Lecture; Microbial Metabolism, Class ppt.ppt

A detail lecture on microbial metabolism, taking through different ways autotrophs and chemothrophs synthesis food and other microorganisms.

1. Microbial
Metabolism

2. Metabolism and the Role of Enzymes
Metabolism:Pertains to all chemical reactions and
physical workings of the cell
Anabolism:A building and bond-making process that
forms larger macromolecules from smaller ones
Requires the input of energy (ATP)
Catabolism:Breaks the bonds of larger molecules into
smaller molecules
Releases energy (used to form ATP)

3. Simplified Model of Metabolism
Relative complexity of molecules
ANABOLISM
ANABOLISM
ANABOLISM
Nutrients
from
outside
or from
internal
pathways
Glycolysis
Krebs cycle
Respiratory
chain
Fermentation
Yields energy Uses energy Uses energy Uses energy
Some assembly
reactions occur
spontaneously
Complex lipids
RNA + DNA
Peptidoglycan
Proteins
Amino acids
Sugars
Nucleotides
Fatty acids
Glyceraldehyde-3-P
Acetyl CoA
Pyruvate
CATABOLISM
Glu
Glucose
Precursor
molecules
Macromolecules
Bacterial
cell
Building
blocks

4. Enzymes: Catalyzing the Chemical Reactions of
Life
•Enzymes
-are catalyststhat increase the rate of chemical
reactions without becoming part of the products
or being consumed in the reaction
-substrates:reactant molecules acted on by an
enzyme
-Have unique active site on the enzyme that fits
only the substrate

5. Enzyme Structure
•Simple enzymes consist of protein alone
•Conjugated enzymes contain protein and nonprotein
molecules
-sometimes referred to as a holoenzyme
-apoenzyme: protein portion of a conjugated
enzyme
-cofactors:inorganic elements (metal ions)
-coenzymes:organic cofactor molecules

6. Conjugated Enzyme Structure
CoenzymeCoenzyme
Metallic
cofactor
Apoenzymes
Metallic
cofactor

7. Enzyme-Substrate Interactions
•A temporary enzyme-substrate union must occur at the
active site
-fit is so specific that it is described as a “lock-
and-key” fit
•Bond formed between the substrate and enzyme are
weak and easily reversible
•Once the enzyme-substrate complex has formed, an
appropriate reaction occurs on the substrate, often with
the aid of a cofactor
•Product is formed
•Enzyme is free to interact with another substrate

8. Enzyme-Substrate Reactions
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E
Substrates
Enzyme (E)
Does
not fit
(a) (b)
ES complex
(c)
Products

9. Cofactors: Supporting the Work of Enzymes
•The need of microorganisms for trace elements arises
from their roles as cofactors for enzymes
-iron, copper, magnesium, manganese, zinc,
cobalt, selenium, etc.
•Participate in precise functions between the enzyme
and substrate
-help bring the active site and substrate close
together
-participate directly in chemical reactions with
the enzyme-substrate complex

10. Cofactors: Supporting the Work of Enzymes
(cont’d)
•Coenzymes
-organic compounds that work in conjunction
with an apoenzyme
-general function is to remove a chemical
group from one substrate molecule and add
it to another substrate molecule
-carry and transfer hydrogen atoms, electrons,
carbon dioxide, and amino groups
-many derived from vitamins

11. Classification of Enzyme Functions
•Enzymes are classified and named according to
characteristics such as site of action, type of action,
and substrate
-prefix or stem word derived from a certain
characteristic, usually the substrate acted
upon or type of reaction catalyzed
-ending –ase

12. Classification of Enzyme Functions (cont’d)
•Six classes of enzymes based on general biochemical
reaction
-oxidoreductases:transfer electrons from one
substrate to another, dehydrogenasestransfer a
hydrogen from one compound to another
-transferases:transfer functional groups from
one substrate to another
-hydrolases:cleave bonds on molecules with the
addition of water

