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Plants & Microbial Sciences > Michaelmas > Flashcards

Michaelmas Flashcards

1
Q

Name a popular method for genetic modification

A

Transformation by A.tumefaciens, by using a Binary plasmid vector
Deactivating viral DNA in plasmid and replacing with useful

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2
Q

What and when was the Green Revolution?

A

1960s
Introduced dwarf species of wheat into agriculture to reduce the height and increase yields, by less energy being used to create stem and less chance of blowing over

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3
Q

List the essential components required for building a synthetic gene and briefly explain their functions.

A
  1. Control Sequences: Allow interaction between host TF, RNA pol, etc.
  2. Marker/Reporter Gene: Used to check the successful integration of the synthetic gene.
  3. Desired Genotypes: Specifies the desired genetic traits to be encoded.
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4
Q

Explain the process of transcription in eukaryotes

A

RNA Polymerase II: Binds to the TATA box but requires additional elements for transcription initiation.
Distal Promoter Elements/Enhancers: Essential for interacting with RNA Polymerase II and initiating transcription.

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5
Q

Outline the steps involved in pre-mRNA processing

A
  1. 5’ Capping: Promotes splicing and protects against degradation.
  2. Poly(A) Tail: Protects against degradation and improves translation efficiency.
  3. Splicing: Removal of introns (non-coding) by the Spliceosome.
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6
Q

Explain how Bacillus thuringiensis (Bt) toxins provide pest resistance

A
  • Produces toxins fatal to insects but not mammals.
  • Toxin ingestion leads to crystalline structure fragmentation.
  • Fragments bind to membrane receptors, forming a pore structure.
  • Heat shock proteins stabilize the expression of foreign genes
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7
Q

Describe the action of the herbicide glyphosate

A
  • Glyphosate inhibits the shikimate pathway in chloroplasts.
  • Results in the plant’s inability to synthesize essential aromatic compounds (phenylalanine).
  • Glyphosate moves effectively, killing the entire plant.
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8
Q

Describe the use of marker or reporter genes in visualizing the activity of foreign traits

A
  1. β-Glucuronidase Enzyme (GUS): Forms a deep blue precipitate.
  2. Green Fluorescent Protein (GFP): Emits green light and is non-toxic, used for distinguishing subcellular structures.
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9
Q

Explain the principles of fluorescence microscopy

A
  • Uses selective filtering for specific colors.
  • Excitation light targets chosen fluorophores.
  • Enables the visualization of specific colors in the sample.
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10
Q

Outline the principles and advantages of confocal microscopy

A
  • Uses a laser beam for illumination.
  • Builds an image by scanning the beam across the sample.
  • Fluorescence passes through a small aperture (confocal pinhole), excluding blur and improving image clarity.
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11
Q

Explain why complex traits do not follow simple Mendelian inheritance patterns.

A

Because multiple genes are involved, leading to many polygenic traits

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12
Q

Discuss how domestication has influenced phenotypic changes in plants

A

Decreases the gene pool, and loss of some genes
Selection for traits such as sweeter, colorful, and seedless fruits and vegetables.

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13
Q

Explain how the Brassica family showcases phenotypic changes arising from a common ancestor.

A
  • Derives from a common ancestor (wild mustard).
  • Phenotypic changes result from exaggerated features in floral buds or vegetative meristems.
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14
Q

List and briefly explain some common traits in crops that have been selected for

A
  • Determinate growth habit.
  • Synchronous ripening throughout the plant.
  • Lower content of bitter compounds.
  • Elimination of seeds.
  • Improved harvest.
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15
Q

Explain the targeted loss-of-gene function in Brassica napus (rapeseed) to prevent shattering and maintain oil yield.

A
  • Pods modified to prevent shattering.
  • Shattering caused by dessication and tension buildup.
  • Mutations like shatterproof1 and shatterproof2 lead to the loss of lignin and separation layers.
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16
Q

Explain the concept of pathway engineering, including the induction of positive-feedback regulatory loops, and provide an example.

A

Fusing a master regulator to a promoter to activate a positive feedback loop in hierarchical transcription cascades.

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17
Q

Describe the function and components of the Light Harvesting Complex in plants.

A
  • Contains pigment-protein complexes.
  • Funnels light to the reaction center.
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18
Q

Explain the role and components of the Reaction Centre in plants, particularly its connection to the Electron Transfer process.

A
  • Pigment-protein complexes with a special pair of chlorophyll.
  • Initiates the Electron Transfer process, to other photosystems.
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19
Q

Outline how Halobacteria capture light in high-salt environments, including the steps involved.

A
  1. Light captured by bacteriorhodopsin.
  2. Conformational change occurs.
  3. Proton from chromophore pushed out of the cell.
  4. Proton diffuses back in, aiding ATP synthesis.
    Differences to Plants:
    - Water is not split.
    - No electron transfer.
    - No Light Harvesting Complex (LHC) or Reaction Centre (RC).
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20
Q

Compare the similarities and differences between Purple Bacteria (Eubacteria) and plants

A

Similarities:
- Bacteriochlorophylls (BChls) in the LHC surround a Reaction Centre (RC).
- Structure of the reaction center similar to PSII.
Differences to Plants:
- BChls absorb a longer wavelength than chlorophyll.
- LHC structure differs from plants.
- Different source for electrons, not water

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21
Q

Describe the characteristics of Green Bacteria (Eubacteria), differentiating between Green Non-Sulphur and Green Sulphur types.

A

Green Non-Sulphur: Filamentous and facultatively aerobic.
Green Sulphur: Anaerobic environments, high salinity.
Similarities:
- Reaction center similar to PSI.
Differences to Plants:
- Form chlorosomes as an LHC.
- Receive electrons from H2S instead of water.

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22
Q

Explain the structure and composition of the Light Harvesting Complex (Chlorosomes) in Green Bacteria

A
  • Contains bacteriochlorophyll c, d, e.
  • Membrane extrinsic structure (chlorosomes), connected to the membrane by a base plate.
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23
Q

Provide information about Cyanobacteria, focusing on their role in the first oxygenic photosynthesis

A
  • First oxygenic photosynthesis 2.5 billion years ago.
  • Two types of LHC: Membrane Intrinsic LHC and Membrane Extrinsic LHC (Phycobilisomes).
    Differences to Plants:
  • Don’t possess chloroplasts.
  • May use bilins to harvest light (or chlorophylls).
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24
Q

Describe the structure and function of Phycobilisomes in Cyanobacteria, including their role in balancing excitation between PSI and PSII.

A

Phycobilisomes:
- Contain bilin to harvest light.
- Mobile on the surface to balance excitation between PSI and PSII.
Test: Bleaching by laser shows recovery of fluorescence in 30s.

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25
Q

Outline the two main hypotheses about the development of photosystems and their evolutionary relationships.

A
  • Two photosystems developed in a single organism, with the loss of one over time.
  • Two classes of photosystems developed independently, followed by genetic fusion or lateral transfer of genetic material.
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26
Q

Summarize the evolutionary derivation of PSII and PSI, and highlight their origins from different bacterial sources.

A
  • PSII derived from purple bacteria.
  • PSI derived from green sulfur bacteria or heliobacteria.
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27
Q

What evidence supports the theory that plastids in plants originated as a result of symbiosis?

A
  • Double membrane resembling cyanobacteria.
  • Double-stranded DNA, uncommon for organelles.
  • Promoters resembling prokaryotes (lacking TATA, having consensus sequences at -35 and -17).
  • 70S ribosomes like prokaryotes.
  • Division process similar to bacteria.
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28
Q

Explain the similarities (4) and differences (4) in the structure and components of chloroplasts in plants and cyanobacteria, highlighting the evidence for ancestral derivation

A

Similarities:
- Presence of plastocyanin in the thylakoid lumen.
- Thylakoid membranes containing Light Harvesting Complex (LHC) and Reaction Center (RC).
- Stroma
- Photosynthetic pigments
Differences:
- Fewer genes in chloroplasts (cDNA) compared to cyanobacteria (entire genome).
- Chloroplasts have additional strucures, such as starch granules
- Chloroplasts have larger more complex organelles
- Use different photopigments

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29
Q

How does the obligate parasitic plant Epifagus differ in terms of chloroplast characteristics?

A
  • An obligate parasitic plant.
  • Lost its photosynthesis genes.
  • Smaller chloroplast DNA (70kb) compared to non-parasitic plants (217kb in germaniums).
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30
Q

List examples of plant mutants affecting the number of chloroplasts

A
  1. Filamentous temperature sensitive (fts) gene: form long filaments at restrictive temperatures
  2. Minicell (MinD): Important in regulating cell division, can lead to the production of larger cells as no division ring is formed
  3. Cav1: unable to move chloroplasts in response to high light, so can lead to photobleaching
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31
Q

Name and describe three types of plastids, and what is the progenitor of plastids called?

