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Engineering of Biological Processes Lecture 1: Metabolic pathways . Mark Riley, Associate Professor Department of Ag and Biosystems Engineering The University of Arizona, Tucson, AZ 2007. Objectives: Lecture 1. Develop basic metabolic processes Carbon flow Energy production.

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engineering of biological processes lecture 1 metabolic pathways

Engineering of Biological ProcessesLecture 1: Metabolic pathways

Mark Riley, Associate Professor

Department of Ag and Biosystems Engineering

The University of Arizona, Tucson, AZ

2007

objectives lecture 1
Objectives: Lecture 1
  • Develop basic metabolic processes
  • Carbon flow
  • Energy production
slide3

Cell as a black box

Cell

Inputs

Outputs

Sugars

Amino acids

Small molecules

Oxygen

CO2, NH4, H2S, H2O

Energy

Protein

Large molecules

metabolic processes
Metabolic processes
  • Catabolic = Breakdown:
    • generation of energy and reducing power from complex molecules
      • produces small molecules (CO2, NH3) for use and as waste products
  • Anabolic = Biosynthesis:
    • construction of large molecules to serve as cellular components such as
      • amino acids for proteins, nucleic acids, fats and cholesterol
      • usually consumes energy
inputs cellular nutrients
Inputs (cellular nutrients)
  • Carbon source
    • sugars
      • glucose, sucrose, fructose, maltose
      • polymers of glucose: cellulose, cellobiose
  • Nitrogen
    • amino acids and ammonia
  • Energy extraction:
    • oxidized input → reduced product
    • reduced input → oxidized product
other inputs to metabolism
Other inputs to metabolism

Compounds General reaction Example of a species

carbonate CO2 → CH4Methanosarcina barkeri

fumarate fumarate → succinate Proteus rettgeri

iron Fe3+ → Fe2+Shewanella putrefaciens

nitrate NO3- → NO2-Thiobacillus denitrificans

sulfate SO42+ → HS-Desulfovibrio desulfuricans

energy currency
Energy currency
  • ATP Adenosine triphosphate
  • NADH Nicotinamide adenine dinucleotide
  • FADH2 Flavin adenine dinucleotide
  • The basic reactions for formation of each are:
  • ADP + Pi → ATP
  • AMP + Pi → ADP
  • NAD+ + H+ → NADH
  • FADH + H+ → FADH2
redox reactions of nad nadh nicotinamide adenine dinucleotide
Redox reactions of NAD+ / NADHNicotinamide adenine dinucleotide

O

O

H

H

H

CNH2

CNH2

+ H+

+ 2 e-

N+

N

R

R

NAD+

NADH

NAD+ is the electron acceptor in many reactions

slide11

NADH

NADH

CO2+NADH

GTP

CO2+NADH

GDP+Pi

FADH2

Glycolysis

Glucose

Glucose 6-Phosphate

Fructose 6-Phosphate

Dihydroxyacetone phosphate

Fructose 1,6-Bisphosphate

Glyceraldehyde 3-Phosphate

2-Phosphoglycerate

Phosphoenolpyruvate

Pyruvate

TCA cycle

Acetyl CoA

Acetate

Citrate

Oxaloacetate

Isocitrate

Malate

a-Ketoglutarate

Fumarate

Succinate

glycolysis
Glycolysis
  • Also called the EMP pathway (Embden-Meyerhoff-Parnas).
  • Glucose + 2 Pi + 2 NAD+ + 2 ADP →
  • 2 Pyruvate + 2 ATP + 2 NADH + 2H+ + 2 H2O
  • 9 step process with 8 intermediate molecules
  • 2 ATP produced / 1 Glucose consumed
  • Anaerobic
pyruvate dehydrogenase
Pyruvate dehydrogenase

Co-enzyme A,

carries acetyl groups

(2 Carbon)

