Cellular Energetics

Topics Covered

• Enzyme Structure
• Enzyme Catalysts
• Environmental Impacts on Enzyme Function
• Cellular Energy
• Photosynthesis
• Cellular Respiration
• Fitness

Enzymes: speed up metabolic reactions by lowering energy barriers

Structure: globular proteins that exhibit tertiary structure

• Enzymes have active sites that interact with substrates
• For an enzyme-mediated chemical reaction to occur, the shape and charge of the substrate must be compatible with the active site of the enzyme.

Enzyme Controlled Reactions:

• Enzymes serve as catabolic proteins that speed up reactions by lowering the activation energy
  • Activation energy: the initial energy needed to start a reaction
• Induced fit model describes how enzymes work. As the substrate enters the active site, it induces the enzyme to alter its shape slightly so the substrate fits better

Process:

• Substrate is held in the active site by weak interactions including hydrogen and ionic bonds.
• R groups of a few of the amino acids that make up the active site catalyze the conversion of substrate to product and the produce departs from the active site
• After the substrates are converted to products, the products are released and the enzyme can be reused

Active-site can lower activation energy by

• Orienting substrates correctly
• Straining substrate bonds (since activation energy is proportional to the difficulty of breaking the bonds, distorting the substrate helps it approach the transition state thus absorbing the amount of free energy needed to be absorbed to achieve that state)
• Provide favorable microenvironment (ex: serve as acidic or basic environment)
• Directly participating in the reaction through brief covalent bonding

Enzymes are affected by:

• Relative concentration of substrates affects the efficiency of the enzyme which affects the product production rate
• Environment
  • Temperature: Heat increases the frequency of enzyme and substrate collison which increases the rate of the reaction. If the temperature is too hot, the enzyme will denature, and if it is too cold, there will not be enough energy to start the reaction. Each enzyme has an optimal temperature.
  • PH: AN environment too acidic or basic results in an inactive enzyme by disrupting the hydrogen bonds of the enzyme which provide the enzyme's shape and structure. Each enzyme has an optimal PH which can differ between different enzymes.
• Cofactors/ coenzymes: non-protein enzyme helper that alter the active site
• Inhibitors: bind to enzymes and decrease their activity. They regulate reactions, eliminate harmful enzymes, or they can be poisonous.
  • Competitive: bind to active site and compete with the substrate
    • They are reversible if they form hydrogen/ionic bonds with the active site, or irreversible if they form covalent bonds or they are toxic
    • This makes a bigger impact at lower substrate concentrations because there is a higher change the inhibitor will get the active site before the substrate
  • Non-competitive bind to allosteric (site other than active site) and change the enzyme’s shape

Regulation of enzyme activity helps control metabolism:

Allosteric Regulation: occurs when a regulatory molecule binds to a protein at one site and

affects the protein’s function at another site

• The binding of an activator stabilizes the active form of the enzyme
• The binding of an inhibitor stabilizes the inactive form of the enzyme
• Cooperativity is a type of allosteric activation. The binding of one substrate molecule to one active site of one subunit of an enzyme causes a change in the entire molecule and locks the subunits in an active position. This mechanism amplifies the response of an enzyme to its substrate.

Regulation of metabolic pathways:

Metabolic pathway: the product of one reaction is the reactant for the next

• Negative Feedback
  • The end product of a metabolic pathway shuts down the pathway
  • Prevents the cell from wasting chemical resources by producing more than what’s needed
• Positive Feedback
  • Tells enzyme to continue spiral of change

Specific Location of Enzymes within the cell:

• Enzymes can reside in membranes, or organelles in eukaryotic cells (like mitochondria)

Cellular Energy:

Laws of Thermodynamics:

1. Energy cannot be created or destroyed, only transformed or transferred
2. Every energy transfer increases the entropy in our universe
   1. No energy transformation is 100% efficient because some is lost as heat
   2. For a reaction to occur spontaneously (without energy input), it must increase the entropy of our universe

The free energy change of a reaction tells us whether the reaction occurs spontaneously

• In a spontaneous Change:
  • The system becomes more stable
  • The released free energy can be harnessed to do work-> energy coupling
  • Energy coupling: use of an energy releasing process to drive an energy requiring one

Life requires a highly ordered system and does not violate the second law of thermodynamics—

• Energy input must exceed energy loss to maintain order and to power cellular processes.
• Cellular processes that release energy may be coupled with cellular processes that require energy.
• Loss of order or energy flow results in death

ATP powers cellular work by coupling energy releasing reactions to energy requiring reactions

