Metabolisme Mikroba

Metabolisme adalah semua reaksi kimia yang terjadi di

dalam makhluk hidup
Metabolisme dibagi 2:
 Catabolic: Reaksi degradative yang melepaskan energi
melalui pemecahan molekul komplek menjadi molekul
sederhana
Often involve hydrolysis, breaking bonds with water.
 Anabolic: Reaction biosynthetic yang membentuk
molekul komplek dari molekul sederhana
Require energy and often involve dehydration synthesis.
Coupling of Anabolic and Catabolic Reactions

– Reaksi Katabolic menyediakan energi yang dibutuhkan

untuk menjalankan reaksi anabolik . ATP menyimpan
energi dari reaksi katabololik dan melepaskannya untuk
menjalankan reaksi anabolik
– Catabolic reactions are often coupled to ATP synthesis:
ADP + Pi + Energy ----------->ATP
– Anabolic reactions are often coupled to ATP hydrolysis:
ATP -----------> ADP + Pi + Energy
– Efficiency: hanya sebagian energi yang dilepas untuk
dapat menjalankan katabolisme, sisanya hilang dalam
bentuk panas. Energy transformations are inefficient.
 MENGAPA MIKROBA MEMERLUKAN ENERGI ?

• Synthesis bagian sel (dinding

sel, membran sel, dan
substansi sel lainnya)
• Synthesis Enzim, Asam
Nukleat, Polysakarida,
Phospholipids, atau
komponen sel lainnya
• Mempertahankan kondisi sel
(optimal) dan memperbaiki
bagian sel yang rusak
• Pertumbuhan dan
Perbanyakan
• Penyerapan hara dan ekskresi
senyawa yang tidak
diperlukan atau waste
products
• Pergerakan (Motilitas)
 REAKSI BIOKIMIA DIKATALIS OLEH ENZIM:
Berperan penting dalam setiap reaksi metabolisme
 DEFINISI DAN KARAKTERISTIK KERJA ENZIM
Protein dengan aktivitas katalitik yang mempercepat
reaksi kimia tanpa ikut dalam reaksi tersebut

Teori Kunci-Anak
kunci

Ukuran molekul
enzim > substrat

Penurunan
energi aktivasi

Reaksi
dipercepat pada
suhu alami
Enzymes
– Protein molecules that catalyze chemical
reactions.
– Enzymes are highly specific and usually catalyze
only one or a few closely related reactions.
Sucrase
Sucrose + H2O -----------> Glucose + Fructose
(substrate) (products)
– Enzymes are extremely efficient. Speed up
reaction up to 10 billion times more than without
enzyme.
– Turnover number: Number of substrate
molecules an enzyme molecule converts to
product each second. Ranges from 1 to 500,000.
Enzymes (Continued)
– The rate of a chemical reaction depends on
temperature, pressure, substrate concentration, pH,
and several other factors in the cell.
– Energy of activation: The amount of energy
required to trigger a chemical reaction.
– Enzymes speed up chemical reactions by decreasing
their energy of activation without increasing the
temperature or pressure inside the cell.
Example: Bring reactants together, create stress on
a bond, etc.
Naming Enzymes
– Enzyme names typically end in -ase.
– There are six classes of enzymes
1. Oxidoreductases: Catalyze oxidation-reduction
reactions. Include dehydrogenases and oxidases.
2. Transferases: Transfer functional groups (amino,
phosphate, etc).
3. Hydrolases: Hydrolysis, break bonds by adding water.
4. Lyases: Remove groups of atoms without hydrolysis.
5. Isomerases: Rearrange atoms within a molecule.
6. Ligases: Join two molecules, usually with energy
provided by ATP hydrolysis.
Enzyme Components
– Some enzymes consist of protein only.
– Others have a protein portion (apoenzyme) and a
nonprotein component (cofactor).
Holoenzyme = Apoenzyme + Cofactor
– Enzyme cofactors may be a metal ion (Mg2+ , Ca2+,
etc.) or an organic molecule (coenzyme). Many
coenzymes are derived from vitamins.
Examples:
• NAD+: Nicotinamide adenine dinucleotide
• NADP+: Nicotinamide adenine dinucleotide phosphate
are both cofactors derived from niacin (B vitamin).
• Coenzyme A is derived from panthotenic acid.
 KOFAKTOR ENZIM
Ada enzim yang mengandung komponen kimia lain
selain protein. Komponen ini disebut kofaktor, suatu
komponen yang bukan protein
 Kofaktor berupa :
Molekul anorganik seperti Fe2+, Mn2+, Cu2+, Na+ atau
molekul organik kecil yang disebut koenzim misalnya
vitamin B, B1, dan B2
 Koenzim yang terikat kuat secara kovalen pada protein
enzim disebut gugus prostetik.
 Enzim yang strukturnya sempurna dan aktif
mengkatalisis, bersama-sama koenzim atau gugus
logamnya disebut holoenzim.
Components of a Holoenzyme
Mechanism of Enzymatic Action
Factors Affecting Enzymatic Action
Enzymes are protein molecules and their three-
dimensional shape is essential for their function.
The shape of the active site must not be altered so
that it can bind specifically to the substrate.
Several factors can affects enzyme activity:
– Temperature: Most enzymes have an optimal
temperature. At low temperatures most reactions
proceed slowly due to slow particle movement. At very
high temperatures reactions slow down because the
enzyme is denatured.
Denaturation: Loss of three-dimensional protein
structure. Involves breakage of H and noncovalent
bonds.
Denaturation of a Protein Abolishes its Activity
 Factors that Affect Enzyme Activity: pH,
Temperature, and Substrate Concentration
Factors Affecting Enzymatic Action
– pH: Most enzymes have an optimum pH. Above or
below this value activity slows down. Extreme
changes in pH cause denaturation.
– Substrate concentration: Enzyme acts at maximum
rate at high substrate concentration.
Saturation point: Substrate concentration at which
enzyme is acting at maximum rate possible.
– Inhibitors: Inhibit enzyme activity. Two types:
• Competitive inhibitors: Bind to enzyme active site.
Example: Sulfa drugs, AZT.
• Noncompetitive inhibitors: Bind to an allosteric site.
Example: Cyanide, fluoride.
Competitive versus Noncompetitive Enzyme
Inhibitors
Factors Affecting Enzymatic Action
– Feedback Inhibition: Also known as end-product
inhibition.
Some allosteric inhibitors stop cell from making
more of a product than it needs.
The end product of a series of reactions, inhibits the
activity of an earlier enzyme.