13. Classification of Enzyme Functions (cont’d)
•Six classes of enzymes based on general biochemical
reaction (cont’d)
-lyases: add groups to or remove groups from
double-bonded substrates
-isomerases: change a substrate into its isomeric
form
-ligases:catalyze the formation of bonds with
the input of ATP and the removal of water

14. Classification of Enzyme Functions (cont’d)
•Each enzyme also assigned a common name that
indicates the specific reaction it catalyzes
-carbohydrase:digests a carbohydrate substrate
-amylase: acts on starch
-maltase: digests maltose
-proteinase, protease, peptidase:hydrolyzes the
peptide bonds of a protein
-lipase: digests fats
-deoxyribonuclease (DNase): digests DNA
-synthetase or polymerase:bonds many small molecules
together

15. Regulation of Enzyme Function
Constitutive enzymes:Always present in relatively constant
amounts regardless of the amount of substrate
Regulated enzymes: production is turned on (induced) or
turned off (repressed) in responses to changes in
concentration of the substrate

16. Regulation of Enzyme Function (cont’d)
Activity of enzymes influenced by the cell’s environment
-natural temperature, pH, osmotic pressure
-changes in the normal conditions causes
enzymes to be unstable or labile
•Denaturation
-weak bonds that maintain the native shape of
the apoenzymeare broken
-this causes disruption of the enzyme’s shape
-prevents the substrate from attaching to the
active site

17. Metabolic Pathways
•Often occur in a multistep series or pathway, with
each step catalyzed by an enzyme
•Product of one reaction is often the reactant
(substrate) for the next, forming a linear chain or
reaction
•Many pathways have branches that provide alternate
methods for nutrient processing
•Others have a cyclic form, in which the starting
molecule is regenerated to initiate another turn of the
cycle
•Do not stand alone; interconnected and merge at
many sites

18. Patterns of Metabolism
A
B
C
D
E
U
O
2
O
O
1
M
N
P
Q
R
M
A
B
C
N
X
Y
Z
V
W
X
Z
Y
Multienzyme Systems
Branched
Convergent
Linear Cyclic
Example:
Glycolysis
Example:
Amino acid
synthesis
T input
Krebs
Cycle
S product
Divergent

19. Direct Controls on the Action of Enzymes
•Competitive inhibition
-inhibits enzyme activity by supplying a
molecule that resembles the enzyme’s normal
substrate
-“mimic” occupies the active site, preventing
the actual substrate from binding
•Noncompetitive inhibition
-enzymes have two binding sites: the active site
and a regulatory site
-molecules bind to the regulatory site
-slows down enzymatic activity once a certain
concentration of product is reached

20. Two Common Control Mechanisms for Enzymes
Competitive Inhibition Noncompetitive Inhibition
SubstrateCompetitive
inhibitor with
similar shape
Active site
Regulatory site
Normal
substrate
Both molecules
compete for
the active site.
Enzyme
Reaction proceeds. Reaction is blocked
because competitive
inhibitor is incapable
of becoming a product.
Product
Reaction proceeds. Reaction is blocked because
binding of regulatory molecule
in regulatory site changes
conformation of active site so
that substrate cannot enter.
Regulatory
molecule
(product)
Enzyme

21. Controls on Enzyme Synthesis
•Enzymes do not last indefinitely; some wear out, some
are degraded deliberately, and some are diluted with
each cell division
•Replacement of enzymes can be regulated according to
cell demand
•Enzyme repression:genetic apparatus responsible for
replacing enzymes is repressed
-response time is longer than for feedback
inhibition
•Enzyme induction:enzymes appear (are induced) only
when suitable substrates are present

22. Enzyme Induction in E. coli
•If E. coli is inoculated into a medium containing only
lactose, it will produce the enzyme lactase to hydrolyze
it into glucose and galactose
•If E. coliis subsequently inoculated into a medium
containing only sucrose, it will cease to synthesizing
lactase and begin synthesizing sucrase
•Allows the organism to utilize a variety of nutrients, and
prevents it from wasting energy by making enzymes for
which no substrates are present

23. Concept Check
Which of the following mechanisms of enzyme control
blocks a reaction catalyzed by an enzyme, by the binding
of a product to a regulatory site on the enzyme?
A.enzyme repression
B.competitive inhibition
C.enzyme induction
D.noncompetitive inhibition
E.None of the choices is correct.

