosphorylate the receiver domain of a response regulator in response to different stresses or external cues.

Answer 815

There is a longer series of phosphorylation events, and an additional component (the histidine phosphotransferase) that is a shuttle protein connecting the cytokinin receptor to the response regulator.

Answer 816

Type A and type B/negative regulators.

Answer 817

The actual transducers at the level of gene expression.

Answer 818

Activated by type B in a feedback loop. Attenuates the response to cytokinins. It can't bind to the DNA; it just steals phosphates from the phosphotransferase in competition with the type B response regulator.

Answer 819

Activation of proton pumps, protein localisation (PIN), cell cycle regulators, primary and secondary metabolism and synthesis of other hormones.

Answer 820

Inhibition of hormone biosynthesis, stimulation of hormone degradation, promotion of hormone sequestration/inactivation and negative regulators of signal transduction (competitors/co-repressors).

Answer 821

Promoter sequences are much less conserved than protein-coding genes.

Answer 822

Compare between closely-related species, or delete certain regions, and test whether there is still responsiveness to the hormone.

Answer 823

Link the hormone enhancers in a tandem repeat/inverted tandem repeat then fused them to a minimal promoter and the reporter gene to generate a very strong output of the reporter to indicate whether the reporter can be perceived.

Answer 824

Isolate domain II, and fuse it with a fluorescent reporter. The protein is stable, but in the presence of auxin, the signal is degraded. If there's a mutation, and TIR1 cannot bind to auxin, then the signal is visible.

Answer 825

DII allows the auxin receptor to connect with the co-repressor.

Answer 826

Hormone-sensitive (linked to GFP) and -insensitive modules (mutated, linked to RFP) can be joined genetically to generate a ratiometric output, independent of the concentartion of the reporter. Green= absence of auxin signalling. Red= auxin signalling, the reference.

Answer 827

The main hormones involved in the regulation of meristem maintenance as well as identity and activity in both roots and shoots.

Answer 828

Auxin is a positive regulator, and cytokinin is a negative regulator.

Answer 829

Auxins are postive regulators.

Answer 830

Cytokinins are negative regulators.

Answer 831

Regulated by gibberellins and brassinosteroids.

Answer 832

Cytokinins are positive regulators.

Answer 833

Auxins are positive regulators.

Answer 834

Auxins and strigolactones are positive regulators, whislt cytokinins are negative regulators.

Answer 835

Gibberellins are positive regulators.

Answer 836

Cytokinins are positive regulators.

Answer 837

Gibberellins and ethylene become more important, whilst auxins are only required for the production of certain organs. The role of hormones in reproductive development may vary, dependent on species.

Answer 838

Abscisic acid is a positive regulator.

Answer 839

Gibberellins are positive regulators.

Answer 840

Gibberellins and ethylene are positive regulators.

Answer 841

Regulated by auxins, ethylene and gibberellins.

Answer 842

Gibberellins and auxins are positive regulators.

Answer 843

Regulated by ethylene and brassinosteroids.

Answer 844

Regulated by auxins and ethylene.

Answer 845

Antagonises gibberellins.

Answer 846

The sex of the flowers.

Answer 847

Ethylene, salicylates and jasmonates.

Answer 848

Production of secondary metabolites, or induction of apoptosis to prevent the spread of infection.

Answer 849

Pathogens and necrotroph parasites. Includes herbivores and fungi.

Answer 850

Biotroph pathogens incl. bacteria, fungi and viruses.

Answer 851

Favourable interactions/symbioses with mycorrhizal fungi.

Answer 852

Signalling moelcules have been hijacked by parasitic plants that only germinate when they sense the presence of their host.

Answer 853

This promotes callus formation by de-differentiation. Changing the concentration of hormone, particularly cytokinins, induces shoot production. Auxins stimulate root production.

Answer 854

To attract seed dispersers with an aroma.

