Enzyme and metabolism (metabolic pathways)

first law of thermodynamics

states that energy cant be created or destroyed, instead can be tramsformed/converted

second law of thermodynamics

states that the total entropy of an isolated system can never decrease over time, and energy transformations are not 100% efficient.

quantity of energy vs. its quality

refers to the relationship between the amount of energy available in a system and its ability to perform work. High-quality energy is easily converted to work, while low-quality energy is less useful for doing work.

free energy (G)

the amount of energy available to do work at constant temperature and pressure in a system.

free energy change (ΔG)

the difference in energy between the products and reactants of a chemical reaction

± ΔG (free energy change)

a negative or positive ΔG indicated whether the reaction is spontaneous or non-spontaneous

• A negative ΔG signifies that a reaction can occur spontaneously

• a positive ΔG suggests that the reaction requires input energy to proceed.

how do you find ΔG?

ΔG = G_{final state} - G_{intial state}

-ΔG (ΔG<0) on a graph

a graph showing that a reaction is spontaneous, indicating a decrease in free energy over time. This progression shows that products are favored.

+ΔG (ΔG>0) on a graph

a graph shows that the reaction is non-spontaneous and requires energy input to proceed, indicating a positive free energy change. This progression indicates that the reactants are favored

free energy in chemical reactions

is the difference in free energy between reactants and products, indicating the spontaneity of a reaction.

what does negative change in free energy mean?

It indicates that the reaction is spontaneous, favoring the formation of products over reactants.

what does ATP stand for?

adenosine triphosphate

ATP (adenosine triphosphate)

is a high-energy molecule that stores and provides energy for various cellular processes.

what does ATP consist of?

It consists of adenine, ribose, and three phosphate groups.

• These components are vital for its energy storage capabilities.

what are some processes that need ATP (energy)?

Some processes that need ATP include protein synthesis, active transport across membranes , muscle contraction, and cell division.

ATP energy coupling

is the process by which ATP transfers energy to driven cellular reactions, connecting exergonic and endergonic processes.

ATP —> ?

ADP + P_i

how much free energy change is produced when ATP —> ADP + P_i?

ΔG = 30.5 kJ/mol of energy released during hydrolysis.

Exergonic reactions

reactions that release free energy, resulting in a net decrease in energy of the system. These reactions typically occur spontaneously.

Endergonic reactions

reactions that require an input of energy to proceed, resulting in a net increase in energy of the system. These reactions do not occur spontaneously.

can exergonic and endergonic reactions be coupled (combined)

Yes, exergonic and endergonic reactions can be coupled to drive the overall reaction forward, where the energy released from an exergonic reaction powers the endergonic reaction.

glutamine synthesis

The process of forming glutamine from glutamate and ammonia, catalyzed by the enzyme glutamine synthetase.

ATP hydrolysis

The process of breaking down adenosine triphosphate (ATP) into adenosine diphosphate (ADP) and inorganic phosphate (Pi), releasing energy that can be used for cellular activities.

combining glutamine synthesis and ATP hydrolysis

Since glutamine synthesis is a exergonic solution and ATP hydrolysis is an endergonic solultion reaction, the energy produced from ATP hydrolysis can be used to drive the synthesis of glutamine, thereby coupling these two processes.

• combined reaction is now spontaneous

energy barriers

are obstacles that must be overcome for a chemical reaction to occur, often requiring an input of energy to initiate.

do spontaneous reactions = instataneous?

No, spontaneous reactions are not necessarily instantaneous; they can occur over varying time scales, and their rate depends on factors such as the activation energy and reaction conditions.

activation energy

The minimum energy required to initiate a chemical reaction.

energy of activation (E_A)

is the energy needed to overcome the energy barriers and allow a reaction to proceed.

reaction conditions

The specific physical and chemical factors that influence the rate and outcome of a chemical reaction, such as temperature, pressure, concentration, and the presence of catalysts.

transition states

The temporary states during a chemical reaction where the reactants are in a partially transformed state before forming products.

• Transition states are high-energy configurations that exist only momentarily.

stressed bonds

Chemical bonds that have been weakened during a reaction, making them more susceptible to breaking.

enzymes

Biological catalysts that accelerate chemical reactions by lowering activation energy.

