Biology Unit 4 (Enzymes and Photosynthesis)

What are the 2 steps of Carbon Fixation?

1. A CO2 molecule is attached to a 5 carbon sugar named ribulose biphosphate (RuBP). This happens due to an enzyme called rubisco 2. This RuBP is very unstable and immediately splits into 6 molecules of 3-phosphoglycerate

Non-competitive inhibitors

A molecule that binds together to another location (allosteric site) on the enzyme and causes a conformational change to alter the active site and the substrate won't bind

Competitive inhibitors

A molecule that resembles the substrate and competes for the active site (ex. carbon monoxide fits in the same place as oxygen in hemoglobin)

What is the calvin cycle?

A pathway that converts carbon dioxide to glucose, occurs in the stroma of the chloroplast

Describe the light reaction cycle

Captures energy from light and transfers it to ADP and NADPH Occurs at the thylakoid membrane (or the plasma membrane in prokaryotes) This is the "photo" part of photosynthesis

What is carbon fixation? Which enzyme does this?

Carbon fixation is the attaching of carbon dioxide (CO2) to a 5 carbon sugar named ribulose biphosphate (RuBP). The enzyme that does this reaction is called rubisco.

What are enzymes?

Catalytic globular proteins

Explain how negative feedback works in biochemical pathways

Reactions are strung together in biochemical pathways (a series of reactions). Each of these is catalyzed by an enzyme, therefore the product of one reaction becomes the substrate of the next reaction. Biochemical pathways are controlled by negative feedback. This controls the accumulation of the end product by inhibiting one of the early enzymes in the pathway

What is an endergonic reaction?

Requires energy (ATP) In this case, enzymes transfer a phosphate from ATP onto a substrate so that it's energized and ready to react Positive change in G

What is chlorophyll?

The green pigment within the chloroplast

Where does the light reaction occur?

The thylakoid membrane

The free energy for the synthesis of glucose in photosynthesis is ΔG = 2780kJ. Describe or draw what this change looks like on a graph of free energy over the progress of the reaction. What term describes this synthesis with respect to its ΔG? Does this synthesis require ATP? An enzyme?

The ΔG given for glycolysis is positive, meaning that energy is put into the system and the change is therefore endergonic. On a graph, the free energy of the substrate CO2 must be lower than the free energy of the product glucose. ATP provides the energy increase to the system. An enzyme is required to transfer the phosphate from ATP to the substrate so the reaction can begin.

Carbamoyl phosphate combines with ornithine to produce citrulline. Aspartate and water are added later. End products are fumarate, urea, and ornithine. Is this pathway linear or a cycle? Explain.

This is a cycle because a product required to start the cycle again is produced by the cycle (ornithine). The Calvin cycle is similar in that it makes RuBP which it requires to start the cycle again, but it also needs CO2 which is not produced by the cycle, just like the carbamoyl phosphate, aspartate, and water are in this cycle.

What is photosynthesis?

the conversion of light energy into chemical energy, coupled with the conversion of carbon dioxide into glucose

What are steps 1 and 2 of reduction?

1. Each molecule of 3-phosphoglycerate (PGA) receives an additional phosphate to become 1-3 biphosphoglycerate 2. ATP provides the energy for this stage and becomes ADP, which goes to the thylakoids for the light reaction

What are the 3 steps of regeneration?

1. Through a series of reactions, 5 G3P are rearranged into 3 molecules of RuBP. ATP is also used here to provide energy for this reaction and the ADP returns to the thylakoids 2. The Calvin cycle can begin again once you have enough RuBP 3. The Calvin cycle must happen 6 times in a row to make glucose because glucose is a 6 carbon molecule

What are steps 3 and 4 of reduction?

3. NADPH (from the light reaction) donates a pair of electrons to remove a phosphate (reducing it) to create 6 molecules of glyceraldehyde 3 phosphate (G3P). The NADP+ now goes to the thylakoids for the light reaction 4. Only one of those G3P leaves the cycle to make glucose (C6H12O6). The rest cycle on to replace RuBP used in the carbon fixation

Explain why plants use ATP to make glucose in photosynthesis and then use glucose to make ATP in cellular respiration instead of just keeping all of its energy in the form of ATP.

