Test 2 Concepts

Glycolysis and Fermentation

What is catabolism and what is its characteristic

The breakdown of macromolecules

• Increase in entropy

• Exergonic

• Energy is available to be transferred out

• That energy may be used to synthesize ATP

What is anabolism and what is its characteristic

Synthesis of macromolecules

• Increase in entropy

• Endergonic

• Energy is required to be transferred in

• That energy usually comes from ATP hydrolysis

What is ATP, what is its structure, and where is energy stored

A high energy nucleotide used to supply energy for cellular reactions

• A ribose

• An adenine (purine)

• 3 phosphate groups linked by phosphoester bonds (where energy is stored)

Why does ATP store so much energy

1) Charge repulsion

• Phosphate groups that are negatively charged are bonded and forced close together. This repulsive force creates a lot of stored energy

2) Lack of resonance stabilization

• Caused by ester and anhydride bonds between phosphate groups

• in ester or anhydride bonds, e- cannot move as freely, moving between 3 oxygens instead of 4

What is mainly used as fuel for ATP synthesis

Glucose

• Metabolic substrates are energy rich macromolecules whose catabolism is linked to ATP production

• Other carbohydrates, fatty acids, & amino acids can also be used, but glucose is most preferred

What is the chemical reaction of glucose catabolism

C6H12O6 + 6O2 ——> 6CO2 + 6H2O

What type of reaction is the catabolism of metabolic substrates

Redox reactions

What does reduction mean in redox reactions

Gaining electrons or hydrogen atoms

What is oxidation in redox reactions

The loss of electrons or hydrogen atoms

Gaining oxygen atoms

What is reduced and what is oxidized in glucose catabolism

Glucose is oxidized

• Carbons lose electrons and gained oxygen atoms

O2 is reduced

• CO2 and H2O formed

What type of reaction is glucose catabolism

A redox and combustion reaction

• CO2 and H2O are formed

• Energy is transformed into heat, meaning it was lost to entropy

What are the principles of substrate catabolism

• Energy is stored in the bonds of metabolic substrates

• e- are the part of the atom that is responsible for chemical bonds

• Thus, the e- in these substrates ‘hold’ the energy

• Catabolic rxns are redox rxns

• Redox rxns transfer e-

• In the catabolism of metabolic substrates, the e- are ultimately transferred to O2

• Transferring the e- directly to O2 = combustion

How much ATP can theoretically be created by Glucose catabolism

93 ATP

How much ATP is actually created by glucose catabolism and why

~36-38 ATP

• Energy from the substrate is lost to entropy

What are the processes associated with glucose catabolism and where does it occur in the cell

1) Glycolysis in cytosol, 10 rxns

2) Products from glycolysis are used in Kreb’s cycle in the mitochondria, 9 rxns

• Also called the citric acid cycle and TCA (tricarboxylic acid) cycle

• O2 is the final e- acceptor

What is nicotinamide adenine dinucleotide (NAD+) and what is its structure

A nucleotide with a nicotinamide nitrogenous base attached to another nucleotide via a pyrophosphate bridge

• nicotinamide has an oxidized and reduced form

What is the role of NAD+ in glucose catabolism and why is it good for its role

Temporarily hold e-

• Can easily be oxidized (NAD+) or reduced (NADH)

What is the first phase of glycolysis and what are the enzymes involved

Investment/activation and cleavage

• glucose phosphorylated twice by ATP then cut into 2 glyceraldehyde-3-phosphates

• Hexokinase phosphorylates glucose and prevents it from being transported out of the cell (produces Glucose-6-phosphate and ATP —> ADP)

• Phosphoglucoisomerase reorganizes glucose-6-phosphate aldehyde structure into ketose (makes fructose-6-phosphate)

• Phosphofructokinase 1 adds another phosphate group to the first carbon of fructose-6-phosphate (results in fructose-1,6-bisphosphate and ATP—> ADP)

• Adolase cuts fructose-1,6-bisphosphate (cut into 1 dihydroxyacetone phosphate and 1 glyceralaldehyde-3-phosphate)

• Triose phosphate isomerase converts dihydroxyacetone into another glyceraldehyde-3-phosphate (results in 2 glyceraldehyde-3-phosphates)

