Chapter 15 microbiology

False

3-Hydroxypropionate cycle and acetyl-CoA pathway can be found in certain Eukaryotes. True or False?

D

All of the following statements about Rubisco are true EXCEPT: a)It is found in carboxysomes in many bacteria. b)It is one of the most prevalent proteins on Earth. c)It consists of small (S) and large (L) subunits. d)It catalyzes the addition of C O2 to xylulose 5 phosphate.

D

All of the following statements about fatty acid biosynthesis are true EXCEPT a)It involves successive condensations of b)malonyl-ACP. c)A dehydratase is used to generate an unsaturated bond. d)N A D H is generally involved in hydrogenation. e)The initial step involves addition of C O2 to acetyl-CoA.

heterocysts

Aquatic cyanobacteria make special _____ that help in nitrogen fixation

NADPH

Biosynthesis usually reduces the substrate, by ____ and by removing oxygen. Cell components such as lipids and amino acids are more reduced than substrates such as CO2 and acetate, so their biosynthesis requires a reducing agent such as _____

ATP; NADPH

Biosynthetic enzymes spend energy by coupling their reactions to the hydrolysis of ____, the oxidation of ____, or the flux of ions down a transmembrane gradient.

carbon concentrating mechanism

CO2 gas diffuses readily through phospholipid membranes, so the gas concentration problem is solved by some species through enzymatic conversion of CO2 into bicarbonate (HCO3-) which gets trapped in the cytoplasm, unable to leak out of the cell membrane. This process is called ____ and is used to regulate the Calvin cycle

Acetyl-CoA pathway

Certain anaerobic soil bacteria and Sulfur-reducing autotrophs use the _____ in carbohydrate synthesis

reverse TCA cycle

Certain bacteria can drive a catabolic pathway to the opposite direction to synthesize carbohydrates. The beginning of this cycle would be ______

3-Hydroxypropionate cycle

Chloroflexus (green filamentous) and some archaea use the _____ for carbohydrate synthesis

carboxysomes

Cyanobacteria use _____ for CO2 fixation

carboxylation and splitting; PGA

First step of the Calvin cycle is _______ : 6C --> 2[3C]; mediated by rubisco, ribulose 1,5-bisphosphate condenses with CO2 and H2O; rubisco generates a six carbon intermediate which immediately hydrolyzes to 2 molecules of _______, one of which contains the fixed CO2

essential elements, reduction, and energy

For all organisms, biosynthesis requires three things which are :

one molecule of G3P

For every three turns of the Calvin cycle, the cycle feeds ______ into biosynthesis

erythrose 4-phosphate

From the pentose phosphate pathway, ____ contributes to the ring structures of aromatic amino acids.

pyruvate carboxylase; PEP carboxykinase; fructose 1,6-biphosphatase; Glucose 6-phosphatase

Gluconeogenisis, the reverse glycolysis cycle, uses the same enzymes as glycolysis, except for TWO which are different at the beginning of the cycle. In the beginning: 2 pyruvate + _______ ---> 2 Oxaloacetate + ______ ----> 2 Phosphoenolpyrvuate + enolase ---> (2) 2-Phosphoglycerate + phosphoglycerate mutase --> (2) 3-Phosphoglycerate + phosphoglycerate kinase --> (2) 1,2-bisphosphoglycerate + glyceraldehyde phosphate dehydrogenase ---> (2) Glyceraldehyde 3-phosphate + triose phosphate isomerase <----> Dihydroxyacetone phosphate + aldolase ---> Fructose 1,6-bisphosphate + ______ --> Fructose 6-phosphate + phosphohexose isomerase ---> Glucose 6-phosphate + ______ ---> GLUCOSE

Reverse (or reductive) TCA cycle

Green sulphur bacteria use the _____ in carbohydrate synthesis

6

How many turns of the Calvin cycle does it take to feed one molecule of glyceraldehyde-3-phosphate into the biosynthesis of glucose?

Fatty acid synthesis

In _____ synthesis from acetyl CoA, Malonyl-CoA (C3) is used first, CoA replaced with ACP (acyl carrier protein), Oxidation→reduction cycle to add C, Two carbon chain per cycle (acetyl-CoA provide 2×C per cycle), 2×NADPH consumed per cycle

Anaplerotic reactions

In ________ intermediates in a pathway are regenerated

nitrogen; sulfur

In addition to carbon, biosynthesis must assimilate ____ and ____ for proteins, phosphorus for DNA, and metals for metal-containing enzymes

Calvin cycle

In each turn of the _____, one molecule of CO2 is condensed with the five-carbon sugar ribulose 1, 5-bisphosphate.

