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Microbial Metabolism > Amino Acid and Nucleotide Biosynthesis
Amino Acid and Nucleotide Biosynthesis
• Amino Acid Synthesis
• Purine and Pyrimidine Synthesis
• Nonribosomal Peptide Antibiotics
• Biosynthesis of Tetrapyrroles
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Microbial Metabolism > Amino Acid and Nucleotide Biosynthesis
Amino Acid Synthesis
• All amino acids are synthesized from intermediates in glycolysis, the citric acid
cycle, or the pentose phosphate pathway.
• Amino acid synthesis depends on the formation of the appropriate alpha-keto
acid, which is then transaminated to form an amino acid.
• Of the 22 amino acids naturally incorporated into proteins, 20 are encoded by the
universal genetic code and the remaining two, selenocysteine and pyrrolysine, are
incorporated into proteins by unique synthetic mechanisms.
Structure of Pyrrolysine
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Microbial Metabolism > Amino Acid and Nucleotide Biosynthesis
Purine and Pyrimidine Synthesis
• A key regulatory step in the synthesis of purines is the production of 5-phospho-αD-ribosyl 1-pyrophosphate (PRPP) by PRPP synthetase, which is activated by
inorganic phosphate and inactivated by purine ribonucleotides.
• Both adenine and guanine are derived from the nucleotide inosine
monophosphate (IMP), which the first compound in the pathway to have a
completely formed purine ring system.
• Unlike purines, pyrimidines are assembled before being attached to 5phosphoribosyl-1-pyrophosphate (PRPP).
Purine structure
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Microbial Metabolism > Amino Acid and Nucleotide Biosynthesis
Nonribosomal Peptide Antibiotics
• Nonribosomal peptides are produced by microorganisms like bacteria and fungi
but are also found in higher organisms such as nudibranchs where they are
thought to be made by bacteria inside these organisms.
• Nonribosomal peptides are synthesized by nonribosomal peptide synthetases,
which, unlike the ribosomes, are independent of messenger RNA.
• The biosynthesis of nonribosomal peptides shares characteristics with the
polyketide and fatty acid biosynthesis.
Actinomycin D
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Microbial Metabolism > Amino Acid and Nucleotide Biosynthesis
Biosynthesis of Tetrapyrroles
• Porphyrins are a group of organic compounds, many naturally occurring, such as
heme.
• Porphyrins are aromatic, obeying Hückel's rule for aromaticity, possessing 4n+2 π
electrons (n=4 for the shortest cyclic path) delocalized over the macrocycle.
• Porphyrin macrocycles are highly conjugated systems and typically have very
intense absorption bands in the visible region, and may be deeply colored.
Structure of Porphine
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Appendix
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Microbial Metabolism
Key terms
• aromatic Having a closed ring of alternate single and double bonds with delocalized electrons.
• genetic code The set of rules by which the sequence of bases in DNA are translated into the amino acid sequence of proteins
• heterocyclic Having one or more atoms other than carbon in at least one of its rings.
• metabolite Any substance produced by, or taking part in, a metabolic reaction.
• peptide A class of organic compounds consisting of various numbers of amino acids, in which the amine of one is reacted with
the carboxylic acid of the next to form an amide bond.
• porphyrin Any of a class of heterocyclic compounds containing four pyrrole rings arranged in a square; they are important in
biochemistry in a form with a metal atom in the central cavity (hemoglobin with iron, chlorophyll with magnesium, etc.).
• PRPP Phosphoribosyl pyrophosphate (PRPP) is a pentosephosphate formed from ribose 5-phosphate by the enzyme ribosephosphate diphosphokinase. It plays a role in transferring phospho-ribose groups in several reactions:
• purine Any of a class of organic heterocyclic base containing fused pyrimidine and imidazole rings; they are components of
nucleic acids
• pyrimidine A diazine in which the two nitrogen atoms are in the meta- positions; it is the basis of three of the bases found in
DNA and RNA, thymine, uracil and cytosine
• pyrrolysine An amino acid found in methanogenic bacteria.
• selenocysteine A naturally-occurring amino acid, present in several enzymes, whose structure is that of cysteine but with the
sulfur atom replaced by one of selenium.
• siderophores Sidereophores are small, high-affinity iron chelating compounds secreted by microorganisms such as bacteria
and fungi, and also grasses. Siderophores are amongst the strongest soluble Fe3+ binding agents known.
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Microbial Metabolism
Actinomycin D
Actinomycin D (also known generically as Actinomycin or Dactinomycin), is the most significant member of actinomycines, which are a class of
polypeptide antibiotics isolated from soil bacteria of the genus Streptomyces. As one of the older chemotherapy drugs, it has been used for many years.
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Microbial Metabolism
Structure of Pyrrolysine
Pyrrolysine (abbreviated as Pyl or O) is a naturally occurring, genetically coded amino acid used by some methanogenic archaea and one known
bacterium in enzymes that are part of their methane-producing metabolism.
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Microbial Metabolism
Purine structure
A purine is a nucleotide (a nucleoside + phosphate group) that is amine based and planar, aromatic, and heterocyclic. The structure of purine is that of a
cyclohexane(pyrimidine group) and cyclopentane(imidazole group) attached to one another; the Nitrogen atoms are at positions 1,3,7,9. Adenine(A) and
Guanine(G) are examples of purines which are involved in the construction of the backbone of the DNA and RNA.
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Microbial Metabolism
What forms a nucleic acid structure?
The four nitrogenous bases present in DNA are adenine (A), guanine (G), cytosine (C) and thymine (T). Adenine and guanine are purines and cytosine
and thymine are pyrimidines.
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Microbial Metabolism
Structure of Porphine
Porphine is the simplest porphyrin, an aromatic organic compound.