24. Learning Outcomes: Section 7.2
6.Name the chemical in which energy is stored in cells.
7.Create a general diagram of a redox reaction.
8.Identify electron carriers used by cells.

25. Energy in Cells
•Energy is managed in the form of chemical reactions
that involve the making and breaking of bonds and the
transfer of electrons
•Exergonic reactions release energy, making it available
for cellular work
•Endergonic reactions are driven forward with the
addition of energy
•Exergonic and endergonic reactions are often coupled
so that released energy is immediately put to work

26. Oxidation and Reduction
•Oxidation:loss of electrons
-when a compound loses electrons, it is oxidized
•Reduction: gain of electrons
-when a compound gains electrons, it is reduced
•Oxidation-reduction (redox) reactions are common in
the cell and are indispensable to the required energy
transformations

27. Oxidation and Reduction (cont’d)
•Oxidoreductases:enzymes that remove electrons from
one substrate and add them to another
-their coenzyme carriers are nicotinamide
adenine dinucleotide (NAD) and flavin adenine
dinucleotide (FAD)
•Redox pair:an electron donor and an electron acceptor
involved in a redox reaction

28. Oxidation and Reduction (cont’d)
•Energy present in the electron acceptor can be
captured to phosphorylate(add an inorganic
phosphate) to ADP or to some other compound to store
energy in ATP
•The cell does not handle electrons as discrete entities
but rather as parts of an atom such as hydrogen
(consisting of a single electron and a single proton)
•Dehydrogenation:the removal of hydrogen during a
redox reaction

29. Electron Carriers: Molecular Shuttles
•Electron carriers resemble shuttles that are alternately loaded and unloaded,
repeatedly accepting and releasing electrons and hydrogens to facilitate transfer of
redox energy
H
+
P
P
P
P
H
++NAD
+ NAD H
Reduced Nicotinamide
From substrate
Oxidized Nicotinamide
Adenine
Ribose
NH
2
2H
2e:
H
C
C C
CC
O
C
H
NH
2
H
C
C C
CC
O
C
N N

30. ATP: Metabolic Money
•Three-part molecule
-nitrogen base (adenine)
-5-carbon sugar (ribose)
-chain of three phosphate
groups bonded to ribose
-phosphate groups are
bulky and carry negative
charges, causing a strain
between the last two
phosphates
-the removal of the terminal
phosphate releases energy
N
N
N
N N
H H
H
H
O
HH
H H
O
O
O
O
P O
O
H
HPP
Adenine
Adenosine
Adenosine
Diphosphate
(ADP)
Adenosine
Triphosphate
(ATP)
HO
OH OH OH
OH
Ribose
OH
Bond that releases
energy when broken
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31. PRACTICE QUESTIONS
Name three basic catabolic pathways, and give an estimate of
how much ATP each of them yields.
Write a summary statement describing glycolysis.
Describe the Krebs cycle.
Discuss the significance of the electron transport system.
Point out how anaerobic respiration differs from aerobic
respiration.
Provide a summary of fermentation.

32. Catabolism
•Metabolism uses enzymesto catabolizeorganic
molecules to precursor moleculesthat cells then use to
anabolizelarger, more complex molecules
•Reducing power:electrons available in NADH and
FADH
2
•Energy:stored in the bonds of ATP
-both are needed in large quantities for anabolic
metabolism
-both are produced during catabolism

33. Overview of the Three Main Catabolic Pathways
Fermentation
ANAEROBIC RESPIRATION FERMENTATION
ATP ATP
AEROBIC RESPIRATION
CO
2
NAD H
ATP
CO
2
NAD H
ATP
NAD H
CO
2
ATP
FADH
2
Using organic
compounds as
electron acceptor
Electron Transport System Electron Transport System
Alcohols, acids
2 ATPs2–36 ATPs36–38 ATPsMaximum net yield
Yields variable
amount of
energy
Yields 2 GTPs
Yields 2 ATPs
CO
2
NAD H
ATP
NAD H
FADH
2 ATP
CO
2
Krebs
Cycle
Krebs
Cycle
Using O
2 as electron acceptor Using non-O
2 compound as electron acceptor
(So
4
2–
, NO
3–, CO
3
2–
)
Glycolysis Glycolysis Glycolysis