2e-; 2H+; 16

In nitrogen fixation: 1) The Fe protein transfers ____ to the Femo center (4 ATP used) 2) Femo protein binds ____ which are reduced to H2 gas and dissipate from the binding site (this step is necessary in order for N2 to bind) (4 ATP used) 3) ____ takes the place of H2 at the binding site (4 ATP used) 4) Successive pairs of H+ and electrons reduce N2--> HN (double bond) NH --> H2N-NH2 --> 2NH2. In the end ____ molecules of ATP are used to fix ONE N2 molecule

Malonyl-CoA

In the 3-Hydroxypropionate cycle: 1st step: Acetyl-CoA condenses with CO2 in the form of a bicarbonate ion (HCO3-) to form ____; 1 ATP used

2; 3-Hydroxypropionate

In the 3-Hydroxypropionate cycle: 2nd step: Reduction by (how many) ____ NADPH yields the key intermediate ______; 1 ATP used

methylmalonyl-CoA

In the 3-Hydroxypropionate cycle: 3rd step: Reduction by NADPH (3-hydroxypropionate ---> Propionyl-CoA by CoA-SH + NADPH and 1 ATP) and condensation with HCO3- (Propionyl-CoA + HCO3- and 1 ATP --->) yields ______ (2 ATP in total)

L-malyl-CoA

In the 3-Hydroxypropionate cycle: 4th step: Methylmalonyl-CoA is converted to succinylcholine-CoA and then to ______

pyruvate

In the 3-Hydroxypropionate cycle: 5th step: Malyl-CoA is cleaved to yield glyoxylate plus acetyl-CoA which reenters the 3-Hydropropionate cycle. Glyoxylate condenses with a third HCO3- (1 ATP) to yield _____

Rubisco

In the Calvin cycle, CO2 fixation (condensation of CO2 and H2O) into ribulose 1,5-bisphosphate is catalyzed by the enzyme ____ (ribulose 1,5-bisphosphate carboxylase/oxygenase), the most abundant protein on Earth.

glyceraldehyde 3-phosphate (G3P)

In the Calvin cycle, after 2 molecules of PGA are reduced by NADPH and ATP is the energy source, the fixed CO2 ends up as ______ where it enters the biosynthetic pathway

3-phosphoglycerate (PGA)

In the Calvin cycle, after one molecule of CO2 is condensed with ribulose 1,5-bisphosphate, the resulting six carbon intermediate splits into 2 molecules of ______ reduced by NADPH

1; 1

In the Calvin cycle, each CO2 fixed sends ____ into biosynthesis and regenerates ___ ribulose 1,5-bisphosphate

FabA

In unsaturated fatty acid synthesis, the gene _____ expresses Dehydratase, which removes H20 and forms a cis double bond in the chain. These kinks provide the cell membrane with protection during low temperatures when stiffness is needed

carboxysomes

Many organisms that fix CO2 contain the Rubisco complex within sub cellular structures called ______, which consists of a polyhedral shell of protein subunits surrounding tightly packed molecules of Rubisco. They take up HCO3- where it is converted to CO2 by the enzyme carbonic anhydrase where it can then be fixed by Rubisco

Glutamate and glutamine

Most bacteria assimilate NH4+ into which two amino acids?

Nitrogen fixation is energy-intensive

Nitrogen fixation is found only in a few organisms and is tightly regulated because ______

Calvin cycle

Photoautotrophs, photoheterotrophs, and lithotrophs (such as cyanobacteria and purple phototrophs) use the ______ for CO2 fixation

NifA; nitrogenase

Regulation of nitrogen fixation: Low O2 and NH4+ up regulate nitrogenase expression. In high O2, ____ is blocked from activating expression of nif; In low O2, ____ expression is activated.

