MTChem2 Module 6: Introduction to Metabolism

Objective

Demonstrate understanding of the role of biomolecules in the manifestation and maintenance of life.
Understand metabolic pathways by which carbohydrates, fats, and proteins are converted into biochemical substances needed for life.

What is Metabolism?

Metabolism encompasses all biochemical reactions within an organism.

When Does Metabolism Occur?

Metabolism happens constantly in cells, involving processes like:
- Protein synthesis
- DNA replication
- RNA transcription
- Membrane transport

Two Subtypes of Metabolism

1. Catabolism:

Breaking down larger molecules into smaller ones.
Releasing energy.
Example: Oxidation of glucose.

2. Anabolism:

Synthesizing larger molecules from smaller ones.
Absorbing energy.
Example: Protein synthesis from amino acids.

Catabolism vs. Anabolism

Catabolism:
- Breakdown of larger molecules
- Releases energy
Anabolism:
- Synthesis of larger molecules
- Absorbs energy

Metabolic Pathway

A series of consecutive biochemical reactions that convert a starting material into an end product.

Types of Metabolic Pathways

1. Linear Pathway:

A series of reactions that generate a final product different from any reactant.

2. Cyclic Pathway:

A series of reactions that regenerates the first reactant.

Anabolic or Catabolic?

Synthesis of starch from glucose units: Anabolic
Hydrolysis of triacylglycerol to glycerol and fatty acids: Catabolic
Formation of nucleotide from phosphate, nitrogenous base, and pentose sugar: Anabolic

Metabolism and Cell Structure

Energy production and utilization within cells.

Prokaryotes vs. Eukaryotes

Key structural differences:
*Prokaryotes: No Nucleus
*Eukaryotes: Has True Nucleus
*Prokaryotes: DNA
*Eukaryotes: Higher Organisms

Key Components of Eukaryotic Cells

Cytoplasm
Nucleus
Cell Membrane

Cytoplasm

Water-based material between the nucleus and outer membrane.

Organelles

Minute structures suspended in the cytoplasm that carry out specific functions.

Ribosomes

Sites of protein synthesis.

Lysosomes

"Suicide bags" containing hydrolytic enzymes for:
- Cellular rebuilding
- Repair
- Degradation

Mitochondria

"Powerhouse" of the cell, generating energy.
Outer Mitochondrial Membrane
Inner Mitochondrial Membrane
Cristae
Mitochondrial Matrix

Mitochondria Details

Small, sausage-shaped organelles where energy production occurs.
Number of mitochondria varies depending on the cell's energy needs.

Parts of the Mitochondria

Outer Membrane:
- 50% lipid, 50% protein
- Freely permeable to small molecules
Intermembrane Space:
- Region between outer and inner membranes
Matrix:
- Where energy production takes place
- Area surrounded by the inner membrane
Cristae:
- Folds of the inner membrane protruding into the matrix

ATP Synthase

Small spherical knobs attached to the cristae.
Site of ATP synthesis.

Important Nucleotide-Containing Compounds in Metabolic Pathways

Coenzymes, Adenosine Phosphates, Flavin Adenine Dinucleotide, Nicotinamide Adenine Dinucleotide, Coenzyme A

Coenzymes

Organic compounds needed for enzyme-catalyzed reactions.
Some act as oxidizing and reducing agents.
- Oxidizing Agent: Causes oxidation
- Reducing Agent: Causes reduction

Electrons and Coenzymes

LEORA: Loss of Electron is Oxidation; Coenzyme is a Reducing Agent.
GEROA: Gain of Electron is Reduction; Coenzyme is an Oxidizing Agent.

Oxidation vs. Reduction

Oxidation:
- Loss of electrons or hydrogen
Reduction:
- Gain of electrons or hydrogen

Adenosine Phosphates

ATP, ADP, and AMP differ by the number of phosphate groups present.

