MBIO 2230 - Topic 5 (carbon)

Why Carbon?

1.) Acts as energy source (releases energy when reduced carbon is oxidized)
2.) A primary component of a majority of the building blocks of life

polymers usually have a ____ carbon content

Structural polymers usually have a high carbon content

GPP (acronym)

Gross primary productivity 

Primary productivity

It forms the base/first step of biomass formation

Carbon fixiation 

A specific process that involves forming organic carbon from inorganic carbon, usually CO₂

Carbon assimilation

The broad process of taking in inorganic carbon and incoporating it into the body in its organic form

Photosynthesis in primordial Earth

They also fixed carbon through photosynthesis, but they did not use electrons from water, instead they used sulfur

Use of sulfer as an electron donor in primordial earth 

The electrons were obtained by splitting sulfur-hydrides (H₂S)

Downside of using sulfer as an electron donor 

It does not produce oxygen 

Two different forms of carbon fixication

1.) Oxygenic photosynthesis
2.) Non-oxygenic photosynthesis

Does non-oxygenic photosynthesis still occur today?

Yes

Oxygenic photosynthesis 

Refers to the use of water as the source of electrons to give to the reduced carbon

The ability to use _ as the source of electrons removed many __  

The ability to use water as the source of electrons removed many constraints  

What constraints were removed when we started using water as an electron source?

It allowed for the production of O2 as a waste product

_ photosynthesis dominates carbon fixation today

Oxygenic 

We cannot understand carbon cycling without understanding…

Plant growth

Chloroplasts

The organelle where photosynthesis occurs in plants

Origin of chloroplasts

They originated from free-living cyanobacteria that were englulfed by eubacteria

Why do plants now dominate carbon fixation (instead of bacteria)

Because of their multi-cellularity

Significance of how multi-cellularity allows plants to now dominate carbon fixation

They have more surface area, therefore there is more area for them to capture sunlight

Carbon uptake at various scales

Cellular --> Organ --> Global

Two processes of photosynthesis

1.) Light-dependent reactions that occurs in the thylakoid membranes
2.) Light-independent reactions (aka the Calvin Cycle) that occurs in the stroma 

Light-dependent reactions (function)

It harvests light energy and uses it to generate reducing power

Light-independent reactions (function)

"It applies the reducing power obtained from the light-dependent reactions to ""fix"" CO₂"

Light-reactions pull electrons from via water _

Light-reactions pull electrons from water via water splitting

Three phases of the Calvin Cycle

1.) Fixation
2.) Reduction
3.) Regeneration

During the light-dependent reactions, photosynthesis converts ____ energy into _ energy

During the light-dependent reactions, photosynthesis converts light energy into chemical energy

ETC in photosynthesis vs. aerobic respiration

1.) The ETC in photosynthesis does not have a continuous downhill movement that releases energy upon oxidation
2.) Instead it involves multiple instances where the electrons are pushed to a higher energy state by capturing light energy 

Gibbs free energy of aerobic respiration vs. photosynthesis 

1.) In respiration, we start off at a high energy state and go down to a lower energy state, resulting in the release of energy
2.) In photpsynthesis, we start off at a low energy state and go to a higher energy state, which is why an input of energy is required in the form of sunlight

Production of oxygen during photosynthesis

It is produced from the stripping of electrons from water at the start of the chain, even before sunlight is used

Why is oxygenic photosynthesis more common than non-oxygenic photosynthesis

Because H2O is much more abundant than H2S

Purpose of light energy

It results in an increase in the electron energy state, allowing the electrons to be added to NADP+ to form NADPH and the phosphorylation of ADP into ATP

Role of ATP and NADPH that was made during the light-dependent reaction

They are used to fix carbon in the light-indepdent reaction

Used up ADP and NADP+ in the light-independent reaction

It is recycled back to the light-dependent reactions, allowing for more ATP and NADPH to be made