34. Getting Materials and Energy
•Nutrient processing in bacteria is extremely varied, but
in most cases the nutrient is glucose
•Aerobic respiration
-a series of reactions that converts glucose to
CO
2and allows the cell to recover significant
amounts of energy
-utilizes glycolysis, the Krebs cycle, and the
electron transport chain
-relies on free oxygen as the final electron and
hydrogen acceptor
-characteristic of many bacteria, fungi, protozoa,
and animals

35. Getting Materials and Energy (cont’d)
•Anaerobic respiration
-used by strictly anaerobic organisms and those who
are able to metabolize with or without oxygen
-involves glycolysis, the Krebs cycle, and the electron
transport chain
-uses NO
3
-
, SO
4
2-
, CO
3
3-
, and other oxidized
compounds as final electron acceptors
•Fermentation
-incomplete oxidation of glucose
-oxygen is not required
-organic compounds are final electron acceptors

36. Glycolysis
•Turns glucose into pyruvate, which yields energy in the pathways that
follow
One reaction breaks fructose-1,6-diphosphate
into two 3-carbon molecules.
Five reactions convert each 3 carbon molecule
into the 3C pyruvate.
Pyruvate is a molecule that is uniquely suited for chemical
reactions that will produce reducing power (which will
eventually produce ATP).
C C C C C C
Fructose-1, 6-diphosphate
C C C C C C
C C CC C C
C C CC C C
Glycolysis
Energy Lost or Gained
Uses 2 ATPs
Overview Details
Three reactions alter and rearrange the
6-C glucose molecule into 6-C fructose-1,6
diphosphate.
Yields 4 ATPs and 2 NADHs
Total Energy Yield: 2 ATPs and
2 NADHs
Glucose
Pyruvate Pyruvate

37. The Krebs Cycle (Citric Acid Cycle):
A Carbon and Energy Wheel
•After glycolysis, pyruvic acid is still energy-rich
•cytoplasm of bacteria and mitochondrial matrix of eukaryotes
-a cyclical metabolic pathway that begins with acetyl CoA,
which joins with oxaloacetic acid, and then participates in
seven other additional transformations
-transfers the energy stored in acetyl CoA to NAD
+
and FAD
by reducing them (transferring hydrogen ions to them)
-NADH and FADH
2carry electrons to the electron transport
chain
-2 ATPs are produced for each molecule of glucose
through phosphorylation

38. The Krebs Cycle
Each acetyl CoA yields 1 GTP, 3 NADHs,
1 FADH, and 2 CO
2molecules.
Total Yield per 2 acetyl CoAs:
CO
2: 4
In the course of seven more
reactions, citrate is manipulated
to yield energy and CO
2and
oxaloacetate is regenerated.
Intermediate molecules on the
wheel can be shunted into other
metabolic pathways as well.
In the first reaction, acetyl CoA
donates 2Cs to the 4C molecule
oxaloacetate to form 6C citrate.
C C C
Energy: 2 GTPs, 6 NADHs, 2 FADHs
Pyruvate
CC CC CC
Details
The Krebs Cycle
Energy Lost or Gained Overview
Pyruvate
The 3C pyruvate is converted to
2C acetyl CoA in one reaction.
Other
intermediates GTP
CO
2
CO
2
Yields:
3 NADHs
1 FADH
2
Citrate
Oxaloacetate
Acetyl CoA
Remember: This
happens twice for
each glucose
molecule that
enters glycolysis.
One CO
2 is liberated and one NADH is
formed.
C C C C
C C C C C C
C CC

39. The Respiratory Chain: Electron Transport
•A chain of special redox carriers that receives reduced
carriers (NADH, FADH
2) generated by glycolysis and the
Krebs cycle
-passes them in a sequential and orderly fashion
from one to the next
-highly energetic
-allows the transport of hydrogen ions outside
of the membrane
-in the final step of the process, oxygen accepts
electrons and hydrogen, forming water