Adenosine Phosphates Details

Adenosine monophosphate (AMP): 1 Adenine, 1 Ribose, 1 Phosphate
Adenosine diphosphate (ADP): 1 Adenine, 1 Ribose, 2 Phosphates
Adenosine triphosphate (ATP): 1 Adenine, 1 Ribose, 3 Phosphates
Phosphoester bond: Phosphate-ribose bonds
Phosphoanhydride bond: Phosphate-phosphate bonds, producing a water molecule

Phosphoryl and Phosphate Groups

Phosphoryl group ( $(P): PO_3^{2-}$ , derived from phosphate ion when it becomes part of another molecule
Phosphate group ( $(Pi): PO4^{3-}$ , derived from phosphoryl when released from ATP/ADP molecules

ATP Structure

*Molecular structure of ATP

Adenine
Ribose
Phosphate groups
High energy bonds

Adenosine 5’- Triphosphate (ATP)

A nucleoside triphosphate formed by adding 3 phosphates to the 5’ -OH group of adenosine (a nucleoside composed of ribose and adenine).
Most prominent member of "high energy" molecules.
Transporter of energy in metabolic processes.

Adenosine 5’- Diphosphate (ADP)

A nucleoside diphosphate formed by adding 2 phosphates to the 5’ -OH group of adenosine.

Adenosine 5’- Monophosphate (AMP)

A nucleoside monophosphate formed by adding 1 phosphate to the 5’ -OH group of adenosine.

ATP Bonds

The phosphoanhydride bonds in ATP and ADP are very reactive and strained, requiring less energy to break.

Other Nucleotide Triphosphates

Uridine Triphosphate (UTP): Involved in carbohydrate metabolism
Guanosine Triphosphate (GTP): Participates in protein and carbohydrate metabolism
Cytidine Triphosphate (CTP): Involved in lipid metabolism

ATP/ADP Hydrolysis & Synthesis

Interconversion of ATP and ADP is key for energy storage and release.
Hydrolysis of ATP cleaves 1 phosphate group, forming ADP and inorganic phosphate ( $HPO4^{2-}$ , or $Pi$ ) releasing 7.3 kcal/mol of energy.

ATP/ADP Hydrolysis & Synthesis (cont.)

Phosphorylation is the reverse reaction, adding a phosphate group to ADP to form ATP, requiring 7.3 kcal/mol of energy.
Energy is absorbed and stored in ATP when synthesized from ADP.
Energy is released when ATP is hydrolyzed to ADP.

ATP Hydrolysis vs. Synthesis

ATP Hydrolysis: $ATP + H2O \rightarrow ADP + HPO4^{2-}$ , releasing 7.3 kcal/mol
ATP Synthesis (Phosphorylation): $ADP + HPO4^{2-} \rightarrow ATP + H2O$ , absorbing 7.3 kcal/mol

Flavin Adenine Dinucleotide (FAD and FADH2)

Required in numerous metabolic redox reactions
Can be seen as containing 3-subunits or 6-subunits
FAD: also a biochemically active form of riboflavin

Flavin Adenine Dinucleotide Structure

Flavin, Ribitol, ADP

Flavin Adenine Dinucleotide

A common biological oxidizing agent.
Four atoms of the tricyclic ring system (2 N and 2 C) participate in the redox reaction.
Active portion of FAD is the flavin subunit.

FAD as Oxidizing Agent

When acting as an oxidizing agent, FAD is reduced to FADH2 by adding 2 Hydrogen atoms.
- Oxidized form: FAD
- Reduced form: FADH2

FAD Reaction Example

$R - C(H) - C(H) - R + FAD \rightarrow R - CH = CH - R + FADH_2$

Nicotinamide Adenine Dinucleotide (NAD+ and NADH)

The six-membered ring containing the positively charged nitrogen atom participates in the oxidation reaction form

Similarities to FAD/FADH2

Coenzyme function
B Vitamin Structural Component (Nicotinamide)
Has 3-subunit and 6-subunit
Has oxidized (NAD+) and reduced (NADH)

Nicotinamide Adenine Dinucleotide

Positive Charge of NAD+: positive charge on the nitrogen atom in the nicotinamide component
Active portion: Nicotinamide subunit

NAD+ Reduction

When the ring is reduced by 2 hydrogen atoms
The ring gains 1 proton & 2 electrons
1 H is left over in the solution

