AP Biology Unit 3: Cellular Energetics

3.1: Enzyme Structure and Catalysis

• Enzymes catalyze biological systems and reactions by lowering the activation energy

  • Higher activation energy causes a slower chemical reaction; reactions require activation energy to get past a transition state, and often they need an enzyme or catalyst to do that

  • Enzymes are proteins

  • Molecules that bind with enzymes at the active site are substrates

  • Enzymes can be used multiple times

• Induced fit means when the protein or enzymes change to better fit a substrate

• Enzymes work by binding to reactant molecules and holding them so that the bond-breaking or making process happens more easily without changing the Gibbs free energy value

  • Temperature and pH can affect enzyme function by causing them to denature

  • All enzymes return to their original state at the end of a reaction

  • Enzymes are specific and usually only bind with one or a couple of substrates

• Activation energy and the rate of a reaction are inversely related

3.2: Enzyme Reaction Velocity and pH

• pH is -log[H+]; hydrogen ions are essentially protons

  • Remember that protein structure is dependent on hydrogen bonding

  • lower H+ ion concentration = higher pH = basic, while higher H+ concentration = lower pH = acidic

• Enzyme structure and function depend on hydrogen bonds, so different pH can affect that

• Inhibition:

  • In competitive inhibition, a substrate that isn’t the intended one binds to the active site instead of the intended one —> the reaction does not take place

    • In allosteric competitive inhibition, the competition won’t bind to the active site, but to an allosteric site; it changes the enzyme so the intended substrate can’t bind to the active site

      • If the intended substrate successfully binds 1st, then the competition can’t bind

    • Competitive inhibitors can be out-competed by lots of substrates and the enzyme can still reach the maximum reaction rate

  • Non-competitive inhibition: both the intended and “inhibitor” substrates can bind to the enzyme, but if they both do the reaction won’t proceed

    • Can’t ever reach the maximum reaction rate because the enzyme is “poisoned” by the inhibitor; the amount of substrate can’t fix this

• Activators increase enzyme activity while inhibitors decrease it

  • Cooperativity occurs when a substrate is an allosteric activator and increases the activity of another active site when it binds

• A cofactor is a non-protein “helper molecule” for enzymes; it attaches temporarily via ionic or hydrogen bonds, or permanently via covalent; examples include inorganic ions

  • Coenzymes are a subset of cofactors but are organic molecules, such as dietary vitamins; they also help enzymes to work!

• Enzyme compartmentalization: enzymes are often stored in specific parts of the cells where they work; they must be in the right environment where they won’t damage the cell and can find the suitable substrates

• Feedback inhibition: the end product of a metabolic pathway acts on a key enzyme that regulates pathway entry, leading to more of the end product not being produced

  • This stops more product from being made until the supply is used up

  • Usually occurs at the 1st committed step, or the 1st irreversible step of the pathway

• Enzyme kinetics graphs: Shows what happens when equal amount of enzyme is added to different substrate concentrations to help find the initial velocity (V0) for all concentrations

  • Each is plotted as (x,y); substrate concentration is x-axis, velocity is y-axis

  • When the graph plateaus, the enzyme is saturated, and all available enzymes are being used; the rate is limited by the enzyme concentration

  • Vmax = the maximum velocity, or the max rate at a certain concentration; it is the y-value of the plateau

  • Substrate concentration ½ of the way to Vmax is km; lower km means higher affinity to bind to substrate, higher km means lower affinity; this doesn’t depend on enzyme concentration

3.3: Cellular Energy

• The 1st law of thermodynamics is conservation of energy; 2nd law says that entropy of the universe only increases

  • An open system interacts with its surroundings, while a closed system is isolated; the ultimate closed system is the universe

  • More possibilities/states contribute to a higher entropy; the increasing of entropy is often irreversible

• Phosphorylation:

  • Adding a phosphate group to a glucose; the negative charge on the phosphate group makes the glucose polar, which means it can’t leave the cell via the phospholipid lipid membrane and diffusion, allowing the cell to retain more glucose molecules

  • ATP and H2O —> ATP + PO4, which is an exergonic (negative Gibbs free energy), coupled with glucose + PO4 —> glucose-6-phosphate (endogonic, or positive Gibbs free energy)

    • This process requires the hydrolysis of ATP into ATP and a phosphate group, which is energetically favorable

    • ATP and glucose to glucose-6-phosphate + ADP is overall negative Gibbs free energy so it can occur spontaneously BECAUSE of the reaction coupling!!