What is the second part of glycolysis and what enzymes do what roles

Oxidation and ATP synthesis

• Glyceraldehyde-3-phosphate dehydrogenase catalyzes the 1st redox rxn (creates 2 1,3-bisphosphoglycerate)

• The 2 G3P is oxidized and NAD+ is reduced to NADH (2 NAD+ —> 2NADH)

• Phosphoglycerokinase catalyzes a substrate-level phosphorylation (creates 2 3-Phosphoglycerates and ADP —> ATP)

• A phosphate is transferred directly from the substrate to ADP

• 1,3-bisphosphoglycerate has enough energy in its bonds to provide the energy to synthesize ATP

What is the third step of glycolysis and what enzymes do what roles

ATP synthesis and pyruvate formation

• Phosphoglyceromutase moves phosphate from 3rd carbon to 2nd carbon (creates 2 2-phosphoglycerate)

• Enolase removes a H from 2nd carbon (creates 2 phosphoenolpyruvate (PEP) and water)

• Pyruvate kinase catalyzes a substrate-level phosphorylation (creates 2 pyruvates and ADP—>ATP)

• A phosphate is transferred directly from the substrate to ADP

• Phosphoenolpyruvate has enough energy in its bonds to provide the energy to synthesize ATP

What is the chemical reaction equation for glycolysis

C2H12O6 + 2NAD+ + 2ADP + 2Pi —> 2 pyruvate + 2NADH + 2H+ + 2ATP

What are the other carbohydrates that can be used as metabolic substrates

Starch, glycogen, lactose, maltose, sucrose

What is fermentation and how does it work

A process that allows glycolysis to continue under anaerobic conditions by

• eliminating pyruvate

• providing another mechanism for NADH to become oxidized back to NAD+

• NAD+ returns to cytosol to participate in redox rxn of glycolysis

Why is fermentation needed

NAD+ is finite in a cell. If all NAD+ is reduced to NADH and cannot be oxidized back, glycolysis will not occur

• Meaning ATP can still be created via substrate-level phosphorylation in glycolysis

• Less ATP is produced but is enough for cell to survive on temporarily

Explain the process of fermentation

After glycolysis, the pyruvate is converted into either lactate or ethanol

• lactate and ethanol are energy rich waste product

• The lactate/ethanol is then reduced to oxidize NADH

What is the chemical reaction of fermentation

C6H12O6 + 2ADP + 2Pi —> 2 lactate + 2 ATP

What enzymes produce lactate and ethanol

For lactate

• Lactate dehydrogenase (LDH) = reduces pyruvate to create lactate and oxidizes NADH into NAD+

For ethanol

• Pyruvate decarboxylase (PDC) = takes out the CO group from pyruvate (creates CO2) and adds a hydrogen

• This produces acetaldehyde

• Alcohol dehydrogenase (ADH) = oxidizes NADH into NAD+ and reduces acetaldehyde into ethanol

What the Cori cycle

The fermentation process the skeletal muscles go through when oxygen levels are low

• Glycolysis occurs but pyruvate is converted into 2 lactates in the skeletal muscles

• Lactate travels through the blood into the liver

• In the liver, NAD+ is reduced into NADH to produce 2 pyruvate

• 2 NADH is oxidized into two NAD+, 6 ATPs are used to creat a glucose

• Glucose travels through the blood and back to the skeletal muscles, and 2 ATPs are produced

• The cycle repeats

What is gluconeogenesis

the process of creating new glucose

• 10 enzyme-catalyzed rxns

• 7 are readily reversible, 3 are not

• Enzymes in glycolysis do not participate in gluconeogenesis

• Products are the same (except for additional oxaloacetate) but in reverse

What enzymes are different in gluconeogenesis

• Pyruvate carboxylase (PC) adds CO2 to the 2 pyruvates and uses ATP (ATP—>ADP) to create oxaloacetate

• Phosphoenolpyruvate carboxykinase (PEPCK) uses GTP (GTP—>GDP) to remove CO2 and create 2 PEP

• Process remains the same but in reverse

• Fructose-1,6-bisphosphate (F1,6BPase) adds water to F1,6BP and removes the phosphate group

• Glucose-6-phosphatase (GPase) adds water to glucose-6-phosphate to remove the phosphate group

