Download Amino Acid Metabolism

What to Know (protease lecture)
• Know the general mechanism of serine
proteases
– what imparts specificity?
– how is the substrate stabilized?
– how is the transition state stabilized?
– what amino acids play key roles and why?
• Understand the major biological roles of the
four different proteases mentioned in the
lecture
Nitrogen Degradation
Things to Know
• What purpose does nitrogen fixation and assimilation
serve in the biosphere?
• What are the key enzymes in nitrogen fixation and
assimilation?
• What are examples of nitrogen fixation and assimilation in
life?
• What are the general concepts for the pathways that form
ammonium from inorganic nitrogen compounds prevalent
in the inanimate environment?
• What are the general concepts of how ammonium ions
are incorporated into organic compounds?
• What are the general concepts of how amino acids are
synthesized and degraded?
Nitrogen Cycles
• Nitrogen in proteins is reduced
• Inorganic nitrogen in the environment is oxidized
as nitrogen gas or nitrate ions
• Two principal routes for nitrogen acquisition from
the environment lead to formation of NH4+
1. Nitrate assimilation
2. nitrogen fixation
• Are animals capable of nitrogen or NO3- fixation?
Nitrogen is cycled between organisms and the
inanimate environment
• Nitrate assimilation – the reduction of nitrate to
NH4+ in plants, various fungi, and certain bacteria, in
a two-step metabolic pathway
• Nitrogen fixation – the formation of NH4+ from N2
gas
Major Pathways for N Acquisition
Denitrifying bacteria:
Exclusively anaerobic, use
NO3- as electron acceptors
Exclusively anaerobic, prokaryotic
process except for bacteria in symbiotic
relationship with green plants
Nitrate Assimilation
aerobic process
Nitrifying bacteria
chemoautotrophs
Nitrate assimilation – the reduction of nitrate to NH4+ in plants, various
fungi, and certain bacteria, in a two-step metabolic pathway
Nitrate assimilation occurs in two steps:
The two-electron reduction of nitrate to nitrite, catalyzed by nitrate
reductase
-
+
NO3 + 2H +2e
- nitrate reductase
NO2- + H2O
The six-electron reduction of nitrite to ammonium, catalyzed by nitrite
reductase
NO2- + 8H+ + 6e-
nitrite reductase
NH4+ + 2H2O
Nitrate Assimilation
Nitrate Reductase contains cytochrome
b557 and molybdenum cofactor (MoCo)
Nitrate Reductase
Nitrate Assimilation is the Principal Pathway for
Ammonium Biosynthesis
Prosthetic Group of Nitrate Reductase
The Reaction of Nitrite
Reductase
Prosthetic Group of
Nitrite Reductase
act as coupled e- transport center
Nitrite
Reductase
Nitrate Assimilation is the Principal Pathway for
Ammonium Biosynthesis
Organisms Gain Access to Atmospheric N2 Via
the Pathway of Nitrogen Fixation
Only occurs in certain prokaryotes
• Bacteria can use nitrogen fixation reactions to convert
atmospheric nitrogen into ammonium ions.
• N2 fixing bacteria can be free-living or as symbionts with
plants.
Nitrogen Fixation
• All nitrogen fixing systems appear to be
identical-- They require 4 key components:
1.
2.
3.
4.
The enzyme known as Nitrogenase,
a reductant (reduced ferredoxin),
ATP
O-free conditions and regulatory controls (ADP
inhibits and NH4+ inhibits expression of nif
genes)
The Nitrogenase Reaction
N2 + 10H+ 8e-
2NH4+ + H2
Two protein components: nitrogenase reductase and nitrogenase
Nitrogenase Complex
Ribbon diagram of nitrogenase reductase (the Fe-protein,
blue); nitrogenase (FeMo) protein, green) complex. Ironsulfur cluster is yellow, ADP in orange, FeMo in cyan,
P=cluster in red.
Organisms Gain Access to Atmospheric N2 Via the
Pathway of Nitrogen Fixation
The triple bond in N2 must be broken during nitrogen fixation.
The Metal Clusters of Nitrogenase
The Nitrogenase Reaction
• The nitrogenase reaction. ATP hydrolysis coupled to electron
transfer from N. reductase to P-cluster.
• This is followed by conformational change in N. reductase so it
does not bind to Nitrogenase.
•ADP-N. reductase dissociates allowing another ATP-N.
reductase to bind.
The Structure of Nitrogenase
Regulation of Nitrogen Fixation
Key Concepts / Amino Acid Metabolism
• The enzymes glutamate synthase, glutamine synthetase,
glutamate dehydrogenase, and aminotransferases are
responsible for the vast majority of nitrogen metabolizing
reactions in most organisms.
• Protein degradation by the protozomal complex releases
oligopeptides that are degraded into individual amino acids.
• The urea cycle uses protons and electrons from ammonium
ions and the amino acid aspartate to generate urea, which is
excreted to maintain daily nitrogen balance.