Chapter 3 & 5: Bioenergetics, Enzymes and Metabolism

What is the difference between anabolism and catabolism

• Anabolism refers to the metabolic pathways that construct large molecules from smaller units, requiring energy input

• catabolism involves breaking down large molecules into smaller units, releasing energy in the process.

What is Metabolism

• all the chemical processes going on continuously inside your body that allow life and normal functioning (homeostasis)

  • two types: Catabolism and Anabolism

What’s the basic principles of the oxidation states of carbon

• The oxidation states of carbon indicate its degree of oxidation or reduction (moving electrons/energy), reflecting how many electrons it has gained or lost.

  • These states can influence the stability and reactivity of organic compounds

• Five oxidation states of carbon (depending on the elements with which carbon shares electrons)

  • Lots of steps to get alkane to carbon dioxide – the end goal

• Carbon dioxide is the most highly oxidized form of carbon found in living organisms

What are the characteristics of exergonic and endergonic rxns and rxn equilibrium 

• Exergonic reactions release energy and occur spontaneously

  • ∆G (energy associated with a chemical reaction) is negative

• Endergonic reactions absorb energy and are non-spontaneous, ex. glycolysis

  • ∆G is positive

• Reaction equilibrium is the point at which the rate of forward and reverse reactions are equal, resulting in stable concentrations of reactants and products.

  • ∆G is 0

What is free energy changes of ATP

• The free energy changes of ATP refer to the energy released when ATP is hydrolyzed to ADP and inorganic phosphate, driving various biochemical processes

  • This energy change is crucial for cellular work, facilitating reactions that require energy input

• Hydrolysis: breaking bonds apart using water

Explain the concept of coupling rxns

• In metabolism, pathways (like glycolysis) must be thermodynamically favorable but not each reaction needs to be thermodynamically favorable because reactions can be coupled – “sharing” potential transfer energy when they share reaction intermediates

  • Coupling reactions involve linking an exergonic reaction to an endergonic reaction, allowing the energy released from the former to drive the latter.

How would you ‘activate a molecule of glucose in the first step of glycolysis by coupling a reaction (including the names of substrate enzyme and product)

• Glucose+ATP→Glucose-6-phosphate (G6P)+ADP

• In glycolysis, glucose is phosphorylated to glucose-6-phosphate by the enzyme hexokinase (or glucokinase in liver cells), using ATP as the substrate, which is converted to ADP.

  • substrates: glucose and atp

  • products: glucose-6-phosphate (G6P)

• this reaction couples the energy released from ATP hydrolysis to activate glucose for further metabolism down the glycolysis pathway

  • this is an irreversible step

What is the difference between ∆G˚ and ∆G

• ∆G˚ represents the standard free energy change under standard conditions

  • change in free energy during a reaction under standard conditions and measured in a test tube

• ∆G indicates the actual free energy change under specific conditions of concentration and temperature

  • changes in free energy associated with a chemical reaction in a cell

What’s the role of a catalyst and how it increases the rate of a rxn

• A catalyst is a substance that accelerates the rate of a chemical reaction without being consumed in the reaction itself.

• It lowers the activation energy required for the reaction to proceed (the transition substrate), allowing reactants to convert to products more efficiently.

  • only affects the rates of reactions

• Enzymes (biological catalysts) are the mediators of metabolism, responsible for virtually every reaction that occurs in a cell.

  • Without enzymes, metabolic reactions would proceed so slowly as to be imperceptible.

  • very specific

What is a active site

• The active site is a region on an enzyme where substrate molecules bind, forming an enzyme-substrate complex.

  • It contains specific amino acids that facilitate the conversion of substrates to products through a precise fit and induced conformation changes.

  • The active site and the substrate have complementary shapes that allow substrate specificity but after binding of substrate to enzyme both will change conformation

    • binding via multiple weak non-covalent interactions

What is meant by maximal velocity

• Maximal velocity, or Vmax, refers to the maximum rate at which an enzyme-catalyzed reaction can proceed when the enzyme is saturated with substrate.