• Glucose produced

How is glycolysis regulated

Can be regulated via allosteric feedback inhibition or activation

Hexokinase inhibited by G6P

Phosphofructokinase-1 (most important regulatory step alongside F-1,6-BPase) is:

• Activated by F2,6BP, and AMP

• Inhibited by ATP and Citrate

Pyruvate kinase is

• Activated by F1,6BP

• Inhibited by ATP and Acetyl CoA

How is gluconeogenesis regulated

Can be regulated by allosteric feedback inhibition and activation

Fructose-1,6-bisphosphatase (the most important regulatory step alongside Phosphofructokinase-1) inhibited by

• F2,6BP

• AMP

Pyruvate carboxylase (PC) activated by Acetyl CoA

What is the important regulator of glycolysis and gluconeogenesis

A metabolite called fructose-2,6-bisphosphate

• synthesized by Phosphofructokinase-2 (PFK-2)

• broken down by fructose-2,6-bisphosphatase (F2,6-BPase)

• Amount of F2,6BP is important in activation of glycolysis and inhibition of gluconeogenesis

• PFK-2 and F2,6BPase are the same enzyme but F2,6BPase is phosphorylated

• Protein kinase determines activation or deactivation of F2,6BP

• Hormonal signal (like glucagon or epinephrine) activates protein kinase

Kreb’s cycle and aerobic respiration

What is the function of pyruvate dehydrogenase

after glycolysis and pyruvate is taken to the mitochondria,

• pyruvate is decarboxylized (CO2 removed)

• This rxn is an oxidative decarboxylation

• Leaves behind an Acetyl group

what does Coenzyme A do

Temporarily holds onto the Acetyl group to protect the energy stored in it for other enzymes in the Kreb’s Cycle

• Coenzyme A + Pyruvate = Acetyl CoA

What are the steps of the Kreb’s Cycle

• Citrate synthase binds the 2 carbons of the acetyl groups to oxaloacetate, creating citrate

• Aconitase converts citrate into isocitrate

• Isocitrate dehydrogenase oxidizes isocitrate and CO2 is removed to form alpha-ketoglutarate (redox and decarboxylation)

• Alpha-ketoglutarate dehydrogenase oxidizes alpha-ketaglutarate, CO2 is removed, then CoA is linked to form succinyl-CoA (redox and decarboxylation step)

• Succinyl-CoA synthase use GDP as the substrate to do a substrate level phosphorylation and creates succinate

• Succinate dehydrogenase oxidizes succinate to fumarate (cofactor for this rxn is FAD which is reduced to FADH2)

• Fumarate hydratase converts fumarate into malate

• Malate dehydrogenase oxidizes malate into oxaloacetate

Why is Flavin Adenine Dinucleotide (FAD) used as a e- carrier in succinate dehydrogenase and not NAD+

difference in redox potential (oxidation of diff. bonds yields e- with diff. lvls of energy)

• NAD+ has a higher redox potential than FAD and will not accept e- with lower energy

• Succinate oxidation does not yield e- with high energy levels

• FAD can hold these lower energy e- bc of its lower redox potential

what is the most important regulatory step of the Kreb’s Cycle and how is it activated/deactivated

Pyruvate dehydrogenase

• Not in Kreb’s cycle; enzyme just before

• Most active in its dephosphorylated form; less active when phosphorylated

• PDH kinase deactivates it; activated by high [ATP]/[ADP]

• PDH phosphatase activates it; activated by low [ATP]/[ADP]

What regulates the Kreb’s cycle

Pyruvate dehydrogenase (active)

• Inhibited by: Acetyl CoA, NADH, ATP

• Activated by: CoA, NAD+, AMP

Isocitrate dehydrogenase

• Inhibited by: NADH

• Activated by: ADP

Alpha-Ketoglutarate dehydrogenase

• Inhibited by: NADH, Succinyl CoA

Malate dehydrogenase

• Inhibited by: NADH

What is the basic outline of aerobic metabolism

• temporary e- carriers NADH & FADH2 deliver their e- to the electron transport chain (ETC)

• At the end of the ETC, the e- are given to oxygen to produce water

• The ETC uses some of the e- energy to transport H+ out of the matrix

• Creates a gradient of H+

• Energy from H+ gradient used to synthesize ATP

What are the four types of e- carriers found in the four ETC complexes

Flavoproteins

• Found at beginning of Complex I and II

• FAD (flavin adenine dinucleotide) and FMN (flavin mononucleotide)

