Ch. 8 Bio

Flashcards covering key vocabulary terms related to metabolism and enzyme function based on the provided lecture notes, including thermodynamics, energy coupling, enzyme regulation, and inhibition.

Metabolism

The totality of an organism's chemical reactions, following the laws of thermodynamics

Metabolic Pathway

begins w/ a specific molecule and ends with a product

• each step is catalyzed by a specific enzyme

Catabolic Pathways

Metabolic pathways

• release energy by BREAKING down complex molecules into simpler ones (exergonic processes), such as cellular respiration or the breaking down of glucose 

  • aka catabolism

Anabolic Pathways

Metabolic pathways

• consume energy to BUILD complex molecules from simpler ones (endergonic processes), such as the synthesis of proteins from amino acids (building up nucleotides)

First Law of Thermodynamics (Law of Conservation of Energy)

• energy in the universe is constant

• law of conservation of energy 

  • energy can be transferred and transformed but not created or destroyed 

• always able to track all energy leaving and entering a system

Second Law of Thermodynamics

• he entropy (disorder) of the universe is always increasing

• The entropy of a closed system is ≥0.

• entropy is the driving force for all physical processes & chemical processes 

Entropy ΔS

A measure of the disorder or randomness within a system

• a primary driving force for physical and chemical processes.

positive entropy (+ΔS)

• favorable

• disorganized; more messy

  • Ex: boiling water

negative entropy (-ΔS)

• unfavorable 

• becoming more ordered

  • creates disorder within surroundings

  • Ex: body systems

What is the universe equation for entropy?

universe = system (your reaction) + surroundings

Entropy in a system vs universe

within a system

• human body is organized (unfavorable -ΔS), meaning entropy may decrease in an organism 

within the universe 

• universe’s total entropy is always increasing (+ΔS) by spontaneous reactions 

  • humans are always giving up heat, increasing disorder of our surroundings or breathing out CO₂

Does evolution or human activity violate the 2nd law of thermodynamics?

No, it does not violate the law. Evolution and human activity contribute to local decreases in entropy, but overall entropy in the universe still increases.

Free Energy Change (ΔG)

• determines if a reaction is favorable or unfavorable

  • related to metabolism 

• a living system’s energy that can do work 

• most basic form of energy currency within the cell 

Negative ΔG

• favorable

• spontaneous

• exergonic reaction where energy is released.

Positive ΔG

• unfavorable

• non-spontaneous 

• endergonic reaction where energy is required.

Gibbs Equation

ΔG = ΔH - TΔS; an equation relating free energy change (ΔG) to enthalpy change (ΔH), temperature (T in Kelvin), and entropy change (ΔS).

Free energy is a combination of what two things?

entropy & enthalpy

Enthalpy ΔH

a change in heat ΔH

Exergonic Reaction

A chemical reaction that releases energy, is spontaneous, and has a negative ΔG.

Endergonic Reaction

A chemical reaction that requires or absorbs energy, is non-spontaneous, and has a positive ΔG.

ATP (Adenosine Triphosphate)

• primary energy currency of the cell

• composed of a ribose, adenine, & 3 phosphate groups

• constantly cycling between its triphosphate and diphosphate forms

  • regenerated by the addition of a phosphate group to ADP.

Energy Coupling

The use of an exergonic process to drive an endergonic one

• mediated by ATP in cells

How does ATP drive unfavorable reactions?

• couple them to ATP hydrolysis

  • alone some reactions have +ΔG (not spontaneous)

• Breaking ATP (ATP → ADP + Pi) releases lots of energy (-ΔG) 

  • ATP transfers a phosphate to the reactant, resulting in a high-energy intermediate (phosphorylated intermediate) 

    • intermediate easily reacts, so the combined ΔG is negative, making the overall reaction favorable 

Main idea: ATP hydrolysis couples with the reaction to flip it from non-spontaneous to spontaneous

Phosphorylation

The addition of a phosphate group to a molecule, often mediated by ATP, can alter the molecule's energy state and reactivity.

Cycle of ATP to ADP + Pi

The continuous process of ATP hydrolysis to ADP and inorganic phosphate releases energy and is crucial for powering cellular processes.

