Bio FInal

Plasmodesmata

Intercellular pores between to neighboring plant cell walls that allow for transport and cytoplasmic continuity. They are about 30x larger than gap junctions. Gating can affect the pore size. They are located within pit fields of the secondary cell wall.

Pectin

A polysaccharide, structural molecule found within plant cell walls.

Cellulose

A linear polymer of glucose molecules (differs from starch and others which are highly branches) that has H bonding between each “chain” making it extremely strong

Cell Wall Formation

1) Vesicles come together “coalesce” at the cell plate

2) Vesicles form the middle lamella, which will be the oldest part of the cell wall

3) Cell wall material is secreted

Plant Genome

Has many duplicated genes but fewer repetitive genes than the human genome.

Cell Wall Composition

This organelles is 25-30% cellulose, 40-55% other polysaccharides and 1-15% of proteins.

Cellulose Microfibril

A specialized plant microfibril that is an H-bonding of 30-250 linear chains of cellulose, each chain of cellulose can be between 25,000 and 2,000 linked glucose (glc) molecules

Nodes

The points on where leaves are attached. The area between two of these is known as the internode.

Apical Buds

The part of the shoot tip where growth occurs. This is the location of the apical meristem, a specialized type of tissue that ordinates more cells.

Axillary bud

A type of bud that can originate lateral growth and contains an lateral meristem. Forms a petiole (where leaf or leaves come off) or can also form thorns.

Dermal Tissue

The outer protective covering (skin) of the plants and forms the first line of defense from damage and pathogens.

Epidermis

In non-woody plants a single layer of tissue of tightly packed cells that forms the dermal tissue. It has a waxy line called the cuticle that prevents water loss.

Xylem

“______ Up” Is an integral part of the plants Vascular system. It is composed of two types of cells in angiosperms and some gymnosperms: The tracheid cells and vessel element cells.

Angiosperms

Flowering plants

Gymnosperms

Trees that often produce cones, name means “naked seeds” also includes Ginkgo and others.

Apolastic movement

Movement within a plant through dead cells or intercellular space (between cell walls rather than through a cytoplasm)

Tracheids

Long, thin, tapered cells of the xylem that allow water to move up through the plant via tension. There are small pits (pit fields) that allow the water to move through without having to diffuse through a secondary wall.

Vessel elements

Shorter, thin walled, end to end cells that form long pipes and are much larger than the tracheid’s. Cell walls have plates with perforations that allows water to freely flow from one cell to the next.

Vascular Cambrium

Adds vascular tissue, such as the xylem within the plant. Cells duplicate increasing the radius of the plant, growing outward. The _____ ________ will be the oldest with younger cells on both sides

Cork Cambrium

Adds cork/bark tissue, but unlike the the vascular cambrium only adds them on the outwards side of the cork cambrium.

Xylem Control

These vessels for upward water movement can control their flow rate by salt content within the sap. In a classic experiment, when potassium is injected the flow rate greatly increases, then drops off after a short plateau.

Root Hairs

The first step in the process of water absorbtion, these increase the surface area on a root and allow for absorption.

Casparian Strip

A “waxy gasket” in the endodermis that prevent apoplastic movement of water and minerals into the stele.

Stele

The center vascular tissue inside of a root

Countertransport

________transport uses gradients of ions to move ions across a membrane, even if its across the potential. A proton pump pumps H+ ions across the membrane, and this increase of gradient on one side allows K+ ions to move to the other side through a potassium channel (even if there is more potassium on the other side). Since both are positive the + charge is equilibrated on both sides.

Symport

This type of transport uses a pH gradient and moves H+ ions and Cl- anion from one side the cell to the other by use of a ____port protein, which has seperate channels for the H+ and Cl-

Stomata

These are small holes in the lead that despite being 1-2% of leaf surface account for \~95% of water loss within the plant. If the plant needs less CO2 uptake, there will be less of these

Guard Cells

These cells line the opening of a stomata. When they are turgid they are open, and allow water to flow out of them, and when they are flacid they are closed. This is controlled by K+ ions and H+ proton pumps. There is a lack of aquaporins to prevent a “short circuit”. ABA can also cause closure.