A

Progenitor: Proplastid
Chloroplasts: Located in leaves, carry out photosynthesis.
Amyloplast: Stores starch.
Elaioplast: Stores oil.

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32
Q

How do chloroplasts exhibit signaling and movement, and what structures do they form for this purpose?

A

Form stomules (stroma-filled tubules).
Act as signaling structures and increase surface area (SA).

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33
Q

Outline the key processes in reaction centers (RCs) and the pigments involved in light harvesting.

A

RC processes:
- Electron transfer from donors and acceptors to PSI.
- Proton gradient across the membrane enables ATP synthesis.
Pigments:
- Chlorophyll and Carotenoids.
- Wavelength absorption differences in vitro and in vivo due to leaf structure.
- Emerson Enhancement effect requires both PSI (700nm) and PSII (680nm) for high photosynthesis rate

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34
Q

Describe the structure of chlorophyll and highlight the differences between Chlorophyll a, Chlorophyll b, and Bacteriochlorophyll.

A

Chlorophyll Structure:
- Porphyrin head with Mg and 4 N for delocalized electrons.
- Phytol chain for anchoring to the lipid membrane.
Differences:
- Chlorophyll b has a formyl group instead of methyl, increasing absorption of blue.
- Bacteriochlorophyll has fewer double bonds, absorbing longer wavelengths.

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35
Q

Explain the characteristics of Carotenoids and their role in light harvesting.

A
  • Triple banded absorption.
  • Alternating single and double bonds.
  • Serve in light harvesting and energy dissipation (NPQ)
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36
Q

How is light captured by Light Harvesting Complexes (LHCs), and what is Resonance Energy Transfer (RET)?

A
  1. Light energy raises from S1 to excited S1*.
  2. Energy is transferred by Resonance Energy Transfer (RET).
    Resonance Energy Transfer:
    - Transfers from chlorophylls to the special pair
    - Works for molecules in close proximity.
    - Depends on correct molecular orientation.
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37
Q

Describe the structure of Photosystem II (PSII) and its major components.

A
  • Major distal LHCs (L + M + S), form a trimeric shape, binding 60% of chlorophyll.
  • Minor distal LHCs are monomeric and bind fewer chlorophylls.
  • Inner antenna complex (CP47, CP43) binds 50 chlorophylls each.
  • PSII core is dimeric with mirror symmetry.
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38
Q

Explain the sequence of electron transfer in Photosystem II (PSII).

A
  1. Electron from the reaction center goes to pheophytin.
  2. Pheophytin transfers to Qa.
  3. Qa passes the electron to Qb and Plastoquinone.
  4. Plastoquinone attracts 2H+ and forms Plastoquinol (PQH2).
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39
Q

Describe the retrieval of electrons in Photosystem II (PSII), including the roles of P680*, tyrosine, and the manganese cluster.

A
  1. P680* oxidizes tyrosine.
  2. Tyrosine is reduced by the manganese cluster.
  3. Manganese gains electrons from the splitting of water.
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40
Q

What is the Oxygen Evolving Complex, and what is its structure?

A
  • Found in PSII
  • Splits water to form oxygen and protons (H+).
    -Structure: 4 Manganese and Calcium atoms.
  • Formation of oxygen requires 4 oxidation events.
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41
Q

Describe the experiment on dark-adapted algae and the conclusions drawn from the O2 yield.

A
  • Experiment to test how water is excited to produce oxygen
  • Flashes of light showed periodic O2 yield with a peak on the third flash.
  • Periodicity of 4 flashes.
    Conclusion:
    S rests in S1 state, and at S4 state, it releases oxygen (reached at the third flash).
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42
Q

Outline the electron transfer from PSII to PSI

A
  • Plastoquinol (PQH2) passes it Cytb6f complex
    THEN EITHER:
    1. Through Rieske protein’s Iron-sulfur clusters to Plastocyanin (PC) leading to PSI.
    2. To cytb563 where plastoquinone picks up 2H+, increasing the H+ gradient.
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43
Q

What is photoinhibition in photosynthesis, and what are its effects on plants?

A

Definition: Light-dependent reduction in the light-dependent reaction of photosynthesis. Occurs when light capture exceeds ATP and NADPH use by the CBB cycle.
Effects:
- Over-reduction of Electron Transport Chain (ETC) leading to PSII and D1 protein damage.
- Production of Reactive Oxygen Species (ROS) bleaching chlorophyll.
- Superoxide production leading to H2O2 formation, attacking lipids, nucleotides, and proteins.

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44
Q

What are the types of photoinhibition, and how do they differ in reversibility?

A
  1. Dynamic/Reversible/Protective Photoinhibition:
    - Reduces photosynthesis efficiency to avoid damage.
  2. Chronic Photoinhibition:
    - Greater damage that is expensive to repair.
    - Sometimes considered irreversible.
    - Associated with much lower rates of photosynthesis.
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45
Q

Explain the mechanisms of photoprotection in plants against photoinhibition.

A
  1. Leaf Structure
    - Shade leaves: Invest less in photoprotection.
    - Sun leaves: Invest more, are better protected from light.
  2. Energy Dissipation:
    - Non-photochemical quenching (NPQ): Conformational change and heat dissipation by carotenoids.
    - Xanthophyll cycle: Conversion from violaxanthin to zeaxanthin.
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46
Q

Describe the Xanthophyll Cycle and its positive attributes in photoprotection.

A
  • Converts violaxanthin to zeaxanthin by de-epoxidases.
  • Zeaxanthin is more photoprotective because it is less efficient at transferring energy
  • Higher xanthophyll to chlorophyll ratio in sun leaves.
  • Operates on a diurnal cycle.
  • Operates within minutes.
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47
Q

What genetic evidence supports photoprotection mechanisms in plants?

A
  1. Over-expression of β-carotene hydroxylase leads to more xanthophyll pigments, enhancing the response to light.
  2. Mutations in npq4 (PsBs) or npq1 (de-epoxidase) result in lower productivity.
    - PsBs is an important signalling receptor for NPQ, upregulation leads to better NPQ
    - Wild type (WT) performs significantly better under varied light intensity.
  3. Over-expression of xanthophyll cycle enzymes and PsbS improves the plant’s ability to track light fluctuations and enhances productivity.
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48
Q

Outline short-term avoidance mechanisms in plants to deal with excess light.

A
  1. Rapid Leaf Movements: Oxalis (shamrock) responds to excessive light by flipping down rapidly.
  2. Reflectance:
    - Changes in trichrome (hair) abundance responding to leaf moisture.
    e.g. Atriplex hymenelytra adjusts reflectance based on leaf moisture.
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49
Q

Explain the reason for long-term avoidance strategies in plants being changing leaf angle and leaf hairs.

A
  1. Leaf Angle:
    - Increases in response to less water.
    e.g. Grasses maintain a relatively angled position.
  2. Leaf Hairs:
    - More hairs increase reflectance.
    e.g. Encelia exhibits differences in hair abundance between moist habitats and desert environments. Farinosa in desert, Californica in moist habitats
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50
Q

What are slow and fast sunflecks, and how does canopy structure influence light absorption in plants?

A

Slow Sunflecks: Movement of the sun.
Fast Sunflecks: Rapid leaf fluttering.
Importance: Allows sunlight to reach the understorey canopy
Evidence - Adenocaulon bicolor (American trailplant):
-Measures the rate of assimilation.
- At low light levels, O2 production slightly exceeds O2 uptake for respiration.
- Flashes of light significantly increase assimilation rate.

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51
Q

What are heliotropism, diahelitropism, and parahelitropism, and how do they relate to light absorption?

A

Heliotropism: Tracking the sun.
Diahelitropism: Leaves that remain perpendicular to the sun’s rays to maximize light capture.
Parahelitropism: Leaves that remain parallel to the sun’s rays.
- Perpendicular orientation absorbs the greatest flux

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52
Q

How do plants respond to gap formation in the canopy?

A

Germinators: Shade-intolerant plants germinate when a gap forms.
Persistors: Shade-tolerant plants germinate and wait until a gap forms before developing.

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53
Q

What is an example of changes to flowering in response to canopy structure?

A

Blue bells flower in early spring, before leave on the trees begin to form and block out light
Characteristic indicates convergent evolution, where both monocot and dicot species adapt to grow in different seasons.

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54
Q

How does canopy structure, particularly Leaf Area Index (LAI), affect light absorption in plants?

A

Higher LAI in erectophiles like grasses that have leaves at a high angle, from horizontal
Changes in LAI during the Green Revolution have led to more gradual light attenuation, benefiting lower plants.

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55
Q

What factors influence photosynthetic capacity in plants?

A
  1. Leaf Angle: Varies within species depending on location.
  2. Leaf Nitrogen: Higher concentration in top canopy leaves.
  3. Leaf Age: Older leaves have a declining photosynthetic rate due to self-shading and resource re-allocation.
  4. Leaf Thickness: Affects gas diffusion, thicker leaves may be less efficient but retain light better.
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56
Q

How does leaf nitrogen concentration vary within the canopy, and what influences it?

