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Chapter 5
Metabolism
Of
Microorganisms
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Metabolism
Metabolism: sum of all chemical reactions within the cell
Two parts:
Catabolism: breakdown of complex organic molecules into simpler
ones - energy is released
Anabolism: building complex organic molecules from simpler ones;
energy is used
Coupling of these reactions is made possible through ATP
So… what does he mean by coupling?”
energy retrieved from catabolism is stored in ATP and later released to
drive anabolic reactions
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Enzymes
type of protein which catalyzes reactions in the cell by lowering the
activation energy
Enzymes are catalysts: not used up during the reaction
enzymes are specific to one reaction (won’t drive a different reaction)
range in size from 10,000 to several million molecular weight
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More about enzymes
Compounds acted upon by the enzymes are called substrates
Maximum number of substrate molecules an enzyme molecule can
convert to product each second is called the turnover number
So how fast are these enzymes? – VERY FAST
typically between 1 – 10,000 reactions per second for each enzyme
Some as many as 500,000 per second for each enzyme molecule!
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Control of Enzymes
What ways might an enzyme’s activity be regulated?
Control at the level of:
Enzyme synthesis (how much enzyme is made/present)
Enzyme activity (how active the enzyme is: turned on/off)
We will examine some factors affecting enzyme control soon…
Naming of enzymes: most end in -ase
Often name indicates their function or the substrate/product they work on
e.g. ligases are enzymes that ligate or join things (example = DNA ligase)
classified by the type of chemical reaction they catalyze (see Table 5.1)
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Composition of Enzymes
(what they’re made of)
All contain proteins: can be entirely protein, some contain other
components
Enzyme components:
Protein portion is called the apoenzyme
Non-protein component is the co-factor
Co-factors can be either organic or inorganic
If a co-factor is complex organic molecule, it is called a coenzyme
When fully assembled they form the holoenzyme
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Important Coenzymes
All of the example on this slide serve as electron carriers
(more on this function later in this chapter)
One of the B vitamins - nicotinic acid (niacin) and compounds derived
from it…
Nicotinamide adenine dinucleotide (NAD+)
Nicotinamide adenine dinucleotide phosphate (NADP+)
flavin mononucleotide (FMN) and flavin adenin dinucleotide (FAD)
Vitamin K
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Other uses for Coenzymes
Coenzyme A (CoA) – functions in decarboxylation reactions
Pantothenic acid (another B vitamin) – Part of CoA molecule
important in breakdown of fats and in reactions of the Krebs cycle
Vitamin E – needed for cellular & large molecule synthesis
Folic acid – synthesis of nucleotides (both purines & pyrimidines)
Biotin – fatty acid synthesis & CO2 fixation reactions
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Inorganic Co-factors
Many co-factors are metal ions (e.g. Mg++)
One use - required by phosphorylating enzymes
Many metabolic trace elements are probably important due to
use as co-factors
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Enzymatic Action
1. Substrate binds to active site on the surface of enzyme
2. Temporary intermediate complex forms - enzyme-substrate complex
3. Substrate transformed (other molecule added, molecule rearranged,
bond broken, etc.)
4. Transformed substrate (product or products) no longer conforms
to the active site, is released from enzyme
5. Unchanged enzyme is ready to react with more substrate molecules
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Some Factors Influencing Enzymes
Temperature
pH
Substrate Concentration
Inhibition
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The Effect of Temperature On Enzymes
Temperature – as temperature begins to
increase, enzymatic activity increases
At some point (unique for each enzyme)
optimum temperature will be reached. -Enzyme operates at peak efficiency
Higher temperatures will cause protein portion
of enzyme to denature,
Denaturing = unraveling protein, kills all future
function of that molecule.
Each enzyme will have a minimum, optimum
and maximum operating temperature
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Effect of pH on Enzyme Activity
As with temperature, enzymes will
have a minimum, optimum and a
maximum pH.
alterations away from the optimum
may affect individual amino acids
altering the protein’s shape &
effectiveness
Extreme pH changes can cause the
protein portion to denature thus
destroying the enzyme.
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Generation of ATP
Three ways that energy is trapped by formation of ATP
(ADP + P = ATP) in the process called phosphorylation
Substrate-Level Phosphorylation: direct transfer of phosphate to ADP
from phosphorylated substrate (from something that has a phosphate)
Oxidative Phosphorylation: electrons transferred from organic
compounds to electron carriers, energy is transferred down an electron
transport chain, which is then used to generate ATP (e.g. NADH and
FADH2)
Photophosphorylation: light energy is trapped and again uses an
electron transport chain to generate ATP
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Energy Production
Oxidation-Reduction reactions: reaction where one substrate loses
electrons (oxidation) and the other gains electrons (reduction)
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Energy Production
In biological systems this often includes the transfer of both the
electron and the accompanying proton (electron + proton = hydrogen),
thus called dehydrogenation reactions
Redox reactions used to extract energy from nutrient molecules
nutrient is oxidized (e.g. - glucose to carbon dioxide) and the energy
eventually trapped in ATP molecule for later use.
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Carbohydrate Catabolism
Three phases – making a total of 38 ATP for each glucose molecule
Glycolysis – splits glucose (6-Carbons) in half making two (3-carbon)
pyruvic acid molecules --- process releases a small amount of energy
and small amount of NADH
Krebs Cycle – extracts energy from pyruvic acids (small amount)
creates lots of NADH and FADH2 for later use in the….
