Cycle 4: Primary Metabolism

Question 1

The two phases of photosynthesis (light reactions and the Calvin cycle)…broadly.

Answer 1

Light Reactions:
- Location: Occur in the thylakoid membrane of chloroplasts.
- Function: Capture and convert light energy into chemical energy (ATP and NADPH).
- Products: Oxygen is released as a byproduct.

Calvin Cycle (Dark Reactions or Light-Independent Reactions):
- Location: Take place in the stroma of chloroplasts.
- Function: Utilize ATP and NADPH from light reactions to convert carbon dioxide into glucose or other carbohydrates.
- Products: Glucose and other organic molecules are synthesized.

Question 2

Structure and function of a photosystem - what do the different parts do?

Answer 2

Structure of a Photosystem:
- Antenna Pigments: Chlorophyll and other pigments that capture light energy.
- Reaction Center: Chlorophyll molecules where light energy is transferred and used for photochemical reactions.

Function of a Photosystem:
- Light Absorption: Antenna pigments capture light energy and funnel it to the reaction center.
- Photochemical Reaction: In the reaction center, light energy is used to initiate electron transfer reactions.
- Electron Transport: Excited electrons move through a series of proteins, generating an electron transport chain.
- ATP and NADPH Production: The electron transport chain produces ATP and NADPH, which are used in the Calvin Cycle for carbon fixation during photosynthesis.

Question 3

Global primary productivity (why so little photosynthesis in oceans…?)

Answer 3

Low chlorophyll concentrations at the equator since there are not enought nutrients present (e.g. iron) - little photosynthesis occurs because nutrient concentration is too low to support it.

Question 4

Definition of photosynthesis, endergonic (why), redox reaction, what gets oxidized, what gets reduced?

Answer 4

• Photosynthesis is a light-dependent reduction of CO2 to carbohydrates.
• It’s endergonic (+ΔG) because it takes low free energy reactants and transforms them to high free energy products.
• H2O is oxidized to O2 and CO2 is reduced to C6H12O6 (LEO says GER!).

Question 5

Extremophile mental floss…shape of a growth vs temperature curve…differences in hexokinase between habitats.

Answer 5

• Growth vs. temperature curve, can be thought of in terms of enzyme activity: increases to optimum (as increased kinetic energy results in more substrate-active site collisions) and collapses past that point (protein denaturation)
• Differences in hexokinase between habitats depends on the tertiary structure (stronger bonding arrangement in tertiary sturcture of hyperthermophiles, and weaker in psychrophiles)
• Hexokinases in extremophiles in different habitats share a common ancestor but have different primary structures, and thus tertiary structures

Question 6

What is bacteriorhodopsin, what does it do? Is it photosynthesis?

Answer 6

• Bacteriorhodopsin is a light-driven proton pump with prokaryotic cell structure
• Has retinal and uses energy of light to pump protons out of the cell (against concentration gradient) - builds up proton gradient outside of the membrane, so that they flow through ATP synthase and regenerate ATP
• Only found in Archaea

Question 7

The structural features of the chloroplast and what goes on where

Answer 7

• Thylakoid membrane is where PSI, PSII, electron transport are
• Lumen is a membrane-enclosed space
• Stroma is where Calvin cycle occurs
• Has its own genome
• Chloroplast membrane is plasma membrane of Archaea bacteria

Question 8

Chloroplast has its own genome…encodes many proteins including one called D1.

Answer 8

• A chloroplast has its own genome, with its own genetic code and ability to do transcription and translation, like that of the D1 protein.
• *

Question 9

What does the electron transport chain do, how does it work.

Answer 9

NADPH is a source of electrons, makes molecules more energy rich.

Light excites P680, to a very easy to oxidize form of P680*. The primary acceptor with slightly stronger affinity steals an electron from P680. Electron flows downwards because all acceptors in the chain have a slightly greater affinity for electrons than the last.

Electrons split from H2O, resulting in protons and O2, acidifying the lumen.

Question 10

Function of ATP synthase

Answer 10

ATP synthase uses protons? to regenerate ATP from ADP??*

Question 11

Relationship between redox potential and ability to oxidize a molecule and in explaining electron flow

Answer 11

More negative redox potential increases ability to oxidize other molecules. More positive redox potential increases affinity for electrons.

Question 12

How redox potential of chlorophyll changes upon photon absorption.

Answer 12

Redox potential increases drastically as P680 is excited to P680*, becoming very easy to oxidize.

Question 13

Why do you need to photosystems.

Answer 13

• Photosystem II involves a lot of post-translation regulation

*

Question 14

Distinction between P680, P680* and P680+ and the processes that covert one to the other.

Answer 14

• P680 is a special chlorophyll.
• A photon of light hits P680 in its ground state and excites it to P680* (higher free energy form)
• An electron is removed from P680* via electron transport, yielding P680+ (strongest oxidixing molecule in biology)

Question 15

Why Chlamy is sometimes negatively phototactic

Answer 15

Chlamy can be negatively phototactic (shy away from high light) due to photosensitivity, since high-intensity light (photons) can be harmful and kill the cell by damaging its proteins.

