Metabolism: Key Processes and Pathways in Energy Production

Metabolism

Sum of all chemical reactions in the body to provide energy and create substance that sustains life

Catabolism

A type of metabolism that simplifies complex molecules so polymers to monomers

Anabolism

Simple molecules to make complex molecules so monomers to polymers

Exergonic

Energy transformation that releases energy so products have less free energy than reactants like ATP hydrolysis

Endergonic Reactions

Require energy input products have more free energy than reactants like energy is used to form bonds

Oxidization

Losing electrons or hydrogen to an oxidizing agent.

Reduction

Any chemical reaction is when a molecule gains electrons and energy. Molecule is reduced when it accepts electrons, the molecule that donates the electron is the oxidizing agent.

Redox

Also known as Oxidation-Reduction Reactions, Oxidation of one molecule is accompanied by reduction of another. Hydrogens are usually moving with electrons when transferred.

Catalyst

The substance that increases the rate of the chemical reaction without having any permanent damage or being consumed in the process.

Enzyme

Proteins that function as a catalyst, it is lower activation energy which basically means the energy you need to start a reaction, does not actually produce reaction.

Enzyme Action

Substrate approaches enzymes activate site. Molecules bind together forming enzyme-substrate complexes. (Lock and key because only a specific substrate will fit.) The enzyme releases the reaction products. Enzymes are unchanged by their reactions. (repeat the process many times)

Cofactor

They are essential function because ⅔ of humans need a non protein cofactor. Some inorganic include iron, copper, magnesium, and calcium ions. Some of them will bind to enzymes and change the shape that will activate the site.

Coenzyme

Organic cofactors that are derived from water soluble vitamins like riboflavin and niacin. Will receive electrons from an enzyme in a metabolic pathway (breakdown or buildup), and will transfer them to another.

Apoenzyme

Protein portion of enzyme, without cofactors.

Holoenzyme

Apoenzymes plus cofactor (active enzyme form) Basically the whole enzyme.

Factors influencing the enzyme Activity

Temperature high and extreme PH can denature the proteins by disrupting the folding pattern (inhibit enzyme activity). Increasing the substrate concentration the reaction rate rises, at saturation the enzyme catalyzes its max. (promotes activity)

Enzyme Inhibition

Can be reversible or irreversible.

Competitive Inhibitor

Binds the active site of an enzyme, basically blocking the substrate from binding, competing with the substrate.

Noncompetitive Inhibitor

These don't interact with the active site, however they alter the shape of it so the substrate does not fit into the enzyme anymore making it not bind, basically denaturing the enzyme.

Allosteric Inhibitor

The region of the enzyme where the noncompetitive inhibitors will bind to change the shape of the enzyme.

Feedback Inhibition

Cellular process that controls the enzyme activity by using the end-product of a reaction allosterically inhibits enzymes from earlier in the pathway, this prevents overproduction of the metabolic product.

ADP

Energy released during a redox reaction and used to produce ATP.

ATP

Generated by the phosphorylation (adding a phosphate) of ADP (ADP+Pi).

Electron Carrier

A molecule that moves electrons from one molecule to another.

NAD+/NADH

Coenzymes that carry high electrons produced through catabolism, e- must be removed to allow them to continue functioning. NAD+: derived from niacin (B vitamin), Nicotinamide Adenine Dinucleotide. NADH: NAD+ 2e- + 2H+ > NADH + H+.

FAD/FADH2

Electron carrier.

Flavin Adenine Dinucleotide

Derived from Riboflavin

FAD+ 2e- + 2H+ > FADH + H+

Chemical reaction involving FAD.

Glycolysis

Breakdown of glucose into pyruvate and produce ATP.

Glucose= Pyruvate

Main takeaway: 2 ATP to jumpstart, break the bond in the middle of the glucose, substrate level phosphorylation 4 ATP, end up adding 2 e- to NAD > NADH, will end up with 2 Pyruvate (C3H4O3).

Net gain of 2 ATP and 2 NADH

However total spent ATP is 4.

Pyruvate

Organic molecule with a 3 C backbone and plays a crucial role for breakdown and synthesis with organisms.

ED pathway

Entner Doudoroff, breakdown of sugar acids and produce pyruvate. Does not involve glycolysis, operates independently.

Pentose Phosphate Pathway

Breakdown of 5 carbon pentose sugars and/or glucose and produces NADH and makes organics.

Substrate Level Phosphorylation

Forming ATP by transfer of high energy phosphate from another organic.

C-C-C-P + ADP > C-C-C + ATP

Chemical reaction demonstrating substrate level phosphorylation.

Fermentation

Lactic Acid Fermentation catalyzing pyruvate and lactate also interconversion of NADH and NAD+.

NAD+ can return to glycolysis

Indicates that NAD+ is recycled in the process.

Ethanolic Fermentation

Decarboxylated to form acetaldehyde to release CO2.

NADH then reduces acetaldehyde to ethanol restoring NAD+

Important to human food and industrial processes.

Terminal Electron Acceptor

Receiving electrons at the end of the ETC.

Respiration

Breaking down organic matter to obtain energy and nutrients.

Oxidation

The chemical reaction in which a molecule gives up electrons and releases energy to an electron acceptor molecule oxidizing agent.

Acetyl-CoA

Coenzyme that delivers acetyl groups to the citric acid to be oxidized for energy production.

Citric Acid Cycle (TCA)

Oxidizes acetyl groups, Acetyl-CoA adds 2 carbons forming citrate.

At the end of the cycle oxaloacetate must be regenerated

Essential for the continuation of the citric acid cycle.

Oxidative Phosphorylation

Electrons are transferred from one electron carrier to another along an electron transport chain.

