U4
Unit 4 - Metabolism (C1.1, C1.2, C1.3)
Important Concepts
C1.1 Enzymes and metabolism
Active site, substrate, enzyme-substrate complex
Active site = location on an enzyme that binds to substrate through induced fit and catalyses a reaction
Substrate = a reactant that bonds with an active site to be catalysed and turned into a final product
Enzyme-substrate complex = a temporary molecule formed when the substrate binds to the enzyme
Induced fit model
The binding of the substrate(s) to the enzyme causes a slight change in the shape of the enzyme to enhance its catalytic activity. (both the enzyme and substrate change shape to better fit together and make the reaction catalyze)
How enzymes lower activation energy
Enzymes allow for a different pathway for the reactants to reach products thus making the reaction faster and more efficient. They also lower the activation energy.
Factors that affect enzyme activity (temperature, pH, substrate concentration)
Temperature = affects the speed at which molecules move around, therefore, as temperature increases, the chances of enzymes colliding with substrates increases. Enzymes have a specific temperature at which they will work the best. This is called the optimal temperature. There is a temperature maximum, once the enzyme is heated too far, it denatures and is no longer able to catalyse reactions.
pH = affects the rate of enzyme activity. Enzymes have an optimal pH at which they work the best. If the pH is increased or decreased from the optimal level, enzyme activity decreases and eventually stops.
Substrate concentration = as substrate concentration increases, enzyme activity also increases, but eventually, it reaches a maximum rate when all the enzyme active sites are full. After this point, adding more substrate won’t speed up the reaction because the enzyme is working at full capacity.
Denaturation of proteins
In conditions, such as high heat or incorrect pH, the bonds holding the tertiary structure together break. The 3-D protein loses its shape & properties. When an enzyme is denatured, the active site is altered and can not bind to the substrate.
Competitive inhibitors and non-competitive inhibitors
Competitive = occurs when an inhibitor mimics the substrate (similar shape) and competes for binding at the enzyme's active site. Increasing substrate concentration can overcome this inhibition
Non-competitive = happens when the inhibitor binds to an allosteric site (not the active site), changing the enzyme's shape and reducing its ability to bind to substrates. This cannot be overcome by increasing substrate concentration.
Know some examples of proteins in the cell
Enzymes
Transport channels (proteins)
Transport pumps (proteins)
Glycoproteins
Cyclic vs linear metabolic pathways
Linear = reactants become products
Cyclic = reactants become products but the some reactants are regenerated to continue the cycle
Anabolic vs catabolic reactions
Anabolic = formation of products
Catabolic = breaking down of complex molecules
Feedback inhibition
A cellular control mechanism, in which the activity of an enzyme is inhibited by the end product of a metabolic pathway
C1.2 Cell Respiration
ATP - structure, function, properties
Structure = nucleotide made of one 5-C sugar, one nitrogenous base, and three phosphate groups
Function = form of useable energy
Properties =
Soluble in water
Stable at neutral pH
Cannot pass through plasma membrane
3rd phosphate group can be removed and reattached
Releases usable energy
Variables affecting the rate of cell respiration - respirometer (instrument)
Temperature
Quantity of seeds
Types of seeds
NAD (oxidized and reduced form)
Oxidized = NAD+
Reduced = NADH
Structure and function of mitochondria
Structure =
Function = site of the link reaction and kreb’s cycle (allows for certain conditions like the proton gradient)
4 stages of cellular respiration (location, reactants and products of each)
Chemiosmosis and concentration gradient of H+
The movement of protons across a membrane through ATP synthase to produce ATP.
Powered by the proton gradient (As electrons are passed through the electron transport chain (ETC), energy is released and used by protein complexes to pump protons (H⁺) from the mitochondrial matrix (NADH & FADH) into the intermembrane space. This creates a high concentration of protons outside the matrix, establishing an electrochemical gradient.