Cytochromes

• Heavily found in Complex III and IV

• Takes e- from Complex III and takes them to Complex IV

• Contain heme groups (has Fe in the center and is easily oxidized)

• Soluble

Coenzyme Q

• Takes e- from Complex I, bypasses Complex II, and takes them to Complex III (Complex I → Complex III)

• Not a protein

• Can also take e- from Complex II and take them to Complex III

• Has a ring group w/ a isoprenyl tail

• Oxidized form is ubiquinene and reduced form is dihydroquinone

Iron-Sulfur proteins

• Basically found in all complexes

• Have Fe

How do e- travel through ETC

• NADH delivers e- to Complex I FMN (flavoprotein) then to Fe-S protein (H+ transported out)

• e^- then given to CoQ (turns to CoQH₂) and is taken to Complex III (H+ transported out)

• In Complex III, e^- are taken to either the Q cycle or Fe-S protein

• Fe-S takes e^- to Cytochrome C, and Cytochrome C take e^- to Complex IV

• In Complex IV, e^- through Cytochrome complex and to Fe-Cu protein (H+ transported out)

• Fe-Cu protein gives e^- to O₂

• FADH first gives its e^- to complex II, not I

• In Complex II, e^- given to Fe-S protein then to CoQ and undergoes the same process as NADH e^-

What is the reduction potential of ETC components

E- can only be passed to a molecule w/ a lower redox potential

• Redox potential of the complexes decreases down the ETC

• Some energy is lost to entropy

• Some energy used to transport H+

How does the oxidation of NADH contribute to the electrochemical proton gradient

e- from NADH allow H+ to be transported 3 times: by complex I, III, and IV

How does the oxidation of FADH2 contribute to the electrochemical proton gradient

e- from FADH allow H+ to be transported two times: by complex III and IV

What is chemiosmotic coupling

Transport of H+ and the resulting electrochemical proton gradient provides energy for the synthesis of ATP through the F0/F1 synthase

How is the ETC inhibited

• Cyanide inhibits the final step of ETC, e- blocked from O2

• Rotenone inhibits first step of ETC, blocks transfer for e- from NADH to Complex I

What can dinitrophenol (DNP) do

A protonophore that allows H+ ions to travel across the membrane easily

• Disrupts H+ gradient

• Doesn’t stop ETC from transporting H+ out, just brings H+ right back in

• Uncoupled e- transport from oxidative phosphorylation

• Energy for ATP synthesis not provided

What is thermogenin

A protonophore and channel forming protein allows H+ to be transported down the membrane

• Energy lost as heat

• Not seen much in adults, very common in babies

• reduces H+ flow into F0/F1 synthase

How does the F0/F1 ATP synthase synthesize ATP

• a H+ passing through a and c subunits and causes a conformational change

  • Causes $\gamma$ subunit to rotate 120 degrees

• Every rotation causes conformational changes in the $\beta$ subunits

What are the three conformations of the beta subunit of F0F1 ATP synthase

Open

• Don’t have a high affinity for binding anything

Loose

• Binds loosely to ADP and phosphate

Tight

• Forces ADP and phosphate close enough for them to bind and make ATP

• Spontaneous rxn

1 subunit is open, 1 is loose, and 1 is tight simultaneously

How much ATP is created from each step and electron carrier

• Glycolysis = 2 ATP

• Kreb’s cycle = 2 ATP

• 10 NADH x 3 ATP = 30 ATP

• 2 FADH2 × 2 ATP = 4 ATP

• Total: 36-38

Why is the number of ATP synthesized indicated as a range?

