Energy, environment, microbiology, and immunity

• Adenosine triphosphate (ATP) is the universal energy supplier in cells
• ATP is a nucleotide with three phosphate groups attached

  
• It is the energy in the phosphate bonds of ATP,

  particularly the end one, that is made available to cells to use to make or break bonds.
• When energy is needed, the third phosphate bond can be broken by a hydrolysis reaction, which is catalysed by the enzyme ATPase. The result is adenosine diphosphate (ADP), a free organic phosphate group (Pi) and energy. Some of this energy is lost as heat and is wasted. The test is used for any biological activity which requires energy e.g. active transport
• adenosine triphosphate + H2O ⇌ adenosine diphosphate + Pi
• the energy needed to drive the synthesis of ATP comes from catabolic (breakdown) reactions or redox reactions.
• An ATP molecule provides an immediate supply of energy for the cells, ready to use when needed.
• ATP is made in a condensation reaction
• Energy is released in catabolic reactions such as cellular respiration
• The main way energy is released is by the removal of hydrogen atoms from several intermediate compounds in a metabolic pathway. When two hydrogen atoms are removed from a compound, they are collected by a hydrogen carrier or acceptor that is reduced. Electrons from the hydrogen atoms are then transferred along a series of carriers known as electron transport chain. The components of the chain are reduced when they receive the electrons, and oxidized again when they transfer the electrons. These redox reactions release a small amount of energy which is used to drive the synthesis of ATP
• The energy from light is used to break the strong hydrogen (O-H) bonds in the water molecules. The hydrogen released is combined with carbon dioxide to form glucose and the oxygen is released into the atmosphere as a waste product.
• Chloroplasts are the site of photosynthesis
• Each chloroplast is surrounded by an outer and inner membrane (the space between is called the inter membrane space) known as the chloroplast envelope
• Inside the envelope is a system of membranes arranged in layers called grana. A single granum is made of layers of membrane discs known as thylakoids. This is where the green pigment chlorophyll is found. The grana are joined together by lamellae, which are extensions of the thylakoid membranes, and act as a skeleton inside the chloroplast, maintaining a distance between the grana, so that they refuse maximum light for better efficiency
• The membrane layer is surrounded by a matrix called the stroma. The stroma contains all the enzymes needed for photosynthesis. The glucose produced can be used in cellular respiration, converted to starch for storage or used in the synthesis of amino acids and lipids
• Chlorophyll is a light-capturing, photosynthetic pigment. It is a mixture of pigments, including chlorophyll a (blue-green), chlorophyll b (yellow-green), the chlorophyll carotenoids (orange carotene and yellow xanthophyll) and also a grey pigment phaeophytin, which is a breakdown product of the others
• Chlorophyll a is found in all photosynthesising plants and in the highest quality of the five pigments
• The different proportions of the pigmentd (besides chlorophyll a) gives the leaves of plants their variety of different greens. Each pigment absorbs and captured light from particular areas of the light spectrum. As a result, much more of the energy from the light falling on the plant can be used than if only one pigment is involved.
• The absorption spectrum describes the different amounts of light of different wavelengths than a photosynthetic pigment absorbs. To find the absorption spectra of different photosynthetic pigments, you measure their absorption of light through different wavelengths
• An action spectrum can be achieved to show the rate of photosynthesis according to the wavelength of light.
• Having different photosynthetic pigments makes a much bigger portion of light available to plants and therefore gives them an adaptive advantage. Different photosynthetic pigments can provide a major adaptation to the habitat, for example aquatic plants are grown so they can absorb the blue light that penetrated the water easily
• 1. 70S ribosomes
  2. thylakoid membrane
  3. thylakoid
  4. grana
  5. starch grain
  6. circular DNA
  7. outer membrane
  8. intermembrane space
  9. inner membrane
  10. lipid droplet
  11. stroma

  
• Chromatography can show the different pigmentd present in a plant. The plant‘s leaves are grounded with propanone and then filtered. Using silica gel or paper as the medium, the pigments travel to the solid medium at different speeds and are separated using a solvent. The Rf value can then be calculated.
• The Rf value is the ratio of the distance travelled by the pigment to the distance travelled by the solvent. It is always between 0 and 1.

