Lec 4 Metabolism and Cell energy

The reactions inThe reactions in the pathways of glycolysis and the citric acid cycle break down glucose into smaller molecules. Therefore, these pathways the pathways

• Catabolic pathways

• Catabolism is the breakdown of molecules into smaller units, producing ATP

What happens to bonds within chemical reactions?

• During chemical reaction, atoms keep chemical identity but the bonds change 

What can occur in human bloodstream due to CO2 (B)?

• cells break down glucose → produce carbon dioxide.

• In animals, this carbon dioxide diffuses out of cells and into the blood.

• Rather than remaining dissolved in solution, most of the carbon dioxide is converted into carbonic acid.

• In an aqueous (watery) environment like the ocean or the blood: carbonic acid exists as bicarbonate ions ( HCO 3 − ) and protons ( H + ) .

How is carbonic acid formed?

• CO2 and water react to form carbonic acid 

• CO2 covalently bonded with double bonds

• H20 covalent bonded to O with two single bonds

  • single covalent bond connecting Carbon and oxygen in CO2 and single covalent bond connecting hydrogen and oxygen in H20 are broken

  • Covalent bond is formed between carbon of CO2 and oxygen of H20, and between one oxygen of CO2 and one hydrogen of H20

• Happens in Aquarius atoms -> oceans become more acidic because more CO2 dissolved in water --> increased carbonic acid 

• reaction is reversible 

• atoms stay the same, but bonds change

What are covalent bonds?

• A chemical bond formed by a shared pair of electrons holding two different atoms together.

• Covalent: sharing e-

What are ionic bonds?

• A chemical bond in which two ions with opposite charges associate with each other due to their difference in electronegativity.

• Not shared from one atom to another: breaking and forming of ionic bonds

What kind of bond is there in the formation of carbonic acid?

• Involve breaking and creating covalent bonds 

What are free radicals (Reactive Oxygen Species)?

• Atoms or molecules in unpaired e - --> unstable and highly reactive (need more to become stable) 

How are free radicals shown in oxygen?

• Oxygen: 8 e- to be stable (not a free radical)

  • Loses e- is becomes unstable and wants to pick e' from the env

  • Common free radical in body

• Single oxygen atom -> 6 (free radical)

  • Need to share 2 e- to be stable

  • b/c so much oxygen -> free radicals common in body and env

What do Reactive Oxygen species (free radicals) lead to?

• Free radical steal e- from other molecules -> cause dmg to cells and tissues 

• Naked eyes 

  • Apple slice oxidized (dmged from oxidation (lose of e-)) 

• Human aging caused by free radicals 

  • Using protection on skin and damaged by free radicals 

What are antioxidants?

• Antioxidants provide e- and serve as reducing agent and limits oxidation dmg to biological structures 

• More e- -> the more capable they are to deal with oxidation 

  • Have a lot of e- to give 

What is a popular antioxidant?

• Selenium 

  • Popular health supplement 

  • Has a lot of e- it can give  

How does selenium act as an antioxidant (slide was confusing)

 

• Fungal species: ability to use selenium and incorporate it to produce proteins -> specialized protein (selenoprotei) 

  • Protein can be used as an antioxidant b/c a lot of e- 

  • Compartments: sulfuer? 

  • Selenprotien can give e- 

• Potential to develop health products (still new) 

What is Gibbs free energy?

• the amount of energy in a system available to do work

  • difference between products and reactents

What are endergonic reactions?

• Reactions with a positive ΔG require an input of energy

• Products have more free energy than reactant: ΔG is positive 

  • Positive: requires input of energy (endergonic reaction) 

• Endergonic (need ATP to start) -> non-spontaneous (need energy to activate it) 

What are exergonic reactions?

• Reactions with a negative ΔG release energy

• Reactant has more free energy -> Negative 

  • Negative: release energy (exergonic reaction) 

• Exergonic -> spontaneous (does not need extra energy to activate) 

What is enthalpy (slide is confusing)?

