Metabolism, cell respiration, and photosynthesis

Approaching the topic:

• Understanding the concepts
  
  
• Application of these concepts
  
  

Metabolism

Definition and mechanism

• Metabolism is the sum of all the chemical reactions taking place inside a living organism, most of which are enzyme-mediated
• These enzymatic reactions when convert large molecules into smaller and simpler ones, it is called catabolism. And when it forms larger molecules from smaller ones, it is called anabolism.
• Enzymes forms active site on which substrate comes and binds and this binding result in much faster “Lock and key model” explains this activity.
• Enzymes lower the activation energy of the reaction, without altering the reactant or product
• Enzymatic mechanism;
  𝑬 + 𝑺 ↔ 𝑬𝑺 ↔ 𝑬 + 𝑷
  • Substrate combines with the active site of the enzyme to form an enzyme- substrate complex.
  • The activation energy is lowered and the substrate is altered in the form of product.
  • The substrate (product) is released from the active site, enzyme can be reused.

Inhibition  ̶  its types

The inhibition of an enzymatic activity occurs due to change in certain factors including pH, temperature and substrate concentration. The alteration in shape of active site or the occupying of a foreign molecule on active site may also cause inhibition.

• Competitive inhibition
  • When a molecule (competitive inhibitor), similar to the shape of substrate tries to occupy the active site of the enzyme, it is called competitive
    
  • Example: Taking sulfa drugs (sulphanilamide) can be helpful to kill bacteria during an It tries to stop the production of paraminobenzoic acid (PABA) by blocking the enzyme which produces it. Stopped production of PABA further stops the formation of folic acid which is a coenzyme of bacteria. It causes death of the bacteria.
• Non-competitive inhibition
  • When a molecule (inhibitor) interacts with another site rather than active site of the enzyme to change the conformation of its active site, then it is called non-competitive
  • The site it occupies is called allosteric site and therefore it is also called allosteric inhibition.
    
• End-product inhibition
  • Many metabolic reactions occur in an assembly-line type of process with each step catalysed by an enzyme to achieve the end
  • When the product is present in sufficient amount, process
  • When the substance (actually a product) binds to the allosteric site of the enzyme in initial steps, it acts as inhibitor and thereby stops the further process, since the product is already
  • Example: The pathway that converts threonine to
    

Cell respiration

Overview and process ̶  Substrate level phosphorylation

Cell respiration is a catabolic pathway.

• A general equation for this catabolic process is;

𝐶₆ 𝐻₁₂𝑂₆ + 6 𝑂₂ → 6 𝐶𝑂₂ + 6 𝐻₂𝑂 + 𝑒𝑛𝑒𝑟𝑔𝑦

• • This is a redox reaction. The oxygen atoms of the reactants gets due to the addition of two hydrogen atoms and the glucose is oxydized.
  • The reduced molecule have much more potential energy than oxidized form of molecule, therefore the energy is released when the glucose gets oxidised.
  • Much of this released energy is evolved as heat and only 30% (of the energy in the chemical bonds of the glucose) is used in the cellin the form of ATPs.
  • Total 36 ATP molecules are produced by cellular respiration but the number comes to 30 ATPs because some of it gets utilised in the process itself.
  • All the living organisms carry out respiration for energy production.
• Processes of respiration follows:
  It follows the common pathway when initiated for all the organisms, referred to as Glycolysis (‘lysis’ means to break). Fate of glycolysis;
  • Glycolysis is the method of slow oxidation of the glucose using various enzymes. It is a sequential process and at every step a bond is broken with the release of energy, which is released in the form of A
  • If no oxygen is available, the pyruvate molecules enter the anaerobic pathway which is followed by fermentation. But if there is the presence of oxygen then it follows aerobic pathway which further has three stages:
    • link reaction
    • Krebs cycle
    • Oxidative phosphorylation

Glycolysis

• In this process of glucose breakdown, 4 molecules of ATP are generated and two are used in the process to conduct. So, net gain of 2 molecules of ATP occurs.
• 2 molecules of NADH are produced which is equivalent to 6 ATP molecules (1 NADH = 3 ATP).
• There is a direct transfer of phosphate group from phosphate bearing molecule (phosphoenolpyruvate) to ADP in order to make ATP. The process is called substrate-level phosphorylation.
• It is an enzyme mediated process. Therefore its regulation is done by enzymes based on the amount of ATP molecules in the cytoplasm.
• The result would be two pyruvate molecules at the end of the cycle.
• This process occurs in both prokaryotic and eukaryotic cell and uses no oxygen i.e. anaerobic.