• ATP serves as a mediator/ vehicle to move energy
• Energy is released from ATP when the terminal phosphate is broken off and bonds in water are broken, then new bonds form (hydrolysis)
• Breaking bonds requires energy, but when ATP is broken, new bonds form, thus releasing energy
• the energy from the energy
• ATP drives energy requiring reactions by phosphorylation, transferring a phosphate group to some other molecule, such as a reactant
  • The recipient molecule is now called a phosphorylated intermediate
• ATP is a renewable energy source

Redox Reactions: involve the gaining or loss of electrons

• Both are required for normal cell respiration
• They are coenzymes that carry protons and electrons from glycolysis and the citric acid cycle to the electron transport chain
• The enzymes NAD dehydrogenase, or FAD dehydrogenase facilitates the transfer of hydrogen atoms from a substrate, to its coenzyme
• If something becomes oxidized, it loses electrons, while something is reduced gains electrons
  • NAD+ (oxidized form) NADH (reduced form which carries 1 proton and 2 electrons)
  • FAD (oxidized form) FAD2 (reduced form which carries 1 proton/hydrogen ion and 2 electrons.

Photosynthesis: process by which light energy is converted to chemical bond energy

Evolution Background: Photosynthesis first evolved from prokaryotic organisms

• Scientific evidence supports the claim that prokaryotic (cyanobacteria) photosynthesis was responsible for the production of an oxygenated atmosphere
• Prokaryotic photosynthetic pathways were the foundation of eukaryotic photosynthesis.
  • Green plants evolved when purple photosynthetic bacteria were plentiful. Green plants used the light available to them.
    • Chlorophyll absorb red and blue wavelengths, thus green wavelengths are reflected, so plants look green

2 main processes of photosynthesis: light dependent and the light independent reactions

First, Plants obtains raw materials

• Receive sunlight through leaves, water and nutrients from roots, and CO2 from stomata (leaves or stem)

Light Dependent: Light energy is converted to chemical energy during the first stage of photosynthesis, which involves a series of chemical reactions known as the light-dependent reactions.

General Information:

• The light-dependent reactions use light energy to make two molecules needed for the next stage of photosynthesis: the energy storage molecule ATP and the reduced electron carrier NADPH. In plants, the light reactions take place in the thylakoid membranes of organelles called chloroplasts.
• Photosystems, large complexes of proteins and pigments (light-absorbing molecules) that are optimized to harvest light, play a key role in the light reactions. There are two types of photosystems: photosystem I (PSI) and photosystem II (PSII).
  • Each photosystem consists of a reaction center containing chlorophyll and a region containing several hundred antenna pigment molecules that funned energy to chlorophyll
• Both photosystems contain many pigments that help collect light energy, as well as a special pair of chlorophyll molecules found at the core (reaction center) of the photosystem. The special pair of photosystem I is called P700, while the special pair of photosystem II is called P680.

Photophosphorylation: electrons are removed from water and passed through PSII and PSI before NADPH is reduced. This process requires light to be absorbed twice, once in each photosystem, and it makes ATP. Here are the general steps:

1. Light absorption in Photosystem 2: When light is absorbed by one of the many pigments in photosystem II, energy is passed inward from pigment to pigment (antenna pigment molecules) until it reaches the reaction center. Energy is absorbed by P680, and the electron from the head of a chlorophyll a is boosted to a higher energy level. The high-energy electron is then captured by a primary electron acceptor.
2. Photolysis: the splitting of water provides electrons to replace those lost chlorophyll a in P680. Photolysis splits water into two electrons, two protons, and one oxygen atom. Two oxygen atoms combine to form one O2 atom which is released into the air as a waste product of photosynthesis.
3. Electron Transport Chain: As the high energy electrons (from P680) travel down the electron transport chain, they lose energy as they go. The flow of electrons is exergonic and provides energy to produce ATP by chemiosmosis (the same way ATP is produced in mitochondria. However unlike mitochondria, this ATP synthase is powered by light).
4. Light Absorption in Photosystem 1: Same thing as photosystem 2. Only difference is that the electrons that leave chlorophyll a are replaced with electrons from photosystem, P680, instead of from an electron from water.
5. NADPH Formation: At the end of the electron transport chain, the electron is passed to NADP+, (along with a second electron from the same pathway) to make NADPH.
6. Chemiosmosis is the process by which ATP is formed during the light reactions: Protons that were released from water during photolysis are pumped by the thylakoid membrane from the stroma into the thylakoid space (lumen). ATP is formed as these protons diffuse down the gradient from the thylakoid space, through the ATP synthase channels, and into the stroma. The ATP produced here powers the Calvin Cycle.