Answer 855

Softening due to changes in cell wall composition. Pigmentation cahnges as chlorophyll is degraded, and plastids are filled with carotenoids and anthocyanins. Secondary metabolites are emitted as volatiles. Starch is degraded into soluble sugars.

Answer 856

Incubation with ethylene.

Answer 857

O2 is required for ethylene syntehsis, so the fruit is kept in a low-O2 environment until it is ready to be sold. Then ethylene is released to promote uniform ripening.

Answer 858

Proceed through a series of transverse and longitudinal divisions that establish axial and radial polarity.

Answer 859

… the tissues that will become the SAM and RAM that then produce new organs can be identified.

Answer 860

Apical and basal asymmetries as well as radial growth.

Answer 861

Periclinal and anticlinal divisions.

Answer 862

The plane of division is in the same direction as the growth of the organ. Leads to new cell files.

Answer 863

The plane of division is placed orthogonally to the growth of the organ being considered. Leads to an increased number of cells across a certain cell file.

Answer 864

Mutants that produce seedlings that lack part of the plant body can be used to infer genetic control over the embryonic development of plant organs. Mutations could cause loss of function, or gain of a new function, which would give a dominant phenotype.

Answer 865

Gurke, fackel, monopterus and gnom.

Answer 866

The nucleus is pushed to the apical region of the cell by the vacuole. This generates asymmetry of division.

Answer 867

The fertilisation event.

Answer 868

Elongation via phosphorylation cascades the push the nucleus upward.

Answer 869

A smaller cell that forms the embryo, and a longer one, which is the suspensor that supports the embryo, acts as a conduit for nutrients and connects it to the maternal tissues.

Answer 870

A change in the direction of cell division, forming 2-4 cells that are largely identical at the apex.

Answer 871

Asymmetric cell division occurs again, establishing an upper and a lower tier of cells.

Answer 872

Auxin fluxes.

Answer 873

They induce periclinal divisions that establish radial expansion of the embryo, which shifts from sink to source of auxins through the activation of biosynthetic and transport genes.

Answer 874

Use reporters or PIN proteins.

Answer 875

On the upper side of plasma membranes, indicating that auxins are pushed upwards towards the embryo.

Answer 876

Mainly PIN1.

Answer 877

They are localised to transmit auxins towards the centre of the structure.

Answer 878

A shift in the plane of division: auxins shift the normal plane of division almost 90° leading to periclinal divisions that make the embryo larger, and define the first separation of tissues in the embryo with the dermatogen becoming the main source of auxins.

Answer 879

This transforms the embryo from a sink to a source of auxins, thereby reversing the direction of travel of auxins, so they travel towards the bottom.

Answer 880

They are re-localised to the bottom of cells to channel auxins towards the bottom.

Answer 881

Mutant seedling unable to produce roots.

Answer 882

The gene for an ARF7 transcription factor, indicating the significance of auxins in root development.

Answer 883

A dominant mutation in iaa12/bodenlos, which causes loss of root development.

Answer 884

iaa12 represses ARF5. In the presence of auxins, iaa12 is degraded. However, the mutated iaa12 is dominant, so is not degraded by auxin.

Answer 885

The mutated iaa12 gene was fused to a known part of mammalian glucocorticoid receptor signalling. This protein keeps the iaa12 mutant protein sequestered outside the nucleus by interactiosn with heat shock proteins. Only in eth presence of glucocorticoids is there a change in conformation taht released the mutated iaa12/bodenlos protein from this complex, allowing it to enter the nucleus.

Answer 886

Through an RNA-seq/microarray, they identified plethora genes, genes unknown at the time, so were termed target of monopterus (TMO) genes and genes encoding PIN proteins. The effect of these on embryonic development was then tested.

Answer 887

Target of monopterus 7, an important transcription factor for defining the structures of the root and root cap.

Answer 888

First root cell in the embryo.

Answer 889

It requires auxin signalling, which is localised upstream, PIN proteins to create an auxin maximum and additional ARFs to specify the identity of the tissue.