A

-Higher concentrations in top canopy leaves due to higher productivity.
- More chlorophyll, which is nitrogen-rich.
Effect on Net Photosynthesis:
- Increasing leaf nitrogen increases net photosynthesis in some plants.

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57
Q

How does leaf aging influence the photosynthetic capacity of plants?

A
  • Maximum photosynthesis rate declines with age.
  • External factor: Reasons include self-shading and resource re-allocation to younger leaves.
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58
Q

What is the importance of leaf structure in determining photosynthetic capacity?

A
  • Leaf structure, including thickness, nitrogen content, angle, and age, is crucial in determining photosynthetic capacity.
  • Different combinations of these factors lead to compatible or incompatible outcomes.
    -For example, long-lived, thick leaves are subject to herbivory and are metabolically expensive, making them highly unlikely.
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59
Q

How do Triose Phosphate Translocators (TPT) function in the export of carbon from chloroplast to cytosol, and what evidence supports their mechanisms?

A
  • Transport mainly Triose Phosphates (TPs), derived from 3-PGA, exchanging TPs for Pi.
    Experiment sourcing 5C and 6C: shows specificity, TPT moves 3C, not 5C or 6C sugars.
  • Transports via a ping pong mechanism
    NOTE: TPT relays information about relative rates of photosynthesis and sucrose synthesis by transporting phosphate.
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60
Q

What are the steps in the production of sucrose from Triose Phosphates?

A
  1. Combination to form Fructose-1, 6-bisphosphate.
  2. Lose a Pi to become Fructose 6 phosphate (F6P).
  3. Conversion between glucoses to form Glucose-1-phosphate.
  4. Formation of UDP-glucose by UDP-G pyrophosphorylase.
  5. Conversion to sucrose by SPS and SPP
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61
Q

How is sucrose synthesis regulated?

A

– Inhibition of FBPase by F-2,6-BP:
1. Enzyme PFK II produces F-2,6-BP from F6P
2. PFKII is activated by Pi, and F6P, and inhibited by DHAP and 3PGA
- High concentrations of F-2,6-BP inhibit FBPase, reducing F6P production, and subsequently, UDP-Glucose.
- High F-2,6-BP concentrations occur at night.

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62
Q

What is the evidence for SPS and SPP?

A
  1. Supply of radio-labelled carbon and subsequent Electrophoresis showed the production pathway from UDP-glucose-> Sucrose P-> Sucrose
  2. Bifluorescence complementation- half of the GFP bound to SPS and the other to SPP. Binding and formation of the complex led to fluorescence being emitted
  3. Increase in one (e.g. SPP) led to the increase in the presence of the other SPS
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63
Q

What are the characteristics, uses, and molecular composition of starch?

A
  • Insoluble carbon store in algae and plants.
  • Has a very ordered structure.
    -Energy for seed germination.
  • Regrowth after fire or herbivory.
  • Food staples like maize, rice, potato, etc.
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64
Q

What is the structure of starch?

A

Made up of amylose and amylopectin
Amylose:
- α-1,4 glucan bonds.
- Few branches.
Amylopectin:
- α-1,4 glucan bonds and α-1,6 glucan bonds.
- Highly branched.

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65
Q

What are transitory and storage starch, and how is their synthesis controlled?

A

Transitory Starch: Generated in photosynthetic cells (chloroplasts).
-Main pathway involves ADPG pyrophosphorylase and starch synthase.
- Controlled by F-1,6-Bpase activity and sucrose synthesis rates.
Storage Starch:
- Generated in non-photosynthetic cells (amyloplasts in roots, etc.).
- Synthesis involves the formation and transport of hexose phosphate.
- Importance highlighted in mutants like shrunken1 maize with a mutation in sucrose synthase.
~~Sucrose synthesis and transport play crucial roles in controlling starch synthesis

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66
Q

What are the main pathways for the production of transitory starch, and what evidence supports the role of enzymes in this process?

A

Glucose 1-P → ADPglucose → α 1,4 glucan.
- Involves ADPG pyrophosphorylase (ADPG PPiase) and starch synthase.
Evidence: Single-point mutations in the gene encoding ADPG PPiase led to a significant reduction in starch production.

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67
Q

How is storage starch synthesized, and what is the importance of enzymes like sucrose synthase and invertase in this process?

A
  1. Degradation of sucrose to F-6-P initially by sucrose synthase/invertase.
  2. Transformation of UDPG to F6P via UDP-G PPiase.
  3. Hexose transported into plastid and converted to ADPG by ADPG PPiase, then to starch
    Transport into plastid: Membrane hexose-P translocator with strict counter-exchange with Pi.
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68
Q

What are fructans, and what is their significance in plants?

A

Water-soluble, non-reducing polymers of fructose.
- Synthesis induced by high sucrose levels.
- Implicated in cold and drought tolerance.
- Difficult to digest, used as a fiber supplement.

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69
Q

Describe the structure of lipids, their uses

A
  • Triacylglycerides (TAGs) or Triglycerides.
  • Glycerol backbone + 3 Fatty acid tails.
  • Produce more ATP per unit carbon compared to carbs.
    Uses:
  • 25% of dietary calories.
  • Biodiesel production through transesterification.
  • Lubricants
  • Energy storage for germination
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70
Q

Explain the synthesis of lipids, including the formation of the glycerol backbone and fatty acids

A

Glycerol Backbone Synthesis:
- From GAP and DHAP (formed by sucrose hydrolysis)
Fatty Acid Synthesis:
- From acetyl CoA through decarboxylation of pyruvate.
- Different lengths and C=C configurations give different properties.

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71
Q

Describe the synthesis of triacylglycerides (TAGs) and the enzymes involved in the transesterification process.

A

TAG Synthesis occurs at the ER
- Transesterification of 3 FAs onto glycerol backbone.
- Catalyzed by Acyltransferases (AT), including GPAT, LPAT, and DGAT.
- Sequentially added on by the three enzymes

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72
Q

How is fatty acid synthesis controlled, and what is the role of the transcription factor WRINKLED 1?

A

Transcription factor WRINKLED 1 (WRI1) regulates fatty acid synthesis.
+ acts as a master regulator
Evidence:
- wri1-1 mutants in Arabidopsis show low lipid content, leading to wrinkling.
- Overexpression of WRI1 in maize increases seed oil content.

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73
Q

Explain the storage of triacylglycerides (TAGs) and the mobilization process, including the involvement of glyoxysomes and the glyoxylate cycle.

A

Storage of TAGs: Oil bodies bud off the ER, having a monolayer of phospholipids encapsulating TAGs.
Mobilization Process (Glyoxylate Cycle):
1. Hydrolysis by lipase releases fatty acids from glycerol.
2. Glycerol is metabolized by glycolysis.
3. Fatty acids undergo β-oxidation and enter the Glyoxylate Cycle, which is more carbon-efficient than the TCA cycle.

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74
Q

How does the Glyoxylate Cycle link to gluconeogenesis, and what enzymes are involved?

A

Glyoxylate cycle is more carbon efficient and uses the enzymes
- Isocitrate Lyase
- Malate synthase
And forms a glyoxylate intermediate, from isocitrate, which bypasses the CO2 losing reactions in the TCA cycle
Link: Enzyme PEP carboxykinase produces phosphoenolpyruvate (PEP) from malate

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75
Q

What are glyoxysomes, and how is the Glyoxylate Cycle regulated for lipid mobilization?

A

Modified peroxisomes located next to oil bodies.
Regulation:
1. Coarse gene expression control, such as the master regulator WRINKLED 1.
2. Fast response to changes in lipid levels, leading to adjustments in enzyme activity.

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76
Q

What are the challenges in measuring photosynthesis?

A

Responsive to surroundings and affected by multiple factors.
Also its involvement with various other processes

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77
Q

Explain the use of chlorophyll fluorescence as a probe for photochemistry and the different pathways of excitation energy.

A

Excitation energy goes to 3 processes:
- Photochemistry
- Dissipation as heat (NPQ)
- Re-emission (fluorescence)

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78
Q

What did the Kautsky and Hirsch experiment demonstrate regarding fluorescence and the competing fates of absorbed light energy?

A

Competing Fates between fluorescence, photochemistry, and heat (NPQ) pathways.
The sum of these pathways always adds up to one.

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79
Q

What is fluorescence yield, and what are the parameters F0, Fm, Fm’ and ΦPSII?

A

Fo: Minimum fluorescence in a dark-adapted state.
Fm: Maximum fluorescence level, from base level.
Fm’: Max fluorescent yield after the first flash.
ΦPSII: Maximum PSII efficiency (effective quantum yield).
NPQ: Non-Photochemical Quenching.

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80
Q

How is ΦPSII, operating ΦPSII and NPQ calculated?