• crucial for various metabolic pathways.

substrates

The reactants that enzymes act upon in a biochemical reaction, typically transformed into products as a result of the enzymatic activity.

lock-and-key model

A theory explaining enzyme specificity where the enzyme's active site is complementary to the shape of the substrate, fitting together like a key in a lock.

active site

The particular region of an enzyme where substrate molecules bind and undergo a chemical reaction.

induced fit model

A theory that explains enzyme specificity by suggesting that the active site of an enzyme changes shape to fit the substrate upon binding, enhancing the catalytic process.

protein denaturation

The process by which a protein's structure is altered, often resulting in the loss of biological activity, due to factors such as temperature, pH, or chemical exposure.

what bonds are effected if temperature is increased

Increased temperature can disrupt hydrogen bonds, ionic bonds, and hydrophobic interactions within proteins, leading to denaturation.

what bonds are effected if pH is increased or decreased

Changes in pH can affect ionic bonds and hydrogen bonds within proteins, potentially leading to denaturation or altered activity.

enzyme inhibition

A process where a molecule impedes the activity of an enzyme, often by binding to its active site or altering its structure, thereby reducing the rate of reaction or preventing substrate binding.

is control of enzyme function important?

Yes, controlling enzyme function is crucial for regulating metabolic pathways, maintaining homeostasis, and ensuring that biological reactions occur at the appropriate rates.

• It allows cells to respond to changes in their environment and manage energy production

inhibitors

molecules that reduce enzyme activity or function by binding to the enzyme.

competitive inhibitors

bind to the active site of an enzyme and compete with the substrate, preventing normal enzyme activity.

noncompetitive inhibitors

bind to an enzyme at a site other than the active site, altering the enzyme's structure and decreasing its activity regardless of substrate presence.

what does allosteric mean?

inhibitors alter enzyme activity by binding at a site distinct from the active site, leading to a conformational change that affects the enzyme's function.

what does reaction rate depend on?

the proportion that is active and the concentration of substrates, enzyme availability, temperature, and pH.

activators

are molecules that bind to an enzyme and increase its activity, often by stabilizing the active conformation of the enzyme.

what affect does activators have on the enzyme?

Activators enhance enzyme activity by promoting the enzyme's active conformation, leading to increased reaction rates.

what affect does inhibitors have on the enzyme?

Inhibitors decrease enzyme activity by binding to the enzyme or its active site, preventing substrate binding or altering its conformation, thereby reducing reaction rates.

feedback inhibition

is a regulatory mechanism in metabolic pathways where the end product inhibits an earlier enzyme, preventing overproduction.

enzymatic pathways

are sequences of enzymatic reactions where the product of one reaction serves as the substrate for the next, facilitating metabolic processes.

phosphorylation

is the addition of a phosphate group to a molecule, commonly regulating enzyme activity and signaling pathways in cells.

kinases

enzymes that catalyze the transfer of phosphate groups from high-energy donor molecules, like ATP, to specific substrates,

• play crucial roles in signaling and metabolic pathways.

dephosphorylation

is the removal of a phosphate group from a molecule, often reversing the effects of phosphorylation and regulating enzyme activity and signaling pathways.

phosphatases

enzymes that catalyze the removal of phosphate groups from molecules, reversing phosphorylation effects and regulating various cellular processes.

metabolic pathways

series of chemical reactions in a cell that convert substrates into products through enzyme-catalyzed steps,

often linked to energy production and biosynthesis.

metabolic pathways’ involvement with glucose

includes the breakdown and synthesis of complex molecules (glucose)

where do molecules store their energy?

in their bonds’ electrons and within chemical bonds

catabolism

the set of metabolic pathways that break down molecules to produce energy. It involves the degradation of complex molecules into simpler ones, often releasing energy in the process.

anabolism

the set of metabolic pathways that construct molecules from smaller units. It involves the synthesis of complex molecules, often requiring energy input.

electron transport

a series of protein complexes and other molecules that transfer electrons from donors to acceptors, generating ATP and proton gradients in aerobic respiration.

if electrons are uncontrolled what happens?

it can lead to oxidative stress, damaging cells and tissues due to the formation of reactive oxygen species.

if electrons are controlled through NADH what happens?

they are transferred efficiently to the electron transport chain, promoting ATP production and minimizing oxidative stress.

electron shuttles

molecules that transport electrons between metabolic pathways, often facilitating their transfer to the electron transport chain.

what does NAD+ stand for?