Bc not all NADH is the same

• In most cells, NADH from cytosol (glycolysis) results in fewer ATP synthesized than NADH produced in the mitochondria

How do we move NADH from the cytosol to the mitochondria

The glycerol phosphate shuttle

• e- from NADH reduce DHAP to form glycerol phosphate that is transported into mitochondria’s inter-membrane space

• e- from glycerol phosphate are then transferred to FAD to form FADH2

• This is due to the loss of redox potential from the e- being transferred

• Energy lost to entropy, so less ATP is made (2 ATP)

What is the malate-asparate shuttle

Cells that have high metabolic demand use a “lossless” transfer system when transporting NADH from cytosol to mitochondria

• Liver, Kidney, cardiac muscle

• Malate and asparate is transported back and forth through the membrane

• Energy not lost, 3 ATP made

What are some examples of membrane translocases

• Pyruvate carrier (Pyruvate and H+ brought into matrix together)

• Dicarboxylate carrier (Malate, Fumarate and Succinate brought in or out depending on concentration)

• Tricarboxylate carrier (Citrate and isocitrate in or out depending on concentration)

• ATP-ADP carrier (ADP in, ATP out)

• Phosphate carrier (Phosphate in, OH- out)

What is the pathway for breaking down fatty acids for fuel for ATP synthesis

$\beta$ oxidation

• Fatty acids cleaved into 2-carbon units

• These 2-carbon units are linked to Coenzyme A and enter the Kreb’s cycle as acetyl-CoA

• Single glucose yields 2 acetyl-CoA

• Fatty acids like palmitic acid can make more (palmitic acid is 16-carbon and yields 8 acetyl-CoA)

How are amino acids used in metabolism

• Very rare; used when sugars are exhausted and fatty acids used

• Amino acids can be used as catabolic substrates that feed into the Kreb’s cycle

• Kreb’s cycle intermediates may be used to synthesize amino acids

Photosynthesis

What are heterotrophs

Organisms that eat other organisms to obtain energy and reduced carbon

what are autotrophs and what are the two types

organisms that obtain energy from inorganic sources and use it to produce their own reduced carbon molecules

• Chemoautotrophs- get energy from reduced inorganic molecules and incorporate it into reduced carbon molecules (chemosynthesis)

• Photoautotrophs- get energy from photons in sunlight and incorporate it into reduced carbon molecules through photosynthesis

What is the chemical equations of photosynthesis

6CO₂ + 12H₂O + sunlight → C₆H₁₂O₆ + 6O₂ + 6H₂O

What are the 2 phases of photosynthesis

Energy Transduction = chlorophyll molecules capture energy from photons and transfer that energy into ATP and NADPH

• Known as light dependent reactions

Carbon fixation = energy from ATP and reducing power form NADPH is incorporated into bonds joining carbon atoms (from CO₂) to make carbohydrates

• Known as light independent reactions, the Calvin cycle, and/or carbon fixation

Where does photosynthesis and its phases occur

Photosynthesis occurs in the chloroplasts of plant cells

• Energy transduction occurs in the thylakoid membranes (looks like a stack of coins; called granum)

• Carbon assimilation occurs in the stroma (space around thylakoids)

Where does energy transduction and carbon assimilation occur in prokaryotes

Phototropic bacteria do not have chloroplasts

• Ex: Cyanobacteria

• Energy transduction occurs in the photosynthetic membrane which are folded inward from the plasma membrane

• Carbon assimilation occurs in carboxysomes

How is the energy from photons absorbed

Molecules called pigments absorb the energy from photons

• Different pigments absorb photons of different wavelengths

• Called their absorption spectrum

What are the most important pigments

chlorophylls

• Has a similar heme structure like the one seen in hemoglobin

Accessory proteins like carotenoids are needed too

What are photosystems and how do they work

Multi-protein complexes that form functional units for photosynthesis

• Have light harvesting complexes and electron transport chains

• Photosystem I

• Photosystem II

• Pigment e^- get excited by light and its redox potential and energy state increases

• Those e^- are then transported to the thylakoid membrane

What are in light harvesting complexes and what are their parts

Contain pigment molecules and chlorophyll which are organized into groups

• Antenna complex = composed of chlorophyll and accessory pigments that capture energy from sunlight into their e^-

• Reaction center = a specialized chlorophyll that accepts excited e^-

what is photoexcitation

a photon strikes a pigment molecule in the antenna complex and the energy is absorbed by an e^-

• The electron becomes excited and jumps from ground state (low energy orbital) to the excited state (high energy orbital)

• The excited state is unstable, so e^- either:

  • Returns to ground state and energy is lost to entropy

  • OR transfer energy to another e^- in chlorophyll, then another and another inside the antenna complex

• The excited e^- reaches the reaction center and is transferred to a specialized chlorophyll molecule that acts as an e^- acceptor

