ch 12 anabolism: the use of energy in biosynthesis

Question 1

where does the calvin cycle occur?

Answer 1

in eukaryotes - stroma of chloroplasts
in cyanobacteria - some nitrifying bacteria and thiobacilli, may occur in carboxysomes

Question 2

3 phases of calvin cycle

Answer 2

carboxylation phase
reduction phase
regeneration phase
3 ATP and 2NADPH are used during the incorporation of 1 CO2

Question 3

carboxylation phase

Answer 3

enzyme ribulose 1,5-biphosphate carboxylase/oxygenase (RuBisCO) catalyzes the addition of CO2 to the 5-carbon molecules RuBP forming a 6-carbon intermediate that rapidly and spontaneously splits into two molecules of PGA

Question 4

reductive TCA cycle

Answer 4

alternative CO2 fixation pathway used by some autotrophs in the bacterial phyla aquificota, proteobacteria, nitrospirota, bacteroidata

Question 5

gluconeogenesis

Answer 5

synthesis of glucose-6-phosphate from noncarbohydrate precursors
shares enzymes with EMP
3 reactions catalyzed by 3 enzymes

Question 6

peptidoglycan synthesis

Answer 6

complex process involving UDP derivatives
bactoprenol phosphate used to transport NAG-NAM-pentapeptide units across cell membrane
final step, transpeptidation, creates cross-links btw the stem peptides on the peptidoglycan strand

Question 7

two ways ammonia is incorporated into the carbon skeleton

Answer 7

• reductive amination pathway: forms glutamate from alpha-ketoglutarate, catalyzed by glutamate dehydrogenase when ammonia conc is high, once glutamate has been synthesized the newly formed amino group can be transferred by transaminases to other carbon skeletons
• glutamine synthetase-glutamate synthase system: assimilate ammonia when levels are low, carboxyl group found in side chain of glutamate reacts with ammonia, and the incorporated nitrogen exists as amide in glutamine, then transfers to generate two glutamate molecules

Question 8

assimilatory nitrate reduction

Answer 8

used by bacteria to reduce nitrate to ammonia and the incorporate it into an organic form
nitrate reduction to nitrite catalyzed by nitrate reductase
- nitrite toxic to those without nitrite reductase (most eukaryotes)

Question 9

nitrogen fixation

Answer 9

the reduction of atmospheric gaseous nitrogen to ammonia
catalyzed by nitrogenase - requires a large ATP expenditure
- only carried out by a few bacteria and archaea (diazotrophs)

Question 10

assimilatory sulfate reduction

Answer 10

reduction of sulfate to sulfide then to hydrogen sulfide
sulfur needed for:
- synthesis of amino acids
- synthesis of several coenzymes
sulfur obtained from:
- either external source or intracellular amino acid reserves
- inorganic sulfate

Question 11

anaplerotic reactions

Answer 11

reactions that replenish depleted tricarboxylic acid cycle intermediates

Question 12

glyoxylate cycle

Answer 12

functions is some bacteria, fungi, and protists
need two enzymes: isocitrate lyase and malate synthase
modified TCA cycle - convert acetyl-CoA to oxaloacetate without the loss of the acetyl-coa carbons as CO2

Question 13

most common phosphorus sources

Answer 13

inorganic phosphate and organic molecules with a phosphoryl group

Question 14

phosphatases

Answer 14

hydrolyze organic phosphate-containing molecules to release inorganic phosphate
gram-negative bacteria have them in the periplasmic space, which allows phosphate to be taken up immediately after release
protists can directly use organic phosphates after ingestion of hydrolyze them in lysosomes and the incorporate the phosphate

Question 15

purine biosynthesis

Answer 15

complex pathway in which seven different molecules contribute parts to the final purine skeleton
- initial products are ribonucleotides
deoxyribonucleotides formed by reduction of nucleoside diphosphates or nucleoside triphosphates

Question 16

pyrimidine biosynthesis

Answer 16

begins with the carbon skeleton of aspartic acid and additional carbon and nitrogen atoms derived from bicarbonate and glutamine
- construction of pyrimidine ring is completed before ribose is attached

Question 17

fatty acid biosynthesis

Answer 17

synthesized from acetyl-coa, malonyl-coa, NADPH by fatty acid synthase complex
intermediates are attached to the acyl carrier protein
double bonds can be added either by using NADPH and O2 or by dehydrating hydroxy fatty acids

Question 18

sterols and isoprenoid lipids

Answer 18

sterols found in eukaryotic membranes
isoprenoid lipids (isoprenes) found in archaeal membranes
isoprenes made from two sterol pathway intermediates

Question 19

lipopolysaccharides

Answer 19

important component of the outer membrane of typical gram-negative bacteria
combines lipid and carbohydrate anabolic pathways
lipid-a core branch and o-antigen branch
current model suggest seven proteins (Lpt proteins) forms a path along which LPS moves from the plasma membrane across the aqueous periplasm