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Opening and closing

\-Light or low CO2 causes opening

\-High CO2 or low water (ABA) causes closing

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Plant Action Potentials

These are 2-100x longer than their counterparts in animals. K+ efflux or Cl- influx drives hyperpolarization. H+ efflux establishes a resting potential. K+ influx causes depolarization (remember, this is the resting potential becoming less negative and more positive)

Sink

A ___ is the part of the plant where carbohydrates are deposited after being produced by a source. It is usually new leafs or other growing parts of the plants, but never a large part of the plant

Dual-Osmometer Model

This model is used to explain how carbohydrates seemingly flow against their gradient in the phloem. Water enters through the membrane at the source and because the tube has positive pressure it is forced through to the sink where the membrane is more permeable. There is always more solute at the source, but this differential permeable membrane system causes flow towards the sink. Can also be called a pressure flow system

Sieve tube element

Unlike tracheid’s and vessel elements, these are alive at maturity. They serve as the major conducting cell of the phloem and are capped by sieve plates with many pores. While alive, they are metabolically inactive and have almost no organelles. Next to them is a companion cell

Companion cells

Cells next to the sieve tube elements that are metabolically active and have wall invaginations to increase surface area.

Cotransporter

More simple than a countertransporter. Uses an H+ gradient on the outside the the sieve tube elements to cotransport sucrose, a neutral molecule, into the cytoplasm of the sieve tube element/member

Phloem Sap

_____ Sap is the fluid inside of the that is usually under pressure do to the pressure flow system and cotransport of sucrose into the fluid. This differs from the xylem sap which is usually under tensions from the transpiration of water out and cohesion. It moves at around 1m per hour compared to 45m per hour of xlyem sap.

Stroma

Not to be confused with Stoma(ta), this is the fluid found within the double membrane of a chloroplast. It surrounds the thylakoids. Stroma is the sight of the so-called “dark reactions” which should really be called the light-independent reactions (calvin cycle).

Granum/Grana (plural)

A stack of thylakoids. Inside the thylakoids, is the thylakoid space which contains the pigment chlorophyll. The thylakoid membranes are the sight of the misnamed “light reactions”

Mesophyll

The tissue of the internal part of the leaf where photosynthesis is mostly conducted.

Van Niel Equation

This Stanford Professor used photosynthetic bacteria, and photosynthetic hydrogen sulfide bacteria to come up with the theory that O2 produced in photosynthesis came from the splitting of water for the H+ rather than CO2. This was later confirmed using radioactively tagged water.

Chlorophyll (pigment)

This is a type of pigment with two main types, A and B which absorb in the BLUE and RED ranges returning back GREEN to the eye. They serve as the major pigments within chloroplasts.

Accessory Pigments

These are types of pigments that absorb in wavelengths other than what Chlorophyll A and B are. Cartenoids and Phycobilins may absorb in the more blue-green spectra or red-orange spectra making photosynthesis possible under unusual wavelengths. They may also be involved in photoprotection.

Porphyrin Ring

The ______ ring is a ring of alternating double and single bonds within a chlorophyll pigment that allows for light absorbtion.

Chlorophyll (structure)

The chlorophyll has a porphyrin ring which is the main center for light absorbtion. In addition to this it has a long hydrocarbon tail which helps to anchor it in the apoprotein.

Apoprotein

This protein hold 13-15 pigment molecules hydrocarbon tails and helps to make up the light harvesting complex.

Photosystem

A reaction center complex ( the central pair of pigment chlorophyll A and an electron acceptor) is surrounded by the light-harvesting complex (many types of pigments, including carotenoids, chlorophyll A and B). There is about 200 chlorophyll A & B and 50 cartenoids.

Light Harvesting Complex

The protein surrounding the reaction center complex protein which contains multiple types of pigments - including chlorophyll A and B and other carotenoids. Acts as an antenna for the reaction center complex and energy is transferred from pigment to pigment

Reaction Center complex

The ________ is surrounded by the light harvesting complex and contains the primary electron acceptor. Due to the molecular bits of the reaction center complex the pair of chlorophyll A’s can excite an electron to the electron acceptor in a redox reaction. This is the first step on the light reaction

Chemiosmotic ATP Synthesis

The steps of this process is

1) Increase the potential energy of an electron

2) Use this to create a pH gradient

3) Use this pH gradient to drive ATP synthesis

ATP Synthase

This transmembrane protein is present in both plants and eukaryote cells. It is driven by a proton gradient that flows past the “turbines” and makes ATP.