Cellular Reaction with NAD+

$R - C(OH) - R + NAD^+ \rightarrow R - C(=O) - R + NADH + H^+$

Coenzyme A (CoA-SH/HS-CoA)

Derivative of Pantothenic Acid (Vit. B5)
Not an oxidizing nor a reducing agent
Abbreviated as CoA-SH/HS-CoA

Coenzyme A Structure

2-Aminoethanethiol, Pantothenic Acid, Phosphorylated ADP
The ADP subunit is phosphorylated
Extra phosphate at C3 of its ribose

Coenzyme A Function

Contains a sulfhydryl group (-SH), making it a thiol (R-SH)
The sulfhydryl group reacts with acetyl groups ( $CH_3CO—$ ) or other acyl groups ( $RCO—$ ) to form thioesters ( $RCOSR'$ )
Acetyl group bonded to coenzyme A produces acetyl coenzyme A (acetyl CoA)

Thioesters

Thioesters, like acetyl CoA, are high energy compounds that release energy when reacting with water.
Acetyl CoA reacts with other substrates in metabolic pathways to deliver its 2-carbon acetyl group, as in the citric acid cycle.
Coenzyme A is continually changing back and forth between its CoA form and acetyl CoA form.

Important Carboxylate Ions in Metabolic Pathways

Hydroxy Derivative: Malic Acid - Malate
Keto Derivative: Oxaloacetic Acid - Oxaloacetate
Unsaturated Derivative: Fumaric Acid - Fumarate
Keto Derivative: α – Ketoglutaric Acid - α – Ketoglutarate
Carboxyhydroxy Derivative: Citric Acid - Citrate

High Energy Phosphate Compounds

Compounds that have a greater free energy of hydrolysis than that of the typical compound.
Contain 1 or more very reactive bonds (strained bond).

Intermediates

Intermediates for the storage of energy and transfer of phosphate groups: ATP, ADP, AMP
Intermediates for the transfer of electrons in metabolic redox reactions: FAD, FADH2, NAD+, NADH
Intermediates for the transfer of acetyl groups: H-S-CoA, acetyl-S-CoA

Biochemical Energy Production Steps

Digestion, Acetyl CoA formation, Citric Acid Cycle, Electron Transport Chain

Digestion

CHO, LIPIDS, PROTEINS
Enzymes: amylase, lipase, pepsin, trypsin & chymotrypsin
Monosaccharides, Fatty Acids + Glycerol, Amino acids

Energy Production

*Overview of Energy Production

I. Recall:

a. Digestion
b. Acetyl CoA formation
c. Citric Acid Cycle
d. Electron Transport Chain

II. Synthesis and Summary Outline of Discussion:

Learning Objective:

Demonstrate understanding of the role of biomolecules in the manifestation and maintenance of life.
Understand metabolic pathways for converting carbohydrates, fats, and proteins into biochemical substances.

Overview of Metabolic Stages

1. Digestion:

Occurs extracellularly (mouth → stomach → small intestines)
End products are building blocks: Monosaccharides, Fatty Acids + Glycerol, Amino acids

2. Acetyl CoA Formation:

Occurs in cytosol and mitochondria
Primary products: 2-C acetyl units, Acetyl CoA + NADH

3. Citric Acid Cycle &,

4. Electron Transport Chain and Oxidative Phosphorylation:

Occur intracellularly in mitochondria
Common metabolic pathway

Citric Acid Cycle

Hans Adolf Krebs: KREBS CYCLE / TRICARBOXYLIC ACID CYCLE
Series of enzyme-catalyzed reactions that occur in the mitochondria.
Series of biochemical reactions in which the acetyl portion of acetyl CoA is oxidized to $CO2$ and the reduced coenzymes ( $FADH2$ and NADH) and energy are produced
Cyclic metabolic pathway that begins with the addition of acetyl CoA to a four-carbon substrate and ends when the same four-carbon compound is produced as a product.

Citric Acid Cycle Steps

THERE ARE A TOTAL OF 8 STEPS.

