U3 AOS 2 - How are biochemical pathways regulated?

U3 - How do cells maintain life?

Study Dotpoints for this AOS ?

Regulation of biochemical pathways in photosynthesis and cellular respiration

• the general structure of the biochemical pathways in photosynthesis and cellular respiration from initial reactant to final product 

• the general role of enzymes and coenzymes in facilitating steps in photosynthesis and cellular respiration

• the general factors that impact on enzyme function in relation to photosynthesis and cellular respiration: changes in temperature, pH, concentration, competitive and non-competitive enzyme inhibitors
  
  Photosynthesis as an example of biochemical pathways

  • inputs, outputs and locations of the light dependent and light independent stages of photosynthesis in C₃ plants (details of biochemical pathway mechanisms are not required) 

  • [Refer to ‘the process of C3 photosynthesis’ mindmap]

  • the role of Rubisco in photosynthesis, including adaptations of C₃, C₄ and CAM plants to maximise the efficiency of photosynthesis

  
  
  

  • the factors that affect the rate of photosynthesis: light availability, water availability, temperature and carbon dioxide concentration

  • [Refer to ‘factors affecting the rate of photosynthesis’ mindmap]
    
    Cellular respiration as an example of biochemical pathways

    • the main inputs, outputs and locations of glycolysis, Krebs Cycle and electron transport chain including ATP yield (details of biochemical pathway mechanisms are not required)

    • the location, inputs and the difference in outputs of anaerobic fermentation in animals and yeasts 

    • the factors that affect the rate of cellular respiration: temperature, glucose availability and oxygen concentration
      
      Biotechnological applications of biochemical pathways

      • potential uses and applications of CRISPR-Cas9 technologies to improve photosynthetic efficiencies and crop yields

      - [Re

      • uses and applications of anaerobic fermentation of biomass for biofuel production.

Biochemical pathway

• a series of linked biochemical reactions that start with an initial reactant that is converted in a stepwise fashion to a final product.

• The product of the one reaction becomes the starting reactant for the next step, until the final product is reached.

• Each step in a biochemical pathway requires the activity of a specific enzyme.

What are the two types of biochemical pathways?

• Anabolic pathways

  • Assemble simple molecules into more complex molecules

  • Require energy (endergonic)

  • E.g. Photosynthesis, creating glucose molecules from carbon dioxide and water

• Catabolic pathways

  • Break down complex molecules into simple molecules

  • Release energy (exergonic)

  • E.g. Aerobic cellular respiration, glucose is broken down into carbon dioxide and water

    

Rubisco, a key enzyme of the photosynthesis pathway, is a relatively slow __ enzyme, acting on just 3 to 10 substrate molecules per second. Green plant cells compensate for this by having a very __ concentration of this enzyme in their chloroplasts.

slow, high

Enzymes

• Enzymes are proteins that are biological catalysts that speed up the rate of metabolic reactions (both catabolic & anabolic) while remaining unchanged at the end of the reaction (can be reused for another reaction)

• Enzymes speed up the rates at which the products of reactions are formed by lowering the activation energy needed for reactions.

Active sites of enzymes

• The active site of an enzyme is a small part of its structure that has a unique 3D shape.

• The shape is complementary to that of its specific substrate molecule.

Factors affecting enzymes?

• Temperature

  • Every enzyme has an optimum temperature at which it operates most efficiently and at that point, the enzyme is operating at its maximum rate.

  • As the temperature falls below optimum, molecular movements slow, resulting in fewer collisions between substrates and enzyme (reduced kinetic energy)

  • As the temperature increases above the optimum, the reaction rate reduces sharply. This occurs because enzymes are proteins and when temperatures exceed the optimum, heat denaturation of the protein occurs

  • 

• pH

  • The level of acidity at which enzymes can operate varies, typically according to the environment in which the enzyme normally operates.

  • Different enzymes have different optimal pH

  • When outside of this pH range the enzyme is considered to have denatured

  • .

• Substrate concentration

  • The increasing concentration of substrate would be expected to result in an increase in the rate of an enzyme reaction. However, after a point all the enzyme is occupied with substrate, meaning the substrate cannot find an enzyme to bind to. Therefore, the reaction plateaus. (enzymes become saturated)

  • 

Cofactors & Coenzymes

• Cofactors

  • Are inorganic molecules e.g. Mg3+, Zn2+

• Coenzymes

  • -Are non-protein organic substances.