  Rf value = distance traveled by photosynthetic pigment/distance travelled by solvent
• In chloroplasts, there are two types of photosystems; Photosystem II (PSII) and Photosystem I (PSI). PSII contains chlorophyll a and b, carotenoids and phycobilins. PSI only has chlorophyll a and some accessory pigments such as chlorophyll b and carotenoids.
• The different photostems are different sized particles attached to the membranes in the chloroplasts. PSI particles are mainly on the lamellae, whereas PSII particles are on the grana.
• Photosynthesis is a two stage process. The light-dependent reactions produce materials that can be used in the light-interdependent reactions. The whole process continues during the hours of daylight, and the light-interdependent reactions can continue when it is dark
• The light dependent stage occurs on the thylakoid membranes of the chloroplasts and has two main functions:

  • to break up water molecules in a photochemical reaction, producing hydrogen ions to reduce carbon dioxide and produce carbohydrates in the light-interdependent stage
  • to produce ATP, which supplies energy to build carbohydrates
• Light is a form of electromagnetic radiation, and the smallest unit of light is a photon.
• When a photon hits a chlorophyll molecule, the energy is transferred to the electrons of the chlorophyll molecule. The electrons are excited and raised to a higher energy levels. If an electron reaches a high enough electron level, it leaves the chlorophyll completely and is collected by a carrier molecule called an electron acceptor. This results in the synthesis of ATP in either cyclic phosphorylation or non-cyclic phosphorylation. These processes occur at the same time
• In both cyclic phosphorylation and non-cyclic phosphorylation, ATP is formed as the excited electron is transferred along an electron transport chain. In non-cyclic phosphorylation, reduced NADP is also formed
• Phosphorylation means adding a phosphate group to ADP
• Cyclic phosphorylation involves only photosystem I (PSI) and drives the production of ATP. When an electron returns to a chlorophyll molecule in PSI, it can be excited again.

  
• In non-cyclic phosphorylation, water molecules are broken down, providing hydrogen ions to reduce NADP. This process involved both photosystem I and II. this
• In non-cyclic phosphorylation, light energy hits photosystem II in the thylakoid membrane, and an electron gains energy and is excited to a higher energy level. This electron is transferred along an energy transport chain to PSI, driving the synthesis of ATP. This allows PSI to receive an electron to replace the one lost in the light-interdependent reactions. However, now the chlorophyll molecule in PSII is missing one electron and is unstable. H+ and OH- ions in the chloroplasts, formed by the photolysis of water are used to replace the lost electrons in the chlorophyll.
• At the same time as non-cyclic phosphorylation, electrons in PSI are also being excited and transferred along an electron transport chain and collected by the electron acceptor NADP. The NADP also collects a H+ from the dissociated water. The reduced NADP and ATP produce the source of reducing power and energy to make glucose. The remaining hydroxide ions react to make water and 4 chlorophyll molecules regain electrons in the production of an oxygen molecule 4OH- - 4e- -> O2 + H2O
• The light-interdependent stage uses the reducing power (reduced NADP) and ATP produced by the light-dependent stage. This stage consists of a series of reactions known as the Calvin cycle and occurs in the stroma of the chloroplast. This results in the reduction of carbon dioxide from the air leading to the synthesis of carbohydrates. The Calvin cycle is controlled by enzymes.
• The Calvin cycle reactions can continue in the dark, and only stop when there is no longer reduced NADP or ATP.
• In the first step of the Calvin cycle, carbon dioxide combines with the 5-carbon compound ribulose biphosphate (RuBP) in the chloroplasts in a process called carbon fixation. This steps involved the enzyme ribulose biphosphate carboxylase/oxygenase (RUBISCO), a rate limiting enzyme in photosynthesis. The result is highly unstable and immediately separates into two molecules: glycerate 3-phosphate (GP, 3-carbon compound) which is then reduced to form gylceraldehyde (GALP). The hydrogen comes from reduced NADP, and the energy required comes from ATP.
• Much of the GALP produced in the Calvin cycle is used to replace the RuBP used in the first step, but some is used to make glucose or transferred directly into the glycolysis pathway for the synthesis of other molecules. The rest is used to make glucose in a process called gluconeogenesis. The GALP that entered cellular respiration is used to provide energy in the form of ATP, and can also combine with phosphates in the soil to produce nucleic acids.