Chapter 8 Flashcards
Metabolism, cell respiration and photosynthesis
Metabolic pathway
any chain or cycle of linked reactions catalysed by enzymes; are linked, enzymatically catalysed reactions
- some are linear, and some are cyclic
- pathway can be complex , w/ many intermediate products before an end product is produced
- some are linked to other metabolic pathways
Activation energy
minimum energy that reacting particles need to possess for a reaction to take place
- enzymes speed up reactions by lowering the activation energy
Enzyme inhibitors
Two types:
- competitive
- non-competitive
Competitive inhibitor
competes w/ substrate for the same active site
- maximum rate of reaction is eventually the same as the reaction without inhibitor
- when substrate conc. increases, rate will increase
- because, there’s more available substrate than inhibitor
- hence, there’s a greater chance of substrate binding to enzyme’s active site and forming product
Non-competitive inhibitor
bind at a site away from the active site
- rate of reaction levels off and never reaches same level it would without inhibitor
- because all enzyme molecules to which inhibitor is attached are effectively blocked from reacting w/ substrate- due to modification of their active site
- hence, fewer enzyme molecules, free of inhibitor, are available to catalyse the reaction
Properties of competitive inhibitor
- It is chemically quite similar to the substrate
- It binds to active site of the enzyme
- Binding of inhibitor to enzyme doesn’t modify its active site
- As conc. of substrate is increased, effect of inhibitor on reaction is reduced
Properties of non-competitive inhibitor
- It has no similarity to the substrate.
- It binds to the enzyme at a site other than active site
- Binding of inhibitor to enzyme modifies its active site, hence preventing binding of substrate- if it does bind, enzyme won’t be able to catalyse reaction
- Increasing conc. of substrate doesn’t decrease impact of inhibitor- hence, rate of reaction is lower than normal at all substrate concentrations.
End-product inhibition
when the enzymes that catalyse the first reaction of the pathway are allosterically inhibited by the end product of the pathway
Allosteric site
a binding site on the surface of an enzyme other than the active site
- in non-competitive inhibition, when inhibitor binds to an allosteric site, it blocks activity of the enzyme
Allosteric inhibition
- binding of a regulatory molecule (usually, the end product of the pathway) to allosteric site changes overall conformation of the enzyme
- this can either enable the substrate to bind to the active sire or prevent binding of the substrate
Synthesis of isoleucine from threonine
- isoleucine can bind to the enzyme that catalyses the first step of the pathway in a non-competitive way
- it binds allosterically to the enzyme and changes conformation of the active site
- hence, substrate can no longer bind to the enzyme
Formula for rate of reaction
Rate (1/s) = 1/ t
t= time taken in seconds
Redox reactions
- involve one compound being oxidised, while another is reduced
- involve gain or loss of e-
- makes electrons carriers of energy that can be used for other processes
Redox reactions and electron carriers
- redox reactions are usually coupled to an e- carrier eg. NAD (Nicotinamide Adenine Dinucleotide)
- reactions often transfer 2 hydrogen atoms to carrier
- e- that are lost from one substance in oxidation are needed or used in another part of the cell
- the reduced NADH+ H+ is transferred to a mitochondrion
- it’s used in electron transport chain to generate ATP
NADP vs. NAD
NADP (Nicotinamide Adenine Dinucleotide Phosphate)
- main carrier for photosynthetic reactions
NAD (Nicotinamide Adenine Dinucleotide)
- used for bulk of respiration reactions
Oxidation
- gain of oxygen
- loss of hydrogen
- loss of electrons
Reduction
- loss of oxygen
- gain of hydrogen
- gain of electrons
Phosphorylation
the addition of a phosphate group to a molecule
- makes whole molecule less stable
- makes it more likely to react or break down into smaller molecules
Glycolysis
the reaction in the cytoplasm where glucose is broken down to pyruvate in a series of linked catalytic steps
Link reaction
In aerobic respiration:
- pyruvate is converted to acetyl coenzyme A
- this is transferred to mitochondria, where it enters the Krebs cycle
- link reaction because it links glycolysis to Krebs cycle
Process of glycolysis
Glycolysis is the first step of cellular respiration and occurs in all organisms
- glycolysis is a metabolic pathway which gives a small yield of 2 ATP and 2 reduced NADH+ H+
- at the end of the glycolytic pathway, 2 molecules of pyruvate are formed
- they’re linked to acetyl CoA in the link reaction if oxygen is available
- this is a decarboxylation reaction as carbon is lost as carbon dioxide
- as pyruvate loses hydrogen, it’s oxidised to acetyl CoA
- overall, conversion of pyruvate to acetyl CoA involves both decarboxylation and oxidation reactions
Krebs cycle
- next step in catabolic breakdown of glucose
- takes place in the mitochondrial matrix
- the acetyl group that enters the Krebs cycle is successively oxidised- it loses hydrogen atoms and e-
- the hydrogen atoms lost are picked up by hydrogen carriers, either NAD or FAD, which are themselves reduced
- oxidation of acetyl group is coupled w/ a loss of CO2 (decarboxylation)
Electron transport chain
- all oxidation reaction in cytoplasm in cytoplasm and mitochondrial matric are linked to electron carriers
eg. NAD and FAD - reduced forms of these molecules carry energy released by oxidation to cristae of mitochondria - they give off e- and hydrogen ions to special protein complexes
- in inner mitochondrial complex, ATP synthase uses a hydrogen ion gradient to synthesis ATP
- both NADH+ H+ and FADH2 release e- to different complexes in ETC, along w/ release of H+ ions into mitochondrial matrix
- e- are successively transferred from one e- carrier to the next along ETC, until they reach cytochrome oxidase, where e- are combined w/ oxygen and hydrogen to form water