• The total amount of energy in a system.

  • interested in the energy available for a cell to do work, or G

• Total energy or enthalpy (H) = energy available to do work (G) + energy lost to entropy (TS)

  • T- absolute temperature in Kelvin

  • S - entropy

• G = H - TS

What is the equation of ΔG?

• 2^nd law of thermodynamics 

• Energy lost due to randomness 

• Temperature is constant 

• compare the total energy and entropy of the reactants with the total energy and entropy of the products to see if there is energy available to do work.

• useful way to see if a chemical reaction takes place spontaneously and whether net energy is required or released

What is ΔG in catabolic reactions?

• macromolecules(have higher energy level) 

• G is negative 

  • reactants have more energy that products

  • decrease in enthalpy, products have more subunits → more disorder = higher entropy 

• Catabolic reaction is spontaneous and release energy (ATP) 

What is ΔG in anabolic reactions?

• Positive G 

  • Energy in products (bigger molecules) higher than reactants

  • Increase ΔH (total energy) 

  • Products more organized -> decrease entropy 

• Requires energy input 

• non-spontaneous 

What is energetic coupling?

• Reactions in the body can have multiple stops 

• is a process in which spontaneous reactions (ΔG < 0) drive a non-spontaneous reaction (ΔG > 0)

• If sum of reactions have a negative G --> reaction will also be spontaneous  

  • Reaction 2 has enough energy to activate reaction 1 -> coupled reaction can still occur 

What do hydrolysis reactions often do?

• break down polymers into their subunits → one product gains a proton and the other gains a hydroxyl group.

What is hydrolysis of ATP?

• ATP + H20 → Pi(inorganic phosphate)(HPO4-2) + ADP

• chemical reaction in which a water molecule is split into a proton (H + ) and a hydroxyl group (OH − ) .

• Exergonic: 

  • less free energy in the products than in the reactants.

  • Delta H

    • Phosphate groups of ATP negative → ATP has 3

    • ADP has 2 → more stable (contains less chemical energy in its bonds) than ATP → value of Delta H neg

  • Delta S: positive

    • Single molecule of ATP broken into two molecules (ADP and Pi) 

  • Delta G

    • spontaneous and releases energy 

How does energetic coupling occur in ATP hydrolysis?

• ATP hydrolysis and formation of glucose 6 phosphate in cellular respiration 

• Inorganic phosphate shared between the reactions  

  • Product of one has to be used as input to the next reaction for this to occur 

• Reaction formed by the coupling will still occur and be spontaneous 

How does  energetic coupling occur for hydrolysis of phosphoenolpyruvate?

• Hydrolysis of phosphenoalpyruavte that drives synthesis of ATP 

• Cell needs to replenish ATP to carry out additional chemical reactions 

• Inorganic phosphate both input and output -> need phosphate group to synthesize ATP

What is the ΔG of ATP considered?

• Allows ATP to drive reaction when being abundant or can be managed when low (intermediate) 

• Reaction of hydrolysis of phosphoenolpyruvate have more negative G than ATP hydrolysis and first two reaction -> produce the ATP by donating a phosphate group to ADP -> will synthesize ATP 

  • ATP hydrolysis has an intermediate energy difference

• Flow of reaction is indicated by yellow arrow 

• When ATP is high -> drive other reaction with a less negative G than ATP hydrolysis 

  • Glucose will reactive a phosphate group from ATP -> form glucose 6 phosphate 

  • Flow: red arrows 

  • ATP is consumed and creates ADP and inorganic phosphate group 

What is ATP and ADP cycling?

• reactions that have a Δ 𝐺 more negative than that of ATP hydrolysis transfer a phosphate group to ADP by energetic coupling

• reactions that have a less negative Δ 𝐺 receive a phosphate group from ATP by energetic coupling.

• Therefore, ADP accepts a phosphate group (and energy), and ATP donates a phosphate group (and energy) as it cycles between ATP and ADP.