Substrate phosphorylation vs oxidative phosphorylation
Substrate phosphorylation = in glycolysis and in krebs cycle ; A process in which ATP is directly generated by transferring a phosphate group from a high-energy substrate molecule to ADP (no enzyme)
Oxidative phosphorylation = process of generating ATP through the electron transport chain and chemiosmosis, where energy from electrons is used to pump protons across the membrane, driving ATP synthesis via ATP synthase.
Aerobic and anaerobic respiration
Aerobic = Respiration that occurs with oxygen. Includes glycolysis, the Krebs cycle, and oxidative phosphorylation, producing a large amount of ATP.
Anaerobic = A form of respiration that occurs without oxygen. Produces less ATP than aerobic respiration and includes processes like fermentation.
Yeast as application of anaerobic respiration
Yeast cells use anaerobic respiration (fermentation) to generate energy in the absence of oxygen, converting glucose into ethanol and carbon dioxide. This process is widely used in brewing, baking, and biofuel production, where the byproducts (ethanol and CO₂) play key roles in fermentation.
The formation of lactate in animal cells due to anaerobic respiration
In animal cells, when there isn't a lot of oxygen, pyruvate produced from glycolysis is converted into lactate to regenerate NAD⁺, allowing glycolysis to continue and produce ATP. This process, known as lactic acid fermentation, helps provide energy in the short term but leads to the buildup of lactate (& oxygen debt), which can cause muscle fatigue.
Use of lipids as respiratory substrates (using lipids in cellular respiration)
Lipids can be used as respiratory substrates when broken down into fatty acids and glycerol. Fatty acids undergo beta-oxidation to form acetyl-CoA, which enters the citric acid cycle, leading to the production of ATP through oxidative phosphorylation.
C1.3 Photosynthesis
Light Dependent Reactions (photolysis, photoactivation, phosphorylation)
Photolysis = the splitting of water into oxygen, protons and electrons
Photoactivation = When the chlorophyll molecules in the reaction centre absorb the energy from a photon, an electron within the molecule becomes excited
Phosphorylation = phosphorylation occurs through a process called photophosphorylation. Photoactivation occurs exciting electrons that pass through the electron transport chain, which creates a proton gradient across the thylakoid membrane. This proton gradient drives ATP synthase, allowing ADP to be phosphorylated to ATP as protons flow back into the stroma. This ATP is then used in the Calvin cycle to help convert carbon dioxide into sugars.
Calvin cycle (Rubisco, RuBP, carboxylation, use of NADH, ATP, products)
Rubisco = The most abundant enzyme. Catalyses reaction between RuBP (5-C) and CO2
Carboxylation = the process where CO₂ is added to a RuBP, by the enzyme Rubisco. This reaction forms an unstable six-carbon compound, which immediately splits into two molecules of 3-PGA, the first stable products of the cycle.
Pigments of photosynthesis (purpose, relation to wavelength)
Plants can use light in the range of 400 to 700 nanometers (nm) for photosynthesis, which includes the visible light spectrum. The most effective wavelengths for photosynthesis are in the blue (430-450 nm) and red (650-680 nm) regions, as these are absorbed most efficiently by chlorophyll and other pigments, providing the energy needed for the process. The center range, green light range, (500-570 nm) is ineffective for photosynthesis because chlorophyll reflects green light, meaning less energy is captured from this wavelength.
How to use paper chromatography to separate pigments
Extract pigments from plant material. (ex; crushing plant leaf)
Spot pigment extract on chromatography paper.
Develop a chromatogram by allowing solvent to move up the paper. (ex; use alcohol as solvent & allow the paper to absorb solvent)
Pigments separate based on solubility and affinity for the paper.
Measure distances, visualize pigments, and calculate Rf values.
Absorption spectrum vs action spectrum
Action spectrum is a graph showing the rate of photosynthesis at each wavelength of light
The absorption spectrum is a graph showing the percentage of light absorbed at each wavelength by a pigment or a group of pigments.