Light Independent Reactions: The Calvin Cycle

General Information: It is a cyclical process that produces 3-carbon sugar PGAL (phosphoglyceraldehyde)

• Three turns of the Calvin cycle are needed to make one G3P molecule that can exit the cycle and go towards making glucose.
• Takes place in the stroma (colorless fluid surrounding the grana within the chloroplast)

In 3 turns of the Calvin Cycle:

Carbon: 3 CO2 molecules combine with 3 RuBP molecules, making 6 molecules of G3P

• 1 G3P exits the cycle and goes towards making glucose while the other 5 are recycled in order to regenerate the 3 RuBP molecules
• 2 G3P molecules are needed to make one molecule of glucose
• ATP: 9 ATP are converted to 9 ADP (6 during the fixation step, 3 during the regeneration step)
• NADPH: 6 NADPH are converted to 6 NADP+ (during the reduction step

Process

1. Carbon fixation: carbon combines with a 5 carbon sugar (ribulose bisphosphate or RuBP), forming a six carbon molecule that splits into 2 3-carbon compounds (3-phosphoglycerate or 3-PGA). Rubisco is the enzyme that catalyzes this first step.
2. Reduction: ATP and NADPH are used to convert the 3-PGA molecules into molecules of a three-carbon sugar, glyceraldehyde-3-phosphate (G3P). This stage gets its name because NADPH donates electrons to, or reduces, a three-carbon intermediate to make G3P.
3. Regeneration: Some G3P molecules go to make glucose, while others must be recycled to regenerate the RuBP acceptor. Regeneration requires ATP and involves a complex network of reactions

Photorespiration:

• The enzyme rubisco fixes oxygen instead of CO2
• Carbon fixation typically exceed oxygen fixation because rubisco’s affinity for C)2 is higher than O2
• This is a wasteful process because it consumes the ATP and NADPH (high energy molecules) because it prevents plants from using energy to synthesize carbohydrates.

Cellular Respiration

Fermentation allows glycolysis to proceed in the absence of oxygen and produces organic molecules, including alcohol and lactic acid, as waste products.

Anaerobic Respiration: Fermentation:

• Anaerobic, catabolic process that consists of glycolysis plus alcohol or lactic acid fermentation (reactions that regenerate NADP+)
• Fermentation can generate ATP during anaerobic respiration only as long as there is an adequate supply of NADP+ to accept electrons during glycolysis
• Obligate anaerobes: cannot live an environment with oxygen so they need to carry out fermentation
• Facultative anaerobes: survive using fermentation, and can tolerate presence of oxygen

Lactic Acid Fermentation:

1. Pyruvate (made from glycolysis) takes an electron from NADPH
2. Pyruvate is reduced while NADPH is oxidized
3. Lactic Acid/ lactate (reduced pyruvate) is formed and NADPH become NADP+

Glycolysis can continue, ATP continues getting made as long as there is glucose and NAD+, fermentation continues

Alcohol Fermentation: process by which cells convert pyruvate from glycolysis into ethyl alcohol and carbon dioxide in the absence of oxygen in order to oxidize NADPH back to NADP+

Aerobic Respiration:

Glycolysis: ATP is produced from substrate level phosphorylation: direct enzymatic transfer of a phosphate to ADP. Only a small amount of ATP is released this way. It occurs in the cytoplasm

End Result:

2ATP+1 Glucose→ 2 pyruvate 4 ATP

2NADP+ + 4 electrons n 4 hydrogen ions= 2NADPH + 2 hydrogen ions

Process: 1). Energy-Requiring phase: in this phase, the starting molecule of glucose gets rearranged and two phosphate groups are attached to it. The phosphate groups make up the modified sugar: now called fructose-1, 6-bisphosphate. This step is catalyzed by the enzyme phosphofructokinase, which can be regulated to speed up or slow down the glycolysis pathway. The fructose-1, 6-bisphosphate molecule is unstable, allowing it to split in half and form two phosphate-bearing tree-carbon sugars. Because the phosphates used in these steps come from ATP, two ATP molecules get used up. Phosphofructokinase (PFK) is an allosteric enzyme. If ATP is available in large quantities, it inhibits PFK by altering the conformation of the enzyme, thus inhibiting the substrate from binding, thus inhibiting glycolysis. Although the 3-carbon sugars formed when the unstable sugar breaks down are different from each other, both can finish the pathway in the end. DHAP is the unfavorable sugar, but it can be converted into glyceraldehyde-3-phosphate, which is the favorable sugar 2). Energy Releasing Phase: In this phase, each 3-carbon sugar is converted into another 3-carbon molecule, pyruvate, through a series of reactions. In these reactions, two ATP molecules and one NADPH molecule are made. Because this phase takes place twice, once for each of the two 3-carbon sugars, it makes four ATP and two NADPH overall.

