Micro Chapter 8: Microbial Metabolism

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Metabolism

Back 1

All chemical reactions and physical workings of the cell

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Anabolism

Back 2

also called biosynthesis- any process that results in synthesis of cell molecules and structures (usually requires energy input). Builds things up.

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Catabolism

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the breakdown of bonds of larger molecules into smaller molecules (often release energy)

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What is one reason you need ATP?

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once you have it, then you can build things.
Slide #3

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Catalyst

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Lowers the amount of energy needed for reaction to take place. Does not get consumed in a reaction. Enzymes are catalysts.

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TRUE/FALSE
Catalysts have an active site for target molecules called substrates.

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TRUE
Most are specific, but not all.

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How do enzymes work?

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Speed up natural reactions.

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Substrates

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reactants
anything an enzyme acts on

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Enzyme structures

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Most are proteins.
Can be simple or conjugated.

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Simple enzymes

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consist of protein alone

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Conjugated enzymes

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Requires a cofactor to function.
Cofactors are either organic molecules or inorganic elements. Fig 8.2

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Apoenzymes

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Proteins levels of molecular complexity called the primary, secondary, tertiary, and quaternary organization

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What is the actual site where the substrate binds in a crevice or groove?

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Active site or catalytic site

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An enzyme is produced with a very specific function in mind, and therefore:

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For a reaction to take place, a temporary enzyme-substrate union must occur at the active site

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Type of cofactors:

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Metallic cofactors
Coenzymes

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Metallic Cofactors

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Include Fe, Cu, Mg, Mn, Zn, Co, Se
Metals activate enzymes, help bring the active site and substrate close together

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Coenzymes

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Organic compounds
Removes a chemical groups
Vitamins: one of the most important components of coenzymes

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Classification of Enzyme Functions

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Site of action
Type of action
Substrate (pretty common)

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Exoenzymes

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break down molecules OUTSIDE of the cell

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Endoenzymes

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break down molecules INSIDE of the cell

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Constitutive enzymes

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Always present and in relatively constant amounts.
Responsible for energy metabolism.

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Regulated enzymes

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production is either induced or repressed in response to a change in concentration of the substrate

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Oxidation

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compound loses electron (OIL)

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Reduction

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compound gains electron (RIG)

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Other transfer reactions by enzymes:

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Aminotransferases
Phosphotransferases
Methyltranferases
Decarboxylases

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The Sensitivity of Enzymes to Their Environment

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Enzymes generally operate only under the natural temperature, pH, and osmotic pressure of an organism’s habitat

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Chemically unstable enzymes are called:

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Labile

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Denaturation

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the weak bonds that maintain the native shape of the apoenzyme are broken

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Competitive inhibition

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The cell supplies a molecule that resembles the enzyme’s normal substrate, which then occupies and blocks the enzyme’s active site

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Noncompetitive inhibition

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The enzyme has two binding sites- the active site and the regulatory site; a regulator molecule binds to the regulatory site providing a negative feedback mechanism

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Enzyme repression

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stops further synthesis of an enzyme somewhere along its pathway. Enzyme not present.

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Enzyme induction

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Turns enzyme production on.

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Exergonic reaction

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a reaction that releases energy as it goes forward

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Endergonic reaction

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a reaction that is driven forward with the addition of energy

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TRUE/FALSE
Redox reactions always occur in pairs.

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TRUE
An electron donor and electron acceptor.

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Most common electron carrier

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NAD
e- carrier, fuels oxidative phosphorylation

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ATP is energy currency

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can be banked, saved, spent and exchanged

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The Molecular Structure of ATP

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Three-part molecule:
-Nitrogen base (adenine)
-5-carbon sugar (ribose)
-Chain of three phosphate groups

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Adenine Diphosphate + phosphate=

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Adenine Triphosphate (ATP)

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Oxidative phosphorylation

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Uses O2

Series of redox reactions occurring during the final phase of the respiratory pathway

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Photophosphorylation

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Sun-driven rxn

ATP is formed through a series of sunlight-driven reactions in phototrophic organisms

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Pathway

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a series of biochemical reactions

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Metabolism

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uses enzymes to catalyze reactions that break down (catabolize) organic molecules to materials (precursor molecules) that cells can then use to build (anabolize) larger, more complex molecules that are particularly suited to them.

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Reducing Power

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this plus energy are needed in large quantities for the anabolic parts of metabolism; they are produced during the catabolic part of metabolism

donate e-

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What is the frequently needed nutrient for catabolism?

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glucose

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Glycolysis

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Most common pathway to break down glucose

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3 major pathways:

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Aerobic respiration
Fermentation
Anaerobic respiration

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Aerobic respiration

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series of reactions that convert glucose to CO2 and allows the cell to recover significant amounts of energy

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Fermentation

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when facultative and aerotolerant anaerobes use only the glycolysis scheme to incompletely oxidize glucose
(supports glycolysis)

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Anaerobic respiration

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does not use molecular oxygen as the final electron acceptor

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Which pathway yields the most ATP?

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Aerobic Respiration (38)
Anaerobic Respiration (36)
Fermentation (2)

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What happens to electrons during aerobic respiration?