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Microbial Metabolism
Which of the following is a necessary component of amino acid
synthesis?
A) Formation of the appropriate alpha-keto acid
B) Formation of intermediates in the pentose phosphate pathway
C) The recruitment of a ribozyme to the site of synthesis
D) The activation and attachment of the appropriate transfer RNA
molecule via an ester bond
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Microbial Metabolism
Which of the following is a necessary component of amino acid
synthesis?
A) Formation of the appropriate alpha-keto acid
B) Formation of intermediates in the pentose phosphate pathway
C) The recruitment of a ribozyme to the site of synthesis
D) The activation and attachment of the appropriate transfer RNA
molecule via an ester bond
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Microbial Metabolism
Which of the following is specific to pyrimidine synthesis?
A) Production of 5-phospho-alpha-D-ribosyl 1-pyrophosphate (PRPP)
B) The use of formyl groups to build carbon-2 and carbon-8
C) Assembly before attachment to 5-phosphoribosyl-1-pyrophosphate
D) The nucleotide inosine monophosphate (IMP) is used to derive
compounds
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Microbial Metabolism
Which of the following is specific to pyrimidine synthesis?
A) Production of 5-phospho-alpha-D-ribosyl 1-pyrophosphate (PRPP)
B) The use of formyl groups to build carbon-2 and carbon-8
C) Assembly before attachment to 5-phosphoribosyl-1-pyrophosphate
D) The nucleotide inosine monophosphate (IMP) is used to derive
compounds
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Microbial Metabolism
Which of the following are characteristics of nonribosomal
peptides:I: Synthesis by specialized nonribosomal peptidesynthetase enzymesII: Have cyclic and/or branched structuresIII:
Dependent on messenger RNAIV: Have pharmacological
properties
A) I, II, IV
B) I, IV
C) I, II, III, IV
D) I, II
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Microbial Metabolism
Which of the following are characteristics of nonribosomal
peptides:I: Synthesis by specialized nonribosomal peptidesynthetase enzymesII: Have cyclic and/or branched structuresIII:
Dependent on messenger RNAIV: Have pharmacological
properties
A) I, II, IV
B) I, IV
C) I, II, III, IV
D) I, II
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Microbial Metabolism
The most important steps in tetrapyyrole biosynthesis, considered
the committment step is:
A) the combination of two 5-ALA molecules to form porphobilinogen
B) the combination of four porphobilinogens to form hydroxymethyl bilane
C) the formation of 5-ALA by reaction of glycine with succincyl-CoA
D) the combination of protoporphyrin IX with iron to form heme
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Microbial Metabolism
The most important steps in tetrapyyrole biosynthesis, considered
the committment step is:
A) the combination of two 5-ALA molecules to form porphobilinogen
B) the combination of four porphobilinogens to form hydroxymethyl bilane
C) the formation of 5-ALA by reaction of glycine with succincyl-CoA
D) the combination of protoporphyrin IX with iron to form heme
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Microbial Metabolism
Attribution
• Wikipedia. "Porphyrin." CC BY-SA 3.0 http://en.wikipedia.org/wiki/Porphyrin#Biosynthesis
• Wikipedia. "Porphyrin." CC BY-SA 3.0 http://en.wikipedia.org/wiki/Porphyrin#Biosynthesis
• Wiktionary. "aromatic." CC BY-SA 3.0 http://en.wiktionary.org/wiki/aromatic
• Wiktionary. "heterocyclic." CC BY-SA 3.0 http://en.wiktionary.org/wiki/heterocyclic
• Wiktionary. "porphyrin." CC BY-SA 3.0 http://en.wiktionary.org/wiki/porphyrin
• Wikipedia. "siderophores." CC BY-SA 3.0 http://en.wikipedia.org/wiki/siderophores
• Wiktionary. "metabolite." CC BY-SA 3.0 http://en.wiktionary.org/wiki/metabolite
• Wiktionary. "peptide." CC BY-SA 3.0 http://en.wiktionary.org/wiki/peptide
• Wikipedia. "Nonribosomal peptide." CC BY-SA 3.0 http://en.wikipedia.org/wiki/Nonribosomal_peptide
• Wikipedia. "PRPP." CC BY-SA 3.0 http://en.wikipedia.org/wiki/PRPP
• Wiktionary. "pyrimidine." CC BY-SA 3.0 http://en.wiktionary.org/wiki/pyrimidine
• Wiktionary. "purine." CC BY-SA 3.0 http://en.wiktionary.org/wiki/purine
• Wikipedia. "Purine metabolism." CC BY-SA 3.0 http://en.wikipedia.org/wiki/Purine_metabolism
• Wikibooks. "Principles of Biochemistry/Nucleic acid III: Sythesis of nucleotides." CC BY-SA 3.0
http://en.wikibooks.org/wiki/Principles_of_Biochemistry/Nucleic_acid_III:_Sythesis_of_nucleotides#De_novo_biosynthesis_of_p
yrimidine
• Wiktionary. "genetic code." CC BY-SA 3.0 http://en.wiktionary.org/wiki/genetic+code
• Wiktionary. "selenocysteine." CC BY-SA 3.0 http://en.wiktionary.org/wiki/selenocysteine
• Wikipedia. "Amino acid." CC BY-SA 3.0 http://en.wikipedia.org/wiki/Amino_acid#Standard_amino_acids
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Microbial Metabolism
• Wikipedia. "Metabolism." CC BY-SA 3.0 http://en.wikipedia.org/wiki/Metabolism#Nucleotide_synthesis_and_salvage
• Wikipedia. "Pyrrolysine." CC BY-SA 3.0 http://en.wikipedia.org/wiki/Pyrrolysine
• Wiktionary. "pyrrolysine." CC BY-SA 3.0 http://en.wiktionary.org/wiki/pyrrolysine
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