Electron Transport Chain – extracts lots of energy from NADH
and FADH2 (Electron carrying molecules)
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Glycolysis
occurs in
cytoplasm
Krebs
occurs in
mitochondria
Electron transport
chain occurs in
mitochondria
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Glycolysis
Glycolysis –splitting of glucose: a 6-carbon molecule into two 3carbon molecules (produced 2 ATP overall)
• Preparatory phase – costs cell energy
• Energy conserving phase – produces energy
Cost = 2 ATP
Gain = 4 ATP & 2 NADH (NADH to be used later)
Produces two pyruvic acids to send through Krebs Cycle
Glycolysis occurs in the cytoplasm of eukaryotes
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Energy Input - COST
Energy Input - COST
Total cost so far = 2 ATP
Total energy gain = 0
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Cost = 0 during this stage
Gain = 4 ATP + 2 NADH (will be used later)
produce 2 pyruvic acid to use in
Krebs Cycle
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Krebs Cycle (Plus Preparatory)
Each cycle of Krebs produces
1 ATP
4 NADH
Since we can run Krebs
twice our total yield is:
1 FADH2
2 ATP
8 NADH
2 FADH2
Krebs Cycle – runs once for each pyruvic acid each glucose broken
produces two pyruvic acids so we can run Krebs twice.
The NADH and FADH2 will be used in the next step to recover many
ATPs
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Electron Transport Chain
NADH enters at first protein – ejects 2 hydrogen ions (one pair of H+)
from the inner membrane of the mitochondria
Ejects two more pairs of H+ at the next two steps in the chain
A total of 3 pairs of H+ have been ejected when an NADH completes
it’s passage along the chain
Each pair of H+ ions passes through an ATP Synthase molecule
making one ATP as they pass through
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FADH2
Also uses the electron transport chain but can’t enter at the first step
must enter at the second step
Because of this it can only move 2 pairs of H+ and will ultimately be
responsible for production of 2 ATP molecules
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Energy Yield
…from Electron Transport Chain
10 NADH = 30 ATP
2 FADH2 = 4 ATP
If you add this to the two we got from Krebs plus the two we gain
from Glycolysis you have a total produced of 38 from the breakdown
of a single glucose molecule
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Anaerobic Respiration
in Prokaryotes
Final Electron acceptor is an inorganic molecule other than O2
Examples include:
NO3 e.g. Pseudomonas & Bacillus makes nitrous oxide, nitrate or
nitrogen gas
–
SO4 e.g. Desulfovibrio makes hydrogen sulfide gas
--
CO3 e.g. Methanobacterium makes methane
Less efficient that Aerobic respiration, produces less total ATP
because of this, anaerobic bacteria tend to grow slower than aerobes
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Fermentation
After the breakdown of glucose to pyruvic acid, other pathways can be
taken – Fermentation is one alternative. Fermentation:
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Releases energy from sugars or other organic molecules
Does not require O2 (but can often occur in presence of O2)
Does not use Krebs or Electron Transport
Uses an organic molecule for electron acceptor
Produces few ATP (one or two per start molecule)
End products contain much of original energy
 ethanol
 lactic acid
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Industrial Uses for Fermentation
Ethanol (ethyl alcohol)
beer, wine, fuel
Acetic Acid
vinegar
Lactic acid
yogurt, sauerkraut etc
methane
fuel
see table 5.4 p 136 for details
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Biochemical Tests for
Bacterial Identification
Useful things for identifying your unknown!
Fermentation Test Medium contains:
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protein
one specific carbohydrate (maltose, fructose, glucose, etc)
pH indicator (color change if use carbohydrate)
Durham tube (glass tube) to collect gas if produced
Purple Carbohydrate Broth
Turns yellow if organism can use
The particular carbohydrate for
energy source – bubble indicates
Gas produced
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Phenol Red Carbohydrate Broth
Turns yellow if organism can use
The particular carbohydrate for
energy source. Bubble indicates
Gas produced
Photosynthesis
Conversion of light energy into chemical energy using light gathering
pigments such as chlorophyll by plants, algae & cyanobacteria
Two major reactions:
Light Reaction – gathers light, harvests energy, releases oxygen
Light-Independant Reaction – CO2 used to produce sugars
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Bacterial Metabolic Diversity
Categorizing bacteria by metabolic styles:
Major Categories include
Chemotrophs – derive energy from chemical sources such as carbon,
sulphur etc
Phototrophs – derive energy from light (usually sunlight)
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Self-feeder vs Other-feeder
Autotrophs – ‘self-feeders’ assemble simple carbon sources such as
CO2 into more complex organic molecules such as carbohydrates to
store energy
Heterotrophs – ‘feeders-on-others’ require complex organic molecules
for a carbon source
Heterotrophs can be further broken into two groups
Saprophytes – feed on dead organic matter
Parasites
- feed on living organic matter
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Thus - Possible Lifestyles:
Photoautotrophs – use light for energy and CO2 for carbon source
Photoheterotrophs – use light for energy but can’t convert CO2 to
sugars, don’t produce oxygen
Chemoautotrophs – energy from reduced inorganic compounds (such
as sulfur, hydrogen sulfide, ammonia), use CO2 for primary carbon
source
Chemoheterotrophs – energy from complex organic molecules,
carbon from complex organic molecules (we do this as humans)
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