Purpose of water in photosynthesis
The purpose of water during photosynthesis is to provide electrons and protons for the light reactions. Water molecules are split (photolysis) by light energy, releasing oxygen, electrons, and hydrogen ions, which are used to generate ATP and NADPH for the Calvin cycle.
Factors affecting the rate of photosynthesis
Temperature
Lack of water
Lack of CO2
Lack of light
Questions to consider
C1.1 Enzymes and Metabolism
What is the function of enzymes in metabolic reactions?
Define a metabolic reaction and explain how enzymes catalyze these reactions.
Metabolic reactions are any biochemical reactions that occur within cells, these reactions are sped up via enzymes. Catalysts speed up reactions by lowering the activation energy required to be overcome. Reactants (substrates) bind to the active sites on enzymes, they are then catalyzed and released as products
Explain enzyme specificity.
What is meant by the "lock and key" model and the "induced fit" model?
The active site of an enzyme and the substrate mold themselves slightly to perfectly fit one another thereby increasing catalytic activity.
How do these models explain enzyme-substrate interactions?
When a substrate binds to an active site it temporarily forms an enzyme-substrate complex.
Describe how temperature, pH, and substrate concentration affect enzyme activity.
What are the effects of increasing temperature on enzyme activity, and why?
Raise in temperature leads to increased kinetic energy which in turn increases the number of successive collisions occurring, meaning a faster reaction rate. The opposite is true in cases of decreased temperature. If temperature is increased drastically it will exceed the optimum temp range leading to damaging the 3D structure of the protein. When the structure is damaged the enzyme denatures and the active site changes shape, meaning substrates can no longer bind.
How does pH affect enzyme structure and function?
Like temperature there's an optimum pH range, when it is decreased or increased it slows eventually stopping all together.
What is enzyme inhibition?
Compare competitive and non-competitive inhibition.
Competitive:
Binds directly to active site
Similar structure to substrate
Can be outcompeted through increase substrate concentration
Non-competitive:
Binds to allosteric site rather than active site
Changes shape of active site leading to denaturation
Cannot be outcompeted through increased substrate concentration
How does each type of inhibition impact enzyme activity?
Describe the difference between anabolism and catabolism.
Provide examples of each type of metabolic pathway
Linear: reactant → product
Cyclical: reactant → product, some of the products are then turned back into reactants to continue a cycle
What is feedback inhibition in metabolic pathways?
Provide an example of feedback inhibition and explain its importance in regulating metabolic processes.
Many enzymes are regulated by chemical substances that bind to a site on the enzyme away from the active site (called the allosteric site)
In a metabolic pathway, the end product acts as an allosteric inhibitor. This controls the amount of product being produced and prevents a buildup of intermediate products
Cellular Respiration
What is the overall purpose of cellular respiration?
Describe how cellular respiration provides energy for the cell.
Cellular respiration turns glucose into usable energy
List the four main stages of aerobic cellular respiration.
Describe what happens during glycolysis, the Link reaction, the Krebs cycle, and the electron transport chain (and chemiosmosis).
Glycolysis:
Glycolysis occurs in the cytoplasm.
It is anaerobic, meaning it does not require oxygen.
The process begins with glucose and ends with two molecules of pyruvate.
The energy yield from glycolysis is 2 ATP and 2 NADH per glucose molecule.
Link Reaction:
3 step process:
Decarboxylation → carbon is removed
NAD+ is reduced to NADH
CoA bonds to the remainder of the initial pyruvate molecules
The link reaction occurs once for each pyruvate, but since two pyruvate molecules are produced from one glucose molecule during glycolysis, the link reaction happens twice for each glucose molecule.
The NADH produced in the link reaction carries electrons to the electron transport chain, contributing to the generation of ATP via oxidative phosphorylation.