  • -They can be loaded and unloaded e.g. NADP+ and NADPH

Cofactor

• non-protein molecule or ion that is essential for the normal functioning of some enzyme

• Can be organic (comprise prosthetic groups, e.g. heme molecules, coenzymes e.g. NAD, NADP, FAD, ATP, Coenzyme A - CoA) or inorganic (do not cointain carbon and include metal ions e.g. Mg²⁺, Cu²⁺, Ca²⁺)

loaded

• the form of coenzymes that can act as electron donors (e.g. NADH, FADH₂)

unloaded

• a form of coenzymes that can act as electron acceptors (e.g. NAD⁺, FAD)

Optimum temeperature

the temperature at which the rate of reaction catalysed by an enzyme is at its highest

denaturation

the loss of enzyme structure due to the breaking of bonds upon heating, irreversibly changing the shape of the active site

competitive inhibition

inhibition in which a molecule binds to the active site of a molecule instead of the usual substrate

Competitive inhibitors

• A competitive inhibitor of an enzyme is a molecule that contains a region with a shape that is similar to that of the substrate

• Therefore it competes to bind to the enzyme with the substrate, lowering the enzyme reaction

non-competitive inhibition

inhibition in which a molecule binds to the allosteric site of an enzyme causing a conformation change in the active site

Non-competitive inhibitors

• In non-competitive inhibition, the inhibitor molecule binds with the enzyme but at a site that is NOT the active site (this region is termed an allosteric site)

• This binding causes a conformational change in the enzyme so the substrate cannot bind to the enzyme anymore

  

allosteric site

location on an enzyme molecule where a compound can bind and alter the shape of the enzyme

allosteric regulation

• the control of the reaction rate of enzymes through conformational changes in enzymes

• Allosteric sites can also be used to regulate biochemical pathways. Two ways allosteric sites can be used are:

  Allosteric inhibitors: their binding produces a change of shape in the enzyme that stops enzyme activity; they act like an OFF switch.

  Allosteric activators: the shape change resulting from the binding produces an increase in enzyme activity; they act like an ON switch 

feedback inhibition

inhibition occurs when the end product of a pathway inhibits an enzymes earlier in the pathway as a negative feedback mechanism; also known as end-product inhibition

allosteric inhibitors

molecules that bind to the allosteric site of an enzyme and stop enzyme activity

allosteric activators

molecules that bind to the allosteric site of an enzyme and increase enzyme activity

Study Dotpoints for Photosynthesis?

Photosynthesis as an example of biochemical pathways

• The general structure of the biochemical pathways in photosynthesis and cellular respiration from initial reactant to final product

• inputs, outputs and locations of the light dependent and light independent stages of photosynthesis in C₃ plants (details of biochemical pathway mechanisms are not required) 

• the role of Rubisco in photosynthesis, including adaptations of C₃, C₄ and CAM plants to maximise the efficiency of photosynthesis

• the factors that affect the rate of photosynthesis: light availability, water availability, temperature and carbon dioxide concentration

Equation for photosynthesis

Two stages of photosynthesis

• Light Dependent Stage

• Light Independent Stage

Chloroplast strucuture

Light Dependent Stage - location, inputs and outputs

Location

• Thylakoid membranes

Inputs:

• 12 H₂O

• 12 NADP⁺

• 18 ADP + P_i

Outputs:

• 6 O₂

• 12 NADPH

• 18 ATP

Light Dependent Stage - Description

The capture of the radiant energy of sunlight by chlorophyll in the thylakoids

The absorption of this energy by electrons in the chlorophyll to become high-energy or ‘excited’ electrons

The splitting of water molecules, that produces electrons, hydrogen ions (H+) (also known as protons) and oxygen

The passage of high-energy of electrons down a chain of electron acceptors during which electrons release their energy

The loading of electrons and hydrogen ions onto NADP+ to form NADPH

Use of this energy to pump protons from the stroma to inside the thylakoid, creating a proton gradient

Passive movement of protons down this gradient back into the stroma produces kinetic energy that is used by the ATP synthase enzyme to produce ATP from ADP and Pi.

Light Independent Stage - Location, inputs and outputs

Location:

• Stroma

Inputs:

• 6CO₂

• 12 NADPH

• 18 ATP

Outputs:

• C₆H₁₂O₆

• 12 NADP⁺

• 18 ADP + P_i

• 6 H₂O

Light Independent Stage

Inorganic CO2 is converted into the carbon in organic molecules, a process termed carbon fixation.

Carbon dioxide molecules are accepted into the Calvin cycle by organic 5C acceptor molecules.

Loaded NADPH coenzymes donate hydrogens and electrons.

ATP supplies energy for the anabolic steps of this cycle.

Glucose is formed as an output.

Factors that Affect the Rate of Photosynthesis

• Light availability

• Water availability

• Temperature

• Carbon Dioxide (CO₂) Concentration

Light Intensity (as a factor affecting the rate of photosynthesis)

LOW: With decreased light intensity the rate of photosynthesis decreases

The optimal light intensity is the one at which the rate of photosynthesis is the greatest.

HIGH: With increased light intensity the rate of photosynthesis increases, Beyond the optimal light intensity, further increases in light intensity have no effect and the rate of photosynthesis stays constant. This is called the light saturation point and it is marked by the flattening or plateauing of the graph. At this point, some other factor is limiting the rate of photosynthesis.