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In plants the H+ comes from the electron transport chain of the Z Scheme and some from the splitting of water to replace the electron in PSII (which comes first in the Z scheme)

Z Scheme

1) Light strikes the light harvesting center and does “the wave”

2) Light excites an electron of the reaction center complex

3) This electron is accepted by the primary electron acceptor

4) H2O is split by an enzyme and an electron fills the whole within P680. It also creates 2H which power ATP synthase. The O’s combine to make O2

5) The electron flows through the electron transport chain, which creates an H+ gradient inside the thylakoid space (1000x more H+ than outside. This will drive ATP synthase)

6) PSI (P700) is excited by light

7) The electron from PSI is accepted by the primary electron acceptor

8) The electron flowing down the ETC fills the gap in the P700

9) The primary electron acceptor of PSI goes down a secondary electron chain and through protein Fd (ferrodoxin)

10) Fd can be used to turn NADP+ into NADPH with 2 electrons and help from the enzyme NADP+ reductase.

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Advantages

\-Produces extra H+ in the thylakoid space due to water splitting

\-Produces NADPH which is needed for the “dark reactions”

Cyclic electron flow

Much more simple than the Z-Scheme

1) Photon strikes Photosystem I, exciting an electron into the primary electron acceptor

2) This electron flows into Fd, protein Ferrodoxin

3) This electron flows through the Cytochrome complex and Pc (part of the ETC in the z scheme too) producing ATP but no O2 or NADPH

4) returns to the P700 and fills the elctron hole

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Advantages

\- Works well in very high sunlight

\-May be evolutionary lefotover

\-Doesnt produce NADPH, which helps to balance the ration as MORE ATP is used the NADPH (but NADPH is still very important!!!!!)

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Cons

\-Shaded plants cannot do this well

\-No NADPH

Calvin Cycle

Steps:

1) 3 CO2 enters and is added to RuBP by the abundant protein Rubisco, this forms a 6 carbon intermediate that it immediatley breaks down into the 3 carbon known as 3PG, not to be confused with (G3P)

2) Using 6 ATP the 3PG (3-Phosphoglycerate) is converted into 1,3-Biphosphoglycerate, which in turn 6 NADPH reduce into 6 \*\*\*\***G3P**\*\*\*\*\*. One G3P is removed, which is is half of one glucose (G3P is also a sugar) The remaining 5 G3P go onto the next step

3) In a series of even more complex reaction the G3P is regenerated by 3 ATP into the 5 carbon RuBP which was the starting point for this all

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Totals

3 CO2 go in

1 G3P comes out

6 + 3 ATP used = 9 ATP

6 NADH used

Per glucose = 18 ATP and 12 NADH per 6 CO2

\*Sometimes there is a 1 turn model that uses 1 CO2, in which case 6 turns cause 1 glucose, consume 3 ATP and 2 NADHP

3PG

This is the first compound to be created from the Calvin-Benson cycle and is a 3 Carbon compound. It is made by using carbon from CO2 and the precursors RuBP which is catalyzed by the enzyme RUBISCO. Since no ATP is used here, this carbohydrate can accumulate in the dark but the compounds following it will not be made. It ISSSSSS dependant on CO2 however.

Rubisco

Catalyzes RuBP into 3PG (3-Phosphoglycerate)

1,3-Bisphosphoglycerate

This 3 carbon intermediate is formed following 6ATP reaction with 3PG but prior to the reaction with the 6 NADPH

Glyceraldehyde 3-phosphate (G3P)

The starting point for the creation of other carbohydrates, and one of the most important molecules to know from the calvin-benson cycle. This molecule is created after 1,3-Bipohophoglycerate is rescued by 6NADPH. When 3CO2 go in, 6 G3P are created and only ONE is pulled out

RuBP

This molecule is created after the remaining 5 G3P come into contact with another 3 ATP. it will be the precursor for 3PG which is catalyzed by Rubisco. Can also have an interaction with O2 also catalyzed by Rubisco.