Answer 890

Downstream of MP (monopterus)/ARF5, cell-to-cell diffusion of auxin and mobile transcription factors specifies the hypophysis.

Answer 891

Cytokinin production. Cytokinins then stimulate periclinal divisions. Targets important for stimulating periclinal division and developing the vasculature are found in the cells above the hypophysis.

Answer 892

When a triple mutant in the plethora genes was created, it had the same phenotype as the monopterus mutation-- absence of a root.

Answer 893

The SAM was converted to a RAM.

Answer 894

Generated early seedlings with a root at both the top and bottom, so Tpl is important for specifying the shoot identity.

Answer 895

PLETHORA and HD-ZIP III. HD-ZIP III is responsible for the shoot domain, and plethora genes are responsible for the root in the early embryo.

Answer 896

Forces the shoot apex to make a root.

Answer 897

HD-ZIP III was mutated, so that it's amino acid sequence doesn't change, but it was resistant to the miRNA. Hyperstable HD-ZIP III (mRNA) rescues the phenotype caused by PLETHORA hyperactivity. Expression of these TFs in the basal domain causes leaf production instead of roots.

Answer 898

Expression of homeotic genes Wuschel and WOX.

Answer 899

The Organising Centre (OC) of the SAM in Layer 3.

Answer 900

The mRNA is found in layer 3, whereas the protein is found in the other cell layers. This indicates that Wuschel is produced is in layer 3, then diffuses through the plasmodesmata to the other cell layers.

Answer 901

Generates larger meristems when mutated, and produces an excess of flowers. Opposite function to Wuschel.

Answer 902

In layers 1 and 2 when Wuschel stimulates its production.

Answer 903

… acts locally to reduce Wuschel expression. This helps to establish two separate domains.

Answer 904

The Organising Centre and Stem Cell Pool.

Answer 905

The receptor for the CLV3 peptide hormone.

Answer 906

Secreted peptides produced via translation and subsequent proteolytic trimming and additional modifications (e.g., sulfurylation, hydroxylation) to be perceived by membrane receptors to initiate a phosphorylation cascade that affects gene expression.

Answer 907

Shoot meristem-less When mutated, it displays early termination at the seedling stage of shoot activity, just like Wuschel.

Answer 908

At the periphery of the SAM.

Answer 909

Stm mainly acts in cytokinin synthesis and signalling, so add exogenous cytokinins, or add the gene for cytokinin biosynthesis with an stm promoter.

Answer 910

Specify primordial identity, and exclude stm expression.

Answer 911

…prevents ARP expression.

Answer 912

It prevents the early production of leaf primordia that would eat away at the available stem cells by creating domains when ARPs (transcription factors) aren't regulated.

Answer 913

Placed in a spiral. This was studied by removing incipient leaves with a laser.

Answer 914

… an area of suppression of new primordia is established in the area surrounding the new primordium.

Answer 915

Convergent localisation of PIN1 proteins that cabalise auxin towards the apex of the primordia.

Answer 916

It inactivates Stm expression, promotes proliferation and promotes expression of ARP genes for primordium identity.

Answer 917

Above a certain auxin threshold, PIN1 localisation is re-directed downwards in anticipation of new vasculature. This leads to an auxin minimum with high Stm activity, right before the maximum, to prevent the formation of primordia right next to each other.

Answer 918

In the region that remains meristematic for the longest.

Answer 919

Promote leaflet and lobe production.

Answer 920

… the shape of leaf primordia and leaflets. Auxin maxima, established via PIN proteins, eventually form leaflets.

Answer 921

Leaf primordia tend to be fully abaxialised.

Answer 922

Complete abaxialisation. PHANTASTICA is a HD-ZIP III gene.

Answer 923

Fully adaxialised genes were generated.

Answer 924

Two transcription factors are mutually antagonistic to separate the two developmental patterns.

Answer 925

Sandwiched between the KANADI and PHANTASTICA trancription factors. Required for leaf blade lateral expansion.

