BIOLOGICAL BASICS OF FERMENTATION INDUSTRIAL ENGINEERINGCELLS(The major categories of life are the animal kingdom, the plant kingdom, and the protist.

(Cells are the structural and functional units of living organisms.(All cells share some structural features.

*Cell membrane: being selectively permeable*Cytoplasm: most of the enzyme-catalyzed reactions of cell metabolism occur*Ribosomes: synthesis of proteins*Nucleus (or nuclear body): replication and storage of the genetic material

(Cells must have very small dimensions.((1) Effective diffusion of nutrient molecules

(2) Large ratio of the surface area of cells to volume

(There are two great classes of cells: prokaryotes and eucaryotes.

Prokaryotic: before the nucleus

(The genetic material is localized in a rather irregular nuclear body or nucleoid, which has no surrounding membrane.

Eukaryotic: well-formed nucleus

(Comparison of prokaryotic and eukaryotic cells:Prokaryotic CellsEukaryotic Cells

Size0.25 m in diameterMost are 1050 m in diameter

Containment of DNAFree in cytoplasm as nucleoidIn nucleus, condensed with proteins into multiple chromosomes

Ploidy (number of copies of the genetic information)Usually haploid ()Almost always diploid () or polyploid

Mechanism of cell replicationSimple division following DNA replicationMitosis () in somatic cells (), meiosis () in gametes ()

Internal compartmentationNoYes, with several different kinds of organells

GlossaryChromosomes (): structures that contain the nuclear DNA of a cellRibosomes (): intracellular structures composed of ribosomal RNA and protein, the sites where protein synthesis occursVacuole (,): a membrane-bound cavity within a cell that may function in digestion, secretion (), storage, or excretion ()Chloroplasts (): membrane-bound organelles of photosynthetic eucaryotes where the biochemical conversion of light energy to ATP occurs; the sites of photosynthesis in eukaryotic organismsNucleolus (): an RNA-rich intranuclear body not bounded by a limiting membrane that is the site of ribosomal RNA synthesis in eucaryotesLysosomes (): an organelle containing hydrolytic enzymes involved in autolytic and digestive processesGolgi apparatus (): a membranous organelle of eukaryotic organisms involved with the formation of secretory vesicles (,) and the synthesis of complex polysaccharidesMitochondria (): a semiautonomous () organelle found in eukaryotic cells, the site of respiration and other cellular processes, consisting of an outer membrane and an inner one that is convoluted ()Respiration (): a mode of energy-yielding metabolism requiring a terminal electron acceptor for substrate oxidation, with oxygen frequently used as the terminal electron acceptorEndoplasmic recticulum (): the extensive array of internal membranes in a eukaryotic cell involved in coordinating protein synthesis

(The protist is further divided into two categories: procaryotes and eucaryotes.

*Bacteria are members of a group of diverse and ubiquitous prokaryotic, single-celled organisms.

(Bacteria occur in a variety of shapes: coccispherical or ovoid; bacillicylindrical or rod-shaped; spirillahelically coiled

*Actinomycetes are members of an order of bacteria in which species are characterized by the formation of branching filaments and/or true filaments.*Blue-green algae (cyanobacteria): prokaryotic, photosynthetic organisms containing chlorophyll a, capable of evolving oxygen by the splitting of water.*Fungi are a group of diverse and widespread unicellular and multicellular eukaryotic organisms, lacking chlorophyll, usually bearing spores, and often filamentous.

*Molds are a type of fungus having a filamentous structure.

*Yeasts are a category of fungi defined in terms of morphological and physiological criteria, typically a unicellular, saprophytic organism that characteristically ferments a range of carbohydrates and in which asexual reproduction occurs by budding.*Algae: a heterogeneous group of eukaryotic, photosynthetic, unicellular, and multicellular organisms lacking true tissue differentiation.*Protozoa: diverse, eukaryotic, typically unicellular nonphotosynthetic microorganisms, generally lacking a rigid cell wall

(Microbial nomenclature follows the binomial system, for example, Bacillus subtilis.

*The first word is the name of the genus and the second word is the species name.

*The genus name is capitalized. When the same genus name is repeated several times, it is abbreviated, for example, B. subtilis.

*The names are given in Latin or are Latinized; they are always italicized.