- transfer of e- along ETC involves a drop in energy state of e-, energy is released
- this energy is used to pump H+ ions across inner mitochondrial membrane into inter-membrane space
Chemiosmosis
- involves pumping of protons (H+ ions) into intermembrane space of mitochondria by using energy released by e- transport along ETC
- this is followed by diffusion of protons into the matrix down a conc. gradient through ATP synthase to produce ATP
- As the last electron acceptor of ETC, oxygen helps maintain hydrogen gradient in the matrix by binding w/ free protons to form water
- Oxygen accepts electrons and binds protons at the same time to form water
- Each molecule NADH + H+ and FADH2 can give rise to 3 and 2 ATP molecules, respectively
- main reason FADH2 generates fewer ATP molecules, is because it donates its electrons to ETC at a later step
Mitochondria
- a range of complex biochemical reactions take place in the mitochondria
- each reaction has a specific requirement
Evolution of mitochondria
- need for conc. gradients and compartmentalisation of various reactions, and increased SA, were evolutionary driving force behind mitochondrion’s structure
- Organisms evolved w/ complex mitochondrial structures probably produced more ATP, giving organism an advantage in poor environmental conditions
Structure and function of the mitochondrion
- Cristae: form a large surface area for electron transport chain and ATP synthase
- Small space between inner and outer membranes (intermembrane space) - Allows fast accumulation of protons needed for chemiosmosis
- Fluid matrix contains enzymes
- enables link reaction and Krebs cycle to proceed at an appropriate rate - 70S ribososomes - synthesises some of the proteins and enzymes needed within the mitochondrion
- Outer mitochondrial membrane
- isolates content of mitochondrion from the cytoplasm; to allow optimum conditions for reactions of aerobic respiration - Naked DNA
- Codes for some of the mitochondrial proteins.
Electron tomography imaging
- allows 3D images of mitochondria to be made- supports idea of the dynamic nature and fluidity of the cristae
- proteins can be visualised within active mitochondria
- used to investigate how active mitochondria function and adjust to cellular energy requirements
The division of photosynthesis into 2 processes
- Light-dependent reactions
2. Light-independent reactions
Light-dependent reaiton
- converts light energy into a flow of excited electrons
Process is made of:
- Photoactivation
- Photolysis
- Electron transport chain
- Chemiosmosis
- ATP synthesis
- NADP reduction
All of these reactions take place in thylakoids (intermembrane space of the thylakoids)
The energy produced from this reaction is transferred to e- carriers, but in the chloroplast, it is in the reduced form of NADP
- light-dependent reaction also generates ATP
NADP to NADPH + H+
Each NADP molecule accepts two hydrogen atoms (i.e. two H+ ions and two electrons) to form NADPH + H+
Light-independent reactions
- also called the Calvin cycle
- takes place in the Stroma (cytoplasm of the chloroplast)
Process:
- Carbon fixation
- Carboxylation of ribulose bisphosphate (RuBP)
- Triose phosphate production
NADPH and ATP produced in light-dependent reactions are used in light-independent reactions
- although these reactions are called light independent, they can only continue for a short while in absence of light
- Once stock of NADPH and ATP runs out, light-independent reactions stop
Electron carriers in photosynthesis and cellular respiration
Photosynthesis: Electron carrier is a reduced form of NADP
Cellular respiration: Electron carrier is a reduced form of NAD
What is photosynthesis?
process during which an organism (usually a plant) uses light energy to carry out chemical reactions to produce sugars or other organic molecules
Photons and chlorophyll
- Visible light consists of photons w/ a particular wavelength
- A shorter wavelength of photon means a higher energy content
- so, a ‘blue’ photon has a higher energy level than a ‘red’ photon, as blue light has a shorter wavelength than red light
- chlorophyll is a light-sensitive molecule that absorbs photons w/ certain wavelengths
- absorption spectrum of chlorophyll shows this
- Hundreds of chlorophyll molecules and other accessory pigments aggregate together w/ a protein to form a protein complex called a photosystem
- these pigments transfer all the energy they’ve absorbed from light photons to central chlorophyll a molecule, it forms reaction centre of photosystem
Accessory pigments
include any pigment, other than chlorophyll a, that can absorb light
- eg/ chlorophyll b and carotenoids
Two types of photosystems
2 types of photosystems embedded in thylakoid membrane:
- photosystem I: sensitive to light wavelengths of 700 nm
- photosystem II: sensitive to light wavelengths of 680 nm
Reaction in photosystem II
- chlorophyll molecules in photosystem II become activated by photons of light and pass on their activation energy to reaction centre
- this passes 2 excited electrons to primary electron acceptor
- then passes 2 e- to plastoquinone, which stays in the thylakoid membrane to pass on e- to the next electron carrier
- this continues all the way to photosystem I
- Photosystem II repeats this one more time, so the reaction centre has lost 4 electrons that must be replaced before a new cycle begins
- reaction centre, due to its oxidised state (it has lost four electrons), now becomes a powerful oxidising agent
- It’s the reason that water molecules can be split to give up their e- to the reaction centre
- photolysis of water generates e- for use in light-dependent reaction, as it constantly replaces electrons lost by photosystem II
Photolysis of water
- the splitting of water molecules into oxygen, hydrogen ions and electrons in the presence of light
- Light isn’t used to split water molecules directly, but to cause loss of electrons from the reaction centre (of photosystem II), which then acts as oxidising agent to trigger the reaction
- oxygen is a byproduct of this photolysis reaction and is the first step in the circle of life.