Name of the Reactions
Enzymes involved
Reactants and Products produced in each step

Condensation
Isomerization
& 4. Oxidation & DECARBOXYLATION
PHOSPHORYLATION
OXIDATION
HYDRATION
OXIDATION

Steps in the Citric Acid Cycle

Formation of citrate, Formation of Isocitrate, Oxidation and Decarboxylation, Oxidation of alpha- ketoglutrate and formation of CO2

Step 1: Formation of Citrate

Oxaloacetate + Acetyl CoA
Enzyme: Citrate synthase
Citrate synthase
H2O
Intermediates: Citryl CoA
Products: Citrate + Coenzyme A
Condensation, Hydrolysis

Step 2: Formation of Isocitrate

Reactant: Citrate (Tertiary Alcohol)
Enzyme: Aconitase
Intermediates: cis-Aconitate
Product: Isocitrate (Secondary Alcohol)
Dehydration, Hydration
*Isomerization = same atoms but with different arrangement
*Secondary alcohols are easier to oxidize than tertiary alcohols.

Step 3: Oxidation of Isocitrate and Formation of CO2

Reactant: Isocitrate
Enzyme: Isocitrate dehydrogenase
Intermediates: Oxalosuccinate
Products: α-ketoglutarate + $CO_2$ + NADH + $H^+$
Oxidation, Decarboxylation

Step 4: Oxidation of α-Ketoglutarate and Formation of CO2

Reactant: α-ketoglutarate + NAD+ + H+ + CoA-SH
Enzyme: α-ketoglutarate dehydrogenase complex
Products: Succinyl CoA (4 Carbons), NADH , $CO_2$ , H+
Released by exhalation

NOTE α 2 is the second involvement of Coenzyme A in the cycle.
Coenzyme A reacts with decarboxylation to produce succinyl CoA

Step 5: Thioester Bond Cleavage in Succinyl CoA and Phosphorylation of GDP

Step 6: Oxidation of Succinate

Step 7: Hydration of Fumarate

Step 8: Oxidation of L-malate to regenerate oxalosuccinate.

These are the Steps In the Citric Acid Cycle

Step 5: Thioester Bond Cleavage in Succinyl CoA and Phosphorylation of GDP

Reactant: Succinyl CoA
Enzyme: Succinyl CoA synthetase
Intermediates: Succinyl Phosphate
Products: Succinate
NOTE
The enzyme “synthase” from step 1 is different from the enzyme “synthetase” from step 5.
“Synthetase” uses a energy from the breaking of a high-energy phosphate bond.

Step 6: Oxidation of Succinate

Reactant: Succinate
Enzyme: Succinate dehydrogenase
Products: Fumarate (trans-double bond)
NOTE
Product in step 6 is a reduced form of flavin adenine dinucleotide.

Step 7: Hydration of Fumarate

Reactant: Fumarate
Enzyme: Fumarase
Products: Malate (4 Carbons)

Step 8: Oxidation of L-Malate to Regenerate Oxaloacetate

Reactant: Malate
Enzyme: Malate dehydrogenase
Products: Oxaloacetate (4 Carbons), NADH, $$H^+$
GOES BACK TO STEP [1]

Total Products produced in Citric Acid Cycle:
✓2 Carbon dioxide
✓3 NADH
✓1 FADH2
✓1 GTP

Synthesis and Important notes in Citric Acid Cycle

The “fuel” for the cycle is acetyl CoA, obtained from the breakdown of carbohydrates, fats, and proteins.
Synthesis and Important notes in Citric Acid Cycle
In redox reactions
- NAD+ = oxidizing agent when a carbon– oxygen double bond is formed
- FAD = oxidizing agent when a carbon– carbon double bond is formed

The three NADH and one FADH2 that are formed during the cycle carry electrons and H+ to the electron transport chain through which ATP is synthesized.
Synthesis and Important notes in Citric Acid Cycle
Four B vitamins are necessary for the proper functioning of the cycle:
- riboflavin (both FAD & α-ketoglutarate dehydrogenase complex)
- nicotinamide (NAD+)
- pantothenic acid (CoA—SH)
- thiamine (α-ketoglutarate dehydrogenase complex).