Kreb’s cycle
It begins with the combination of acetyl-CoA (from glucose, fatty acids, or amino acids) and oxaloacetate, forming citrate (6 carbons). Through a series of reactions, citrate is broken down, releasing 2 molecules of CO₂ and transferring high-energy electrons to NADH and FADH₂. These electron carriers will later donate electrons to the electron transport chain to generate ATP.
Key outputs per cycle (for one acetyl-CoA):
3 NADH
1 FADH₂
1 ATP (or GTP)
2 CO₂
The cycle regenerates oxaloacetate, enabling it to repeat. For each glucose molecule, the cycle turns twice, producing a total of 6 NADH, 2 FADH₂, 2 ATP, and 4 CO₂. The Krebs cycle is a central part of aerobic respiration, providing energy for cells.
ETC
Electron Donation: The high-energy electrons from NADH and FADH₂ (produced in glycolysis, the link reaction, and the Krebs cycle) are passed to protein complexes in the inner mitochondrial membrane (Complexes I-IV).
Electron Transport: Electrons move through the protein complexes (I, II, III, and IV), releasing energy at each step. This energy pumps protons (H⁺) from the mitochondrial matrix into the intermembrane space, creating a proton gradient.
Oxygen as the Final Electron Acceptor: At the end of the chain, electrons combine with oxygen (O₂) and protons to form water (H₂O). Oxygen is the final electron acceptor, preventing a backup of electrons and enabling the chain to continue.
ATP Synthesis: The proton gradient created by the electron transport chain generates a potential energy difference (proton motive force) across the inner membrane. Protons flow back into the matrix through ATP synthase, a protein complex that uses this flow to synthesize ATP from ADP and inorganic phosphate (Pi).
Approximately 32-34 ATP (from NADH and FADH₂) are produced via oxidative phosphorylation (ATP synthase).
Water is produced as a byproduct.
What is the role of NAD⁺ and FAD in cellular respiration?
How do these molecules function as electron carriers in the process of cellular respiration?
Carrying H+ and electrons, these molecules donate their electrons to enzymes during ETC where they power the enzymes to pump the H+ through, creating a concentration gradient of H+ protons.
Where do they come from in a cell?
These NAD come from glycolysis, the link reaction and the Krebs cycle
Describe the process and location of glycolysis.
Happens around the cell in the cytoplasm
What are the reactants and end products of glycolysis, and how is ATP produced in this step?
The reactants of glycolysis are glucose and the products are pyruvates the ATP produced is by substrate level phosphorylation.
What happens during the Link Reaction?
2 pyruvate turns into acetyl CoA
Decarboxylation
NAD→ NADH (Reduction)
Where does it take place?
In the matrix of the mitochondria
What are the three modifications made to pyruvate?
Decarboxylation, reduction, and it goes through altering into acetyl-Coa
What happens during the Krebs cycle?
What are the key products of the Krebs cycle, and how do they contribute to the generation of ATP?
4 CO2, 6 NAD + 6 H = 6 NADH, 2 FADH2, 2 ATP
Explain the role of the electron transport chain in aerobic respiration.
Where does the electron transport chain occur?
How does the flow of electrons through the chain lead to ATP production?
What is chemiosmosis and its role in ATP production?
How does the proton gradient facilitate ATP synthesis?
What is the role of oxygen in cellular respiration?
Explain how oxygen is used in the final steps of electron transport and why it is critical for ATP production.
Due to its high electronegativity, once electrons have passed through the carrier enzymes they are attracted to O2 where they combine with H+ to form H2 once the H2 has formed it bonds with the O2 to make H2O after which it leaves the cell. Without oxygen aerobic respiration wouldn’t be possible meaning anaerobic respiration would occur, yielding only 2 ATP rather than 32.
Compare and contrast aerobic and anaerobic respiration.
What are the differences in efficiency between aerobic and anaerobic respiration?