A

ΦPSII = (Fm - Fo) / Fm
NPQ = (Fm - Fm’) / Fm’
Operating ΦPSII = (Fm’ - Fo’) / Fm’

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81
Q

How do NPQ and PSII efficiency dynamically adjust in response to high light exposure?

A
  • Rate of change of ΦPSII efficiency decreases rapidly in high light.
  • Rate of change of NPQ activity is slower but still responsive to high light.
    – First exposure to light is when all reaction centres are open and NPQ not yet induced, so measures Fm, also used to test the health of a plant
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82
Q

Describe the relationship between [CO2] and ΦPSII, and how a decrease in CO2 affects ΦPSII.

A

Decrease in CO2 for the Calvin-Benson-Bassham (CBB) cycle leads to a decrease in ΦPSII.
More energy will be released via the NPQ or fluorescence pathway

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83
Q

How is CO2 assimilation and stomatal conductance measured, and what is the role of gas exchange cuvettes?

A
  • Enclose leaves in a gas exchange cuvette.
  • Measure gas composition before and after to determine steady-state rates of gas exchange.
  • Calculate net release by multiplying by flow rate and dividing by measured leaf area.
    REMEMBER: Need to standardize for the leaf area
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84
Q

How is gas exchange controlled, and what is the role of stomata and guard cells in this process?

A

Gas exchange controlled by the opening and closing of stomata.
Stomata are controlled by guard cells, which change due to turgor pressure

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85
Q

What are the potential biochemical limitations to photosynthesis?

A
  1. Diffusion rate
  2. Biochemistry
    - Rubisco capacity @low CO2 limiting
    - RuBP regeneration @intermediate CO2
    - Use of products @ high CO2 limiting
    By modelling A (CO2 assimilation) against [CO2] this eliminates the effect of diffusion
    Michaelis- Menten Graph plot shows how well the Rubsico limiting line fits for low CO2
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86
Q

Why is water transport crucial for photosynthesis, and how do changes in climate impact plant growth?

A

Crucial for photosynthesis
Important for nutrient transport
Deficiency leads to stunted growth

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87
Q

Describe the movement of water in the Soil-Plant-Atmosphere Continuum, and what influences water potential?

A
  • Water moves along the water potential (ψ) gradient.
  • Biggest change in ψ is due to water evaporation (from -3 to -30) at the leaf.
  • Water potential is influenced by osmotic pressure, matric potential, and solute potential.
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88
Q

Define water potential and its components, including osmotic pressure, matric potential, and solute potential.

A

Water Potential: Tendency for water to move.
Osmotic Pressure: Pressure required to stop the movement of pure water.
Matric Potential: Caused by adhesion of water molecules to non-dissolved structures.
Solute Potential: Chemical potential energy of water, numerically equivalent to osmotic pressure.

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89
Q

How does tissue withdraw water from the xylem, and what experiment is used to understand this process?

A

Tissue withdraws water by accumulating solutes, reducing water potential.
Experiment: Pressure bomb - cut stem, alter pressure until water comes out, pressure required equals tension in the stem holding water.

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90
Q

What is field capacity, and how does soil moisture availability affect plant wilting?

A

Field Capacity: Water retained in capillaries.
- Continuous water loss leads to wilting when matric potential is too negative.
- Dry soil has a strong negative matric potential.

91
Q

How does an increase in inorganic ions lead to root pressure, and what is the role of guttation?

A
  • Increase in inorganic ions drives water into the root steele, creating positive root pressure.
  • Guttation is the exuding of water onto the surface through hydathodes, aiding in temperature control, nutrient uptake, and maintaining turgor pressure. Usually occurs at night, different to morning dew because extruded from plant and not formed by condensation
92
Q

What is the role of guttation?

A
  • Temperature control
  • Repair cavitation
  • Maintain water flow
  • Maintain turgor pressure
93
Q
A
94
Q

How does increasing solute concentration combat decreasing water potential, and what are some examples of compatible solutes?

A

Increasing solute concentration makes water potential more negative.
Examples: Proline, glycine, mannitol - compatible solutes that don’t disrupt protein hydration.

95
Q

What are tracheids and vessels, and how does their structure influence water transport efficiency?

A

Tracheids: Long, thin, overlapping cells.
Vessels: Short, wider cells with perforated end plates.
Structure influences hydraulic conductance, with wider vessels being more efficient but potentially riskier.
- Gymnosperms (pines and conifers)

96
Q

How is hydraulic conductance related to vessel radius, and what is the seasonal variation in vessel diameter?

A

Hydraulic conductance is proportional to the fourth power of vessel radius (Poiseuille’s Law).
Seasonal variation includes wider vessels during growing seasons.

97
Q

What is cavitation, and what causes it? How is embolism related, and how do plants mitigate cavitation?

A

Cavitation: Formation of an air pocket, leading to water flow blockage.
Causes: High tension in the water column, freeze-thaw cycles, pathogens.
Emboli: Air bubbles blocking vessels.
- Plants mitigate cavitation through redundant vessels and the rate of embolism repair.

98
Q

How is gas forced back into solution during cavitation repair?

A
  1. Gas Repair: Gas is forced back into solution by increasing local pressures.
  2. Xylem Parenchyma: Provides ions and sucrose to xylem, lowering water potential.
  3. Pit Geometry: Ensures synchronous filling, preventing air bubble reforming.
99
Q

How do aquaporins control water movement in mesophyll cells, and why is this control important?

A

Aquaporins control water movement through mesophyll cells.
- Too much water in mesophyll cells can affect CO2 uptake. So control is required
Evidence: Inhibitors like mercuric chloride have effects similar to adding ABA.

100
Q

How can aquaporins aid in preventing excessive guttation fluid in mesophyll cells?

A

Aquaporins can close to prevent guttation fluid from flooding mesophyll cells.
This helps maintain proper water balance and prevents potential issues with CO2 uptake.

101
Q

What traits are strongly correlated with drought tolerance in plants?

A
  • Low stomatal conductance
  • Ability for osmotic adjustment
  • Hydraulic conductance
  • Turgor pressure
102
Q
A
103
Q

Describe the characteristics of Mediterranean vegetation and climate, including types of plants like sclerophylls and malacophylls.

A

Climate: Wet winters, dry summers.
Sclerophylls (Resprouters): Hard leaves, resprout after fire.
Malacophylls (Seeders): Soft leaves, regrow from seeds after fire.
Geophytes (Bulbs): Stay underground as bulbs to avoid drought.

104
Q

What does the Klimadiagramm show, and how is it interpreted?

A

Shows precipitation and temperature of a location.
If temperature exceeds precipitation, evaporation is high, indicating a dry climate.

105
Q

Compare the gas exchange characteristics of sclerophylls (resprouters) and malacophylls (seeders).

A

Sclerophylls
- Hard leaves
- Water savers
- Low CO2 assimilation
- Great WUE
Malacophylls
- Soft leaves
- Water spenders
- HighCO2 assimilation
- Low WUE

106
Q

What defines drylands, and how is the aridity index calculated?

A

Drylands: Areas with average rainfall less than potential moisture loss through evaporation and transpiration.
Aridity Index: Ratio of Precipitation (P) to Potential Evapotranspiration (PET)

107
Q

Define hyper-arid, semi-arid, and dry sub-humid areas, and provide examples.

A

Hyper-arid: Water deficit all year round, no crop growth without irrigation.
Semi-arid: Water deficit for most of the year, short periods of crop growth (e.g., Almeria, Spain).
Dry Sub-humid: Alternates between drought and excess water (e.g., Australia).

108
Q

What percentage of the world can be classified as dryland, and where are these regions primarily located?

A

47% of the world can be classified as dryland.
Especially prevalent between the Tropics.

109
Q

What are the effects of decreased water on canopy structure, and how does it impact plant characteristics?

A
  • Decreased plant density.
  • Reduction in plant height, affecting hydraulic conductance.
  • Multi-stemmed plants to avoid cavitation.
  • Shedding twigs or segmentation to prevent cavitation.
  • Increase in solute potential.
110
Q

How do plants in semi-arid environments tap into water reserves, and what are phreatophytes?

A

Water Tapping: Plants tap into groundwater reserves.
Phreatophytes: Plants like Boscia with deep roots (e.g., 68m underground in the Kalahari desert).

111
Q

Explain the concept of hydraulic lift and shift, and when does it occur?

A

Occurs at night when transpiration is suppressed.
- Water moves from groundwater storage into roots and up the plant.
- Soil is recharged as water moves out at night due to lower water potential in the soil
- During the day, transpiration occurs and water potential is lower in roots, so water moves back into the plant

112
Q

How is water use tracked using stable isotopes, and what natural markers are used?

A

Stable Isotopes: Changes in heavy and light O and H concentrations.
- Markers: Compared with the Standard Mean Oceanic Water (SMOW) (δ).
- Experiment: Water enriched with a heavy isotope, with evaporation revealing differences in isotopic composition based on temperature. As lighter is evaporated before

113
Q

How do succulents adapt to drought, and what strategies do they employ?