Answer 926

Already present in the embryo.

Answer 927

Elongation Zone.

Answer 928

Cell division over cell differentiation because you have to make new cells before they can eb differentiated. After a few days, they re-balance.

Answer 929

To detect gravity.

Answer 930

Generates a signalling cascade, and is perceived by a receptor that impacts WOX5, a wuschel transcription factor that's important for cell differentiation at the root cap.

Answer 931

You lose the activity of the undifferentiated, dividing cells root cap cells, just underneath the QC. Immediatley, meristem cells and cell expansion are lost.

Answer 932

Targets of monopterus.

Answer 933

Partly by directing auxin syntehsis and transport in the RAM.

Answer 934

Reduced root development and reduced auxin synthesis.

Answer 935

Diffusible transcription factors, diffusible small RNAs, auxin gradients and signalling peptide gradients.

Answer 936

GRAS-type and WOX-type transcription factors.

Answer 937

MicroRNA165/166 targets HD-ZIP III transcription factors.

Answer 938

Local IAA synthesis,a nd trasnport via PIN efflux and influx carriers

Answer 939

Transcription and translation, post-translation modification and export. Peptide signalling impacts PLETHORA activity, and thus, auxin synthesis.

Answer 940

Cytokinin production, and auxin activity minima.

Answer 941

To activate expansin genes, and decrease apoplastic pH to make the cell wall easier to expand. They also increase turgor pressure by increasing the uptake of water into the vacuole.

Answer 942

Cell wall-modifying enzymes such as expansins. Turgor pressure produced by water uptake into the vacuole. Direct constraints by cellulose fibrils placed perpendicular to the growth axis for longitudinal expansion.

Answer 943

The barrier in roots is characterised by suberinisation of the cell walls of the epidermis, so that they are impermeable as suberinisation makes them waterproof.

Answer 944

Cell wall system.

Answer 945

Cytoplasm system.

Answer 946

By suberin enrichment at the cell walls and lignin deposition (especially at junction between endodermis cells)-- the Casparian strip.

Answer 947

A diffusible signal from the edges of cortex cells. Root hair cells develop from cells in contact with two cortex cells because cortex cells typically release signalling molecules from their corners.

Answer 948

Organise the production of monolignols that need to be polymerised by peroxidase and NADPH oxidases to form lignin. It's an amorphous that's difficult to cross, if you're water or a pathogen.

Answer 949

Lateral primordia are specified early on, but lateral roots emerge quite late on.

Answer 950

Auxin maxima direct anticlinal and periclinal divisions to form the lateral root primordia. Auxin export into the above-lying cells softens their cell walls to enable penetration and emergence of the lateral roots.

Answer 951

Oscillations in auxins in the external cells of the stele. They are activated at a certain distance from the differentiation zone.

Answer 952

Most meristem types of a plant.

Answer 953

Molecular gradients.

Answer 954

Establishment of auxin maxima.

Answer 955

The intertwined activity of lots of transcriptional regulators.

Answer 956

… self-organising system.

Answer 957

Provides little more than the paternal genome.

Answer 958

By fertilisation.

Answer 959

Organelles, RNA and proteins and yolk (constituent molecules and energy supplies for synthesis and growth-- the nutrients).

Answer 960

The oocyte contents and the genome.

Answer 961

A form of cell division specific to the early embryo.

Answer 962

Occur perpendicular to each other through an axis.

Answer 963

By polar bodies.

Answer 964

The first divisions separate the left and right sides of the body. Typical, but not universal for bilaterians.

Answer 965

There are 2 cell divisions perpendicular to each other, but the 3rd is twisted at an angle either clockwise or anticlockwise to give spiral cleavage.

Answer 966

Sinistral.

Answer 967

Equal or unequal division.

Answer 968

The first 4 blastomeres are of similar size.

