IB Biology - Metabolism HL

What is the activation energy?

What is the activation energy?

The energy necessary for reactants to take part in a reaction, the energy is needed to break bonds within the reactant.

What does exothermic mean?

That a reaction releases more energy than the activation energy

How do enzymes affect activation energy?

They lower it

Describe the chemical effect enzymes have on reactants, mention the transitionary state.

The active site causes changes within the substrate molecule, weakening its bonds. The substrate changes into a transition state, different from the transition state during the reaction when an enzyme isn’t involved.

• The transition state during enzyme active site binding has less energy and that’s how enzymes lower activation energy

Know how to calculate rates of reaction. What is the standard unit for time in rate?

Per second/s^(-1)

What are the two types of enzyme inhibitors we need to know?

Competitive and noncompetitive

What does enzyme inhibition do?

Reduce the activity of enzymes or prevent enzyme activity completely

Make 3 points contrasting competitive inhibition and noncompetitive inhibition.

• While non-competitive inhibitors don’t have similar chemical features to the substrate they inhibit, competitive inhibitors do.

• While non-competitive inhibitors don’t bind to the active site (they bind to a site which changes the active site shape, allosteric site)

• Competitive inhibitors occupy the active site, non-competitive inhibitors don’t

Describe how rate of reaction is impacted by competitive inhibition as substrate concentration changes.

The activity (rate) of an enzyme is reduced if a fixed low concentration of a competitive inhibitor is added, but as the substrate concentration rises, the effect of the inhibitor becomes less and less until it’s negligible (@ same graph spot as uninhibited reaction)

Describe how rate of reaction is impacted by noncompetitive inhibition as substrate concentration changes.

The activity of the enzyme is reduced at all substrate concentrations if a fixed low concentration of non-competitive inhibitor is added and the percentage reduction is the same at all substrate concentrations.

Describe competitive inhibition.

The inhibitor and substrate compete for the active site

• When the substrate binds to the active site, the inhibitor can’t and vice versa

• As the substrate conc. increases, a substrate rather than an inhibitor is increasingly likely to bind to a vacant active site

• @ very high substrate concentrations and low inhibitor conc. the substrate almost always wins the competition and binds to the active site so the enzyme activity is nearly as high as when there’s no inhibitor

Describe non-competitive inhibition.

The substrate and inhibitor aren’t competing for the same site because the inhibitor binds somewhere else on the enzyme that’s not the active site (allosteric site)

• The substrate can’t prevent the binding of the inhibitor even at very high substrate concentraiions

• The same proportion of enzyme molecules is inhibited at all substrate concentrations. Even a very high substrate conc. the enzyme activity rate is lower than when there is no inhibitor

Describe an example of competitive inhibition (we have to know a named example).

In the reaction with succinate and succinate dehydrogenase to convert succinate into fumarate; malonate acts as a competitive inhibitor

Describe an example of noncompetitive inhibition (we have to know a named example).

In the reaction that turns arginine into nitric oxide and citrulline, morphine inhibits nitric oxide synthase. Works for when people go into septic shock to reduce their blood pressure.

Make a list of the possible features of metabolic pathways.

• Enzyme catalysis for each reaction in the pathway

• All the reactions occur inside cells

• Some pathways build up organic compounds (anabolic), while some break others down (catabolic)

• Some metabolic pathways consist of reaction chains

  • For example glycolysis

• Some metabolic pathways consist of reaction cycles

  • For example the Krebs cycle

Define end-product inhibition.

When the product of the last reaction in a pathway inhibits the enzyme that catalyses the first reaction.

How does end-product inhibition work?

• The end product acts as a substrate for the first enzyme’s allosteric site.

• When it binds, the structure of the enzyme is altered so that the substrate is less likely to bind to an active site

• Binding of the inhibitor is reversible and if it detaches the enzyme returns to its original conformation, so the active site can bind the substrate again.

• This helps regulate end-product to avoid excess

• As the level of end product falls, more and more of the enzymes that catalyse the first reaction will start to work and the pathway will become activated

What is an allosteric enzyme?

An enzyme that has two non-overlapping binding sites, one of which is the active site and the other is the allosteric site.

Describe a named example of end-product inhibition.

The inhibition of threonine dehydratase by isoleucine.

• Isoleucine is the end product of the pathway and inhibits threonine dehydratase which catalyses the first step in converting threonine into isoleucine

How are inhibitors being used to fight malaria?