A

Drought Avoidance: Succulents store water to take advantage of short rain events.
Root Sensitivity: Roots are sensitive to soil water deficit.
Cortex Shrinkage: Cortex shrinks to isolate tissue.
Protection: Protect mature roots by cavitating new roots.

114
Q

What did Todd Dawson’s analysis of Acer saccharum twigs and nearby herbaceous plants reveal about water use?

A

Tree mainly used groundwater, tapping.
Evidence: Herbaceous Plants Analysis: Gradient in isotope ratio, plants closer to Acer saccharum used groundwater from hydraulic lift. So water is used by surrounding plants by soil being recharged

115
Q

How is the rate of starch regulated, why is it important?

A

Rate of breakdown controlled by diurnal cycles
- Altered by day and night length
- Important to ensure store doesn’t run out over night

116
Q

How does mineral availability in soil depend on soil horizons, and what is Cation Exchange Capacity (CEC)?

A

Layers of soil influenced by bedrock and weathering.
Breakdown of organic matter contributes to humic content
- Soil is negatively charged, binding to cations.
- Influenced by size, pH, and humic content.
- Larger particles have greater CEC.

117
Q

What are macronutrients and micronutrients, and what are the uses of various nutrients in plants?

A

Macronutrients: Required in high concentration (e.g., N, P, K).
Micronutrients: Required in small amounts (e.g., Fe, Boron).
K+, Ca2+, Mn, Mg2+: Osmotic relations, signaling, cofactors.
Fe, Zn, Cu: Redox reactions.

118
Q

Explain the dose-response relationship and the concept of critical concentration in plant nutrition.

A

Too low: Deficiency (e.g., Ca2+ cork spot).
Perfect: Adequate zone.
Too high: Toxicity (e.g., leaf tip necrosis in barley).
Critical Concentration at 10% reduction in growth, past that leads to rapid recline

119
Q

How is mineral uptake species-specific, and what does an experiment with Avenella and Urtica reveal?

A

Adequate zones vary between species.
- Avenella (common in deficient soils) grows well at low phosphate concentrations.
- Urtica (nettle) grows better at increasing concentrations, while Avenella saturates early.

120
Q

Describe apoplastic flow, symplastic flow, and coupled-transcellular pathways in nutrient uptake.

A

Apoplastic Flow:
- Travels in the aqueous phase.
- Blocked by exodermis.
Symplastic Flow:
- Travels in cells via plasmodesmata.
- Not blocked by endodermis.
Coupled-Transcellular Pathway:
- Influx and efflux protein transporters.
- Movement in and out of cells.

121
Q

How is hormonal control involved in the movement of nutrients, regulatedby suberin deposition in the endodermis?

A

ABA promotes deposition of suberin, Ethylene promotes suberin removal.
- Suberinization (deposition of suberin) is hormonally controlled.
Endodermis: Contains Casparian strip and suberin lamellae.

122
Q

Differentiate between low affinity transporters (LATS) and high affinity transporters (HATS)

A

LATS: channels, present at high concentrations
HATS: Antiporters and symporters, activated when concentrations are low

123
Q

What are the essential uses of potassium (K+) in plants?

A
  1. Ribosome Function: Crucial for ribosome activity.
  2. Metabolism (Pyruvate Kinase): Involved in metabolic processes.
  3. Osmotic Relations: Plays a role in maintaining osmotic balance.
    Deficiency: Leads to increased vulnerability to infections.
124
Q

Describe the basic movements of potassium (K+) in different soil concentrations.

A

High Soil [K+]:
- Passive movement into root epidermis.
- Active movement into the vacuole.
Low Soil [K+]:
- Active movement into root epidermis.
- Active movement out of the vacuole into the cytosol.

125
Q

Describe the functional domains of the H+ ATPase

A

Sets pH gradient, used for secondary active transport.
Functional Domains:
N = binds to ATP.
R = regulatory, phosphorylation leads to activation and 14-3-3 protein binding.

126
Q

How does the HAK5 transporter contribute to potassium (K+) uptake during K+ depletion?

A

Active transporter.
Allows movement of K+.
Negative charge also transports Caesium.

~During low concentrations, demonstrated by experiments with Rb+ (a K+ tracer) and changes in pH.

127
Q

Describe the mechanism of potassium (K+) uptake from K+-replete soils, focusing on AKT1.

A
  • Inward rectifier channel.
  • Passes K+ better inward than
    outward.
    Experiment: Patch clamp electrophysiology.
128
Q

Explain the roles of SKOR in loading xylem and unloading phloem, with insights from experiments.

A

SKOR (Stelar K Outward Rectifier):
- Atskor mutant shows reduced K+ accumulation in the shoot.
- Promotes unloading into sink tissues
- Promotes loading into the xylem

129
Q

Explain the role of vacuolar transport in potassium (K+) accumulation, especially under replete conditions.

A

Critical for osmotic relations.
- Involves H+ ATPase, NHX1/2 antiporters, and V-PPase.
- Graphs illustrate differences in vacuolar K+ content between WT and mutants.

130
Q

Describe the role of TPK1 in the release of potassium (K+) and the factors influencing its activation.

A
  • Activated by Ca2+ and 14-3-3 proteins.
  • Acts as a dimer on the tonoplast.
  • Not able to release during K+ starvation.

~~ Involved in the release of potassium from vacuoles

131
Q

What triggers K+ retention in roots, and how is K+ sensing and triggering regulated?

A

Triggers: Ethylene production inhibits elongation and triggers HAK5.
Low K+:
- Increased suberin deposition in the endodermis.
- Downregulation of SKOR (less xylem unloading).
- ABA responses.

132
Q

What are the essential roles of nitrogen in plants?

A

Amino Acids: Fundamental building blocks of proteins.
Nucleotides: Key components of DNA and RNA.
Secondary Metabolites: Various compounds contributing to plant physiology.

133
Q

What are the characteristics and effects of nitrogen deprivation in plants?

A
  • Stunted Growth: Impaired overall plant development.
  • Decreased Photosynthetic Capacity: Reduction in the ability to perform photosynthesis.
    -Chlorosis: Yellowing of leaves due to insufficient chlorophyll.
  • Poor Grain Quality: Affects the quality of harvested grains.
134
Q

How is nitrogen fixed, and what is the role of Nitrogenase?

A

Nitrogen to Nitrate: Nitrogenase, found in diazotrophs like Rhizobia and Cyanobacteria.
Examples: Rhizobia (legumes) and Cyanobacteria are bacteria involved in nitrogen fixation.
- Or via nitroplast Coale et al., 2024

135
Q

Describe the different forms of nitrogen uptake and the associated transporters.

A

Acidic (ammonium, amino acids),
Higher pH (nitrate)
Arctic soils (amino acids)

Nitrate Transporters: NRT1 (Low affinity), NRT2 (High affinity).
Ammonium Uptake: Involves AMT family (HAT and LAT).
Amino Acid and Urea Uptake: Mediated by specific transporters.

136
Q

Outline the steps involved in nitrate assimilation.

A

Nitrate → Nitrite:
- Nitrate Reductase: Transfers electrons from NADPH or NADH.
- Components: FAD, Cytochrome b557, Molybdopterin.
Nitrite → Ammonium:
- Nitrite Reductase: Contains Fe-S clusters and Siroheme, found in plastids.

137
Q

What is the GS-GOGAT cycle, and how does it facilitate nitrogen assimilation into amino acids?

A

Glutamine Synthetase (GS): Converts ammonium and glutamate to glutamine.
GOGAT: Transaminase enzymes facilitate the transfer of amine (NH2) to an oxo acid.
Regeneration: Allows glutamate to be regenerated for reincorporation into the cycle.

~~Crucial for incorporating nitrogen into amino acids in plants.

138
Q

How is nitrogen stored in plants, and what are the different storage forms?

A

Short Term Storage:
- Excess stored in vacuole via H+/NO3- antiporter.
Medium Term Storage:
- Protein and non-protein amino acids like Asparagine and Canavanine.
Long Term Storage:
- High molecular weight proteins (e.g., Globulins in legumes, Prolamins in cereals).

139
Q

Explain how nitrogen is remobilized in plants and its significance.

A

Break down into amino acids and nitrate.
Annual Plants: Up to 90% of nitrogen remobilized to seeds, controlled by NRT1 and NRT2.

140
Q

How is nitrogen reassimilated in plants, particularly after remobilization?

A

GS in Cytosol: Captures ammonium from remobilization.
GS in Chloroplast: Captures ammonium released during photorespiration.
Reassimilation involves capturing released ammonium and incorporating it back into nitrogen metabolism.

141
Q

Describe the interplay between carbon and nitrogen in plants.