Enzyme 1 Enzyme 2 Enzyme 3

A --------> B -------> C --------> D
Enzyme 1 is inhibited by product D.
Feedback inhibition is used to regulate ATP, amino
acid, nucleotide, and vitamin synthesis by the cell.
Feedback Inhibition of an Enzymatic
Pathway
 Energy Production
Oxidation-Reduction or Redox Reactions:
Reactions in which both oxidation and
reduction occur.
Oxidation: Removal of electrons or H atoms
Addition of oxygen
Associated with loss of energy
Reduction: Gain of electrons or H atoms
Loss of oxygen
Associated with gain of energy
Examples: Aerobic respiration & photosynthesis
are redox processes.
Oxidation-Reduction Reactions
Aerobic Respiration is a Redox Reaction

C6H12O6 + 6 O2 -----> 6 CO2 + 6 H2O + ATP

Glucose oxygen oxidized reduced
 ATP Production
Some of the energy released in oxidation-reduction
processes is trapped as ATP; the rest is lost as heat.
Phosphorylation reaction:
ADP + Energy + P ---------> ATP
There are three different mechanisms of ATP
phosphorylation in living organisms:
1. Substrate-Level Phosphorylation:
– Direct transfer of phosphate from phosphorylated
compound to ADP.
– Simple process that does not require intact membranes.
– Generates a small amount of energy during aerobic
respiration.
Two Mechanisms of ATP Synthesis:
Oxidative and Substrate Level Phosphorylation
2. Oxidative Phosphorylation:
– Involves electron transport chain, in which electrons are
transferred from organic compounds to electron carriers
(NAD+ or FAD) to a final electron acceptor (O2 or other
inorganic compounds).
– Occurs on membranes (plasma membrane of procaryotes
or inner mitochondrial membrane of eucaryotes).
– ATP is generated through chemiosmosis.
– Generates most of the ATP in aerobic respiration.
3. Photophosphorylation:
– Occurs in photosynthetic cells only.
– Convert solar energy into chemical energy (ATP and
NADPH).
– Also involves an electron transport chain.
 Carbohydrate Catabolism
 Most microorganisms use glucose or other
carbohydrates as their primary source of energy.
 Lipids and proteins are also used as energy sources.
Two general processes are used to obtain energy
from glucose: cellular respiration and
fermentation.
 Carbohydrate Catabolism
I. Cellular respiration:
– ATP generating process in which food molecules
are oxidized.
– Requires an electron transport chain.
– Final electron acceptor is an inorganic molecule:
• Aerobic respiration final electron acceptor is oxygen.
Much more efficient process.
• Anaerobic respiration final electron acceptor is another
inorganic molecule. Energetically inefficient process.
II. Fermentation:
– Releases energy from sugars or other organic
molecules.
– Does not require oxygen, but may occur in its
presence.
– Does not require an electron transport chain.
– Final electron acceptor is organic molecule.
– Inefficient: Produces a small amount of ATP for
each molecule of food.
– End-products are energy rich organic
compounds:
• Lactic acid
• Alcohol
Aerobic Respiration versus Fermentation
 Cellular Respiration
I. Aerobic Respiration
C6H12O6 + 6 O2 -----> 6 CO2 + 6H2O + ATP
Glucose oxygen oxidized reduced
 Most energy efficient catabolic process.
 Oxygen is final electron acceptor.