Answer 969

The blastomeres are of very different sizes. Blastomeres inhierit different-sized portions of the oocyte cytoplasm, which is exaggerated in unequal division. This has implications later in development for determining cell types.

Answer 970

The direction in which the shell coils.

Answer 971

By taking an embryo after 3 divsions, then moving around the top layer of cell, so it was in the other direction. This flipped their development.

Answer 972

… usually inversely correlates with the number of eggs she lays.

Answer 973

The whole cell divides.

Answer 974

Cell division is confined to just the top cell layer, which is an adaptation for extreme maternal nutrient provision. Occurs in embryos with a lot of yolk, thereby restricting cleavage. Seen in teleost fish.

Answer 975

Consists of a layer of cells on the outside (blastoderm) and a cavity in the middle (blastocoel).

Answer 976

Because the space it can take up is distorted by the yolk.

Answer 977

To enable gastrulation.

Answer 978

Cells move into the embryo to create a multi-layered embryo. This goes on to make the 3 germ layers in most animals.

Answer 979

Nervous system and epidermis.

Answer 980

Gut and associated digestive and respiratory systems.

Answer 981

Muscles, skeleton, excretory system and gonads.

Answer 982

Differentiation, pattern fomration and movemnet.

Answer 983

The process by which cells come to display a specific phenotype related to a specific set of functions.

Answer 984

The process of organising cells in time and space.

Answer 985

A.k.a. morphogenesis. Movement of cells or groups of cells to form shapes and structures. E.g., gastrulation and neural crest migration.

Answer 986

John Gurdon (1962) transplanted nuclei from tadpole epithelial cells into the enucleated oocytes of Xenopus laevis. Nobel Prize for Physiology and Medicine in 2012. Demonstrated that differentiated cells in thes eorgansism retained the genetic material to build a whole new organism.

Answer 987

The formation of muscle tissue from myoblast precursors. After cell division, cells align tehn fuse into myotubules to form a muscle fibre.

Answer 988

Encodes a bHLH transcription factor tahts atrts a cascade of gene expression. This is generic across the animal kingdom. Even in jellyfish, homologous myogenic genes are used to make muscles.

Answer 989

The existing phenotype is overriden, and the ecll is forced into the myoblast differentiation pathway. Add MyoD to a fibroblast in culture, which activates muscle genes, so that the fibroblast differentiates as a myoblast.

Answer 990

Encoding transcription factors have been identified for other cell types.

Answer 991

Lineage-dependent mechanisms and by organising fileds of cells.

Answer 992

Patterning by asymmetric cell division. Cells differentiate according to the axis of cell division. Some cells will get more cytoplasm than others, so will get more determinants.

Answer 993

Proteins or RNA that confer a property to cells.

Answer 994

Local patterns of differentiation when few cells are involved.

Answer 995

… almost the whole body is built by asymmetric cell division, such as in C. elegans, in which in adult hermaphrodite has 959 cells. It would be unfeasibly complex for animals with billions of cells.

Answer 996

Patterning by intercellular signalling.

Answer 997

Each cell has the potential to develop as blue, white or red. The position of each cell is defined by concentration of the morphogen. Positional value is interpreted by the cells which differentiate to form a pattern. Cells differentiate according to their position relative to a signal, irrespective of their lineage.

Answer 998

Point source release of a signal, then it diffuses away from the source. This means cells can determine their position in the embryo by how far away they are from the source based on the level of signal.

Answer 999

Maternal bicoid mRNA is anchored at the anterior end of the oocyte. When it is translated, the protein diffuses (as it is not anchored) , and forms a gradient. The protein activates different genes at different concentrations, leading to stripes of gene expression. This si the first step to making a segmented body in this species.

Answer 1000

Gene expression was shifted backwards. This is a gain of function experiment.

Answer 1001

Removing the bicoid gene by mutation. This removed the head and thorax, so it was just a large abdomen.

Answer 1002

The embryo began to start developing a head in the middle.

Answer 1003

A transcription factor. Transcription factors have to be able to enter the nucleus to get into the egg.