Plateaus where further increase in light will not increase rate

Water availability (as a factor affecting the rate of photosynthesis)

LOW: If soils dry out and the water supply becomes too little, the rate of photosynthesis declines and then stops because closed stomata prevent the uptake of carbon dioxide needed for the Calvin cycle.

HIGH: If the water supply increases too much causing waterlogging of the soil, the rate of photosynthesis will also decline and stop because the lack of oxygen for cellular respiration in root cells stops water uptake.

Temperature (as a factor affecting the rate of photosynthesis)

LOW: At low temperatures, low collision rates produce a low rate of photosynthesis.

HIGH: As the temperature rises, the rate of photosynthesis initially increases as the rate of molecular collisions increases.

Once the optimal temperatures of the enzymes involved are exceeded, the rate of photosynthesis decreases rapidly as heat denaturation of enzymes begins.

Carbon Dioxide (CO2) Concentration (as a factor affecting the rate of photosynthesis)

As the concentration of carbon dioxide is progressively increased, the rate of photosynthesis will increase until it plateaus off due to limiting factors.

Potential Limiting Factors

The enzymes involved in carbon fixation are working at their maximum rate so that no further increase in rate is possible

Availability of essential coenzymes, such as NADPH

C₃ Plants

• plants that carry out the original Calvin cycle using Rubisco and are prone to photorespiration

• 85% of all terrestrial plants in the world

  

C₄ Plants:

• plants that carry out an adapted Calvin cycle, in which carbon fixation and glucose production occur in different cells (Carbon fixation occurs in the mesophyll cells and glucose production in the bundle sheath cells)

• 3% of all terrestrial plants in the world

• Mechanism:

  • Carbon fixation in mesophyll cells

    Uses enzyme PEP carboxylase to join CO2 to PEP

    PEP carboxylase can only bind to CO2

    Product is malic acid

  • Calvin cycle in bundle sheath cells

    Malic acid is converted to pyruvate and CO2

    Rubisco fixes this CO2 for glucose production via the Calvin cycle

    

CAM (crassulacean acid metabolism) Plants:

• plants that thrive in arid conditions and have their two stages of the Calvin cycle occurring at different times (carbon fixation occurring only during the night, glucose production occurring only during the day)

• 8% of all terrestrial plants in the world

• Mechanism

  • Carbon fixation only occurs at night

    Stomata only open at night

    Uses enzyme PEP carboxylase to join CO2 to PEP

    Products (including malic acid) are stored in vacuoles

    Occurs in mesophyll cells

  • Calvin cycle in only occurs in the day

    Stomata are closed

    Products are released from storage and broken down into CO2

    Rubisco fixes this CO2 for glucose production via the Calvin cycle

    Occurs in mesophyll cells

    

What conditions is photorespiration likely to occur in?

• As temperature increases

  • At low temperatures, Rubisco preferentially binds carbon dioxide.

  • As temperatures increase, the ability of the Rubisco enzyme to distinguish between CO2 and O2 decreases

  • Therefore, Rubisco will increasingly bind oxygen.

• As conditions dry out

  • C3 plants close their stomata to prevent water loss.

  • This blocks the entry of CO2 needed as input to the Calvin cycle and limits the exit of O2 produced in the light-dependent stage of photosynthesis.

  • Results in high concentration of oxygen.

Study Design Dotpoints for Cellular Respiration?

• The general structure of the biochemical pathways in photosynthesis and cellular respiration from initial reactant to final product

• the main inputs, outputs and locations of glycolysis, Krebs Cycle and electron transport chain including ATP yield (details of biochemical pathway mechanisms are not required)

• the location, inputs and the difference in outputs of anaerobic fermentation in animals and yeasts 

• the factors that affect the rate of cellular respiration: temperature, glucose availability and oxygen concentration

Cellular respiration - Chemical & Word equation

The two types of cellular respiration

Aerobic and anaerobic

Aerobic cellular respiration: Glycolysis - Location, Inputs and Outputs

Location:

• Cytosol

Inputs:

• C₆H₁₂O₆

• 2 ADP + 2 P_i

• 6 NAD⁺ + 2H⁺

Outputs:

• 2 pyruvate (2 × 3C)

• 2 ATP

• 2 NADH

Aerobic cellular respiration: Krebs Cycle - Location, Inputs and Outputs

Location:

• Mitochondrial matrix

Inputs:

• 2 AcetylcoA

• 2 ADP +

Anaerobic fermentation

Occurs without the presence of oxygen

Takes place entirely in the cytosol

Significantly less ATP produced

ATP is produced significantly faster that aerobic cellular respiration

Both pathways start with glycolysis – creating 2 ATP

Two pathways for anaerobic fermentation

• Lactic acid fermentation (For lactic acid fermentation, the reaction, catalysed by the enzyme lactate dehydrogenase, produces lactic acid)

• Alcohol fermentation (For alcohol fermentation, the end product is the alcohol, ethanol, that is produced in a two-step reaction, each catalysed by a specific enzyme.)