Chapter 8

Metabolism

• All chemical and physical workings of a cell

• Both types of pathways are required for maintaining the cell’s energy balance

• Both types of reactions are governed by biological catalysts known as enzymes

• Two types of chemical reactions:

  • Catabolism

  • Anabolism

Catabolism

• Degradative

• Breaks the bonds of larger molecules forming smaller molecules

• Releases energy

Anabolism

• Biosynthesis

• Process that forms larger macromolecules from smaller molecules

• Requires energy input

Enzymes

• Biological cataclysts (not consumed in the reaction)

• Increase the rate of a chemical reaction by lowering the activation energy - which is the resistance to a reaction

• The enzyme is not permanently altered in the reaction

• Promotes a reaction by serving as a physical site for specific substrate molecules to position

• Exhibits primary, secondary, tertiary, and quaternary structure

Simple enzymes

Consist of protein alone

Conjugated enzyme

• a.k.a. holoenzymes

• Contain protein and nonprotein molecules

• Apoenzyme - protein portion

• Cofactors - nonprotein portion

  • Metallic cofactors - iron, copper, magnesium

  • Coenzymes, organic molecules: vitamins

Specificity of enzymes and their active sites

• Enzymes are very specific to their substrate

• The substrate is the molecule the enzyme binds

• Site for substrate binding is the active site, or catalytic site

• A temporary enzyme-substrate union occurs when substrate moves into the active site - induced fit (enzyme “hugs” the substrate, loosening the bonds of the substrate, and thus lowering activation energy)

• Appropriate reaction then occurs

• Product is formed and released

Holoenzyme formation

To form an active holoenzyme, the binding of a coenzyme or cofactor to an apoenzyme is often required

Enzyme regulation

• Two forms of enzyme regulation:

  • Competitive inhibition

    • Substance that resembles the normal substrate competes with the substrate for the active site

  • Noncompetitive inhibition

    • Enzymes are regulated by the binding of molecules other than the substrate away from the active site

      • Enzyme repression - inhibits at the genetic level by controlling synthesis of key enzymes - binding to the active site

      • Enzyme induction - enzymes are made only when suitable substrates are present - binding to an allosteric site

Allosteric inhibitor

Binding of an allosteric inhibitor reduces enzyme activity, but binding of an allosteric activator increase enzyme activity

Feedback inhibition

Where the end product of the pathway serves as a noncompetitive inhibitor to an enzyme early in the pathway, is an important mechanism of allosteric regulation in cells

Enzyme regulation via Transcription repression

1. DNA

2. RNA

3. Protein

4. Folds to form functional enzyme structure

5. Enzyme + Substrate → products

6. Excess product binds to DNA and shuts down further enzyme production

Environmental regulation of enzymes

• Activity of an enzyme is influenced by the cell’s environment

• Enzymes operate under temperature, pH, and osmotic pressure of organism’s habitat

• When enzymes are subjected to changes in organism’s habitat they become unstable

  • Labile: chemically unstable enzymes

  • Denaturation: weak bonds that maintain the shape of the apoenzyme are broken

Exoenzymes

• Transported extracellularly, where they break dowon large food molecules or harmful chemicals

• i.e. cellulase, amylase, penicillinase

Endoenzymes

• Retained intracellularly and function there

• Most enzymes are this type

Constitutive enzymes

• Always present

• Always produced in equal amounts or at equal rates, regardless of the amount of substrate

Regulated enzymes

• Not constantly present

• Production is turned on (induced) and off (repressed) in response to changes in the substrate concentration

Synthesis (condensation reactions)

• Anabolic reactions to form covalent bonds between smaller molecules

• Require ATP

• Release one molecule of water for each bond formed

Hydrolysis reactions

• Catabolic reactions that break down substrates into small molecules

• requires the input of water to break bonds

Energy

The capacity to do work or to cause change

First law of thermodynamics

• Energy cannot be created or destroyed

• Energy is just transformed

• Forms of energy include: Thermal, radiant, electrical, mechanical, atomic, and chemical

Energy converting organelles

• Mitochondria

  • Catabolic energy conversion

  • Glucose → CO₂ + energy

• Chloroplast

  • Anabolic energy conversion

  • CO₂ + energy → Glucose

ATP/ADP cycle

• The energy release from dephosphorylation of ATP is used to drive cellular work, including anabolic pathways

• ATP is generated through phosphorylation, harnessing the energy found in chemicals or from sunlight

Cell energetics

• Cells manage energy in the form of chemical reactions that make or break bonds and transfer electrons

• Endergonic reactions

  • Consume energy

  • Anabolic metabolism

  • Gain electrons - reduction

  • Energy + A + B →with enzyme help→ C

• Exergonic reactions

  • Release energy

  • catabolic metabolism

  • Lose electrons - oxidation

  • X + Y → with enzyme help→ Z + energy

• Energy released is temporarily stored in high energy phosphate molecules - the energy of these molecules is used in all endergonic cell reactions

Redox reactions

• Always occur in pairs

• There is an electron donor and an electron acceptor which constitutes a redox pair

• Process salvages electrons and their energy

• Released energy can be captured to phosphorylate ADP or another compound

Electron carriers

• Repeatedly accept and release electrons and hydrogen to facilitate the transfer of redox energy

• Most electron carriers are coenzymes:

  • NAD

  • FAD

  • NADP

  • Coenzyme A

  • Compounds of the respiratory chain

Adenosine Triphosphate (ATP)

• Metabolic “currency”

• Three part molecule consisting of:

  • Adenine - a nitrogenous base

  • Ribose - a 5-carbon sugar

  • 3 phosphate groups

• Removal of the terminal phosphate releases energy

• ATP utilization and replenishment is a constant cycle in active cells

Formation of ATP

• ATP can be formed by three different mechanisms:

  1. Substrate-level phosphorylation - transfer of phosphate group from a phosphorylated compound (substrate) directly to ADP

  2. Oxidative phosphorylation - series of redox reactions occurring during respiratory pathway

  3. Photophosphorylation - ATP is formed utilizing the energy of sunlight

Bioenergetics

Study of mechanisms of cellular energy release

Catabolism of fuels

• Primary catabolism of fuels (glucose) proceeds through a series of three coupled pathways:

  1. Glycolysis

  2. Formation of Acetyl Co-A

  3. Kreb’s cycle (citric acid cycle)

  4. Respiratory chain, electron transport chain

Aerobic respiration

• Series of enzyme-catalyzed reactions in which electrons are transferred from fuel molecules (glucose) to oxygen as a final electron acceptor

• Glycolysis - Glucose (6C) is oxidized and split into two molecules of pyruvic acid (3C), NADH is generated

• Formation of Acetyl Co-A - pyruvic acid (3C), generates 1 CO₂ and NADH is generated

• Kreb’s (citric acid) cycle- Processes Acetyl Co-A and generates 2 CO₂ molecules, NADH, and FADH₂ are generated

• Electron transport chain - accepts electrons from NADH and FADH - generates energy through sequential redox reactions called oxidative phsophorylation

Glycolysis

• The energy investment phase of the Embden Meyerhof-Parnas glycolysis pathway uses two ATP molecules to phosphorylate glucose

• Forms two glyceraldehyde 3-phosphate (G3P) molecules

• The energy payoff phase harnesses the energy in the G3P molecules, producing four ATP molecules, two NADH molecules, and two pyruvates

• The ATP made during Glycolysis is a result of substrate-level phosphorylation

Acetyl Co-A production

• Pyruvate hydrolyzes a CO₂ and is replaced by Co-A

• NADH captures the electron released

Citric Acid Cycle (Kreb’s cycle)

• Also known as tri-carboxylic acid cycle (TCA)

• Incoming two-carbon acetyl results in the main outputs per turn of two CO₂, three NADH, one FADH₂, and one ATP (or GTP) molecules made by substrate-level phosphorylation

• Two turns of the Kreb’s cycle are required to process all of the carbon from one glucose molecule

Kreb’s intermediates

Many organisms use intermediates from the Kreb’s cycle, such as amino acids, fatty acids, and nucleotides, as building blocks for biosynthesis

Electron Transport Chain

• Final processing of electrons and hydrogen

• Chain of redox carriers that receive electrons from reduced carriers (NADH and FADH₂)

• ETC shuttles electrons down the chain, energy is released and subsequently captured

• The end result is a build up of protons across a membrane generating a high concentration gradient

The Terminal Step

• Oxygen accepts 2 electrons from ETS and then picks up 2 hydrogen ions from the solution to form a molecule of water

• Oxygen is the final electron acceptor in aerobic respiration

• 2H⁺ + 2e^- + 1/2O₂ → H₂O

Oxidative Phosphorylation

• ATP synthase is a complex integral membrane protein through which H⁺ flows down and electrochemical gradient

• This provides the energy for ATP production by oxidative phosphorylation

• This process is called chemiosmosis

Chemiosmosis

• As the electron transport carriers shuttle electrons, they actively pump hydrogen ions across the membrane, setting up a gradient of hydrogen ions - proton motive force

• Hydrogen ions diffuse back through the ATP synthase complex causing it to rotate (mechanical energy)

• This causes a 3-D change resulting in the production of ATP

Anaerobic respiration

• Functions like aerobic respiration except it utilizes oxygen containing ions rather than free oxygen, as the final electron acceptor

  • Nitrate (NO₃^-), nitrite (NO₂^-), and sulfate (SO₄^-2)

• Most obligate anaerobes use the H+ generated during glycolysis and the Kreb’s cycle to reduce some compound other than O₂

Fermentation

• Incomplete oxidation of glucose or other carbohydrates in the absence of oxygen

• Uses organic compounds as terminal electron acceptors

• Yields a small amount of ATP

• Production of ethyl alcohol by yeasts acting on glucose

• Formation of acid, gas, and other products by the action of various bacteria on pyruvic acid

Crossing pathways of metabolism

• Many pathways of metabolism are bi-directional or amphibolic

• Catabolic pathways contain molecular intermediates (metabolites) that can be diverted into anabolic pathways

• Pyruvate acid can be converted into amino acids through amination

• Amino acids can be converted into energy sources through deamination

• Glyceraldehyde-3-phosphate can be converted into precursors for amino acids, carbohydrates, and fats

Photosynthesis

• The ultimate source of all the chemical energy in cells comes from the sun

• 6CO₂ + 6H₂O → with light → C₆H₁₂O₆ + 6O₂

• Occurs in two stages:

  • Light-dependent Reactions

  • Light-independent Reactions

• In Eukaryotes, takes place in Chloroplasts, which contains thylakoids stacked into grana

• Eukaryotes and cyanobacteria carry out oxygenic photosynthesis, producing oxygen

• Other bacteria carry out anoxygenic photosynthesis, which does not produce oxygen

Light-dependent reactions

• Photons are absorbed by chlorophyll, carotenoid, and phycobilin pigments

• Water split by photolysis, releasing O₂ gas and provides electrons to drive photophosphorylation

• Released light energy used to synthesize ATP and NADPH

Light-independent reactions

• a.k.a. Dark reactions or calvin cycle

• uses ATP to fix CO₂ to ribulose-1, 5-biphosphate and convert it to glucose