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they are transferred from fuel molecules to oxygen as a final electron acceptor.

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Pyruvic acid

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From glycolysis serves an important position in several pathways

Different organisms handle it in different ways

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Krebs cycle

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Takes place in the cytoplasm of bacteria and in the mitochondrial matrix in eukaryotes

Produces reduced coenzymes NADH and FADH2, 2 ATPs for each glucose molecule

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How many NADH do you get at end of glycolysis, Krebs Cycle, e- transport chain?

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Glycolysis: 2
Krebs: 8
e- transport: 0

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How many FADH2 do you get at end of glycolysis, Krebs Cycle, e- transport chain?

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Glycolysis: 0
Krebs: 2
e- transport: 2

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How many ATP do you get at end of glycolysis, Krebs Cycle, e- transport chain?

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Glycolysis: 2
Krebs: 2
e- transport: 38

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What product do you get at the end of e- transport chain?

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H2O

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Denitrification:

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when enzymes can further reduce nitrite to nitric oxide, nitrous oxide, and nitrogen gas- important in recycling nitrogen in the biosphere

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What is the single biggest advantage of fermentation?

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Permits independence from molecular oxygen

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Products of fermentation

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Alcoholic beverages
Organic acids
Dairy products
Vitamins, antibiotics, and even hormones

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Two general categories of fermentation products:

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Alcoholic fermentation
Acidic fermentation

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Alcoholic fermentation products:

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ethanol
CO2

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Acidic fermentation products:

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Lactic acid
Mixed acid
*extremely varied pathways

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Lactic acid

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bacteria ferment pyruvate and reduce it to lactic acid

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Mixed acid fermentation

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produces a combination of acetic, lactic, succinic, and formic acids and lowers the pH of a medium to about 4.0

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Proteases

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break proteins down to their amino acid components

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Deamination

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the way amino acid groups are removed from proteins

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Amphibolism

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take a catabolic pathway and make it an anabolic pathway (vice versa)

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gluconeogenesis

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new glucose formation

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How are fats degraded to acetyl?

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beta oxidation

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Amination

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Two metabolites of carbohydrate catabolism that the Krebs cycle produces are essential intermediates in the synthesis of amino acids

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Transamination

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Amino acids and carbohydrates can be interchanged

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Anabolism

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formation of macromolecules

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Carbohydrate Biosynthesis

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Several alternative pathways.

Cells can make the CHO they need.

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Amphibolism

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take a catabolic pathway and make it an anabolic pathway (vice versa)

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gluconeogenesis

Back 77

new glucose formation

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How are fats degraded to acetyl?

Back 78

beta oxidation

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Amination

Back 79

Two metabolites of carbohydrate catabolism that the Krebs cycle produces are essential intermediates in the synthesis of amino acids

Front 80

Transamination

Back 80

Amino acids and carbohydrates can be interchanged

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Anabolism

Back 81

formation of macromolecules

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Carbohydrate Biosynthesis

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Several alternative pathways.

Cells can make the CHO they need.

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Two phases of photosynthesis

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Light-dependent reactions

Light-independent reactions

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How is light absorbed for light-dependent reactions?

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Through photosynthetic pigments

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Photosynthetic pigments:

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Chlorophylls (green)
Carotenoids (yellow, orange, or red)
Phycobilins (red or blue-green)

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What do light dependent reactions generate?

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ATP (which can be used in light-independent reactions).

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What do light=independent reactions generate?

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Glucose

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Oxygenic photosynthesis

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oxygen-releasing

occurs in plants, algae, and cyanobacteria- dominant type on earth

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Anoxygenic photosynthesizers

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non-oxygen-producing

many are strict anaerobes

Front 90

Amphibolism

Back 90

take a catabolic pathway and make it an anabolic pathway (vice versa)

Front 91

gluconeogenesis

Back 91

new glucose formation

Front 92

How are fats degraded to acetyl?

Back 92

beta oxidation

Front 93

Amination

Back 93

Two metabolites of carbohydrate catabolism that the Krebs cycle produces are essential intermediates in the synthesis of amino acids

Front 94

Transamination

Back 94

Amino acids and carbohydrates can be interchanged

Front 95

Anabolism

Back 95

formation of macromolecules

Front 96

Carbohydrate Biosynthesis

Back 96

Several alternative pathways.

Cells can make the CHO they need.

Front 97

Two phases of photosynthesis

Back 97

Light-dependent reactions

Light-independent reactions

Front 98

How is light absorbed for light-dependent reactions?

Back 98

Through photosynthetic pigments

Front 99

Photosynthetic pigments:

Back 99

Chlorophylls (green)
Carotenoids (yellow, orange, or red)
Phycobilins (red or blue-green)

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What do light dependent reactions generate?

Back 100

ATP (which can be used in light-independent reactions).

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What do light-independent reactions generate?

Back 101

Glucose

Front 102

Oxygenic photosynthesis

Back 102

oxygen-releasing

occurs in plants, algae, and cyanobacteria- dominant type on earth

Front 103

Anoxygenic photosynthesizers

Back 103

non-oxygen-producing

many are strict anaerobes