CHAPTER 6

6.1 Elements of life

o A) Macromolecules
O, H, N, S, P ,C
K, Ca, Mg, Fe, Na+, K+
o B) Micromolecules
Mn, K+, Zn(transcript factor), Co, Mo, Ni, Cu
Make up enzymes and cofactors
Table 6.1

MOLECULE
Proteins
Lipids
Carbs
Nucleic acids

Elements
CHONS
CHOP
CHO
CHOPN

6.2
o

2 main functions of electrons

Energy (E- move through ETC to provide energy )
Reduce Molecules (in biosynthesis so that they can form organic molec)
Carbon
Description: Energy
Description
Electron
Description
Sources
Sources
Sources
Autotrophs
CO2 sole
Phototrophs
Light
Lithotrophs
Reduced
carbon
inorganic esource
source
Heterotrophs Preformed
Chemotrophs Oxidation
Organotrophs Organic
organic
organic or
molec emolec
inorganic
source
o

Cometabolism= digests pesticides. Degraded in presence of growth promoting nutrient

that is digested also
6.3 Nutritional Types of Microorganisms
o 2 main sources of energy
1) light
2) oxidizing organic or inorganic

Table 6.3- 5 Major Nutritional Types of Microorganisms

NUTRITIONAL TYPE
CARBON
ENERGY
ELECTRON
SOURCE
SOURCE
SOURCE
Photolithoautotroph
CO2
Light
Inorganic

Photoorganoheterotroph
Chemolithoautotroph***

Chemolithoheterotroph

Preformed
organic C
CO2

Preformed
Organic C
Chemoorganoheterotroph Preformed
Organic C

Light

Organic

Inorganic

Inorganic

Inorganic

Inorganic

Organic

Organic

EXAMPLES
Cyanobactiera
Sulfur bacteria
Diatoms
Green non sulfur
bacteria
Nitrifying bacteria
Iron-oxidizing
bacteria
Methanogens
Sulfur oxidizing
bacteria
Sulfur oxidizing
bacteria
Nonphotosynthetic
microbes
Pathogenic
microbes

o
6.4 Nitrogen, Phosphorus, Sulfur
o 3 Main elements necessary for microbial growth
Sulfur, Phosphate, & Nitrogen
o Nitrogen
Synthesize amino acid
Can be obtained from either organic or inorganic sources (Nitrate)
Enzymes used: Glutamate dehydrogenase, glutamine synthesis, glutamate
synthase (Ch 11)
Processes: assimilatory nitrate reduction & Nitrogen fixation [N2 NH3]
(Ch 11)
o Sulfur
Nitrogen can be obtained from organic or inorganic sources
Synthesize: methionine & cysteine
o Phosphorus
Can only be obtained from inorganic sources, produced in periplasm

o
6.5 Growth Factors
o Definition= organic compounds that cannot be synthesized by an organism but are
essential for its growth
3 major types growth factors/Cofactors????:
1) amino acids
o Used for protein synthesis

2) purines & pyrimidines

o Used for Nucleic acid synthesis
3) vitamins
o Small organic molecules that make up coenyzmes
NOTE: molec function as coenzymes NOT cofactors
o Fun fact: microbes synthesize growth factor: vitamin for human consumption
ie: riboflavin, vitamin B12
6.6 Uptake of Nutrients
o Bacteria & Archaea take up nutrients via:
1)Facilitated Diffusion
Permeases= carrier proteins, embedded in plasma membrane
o Selective
o Carrier proteins experience a saturation effect
o Only transport closely related solutes
o Example: BACTERIA: aquaporins (Claudio says not selective) &
ARCHAEA & EUKARYOTES most prominent
o No metabolic energy
Diffusion across selectively permeable membrane via carrier proteins
2) active transport
o Solute moves against concentration gradient
o Used often by microbes
o 2 types of active transport proteins:
A) Primary Transporter
Energy from ATP hydrolysis
ATP-Binding Cassette Transporters (ABC
transporters)
o Uniport= single molecule transported
via ABC transporters