40. The Respiratory Chain: Electron Transport (cont’d)
•Principal compounds in the electron transport chain:
-NADH dehydrogenase
-flavoproteins
-coenzyme Q (ubiquinone)
-cytochromes
•Cytochromescontain a tightly bound metal ion in their
center that is actively involved in accepting electrons and
donating them to the next carrier in the series

41. The Respiratory (Electron Transport) Chain
Reduced carriers (NADH, FADH) transfer electrons and H
+
to first
electron carrier in chain: NADH dehydrogenase.
These are then sequentially transferred to the next four to six
carriers with progressively more positive reduction potentials.
The carriers are called cytochromes. The number of carriers varies,
depending on the bacterium.
Simultaneous with the reduction of the electron carriers,
protons are moved to the outside of the membrane, creating a
concentration gradient (more protons outside than inside the
cell). The extracellular space becomes more positively charged
and more acidic than the intracellular space. This condition
creates the proton motive force, by which protons flow down the
concentration gradient through the ATP synthase embedded in the
membrane. This results in the conversion of ADP to ATP.
Once inside the cytoplasm, protons combine with O
2to
form water (in aerobic respirers [left]), and with a variety of
O-containing compounds to produce more reduced compounds.
Anaerobic respiration yields less per NADH and FADH.
Aerobic respiration yields a maximum of 3 ATPs per
oxidized NADH and 2 ATPs per oxidized FADH.
The Respiratory (Electron Transport) Chain
Anaerobic
respirers
Aerobic
respirers
Cytoplasm
H
2O
NO
2
–
HS
–
O
2
H
+
Cell
membrane
With ETS
Cell wall
H
+
H
+
H
+
H
+
H
+
H
+
H
+
H
+
H
+
H
+
H
+
H
+
H
+
H
+
Cytochromes
NAD H
ATPADP
ATP
synthase
NO
3
–
SO
4
2–

42. The Electron Transport Chain (cont’d)
•Electron transport carriers and enzymes are embedded in the cell
membrane in prokaryotes and on the inner mitochondrial membrane
in eukaryotes
Intermembrane
space
Cristae
H
+
ions

43. The Electron Chain (cont’d)
•Released energy from electron carriers in the electron
transport chain is channeled through ATP synthase
•Oxidative phosphorylation:the coupling of ATP
synthesis to electron transport
-each NADH that enters the electron transport
chain can give rise to 3 ATPs
-Electrons from FADH
2enter the electron transport
chain at a later point and have less energy to
release, so only 2 ATPs result

44. The Terminal Step
•Aerobic respiration
-catalyzed by cytochrome aa
3, also known as
cytochrome oxidase
-adapted to receive electrons from cytochrome c,
pick up hydrogens from solution, and react with
oxygen to form water
2H
+
+ 2e
-
+ ½ O
2H
20

45. The Terminal Step (cont’d)
•Most eukaryotes have a fully functioning cytochrome
system
•Bacteria exhibit wide-ranging variations in this system
-some lack one or more redox steps
-several have alternative electron transport
schemes
-lack of cytochrome coxidase is useful in
differentiating among certain genera of bacteria

46. The Terminal Step (cont’d)
•A potential side reaction of the respiratory chain is the
incomplete reduction of oxygen to the superoxide ion
(O
2
-
) and hydrogen peroxide (H
2O
2)
•Aerobes produce enzymes to deal with these toxic
oxygen products
-superoxide dismutase
-catalase
-Streptococcuslacks these enzymes but still
grows well in oxygen due to the production of
peroxidase

47. The Terminal Step (cont’d)
•Anaerobic Respiration
-the terminal step utilizes oxygen-containing ions,
rather than free oxygen, as the final electron
acceptor
Nitrate reductase

NO
3
-
+ NADH NO
2
-
+ H
2O + NAD
+
•Nitrate reductasecatalyzes the removal of oxygen from
nitrate, leaving nitrite and water as products