  • It indicates the efficiency and capacity of the enzyme under optimal conditions.

What is meant by Km

• Km, or Michaelis constant, is the substrate concentration at which an enzyme-catalyzed reaction reaches half of its maximal velocity (Vmax)

• It reflects the affinity of the enzyme for its substrate; a lower Km indicates higher affinity.

What is glycated hemoglobin and how can it be used to determine average blood glucose levels over a period of time

• Glycated hemoglobin (GHB), or A1c, is a form of hemoglobin that is chemically linked to glucose

• Is used to measure “average” blood glucose concentrations over time (over the previous two months) making it a crucial marker for diagnosing and managing diabetes

  • when you have excess glucose it then forms complexes, which causes a lot of problems

What’s the definition of AGE with respect to glycated proteins

• AGE, or Advanced Glycation End-products, are harmful compounds formed when proteins or lipids (not just hemoglobin) bond with sugars, which can accumulate and contribute to various chronic diseases, including diabetes and cardiovascular issues.

• The more of this that occurs, the higher the potential damage

What are inhibitors and explain how it being covalent or not affects it?

• Inhibitors are substances that decrease the activity of enzymes by binding to them

  • Irreversible inhibitors bind tightly to the enzyme → permanent (often covalently)

  • Reversible inhibitors bind loosely to the enzyme → temporary (non covalently)

What is competitive inhibition

• Reversible inhibition

• Is a process where a substance similar to the substrate competes for binding to the active site of an enzyme, reducing the enzyme's activity and slowing down the reaction rate.

  • usually resemble the substrate in structure but high enough levels of substrate can compete out the inhibitor

What is non-competitive inhibition

• Reversible inhibition

• Is a type of enzyme inhibition where an inhibitor binds to an enzyme at a site other than the active site, altering the enzyme's shape and function (conformation), thus decreasing its activity regardless of substrate concentration.

  • Allosteric inhibitors

What does allosteric inhibition mean

• Allosteric inhibition refers to a regulatory mechanism where an inhibitor binds to an allosteric site on an enzyme, causing a conformational change that decreases the enzyme's activity and prevents substrate binding.

• Allosteric modulation of enzymes can inhibit or activate enzyme activity

  • PKA (protein kinase A) is activated by catalytic subunits and cAMP

What is the role of NADH and FADH2

• NADH and FADH2 are coenzymes that function as electron carriers in cellular respiration, transferring electrons to the electron transport chain to produce ATP during oxidative phosphorylation

  • all of this takes place in the mitochondrial matrix and the citric acid cycle, hence is why we are generating so many of these electron carriers

• NADH carries 2 electrons that will be passed on to the electron transport chain and will ultimately be transferred to molecular oxygen which ultimately results in the formation of ATP

• FADH2 also carries 2 electrons that follow the same pathway

What happens to the carbons from glucose when glucose is used to generate ATP

• The carbons from glucose are converted into carbon dioxide through the processes of glycolysis, the citric acid cycle, and the subsequent oxidation of pyruvate.

  • This release of carbon dioxide occurs as glucose is metabolized for energy

  • conserved energy is used to pump protons from matrix to intermembrane space where it ultimately leads to atp being made (down the transport chain)

• Ultimately, carbons get excreted from glucose

What are the 3 conformations of ATP synthase and what happens at each step (that is the synthesis of ATP)

• know the 3 subunits (alpha and beta x3) which change conformations, substrates involved (ADP) – moving 120 degrees resulting in ATP – moving another 120 degrees will release the ATP

• ATP synthase has three conformations: open (O), loose (L), and tight (T).

  • In the open conformation, ADP and inorganic phosphate enter

  • In the loose conformation, they are held together

  • In the tight conformation, ATP is synthesized, which is then released back into the mitochondrial matrix.