Glycolysis

Link reaction and the Krebs cycle

• Pyruvate enters the matrix of the mitochondria and performs decarboxylation link reaction to form 2-C acetyl coenzyme A (acetyl CoA).
• Acetyl CoA usage depends upon the cellular ATP levels. If the ATP levels are low then it will enter the Krebs cycle but if the ATP level is high enough then it can be synthesised into lipid for storage
• Series of steps in Krebs cycle are:
  • Acetyl CoA combines with oxaloacetate (4-C) and form citrate (6-C).
  • Citrate is oxidized to (5-C) by releasing carbon as CO₂. NAD⁺ gets reduced to NADH.
  • 5-C gets oxidized and decarboxylated to (4-C) and again reducing NAD⁺ to NADH.
  • This 4-C compound undergoes many enzymatic steps to produce NADH, FADH₂ and ATP molecules and then form oxaloacetate again, to start the cycle over again.

    

    

• Points to be noted:
  • Krebs cycle will run twice for complete oxidation of one glucose molecule because one cycle process one pyruvate
  • From this cycle, 2 molecules of ATP, 6 molecules of NADH, 2 molecules of FADH₂ are produced and 4 molecules (2 from link reaction + 2 from Krebs cycle) of CO₂ are
  • 4 molecules (2 from glycolysis) of ATP are produced until this

Electron transport chain (ETC)  ̶  Oxidative phosphorylation

• It is the series of protein complexes called cytochromes (they contain haem group) and organic molecules to pass on the electrons from one member of the chain to another (due to energy gradient) in a series of redox
• These complexes are embedded in the inner membrane and in the cristae of the
• These embedded molecules are easily reduced or oxidised and therefore brings out redox
• The electron receiving molecule has higher electronegativity to attract the electrons, and when the electrons get transported, a certain amounts of energy are released. This energy is harnessed by the cell to carry out phosphorylation.
• The coenzymes NADH and FADH₂ released in previous cycles act as the sources of
  
• NADH allows the production of three ATPs and FADH₂ allows the production of 2 ATP molecules.
• At last Oxygen accepts electron due to its high electronegativity which combines with the protons to form
• Energy difference between the embedded molecules which aloe the phosphorylation to occur in which the ADP molecule turns into
• Chemiosmosis is the process in which movement of protons occurs to provide energy for
• An enzyme called ATP synthase is embedded in the inner membranes of the mitochondria which facilitates ions
  • The energy for protons transfer from mitochondrial matrix to intermembrane space is provided by electrons.
  • The hydrogen ion gradient created due to this transfer causes the protons to transfer passively from intermembrane space to the matrix by ATP synthase.

    

Photosynthesis

Overview and process

The conversion of the light energy into the chemical energy is called photosynthesis. It forms the basis of food for every organism on the earth. Plants and certain bacteria are autotrophic which can use sunlight and inorganic matter to convert into useful organic matter (sugar). It is an anabolic process.

Equation,    6 𝐶𝑂₂ + 12 𝐻₂𝑂 →  𝐶₆𝐻₁₂𝑂₆ + 6 𝐻₂𝑂 + 6 𝑂₂

How plants absorb the light energy?

• In the leaves of the plants, there is a presence of green colour organelle called chloroplast which contains the light absorbing pigment chlorophyll in it.
• Plants use the human visible spectrum of electromagnetic waves as a light to make
• Chloroplasts itself are green in colour, therefore they reflects back green light and absorbs red and blue light. This is the reason why plants show much more efficient photosynthesis in blue and red
• Photosynthesis completes in two stages:
  • Light-dependent reactions
  • It is a non-cyclic reaction occurs in thylakoids and the stack of thylakoids is called granum.
  • Presence of pigments like chlorophyll, xanthophyll and carotenoids trap light energy and convert it into the chemical energy (ATP).
  • Organized structure of these pigments in thylakoid membrane is called photosystem. It includes chlorophyll a, accessory pigments and a protein matrix.
  • Photosystem contains even more complex structure within called reaction centre. It contains chlorophyll a molecules, protein matrix and a primary electron acceptor.
  • Types of photosystem; Photosystem I and Photosystem II. Photosystem II (P680) works efficiently at 680 nm wavelength of light while the photosystem I (P700) works efficiently at 700 nm.

    

• Light-independent reactions
  • It happens at night.
  • It occurs in stroma of the chloroplast.
  • ATP and hydrogen produced in the daylight is now used to convert CO₂ and H₂O into glucose.
    6𝐶𝑂₂ + 6𝐻₂𝑂 → 𝐶₆𝐻₁₂𝑂₆ + 6𝑂₂
    Glucose
  • It involves Calvin cycle.
  • The reactions occur as;
    • RuBP combines with CO₂ (carbon fixation catalysed by rubisco) and forms an unstable 6-C compound.
    • Unstable 6-C compound is broken down into two glycerate 3-phosphate molecules which are the converted into triose phosphate (reduction).
    • Now some of the triose phosphate molecules leave the cycle but some continues it to regains RuBP molecules (using ATP).

      

Points to be noted:

• One molecule of glucose and 6 molecules of RuBP is
• 18 molecules of ATP and 12 molecules of NADPH are necessary to produce one molecule of
• Triose phosphate can be used to produce disaccharides and