Prekrebs: converts pyruvate to Acetyl COA

• Pyruvate enters the mitochondria through a transport protein since it is charged
• The end result is: 2 acetyl COA, 2 CO2, 2 NADPH, and 0 ATP

1. Pyruvate’s carboxyl group is already fully oxidized because it gave off its electrons. Thus, the carboxyl group turns into CO2 and is released
2. The remaining 2-carbon fragment is oxidized, forming acetate. Extracted electrons are transferred to NAD+ which stores the electrons as NADPH.
3. COA (a sulfur containing compound) attaches to acetate forming acetyl CoA! (this process repeats twice since there are 2 pyruvates)

Krebs Cycle: ATP is produced through substrate-level phosphorylation

The main function of the Krebs cycle is to produce electron carriers that can be used in the last step of cellular respiration.

Takes place in the matrix of mitochondria

• It takes acetyl CoA as its starting material, and in a series of redox reactions, harvest musch of its bond energy in the form of NADH, FADH2 and ATP
• Carbon cycles happens twice, once for each acetyl CoA
• End Result: 6NADPH, 2FADH2, 4CO2, and 2ATP

Process:

1. Acetyl CoA combines with a four-carbon acceptor molecule called oxaloacetate in order to form a six-carbon molecule called citrate.
2. Citrate is converted into its isomer, isocitrate
3. Isocitrate is oxidized and releases a molecule of carbon dioxide forming a 5 carbon molecule called a-ketoglutarate, and NAD+ is reduced to NADH. The enzyme catalyzing this step, isocitrate dehydrogenase is important in regulating the speed of the citric acid cycle.
4. A-ketoglutarate is oxidized and reduces NAD+ to NADH and releases a CO2 in the process. The four-carbon compound attaches to a Coenzyme A, forming an unstable compound: succinyl CoA
5. CoA of succinyl CoA is replaced by a phosphate group. The phosphate group is then transferred to ADP to make ATP. The four carbon molecule produced is called succinate
6. Succinate is oxidized, forming another four carbon molecules called fumarate. In this step, 2 hydrogen atoms (with their elections) are transferred to FAD, producing FADH2
7. Water is added to fumarate, converting it into another four carbon molecule called malate
8. Malate is oxidized, forming oxalate and another NAD+ is reduced to NADH

Oxidative Phosphorylation : phosphorylation of ADP into ATP by the oxidation of carrier molecules NADH and FADH2.

• Oxidative Phosphorylation: NAD and FAD lose protons to the electron transport chain which creates a steep proton gradient. The gradient powers the phosphorylation of ADP into ATP during chemiosmosis.

Electron Transport Chain:

• NADPH and FADH2 shuttle high energy electrons extracted in the previous steps into the ETC in the cristae membrane. The electrons move down the chain, eventually to the final electron acceptor, oxygen (which is very electronegative)
• NADH and FADH2 help create a proton gradient as they power protein pumps with the electrons they lost as they were oxidized. The proton pumps pump the hydrogen ion lost from the carrier molecules while they are oxidized, into the intermembrane space, thus creating a proton gradient (lots of protons in intermembrane space, little in the Mitochondrial matrix).

Chemiosmosis:

• As protons glow back down the gradient, through ATP-Synthase channels, they generate energy to phosphorylate ADP into ATP

This step creates the most ATP molecules during cellular respiration.

Fitness

• Variation at the molecular level provides organisms with the ability to respond to a variety of environmental stimuli.
• Variation in the number and types of molecules within cells provides organisms a greater ability to survive and/or reproduce in different environments.
  • Different types of phospholipids in cell membranes allow the organism flexibility to adapt to different environmental temperatures.
  • Different types of hemoglobin maximize oxygen absorption in organisms at different developmental stages.
  • Different chlorophylls give the plant greater flexibility to exploit/ absorb incoming wavelengths of light for photosynthesis.
• Natural Selection (on the organism level) components needed for this mechanism
  • Variation (exists among individuals of the same species)
  • Reproduction (results in overpopulation)
  • Competition (not enough resources are available for all)
  • Fitness (those more fit survive)
  • Evolution: survivors reproduce, fit alleles become more common