Photorespiration

This happens in hot/arid climates where stomata close and O2 builds up in the plant. Rubisco can join O2 to RuBP (called an Oxygenase reaction) which leads to a molecule called Glycolate. To deal with Glycolate it must be diffused to the peroxisome. This process results in use of ATP (respiration) and release of CO2, which is net harm to the plant. It makes NO SUGAR either.

Bundle Sheath Cells

Part of the Kranz anatomy, these are cells that are ringed and tighly packed around the vessels within the leaf. And kranz anatomy also has the mesophyll cells packed tightly around these cells.

C4 Fixation

This fixation pathway uses PEP Carboxylase which doesnt have any affinity for O2 and a very high afinity for CO2. Through a series of molecules it stores CO2 into a 4 carbon molecule which can be sent to the bundle sheath cells to be processed like normal, using the C3 pathway. It is separating the process spacialy. Rather than RuBP the primary CO2 accepter is PEP (hense pep carboxylase).

CAM Fixation

Like C4 Fixation it uses PEP Carboxylase to produce 4C compound. At night the stomata are open and allow CO2 to enter the plant which is fixed by PEP Carboxylase. During the day this 4C can act as the CO2 needed when the stomata are closed to prevent water loss and can go through the C3 pathway to produce sugar. Rather than RuBP the primary CO2 accepter is PEP (hense pep carboxylase).

Phytohormons

Hormones made by plants that regulate growth, death, reproduction, and death through genetically programmed options

Classical Hormones

Auxin (IAA), Cytokinin (Ck), Gibberellin (GA), Abscisic Acid (ABA), Ethylene

Hormone pathways

1) Signal response pathway in which a single receptor binds to a single hormone and through this a pathway lets of a single response

2) Branching pathway: A single hormone bonds to a single receptor, but partway through the pathway splits into two (or more?) and leads to at least two responses

3) Cross talk pathway: Two different receptors and hormones leads to the same genetic response

4) Different receptor: Different receptor of the same hormone (say the hormone in signal response) leads to a different pathway and a different response

Phytohormone Cell Surface Recognition

Recognition here may involve two different possible signaling pathways. The first is a phosphorylation cascade, where a Phosphate from ADP is added onto an inactivated protein kinase in multiple series to finally activate a protein and lead to a cellular response. The second way is through G-proteins and secondary messengers such as Calcium channels gated by IP3 (a secondary messenger)

Gametogenesis

The process by which haploid male and female gametes are formed

Fertilization

Fusion of the male and female gametes (pollen and ovum) to form the diploid zygote

Embryogenesis

This is the development of the seed from the time it is fertilized to the time of dormancy. The basic body plan is laid out.

Plant Embryo

This is the lifestage following fertilization. It is the mini plant encased in the endosperm and maternal tissue. The zygote develops first a suspensor, then into a heart stage embryo. The torpedo shaped embryo is last and contains the basic body plan. This includes the cotyledons (mini leaves), root apex, suspensor etc.

Double fertilization

When fertilization occurs both the double polar nuclei is fertilized, which will become the 3n endosperm, similarly the egg is fertilized to form the 2n embryo.

Embryo Developmental Stages

1. Fertilization and embryogenesis, develop into mini plant with a basic body plan and organs needed for growth. Hormones auxin, gibberellin, and Cytokinins are active

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\-The hormone auxin in embryonic formation drives pattern formation and differentiation. Without it you would not get the distinct organs we see inside the plant.

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1. The seed accumulates reserves. The only hormone active is ABA. The seed has its highest water content.
2. The seed desiccates enters developmental arrest. Loses most of its water
3. Reserve mobilization. When the time is right GA will be released (which promotes amylase activity) and causes the mobilization of starch into sugar within the seed.

Cotyledon

An embryonic leaf of plants

Plant Maternal Tissue

Seed development happens within the plants maternal tissue, which sometimes is enlarged to protect and nourish the seed. As laymen we call this fleshy bit the fruit. This fruit helps to aid in seed dispersal (if animals eat it). Like seed development, fruit development needs

\-A seed

\-Hormons IAA (auxin), GA (giberellins) and cytokininins

\-In absence of a seed, very high auxin levels can still promote a fruit

\-Ripening is stimulated by ethylene

Classical hormone functions in seed development

\-IAA (Auxin) is used in early embryogenesis for cell/organ differentiation

\-GA, CK are used in nutrition of early embryo in addition to fruit development with auxin

\-ABA is used for reserve accumulation and in preperation for dessication

\-GA is used for breaking down reserves and releasing them to the plant and ABA works antagonistically to this

\-Ethylene works to ripen fruit

Etioliation

Physical adaptions for growing in darkness. Elongated stem, lack of chlorophyll, long weak stems, pale yellow color.