*The genus names have meanings:

Bacillus: a small rod; Lactobacillus: a small milk rod; Micrococcus: a small grain; Clostridium: a small spindle; Pasteurella: after Louis Pasteur, Latinized; Salmonella: after Daniel E. Salmon, Latinized; Saccharomyces: sugar fungus.

BIOENERGETICS

(Living organisms require energy for growth and maintenance.

(The energy needs of all organisms are provided, directly or indirectly, by solar energy.

(Living organisms exchange energy and matter via the environment.

(Metabolic pathways are promoted by sequential enzyme systems.

* Linear pathway:

* Circular or cyclic pathway:

(Metabolism consists of catabolic (degradative) pathways and anabolic (biosynthetic) pathways.

(Catabolic pathways converge to a few end products.

( Biosynthetic (anabolic) pathways diverge to yield many products.

(There are important differences between corresponding catabolic and anabolic pathways.

(In the cell, energy is trapped in organic compounds with high-energy bonds.

(Adenosine triphosphate (ATP) is one of the most important high-energy compounds in cellular metabolism.

*Hydrolysis of ATP:

ATP + H2O ADP + HPO42G( = 7.3 kcal/mol

ADP + H2O AMP + HPO42G( = 7.3 kcal/mol

AMP + H2O Adenosine + HPO42G( = 3.4 kcal/mol

(It is common for the terminal phosphate only to be involved in reactions.

*Coupled reactions:

A + B C

C + D E

A + B + D E

*Analog compounds of ATP, such as GTP, UTP and CTP, also store and transfer high-energy phosphate bond, but not to the extent of ATP.

ELECTRON TRANSPORT

( Electron-transferring reactions are oxidation-reduction reactions.

(Free-energy changes accompany electron transfers.

wheren = number of electrons transferred

F = Faradays constant, 23.06 kcal mol1 volt1 or 96.5 kJ mol1 volt1

= standard potential difference, volt

* Electron transport from NADH to O2:

NADH ( NAD+ + H+ + 2e = +0.32 volt

O2 + 2H+ + 2e( H2O = +0.82 volt

NADH + H+ + O2 ( NAD+ + H2O = 1.14 volt

(G( = 2 ( 96.5 ( 1.14 = 220 kJ/mol

* Synthesis of ATP: ADP + Pi + H+ ( ATP + H2O G( = 30.5 kJ/mol

(How many moles of ATP are formed by oxidizing 1 mole of NADH or FADH2?

MAJOR METABOLIC PATHWAYS

Glycolysis

( 80% of the glucose used is broken down by glycolysis.

Overall equation:

Glucose + 2ADP + 2Pi + 2NAD+ ( 2 pyruvate + 2ATP + 2NADH

(Glycolysis has two phasesenergy investment phase and energy generation phase.

(The Entner-Doudoroff pathwaya variation of glycolysis

Overall equation:

Glucose + ADP + Pi + NAD + NADP

2 pyruvate + ATP + NADH + NADPH

(Pyruvate follows different catabolic pathways depending on the organism and the metabolic conditions.

(Ethanol production: Zymomonas mobilis (bacteria) versus Saccharomyces uvarum (yeast)

Citric Acid Cycle (or Tricarboxylic Acid Cycle)

(Provide both the carbon skeletons needed as starting materials in biosynthesis and the energy needed for the reactions.

StoichiometryGlycolysis: Glucose + 2ADP + 2Pi + 2NAD+ ( 2 pyruvate + 2ATP + 2NADH

Decarboxylation of pyruvate:

Pyruvate + NAD+ + CoA-SH ( acetyl-CoA + NADH + CO2

Citric acid cycle:

Acetyl-CoA + 3NAD+ + FAD + ADP + Pi

( 2CO2 + CoA-SH + 3NADH + 3H+ + FADH2 + ATP

Catabolism of glucose through glycolysis and citric acid cycle:

Glucose + 10NAD+ + 2FAD + 4ADP + 4Pi

( 6CO2 + 10NADH + 10H+ + 2FADH2 + 4ATP

[Problem] Yeast can grow both aerobically and anaerobically on glucose. When yeast, which has been maintained under anaerobic conditions, is exposed to oxygen, the rate of glucose consumption decreases. Why?

Anaerobically: energy production = 2ATP

Aerobically: energy production = 38ATP

The net result in the presence of O2 is a marked increase in the ATP/ADP ratio. This inhibits phosphofructokinase and thus decreases the amount of glucose utilized via glycolysis.

Glyoxalate Cycle

(The glyoxalate cycle is a modification of the citric acid cycle.