Question 16

P680 is bound to the protein D1….consequences to D1 of excessive P680+ generation (occurs under high light).

Answer 16

Excessive P680+ generation due to high light exposure results in an excess of strong oxidizing agent, stealing electrons from the D1 protein, damaging it.

Question 17

Understanding that PSII is constantly being damaged and thus needs to be repaired.

Answer 17

• Active PSII’s D1 protein is damaged through overexposure to light. The D1 protein is damaged and replaced every 20min or so.
• Under low light conditions, the rate of damage = rate of repair, so that D1 abundance stays constant.
• Under high light conditions, the rate of damage > rate of repair, so that D1 abundance decreases.

Question 18

Role of chloroplast protein synthesis in the repair cycle.

Answer 18

Chloroplast protein synthesis is used to replace the damaged D1 protein and repair PSII, from inactive to active state.

Question 19

Basic understanding of the Calvin cycle (can you work through Figure 6.17 alone?)

Answer 19

see fig 6.17, turquoise cycle

Question 20

Where does it take place, what does it do…why did this thing evolve in the first place?

Answer 20

Where: stroma of chloroplasts

What: convert carbon dioxide into carbs, using ATP and NADPH

Why Evolution: mechanism for photosynthetic organisms to utilize sunlight as an energy source, reduce dependence on external food sources, and convert inorganic carbon (CO2) into organic molecules

Question 21

Understand in broad terms the three phases: Fixation, Reduction, Regeneration.

Answer 21

• Fixation: CO2 is captured and incorporated into RuBP with the help of RuBisCO.
• Reduction: ATP and NADPH, produced during the light reactions of photosynthesis, provide energy to convert the resulting molecules into G3P.
• Regeneration of RuBP: Some G3P molecules are used to regenerate the initial RuBP, ensuring the continuation of the cycle.

Question 22

Know what the follow are: Rubisco, RuBP, PGA and G3P. (don’t need to know what the abbreviation stands for).

Answer 22

• Rubisco (enzyme helps incorporate CO2 with RuBP)
• RuBP (substrate, a five-carbon sugar molecule)
• PGA (intermediate, during carbon fixation)
• G3P (three-carbon sugar, half a glucose molecule)

Question 23

Basic differences between anoxygenic and oxygenic photosynthesis….requirements for light…

Answer 23

• Anoxygenic photosynthesis: electron transport with only one photosystem (I or II, depending on bacteria), wihich make ATP and NADPH
• I converts H2S to S
• II converts Fe2+ to Fe3+
• *light requirements

Question 24

What was the huge evolutionary advantage of oxygenic photosynthesis over anoxygenic photosynthesis

Answer 24

Oxygenic photosynthesis uses both Type I and II photosystems and have the evolutionary advantage that H2O is much more prevalent than H2S and Fe2+, which outweighs the disadvantage that it requires more energy.

Question 25

Intracellular location and metabolic purpose of: glycolysis, citric acid cycle. Which produce/consume….ATP, NADH, O2….

Answer 25

• Glycolysis occurs in the cytosol, uses glucose, produces ATP and pyruvate
• Citric acid cycle occurs in the mitochondrion, oxidizes pyruvate to acetyl-CoA, produces ATP and electrons carried by NADH and FADH2
• Oxidative phosphorylationg produces ATP

Question 26

Identify the starting and ending molecules of each.

Answer 26

**

Question 27

relative free energy changes that occur during the process and the free energy of various intermediate compounds (eg. glucose vs. pyruvate vs. CO2)

Answer 27

**
Cellular respiration is exergonic

Question 28

understanding of substrate-level phosphorylation.

Answer 28

With the help of an enzyme:
- a phorphorylated donor molecule combines with ADP
AND becomes
- an unphosphorylated product molecule AND ATP

Question 29

Thermodynamics of respiration…explain how its a redox process.

Answer 29

Glucose gets oxidized to carbon dioxide. Oxygen gets reduced to water.

Question 30

Role of mitochondria in Chlamy cells.

Answer 30

• Synthesizes ATP using electron transport chain and ATP synthase complexes
  *

Question 31

Overview of metabolism: catabolism vs anabolism…link to thermodynamics (deltaG)

Answer 31

Catabolism refers to exergonic reactions that release ATP - these reactions break down energy-rich molecules into energy-poor molecules.

Anabolism refers to endergonic reacts that require ATP to occur - these reactions transfrom precursor molecules to cell macromolecules.

Question 32

Thinking about ATP and NADH in terms of ratios.

Answer 32

Catabolic processes turn ADP into ATP. Anabolic processes turn ATP into ADP.

IF inhibition of glycolysis, the respiratory pathway shuts down and the pool size of ADP increases relative to ATP.

What happens if light level changes?

Question 33

Concept of energy coupling….and how one could actually say endergonic reactions don’t actually occur.