B) Secondary Transporter
Energy from PE of ion gradient
Antiport= sodium move out, proton move
insubstance move in opposite direction
Symport= proton & lactose simultaneously
enter cellsubstance linked move in same
direction
3) Group translocation
o
o Passive Diffusion
High concentration Low concentration
O2, CO2, H2O move via this method
No metabolic energy required
o

CHAPTER 11

11.1 Principles of Biosynthesis

1) Macromolecules synthesized from limited monomers
Save genetic storage capacity, biosyn raw materials, energy
2) Many have same enzymes for both catabolic & anabolic
Saves materials & energy
3) Some enzymes are irreversible
Allow independent regulation
Although many same enzymes, catabolic & anabolic pathways not
identical permits independent regulation
4) Anabolic pathways must operate irreversibly to be efficient
Couple ATP & drive biosynthesis to completion
5) Catabolism & Anabolism are physically separated
only eukaryotes are anabolic/catabolic rxns in separate compartments
(since they have membrane bound organelles)
Prokaryotes utilize carboxysomes
6) Catabolism & anabolism use different cofactors
Catabolism: NADH
ANABOLISM: NADPH
o Metabolism 2 components:
anabolism
ATP | NADPH | precursor metabolites
synthesize cell components
require energy, use energy from catabolic reactions
catabolism
degrades, produce energy
o Supramolecular systems & organelles= macromolecules assemble into supramolecular
structures spontaneous via self-assembly (ie: ribosomes)
Prototroph= synthesize own precursor metabolites, bacteria have no nutritional requirement
Auxotroph= special requirements for metabolites, bacteria have 1+ nutritional requirement
11.2 Precursor Metabolites
o Central metabolic pathways
Embden Meyerhof
Pentose phosphate
Entner Doudoroff
EMP (Embden)
PP (Pentose)
EDP (Entner)
TCA
Pentose-5-phosphate
Purines &
(PP)
pyrimidine
Purinesvitamins
& cofactors
Glucose-6-phosphate

Sugar nucleotides

Pentose 5 phosphate

Fructose 6 phosphate

Fructose 6 phosphate
Amino sugars

Dihydroxyacetonephosphate

Dihydroxyacetonephosphate
Sedoheptulose-7phosphate

Nicotinamide coenzymes &

glycerol-3phosophatephospholipids
Fructose-6phosphate

Erythros-4-phosphate

Fructose-6phosphate

3-Phosphoglycerate

(3CPHASE)
Serine family
(tryptophan, glycine,
cysteine)

Heptose in LPS
Erythros-4phosphate
Aromatic family
(tyrosine &
tryptophan) &
vitamins|cofactors
(ubiquinone)

Phosphoenolpyruvate
Phosphoenolpyruvate Serine family
(tryptophan, glycine,
cysteine)
Pyruvate

Pyruvate family
(leucine, alanine)

Acetyl Coenzyme A

Fatty acid, murein,

leucine

Oxaloacetate

2-oxoglutarate

Succinyl coenzyme A

o
11.3 CO2 Fixation via Autotrophs Energetically expensive
o 1) Calvin cycle

Oxaloacetate

Acetyl
coenzyme A

Asparate
Family
Methionine
Glutamate
fam
-glutamate
-glutamine
heme
heme

Reverse of EMP
3ATP & 2NADPH/ 1 CO2 | total: 3x6=18ATP, 2x6=12NADPH, 6 carbons
Also called reductive pentose phosphate
Archaea dont use calvin cycle
EUKARYOTES= occur stroma
BACTERIA= occur carboxysomes
3 phases
1) carboxylation phase
2)reduction phase
3)Regeneration phase
CarboxylationReduction PhaseRegeneration Phase

Rubulose 1,5 biphosphate (RuBP)enzyme [split spontaneously to PGA] catalyze CO2 RuBP2 PGA-
o
o
o
o
o
o
o

2)reductive TCA cycle

3) acetyl-CoA pathway
4)hydroxypropionate cycle
5)????
6)???