• ATP–ADP cycle is at the core of energetic coupling between catabolic and anabolic reactions

Why is ATP useful?

• Dynamic system that depends on wether there is enough ATP or not

  • Body can use different reactions to create or consume ATP

  • Hydrolysis reaction is intermediate

• Other molecules are not intermediate so they cannot be used as currency of energy 

• intermediate ΔG

  • 1^st example: ATP is consumed

  • 2^nd: ATP is synthesized 

    • ATP useful because it can consumed and synthesized

What does both exergonic and endergonic reactions both need?

• all chemical reactions require an initial input of energy to proceed

• exergonic: the energy released is more than the initial input of energy → net release of energy.

What is a transition state?

• New compound forming -> brief transition state where old bonds are breaking and new bonds are forming 

• Transition state (unstable) -> has lots of free energy 

• highest free energy value = transition state

• Example 

  • Carbonic acid formation from CO2 and water 

  • Both reactants are most stable than transition state 

  • Reaction requires input of energy to reach the transition state (EA) 

    • Need energy to put it two work 

What is activation energy (EA)?

• all reactions require an input of energy to proceed

• energy input necessary to reach the transition state

What happens after the transition state is reached (b)?

• the reaction proceeds

• products are formed,

• energy is released into the surroundings (the downhill portion of the curve)

What are enzymes?

• protein catalysts that can increase the rate of biochemical reactions by stabilizing the transition state and decreasing free energy (decreasing curve)

• accelerates the reaction by reducing E

  • lowers obstacle

• Delta G is the same with and without the enzyme

What is a substrate?

In a chemical reaction catalyzed by an enzyme, the reactant is often referred to as the substrate

How does an enzyme decrease EA (I)?

• Low Ea -> lower energy required for reaction to work 

• Enzyme: product of proteins 

  • Catalyzes reaction by lowering EA 

• Substrate (S) is converted to Product (P)

• In presence of E → substrate forms couples with the enzyme (enzyme-substrate, ES)

• ES converted to enzyme product (EP)

• Last: complex disassociates and releases enzyme and product

• Enzyme forms complex with substrate ES (enzyme-substrate complex) 

  • Requires less EA to start reaction 

  • Substrate is changed into different product (ES) -> structure also changes 

  • Substrate is converted into product while still working with enzyme complex -> change to EP (enzyme product complex) -> complex dissociate and release enzyme (impacts shape of product) 

  • Enzyme does not change, substrate of product changes 

What do specific interactions between enzyme and the substrate in the complex do?

• stabilize the transition state → reduce activaiton energy

How are active sites formed?

• Enzyme active site is small compared to enzyme itself 

  • Only need small cavity to combine with substrate 

  • active sits made of amino acids → only a few amino acids actually catalyze (b)

• Active amino acids can be spaced far apart in peptide chain 

  • Peptide are synthesized will have few sites that will work an active site when folded together 

 

Why are enzymes so large?

• because each of these amino acids occupies a specific spatial position to align with the reactive group on the substrate.

• If the few essential amino acids were part of a short peptide, the alignment of chemical groups between the peptide and the substrate would be difficult

  • the length of the bonds and the bond angles in the peptide would constrain its three-dimensional structure.

How is enzyme shape changed?

• The enzyme active site binds the substrate and converts it to the product.

• The interactions between the substrate and the active site will decrease the activation energy required for the reaction

• Enzymes are proteins with active sites to facilities reactions 

  • ES complex will meet active site to combine with reactant  

    • Active site will change reactent to products 

  • Interactions between substrte and active site -> decreases EA 

• Enzymes needed by many biological reactions -> not enough EA to make them happen → they go slower

How does enzyme specificity work?