ATP is unstable and short-lived, so ATP cannot be stored for use during the night or on cloudy days. Glucose, however, is extremely stable and can be stored as a monosaccharide, with another sugar as a disaccharide, or as a polysaccharide long-term.

What is the induced fit model?

As the substrate fits into the active site of the enzyme, the active site will change shape more to help the reaction happen more efficiently

Where does the light reaction occur?

At the thylakoid membrane of the chloroplast in plants and in eukaryotic phytoplankton. It also occurs in the cell membrane of photosynthetic bacteria

Discuss carbon fixation. Explain what it is, how it occurs, where it occurs (cellular location and type of organism), and when it occurs (which step of the pathway).

Carbon fixation is the first step of three in the Calvin cycle, which happens in the chloroplast (found in the fleshy tissue called mesophyll) in plant cells. In this step, carbon dioxide (CO2) us attached to a 5 carbon sugar named RuBP by an enzyme called rubisco, making PGA, which continues through the Calvin cycle.

What are catalysts?

Chemical agents that speed up reactions without getting used up in the reaction and can be used over and over again

What is the difference between chlorophyll a and b?

Chlorophyll a: absorbs blue violet and red light, reflects green light Chlorophyll b: absorbs blue and orange light, reflects yellow green light, doesn't participate directly in the light reaction but transfers the absorbed light energy to chlorophyll a

Photosynthesis formula

Chlorophyll and sunlight involved in the arrow

What organelle does photosynthesis?

Chloroplast

What are the 2 types of enzyme inhibitors?

Competitive inhibitors and non-competitive inhibitors

What happens in photosystem II?

Contains chlorophyll Sunlight activates 2 electrons from the chlorophyll molecules which will be used in the next step-> the electron transport chain

Explain why "dark reaction" is a misleading name for the Calvin Cycle.

Dark reaction is a misleading name because, while the Calvin Cycle doesn't require sunlight, it requires ATP and NADPH from the light reaction, which can't be created without sunlight. Thus, the Calvin Cycle doesn't indirectly require sunlight.

Describe the chloroplast structure

Double membraned structure Inside are disc-like structures called thylakoids that stack up to make granum Space around the granum is called stroma

What do enzymes require and what happens if they don't have these conditions?

Each enzyme has an optimal condition in which it functions. If this optimal condition is altered, the enzyme can denature from its quaternary to primary structure

What are the 2 parts of light reaction?

Electron transport chain (transports electrons) Phosphorylation (adding a phosphate to ADP to make ATP)

Explain what causes electrons increase in energy during the light reaction

Electrons are initially excited by sunlight entering photosystem II, then again by sunlight in photosystem I.

What happens in the electron transport chain?

Electrons from the chlorophyll in photosystem II are passed onto the electrons transport chain These electrons had a great deal of energy from the sunlight they received and use this energy in the electron transport chain to create the hydrogen ion gradient by moving the H+ from the stroma to the thylakoids

Contrast endergonic and exergonic reactions by their delta G and by what they require.

Endergonic reactions require ATP and have a positive change in G. Exergonic reactions don't require ATP and have a negative change in G.

What are enzyme inhibitors? Are they reversible?

Enzyme inhibitors bind to the enzyme and trigger a conformational change to change the enzyme. This is usually reversible

What happens in photosystem I?

Excites the electrons again, once they have used up all their energy. These energized electrons attach themselves to NADP+ which will carry them to the next stage of photosynthesis (Calvin cycle)

Where in the plant is the chloroplast found?

Found in all the green parts of the plant, primarily in the fleshy tissue of the leaf mesophyll

How is ATP generated in the light reaction?

H+ are very concentrated in the thylakoid and exit back to the stroma by the only available path: through the H+ channel in ATP synthase. As the H+ pass through, they spin ATP synthase like a turbine. ATP synthase uses this kinetic energy to add a phosphate to ADP to make ATP. ATP is made on the stroma side.

Describe all of the events of the light reaction with respect to the electrons.

