Chapter 5, part A
Microbial Metabolism
• Life fundamental feature:
–
growth (metabolism)
– reproduction (heritable genetic information)
What do all organisms need?
• Organic compounds in life organisms
•
•
•
•
•
Carbohydrates – sugars
Lipids – fatty acids
Proteins – amino acids
Nucleic acids - nucleotides
Vitamins
Carbon
• Chemical reactions involve the making or breaking of bonds
between atoms.
– A change in chemical energy occurs during a chemical reaction.
• Endergonic reactions absorb energy.
Energy
– Synthesis reaction
• Exergonic reactions release energy.
– Decomposition Reactions
• Metabolism is the sum of all chemical reactions that occur in
living organisms to maintain life.
– Catabolism is breakdown and the energy-releasing processes.
• Provides energy and building blocks for anabolism.
– Anabolism is biosynthesis and the energy-using processes
• Uses energy and building blocks to build large molecules
• Role of ATP in Coupling Reactions
Nutritional ( metabolic) types of organisms
– Trophe = nutrition
• Sources of energy
– Chemotrophs: Energy is released from breaking chemical bond in
compound
– Phototrophs: Light is absorbed in photo receptors and transformed
into chemical energy.
• Sources of carbon
– Autotrophs: Carbon dioxide (CO2) is used as source of carbon
Heterotrophs: Organic compounds are metabolized to get carbon for
growth and development.
Chemical reactions - Collision theory
• The collision theory states that chemical reactions can occur when
atoms, ions, and molecules collide.
• Reaction rate:
– Activation energy - needed to disrupt electronic configurations.
– Frequency of collisions – depends on concentration of the atoms and
molecules
• Reaction rate can be increased by:
– Increasing temperature or pressure.
– Lowering the activation energy - Catalysts
• Enzymes - biological catalysts
Enzymes
• Like all catalysts, enzymes work by lowering the activation
energy for a reaction, thus dramatically increasing the rate of the
reaction
AB
Enzyme
Substrate
A + B
Products
Reaction
without enzyme
• Enzymatic reactions –
– Substrates The material or substance
on which an enzyme acts
(The molecules at the
beginning of the process)
– Enzyme
– Products The molecules at the
end the reaction
Reaction
with enzyme
Reactant (Substrate)
Activation
energy
with
enzyme
Initial energy level
Final energy
level
Products
Activation
energy
without
enzyme
Enzymes
• Enzymes are biomolecules that catalyze ( increase the rates of)
chemical reactions.
– Almost all enzymes are proteins.
– RNA molecules called ribozymes are capable of performing specific
biochemical reactions
• Peptidyl transferase is catalysed by the rRNA component of the large
ribosomal subunit.
• Although most ribozymes are quite rare in the cell,
their roles are sometimes essential to life
Enzymes
• Like all proteins, enzymes are made as long, linear chains of amino
acids
– Each unique amino acid sequence (peptide) produces a specific structure (a
three-dimensional product) , which has unique properties.
– Active site
• The structure and chemical properties of the active site allow the
recognition and binding of the substrate
Figure 5.2
Enzymes
• Enzyme-substrate complex - Substrates bind to the active site of the
enzyme
• Bind through hydrogen bonds, hydrophobic interactions, temporary covalent
bonds (van der waals) or a combination of all of these
• The active site modifies the reaction mechanism in order to decrease the activation
energy of the reaction.
• The product is usually unstable in the active site, it is released and
returns the enzyme to its initial unbound state.
• The turnover number is generally 1-10,000 molecules per second.