      • When a favorable and unfavorable reaction are linked using a shared intermediate to create an overall negative deltaG

  • Also, this reaction uses the enzyme hexokinase, because the glucose needs to bind with the phosphate and the hexokinase supplies ions to allow the glucose to carry out a nucleophilic attack on the phosphate; this is energetically favorable (spontaneous) because of that enzyme

• Metabolism means taking energy and making it useful

  • Catabolism is breaking down of energy into building blocks, while rebuilding is anabolism

3.4: Photosynthesis

• General equation: nCO2 + nH2O + photons —> (CH2O)n [carbohydrates] +nO2

  • Glucose can provide fuel via cellular respiration or fermentation by being converted to ATP

  • Glucose can also provide fixed carbon; carbon from CO2 is incorporated into organic molecules (carbon fixation); carbon that is fixed and incorporated into sugars via photosynthesis can be used to build macromolecules

• Photoautrophs are self-feeders that use light, while humans are heterotrophs (different feeders)

• In the chloroplast, thylakoids are stacked in grana

  • There is also chlorophyll, stroma (space around grana), and thylakoid space

• There are two parts to photosynthesis: the light-dependent reactions use light and H2O to make ATP from ADP and reduce NADP+ to NADPH, as well as make O2 as a byproduct

  • Light-independent reaction, or Calvin Cycle, uses ATP, NADPH and CO2 to make sugar (glucose)

Light-dependent reactions:

• Take place in the thylakoid membrane

• In PSII:

  • Photons excite electrons and they move to a higher energy state

  • Those high-energy state elections are transferred by molecules from high to low

  • P680, a special pair, oxidizes water to get oxygen and H+ (to contribute to the higher H+ concentration; the O2 is a byproduct of this reaction

  • As electrons move down the the electron transport chain, energy is released and that energy drives the pumping of H+ in a concentration gradient from the stroma into the thylakoid interior; H+ from the water also adds to this from when water was broken down

  • H+ passes through ATP synthase and produces ATP via chemiosmosis

• After all that, in PSI, an electron joins P700 and goes down the electron transport chain

  • NADPH is made from NADP+ via NADP+ reductase

  • Once again, when the protons form the H+ gradient, ATP is made via chemiosmosis

• Cyclic photophosphorylation is when electrons repeatedly go through PSI but don’t end up in NADPH; sometimes occurs when there is too much NADPH already there, or when plants need extra ATP

• Via non-cyclic photophosphorylation, electrons are removed from water and passed through PSII and PSI before ending up in NADPH

Calvin Cycle, or light-independent reactions:

• Takes place in the stroma, not the thylakoid membrane; uses ATP and NADPH to fix carbon from CO2

• Carbon fixation: CO2 combines with 5-carbon acceptor (RuBP) to make a 6-carbon compound which splits into 2 molecules of a 3-carbon compound (3-PGA); this is catalyzed by rubisco

• Then, in reduction, ATP and NADPH are used to convert the 2 3-PGA into 3-carbon sugars (G3P); NADPH reduces the intermediate to make G3P

• Next, in regeneration: some G3P molecules go to make glucose while some are recycled to generate the RuBP acceptor; regeneration uses ATP and a complex network of reactions

• In 3 turns of the Calvin Cycle, 3 CO2 combines with 3 RuBP, making 6 G3P —> 1 G3P go towards making glucose and exits, while 5 are recycled, regenerating 3 RuBP acceptors

  • 9 ATP are converted to 9 ADP (6 during reduction, 3 during regeneration)

  • 6 NADPH —> 6 NADP+ during reduction

• So, one G3P has 3 fixed carbons and it takes 2 G3Ps to make 1 6-carbon glucose; it takes 6 turns of the cycle, of 6CO2, 18 ATP, and 12 NADPH to make 1 molecule of glucose????

Photosynthesis evolution

• Cyanobacteria are a type that can do photosynthesis

  • Ancestors of cyanobacteria changed the atmosphere by producing oxygen

• The Great Oxygenation Event (GOE) introduced oxygen to the atmosphere in a larger percentage

  • Because of endosymbiotic theory, we believe chloroplasts are descendants of the ancestors of cyanobacteria

3.5: Cellular Respiration

• Breaking a larger molecule into smaller ones is catabolic, remember?

• Cellular respiration general reaction: C6H12O6 —> 6CO2 + 6H2O; delta G = -686 kcal/mol

• Electron carriers: NAD+ and FAD; when they gain electrons, they gain hydrogen too; when they drop off electrons, go back to OG state

  Steps of cellular respiration:

• Glycolysis: 6-carbon sugar —> 2 molecules of pyruvate, ATP is made, NAD+ —> NADH

• Then, pyruvate oxidation: pyruvates go into mitochondrial matrix and make acetyl CoA (bound to coenzyme A); CO2 is released and NADH is generated

• Then: citric acid cycle: acetyl CoA and 4-carbon molecule regenerate the OG 4-carbon starting molecules; ATP NADH, FADH2 produced from this

• Finally: oxidative phosphorylation (uses O2): NADH and FADH release electrons; that energy is used for protons to flow; at the end of the electron transport chain, H2O is formed

  • Glycolysis can happen without oxygen, via fermentation

    Anaerobic pathways: (not enough oxygen)

  • Anaerobic cellular respiration: similar to regular aerobic respiration, but different molecule (NO3-, etc) is used at the end of electron transport chain, not O2

• Fermentation: Only energy extraction process is glycolysis; pyruvate is made bbuty this doesn’t go through the electron transport chain; NADH drops off electrons as it goes, allowing glycolysis to keep going

• Lactic acid fermentaiton: NADH transfers electrons to pyruvate and lactate

• Alchohol fermentation (yeast cells): NADH donates electrons to pyruvate derivative (ethanol)