The Structure of informational macromolecules: DNA and RNA Flashcards
*Understand what Nitrogen fixation is. Know how this is done.
Nitrogen fixation- process of converting N2 to ammonia, NH3+. A few organisms such as diazotrophic (nitrogen-fixing) bacteria can convert nitrogen gas (N2) into biochemically more useful NH3.
*Understand how Nitrogen is incorporated into the building blocks of amino acids.
first Nitrogen (N2) fixed into ammonia (NH3) (by reductase and nitrogenase functions).
Then incorporate ammonium ion into versatile amino acids. Alpha-ketoglutarate and glutamate play role as acceptor of ammonium ion:
1. NH4+ and alpha-ketoglutarate and NAD(P)H will react to form GLUTAMATE (and NAD (P)+ and water) by enzyme glutamate DH
2. Glutamate will react with NH3+ through hydrolysis of ATP to form GLUTAMINE by glutamine synthetase
(Glutamate will be phosphorylated by ATP to form acyl-phosphate intermediate, then intermediate react with NH3+ to form glutamine)
*Where do carbon skeletons come from to generate amino acids?
The carbon skeletons for amino acid synthesis are provided by INTERMEDIATES of GLYCOLYTIC pathway, CITRIC ACID Cycle, and PENTOSE phosphate Pathway.
*Understand the biosynthetic families of amino acids
6 biosynthetic families of aa:
Citric Acid-oxaloactetae form aspartate. Aspartate can make asparigine, methionine, and thereonine and lysine. Threonine can make isoleucine
Citric Acid - alpha-ketoglutarate form glutamate. Glutamate form glutamine, proline and arginine
Glycolysis- pyruvate form Alanine, valine and leucine
Glycolysis- 3-phosphoglycerate intermediate make serine. Serine can make cysteine and glycine
Glycolysis and pentose phosphate pathway - PEP intermediate and erythose 4-P form Phenylalanine, Tyrosine and tryptophan. Phenylalanine also form tyrosine (1 step)
pentose phosphate pathway- intermediate ribose 5-phosphate will form HISTIDINE
Essential amino acids: , threonine phenylalanine, leucine, methionine Histidine, lysine, isoleucine, tryptophan, valine
*Understand the difference between essential and nonessential amino acids.
Essential amino acids: aa that are required in the diet. These aa have COMPLEX synthetic pathways and CANNOT be synthesized by humans
Non-essential amino acids: CAN be synthesized from HUMANS and are made by SIMPLE reactions.
a deficiency in one essential amino acids can have severe physiological consequences.
*what do the co-factors “tetrahydrofolate and S-adenosyl methionine (SAM) do”
tetrahydrofolate- coenzyme essential for synthesizing aa and nucleotides; versatile carrier of activated 1-carbon units. (inhibition of THF will inhbit cancer cell growth. THF important for DNA replication and cell growth.
THF consist of pteridine ring, p-aminobenzoate and chain of glutamate residues.
S-adneosyl methionine- active donor of methyl group, has High energy phosphoryl transfer- adenosyl group linked to sulfur atom. formation of SAM leads to activation of methyl group in methionine.
SAM also activated methyl donor in synthesis of phosphatidylcholine from phosphatidlyethanoamine.
What chemical is the atmosphere 80% of? What makes it unique?
The atmosphere is approx. 80% of Nitrogen gas (N2) which is an unreactive molecule. It is not available to majority of organisms. Only bacteria that live in root nodules of yellow clover, alfafa, soy beans can convert nitrogen gas into ammonia, which can be used to synthesize glutamate and then other aa.
Describe the steps to Nitrogen fixation. in aqueous solution, what does ammonia (NH3) require? What is ATP used for in process?
Nitrogen gas (N2 is a strong triple bonded molecule)
The Nitrogen complex of diazotrophic organisms complete fixation of N2 into Nh3.
Complex has two components:
1. REDUCTASE provides high-energy Electrons, in form of ferrodoxin, for reducing power
2, The NITROGENASE uses the electrons to reduce N2 to NH3 with rxn: (N2 + 8e- +8H + 16 ATP and 16 H2O to form 2 NH3 + h2, + 16 ADP and 16Pi) Requires ATP hydrolysis
in aqueous solution: ammonia requires a PROTON to form NH4+
ATP is required not to power reaction, but to make exergonic reaction kinetically feasible.
What is the role of glutamate?
Glutamate serves a nitrogen source for biosynthetic reactions, such as synthesis of amino acids from ketoacids. (NH4+ alphaketogluatarate + NadH + H form glutamate and NAD (P) + H20)
How many electrons are required for reducing N2 to NH3? How many ATP required.
What is the site of Nitrogen fixation?
Need 8 electrons that come from ferrodoxin and go to reductaste. for each electron transfer need 2 ATP, so 16 ATP total.
MoFe factor-site of nitrogen fixation
What are the nitrogen donors?
Glutamate and Glutamine are the nitrogen donors.
Glutamine- also transport for nitrogen in blood.
How are alanine and aspartate made.
Alanine and aspartate are nonessential (made in 1 simple step, made by humans)
Oxaloacetate and glutamate make ASPARTATE and alpha-ketoglutarate
PYRUVATE and glutamate make ALANINE and alpha-ketoglutarate