Answer 33

ATP can be used to drive non-spontaneous reaction through energy coupling. Endergonic reactions only occur thanks to a coupled reaction mechanism, where the product of ATP hydrolysis (phosphate group) adds to the substrate (energy transferred to phosphate), making the overall reaction exergonic!

Endergonic reactions don’t occur because they must be coupled with exergonic reactions to occur.

Question 34

Process of electron transport from NADH or FADH2 to O2….the basics

Answer 34

Oxidizing NADH and phosphorylating ADP???
Complex I and IV pump protons (we never run out of protons) from inside the mitochondria into the intermembrane compartment. NADH enters in Complex I and is turned to NAD+, FADH2 enters in Complex II and is turned to FAD, O2 turns into H2O in Complex IV

Question 35

Oxidation of FADH2 comes after Complex I….why is that important?

Answer 35

Some free

Question 36

Where does proton pumping take place.

Answer 36

Pumped into intermembrane compartment through Complex I and IV, pumped out through ATP Synthase

Question 37

Definition of oxidative phosphorylation, chemiosmosis

Answer 37

Oxidative phosphorylation is the process within cellular respiration where electrons are transferred through an electron transport chain located in the inner mitochondrial membrane.*

Chemiosmosis - use proton gradient to do work, in this case, synthesize ATP

Question 38

Why chemiosmosis is built of proton gradients….(why not other molecules).

Answer 38

Chemiosmosis is built off protein gradients because the aqueous environment is in equilibrium and will replenish the protons.

Question 39

Importance of redox-active cofactors in electron transport (requirements for iron Fe).

Answer 39

Redox-active cofactors are required to steal a protein and pass it on to the next one, like a staircase of decrease redox potentials

Question 40

Understand why electrons move spontaneously down the chain

Answer 40

Electrons move spontaneously down the chain because each cofactor has decreasing redox potential, with increased electron affinity.

Question 41

Concept of coupling electron transport with ATP synthesis….and concept of uncoupling

Answer 41

Electron transport chain uses electrons? to convert O2 to H2O, resulting in a proton.

This proton reacts with ATP synthase converting ADP to ATP.

Uncoupler means there is no conservation of free energy, only heat is generated.

Question 42

Physiological role of regulated uncoupling using uncoupling proteins (e.g. babies and bears!)

Answer 42

Proton rush generates heat. Uncoupling is a metabolic way to generate heat during hibernation.

Question 43

Link between uncoupling expression and obesity (go to FORUM for discussion and answer on this).

Answer 43

Uncoupling**
where’s the chicken wings
those fuckers who stay thin

Question 44

Why chemical uncouplers (dinitrophenol) are toxic…..how does it alter metabolism.

Answer 44

Uncoupling results in the bypassing of conversion of ADP to ATP.*

Question 45

How metabolism shifts in response to low oxygen…how is that controlled.

Answer 45

In response to low oxygen, anaerobic respiration occurs, with a much lower ATP yield and with fermentation. Low oxygen concentration activates pyruvate dehydrogenase kinase, which inhibits pyruvate dehydrogenase complex.

Neurons cannot use fermentation, because it requires more ATP than other cells to function.

Question 46

What is the warburg effect.

Answer 46

The Warburg effect refers to the phenomenon where even in sufficient oxygen concentrations, (almost universally) cancer cells perform aerobic glycolysis.

Question 47

How cancer cells remodel normal respiration…role of glucose transporter, hexokinase, and pyruvate dehydrogenase kinase.

Answer 47

Because cancer cells rely on fermentation, they massively up-regulate glucose (glucose transporter transports way more glucose). More hexokinase to turn glucose to pyruvate. Pyruvate dehydrogenase kinase shows constitutive expression - always blocking pyruvate dehydrogenase complex

Question 48

basics of cancer detection based on metabolism (using radioactive forms of glucose).

Answer 48

Patient drinks radioactive glucose, concentrates in tumour cells due to high upregulation of glucose uptake in cancer cells, shows locations of tumours.

Question 49

BIG PICTURE…compare and contrast oxidative phosphorylation and the light reactions of photosynthesis (here is one thing - they both have ATP synthase that is linked to chemiosmosis)

Answer 49

Comparison:
- Both processes involve the movement of electrons through an electron transport chain and the pumping of protons across a membrane to create an electrochemical gradient.
- Both processes use ATP synthase to harness the energy of the electrochemical gradient for ATP synthesis.
- Oxygen serves as the final electron acceptor in oxidative phosphorylation, while NADP⁺ acts as the final electron acceptor in the light reactions of photosynthesis.

Contrast:
- Oxidative phosphorylation occurs in the mitochondria, whereas the light reactions occur in the chloroplasts.
- Cellular respiration uses organic molecules as electron donors, whereas photosynthesis uses light as the initial energy source and water as an electron donor.
- The final electron acceptor differs, with oxygen in cellular respiration and NADP⁺ in photosynthesis.
*