E + S ⇌ ES → EP ⇌ E + P
Enzymes are not used up in that reaction
Enzymes
Apoenzyme: protein
Inactive
Cofactor: Nonprotein component
NAD+, (NADH)
NADP+, (NADPH)
FAD
Coenzyme: Organic cofactor
Vitamins
Coenzyme A
Holoenzyme: Apoenzyme + cofactor
Active
Figure 5.3
Factors Influencing Enzyme Activity
1. Effect of Substrate Concentration on Enzyme Activity
* Point of saturation
[E][S]
Substrate
[P1][P2]
Product1 + Product2
Factors Influencing Enzyme Activity
2. Effect of Temperature on Enzyme Activity
* Optimal temperature
3. Effect of pH on Enzyme Activity
* Optimal pH
• Enzymes can be denatured by temperature and pH
Figure 5.5b
Inhibitors of Enzyme Activity
1. Competitive inhibition – competition for the active site
Figure 5.7a, b
Inhibitors of Enzyme Activity
2. Noncompetitive inhibition
Figure 5.7a, c
Feedback inhibition of biochemical pathways
• The term feedback inhibition refers to a situation in which the
substances at the end of a long series of reactions inhibits a
reaction at the begining of the series of reactions.
Figure 5.8
Metabolic Pathways
• A metabolic pathway is a sequence of chemical reactions
occurring within a cell
– In each pathway, a principal chemical is modified by chemical reactions.
E2
E1
Starting molecule
–
intermediate A
E3
intermediate B
end product
Enzymes catalyze these reactions often require dietary minerals, vitamins, and
other cofactors in order to function proper
• Metabolic pathways are determined by enzymes.
• Enzymes are encoded by genes.
Enzymes
• Enzymes are usually very specific as to which reactions they
catalyze and the substrates that are involved in these reactions
• Enzyme Classification
– Oxidoreductase: Oxidation-reduction reactions
– Transferase: Transfer functional groups
– Hydrolase: Hydrolysis
– Lyase: Removal of atoms without hydrolysis
– Isomerase: Rearrangement of atoms
– Ligase: Joining of molecules, uses ATP
Oxidation-Reduction
• Oxidation is the removal of electrons.
• Reduction is the gain of electrons.
• Redox reaction is an oxidation reaction paired with a reduction
reaction.
Figure 5.9
Oxidation-Reduction
• In biological systems, the electrons are often associated with
hydrogen atoms.
– Transfer of electrons or hydrogen atoms from one molecule
(hydrogen or electron donor) to another (the acceptor)
• Biological oxidations are often dehydrogenations.
Figure 5.10
Energy production - Catabolism
• Cells use biological oxidation-reduction reactions in catabolism
to breakdown organic compounds
– Release energy associated with the electrons that form bonds between their
atoms
( C6H12O6)
highly reduced compounds
(with many hydrogen atoms)
(substrate)

CO2 + H2O + energy
highly oxidized compounds
(products)
• Energy released during certain metabolic reactions can be trapped
to form ATP
– Addition of PO4- a to a molecule is called phosphorylation
– ATP is generated by the phosphorylation of ADP.
The Generation of ATP
• Generate ATP – serves as a convenient energy carrier
• During substrate-level phosphorylation, a high-energy from an
intermediate in catabolism is added to ADP.
• During oxidative phosphorylation, energy is released as electrons
are passed to a series of electron acceptors (an electron transport
chain) and finally to O2 or another inorganic compound.
• During photophosphorylation, energy from light is trapped by
chlorophyll, and electrons are passed through a series of electron
acceptors.
• The electron transfer releases energy used for the synthesis of
ATP.
Catabolism Metabolic Pathways
1
2
+ATP
+ATP
+ATP
3
Carbohydrate Catabolism
• Most of a cell’s energy is produced from the oxidation of
carbohydrates.
• Glycolysis - the most common pathway for the oxidation of glucose.
– Glucose is the most commonly used carbohydrate.
• One glucose molecule.
• End-product - Pyruvic acid
• 2 ATP and 2 NADH molecules
are produced
• Alternatives to Glycolysis
– The pentose phosphate pathway
• Used to metabolize five-carbon sugars;
• One ATP and 12 NADPH molecules are produced from one glucose
molecule.
– The Entner-Doudoroff pathway
• One ATP and two NADPH molecules from one glucose molecule.