  • pyruvate + NAD+ + CoA-SH →
  • acetyl CoA + CO2 + NADH + H+
  • Occurs in the cytoplasm
  • Acetyl CoA is transferred into the mitochondria of eukaryotes
citric acid cycle
Citric Acid Cycle
  • The overall reaction is:
  • Acetyl-CoA + 3 NAD+ + FAD + GDP + Pi + 2 H2O →
  • 3 NADH + 3H+ + FADH2 + CoA-SH + GTP + 2 CO2
  • 2 ATP (GTP) produced / 1 Glucose consumed
  • Anaerobic
oxidative phosphorylation respiration
Oxidative phosphorylation – (respiration)
  • Electrons from NAD and FADH2 are used to power the formation of ATP.
  • NADH + ½ O2 + H+ → H2O + NAD+
  • ADP + Pi + H+ → ATP + H2O
  • 32 ATP produced / 1 Glucose consumed
  • Aerobic
overall reaction
Overall reaction
  • Complete aerobic conversion of glucose
  • Glucose + 36Pi + 36 ADP + 36 H+ + 6O2→
  • 6 CO2 + 36 ATP + 42 H2O
products of anaerobic metabolism of pyruvate
Products of anaerobic metabolism of pyruvate

Succinate

Acetyl CoA

Acetate

Lactate

Malate

Ethanol

Pyruvate

Oxaloacetate

Acetaldehyde

Acetolactate

Acetoacetyl CoA

Formate

CO2

Acetoin

Butanol

H2

Butylene glycol

Butyrate

fermentation
Fermentation
  • No electron transport chain (no ox phos).
  • Anaerobic process
  • Glucose (or other sugars) converted to
  • lactate, pyruvate, ethanol, many others
  • Energy yields are low. Typical energy yields are 1-4 ATP per substrate molecule fermented.
  • In the absence of oxygen, the available NAD+ is often limiting. The primary purpose is to regenerate NAD+ from NADH allowing glycolysis to continue.
slide19

NADH

NADH

CO2+NADH

GTP

CO2+NADH

GDP+Pi

FADH2

Glycolysis

Glucose

Glucose 6-Phosphate

Fructose 6-Phosphate

Dihydroxyacetone phosphate

Fructose 1,6-Bisphosphate

Glyceraldehyde 3-Phosphate

2-Phosphoglycerate

Phosphoenolpyruvate

Pyruvate

Lactate

TCA cycle

Acetyl CoA

Acetate

Ethanol

Citrate

Oxaloacetate

Isocitrate

Malate

Fermentation

a-Ketoglutarate

Fumarate

Succinate

slide20

Lactate

CH3CHOHCOO

NAD+

NADH

Glycolysis

Glucose

C6H12O6

Pyruvate

CH3CCOO

CO2 + H2O

O

O2

H+

Ethanol

CH3CH2OH

CO2

NAD+

Acetaldehyde

CHOCH3

NADH

types of fermentation
Types of fermentation
  • Lactic acid fermentation (produce lactate)
    • Performed by:
      • Lactococci, Leuconostoc, Lactobacilli, Streptococci, Bifidobacterium
      • Lack enzymes to perform the TCA cycle. Often use lactose as the input sugar (found in milk)
  • Alcoholic fermentation (produce ethanol)
alcoholic fermentation
Alcoholic fermentation
  • Operates in yeast and in several microorganisms
  • Pyruvate + H+ ↔ acetaldehyde + CO2
  • Acetaldehyde + NADH + H+ ↔ ethanol + NAD+
  • Reversible reactions
  • Acetaldehyde is an important component in many industrial fermentations, particularly for food and alcohol.
yeasts
Yeasts
  • Only a few species are associated with fermentation of food and alcohol products, leavening bread, and to flavor soups
    • Saccharomyces species
    • Cells are round, oval, or elongated
    • Multiply by budding
cell metabolism
Cell metabolism

If no oxygen is available

Glucose → lactic acid + energy

C6H12O6 2 C3H6O3 2 ATP

Anaerobic metabolism

Lactic acid fermentation

Alcoholic fermentation

cell metabolism25
Cell metabolism

Glucose + oxygen → carbon dioxide + water + energy

C6H12O6 6 O2 6 CO2 6H2O 36 ATP

If plenty of oxygen is available

Aerobic metabolism

summary of metabolism
Summary of metabolism
  • Pathway NADH FADH2 ATP Total ATP (+ ox phos)
  • Glycolysis 2 0 2 6
  • PDH 2 0 0 6
  • TCA 6 2 2 24
  • Total 10 2 4 36
  • or,
  • Fermentation 1-2 0 0-2 1-4