Β-oxidization

Metabolic process that breaks down fatty acids to produce energy.

Oxaloacetate

A natural chemical compound that plays a key role in energy production in the body.

Citrate/Citric Acid

Intermediate in the citric acid cycle.

Electron Transport Chain

Series of compounds which carry out membrane reactions, moving electrons from donors to acceptors.

Aerobic Respiration (ETC)

Drops it off on oxygen, so oxygen is our terminal electron recipient.

Anaerobic Respiration

Drop it off in something that is not oxygen like sulfur or nitrate.

Chemiosmosis

Process where ATP is generated using the energy coming from the ETC.

ATP synthase

Cells produce special transporters; transporter and enzyme ADP + P = ATP

Proton Pump

Energetic electrons from NADH pass down the ETC causing some carriers in the chain to pump actively transporting protons across the membrane

Proton Motive Force

Concentration gradient causing excess H+ on one side of the membrane causing accumulation creating electrochemical gradient that has potential energy

Photosynthesis

Light dependent reactions involve photosystems absorbing photon of light -> chemical energy; Electrons travel through ETC making ATP and NADPH

Light independent reactions

Chemical energy from ATP and NADPH is stored in carbs; CO2 is fixed to produce organic molecules

Oxygenic photosynthesis

Carried out by plants, algae, and cyanobacteria; 6 CO2 + 6H2O -> glucose + O2

Anoxygenic photosynthesis

Carried out by purple/green sulfur bacteria; 6 CO2 + 12 H2S -> glucose + O2 + sulfur

Photosystem

Part of the photosynthesis; Chlorophyll and other pigments are packed into thylakoids of chloroplast

Calvin Cycle/Carbon Fixation

Dark reaction; doesn't need photon of light to function; The binding of C to organic molecules CO2 -> organic molecules; Cycles 3 CO2 + G3P; you need 2 G3P to make one glucose; 6 CO2 + 18 ATP + NADPH = glucose

Photoautotroph

Energy source from light - carbon source CO2

Photoheterotroph

Energy source from light - carbon source organic compounds

Chemoautotrophs

Energy source from inorganic chemicals - carbon source CO2

Chemoheterotrophs

Energy source from chemical source - carbon source organic compounds

Overall Chemical Reaction for Cellular Aerobic Respiration

C6H12O6 + 6O --> 6H2O + 6CO2

Endergonic reactions

Require energy to occur, while exergonic reactions release energy

Oxidation

Is the Loss of electrons

Reduction

Is the Gain of electrons (negative charge reduces the total charge) [use OIL RIG to remember]

Enzyme Activity

Enzymes are catalysis (catalysts lower the activation energy of a reaction, but are not consumed in the reaction)

Ribozymes

RNA catalysis

Substrate

An enzyme's target is its substrate, which binds to the active site on the enzyme for the reaction

Denaturation

Of the enzyme (by heat or pH) destabilizes the shape and inhibits the function

Inhibitors

Can bind to this site (competitive inhibition); Inhibitors which bind elsewhere are non-competitive allosteric inhibitors

Feedback inhibition

Involves a product of a metabolic pathway inhibiting enzymes in the pathway; This prevents the cell from making too much of any one product

NAD+

Can carry 2 electrons and gains hydrogen in the process forming NADH

FAD

Can carry 2 electrons and 2 hydrogens, forming FADH2

Glycolysis

Breakdown of glucose [catabolic]; Forms Pyruvate, ATP and NADH

Entner-Doudoroff

Breakdown of non-glucose sugar like molecules [catabolic]; Forms Pyruvate, ATP, NADH and NADPH

Pentose Phosphate Pathway

Uses intermediates of Glycolysis or ED to build organics [anabolic]; NADPH (electron donor [reducing agent]), and ATP [energy] are used to form carbon bonds

Anaerobic Fermentation

Occurs when oxygen (or respiration cannot be run) is absent; NAD+ is required for glycolysis to continue, so the cell needs to revert NADH to NAD+ to continue

Lactic Acid Fermentation

NADH and H+ attach 2 hydrogens to pyruvate, forming lactic acid; CH3-[CO]-COOH + NADH + H+ --> CH3-[HCOH]-COOH + NAD+

Ethanol Fermentation

Decarboxylates pyruvate forming acetaldehyde and CO2; CH3-[CO]-COOH --> CO2 + CH3-CHO; CH3-CHO + NADH + H+ --> CH3-CH2OH + NAD+

Cellular Respiration (Aerobic)

If the cell has enough oxygen the pyruvate can be further catabolized; The electrons and hydrogens will be removed and sent to an electron transport system (ETS) and the carbons will form CO2

Pyruvate Transition Step (Decarboxylation)

In order to enter the citric acid cycle, pyruvate must be chemically modified; A coenzyme (Coenzyme A or CoA) is bonded to the carbons of pyruvate forming acetyl CoA

Citric Acid Cycle

Acetyl-CoA (2 carbons) is bonded to Oxaloacetate (a 4-carbon molecule) to form citrate (6 carbons); This cycle extracts energy by removing the new carbon atoms to regenerate the Oxaloacetate

Electron Transport Chain

A series of membrane bound proteins that accept high energy electrons and slowly release the energy by passing them around

ATPase

A protein which allows H+ ions to flow across the membrane; As the H+ ions flow down their gradient, ATPase uses this energy to bond ADP to Phosphate making ATP

Photosynthesis Light Reactions

Require sunlight to function; Pigments embedded in the thylakoid membrane of chloroplasts absorb photons of light

Calvin Cycle

Also known as the "dark reactions"; These do not require light or photosystems, they use the products of the light reaction though.