In the first photosystem embedded in the thylakoid membrane of the chloroplast, chlorophyll's electrons absorb energy from sunlight and become so excited that they escape to enter the electron transport chain. Since chlorophyll is then short two electrons, it takes them from water inside the thylakoid. This action leaves chlorophyll ready to absorb more light but also splits the water to produce ½ O 2 and 2H + ions. The oxygen diffuses out of the chloroplast and into the atmosphere. The high-energy electrons are passed from one membrane protein to the next along the electron transport chain, losing energy as they go. In the second photosystem, chlorophyll's electrons absorb energy from light and become so excited that they escape to enter the last protein of the electron transport chain. Since chlorophyll is then short two electrons, it takes them from the first part of the electron transport chain (the same electrons from before, that originally came from the first photosystem). The high-energy electrons at the end of the electron transport chain are accepted by NADP+, which combines with H+ to form NADPH.

Explain the steps of ATP production in photosynthesis.

In the light reaction, ATP synthase is energized by H+ ions traveling down the gradient and into the stroma and uses that kinetic energy for phosphorylation- to add a phosphate to ADP to make ATP. That ATP travels to the Calvin cycle where it gives its phosphates to PGA, becoming ADP and traveling back to the light reaction to become ATP again. ATP is also used in the Calvin cycle to add a phosphate to G3P, making RuBP and ADP. That ADP also travels back to the light reaction to become ATP again.

Explain the role of NADP+/NADPH in photosynthesis. Include the exact steps in the light reaction and the Calvin cycle.

In the light reaction, NADP+ uses the energy from the electrons and an H+ from the H+ ion gradient to become NADPH, which carries electrons from the thylakoid membrane to the Calvin Cycle in the stroma. In the Calvin cycle, NADPH uses its energy to detach a phosphate from what will become G3P during reduction, thereby turning into NADP+ again and returning to the light reaction to start the process over.

Where does the calvin cycle occur?

In the stroma of the chloroplast in plants. It also occurs in the cytoplasm of photosynthetic bacteria.

Why does it take 2 turns of the Calvin cycle to produce one glucose?

It takes two turns of the Calvin cycle to produce one glucose because when 3CO2 are put into the cycle, only 3 G3P are released to make glucose, and glucose requires 6 G3P. When the cycle has spun twice, one glucose will be produced

What are the two types of photosynthesis?

Light Reaction and Calvin Cycle

What is metabolism and why does it require enzymes?

Metabolism is the sum of all reactions in an organism. Metabolism requires enzymes to convert matter and transfer energy

Explain the function of NADP+

NADP+ picks up high energy electrons at the end of the electron transport chain along with a H+ to become NADPH. NADPH carries the high energy electrons to the Calvin Cycle.

What are the 3 products of light reaction?

Oxygen (O2) ATP An electron carrier (NADPH)

What is an exergonic reaction?

Requires no ATP Enzymes lower the activation energy because body heat helps break the bonds in the substrate and starts the reaction Negative change in G

Explain what causes electrons to decrease in energy during the light reaction

That energy is used up in motion- the electron transport chain moves electrons along the thylakoid membrane and pushes H+ ions from the stroma to the inner thylakoid which causes it to lose energy. It also loses energy when creating NADPH.

The Calvin cycle has also been called the dark reaction or light-independent reaction because it doesn't capture or use solar energy. These names are misleading, however, because the Calvin cycle, like the light reaction, only occurs in the light. Explain why this is true.

The Calvin cycle requires ATP and NADPH, which are products of the light reaction. Because these chemicals are unstable and short-lived, they are available to the Calvin cycle only when the light reaction is running. Only during the day is there enough sunlight to excite chlorophyll's electrons for the light reaction to operate.

Describe ONE way the H+ gradient is created. Explain how the gradient is used.

The H+ gradient is created when hydrolysis breaks down H2O molecules to replace electrons in photosystem II. The gradient is used here to give ATP synthase kinetic energy so it can add a phosphate to ADP to make ATP. This ATP will go onto the Calvin Cyle and assist in making glucose.

How is ATP created in the light reaction?