In the malarial parasite (Plasmodium) there are metabolic pathways too, and by using bioinformatics to search for potential enzyme inhibitors for those pathways, doctors are able to research anti-malarial drugs with a “clearer vision”

Info card: Glycolysis brief summary (for more in depth visit the mnemonics page)

• One glucose is converted into two pyruvates

• Two ATP molecules are used per glucose but four are produced so there’s a net yield of two ATP molecules

  • This is a small yield of ATP per glucose but it can be achieved without the use of any oxygen

• Two NADs are converted into 2 reduced NADS

What is glycolysis? Where does it happen? Describe the “versatility” of glycolysis.

• The first stage of cell respiration with glucose as the substrate

• In the cytoplasm

• It can form part of both aerobic and anaerobic respiration

What does it mean for a molecule to be oxidized? Reduced?

Oxidized:

• Addition of oxygen atoms to a substance

• Removal of hydrogen atoms from a substance

• Loss of electrons from a substance

Reduced:

• Removal of oxygen atoms from a substance

• Addition of hydrogen atoms to a substance

• Addition of electrons to a substance

How is the oxidation of substrates carried out in respiration?

By removing pairs of hydrogen atoms.

• Each hydrogen has one electron, so while taking hydrogens from substances, oxidation also takes electrons. The hydrogen are accepted by a hydrogen carrier which is therefore reduced (most commonly NAD)

Describe the reduction reaction of NAD.

NAD + 2H → reduced NAD

or

NAD^(+) + 2H → NADH + H^(+)

What is phosphorylation? What is the effect?

Phosphorylation is when a phosphate group is added to an organic molecule (PO4)^(3-)

The effect is to make the organic molecule less stable and more reactive for the next part of the pathway.

• It can turn an endothermic reaction that will occur at a very slow rate to a rapid exothermic one

What happens to pyruvate if there is oxygen available? and if there’s not?

If oxygen is available

• Pyruvate undergoes the link reaction, producing a reduced NAD and CO2, to form an acetyl CoA

If oxygen isn’t available

• Ethanol + CO2 is produced (in yeast)

• Lactate is produced (in humans)

Describe the link reaction briefly.

Enzymes from the mitochondrial matrix remove hydrogen and carbon dioxide from the pyruvate.

• The hydrogen is accepted by NAD

• Removal of hydrogens is oxidation

• Removal of carbon dioxide is decarboxylation

• The link reaction is therefore an oxidative decarboxylation

The product of this is an acetyl group which is attached to coenzyme A to form acetyl CoA

Very briefly (one sentence) describe the krebs cycle.

Acetyl CoA joins a 4 carbon compound (oxaloacetate) to form a 6 carbon compound (citrate), and citrate is converted back into oxaloacetate in the other reactions of the cycle.

What is the electron transport chain?

A series of electron carriers located in the inner membrane of the mitochondrion including the cristae

What happens in the electron transport chain?

• Reduced NAD supplies 2 electrons to the first carrier in the chain (from oxidation earlier in cell respiration)

• As the electrons go along the chain they give up energy, and some of the electron carriers act as proton pumps and use this energy to pump H+ ions from the mitochondrial matrix into the intermembrane space.

• Reduced FAD also feeds electrons into the electron transport chain, but at a late stage than NAD

  • Whereas electrons from reduced NAD cause protein pumping at 3 stages in the e.t.c, the electrons from reduced FAD cause proton pumping at only 2 stages

What is the role of oxygen in cell respiration?

Terminal electron acceptor at the end of the electron transport chain

• The oxygen accepts electrons and at the same time oxygen accepts free protons to form water

What happens if oxygen isn’t available at the end of the electron transport chain?

If oxygen isn’t available, electron flow along the e.t.c stops and reduced NAD ceases conversion back to NAD.

Supplies of NAD in the mitochondrion run out and the link+krebs cycle can’t continue. Only glycolysis can, with a small ATP yield.

Thus Oxygen greatly increases the ATP yield per glucose of cell respiration.

Describe the process of chemiosmosis.

As electrons are passed along the electron transport chain, energy is released and used to pump H+ ions into thee inner mitochondrial membrane, thus creating a concentration gradient/potential energy

ATP synthase in the inner mitochondrial membrane allows protons to diffuse back across the membrane to the matrix

ATP synthase uses the energy that the protons release as they diffuse down the conc. gradient to produce ATP

Chemiosmosis - The generation of ATP using energy released by the movement of hydrogen ions across a membrane

What is a paradigm shift? An example?

A fundamental change in the basic concepts and experimental practices of a scientific discipline

An example of a paradigm shift was in the 1960s when Peter Mitchell proposed chemiosmosis and caused a paradigm shift in the field of bioenergetics.

Describe the function of the outer mitochondrial membrane.

Separates the contents of the mitochondrion from the rest of the cell, creating a compartment with ideal conditions for aerobic respiration

Describe the structure and function of the fluid matrix.

Fluid inside the mitochondrion

Contains enzymes for the Krebs cycle and link reaction

Note: Also contains 70S ribosomes and a naked loop of DNA

Describe the structure and function of the space between inner and outer membranes.