• When the e^- acceptor becomes reduced, the electromagnetic energy has been transformed to chemical energy

What is resonance energy transfer

When excited e^- transfer energy to another e^- in chlorophyll, then another and another inside the antenna complex until an excited e^- is transported to the reaction center

How does the excited e^- travel through Photosystem I

Excited e^- energy is so high it is transported to the e^- acceptor P700

• From P700, e^- is transported through a series of specialized chlorophyll molecules and iron-sulfur complexes

• e^- then transferred from ferredoxin (iron-containing protein) to NADP⁺ to make NADPH

  • Transport causes e^- to lose some energy in each step

  • Note that this is after Photosystem II

How does the excited e^- travel through Photosystem II

Energy from photons bounces from different e^- until eventually exciting an e^- in the P680 e^- acceptor

• the excited e^- is transported to plastoquinone and reduces it to plastoquinol

• plastoquinol passes e^- to the cytochome b₆/f complex (not apart of any of the photosystems; it is its own separate complex)

• The cytochrome b₆/f complex passes e^- to plastocyanin and also H+ ions from the thylakoid lumen to the stroma

• e^- passed to Photosystem I

• H+ gradient is created and is used in ATP synthesis

What is the process of e^- through the ETC in the thylakoid membrane

• e- from splitting water into O₂ are taken to photosystem II

• Photons energize e^- in photosystem II until one reaches its' reaction center, P680

• then to plastoquinone where it reduces it to plastoquinol

• Plastoquinol takes excited e^- to the cytochrome b₆/f complex

• From there, e^- is taken to plastocyanin, where lost e^- are replaced

• e^- then transported to P700 in photosystem I

• From P700, e^- taken to ferrodoxin protein to make NADP to NADPH

• H+ are transported from Photosystem II, Q cycle, and Photosystem I, which creates a electrochemical proton gradient

• H+ ions travel through CF₀/CF₁ ATP synthase from the stroma to the thylakoid membrane, and ATP is produced

How does Photosystem I replaces lost e^-

By accepting them from plastocyanin, a soluble protein which shuttles e^- from the end of Photosystem II

What is oxygenic photosynthesis

The process Photosystem II undergoes to replace e^- lost from being excited and leaving a chlorophyll molecule

• Enzymes in Photosystem II splits water and produces oxygen

• 2H₂O → 4H⁺ + 4e^- + O₂

• If this doesn’t occur, a radical (an unpaired e^-) could occur, making it unstable

What is the chemical equation of energy transduction

8 photons + 2H₂O + 2ADP + 2P_i + 2NADP⁺ → 0₂ + 2ATP + 2NADPH

• Ultimate goal of energy transduction is to make ATP and NADPH

What is cyclic photophosphorylation

Photosystem I ferrodoxin occasionally transfers e^- to the cytochrome b₆/f complex instead of using them to reduce NADP⁺

• ATP requirement > NADPH requirement for carbon fixation

• e^- undergo another trip through photosystem I to create more ATP

• Allows for more H+ transport from the stroma to the thylakoid membrane, which leads to more ATP synthesis

• Happen randomly

What is the first phase of the Calvin Cycle

Carbon fixation

• CO₂ is combined with ribulose bisphosphate (RuBP) and the product is cleaved, producing two molecules of 3-phosphoglyecrate

• In biology, CO₂ is considered inorganic

• Fixing (linking) the carbon to organic groups makes it organic

What is the second step of the Calvin Cycle

Reduction

• The 3-phosphoglycerates are phosphorylated by ATP and reduced by NADPH to convert them to glyceraldehyde-3-phosphate (G3P)

• Some of the G3P is used to make larger sugars

What is the third step of the Calvin Cycle

Regeneration

• The remaining G3P is used in rxns that regenerate RuBP

How does the Calvin Cycle work

• One turn around the Calvin Cycle fixes one CO₂

• But G3P is a triose and has 3 carbons

• So, we need to make 3 turns around the Calvin Cycle to make one sugar

• 3 molecules of CO₂ are fixed simultaneously

What is the full process of the Calvin Cycle

• In Carbon Fixation, three CO₂ are each added to 3 RuBP

• RuBP has 5 carbons, so after adding CO₂ the products have 6 carbons (18 C total)

• The products are cleaved into 3-carbon molecules, creating 6 3-phosphoglycerate