(In plants and microorganisms, the glyoxalate cycle converts fats to carbohydrates.

( The biosynthetic capacity is absent in animals.

Overall reaction:

2 Acetyl-CoA + NAD+ + 2 H2O

succinate + 2 CoA-SH + NADH + 3H+

Pentose Phosphate Pathway

(Serve four purposes: (1) production of NADPH, (2) synthesis of ribose phosphate, (3) production of ATP, and (4) synthesis of glucose.

(The pentose phosphate pathway operates in two phasesoxidative and nonoxidative.

(a) Oxidative phase: generation of reducing power as NADPH

(b) Nonoxidative phase: tailoring pentose phosphates to meet metabolic needs

(Balanced equations in pentose phosphate pathway:

* Generation of NADPH and ribose-5-phosphate

Glucose-6-phosphate + 2NADP+ ( ribose-5-phosphate + CO2 + 2NADPH + 2H+ * Conversion of pentose phosphate to six-carbon and three-carbon sugar phosphates

3 Pentose-5-phosphate ( 2 fructose-6-phosphate + glyceraldehyde-3-phosphate* Conversion of ribose-5-phosphate to glucose-6-phosphate

6 Ribose-5-phosphate +H2O ( 5 glucose-6-phosphate + Pi* Complete oxidation of one mole of hexose phosphate to CO2

Hexose-6-phosphate + 12NADP+ ( 6CO2 + 12NADPH + 12H+ + Pi

Biosynthesis of Amino Acids(The biosynthesis of the 20 L-amino acids found in proteins represents the formation of six families of related amino acids.

(Transamination is the essential process for the synthesis of all of the amino acids.

(1)-Ketoglutarate (in citric acid cycle) ( glutamate ( glutamine, proline, arginine

(2) Oxaloacetate (in citric acid cycle)( aspartate ( asparagines, methionine, threonine (( isoleucine), lysine

(3) 3-Phosphoglycerate (in glycolysis) ( serine ( cysteine, glycine

(4) Pyruvate (in glycolysis) ( alanine, valine, leucine

(5)Phosphoenolpyruvate (in glycolysis) + erythrose 4-phosphate (in pentose phosphate pathway) ( phenylalanine, tyrosine, tryptophan

(6) Ribose 5-phosphate (in pentose phosphate pathway) ( histidine

Catabolism of Amino Acids

(The turnover of protein within cells is surprisingly rapid.

( The halflifes of proteins vary from a few minutes to a few weeks.

( Enable a cell to respond quickly to changing metabolic conditions.

(Fates of amino acids released during protein turnover:

(1) Incorporated in new proteins

(2) Producing ATP

(3) Converted to carbohydrates or fatty acids

(The first phase in the degradation of most amino acids is deamination.

*Transfer of -amino groups is catalyzed by transaminases.

Lipid Metabolism

(Lipases can cleave the fatty acids from the glycerol portion of a triglyceride lipid molecule.

(Fatty acids are oxidized in two stages:

(1) -Oxidation to yield acetyl-CoA and ATP

Palmitoyl-S-CoA + 7CoA-SH + 35ADP + 35Pi + 7O2

( 8 acetyl-S-CoA + 35 ATP + 42H2O

(2) Oxidation of acetyl-CoA via the citric acid cycle

8 Acetyl-S-CoA + 96ADP + 96Pi + 16O2

( 16CO2 + 8CoA-SH + 96ATP + 104H2O

(Common reaction steps in the fatty acid oxidation cycle and citric acid cycle:

(Cells often follow the same enzyme reaction pattern for bringing about analogous metabolic reactions.(Acetyl-CoA has two possible fates:

(1) Being oxidized to CO2 via the citric acid cycle

(2) Being converted into ketone bodies to be circulated to the peripheral tissues

( The metabolism of aliphatic hydrocarbons is closely related to fatty acid metabolism.

(Fatty acid biosynthesis is not a simple reversal of -oxidation.

(The intermediates are bound to an acyl carrier protein (ACP or ACP-SH) rather than to CoA.

Acetyl-CoA + 7 malonyl-CoA + 14NADPH + 20H+

( CH3(CH2)14COO + 7CO2 + 8CoA-SH + 14NADP+ + 6H2O

A Summary of Metabolic Pathways

*Metabolic reactions can be classified in three major categories: fueling reactions, biosynthesis reactions, and polymerization reactions.

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