De-etiolation

Informally known as greening, when an etiolated plant reaches the light stem elongation slows, leaves expands, and greening occurs.

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\-Leaves expand

\-Stem elongation is inhibited or slows down

\-Chloroplast develop thylakoid stacks (grana) which are filled with chlorophyll

\-Genes involved with photosynthesis are induced

Secondary Messengers

Small molecules or ions that amplify a signal from a receptor and carry it to the proteins or nucleus that will initiate a gene response. Some examples are Ca2+ which can increase 100x in the cell and cyclic GMP (cGMP)

Gibberellic Acid (Seed)

This hormone, in seeds, is responsible for both reserve mobilization and germination. It, when released by the embryo travels into the aleurone where alpha amylase is made. Alpha amylase causes hydrolyzation of the starch in the endosperm which produces glucose that is then used by the embryo in growth.

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*IMPORTANT* - Why don’t young seeds germinate

1) ABA works antagonistically to prevent seed germination, ABA levels are very high and \[blank\] levels are very low

2) Young seeds are less responsive to \[blank\], the takeaway being that plants hormone sensitivity varies throughout development

Gibberellic Acid (Plant growth)

This hormone, when sprayed onto dwarf plants, causes rapid growth into plants of normal size. Plant that are considered dwarf are lacking in response to this hormone. Identification of dwarf plants lack of response to this hormone led to the green revolution.

GA Control and Reception

This hormones control pathway is as follows


1. May be received at the surface by a specific receptor
2. Secondary messenger cGMP leads to a de-repression event
3. cGMP also leads to synthesis of positive inducer
4. \[Hormone\] Is synthesized
5. Secretion is promoted by secondary messenger Ca2+

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Therefore this hormone is mainly controlled by a increase in transcription and secretion, but not by enzyme activation and only maybe to translation & protein stability

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Process is antagonized by hormone ABA at the transcription level

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De-Repression

This is the effect of many receptor pathways

1) A receptor-hormone complex binds to a repressor sitting on top of a transcription factor

2) The repressor is marked by the protein ubiquitin, a protein highly conserved across all forms of life. This marks it for destruction by the proteasome

3) The proteasome comes in and breaks down the repressor protein into its component peptides

4) Proteasomes, receptors, hormones, and ubiquitin are left untouched and go on to be used again. receptor-hormone complex is no longer bound together

Triple Response

A response in etiolated seedling that is initiated by ethylene gas

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1) Radial swelling (the plant is getting thicker and wider)

2) Plant maintains an apical hook or it is enlargened

3) Agravitropic growth

Apical Hook

The two cotyledon stay pressed together and are pointed in a way that they form a hook shape at the top of the plant. This is part of the triple response

Agravitropic growth

Literally meaning a plant not displaying gravitropism (growing in response, or away from gravity), but in context of this class means ability to grow around things instead of straight up. Part of the triple response.

Ethylene radial swelling

This hormone is responsible for radial swelling within seedlings. This happens by reorienting the deposition of cellulose microfibrils within the cells of the shoot. The microfibrils are oriented vertically so that turgor pressure will cause horizontal swelling.

MAPKKK

A highly conserved secondary messenger found in plants, yeast, and vertebrates. This reflects the idea that secondary messengers are highly conserved throughout kingdoms.