A very small space between membranes where high proton concentration can be formed during chemiosmosis

Protons are pumped into this space by the electron transport chain.

Describe the structure and function of the cristae.

Tubular or shelf-like projections of the inner membrane which increase the surface area available for oxidative phosphorylation.

Describe the function of the inner mitochondrial membrane.

Contains electron transport chains and ATP synthase, which carry out oxidative phosphorylation.

What is electron tomography used for? What has it revealed about mitochondrion?

To obtain 3D images of active mitochondria

Electron tomography has revealed that cristae are connected with the intermembrane space between the inner and outer membranes via narrow openings (essentially spaces between the projections)

Cristae shape and volume change when a mitochondrion is active, but the “how” of this is still being researched

• I doubt this will come up but you can never be too sure^

Refer to the mnemonic sheet for respiration processes and explanations. I also recommend this video: https://www.youtube.com/watch?v=TouJivLX3Gc&ab_channel=LanternaEducation or search up lanterna respiration HL

Be able to identify the following on an image of a chloroplast; granum, thylakoid space, stroma, liquid droplet, thylakoid membranes, starch grain, inner and outer chloroplast membrane, 70S ribosomes

Describe the structure and function of the granum.

A stack of thylakoids for absorption of as many of the available photons of light as possible.

Describe the structure and function of the thylakoid space.

Spaces with small volume for steep proton gradient build up after relatively few photons of light have been absorbed

Describe the structure and function of the stroma.

Fluid-like, containing all the enzymes of the calvin cycle and very large quantities of rubisco

• Also contains naked DNA and 70S ribosomes

Describe the structure and function of the thylakoid membranes.

Large surface area

Provides a larger area for light-absorbing photosystems, also provides a site for electron flow, the generation of a proton gradient and chemiosmosis

Describe the structure and function of the starch grain.

Sac-like structure

For storage of carbohydrate produced by photosynthesis until it’s exported from the carbohydrate, kind of like a shipping warehouse

Describe the structure and function of the inner & outer membrane.

Is the chloroplast envelope

Creates a compartment in which enzymes and other components of photosynthesis can be concentrated

Refer to the mnemonic sheet for photosynthesis processes and explanations. I also recommend this video: https://www.youtube.com/watch?v=kAI2p4I2NQc&ab_channel=LanternaEducation or search up lanterna photosynthesis HL

What did Calvin’s experiment do?

Discover the Calvin cycle

Describe Calvin’s experiment until the fixation of samples.

A suspension of Chlorella was placed in a thin glass vessel (lollipop vessel) and was brightly illuminated (Chlorella is a unicellular alga).

• The Chlorella was supplied with CO2 and HCO3^(-)

• Before the experiment started, the carbon sources were switched from 12C(carbon-12) to 14C(carbon-14 (isotope))

Calvin and his team took algae samples at short timed intervals and killed and fixed them with hot methanol

Describe what Calvin did with his samples to measure the amount of products of photosynthesis.

They extracted the Carbon compounds, separated them by double-way paper chromatography and found which carbon compounds in the algae contained radioactive 14C by autoradiography.

They then looked at the amount of labelled carbon compounds and discovered that glycerate-3-phosphate was more labelled than any other compound indicating that it’s the first product of carbon fixation, so on so forth.

Think about the setup for Calvin’s experiment, cross-reference it with the image on the other side of this card.

What were the 3 experimental techniques that Calvin used to make his CO2 fixation mechanism conclusions?

Radioactive labelling

Double-way paper chromatography

Autoradiography

Describe radioactive labelling in Calvin’s case.

Radioisotopes of elements have the same chemical properties as other isotopes but can be distinguished by being radioactive

• They can therefore be used to label organic compounds in biochem

• Carbon-14 was suitable in this case, carbon dioxide and HCO3^- could have been used with Carbon-14

Describe double-way paper chromatography.

Separating organic compounds

• A spot of the mixture is placed in one corner of a large chromatography paper

• A first solvent is run up through the paper to separate the mixture partially in one direction.

• The paper is dried and then a second solvent is run up at 90 degrees to the first spreading the mixture in a second dimension.

This was ideal for separating and identifying the initial products of carbon-fixation

Describe autoradiography in Calvin’s case.

Using X-Ray film to find the location of radioisotopes. When atoms of Carbon-14 decay, they give off radiation which makes a small spot in an adjacent X-ray film

• To find radioisotopes in a sheet of chromatography paper it’s placed next to a sheet of film that’s the same size

• The two sheets are kept together in darkness for several weeks and the X-ray film is developed. Black patches appear in areas where the adjacent chromatography paper contained radioisotopes