• In Reduction, each 3-phosphoglycerate is reduced to 6 G3P using 1 ATP and 1 NADPH (6 ATP and NADPH total)

• 1 G3P leave to be converted into glucose, leaving 5 G3P (15 C total)

• In Regeneration, the 5 G3P are recombined using energy from 3 ATP to make 3 Ribulose-1,5,bisphosphate (15 C total)

What happens to the G3P that was taken out of the Calvin Cycle

carbohydrate anabolism

• glycolytic enzymes convert trioses to hexoses, disaccharides, and starch

How are Calvin Cycle enzymes regulated

• Indirectly regulated by light

  • Enzymes don’t react directly to sunlight, but effect of light can activate them

  • e^- can be transported to ferredoxin then to thioredoxin

  • Thioredoxin reduces disulfide bonds in several Calvin Cycle enzymes to activate them

  • Without light, e^- transport ceases and the bonds spontaneously oxidizes, which inactivates the enzymes

  • This keeps the Calvin Cycle enzymes from using up all of the ATP and NADPH at night since they aren’t replaced in the dark

What is Rubisco

The enzyme that fixes CO₂ (ribulose 1,5-bisphophate carboxylase)

• Found in all photosynthetic organisms

What is the one issue with Rubisco

It does not have good substrate specificity

• Both CO₂ and O₂ can bind to the active site, causing a competition

• CO₂ and O₂ concentration determines enzyme activity

• Higher CO₂ concentration means ribulose carboxylase activity is more likely to occur

• Higher O₂ concentration means ribulose oxidase activity is more likely to occur

What are the products of Rubisco

If CO₂ binds, two 3-phosphoglycerates are made

If O₂ binds, one 3-phosphoglycerate and one phosphoglycolate is made

• Phosphoglycolate is not useful as it can’t be used to directly make a glucose

What is photorespiration

The glycolate pathway that converts phosphoglycolate into 3-phosphoglycerate

• Inefficient, consumes ATP and releases previously fixed carbon as CO₂

• Wasteful process and drastically lowers the rate of photosynthesis and net gain of new sugars

How does the O₂ concentration in plant cells increase if stomata are usually open to regulate gas exchange

Gas exchange vs. water preservation

• Normally stomata are open during the day and closed at night

• However, water is lost to evaporation when it is open

• On hot, dry days, excessive water may be lost through open stomata, thus plants close them

• Closing stomata decreases CO₂ delivery and decreases carbon fixation

• Energy transduction continues, so oxygen levels increases, which increases rate of photorespiration

• Some plants have found alternatives to avoid photorespiration

How do plant cells overcome photorespiration

• The C₄ pathway

  • Plants from hot, dry habitats (sugarcane and corn)

  • Difference in how and where the carbon is fixed

• Crassulacean acid metabolism (CAM)

  • Plants like succulents and bromeliads like pineapple

  • Carbon fixation and Calvin Cycle separated by time

  • Fix CO₂ in the day

  • Do Calvin Cycle at night

How does the C₄ pathway work

CO₂ is fixed in the mesophyll cells to form 4-carbon molecules

• 4C molecules are transported into bundle-sheath cells where Calvin Cycle occurs

• 4C molecules release a CO₂, which rubisco uses to form 3-phosphoglycerate and initiates the Calvin Cycle

• The process raises the concentration of CO₂ in the bundle sheath cells

• The enzymes involved are very specific; they only bind to CO₂ so photorespiration occurs

What is the Hatch-Slack Cycle

The reactions that make the C₄ pathway possible

• In mesophyll cells, CO₂ is fixed to PEP and makes oxaloacetate which is reduced to malate

• Malate is transported into the bundle-sheath cells and decarboxylated to release the CO₂ in the bundle sheath cells

• The decarboxylated product is pyruvate, which is transported back to the mesophyll cells and is converted back to PEP

How does CAM photosynthesis work

• During the night, CAM plants take in CO₂ and fix it to produce malate using the Hatch-Slack cycle (same as C₄) plants

• During the day, malate is released from the vacuoles

• Again, using the Hatch-Slack pathway, CO₂ is released and made available to be used by the Calvin cycle

Endomembrane system and the endoplasmic reticulum

What is protein targeting

What is the secretory pathway