A
  • Importance for Nitrogen Fixation: Carbon skeletons crucial for nitrogen fixation.
  • Rubisco and Nitrogen: Nitrogen essential for Rubisco activity, required for carbon fixation.
  • Loss of Nitrogen: Occurs during photorespiration.
142
Q

What are the advantages and disadvantages of using nitrogenous fertilizers in agriculture?

A

Adv- Increases yield, averts hunger crisis
Diasdv- environmental pollution, energy intensive (Harber-process)

143
Q

What are the essential roles and uses of phosphorus (Pi) in plants?

A
  • Energy Stores: Found in ADP and ATP molecules.
  • Phospholipids: Constituent of cell membranes.
  • Nucleic Acids: Essential for the structure of RNA and DNA.
  • Protein Regulation: Involves phosphorylation of enzymes and transporters.
144
Q

How is phosphorus stored in plants, and what are the storage forms?

A

Phytate in Seeds: Storage form of phosphorus in seeds.
Polyphosphates in Vacuole: Another form of phosphorus storage in the vacuole.

145
Q

What are the consequences of phosphorus deprivation in plants?

A

Low Metabolism: Leads to stunted growth.
Chlorosis: Results in yellowing of leaves.
Sulpholipids: Substituted for phospholipids in membranes.
Poor Frost Resistance: Impaired ability to withstand frost.

146
Q

How is phosphorus remobilized in plants, and in what form?

A

Phosphorus is mobilized in the form of phosphate anions during nutrient redistribution.

147
Q

What factors affect the availability of phosphorus in soils?

A
  1. Binding Elements: Phosphorus is bound to iron, aluminum, and calcium in soils.
  2. Optimal pH: Neutral pH enhances phosphorus availability.
148
Q

How can phosphorus availability be increased in soils?

A

Microbial Activity: Microbes secrete phosphatase to release phosphate.
NPK Fertilizer: Although harmful to the environment, it can increase phosphorus availability.

149
Q

What are the mechanisms through which plants acquire phosphorus?

A
  1. Mycorrhizal Symbiosis: Aims to move out of the depletion zone created by roots.
  2. Root Architecture Changes (Cluster Roots): Formation of cluster roots, controlled by auxin patterning.
  3. Root Architecture Changes (Basal Roots): Increase in basal roots to move out of the depletion zone.
150
Q

How do Brassicas, like Arabidopsis, sense, signaland respond (4) phosphorus deprivation?

A
  1. Sensing: LPR multicopper oxidases in the root cap ER are involved in sensing low phosphorus levels causes Fe- mediated ROS production
  2. Response:
    - Involves cessation of root growth
    - increased lateral root production
    - Malate secretion
    - Callose deposition.
  3. Signaling: Auxin plays a role in changing root structure in response to phosphorus levels.
151
Q

What are some key genes involved in the response to phosphorus deprivation in Arabidopsis?

A
  1. Master Regulator: PHR1 (Phosphate Starvation Response):
    - Upregulates high-affinity Pi symporters (Pht1 and Pht4).
  2. High Affinity H+ Symporters (Pht1 and Pht4):
    - Found on root hair cells and secrete H+ to increase soil acidity.
  3. Transport of Transporters to Membrane (PHF1):
    - Facilitates the transport of Pht1 and Pht4 to the plasma membrane from the ER.
  4. Xylem Loading (Aided by PHO1):
    - PHO2 is a negative regulator suppressed by PHR1 via microRNAs.
152
Q

What changes in phosphate movement occur from the vacuole in deprivation conditions?

A
  • Transporters (VPE1 and VPE2) found in rice
  • Double mutant leads to greater conc of Pi in vacuole
  • Increase in expression of transporters in Pi deficiency
    (Xu et al., 2019)
153
Q

How is phosphorus deprivation signaling coordinated between shoots and roots?

A

Cytokinin and Phosphate Signaling Reduction in Shoots
Stimulates changes in root architecture and nutrient uptake.

154
Q

What is the importance of sulfur in plants, and how is it assimilated?

A

Essential for photosynthesis, respiration, and cell membrane structure.
Assimilation: SO4²- is taken up via H+ symporters, assimilated into cysteine, and stored as glutathione.
Can also replace Phosphate when Pi levels are low to form sulpholipids

155
Q

What are the primary roles of iron (Fe) in plant physiology?(4)

A
  1. Efficient Electron Acceptor: Iron efficiently accepts electrons in various cellular processes.
  2. Enzyme Cofactor: Serves as a crucial cofactor for enzymes involved in respiration and photosynthesis.
  3. Haem and Fe-S Clusters: Iron is stored in haem (siroheme) and Fe-S clusters, primarily in chloroplasts.
  4. Fenton Catalyst: In its free form, iron acts as a Fenton catalyst, catalyzing the production of hydroxyl radicals.
156
Q

How is iron stored in plant cells (4)?

A

Ferretin (Seeds): Captures iron to prevent cytosolic toxicity, predominantly located in plastids.
Vacuole: Iron is stored and loaded into the vacuole by VIT1 and FPN2 transporters.
Apoplast: Iron is also stored in the apoplast, bound to pectin.
Chelation: Chelated to form phytate and stored in seeds of cereals.

157
Q

What are the consequences of iron deficiency in plants?

A

Chlorophyll Synthesis Inhibition: Impairs the synthesis of chlorophyll.
Stunted Growth: Results in overall growth inhibition.
Nitrogen Assimilation Impairment: Affects nitrogen assimilation processes.
Vein Chlorosis: Leads to yellowing of leaf veins.

158
Q

What factors influence the concentration of iron in plants, and what is the optimal pH for iron availability?

A

Optimal pH: Around 6.5 for iron availability.
Rhizosphere Acidification: Root H+ ATPases secrete H+ to acidify the rhizosphere, enhancing iron solubility.

159
Q

What is the iron uptake strategy employed by dicots and non-graminaceous monocots e.g. Arabidopsis and tomatoes?

A
  1. Rhizosphere Acidification (AHA2): Root H+ ATPases secrete H+ to acidify the rhizosphere.
  2. Iron Solubilization: This acidification solubilizes Fe3+ in the soil.
  3. Phenolic Chelators: Phenolic chelators are secreted to bind to iron.
  4. Ferric Chelate Reduction (FRO2): Membrane-bound Fe3 reductases reduce ferric chelate.
  5. Iron Uptake (IRT1): Fe2+ is transported into the cytosol.
    Connorton et al., 2017
160
Q

How do grasses, including monocots, employ a different strategy for iron uptake?

A
  1. Chelator Secretion(TOM1): Grasses secrete chelators like Nicotianamine (NA) to capture Fe3+
  2. Specific Transporters (YS1): Fe3+ is taken up by specific transporters like
    - Take up (Fe+) can also be via IRT1 directly
    - Or apoplastically through the Casparian strip in Fe deficiency
    Connorton et al., 2017
161
Q

How is iron transported and taken up by plant cells?

A
  • Xylem Transport: Chelated to citrate for transport into the xylem.
  • Chloroplast Uptake: Utilizes the CIP1 permease for incorporation into chloroplasts.
  • Plastids: Involved in the incorporation of iron into haem and Fe-S clusters, e.g., ferredoxin.
162
Q

How is iron remobilized in plants, especially during deprivation?

A

ABA signalling (stress)
1. Vacuole
- In VIT1
- Out NRAMP3/4
2. Ferritin degradation
= Bound to Nicotianamine (NA) when in Fe2+ state in symplast

163
Q

How is iron interlinked with sulfur, phosphorus, and abscisic acid (ABA) in plant physiology?

A

Balancing S and Fe: Required for forming Fe-S clusters.
Fe and S Interplay: High Fe induces S efflux via SULTR transporters; low S decreases Fe uptake by Ferretin.
ABA Role: ABA alleviates chlorosis by promoting Fe uptake

164
Q

What is the importance of boron in plants, and how is it taken up?

A

Essential for wall integrity and rigidity, binding to pectins.

Uptake: As H(BO)3, via NIP channels; transported through Casparian strip via BOR transporters.

165
Q

What are the consequences of boron deficiency and toxicity in plants?

A

Deficiency: Leads to stunted growth and male sterility, upregulates transporters.
Toxicity: Causes leaf necrosis and root growth inhibition, involves ubiquitination for transporter endocytosis.

166
Q

What differences are observed in the boron uptake of Sahara and Clipper Barley?

A

Sahara Barley: Shows greater boron efflux from roots and less in shoots, indicating efficient transporter (BOT1) activity.
Clipper Barley: Accumulates more boron in leaf blades, potentially reaching toxic levels and inhibiting growth.

167
Q

What insights were gained from QTL analysis comparing Sahara and Clipper Barley boron efflux?

A

BOT1 Efficiency: Sahara BOT1 is a more efficient transporter than Clipper BOT1, differing in only 2 amino acids.
QTL analysis reveals the genetic basis of boron uptake efficiency and its impact on plant tolerance.