Aerobic respiration is far more efficient at generating ATP than anaerobic respiration. However, anaerobic respiration is useful when oxygen is scarce or during short bursts of intense activity.
Aerobic Respiration: 38 ATP/glucose.
Anaerobic Respiration: 2 ATP/glucose
In anaerobic respiration pyruvate is converted into lactic acid (in animals) or ethanol and carbon dioxide (in yeast), rather than proceeding to the Kreb’s cycle and the electron transport chain.
Describe lactic acid fermentation and alcoholic fermentation as examples of anaerobic pathways.
Lactic acid:
Alcoholic fermentation:
What are the net products of cellular respiration in terms of ATP?
How many ATP molecules are produced from one molecule of glucose in aerobic respiration?
Theoretically the number of ATP produced from one glucose is around 32-36
Compare the use of carbohydrates vs. lipids as respiratory substrates
Photosynthesis
What is the function of photosynthesis in plants and algae?
Why is photosynthesis essential for life on Earth?
Photosynthesis is the primary process that sustains life on Earth by producing food, oxygen, and maintaining atmospheric balance. Without photosynthesis, Earth would not have the resources necessary to support life as we know it. Plants are at the bottom of the food chain, which provide energy for all other living organisms.
Describe the two main stages of photosynthesis.
What occurs during the light-dependent reactions and the Calvin cycle?
Light-Dependent reactions
Photon absorption : Light energy (photons) is absorbed by chlorophyll and other pigments in the thylakoid membranes. This excites electrons in chlorophyll, raising them to a higher energy state.
Water Splitting (Photolysis): Water molecules are split into O₂, protons (H⁺), and electrons (e⁻) by the enzyme photolysis. Oxygen is released as a byproduct.
Electron Transport Chain (ETC): Excited electrons move through the electron transport chain (ETC) in the thylakoid membrane. As electrons pass through, energy is used to pump protons (H⁺) into the thylakoid lumen, creating a proton gradient.
ATP Synthesis (Chemiosmosis): The proton gradient drives ATP synthase, which synthesizes ATP from ADP and inorganic phosphate (Pi) as protons flow back into the stroma.
NADP⁺ Reduction: Electrons from the ETC are transferred to NADP⁺, reducing it to NADPH (with the help of protons from the stroma). NADPH is used in the Calvin cycle.
Calvin Cycle
Carbon Fixation: Ribulose bisphosphate (RuBP) (5-carbon sugar) combines with CO₂ from the atmosphere, catalyzed by the enzyme RuBisCO. This produces an unstable 6-carbon compound that immediately splits into two molecules of 3-phosphoglycerate (3-PGA).
Reduction Phase:
ATP and NADPH (from the light-dependent reactions) are used to convert 3-PGA into glyceraldehyde-3-phosphate (G3P), a 3-carbon sugar.
ATP is used to phosphorylate 3-PGA, and NADPH provides electrons to reduce it.
Regeneration of RuBP:
Some of the G3P molecules exit the cycle to form glucose and other carbohydrates.
The remaining G3P molecules are used, along with ATP, to regenerate RuBP, which is required to continue the cycle.
End Products:
G3P (glyceraldehyde-3-phosphate) can be used to form glucose, starch, and other carbohydrates that are vital for plant growth and energy storage.
Where in the cell do the light-dependent reactions and the Calvin cycle take place?
Discuss the role of the chloroplast in each of these stages.
What is the role of chlorophyll in photosynthesis?
Where does chlorophyll absorb light energy, and how is this energy used in the light-dependent reactions?
Once the light photons hit psII or psI the chlorophyll within them begin to vibrate, triggering the next and so on until it reaches the electrons to charge them.
Explain the light-dependent reactions of photosynthesis.
Light dependent reactions of photosynthesis are reactions which require light.
What are the key products (ATP, NADPH, oxygen) of the light-dependent reactions, and how are they used in the next stage?