Aerobic Respiration occurs in three stages:

1. Glycolysis
2. Kreb’s Cycle
3. Electron Transport & Chemiosmosis
Based on producing of energy, bacteria
divided of 3 :
1. Producing energy by anaerobically reaction
2. producing energy by aerobically
3. producing energy through photosynthesize

Energy Produced anaerobically have 4

pathways
1. Embden-Meyerhoff (glycolysis)
2. Pentose-fosfat trace
3. Entner-Doudoroff
4. Fermentation
Energy production through aerobe process
consisted of :
1. Electron transport chain/respiration chain
2. Tricarbonate cyclic Acid/krebs cycles

NOTE:
Glycolysis (Embden-Meyerhoff),
pentosa phosphate and Entner Dou- doroff
are the pathways which change glucose to
be pyruvate acid. Pyruvat acid is a middle
point/navel of carbohyd rate
fermentation.
Produce energy through anaerobically process.

Glycolysis : Glucose -pyruvate acid (+ 2 ATP;

- 4 ATP)
Heterotrophic bacteria are able to use organic
compound as a source of energy (CH, organic acid,
patty acid, amino acid), but the most prominent is
CH especially Glucose. A breakdown of glucose
through glycolysis, pentosa phosphate and Entner
Doudoroff. O2 isn’t as a requirement for
processing of glykolysis to yield energy, either for
anaerobe mo or aerobe mo.
Glikolisis
Entner–Doudoroff (ED) pathway
Jalur
Entner Duodorf
 Glucose (C6)
ATP
Glycolysis or Glucose 6-phosphate
Embden-Meyerhof Fructose 6-phosphate
Pathway ATP
Fructose 1,6-diphosphate

Triose 3-phosphate (C3)

NAD
1,3-Diphosphoeycerate
ATP
NADH2
3-Phosphoglycerate x2
2-Phosphoglycerate
Fermentation
Phosphoenolpyruvate
ATP
Reduced Compound Pyruvate (C3)
Pentose phosphate pathway:

This pathway is to dissimilate CH include the

formed of phosphate sugar that has 6 C
atom (hexose mono phosphate) & phosphate
sugar that has 5 C ( pentose phosphate).
Glucose is oxidized through pentose
phosphate followed by releasing a pair of
electron. The electron enter into electron
transport chain.
Pentose phosphate pathway is used in DNA
synthesize because synthesis of DNA use
pentose phosphate as DNA back bone.
Glucose 6 phosphate is oxidized to 6-
phosphogluconate, and then undergo
decarboxylate and more re-oxidize to be D-
ribulose 5-phosphate + CO2.
Glucose 6 phosphate + 2 NADP+ H2O  D-
ribulose 5 phosphate +CO2+ 2NADPH2.
Pentose phosphate (PP) pathway
Jalur
Pentosa
Pospat
Three Stages of Aerobic Respiration
 Cellular Respiration
I. Stages of Aerobic Respiration
1. Glycolysis: “Splitting of sugar”.
– Glucose (6 C) is split and oxidized to two
molecules of pyruvic acid (3C).
– Most organisms can carry out this process.
– Does not require oxygen.
Net yield per glucose molecule:
– 2 ATP (substrate level phosphorylation)
– 2 NADH
In Glycolysis Glucose is Split into Two
Molecules of Pyruvic Acid
 Cellular Respiration
I. Stages of Aerobic Respiration
2. Krebs Cycle (Citric Acid Cycle):
– Before cycle can start, pyruvic acid (3C) loses one carbon
(as CO2) to become acetyl CoA (2C).
– Acetyl CoA (2C) joins oxaloacetic acid (4C) to form citric
acid (6C).
– Cycle of 8 oxidation-reduction reactions that transfer
energy to electron carrier molecules (coenzymes NAD+ and
FAD).
– 2 molecules of carbon dioxide are lost during each cycle.
– Oxaloacetic acid is regenerated in final step.
Net yield per glucose molecule:
• 2 ATP (substrate level phosphorylation)
• 8 NADH
• 2 FADH2
 Pyruvic Acid is Converted to Acetyl CoA
Before the Kreb’s Cycle Starts

Notice that carbon dioxide is lost.