168
Q

What are the economical consequences of water deficit and drought in plants?

A
  • Threat to Food Security: Results in an average annual loss of $123 billion, impacting 1/3 of global food production on irrigated land.
  • Yield Reduction: A 40% reduction in water availability leads to a 20-30% reduction in wheat and maize yields.
169
Q

What are the consequences of water deficiency in plants, particularly regarding photosynthesis? (5)

A
  • Inhibition of Photosynthesis: Due to stomatal closure.
  • Increase in ROS: Resulting from decreased photosynthesis.
  • Cellular Damage: Caused by reactive oxygen species (ROS).
  • Reduced Growth: Due to lower water potentials.
  • Reduced Nutrient Uptake: Resulting from reduced transpiration efficiency.
170
Q

List the three main strategies employed by plants to resist drought.

A
  • Drought Escape: Involves early maturity, rapid plant development, and seasonal growth.
  • Drought Avoidance: Aims to maintain optimal water content through mechanisms like stomatal closure and changing leaf structure.
  • Drought Tolerance: Focuses on minimizing damage, utilizing strategies like osmotic adjustment and antioxidant defense mechanisms.
171
Q

What are the key features of drought escape strategies in plants?

A
  • Early Maturity: Accelerated plant maturation.
  • Rapid Plant Development: Swift growth to complete the life cycle quickly.
  • Seasonal Growth: Adaptation of growth patterns to specific seasons.
172
Q

How do plants employ drought avoidance mechanisms to maintain optimal water content?

A
  • Minimize Water Loss: Achieved through stomatal closure (reduced transpiration) and leaf rolling.
  • Changing Leaf Structure: Structural modifications to reduce water loss.
  • Increased Water Uptake: Enhanced water uptake from roots, often involving deeper primary roots and minimal lateral roots.
173
Q

What strategies do plants employ to minimize damage and exhibit drought tolerance?

A
  • Osmotic Adjustment: Inclusion of compatible solutes in roots to lower water potential and drive water uptake.
  • Compatible Solute Examples: Mannitol, proline, glycine.
  • Antioxidant Defense Mechanisms: Utilization of carotenoids, ROS-detoxifying enzymes, and Late Embryo Abundant (LEA) proteins.
174
Q

How do plants benefit from symbiosis with arbuscular mycorrhizal fungi?

A

Arbuscular Mycorrhizal Fungi: Form symbiotic relationships with plants.
Evidence: Confocal microscopy analyzes the location of fungi.
Benefits: Bring phosphate and nitrogen to the plant in exchange for carbon.

175
Q

What are the key mechanisms involved in plants sensing and signaling during water deficit?

A
  • Osmotic Sensing: Changes in concentrations lead to conformational changes in receptors like histidine kinase.
  • Mechanosensitive Channel: Turgor pressure changes activate mechanosensitive channels like calcium-permeable channel (OSCA1).
  • Cell Wall Integrity: Changes in turgor pressure affect cell wall integrity, triggering responses like protein detachment (e.g., CrLK).
176
Q

How does abscisic acid (ABA) contribute to the plant’s response to drought?

A

Increase in ABA: Leads to stomatal closure.
Plastid Release: ABA is released from plastids in the roots.
Guard Cell Action: Acts on guard cells to regulate stomatal aperture.

177
Q

How does drought impact transcriptional activation in plants, and what is an example of a transcription factor involved?

A

Enhancer Binding: Binding to enhancers increases transcription of proteins related to drought tolerance.
Example: DREB (Drought Responsive Element-Binding) is a transcription factor involved.

178
Q

Provide examples of crops developed for drought resilience and describe one of them.

A

Sahbhagi Dhan (SD) Rice:
- Developed through conventional breeding, altering flowering times to avoid drought.
Kindandan Patong (KP) Rice:
- Develops deeper roots with a greater root angle to enhance water uptake.
- Changes are attributed to different expression of DRO1 (Deep Root1).

179
Q

Define flooding and highlight its significance in terms of food security.

A

Flooding: An area covered with excess water, impacting plant growth.
Food Security: Flooding accounts for 9% of overall hazards, reducing nutrient availability and posing a threat to food production.

180
Q

What are the problems associated with flooding, particularly in terms of diffusion rates and gas levels?

A

Reduced Diffusion Rates: Hindered movement of gases and nutrients.
- Reduced CO2 Levels: Leads to decreased photosynthesis.
- Reduced O2 Levels: Result in a lack of anaerobic respiration, causing anoxia.

181
Q

Outline the three main strategies employed by plants to resist flooding.

A

Escape: Altering the timing of the growth cycle, such as flowering before flooding.
Avoidance: Involves adaptations in root development, shoot development, and metabolic adjustments.
Tolerance: Includes metabolic adjustments, fermentation, and the use of antioxidants to counteract damage from reactive oxygen species (ROS).

182
Q

How do plants sense excess water, and what is the downstream effect?

A

Sensing Oxygen Levels: Leads to the accumulation of ethylene
- lack of oxidation of cysteine on ERF- VII
- lack of arginine addition
- No ubiquitination by E3 ligase
Increase Ethylene: increases GA

183
Q

What transcription factor is involved in the response to excess water, and how is its activity regulated?

A

Transcription Factor: Ethylene responsive factor group VII (ERF-VII).

Regulation: Under normal oxygen conditions, ERF-VII is degraded by plant cysteine oxidases (PCO).

184
Q

How do the plant hormones ethylene and gibberellins contribute to the response to flooding?

A

Ethylene: A gaseous hormone promoting fruit ripening; its diffusion is reduced during flooding.
Gibberellins: Promote cell elongation, contributing to shoot development.

185
Q

Provide examples of crops with improved resilience to flooding and describe one of them.

A

Deep-water Rice (Escape):
- Rapidly elongating stems, activated by ethylene.
- Ideal for long-term steadily rising flood climates.
- Increased gene expression of SD1 and Snorkel 1/2 in deepwater rice

186
Q

Describe the submergence tolerance strategy in plants and provide an example.

A
  • SUB1 is activated, triggering DELLA, inhibiting elongation.
  • Ideal for short-term (14days) climate changes like flash flooding
187
Q

Explain the role of DELLA in the plant’s response to flooding.

A

DELLA: Binds the transcription factor that promotes elongation.
- GA binds to DELLA, leading to its degradation.

188
Q

How do plants deal with the production of harmful ROS?

A

Secretion of anti-oxidants

189
Q

How does the pH of the thylakoid lumen function as a regulator of photoprotective responses?

A
  • pH correlates to the concentration of H+
  • A H+ gradient is important in the functioning of ATPsynthase
  • Requires a greater concentration of H+ in the thylakoid lumen, which then moves to the stroma of the chloroplast
  • H+ is also required to activate PsbS to trigger NPQ when excess light hits the cell
190
Q

Why do plants have such large gene families for mineral transporters?

A

-Different transporters for different affinities, different conc such as HAK5 and AKT1
- Many minerals are required and they can have different charges and be of different sizes, Phosphate, Nitrate, K+, etc.
- Expression on different membranes as part of uptake and storage, e.g. transporters on the tonoplast are different to transporters on the cell membrane
- Greater family allows for greater diversity and ability to adapt

191
Q

Explain how the leaf traits of Mediterranean plants reflect their climate.

A
  • Sclerophyllous leaves (thick and leathery) = against desiccation
  • Small leaves - reduce water loss
  • Succelence - store water in stem
  • Leaf rolling - prevent transpiration
  • Aromatic compounds to protect the plant from excess light
192
Q

How does a diversity of transporters help plants acquire nitrogen?

A
  • Low and high concentrations, varying high and low affinity transporters
  • Encode for H+ ATPases as well, that drive secondary active transport
  • NRT1 = low affinity, and NRT2 = high affinity
  • Can transport different forms of nitrogen compounds, nitrate, ammonium, urea, peptides etc.
193
Q

If a root were experiencing S deprivation, how would it adapt its Fe nutrition and why?

A
  • Alter Fe as a main use of Fe is in Fe-S clusters
  • So matching of content needs to be generated
  • Achieved by regulating siderophore production
  • Changes to root architecture to match S conc
194
Q

How does potassium reach the root xylem?

A

Deplete soils
HAK5 - high affinity uptake, coupled with H+
Replete soils
AKT1 - low affinity uptake
- Movement symplastic (cytoplasm) or apopastically
SKOR - outward rectifying channels that move K+ into the xylem

195
Q

Boron has the narrowest concentration range between deficient and toxic levels in soils. How do plants cope?

A
  • Sequester into vacuoles to reduce toxicity e.g. via BOR1 transporters
  • Selective transporter to block uptake
196
Q

How were mutants and transgenic plants used in the elucidation of the biosynthesis of starch? (3)

A
  1. Shrunken maize- reduced starch synthesis led to small, wrinkled kernels
  2. Sucrose mutants- reduced production of starch, because of knock on reduction in fructose and UDP-G
  3. Starch synthase mutant - build up of ADPG, but no starch
197
Q

How does the photosynthetic apparatus of land plants and photosynthetic bacteria
differ?