________ energy from the light reactions is used to _______ the C in CO2 

Chemical energy from the light reactions is used to *reduce* the C in CO2 

The carbon fixing enzyme used in the calvin cycle

RuBisCo

Starting molecules of the calvin cycle 

Ribulose 1,5 bisphosphate + CO2

What we have to know about the Calvin cycle 

1.) 1 carbon is added to a 5 carbon sugar to form two 3 carbon molecules
2.) ATP and NADPH (the reducing power) is then used to reduce the 3 carbon molecule

C3 photosynthesis

The most common carbon fixation pathway, which involves forming two 3-carbon molecules from a 1 carbon molecule and 5-carbon molecule

Significance of the half-reactions of photosynthesis 

They are spatially separated within the cell, specifically within the chloroplast

Oxidation (O) half-reaction of photsynthesis is in the…

Thylakoid membranes

Reduction (C) half-reaction of photsynthesis is in the…

Chloroplast stroma

Are the light-driven reactions and calvin cycle always paired together?

No, sometimes a different energy source is used, while sometimes a different form of C is used

Two potential energy sources for photosynthesis 

1.) Light
2.) Chemical (oxidation of reduced chemical)

Two potential sources of C for photosynthesis 

1.) Inorganic C (CO2)
2.) Organic C 

Photo uses what as an energy source?

Light

Chemo_ uses what as an energy source?

Chemicals 

_autotroph uses what as a C source?

Inorganic C

_heterotroph uses what as a C source?

Organic C

Organism that utilizes light as an energy source and oganic C as a carbon source is called a…

Photoheterotroph

Organism that utilizes chemicals as an energy source and inorganic C as a carbon source is called a…

Chemoautotroph

Chemoautotrophy example 

The use of iron as an energy source and CO2 as a carbon source

How do the reactants for photosynthesis get to the site at which photosynthesis happens? 

1.) Water --> Roots + Vasculature
2.) CO2 --> Stomata pores + Guard cells

How does water go up the vasculature from the roots to the leaves?

It is pulled from the top, as a result of the loss of water from the leaves, as well as capillary action and surface tension

Opening and closing of stomata (when)

It opens and closes in response to the environment

Opening and closing of stomata (how)

By adjusting the pressure on the guard cells

The ‘most limiting resource’ concept in relation to photsynthesis 

It refers to the fact that the amount of photosynthesis that occurs depends on the capacity of its components, which is limited by the component that runs out first

What could potentially limit the amount of carbon being fixed?

1.) RuBisCo
2.) CO2
3.) H2O

How can RuBisCo be the limiting factor?

It requires a lot of nitrogen, therefore it could potentially be limited nitrogen

Two parts of RuBisCo as an enzyme

1.) Carboxylase
2.) Oxygenase

Carboxylase part of RuBisCo

The part that performs carbon fixation

Oxygenase part of RuBisCo

It is when the enzyme sometimes accidentally grabs O2 instead of CO2, wasting energy as a result, as well as producing a toxic product that is hard to get rid of 

Origin of oxygenase 

It is predicted to be a relic of primordial earth, from the fact that it started off with working in an anoxic environment

How can water be a limiting factor

When the pores open to let CO2 in, it may also cause water to leave

Why can’t plant leaves just freely exchange gases with the atmosphere (i.e. why can't they leave their pores open all the time)?

Because it gives water the opportunity to leave 

Advantage of rising CO2 concentrations to plants

It allows them to leave their pores open for a shorter amount of time, as they can take in a lot of CO2 in that small time. 

CO2 phase (outside vs. inside)

The CO2 diffuses into the leaf in the gas phase, but it dissolves in the water once inside

What does the CO2 have to do once inside the leaf?

It has to go in further, in order to reach the active site of RuBisCo in the chloroplast

Is CO2 soluble in water

Yes

Influence of temperature on solubility (for O2 and CO2)

As temperature goes up, the solubility of the molecules decreases

How might the rate of photorespiration change with temperature? 

The rates of photorespiration increases as the temperature rises

Why does the rates of photorespiration increase as the temperature rises

1.) At lower temperatures, CO2 is more soluble than O2, therefore RuBisCo would have a higher affinity for CO2
2.) At higher temperatures, O2 is more soluble than CO2, therefore RuBisCo would have a higher affinity for O2

Photorespiration

It's when RuBisCo ends up binding O2 instead of CO2 during photosynthesis

CO2 not only dissolves in water, but it also _ with water

Reacts

CO2 reacting with water

It forms a hydrogen ion and hydrogencarbonate (HCO₃^-), which can then further react with each other to form 2H+ and carbonate (CO₃^2-).