• energy that comes in from catabolism (exergonic, energy-releasing processes)

• energy that is released is used for cellular work (endergonic, energy-consuming processes)

Enzymes

• Catalytic proteins (or RNA)

• lowers activation energy, increasing reaction rates

• catalyze metabolic reactions

  • unchanged by reaction, but changes the reaction

catalyst

chemical agent thats speeds up reactions w/o being consumed by that reaction 

Activation Energy (Ea)

The initial energy investment required to start a chemical reaction; the energy barrier that must be overcome for reactants to reach the transition state.

How do enzymes lower the activation barrier?

Enzymes catalyze reactions by lowering the E_A barrier = faster reaction

-don’t affect the change in free energy ΔG, instead, they speed up reactions that would occur eventually

4 main ways:

• orienting substrates correctly

• straining substrate bonds (so its easier to break) 

• providing a favorable microenvironment ( ex: different pHs)

• covalently binding to substrate 

  • An enzyme is a catalyst, so it can’t permanently covalently bond

Steps of an enzyme lowering activation barrier:

1. substrates enter active site

2. substrates are held by non-covalent bonds

3. E_A is lowered

4. substrates converted to products

5. products are released

6. free enzyme (cycle restarts)

Rates not equilibria, not ΔG

Enzymes only speed up how fast a reaction reaches equilibrium 

• they don’t decide wether a reaction will happen (ΔG) or if it’s favorable or the final equilibrium point 

  • enzymes only change the rate, which is speed, not equilibrium, which is the ratio of products and reactants, nor free energy ΔG, deciding if a reaction can even occur 

Substrate

A specific reactant molecule that an enzyme acts upon; binds to the enzyme's active site

• reactant = ligand = specific to each enzyme 

enzyme substrate complex

Enzyme and substrate are temporarily stuck together, helping reaction happen faster and releasing the product

Active Site

The specific region of an enzyme where the substrate binds and where the chemical reaction occurs.

Induced Fit

the enzyme changes its shape slightly upon binding to the substrate, enhancing the fit and optimizing the catalytic activity

• closing of the enzyme around a substrate 

  • makes drug discovery hard because ppl though it was a “lock & key” mechanism however its not since the shape adapts to the substrate

Cofactors

Non-protein enzyme helpers

• required by many enzymes for catalytic activity

• can be inorganic (e.g., metal ions) or organic (coenzymes).

Coenzymes

Organic cofactors

• ex: many vitamins

  • body cant directly make them but enzymes require them as prosthetic groups

prosthetic groups

helper groups that allow enzymes to function

Enzyme Inhibitors

Molecules that decrease the activity of an enzyme, including competitive and noncompetitive types.

Competitive Inhibitors

• molecules bind to the active site

• competes with substrate blocking it’s entry to the enzyme, thus reducing the rate of the reaction.

Noncompetitive Inhibitors

• Molecules bind to a location other than the active site (allosteric site), causing a change in the enzyme's shape that makes the active site less effective 

• substrate can no longer fit into active site 

4 ways regulation of enzyme activity helps control metabolism

1. switching on or off the genes that encode specific enzymes

2. regulating enzyme activity

   1. allosteric regulation & cooperativity

3. feedback regulation

4. enzyme localization

Allosteric Regulation

• either inhibits or stimulates an enzyme’s activity

  • regulatory protein binds to a protein at one active site and affects the function at another site

Allosteric Activator

A regulatory molecule that binds to an allosteric site and stabilizes the active form of an enzyme, increasing its catalytic activity.

Allosteric Inhibitor

A regulatory molecule that binds to an allosteric site (other than the active site) and stabilizes the inactive form of an enzyme, decreasing its catalytic activity.

Cooperativity

• specific type of allosteric activation

  • regulator molecule and substrate are the SAME molecule 

  • substrate goes into active site 

• one substrate molecule primes as an enzyme to bind additional substrates tightly or weaker 

  • one active site affects a different active site 

Feedback Inhibition/ regulation

• regulatory mechanism

• end product of a metabolic pathway regulates the pathway

  • end product binds allosteric site of first enzyme → shuts pathway off → saves reasources

• prevents the cell from wasting chemical resources by overproducing that product.

Enzyme Localization (Compartmentalization)

• method of controlling metabolic pathways

• localizing specific enzymes within particular organelles or structures within the cell

  • such as cellular respiration enzymes in mitochondria

  • by keeping enzymes close to substrates or away from them, they can turn metabolic pathways on or off quickly

• moving or grouping enzymes where they’re needed so reactions can happen fast or slow down

Compartmentalization

• occurs only within mitochondria

• substrates must be transported into mitochondria

  • cellular regulation