Answer 1004

It has syncytial early development: mitosis occurs, but there's no cytokinesis or cell membrane formation. Though after a while, cellularisation occurs, and cell membranes do form.

Answer 1005

Most animal embryos are fully cellular the whole time, so this process must occur by intercellular signalling.

Answer 1006

Patterning along embryo axes: the 3 axes are controlled by signals.

Answer 1007

Anterior-posterior, dorsal-ventral and mediolateral (left-right).

Answer 1008

Controls the anterior-posterior axis.

Answer 1009

Controls the dorsal-ventral axis.

Answer 1010

Two different signalling proteins secreted by some cells that diffuse through the extracellular matrix then bind to plasma membrane receptors. This triggers a signal transduction cascade in the cell that affects gene expression in the nucleus.

Answer 1011

… the cells don't differentiate. They change their internal specification (their gene expression and epigenetics) to give them a memory of the signal they've seen before. This is an intermediate transcriptional state.

Answer 1012

Cells acquire a positional identity relative to a signal without this immediately leading to differentiation, e.g., Hox genes.

Answer 1013

… cells have been given a position in the embryo, but they're not actively differentiating accordingly. They're just carrying that information on to the next stage in development.

Answer 1014

In overlapping domains along the anterior-posterior axis, and give identity to these domains.

Answer 1015

Biochemistry, and forward genetics.

Answer 1016

Generate fractionated extracts of biological tissue, then carry out enzyme assays to identify whether the proteins have roles in development. E.g., identified Bmp and FGF.

Answer 1017

Bone morphogenesis protein. First identified in fractionated, powdered bone in the 1970s, but it doesn’t just act in bone. An intercellular signalling protein.

Answer 1018

Fibroblast Growth Factor. Also an intercellular signalling protein. Causes cells in a culture to divide faster, so affects growth. It also controls other developmental processes. Extracted from the pituitary gland, first in the 1980s.

Answer 1019

Outside the cells, unlike transcription factors, so they're easier to study as you just have to add the proteins.

Answer 1020

Mutated strains of animals in which there are development defects, implying the mutation is in a gene that controls development.

Answer 1021

William Bateson (1894) Materials for the study of variegation with especial regard to the discontinuity in the development of species.

Answer 1022

This means the sperm carry different de novo mutations. The female is wildtype, so most of the mutations (as most are recessive) are hidden by heterozygosity in the offspring. To reveal the mutant phenotype, cross the offspring with each other a homozygous recessive individual is produced.

Answer 1023

The identification of 100s of genes controlling development. These were then mapped, and the genes carrying the mutations were cloned.

Answer 1024

Control of transcription (transcription factors and epigenetic modifiers). Intercellular communication (signalling, e,g., genes encoding signal molecule receptors).

Answer 1025

Most of the genes identified were conserveda cross different animals, where they performed similar functions. They were inherited from a common ancestor, so can be traced quite far back evolutionarily.

Answer 1026

The fraction of genes in an organism's genome whose products control development.

Answer 1027

Over 500 mya mostly in the Pre-Cambrian, and some in the Cambrian. It's an ancestral trait in most animals.

Answer 1028

Some lineages have lost these genes, and others have duplicated genes to create gene families. The earliest-diverging animals, such as Porifera, have fewer of these genes.

Answer 1029

A posterior signal: the anterior end gets low levels of Wnt signa, whilst the posterior end gets high levels of Wnt signal.

Answer 1030

Drosophila.

Answer 1031

Acts along the oral-aboral axis. Some use this to suggest that the rear-end/oral-end is homologous to a mouth.

Answer 1032

Wnt signalling works by controlling the nuclear import of the β-catenin protein. In some model species, this is what has been observed, rather than the Wnt signal itself. Wnt is also involved in the specification of the endoderm and mesoderm, which is linked to the anterior-posterior axis specification.

Answer 1033

The dorsal side.

