Lecture 16: Amino Acid Metabolism

All nitrogen in the biosphere would eventually be converted into

N2

Fully oxidized nitrogen

nitrate

Fully reduced nitrogen

ammonia

Nitrogen fixation

atmospheric dinitrogen (N2) is reduced to a biologically useful form ammonium (NH4+)

Nitrogen fixation equation

N2 + 6H+ + 6e− → 2NH3

Non-biological nitrogen fixation requires

400°C and several hundred atmospheres of pressure

Dinitrogenase reductase

conveys electrons one at a time from the initial electron source to dinitrogenase, in an ATP-requiring reaction

Dinitrogenase

uses the electrons obtained from dinitrogenase reductase to reduce nitrogen to ammonia

Nitrogenase complex transfers

8e− at the cost of 16 ATP

One electron at a time is transferred from ___ to dinitrogenase reductase

ferredoxin

___ and ___ are the gateway to biologically accessible nitrogen

glu; gln

Free ammonia is

highly toxic

Due to ammonia’s toxicity, it is incorporated into biomolecules through

glutamate and glutamine

_________ is the source of amino groups for most amino acids (via transamination)

glutamate

Glutamine contains an activated nitrogen (amide), so it can act as ______ for more complex structures (nucleotides and complex amino acid side chains)

donor

Glutamine synthetase controls

the flow of new nitrogen into the cell

Feedback inhibitors in conversion of glutamate → glutamine

His, Trp, carbamoyl-P, CTP

Reflect metabolic status in conversion of glutamate to glutamine

AMP, Gly, Ala

These inhibitors work

additively (they are all potential sources of N)

Transamination

interconversion of amino acids and alpha-keto acids

Aminotransferases require

pyridoxal phosphate prosthetic group

PLP ↔ PMP acts as an

amino group carrier

PLP ↔ PMP serves as the intermediate carrier of the

amino group during transamination (double displacement)

Glutamine amidotransferases

transfer glutamine amide nitrogen to hydroxyl compounds

Proteins can be broken down to provide

metabolic fuel (amino acids)

Ingested protein or tissue breakdown results in

free amino acids

NH4+ is shuttled to the liver on

Gln

Glumate

charged, cannot easily pass through cell membranes

NH4+ shuttle reaction (other tissues to liver)

Glu + NH4+ -> Gln

Gln

transports ammonia in the bloodstream to the liver

NH4+ rxn in liver

Gln → Glu + NH4+

In active muscle, ___ is used to transport ammonia

alanine

Muscle cells utilize high rates of _____

glycolysis (lots of pyruvate)

Transamination in muscle cells

pyruvate + glutamate → α-KG + alanine

Amino groups are collected in the

liver

Nitrogen transported to the ____ is removed, producing _____ ____

liver; ammonia; NH4+

Major excretory forms of nitrogen

ammonia, urea, uric acid

Ammonia (NH3)

alkaline, accumulation raises pH, potent neurotoxin, used mostly by aquatic animals

Uric acid

insoluble, excretion can occur with low H2O loss

Urea

neutral but excretion requires high H2O loss

Urea cycle

removes excess nitrogen

Urea production occurs exclusively in the (location in body)

liver

Urea Cycle: Enzymes are in the ____ ___ and the ____

mitochondrial matrix; cytoplasm

The urea cycle maximizes what and minimizes what

maximizes N removal while minimizing C loss

Excess nitrogen is removed via

the urea cycle

The urea cycle is physically and metabolically linked to the

CAC

____ enters the urea cycle via _____ _____, which is formed from NH4+ and HCO3−

NH3; carbamoyl phosphate

Urea cycle is catalyzed by _____ _____ ____ (_____), a key __ enzyme

carbamoyl phosphate synthase I (CPS I); regulatory

CPS I is a _____ ____ (location) enzyme

mitochondrial matrix

Urea cycle occurs partly in the ____ and partly in the _____

cytoplasm; mitochondria

The shunt allows the urea cycle to balance its energy costs by

funneling fumarate into the CAC, generating NADH

This linkage prevents the loss of

carbon skeletons while maintaining a continuous flow of nitrogen toward excretion

Regulation of the flux through the urea cycle

sufficient energy to keep the citric acid cycle going

______________ (____) acts as an overall sensor of the urea cycle

N-acetylglutamate (NAG)

The urea cycle is subsidized by

CAC

Net cost of urea cycle

1.5 ATP

Deaminated carbon skeletons can be used to

build glucose or ketone bodies

Glucogenic

produce oxaloacetate for GNG

Ketogenic

produce ketone bodies

Co-factors in amino acid catabolism

PLP, biotin, THF, AdoMet

PLP type of rxn

transamination

Biotin type of rxn

one-carbon transfer (CO2)

THF type of rxn

one-carbon transfer (intermediate oxidation states)

AdoMet type of rxn

one-carbon transfer (CH3−)

THF

picks up methyl groups and shuttles them in different redox states

THF lacks energy to act as a

methyl donor

AdoMet

takes 3 ATP equivalents to generate SAM; methyl groups are recycled from THF; activated molecule that can transfer a methyl group

3-carbon rule

if an amino acid has a 3-carbon backbone and a functional group on the beta carbon, that group is removed (leaves you with pyruvate)

3-carbon rule is a catabolic pathway for

Trp, Ala, Ser, Cys

5-carbon rule

amino acids with 5 continuous carbons (proline, arginine, histidine, glutamine) are processed until they become glutamate; glutamate is transaminated into α-ketoglutarate

_____ (______) can only make about half of the amino acids needed for protein synthesis

Vertebrates (heterotrophs)

Essentials

vertebrates must consume these amino acids in their diet; lack pathways to synthesize them

Conditionally essential

vertebrates can make these amino acids, but they are resource-intensive to make

Nonessential

vertebrates can make these amino acids

In autotrophs, several amino acids are derived from _____ and pyruvate

oxaloacetate and pyruvate

In autotrophs, pyruvate can generate what amino acids

alanine, valine, leucine, isoleucine

In autotrophs, oxaloacetate can produce what amino acids

aspartate -> asparagine, methionine, lysine, threonine

_______ is an essential amino acid for vertebrates

histidine

Histidine is derived from

PRPP, ATP, Gln, Glu

The 5-phosphoribosyl-1-pyrophosphate precursor is synthesized from

ribose-5-phosphate

PRPP is an intermediate in the biosynthesis of

Trp, His, nucleotides

Regulation of amino acid biosynthesis—enzyme multiplicity

enzyme isoforms enable branched control of the pathway

Regulation of amino acid biosynthesis—sequential feedback

the product inhibits the enzyme immediately preceding the branch point; this causes an accumulation of the intermediate

Regulation of amino acid biosynthesis—concerted

example of feedback inhibition

Concerted

the enzyme only shuts down if two or more specific end-products bind at the same time

Regulation of amino acid biosynthesis—cumulative

example of feedback inhibition

Cumulative

each end product slightly inhibits the starting enzyme; no single product can shut it down entirely, but if all are present, the enzyme stops completely