Reduction of PGA to G3P; G3P

Second step of the Calvin cycle involved ______; the carboxyl group of each PGA is phosphorylated by ATP----> phosphorylated carboxyl group is hydrolyzed and reduced by NADPH, forming _____

fatty acids

Synthesis of _____ occurs by a cyclic process catalyzed by the fatty acid synthase complex

ribulose 1,5 bisphosphate

The Calvin cycle begins with CO2 fixation by _____, a key intermediate that can derive from the pentose phosphate cycle.

nitrogen fixation

The Fe protein and the Femo center are used in ______

Calvin cycle

The _____ is a light-independent cycle

succinylcholine-CoA

The _____ molecules from the TCA cycle can serve as the foundation of several kinds of amino acids, as well as vitamin B12

regulation, competition and predation, and genome loss and cooperation

The genomic and energetic costs of biosynthesis lead microbes to evolve several strategies to control these costs which include:

D

The level of nitrogen fixation is highest under which of the following conditions? a)High levels of O2 and low levels of NH4+ b)Low levels of O2 and high levels of NH4+ c)High levels of O2 and high levels of NH4+ d)Low levels of O2 and low levels of NH4+

reductive pentose phosphate cycle (Calvin cycle)

The majority of biomass on Earth consists of carbon fixed by chloroplasts and bacteria through the _____ which recycles a pentose phosphate intermediate; used by oxygenic phototrophic bacteria (cyanobacteria) and chloroplasts of algae and multicellular plants, facultatively anaerobic purple bacteria, and lithoautotrophic bacteria

carbohydrates, lipids, and amino acids

What can bacterial microbes synthesize?

NADPH

What is the reducing cofactor typically used in bacteria biosynthesis?

Fatty acid synthesis via acetyl-CoA

What synthesis is this? 1) Malonyl-CoA (C3) 2) CoA replaced with ACP (acyl carrier protein) 3) Oxidation→reduction cycle to add C 4) Two carbon chain per cycle (acetyl-CoA provide 2×C per cycle) 2×NADPH consumed per cycle

E

Which of the following pathways is a route for C O2 fixation? a)Reductive acetyl-CoA pathway b)Reductive, or reverse, TCA cycle c)3-hydroxypropionate cycle d)Choices A and B e)Choices A, B, and C

glucose catabolism; TCA cycle

____ and ____ are both reversible processes through which autotrophs can synthesize entire sugar molecules, starting with CO2 and working up.

pyruvate

____ provides the backbone of several amino acids with aliphatic side chains

Purines; pyrimidines

_____ and ______ are built on ribose 5-phosphate.

autotrophy

_____ assembles carbon and water into small molecules such as acetyl-CoA, which then serve as substrates or building blocks for the cell.

heterotrophy

_____ breaks down larger molecules such as carbohydrates and peptides to release acetyl-CoA and other small substrates.

4; Nitrogenase

_____ cycles of reduction are required to convert a molecule of N2 to 2 NH3 (NH4+ at pH 7). The ____ complex catalyzes this energy-intensive process

chemosynthesis

_____ fixes CO2, but without light

FabA

_____ gene is a temperature-sensitive gene used in unsaturated fatty acid biosynthesis that makes dehydratase (makes kink in chains)

gluconeogenesis

_____ is the reverse cascade of glycolysis; uses pyruvate carboxylase, oxaloacetate, etc.

Acetyl-CoA

_____ pathway uses H2 as an energy source and THF as an intermediate for CO2 fixation

glycerol 3-phosphate (G3P)

_____ provides the glyceride backbone of lipids in the TCA cycle.

erythromycin

______ biosynthesis is similar to fatty acid chain biosynthesis but uses ketone

lithoautrophic bacteria and archaea

_______ use the reductive (reverse) TCA cycle, reductive Coenzyme pathway, and 3-hydroxyprioponate cycle to assimilate CO2

Aromatic amino acids

________ are synthesized via a branched pathway involving chorismate

photosynthesis or photoautotrophy

in ____ single carbon molecules are fixed into organic biomass

eukaryotes

in _____, anaplerotic reactions fix CO2 to regenerate TCA intermediates

3-Hydroxypropionate cycle

in ______ CO2 is converted to HCO3- to be incorporated into this cycle

oxaloacetate; 2-oxoglutarate

other amino acids derive their carbon skeleton from TCA cycle intermediates _____ and ______, which incorporate nitrogen in the form of ammonium ions (NH4+)

NADPH

the phosphoryl group of ____ does not participate in energy transfer

regeneration of ribulose 1,5-bisphosphate; 5

third step of the Calvin cycle is the _____; Of every six G3P resulting from three cycles of fixing CO2, ____ G3P enter a complex series of reactions to regenerate 3 molecules of ribulose 1,5 bisphosphate and the remaining G3P enters biosynthesis