Answer 1034

A ventral signal: it has a high level on the ventral side, and a low level on the dorsal side. It's not strictly on the ventral side; it's slightly skewed off.

Answer 1035

A dorsal signal: it's high on the dorsal side, and low on the ventral side. This has led to speculation on axis-inversion: the asymmetric distribution of the signal is a common trait, tehn the axis was inverted at some point in evolution, but the reality is likely simpler.

Answer 1036

Bmp signal is asymmetrically distributed/polarised in the animal. Cnidarians pre-date the evolution of bilateral symmetry, so why do they have Bmp signalling? It's unresolved, but it is evidnece that Bmp signalling evolved early on in animal evolution.

Answer 1037

Hox genes.

Answer 1038

Clusters of homologous genes in a tandem array. They encode transcription factors that bind to DNA through the Homeodomain. Expressed in subdomains along the anterior-posterior axis.

Answer 1039

The position of the gene in the chromosome predicts where it will be expressed along the anterior-posterior axis.

Answer 1040

Shared evolutionary ancestry.

Answer 1041

Wnt signalling.

Answer 1042

Even Cnidarians have a small cluster of Hox genes. Their evolution can be traced back to at least the common ancestor of the Cnidaria and Bilateria.

Answer 1043

Gene duplication. Either whole genome duplication, or tandem gene duplication

Answer 1044

Whole Genome Duplication. In early vertebrate evolution, the Hox gene cluster duplicated to give 4 clusters on different chromosomes.

Answer 1045

Creates linked copies of a gene. During meiotic recombination, slippage, or unequal crossover occurs. This means that, of the two gametes produced, one will have two copies of a gene, and the other will have 0 copies of that gene. If the gamete with two copies does the fertilisation, the offspring receives 2 copies. These are alleles at this point, but selection can act to fix it, so the gene is duplicated in the offspring.

Answer 1046

… most other genes display evolution by gene duplication and divergence.

Answer 1047

Changes in their protein-coding sequence, or by changes in their expression (a more significant route).

Answer 1048

HoxA2 and HoxA3 originally had the same sequence as they were derived by tandem duplication, but they diverged. Their sequences changed in the Homeodomain, so they can regulate different subsets of genes.

Answer 1049

Segmented, and derives from anterior-posterior segmented mesoderm.

Answer 1050

This is due to the changes in the distribution of Hox gene expression in different lineages. Hox gene expression boundraies, which control identity along the anterior-posterior axis, have shifted.

Answer 1051

Makes a thoracic vertebrae in a mouse, and a cervical vertebrae in a chicken.

Answer 1052

We can infer that this was due to changes in Hox gene expression boundaries.

Answer 1053

By re-using Hox gene systems.

Answer 1054

Forelimbs and hindlimbs start out as buds/outgrowths on the flank that grow out over days, weeks or months depending on the species to form organs. This evolved from a simpler system in the Devonian that formed the lobe fins of fish.

Answer 1055

Hoxa genes are found along the anterior-posterior axis, and Hoxd genes are found on the dorsal-ventral axis in limbs.

Answer 1056

Transcription factors bind to enhancers. The combination of those dictates when and where genes are expressed. This combinations can be changed.

Answer 1057

Enhancer sequences evolve, so that the binding of a transcription factor is lost, or another transcription factor can bind. Or a new transcription factor evolves by duplication and divergence to recognsie a new DNA sequence.

Answer 1058

This is modularity. Chnaging the module cahnge steh pattern of gene expression.

Answer 1059

Many genes have multiple different enhancers, so an enhancer can be evolved, whilst keeping the others stable.

Answer 1060

Its expression in a certain cell type could be reduced, increased or eliminated. It could also be expressed in a different cell type altogether, which means there is a signalling molecule that can affect cells quite a long distance away.

Answer 1061

Transcription factors tend to be tied to the differentiation of a certain cell type, so this could lead to the activation of the muscle program in a different place.

TT_Building_a_Phenotype Flashcards

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