Kreb’s Cycle: Two Carbons In & Two Out
 Cellular Respiration
I. Stages of Aerobic Respiration
3. Electron Transport Chain and Chemiosmosis:
– Electrons from NADH and FADH2 are released to chain
of electron carriers.
– Electron carriers are on cell membrane (plasma
membrane of bacteria or inner mitochondrial
membrane in eucaryotes).
– Final electron acceptor is oxygen.
– A proton gradient is generated across membrane as
electrons flow down chain.
– ATP is made by ATP synthase (chemiosmosis) as protons
flow down concentration gradient.
Net ATP yield:
– 2 FADH2 generate 2 ATPs each: 4 ATP
– 10 NADH generate 3 ATPs each: 30 ATP
Electron Transport Chain in Aerobic Respiration:
Oxygen is Final Electron Acceptor
 Chemiosmosis in Aerobic Respiration:
ATP Synthesis Requires Intact Membranes
Summary of Aerobic Respiration in Procaryotes
Total Yield from Aerobic Respiration of 1 Glucose
molecule: 36-38 molecules of ATP
In procaryotes:
C6H12O6 + 6 O2-----> 6 CO2 + 6 H2O + 38 ATP
In eucaryotes:
C6H12O6 + 6 O2 -----> 6 CO2 + 6 H2O + 36 ATP
Yield is lower in eucaryotes because transport of
pyruvic acid into mitochondria requires energy.
 Cellular Respiration
II. Anaerobic Respiration
 Final electron acceptor is not oxygen.
 Instead it is an inorganic molecule:
 Nitrate (NO3-): Pseudomonas and Bacillus. Reduced to
nitrite (NO2-):, nitrous oxide, or nitrogen gas.
 Sulfate (SO42-): Desulfovibrio. Reduced to hydrogen
sulfide (H2S).
 Carbonate (CO32-): Reduced to methane.
 Inefficient (2 ATPs per glucose molecule).
 Only part of the Krebs cycle operates without oxygen.
 Not all carriers in electron transport chain participate.
 Anaerobes tend to grow more slowly than aerobes.
 Fermentation
– Releases energy from sugars or other organic molecules.
– Does not require oxygen, but may occur in its presence.
– Does not require Krebs cycle or an electron transport
chain.
– Final electron acceptor is organic molecule.
– Inefficient. Produces a small amount of ATP for each
molecule of food. (1 or 2 ATPs)
– End-products may be lactic acid, alcohol, or other energy
rich organic compounds.
 Lactic Acid Fermentation: Carried out by Lactobacillus
and Streptococcus. Can result in food spoilage. Used to
make yogurt, sauerkraut, and pickles.
 Alcohol Fermentation: Carried out by yeasts and
bacteria.
Fermentation is Less Efficient Than Aerobic Respiration
Alcohol and Lactic Acid Fermentation
Fermentation: Generates Various Energy Rich,
Organic End-Products
Catabolism of Various Organic Food Molecules
 Photosynthesis
6 CO2 + 6 H2O + Light -----> C6H12O6 + 6 O2
Light Dependent Reactions
– Light energy is trapped by chlorophyll.
– Water is split into oxygen and hydrogen.
– NADP+ is reduced to NADPH.
– ATP is made.
 Light Independent Reactions
– Do not require light.
– CO2 from air is fixed and used to make sugar.
– Sugar is synthesized, using ATP and NADPH.
 Metabolic Diversity
Living organisms can be classified based on
where they obtain their energy and carbon.
Energy Source
– Phototrophs: Light is primary energy source.
– Chemotrophs: Oxidation of chemical compounds.
Carbon Source
– Autotrophs: Carbon dioxide.
– Heterotrophs: Organic carbon source.
 Four Groups Based on Metabolic Diversity
1. Chemoheterotrophs:
– Energy source: Organic compounds.
– Carbon source: Organic compounds.
• Examples: Most bacteria, all protozoans, all fungi, and all animals.
2. Chemoautotrophs:
– Energy source: Inorganic compounds (H2S, NH3, S, H2, Fe2+, etc.)
– Carbon source: Carbon dioxide.
• Examples: Iron, sulfur, hydrogen, and nitrifying bacteria.
3. Photoheterotrophs:
– Energy source: Light.
– Carbon source: Organic compounds.
• Examples: Purple and green nonsulfur bacteria.
4. Photoautotrophs:
– Energy source: Light.
– Carbon source: Carbon dioxide.
• Examples: Plants, algae, photosynthetic bacteria
Organisms Are Classified Based on Their
Metabolic Requirements