Solubility of HCO₃^-

It is much more soluble than CO2

Significance of HCO₃^- formation

A lot of CO2 ends up being lost in the formation of hydrogencarbonate, which is bad because it is not a substrate of RuBisCo

How do plants solve their HCO₃^- problem

Carbonic anhydrase, an enzyme that reverses the chemical transformation of CO2 into hydrogencarbonate

Innovations of life around trade-offs and constraints 

1.) C4 photosynthesis
2.) CAM photosynthesis

C4 photosynthesis

It spatially separates the entry of CO2 and the Calvin cycle, as well as using PEP carboxylate to help solve the HCO₃^- problem

How C4 photosyntesis works

1.) The hydrogencarbonate reacts with PEP to form the 4-carbon malate, using PEP carboxylase
2.) The malate is then moved to where RuBisCo is, where the CO2 gets split off, to be used for the Calvin Cycle
3.) This forms pyruvate, which is once again formed into PEP

Spatial separation in C4 photosynthesis

This allows RuBisCo to be surrounded with a high concentration of CO2, reducing the occurrence of photorespiration

What does it mean to add or remove CO2 from an organic molecule? 

Adding = Carboxylation
Removing = Decarboxylation

The removal of CO2 from malate is a - process and involves various -____

The removal of CO2 from malate is a multi-step process and involves various co-factors

Rate of diffusion of CO2 depends on the __________ gradient 

Concentration

Rate of diffusion of CO2 depending on the concentration gradient 

Faster diffusion occurs when there is more CO2 outside the cell than inside

Is it good for HCO₃^- to constantly be made once CO2 is inside?

Yes, because the constant formation of HCO₃^- offsets equilibrium, allowing CO2 to diffuse inside faster (since it has a low concentration), therefore allowing the plants to close the stomata more often

As we go further down _ in America, the more plants that use __ photosynthesis

As we go further down south in America, the more plants that use C4 photosynthesis

What are the environmental conditions under which C4 photosynthesis provides an advantage? 

Hot and dry conditions

Why does the problem of photorespiration increase as environments get hotter and drier? 

1.) This is because the plant prioritizes conserving water, therefore it keeps the pores closed, even if there is no more CO2, causing RuBisCo to use the only substrate available, O2 
2.) This is why hotter and drier environments usually have C4 photosynthesis

CAM photosynthesis 

It tempoerally separates CO2 uptake and the Calvin cycle process

How does CAM photosynthesis work

1.) At night, the stomata are open (loses less water), allowing CO2 to come in and form HCO₃^- 
2.) Malate is then formed, but it gets stored in a vacuole
3.) In the morning, the stomata close, allowing the malate to leave the vacuole 
4.) CO2 is cleaved off from the malate and photosynthesis can occur regularly with help from the sun

Adaptation type that help with the problem of limited sunlight

The adaptation is in the growth of the organism as a whole, rather than in the mechanics of photosynthesis

Adaptations that help with the problem of limited sunlight (example)

Climbing vines and woody stems, which helps support taller growth, allowing the tree to better access sunlight

Limitations differ among ____________ and _______ cycles frequently interact 

Limitations differ among environments and element cycles frequently interact 

Is phosphorus always the limiting factor for algal blooms

No 

Iron as a limiting factor 

1.) It is most commonly used a cofactor, but it can only be seen in trace amounts
2.) Better growth can be achieved if it's at higher concentrations

The efficient use of water is influenced by ____ traits

Many

Efficient use of water

It refers to being able to produce a certain amount of biomass, but the less water used, the better

Gross vs. net carbon fixation

Gross = The total amount of carbon that was fixed in photosynthesis (without loss)
Net = The total amount of carbon fixed, minus the amount of fixed carbon that was lost, representing the actual amount of biomass of a plant