Biochemical Energy Production: Electron Transport Chain

*also frequently called the respiratory chain
*a multistep process that relies on four enzyme systems as well as mobile electron carriers

ELECTRON TRANSPORT CHAIN (ETC)

a series of biochemical reactions in which electrons and hydrogen ions from NADH and FADH2 are passed to intermediate carriers and then react with molecular oxygen to produce water.
NADH and FADH2 are oxidized in this process.
The complexes are situated in the inner membrane of the mitochondria, arranged so that electrons can be passed to progressively stronger oxidizing agents

FOUR COMPLEXES OF ETC:

Complex I: NADH–coenzyme Q reductase
Complex II: Succinate–coenzyme Q reductase
Complex III: Coenzyme Q–cytochrome c reductase
Complex IV: Cytochrome c oxidase

ELECTRON TRANSPORT CHAIN

COMPLEX I NADH-Coenzyme Q Reductase
COMPLEX III Coenzyme Q-Cytochrome C Reductase
COMPLEX IV Cytochrome c Oxidase
COMPLEX II Succinate-Coenzyme Q Reductase

COMPLEX I: NADH-COENZYME Q REDUCTASE

Used in complex III

from the citric acid cycle, is the source for the electrons that are processed through complex I.
This is the largest of the four protein complexes
Complex I contain more than 40 subunits

NADH Process

The result: the transfer of electrons from NADH to coenzyme Q (CoQ)
Interaction of NADH with flavin mononucleotide (FMN)
The NADH is oxidized to NAD+ as it passes two hydrogen ions and two electrons to FMN, which is reduced to FMNH2.

COMPLEX II: SUCCINATE-COENZYME Q REDUCTASE

NOTE Used in complex III

Complex II contains only four subunits.
FADH2, the coenzyme generated in the citric acid cycle is used. That is why the term “succinate” is in the name of complex II.

FADH Process:

COMPLEX III: COENZYME Q- CYTOCHROME C REDUCTASE

Used in complex IV

Complex III contains 11 different subunits.
Present are iron–sulfur (FeS) proteins and cytochromes
A cytochrome is a heme-containing protein in which reversible oxidation and reduction of an iron atom occur.
Initial substrate - CoQH2 molecules
End result - Cyt C = move laterally in the intermembrane space
Cyt c (Cytochrome c) delivers its electrons to complex IV

COMPLEX IV: CYTOCHROME C OXIDASE

PRODUCT End of ETC

Complex IV contains 13 subunits.
Electron movement flows from cyt c to cyt a to cyt a3.
In the final step of electron transfer, the electrons combine with oxygen to form water
Electrons pass through both copper and iron centers and in the last step interact with molecular O2.
*PRODUCT - Water

SUMMARY OF ETC:

COMPLEX NAME / No. OF PROTEINS / PROSTHETIC GROUPS
I NADH-CoQ Reductase / >40 / FMN
II Succinate-CoQ Reductase / 4 / FAD, Cyt b
III CoQ-Cyt c Reductase / 11 / Cyt b, Cyt c, Fe-S centers
IV Cyt c Oxidase / 13 / Cyt a, Cyt a3, Cu-Fe centers

Oxidative Phosphorylation (OP)

the biochemical process by which ATP is synthesized from ADP as a result of the transfer of electrons and hydrogen ions from NADH or FADH2 to O2 through the electron carriers involved in the electron transport chain
PRODUCT: ATP = energy

SYNTHESIS OF THE MODULE

STAGES / STARTING MOLECULE / END PRODUCT / LOCATION ENERGY / SHUTLLED TO OP

Krebs Cycle (CAC) / Acetyl CoA / Carbon dioxide / Matrix of mitochondria / NADH, FADH2, ETC
ETC / Electrons / ATP, H2O / Inner membrane of mitochondria / OP
OP / Electrons / ATP / Inner membrane of mitochondria

Module Summary

2 acetyl CoA = Products?

2 CO2 * 4 CO2
3 NADH * 6 NADH
1 FADH2 * 2 FADH2
1 GTP * 2 GTP