Nicotinamide adenine dinucleotide, a coenzyme involved in redox reactions.

what does NAD+ do?

NAD+ acts as an electron carrier in redox reactions, accepting electrons and becoming reduced to NADH, which then participates in cellular respiration and energy production.

energy state varies between …?

NAD+ and NADH, with NAD+ being oxidized and NADH being reduced.

oxidized form …?

of NAD+, which donates electrons.

reduced form …?

of NADH, which accepts electrons.

NAD⁺ + H⁺ + 2 e^- —> ?

NADH

what is NADH?

NADH is the reduced form of NAD+, which plays a crucial role in metabolic processes by accepting and carrying electrons.

What was the “first supper” for cells?

the first cells used glucose as a source of ATP energy

glycolysis

earliest pathway to have evolved. It is the metabolic process that breaks down glucose into pyruvate, producing ATP and NADH in the process.

how many series of enzymatic reactions does gylcolysis have?

10 series of enzymatic reactions, includes phosphorylation, isomerization, redox reactions, substrate level phosphorylation (ATP synthesis)

where is glycolysis found?

Glycolysis is found in the cytoplasm of both prokaryotic and eukaryotic cells.

energy investment phase

The initial phase of glycolysis, where ATP is consumed to phosphorylate glucose and prepare it for breakdown. This phase includes the first five reactions of glycolysis.

energy payoff phase

The phase of glycolysis where ATP is produced through substrate-level phosphorylation, resulting in a net gain of ATP and the production of pyruvate. This includes the last five reactions of glycolysis.

ATP production in glycolysis

The process in glycolysis where a 4 ATP molecules are produced through substrate-level phosphorylation, resulting in a net gain of 2 ATP molecules after accounting for the 2 ATPs used in the energy investment phase.

what is the substrate of an enzyme? (ATP production in glycolysis)

ADP

what is the product of an enzyme? (ATP production in glycolysis)

ATP

fermentation

ethanol fermentation

ethanol and primate evolution

ethanol and the dawn of civilization

lactic acid fermentation

studying fermentation

pyruvate

is a key intermediate in glycolysis, produced from glucose and converted into lactic acid during fermentation in the absence of oxygen.

pyruvate oxidation

is the process in which pyruvate is converted into acetyl-CoA, producing NADH and releasing carbon dioxide. This occurs in the mitochondria and links glycolysis to the citric acid cycle.

citric acid cycle

is a series of chemical reactions used by all aerobic organisms to generate energy through the oxidation of acetyl-CoA, producing ATP, NADH, and FADH₂ while releasing carbon dioxide.

electron transport chain

a series of proteins and other molecules located in the inner mitochondrial membrane

• transfers electrons through redox reactions.

• This process generates a proton gradient that ultimately drives ATP synthesis.

sequential redox reactions

that occur in the electron transport chain

• facilitates in the transfer of electrons from electron donors to electron acceptors

• results in energy release and the pumping of protons across the membrane.

proton motive force

the force generated by the proton gradient across the inner mitochondrial membrane during oxidative phosphorylation.

• This gradient drives protons back into the mitochondrial matrix through ATP synthase, facilitating ATP production.

what are the 3 main e^- acceptors used for bacteria?

• Sulphate (SO₄ ^-2)

• nitrite (NO₂^-)

• ferric iron (Fe³⁺)

what does a large difference ΔG mean? (electron transport chain)

a large difference in free energy (ΔG) means that more protons can be pumped, a larger proton motive force can be generated, and more ATP can be made by ATP synthesis

ATP production

is the process by which adenosine triphosphate (ATP) is synthesized from ADP and inorganic phosphate, primarily through oxidative phosphorylation and substrate-level phosphorylation.

chemiosmosis

the movement of H⁺ down its concentration gradient to generate ATP via ATP synthase in the mitochondria.

ATP synthase

a proton channel on the inner membrane of mitochondria that synthesizes ATP from ADP and inorganic phosphate using the energy provided by the proton motive force.

more NADH or FADH₂ produced means …?

increased electron transport chain activity and ATP generation due to enhanced substrate availability for oxidative phosphorylation.

photosynthesis

the process by which green plants, algae, and some bacteria convert light energy into chemical energy in the form of glucose, using carbon dioxide and water.

anoxygenic

photosynthesis that does not produce oxygen, often carried out by certain bacteria using alternative electron donors.