Biochemistry II: Biosynthesis of Amino Acids, Nucleotides, and Related Molecules

This set of vocabulary flashcards covers the biosynthesis of alanine, aspartate, aromatic amino acids, histidine, and the de novo and salvage pathways for nucleotides, including the regulation and mechanism of ribonucleotide reductase and thymidylate synthase.

Alanine Biosynthesis

Synthesized from pyruvate by transamination from glutamate.

Aspartate Biosynthesis

Synthesized from oxaloacetate by transamination from glutamate.

Asparagine Synthetase

The enzyme that catalyzes the synthesis of asparagine by amidation of aspartate, using $NH_4^+$ donated by glutamine.

Essential Amino Acids from Pyruvate and Oxaloacetate

Methionine, threonine, lysine, valine, isoleucine, and leucine.

Chorismate

A key intermediate in the synthesis of the aromatic amino acids tryptophan, phenylalanine, and tyrosine in bacteria and plants.

Tryptophan Synthase

An enzyme with an $\alpha_2\beta_2$ subunit structure that catalyzes the formation of tryptophan from indole-3-glycerol phosphate and requires pyridoxal phosphate.

Phenylalanine Hydroxylase

Catalyzes the hydroxylation at C-4 of the phenyl group of phenylalanine to form tyrosine in animals.

Conditionally Essential Amino Acid

A classification for tyrosine because it can be synthesized from phenylalanine.

Histidine Precursors

The three precursors are PRPP, the purine ring of ATP, and glutamine.

De Novo Pathways

Nucleotide synthesis pathways that begin with precursors such as amino acids, ribose 5-phosphate, $CO_2$, and $NH_3$, where bases are synthesized while attached to ribose.

Salvage Pathways

Pathways that recycle the free bases and nucleosides released from nucleic acid breakdown.

Inosinate (IMP)

The first intermediate in de novo purine synthesis to have a complete purine ring.

Aspartate Transcarbamoylase (ATCase)

The enzyme catalyzing the first committed step in pyrimidine synthesis; it is inhibited by the end-product CTP and accelerated by ATP.

Ribonucleotide Reductase

An $\alpha_2\beta_2$ dimer enzyme that converts ribonucleotides to deoxyribonucleotides.

Thioredoxin

An intermediate hydrogen-carrying protein with pairs of $-SH$ groups that carries a pair of hydrogen atoms from NADPH to the ribonucleoside diphosphate.

Glutaredoxin

A protein that transfers reducing power from glutathione (GSH) to ribonucleotide reductase.

Thymidylate Synthase

An enzyme that catalyzes the conversion of dUMP to dTMP by transferring a one-carbon unit from $N^5,N^{10}\text{-methylenetetrahydrofolate}$.

Dihydrofolate Reductase

An enzyme that reduces dihydrofolate to tetrahydrofolate.