48. Anaerobic Respiration (cont’d)
•Denitrification
-some species of Pseudomonas and Bacillus
possess enzymes that can further reduce
nitrite to nitric oxide (NO), nitrous oxide (N
2O),
and even nitrogen gas (N
2)
-important step in recycling nitrogen in the
biosphere
•Other oxygen-containing nutrients reduced
anaerobically by various bacteria are carbonates and
sulfates
•None of the anaerobic pathways produce as much
ATP as aerobic respiration

49. After Pyruvic Acid II: Fermentation
•Fermentation
-the incomplete oxidation of glucose or other
carbohydrates in the absence of oxygen
-uses organic compounds as the terminal
electron acceptors
-yields a small amount of ATP
-used by organisms that do not have an electron
transport chain
-other organisms revert to fermentation when
oxygen is lacking

50. Fermentation (cont’d)
•Only yields 2 ATPs per molecule of glucose
•Many bacteria grow as fast as they would in the
presence of oxygen due to an increase in the rate of
glycolysis
•Permits independence from molecular oxygen
-allows colonization of anaerobic environments
-enables adaptation to variations in oxygen
availability
-provides a means for growth when oxygen
levels are too low for aerobic respiration

51. Fermentation (cont’d)
•Bacteria and ruminant cattle
-digest cellulose through fermentation
-hydrolyze cellulose to glucose
-ferment glucose to organic acids which are absorbed
as the bovine’s principal energy source
•Human muscle cells
-undergo a form of fermentation that permits short
periods of activity after the oxygen supply has been
depleted
-convert pyruvic acid to lactic acid, allowing
anaerobic production of ATP
-accumulated lactic acid causes muscle fatigue

52. Fermentation
Pyruvic acid from glycolysis can itself become the electron
acceptor.
Pyruvic acid can also be enzymatically altered and then serve as
the electron acceptor.
The NADs are recycled to reenter glycolysis.
The organic molecules that became reduced in their role as
electron acceptors are extremely varied, and often yield useful
products such as ethyl alcohol, lactic acid, propionic acid,
butanol, and others.
CC
O
H
H
H
H
CC C
H
H
H
H
O
C C
H
H
H
H
H
C C C
Lactic acid
OH
OH
NAD
+
Ethyl alcohol
OH
Acetaldehyde
CO
2
Pyruvic acid
Remember: This
happens twice for
each glucose
molecule that
enters glycolysis.
Fermentation
NAD H NAD H

53. Products of Fermentation in Microorganisms
•Alcoholic beverages: ethanol and CO
2
•Solvents: acetone, butanol
•Organic acids: lactic acid, acetic acid
•Vitamins, antibiotics, and hormones
•Large-scale industrial syntheses by microorganisms
often utilize entirely different fermentation
mechanisms for the production of antibiotics,
hormones, vitamins, and amino acids

54. Catabolism of Noncarbohydrate Compounds
•Complex polysaccharides broken into component
sugars, which can enter glycolysis
•Lipids broken down by lipases
-glycerol converted to dihydroxyacetone
phosphate, which can enter midway into
glycolysis
-fatty acids undergo beta oxidation, whose
products can enter the Krebs cycle as acetyl CoA

55. Catabolism of Noncarbohydrate Compounds
(cont’d)
•Proteins are broken down into amino acids by
proteases
-amino groups are removed through
deamination
-remaining carbon compounds are converted
into Krebs cycle intermediates or decarboxylated

56. Anabolism:
Formation of Macromolecules
•Two possible sources for monosaccharides, amino
acids, fatty acids, nitrogenous bases, and vitamins
-enter the cell from the outside as nutrients
-can be synthesized through various cellular
pathways

57. Anabolism:
Formation of Macromolecules (cont’d)
•The degree to which an organism can synthesize its
own building blocks is genetically determined and varies
from group to group
-autotrophs only require CO
2as a carbon source
and a few minerals to synthesize all cell
substances
-some heterotrophs such as E. colican
synthesize all cellular substances from a few
minerals and one organic carbon source such as
glucose