The reactants of the light reaction are water, and light photons. Meanwhile the products are ATP and NADPH which is used throughout the calvin cycle. The ATP is energy used throughout the calvin cycle and NADPH carries potential energy.
Describe the Calvin cycle.
How does ATP and NADPH from the light-dependent reactions contribute to the Calvin cycle?
The Calvin cycle requires ATP that is used up from the light dependent reactions, meanwhile NADPH carries electrons which are used for the calvin cycle.
What is carboxylation?
Carboxylation is when Carbon Dioxide is diffused inside of the cell. This only happens at the beginning of the Calvin cycle.
What are the reactants and products of the Calvin cycle?
Reactants of the calvin cycle are CO2, ATP, NADPH while the products are Triose phosphate, ADP, and NADP
What is the role of NADP⁺ in photosynthesis?
How does NADP⁺ function in the light-dependent reactions, and why is it reduced to NADPH?
NADP⁺ is reduced to NADPH in the light-dependent reactions to capture high-energy electrons, which are then used in the Calvin cycle to build organic molecules like glucose.
What factors affect the rate of photosynthesis?
How do temperature, light intensity, and carbon dioxide concentration affect the rate of photosynthesis?
Temp, light and [CO2] are all limiting factors
Temperature ; Affects enzyme activity. Too high or too low temperatures can reduce the rate of photosynthesis.
Light intensity ; At low light levels, increasing light intensity boosts photosynthesis, but after a certain point, it has no further effect.
CO2 concentration ; Higher CO₂ levels increase the rate of photosynthesis, but only up to a certain saturation point where other factors become limiting.
Explain the concept of the action spectrum and absorption spectrum.
How do the absorption properties of chlorophyll relate to the action spectrum of photosynthesis?
Absorption spec = graph showing the % of light absorbed at each wavelength by a pigment or a group of pigments.
Action spec = graph showing the rate of photosynthesis at each wavelength of light
Chlorophyll absorbs light most efficiently in the red and blue regions of the spectrum, but it reflects green light, which is why plants appear green.
The action spectrum of photosynthesis shows the overall rate of photosynthesis at different wavelengths of light. It closely matches the absorption spectrum of chlorophyll, meaning photosynthesis happens most effectively in the red and blue light regions where chlorophyll absorbs the most light.
How does the structure of the chloroplast facilitate photosynthesis?
Describe the structure of the thylakoid membrane, thylakoid lumen and stroma, and their role in the light-dependent and light-independent stages.
The thylakoid membrane is where light energy is captured (in photosystems) and used to produce ATP and NADPH. The light is absorbed & energy travels along an ETC.
The thylakoid lumen stores protons (conc. gradient) to help create ATP.
The stroma is where carbon fixation occurs to produce sugars in the light-independent reactions.
How does the process of photosynthesis compare to cellular respiration?
Discuss how the products of photosynthesis (glucose and oxygen) are used in cellular respiration and vice versa.
Photosynthesis produces glucose and oxygen, which are used in cellular respiration to generate energy.
Products of photosynthesis : Glucose (C₆H₁₂O₆) stores energy from the sun. Oxygen (O₂) is released as a byproduct.
Cellular respiration produces carbon dioxide and water, which are used in photosynthesis to make glucose and oxygen again. This creates a cycle that sustains life on Earth.
Products of cellular respiration : glucose is broken down in glycolysis and further processed in the Krebs cycle to produce ATP. Oxygen is used in the final step of cellular respiration (the electron transport chain) to help make more ATP.
Explain the importance of the proton gradient in the light-dependent reactions.
How is the proton gradient generated, and how does it contribute to the production of ATP?
Proton gradient generation: Light energy splits water molecules (photolysis) and pumps protons across the thylakoid membrane via the electron transport chain (from stroma) (some protons are provided from photolysis. ATP production: The proton gradient created by these processes powers ATP synthase, which produces ATP from ADP and inorganic phosphate (Pi) as protons flow back into the stroma.