Ethylene

The main takeaways from this hormone are


1. Controlled by environmental signals and positive feedback

\-Pressure, lack of light, and fruit ripening (autocatalysis)


2. Alters macroscopic growth by changing the deposition of microfibrils
3. The receptor for this hormone are located on the endoplasmic reticulum as it is able to pass through the plasma membrane easily
4. There are multiple types of receptors
5. The signaling mechanism is the same that is conserved throughout many kingdoms (MAPKKK)
6. Induction of response is through a derepression event


1. Does NOT use ubiquitin

Gibberellic Acid

1. This hormone is possibly received at the cell surface despite being membrane soluble
2. This hormone was discovered through a bioassay involving a rice fungus
3. This hormone works by increasing induction of transcription (by derepression)
4. This hormone is antagonistic to ABA or rather ABA is antagonistic to it
5. Sensitivity to this hormone varies by developmental stage - a developing seed is insensitive to it but a mature seed is sensitive ~~d~~

Det mutant

Standing for De-ETiolated this is a mutation that causes the plant to exhibits greening at the wrong times (such as when grown in the dark) or to exhibit too much greening, resulting in short bushy plants.

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A possible type of this mutant results from defective brassinosteroid signaling/response. BR’s work in concert with auxins and GAs (which both cause vertical growth), so when BRs are not working a short bushy plant is the result.

Brassinosteroid Signaling

The signaling of this hormone, like others, is follows


1. Receptor located on the plasma membrane
2. BR’s bind to it causing an inhibition of a repressor kinase through phosphorylation events
3. Gene expression
4. Cell wall loosening and cell wall synthesis leads to cell expansion and plant growth
5. BR production inhibited (negative feedback)

Brassinosteroid

This hormone

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1. Work synergistically with other hormones such as GA and Auxin to promote growth
2. Mutants of this hormone results in “Det” which are small bushy, greened out plants
3. This hormone is membrane soluble but perceived on the plasma membrane
4. Works via negative feedback, and is a de-repressor


1. This is not the same as those using ubiquitin though
5. Induce growth by cell wall loosening, cell division

Phototropism

The differential cell elongation of a plant due to the response to blue light. To grow torwards the light the side of the plant “shaded” or not facing the light will grow more compared to the side with the light.

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If the apex (tip) is cut off the plant can not exhibit _____

If the apex is shaded/blinded the plant can not exhibit _____

Acid Growth (Auxin)

This hypothesis is used to explain the rapid effects of auxin on cell elongation

1) Auxin increases activity of proton pumps which pump H+ ions into the cytoplasm/cell wall

2) This increased H+ decreases the pH

3) Wedge shaped proteins called expansins separate the microfibrils from the polysaccharides

4) Polysaccharides are cleaved by cell wall loosening enzymes

5) Microfibrils can now slide past eachother if significant turgor pressure exists

Apical Dominance

The phenomenon whereby the main, central stem of the plant is dominant over other side stems. This is mainly controlled by the hormone Auxin.

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In an experiment where an agar block is placed on top of the apex with no auxin, the lateral buds grow to create new branches

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In the same experiment, an agar block containing auxin is placed on the top, and this inhibits the growth of lateral buds.

Effects of Auxin

This hormone promotes

\-Embryonic pattenn formation

\-Root meristem formation and growth

\-Vascular differentiation

\-Lateral organ initiation

\-Cell elongation

\-Apical dominance

Auxin

This hormone

\-Is distributed asymmetrically through the plant

\-A bioassay using agar placed between the apex and the rest of the coleoptile led to its discovery

\-Uses a pH pump for chemiosmotic transport and for cell wall lossening

\-Rapid and long term affects (rapid cell well loosening, long term increased synthesis)

\-Recognized at cell surface AND internally

\-Multiple receptors

\-Derepression

Auxin Organ Initiation

For this hormone to initiate new organ growth there will be a hot spot of auxin accumulation through an auxin promoter surround by an auxin transporter.

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These hot spots of promoters and transporters move around the meristem creating new organs

Auxin - Cytokinin Antagonism

In the shoot, auxin promotes apical dominance and reduces lateral growth, conversely cytokinin promotes lateral growth.

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In the roots auxin promotes lateral roots and inhibited by CK.

Totipotent

Nearly all plant cells are _____. Meaning they have the ability to differentiate into other cell types and regenerate a whole plant given the right conditions. These conditions for organogenesis are controlled by an auxin/cytokinin ratio.

Auxin/Ck Ratios

High CK / Low Auxin = Some shoots, lots of callus, no roots

High auxin / low ck = Lots of roots

Intermediate both = properly differentiated plant

Intemediate CK / low auxin = ball of callus