• Does not involve glycolysis
• Pseudomonas, Rhizobium, Agrobacterium
Preparatory stage
Glycolysis
Energy-Conserving Stage
• 2 ATPs are used
• Glucose is split to form 2
Glucose-3-phosphate
•
2 Glucose-3-phosphate oxidized to
2 Pyruvic acid
– 4 ATP produced
– 2 NADH produced
1 molecule Glucose
6
1,3-diphosphoglyceric acid
7
3-phosphoglyceric acid
8
9
•
1 Glucose + 2 ATP + 2 ADP + 2 PO4– + 2 NAD+
2 pyruvic acid + 4 ATP + 2 NADH + 2H+
substrate-level phosphorylation,
2-phosphoglyceric acid
Phosphoenolpyruvic acid
(PEP)
10
2 molecules Pyruvic acid
Figure 5.12.2
Carbohydrate Catabolism
• The two major types of glucose
catabolism are:
– Respiration, in which glucose
is completely broken down
• To CO2 and H2O - aerobic
respiration
• To NO2–, N2 , H2S, CH4 and H2O
– anaerobic respiration
– Fermentation, in which
glucose is partially broken
down (organic molecule)
Respiration - Intermediate Step
• Pyruvic acid (from glycolysis) is
oxidized and decarboyxlated
2 Pyruvic acid
2 NADH
Figure 5.13.1
Respiration - Krebs Cycle
• Oxidation of acetyl CoA produces NADH and FADH2
2 Acetyl CoA
6 NADH
2 FADH2
Figure 5.13.2
Respiration - The Electron Transport Chain
• A series of carrier molecules that are, in turn, oxidized and
reduced as electrons are passed down the chain.
10 NADH
2 FADH2
• Energy released can be used to produce ATP by chemiosmosis
Chemiosmosis
• Protons being pumped across the membrane generate a proton
motive force as electrons move through a series of acceptors
or carriers.
• Energy produced from movement of the protons back across the
membrane is used by ATP synthase to make ATP from ADP .
• Electron carriers are located:
• In eukaryotes
– in the inner mitochondrial
membrane;
• In prokaryotes
– in the plasma membrane.
• oxidative phosphorylation
Figure 5.17
• ATP produced from complete oxidation of 1 glucose
using aerobic respiration
Pathway
Glycolysis
By substratelevel
phosphorylation
2
By oxidative
phosphorylation
From
From
NADH
FADH
6
0
Intermediate
step
Krebs cycle
0
6
2
18
4
Total
4
30
4
• 36 ATPs are produced in eukaryotes.
Respiration
• Aerobic respiration
– The final electron acceptor in the electron transport chain is
molecular oxygen (O2).
• Product - H2O
• Anaerobic respiration
– The final electron acceptor in the electron transport chain is
not O2. .
Electron acceptor
NO3–
SO42–
(nitrate ion )
(sulfate ion)
CO32 – (carbonate ion)
Products
NO2– (nitrite ion) , N2 O or N2 + H2O
H2S + H2O
CH4 + H2O
Respiration
Pathway
Eukaryote
Prokaryote
Glycolysis
Cytoplasm
Cytoplasm
Intermediate step
Cytoplasm
Cytoplasm
Krebs cycle
Mitochondrial
matrix
Mitochondrial
inner membrane
Cytoplasm
ETC
Plasma
membrane
Learning objectives
• Define metabolism, and describe the fundamental
differences between anabolism and catabolism.
• Identify the role of ATP as an intermediate between
catabolism and anabolism.
• Identify the components of an enzyme.
• Describe the mechanism of enzymatic action.
• List the factors that influence enzymatic activity.
• Explain what is meant by oxidation–reduction.
• List and provide examples of three types of
phosphorylation reactions that generate ATP.
• Explain the overall function of biochemical pathways.
• Describe the chemical reactions of glycolysis.
• Explain the products of the Krebs cycle.
• Describe the chemiosmosis model for ATP generation.
• Compare and contrast aerobic and anaerobic respiration.