• Enzyme specific for certain substrates (structure of active sites) 

  • induced fit mode: shape of substrate may influenced by binding to active site

  • fit becomes closer as substrate and enzyme interact → not rigid structures → mold to some degree to each other

• Specificity of enzyme is the basis of biosensors / bioengineering 

• Signals released when only the exact biological molecules can be detected  

  • Once they have identified and combined with certain molecule -> release signal 

  • Wrong binding -> cannot bind -> no following reaction -> no signal 

What is an activator?

• A compound that increases the activity of an enzyme;

  • also, a protein that binds to a DNA sequence and turns on transcription.

What is an inhibitor?

• A compound that decreases the activity of an enzyme.

What are the types of inhibitors? 

• Reversible or irreversible depening on how they interact with enzyme 

• Covalent or ionic bonds -> strong -> inhibition is irreversible and cause dmg 

• Weak intermolecular -> reversable 

What is a competitive inhibitor?

• binds to active site -> substate can not form enzyme substrate complex anymore -> reaction is inhibited 

  • Share same active site 

  • Usually similar structure as substrate to compete with it for active sites 

What is an allosteric site?

a binding site on an enzyme or receptor that is distinct from the enzyme's active site

What is a non-competitive inhibitor?

• active site + allosteric site

• inhibitor binds with alternative site 

  • Usually have diff structure than substrate  

  • Binding of inhibitor to enzyme will change shape of enzyme 

    • Active site also changes 

  • Substrate not able to combine with active site 

• Can be influenced by inhibitor 

What are allosteric enzymes?

• an enzyme that is activated or inhibited when binding to another molecule changes its shape.

• Enzymes that are regulated by molecules that bind at sites other than their active sites

What can the activity of allosteric sites be influenced by?

• inhibitors a

• activators

What role do allosteric enzymes play?

• Allosteric enzymes play imp role in chemical regulations of reaction (and metabolic pathway) 

  • Reduce or stop amount of chemical reactions

Allosteric enzyme example

• bacterium has enough isoleucine → shut down pathway to not waste energy by synthesizing more → cell relies on enzyme inhibitor

• synthesize of isoluencine (inhibitor), reactant is threonine

• 5 reactions

  • P1-P4: intermediate products

• Once enough isoleucine (product) is made -> whole process will be inhibited by product itself

  • Isolucine is allosteric inhibitor 

  • Extra isolunece will bind to first enzyme in path way (theorine dehydrates) at a site distinct from the active site

    • theorine = allosteric enzyme

  • binding of isoleucine -> changes shape of enzyme and inhibit further production from the beginning

• Negative feedback: uses products as allosteric inhibitor to stop reaction from beginner

  • final product inhibits the first step of the reaction

What does the rate of reaction depend on (b)?

• activity of threonine dehydratase = rate of the reaction → depends on the concentration of substrate

• low concentration of threnonine = low reaction rate

• high concentration = enzyme activity increases 

• At a particular threshold, a small increase in threonine concentration results in a large increase in reaction rate.

• Finally, when there is excess substrate, the reaction rate slows down.

Why are some mushrooms toxic to human beings?

• Amatoxins are selective inhibitors of RNA polymerase II, which is a vital enzyme in the synthesis of messenger RNA (mRNA), microRNA, and small nuclear RNA (snRNA).

Why is RNA polymerase complex (Pol II) important?

• RNP II important for transcription and protein production 

• Cover image 

  • How RNP works in body to make RNA 

• RNP II needs to bind directly to DNA template to make RNA 

How does amatoxins work to be inhibitors?

• Amatoxin (red) combine to RNP II -> enzyme cannot bind to DNA template (competitive inhibitor) 

• Toxin can travel through stream and reach other organs -> dmg to liver, heart, brain 

  • Inhibition + organ failture = irreversible 

What is the phylogenetic analyses of RNP II?

• Many polyphyletic becomes monophyletic 

• RPP I and II have been used more and is more robust -> more popular 

What are mycotoxins?

• a toxic secondary metabolite produced by fungi

• Many fungi can product toxin 

• Fungal tree of life 

  • Diversity produced from a handful of fungal species