The H+ ion gradient is now used to energize the ATP synthase which adds a phosphate to ADP to create ATP

What is activation energy?

The amount of energy it takes to start a reaction

Describe the events of the Calvin Cycle, accounting for all substrates and products. Tell why the first step is particularly important.

The enzyme Rubisco adds one carbon dioxide each onto 3 molecules of a five carbon (5C) sugar to make three molecules of a 6C sugar. This step, called carbon fixation, can only be done by plants, photosynthetic bacteria, and eukaryotic phytoplankton. However, carbon fixation is necessary for all carbon-based life on earth, since we are all made of macromolecules containing carbon skeletons. Every carbon in every one of our carbohydrates, proteins, lipids, and nucleic acids was at some time part of a carbon dioxide molecule in the air or water until it entered a plant (or other photosynthetic organism) and encountered the enzyme Rubisco. The three 6C sugars split to make six 3C sugars which are phosphorylated by ATP and reduced by NADPH to make another 3C sugar called glyceraldehyde phosphate (G3P). The six molecules of G3P are then divided, with five of the 3C molecules rearranged and phosphorylated into three 5C molecules (5x3 = 3x5). These three 5C molecules are both end products and initial substrates of the process, thereby defining the Calvin cycle as a cycle. The remaining one of the six G3P exits the cycle and combines with another G3P to form glucose. Thus, it takes two turns of the Calvin cycle, including six molecules of CO 2, to make the two G3P needed to make one glucose. Each ADP and each NADP + return to the light reaction to pick up another phosphate and pair of high-energy electrons, respectively.

What happens to the hydrogen ions in the light reactions?

The hydrogen ion gradient is built in 2 ways. First, when water is split by photosystem II, it produces 2H+ inside the thylakoid. Second, one of the proteins in the electron transport chain uses energy from the transported electrons to pump H+ from the chloroplast stroma to the thylakoid.

What is a photosystem?

The light-harvesting complex found in the thylakoid membrane. The thylakoid membrane has a variety of different components that do specific jobs in the light reaction

How are competitive inhibition and non-competitive inhibition the same?

The two inhibitors are the same in that they prevent a substrate from binding to the enzyme's active site

The GL oxidase step has a delta G of 45 KJ/mol. What term describes this reaction? What does this reaction require?

This is an endergonic reaction because it has a positive change in G. This reaction requires ATP and an enzyme.

How do enzymes affect activation energy?

Thye lower the activation energy so that the reactions happen at lower temperatures or with less energy needed

Describe the Calvin Cycle

Transfers energy from ATP and NADPH to glucose for storage Occurs in the stroma of the chloroplast (or the cytoplasm in prokaryotes)

Describe the most likely way a pathway would be controlled by non-competitive inhibition.

Vitamin C (the product) would send a message to GP phosphatase to stop the reaction because enough of the product had been made. It would send the message to that enzyme specifically because it is early in the reaction and would conserve the most energy. Non-competitive inhibition works by the non-competitive inhibitor binding to an allosteric site and causing a conformational change in the enzyme's active site, preventing the substrate from entering.

How are the electrons replaced in the chlorophyll?

Water is broken down inside the thylakoid to recover these electrons. This releases oxygen into the air. The 4 hydrogens are going to be used to build a gradient inside the thylakoid

In photosynthesis, what molecule splits the water? Why does it do that?

Water splits to replace 2 electrons that were excited and moved to the electron transport chain in photosystem II, which is found in the thylakoid membrane of chloroplasts, specifically in the chlorophyll (a green pigment).

What are some factors that affect the activity of enzymes?

pH change and increased temperature non-protein helpers: Cofactors- inorganic molecules (ex. metal ions) Coenzymes- organic molecules (ex. vitamins)

Write as much of the photosynthesis formula as you can remember. Then use your notes to correct it or fill it in. Underneath it, write whether each chemical belongs to the light reaction or to the Calvin cycle.

sunlight + 6 CO 2 + 6 H 2 O ----> 6 O 2 + C 6 H 12 O 6 light rxn/ Calvin cycle/ light rxn/ light rxn. Calvin cycle