A

Pigments
- Land plants use cholorophyll
- Bacteria use bacteriochlorophyll, bacteriorhodopsin and bilins (cyano)
Source of e-
- Land plants (H2O)
- Many bacteria (H2S), or cyano (H2O)
Photosystems
- Land plants PSI and PSII
- Bacteria mainly one PS that harvest light e.g. GSB and purple, except cyano

198
Q

How does the pH of the thylakoid lumen function as a regulator of photoprotective responses?

A
  1. Protonation of PsbS regulates NPQ activation
  2. Regulates activity of enzymes in Xanthophyll cycle
    - de-epoxidases (VDE) for zeaxanthin
  3. Signals stress as pH gradient is present in ETC
199
Q

How do measurements of water potential and hydraulic conductance help to define tolerance of plant groups to water deficits?

A

Hydraulic conductance
- Measure of ease of water movement
- Higher = more drought tolerant
- Maintain turgor pressure
Water potential
- Used to locate source of water
- Drought tolerant able to maintain, to drive water movement

200
Q

What are ‘degree-days’ and why are they useful when assessing plant responses to temperature?

A
  • Measurement to quantify heat accumulation and the effect on development
  • Used to predicting effect on germination, flowering etc.
  • Monitoring the effects of climate change
  • Comparative analysis for different regions or years
201
Q

Describe the functional elements of an Agrobacterium tumor-inducing plasmid.

A
  • OR – origin replication
  • OriT – origin for T-DNA transfer
  • Vir region – facilitates transfer of T-DNA into the plant, via T4SS
  • T-DNA section that is inserted, which causes pathology
  • Selectable markers – ensure and check that transformation has occurred
202
Q

What is in the chloroplast stroma?

A
  • H+ ions among others
  • Rubisco enzymes
  • Ribosomes
  • Chloroplast genome
  • mRNA
  • Starch granules
203
Q

How are the levels of SPS and SPP regulated?

A
  1. Post-translational
    - Phoshorylation leads to inactivation
  2. Allosteric
    Pi - inhibitory
    G6P - activator
  3. Coregulation - due to complementation of proteins
  4. Hormonal
    - Cytokining promote, ABA supress
204
Q

Describe two ways in which plants manage the risk of cavitation.

A
  1. Hydraulic lift
    - Deep roots to tap into groundwater sources and maintain flow of water
  2. Tracheids (gymnosperms)
    - Narrow to prevent risk of cavitation
    - Bordered pits to prevent runaway cavitation, by allowing them to be sealed off
  3. Osmotic adjustment
    - Control the production of solutes to ensure efficient and consistent water flow occurs
205
Q

How do measurements of water potential and hydraulic conductance help to define tolerance of plant groups to water deficits?

A

Water potential
- Lower better, can drive more water in from drier soils
- Due to osmotic adjustment
Hydraulic conductance
- Higher means easier water movement
- Increases risk of cavitation

206
Q

What is xylem cavitation and how is it repaired?

A

Cavitation- Water flow is blocked due to an air embolism
Repair
- Increase in compatible solutes, lowers water potential
- Xylem formation
- Lignin deposition (prevent)
- Hydraulic segmentation to prevent spread

207
Q

Describe the characteristics of sclerophylls.

A
  • Thick cuticle
  • High lignin content (leathery)
  • Few stomata
  • Higher water use efficiency (WUE)
208
Q

Describe the characteristics of malacophylls

A
  • Low water use efficiency
  • Soft thin, larger leaves
  • Abundant mesophyll cells for photosynthesis
209
Q

Compare cavitation in dry and cold habitats for plants.

A

DRY
- Caused by increased tension which increases air bubble formation
- Adapt by hydraulic segregation and deeper roots
COLD
- Freeze-thaw embolisation, due to freezing and melting forming air bubbles
- Narrow vessels and anti-freeze proteins

210
Q

What transport proteins are involved in the movement of Na+?

A

NHX1 (tonoplast)
- Na+ moved in in exchange for H+
SOS1 (plasma membrane)
- Antiporter moves Na+ out
HKT1 (plasma membrane)
- HA transporter moving Na+ in

211
Q

What is the difference between amylopectin and amylose?

A

Amylose
- 1,4 glycosidic bonds
- Coiled structure
- Long term store
Amylopectin
- 1,6 and 1,4 glycosidic bonds
- More soluble
- Branched structure
- Readily accessible

212
Q

What is the evidence that starch is synthesized via starch synthase rather than starch phosphorylase?

A

Genetic evidence
- Mutants led to reduced starch, increase in ADPG
- Overexpression led to greater starch
Enzymatic activity
- Detected in tissues that are producing starch

213
Q

What is branching enzyme, and how was the gene encoding it discovered?

A

Catalyses formation of 1,6 glycosidic bonds for amylopectin
Discovery
- Mutants and sequencing via PCR to identify changes

214
Q

What is the evidence for the existence of glyoxysomes?

A
  1. Electron microscopy
  2. Genetic (mutants)
    - defects in fatty acid metabolism
  3. Biochemical isolation
    - isolate enzymes involved in the cycle (MS and IL)
215
Q

What is the difference between fine and coarse control of enzyme activity? Give an example of each.

A

Fine - Rapid, reversible modifications
e.g. allosteric or Pi
- Regulation of PFK allosterically by ATP and citrate
Coarse- Change in enzyme conc through expression and synthesis
- porin expression OmpC and OmpF, in differing concentrations

216
Q

Why do elevated concentrations of atmospheric CO2 only lead to a transient stimulation of the rate of net photosynthesis?

A
  1. Limiting factors
    - Other limiting factors such as RuBP regeneration
    - Rate of Rubisco
  2. Acclimation
    - Downregulate to counteract initial stimulation
  3. Feedback inhibition
    - No increase in demand so no increase in production
    - Avoid large accumulation of solutes
217
Q

What is the evidence that chloroplasts can be moved within leaf cells, and why is this movement important?

A

Cav1 mutant - unable to move chloroplast in response to high blue light
- Microscopy can be used to localise the chloroplasts
Importance
- Prevent photodamage
- Optimise photosynthetic efficiency e.g. during shading

218
Q

How does the photosynthetic apparatus of land plants and photosynthetic bacteria differ?

A
  1. Location
    Land plants located in chloroplasts that specialised organelles
    Bacteria located on the plasma cell membrane
  2. Pigment
    Land plants - use chlorophyll
    Bacteria - use bilins, bacteriochlorophyll and bacteriorhodopsin
  3. Photosynthetic systems (PS)
    Land = have PSII and PSI
    Bacteria = Cyano has both, purple has PSII similarity and GSB has PSI similarity
  4. Source of e-
    Land = water to produce oxygen
    Bacteria = H2S mainly, except Cyano
219
Q

Summarize the organisation of photosystem II proteins and how this allows resonance energy transfer and then photochemistry. (4)

A

Reaction centre with D1 and D2 proteins
Light harvesting around (containing pigments)
1. Become excited
2. Able to pass on excited to the P680 in the RC
3. E- transfer in ETC
4. energy released when e- transferred drives movement of protons for ATP synthesis

220
Q

How are carotenoids useful?

A
  1. Light harvesting
  2. Photoprotection
    - inefficient energy transfer
  3. Precursor to hormones
  4. Antioxidant activity
221
Q

What are the advantages and disadvantages for a plant to store triglycerides in their seeds rather than just starch?

A

Adv
- Other form of energy store
- More efficient store, higher energy content per gram
- Require less water for storage
- Good long term store
Disadv
- Requires specific enzymes
- Complex metabolism pathway

222
Q

How is the F-1,6-Bpase (FBPase) regulated in the chloroplast?

A

Redox of the disulphide bond by ferredoxin
- Light = reduction = no S-S = active and vice versa

223
Q

How is the production of starch and sucrose linked?

A
  1. Triose C usage
    - Decrease in sucrose synthesis leads to increase in starch synthesis
  2. Sucrose conc
    - Used to form storage starch
  3. Pi changes
    - Release of Pi from Sucrose, alters 3PGA:Pi which alters rate of ADPG PPiase
  4. Diurnal cycles
    - Starch breakdown at night to form sucrose, sucrose formed throughout
224
Q

List examples of the role of Pi as an allosteric regulator

A
  1. SPS
    - Pi of Serine158 leads to inactivation
  2. F-2,6-BPase
    - Increase in Pi leads to inactivation
  3. AGP-ase
    - Increase leads to decrease in production of ADPG
  4. PHF1
    - Decrease in Pi, promotes its action of transporting transporters to the membrane
  5. Ph transporters
    - Deficiency leads to increase in HAT (Pht1 and Pht4)

Plants & Microbial Sciences (4 decks)

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