Biosynthesis in Microbial Cells: Sugars, Amino Acids, Nucleotides, and Lipids

Lecture 12: Biosynthesis

Overview

This study guide covers the biosynthetic pathways in prokaryotes, focusing on the synthesis of sugars, polysaccharides, amino acids, nucleotides, and lipids. Understanding these processes is essential for appreciating how microorganisms build cellular components and store energy.

Synthesis: Sugars and Polysaccharides

Polysaccharide Biosynthesis in Prokaryotes

Polysaccharides are crucial for bacterial cell structure and energy storage. Their synthesis involves activated forms of glucose.

• Polysaccharides are large carbohydrate molecules that serve as structural components (e.g., cell wall) and energy reserves.

• In prokaryotes, polysaccharides are synthesized from activated glucose derivatives:

  • Uridine diphosphoglucose (UDPG): Precursor for cell wall polysaccharides.

  • Adenosine diphosphoglucose (ADPG): Precursor for glycogen synthesis.

• Synthesis occurs by adding activated glucose to a preexisting polymer fragment.

Example: UDPG is used in the biosynthesis of peptidoglycan, a major cell wall component in bacteria.

Gluconeogenesis

When cells grow on non-glucose carbon sources, they must synthesize glucose via gluconeogenesis.

• Gluconeogenesis is the process of synthesizing glucose from non-carbohydrate precursors.

• Uses phosphoenolpyruvate (PEP), an intermediate of glycolysis, as the starting material.

• PEP can be synthesized from oxaloacetate, an intermediate in the citric acid cycle.

Equation:

$\text{Oxaloacetate} \rightarrow \text{Phosphoenolpyruvate} \rightarrow \text{Glucose}$

Example: Gluconeogenesis is essential for bacteria growing on acetate or amino acids as carbon sources.

Pentose Phosphate Pathway

Pentoses (C5 sugars) are needed for nucleic acid synthesis and are produced via the pentose phosphate pathway.

• Pentoses are five-carbon sugars (e.g., ribose for RNA, deoxyribose for DNA).

• Formed by removal of one carbon atom from a hexose.

• Pentose phosphate pathway oxidizes glucose to CO2, NADPH, and ribulose 5-phosphate.

• NADPH produced is used as a reductant in biosynthetic reactions (e.g., fatty acid biosynthesis).

• The pathway also produces sugars with 4-7 carbons, which can be converted to hexoses for various purposes.

Equation:

$\text{Glucose-6-phosphate} \rightarrow \text{Ribulose-5-phosphate} + \text{NADPH} + \text{CO}_2$

Example: Ribose-5-phosphate is a precursor for nucleotide synthesis.

Synthesis: Amino Acids

Amino Acid Biosynthesis Pathways

Amino acids are synthesized through complex, multistep pathways and are grouped into families based on shared biosynthetic steps.

• Carbon skeletons for amino acids are derived from intermediates of glycolysis and the citric acid cycle.

• Examples of families:

  • Alanine family: Alanine, valine, leucine (from pyruvate)

  • Serine family: Serine, glycine (from 3-phosphoglycerate)

  • Aromatic family: Phenylalanine, tyrosine, tryptophan (from chorismate)

  • Aspartate family: Aspartate, asparagine, methionine, threonine, lysine (from oxaloacetate)

Example: The synthesis of glutamate from α-ketoglutarate (citric acid cycle intermediate).

Incorporation of Amino Groups

The amino group (-NH2) in amino acids is typically derived from inorganic nitrogen sources, such as ammonia.

• Ammonia is incorporated by glutamate dehydrogenase or glutamine synthetase.

• Amino groups are transferred by transaminase or glutamate synthase.

Key Reactions:

• $\alpha\text{-Ketoglutarate} + \text{NH}_3 + \text{NADH} \rightarrow \text{Glutamate} + \text{NAD}^+$

• $\text{Glutamate} + \text{NH}_3 + \text{ATP} \rightarrow \text{Glutamine} + \text{ADP} + \text{P}_i$

• $\text{Glutamate} + \text{Oxaloacetate} \rightarrow \alpha\text{-Ketoglutarate} + \text{Aspartate}$

• $\text{Glutamine} + \alpha\text{-Ketoglutarate} + \text{NADH} \rightarrow 2\ \text{Glutamate} + \text{NAD}^+$

Example: Transamination reactions are essential for the synthesis of non-essential amino acids.

Synthesis: Nucleotides

Purine and Pyrimidine Biosynthesis

Nucleotide biosynthesis is complex, involving the assembly of purine and pyrimidine rings from various carbon and nitrogen sources.

• Purines (adenine, guanine) are constructed atom by atom; the purine skeleton is inosinic acid.

• Once purines are attached to ribose in triphosphate form, they are ready for incorporation into DNA or RNA.

• Pyrimidines (thymine, cytosine, uracil) are derived from orotic acid; the pyrimidine skeleton is uridylate.

Example: Inosinic acid is the precursor for both adenine and guanine nucleotides.

Synthesis: Fatty Acids and Lipids

Fatty Acid Biosynthesis

Fatty acids are key components of lipids, serving structural and energy storage roles. Their biosynthesis involves acyl carrier proteins (ACPs).

• Fatty acids are synthesized two carbons at a time using acyl carrier proteins (ACPs).

• Each C2 unit comes from malonate (attached to ACP as malonyl-ACP; third carbon released as CO2).

• ACP holds the growing fatty acid chain until it reaches its final length.

Equation:

$\text{Malonyl-ACP} + \text{Fatty acid chain} \rightarrow \text{Elongated fatty acid} + \text{CO}_2$

Example: Synthesis of palmitate (C16 fatty acid) involves six cycles of two-carbon addition.

Variation in Fatty Acid Composition

The composition of cellular lipids varies between species and can change with growth temperature.

• Lower growth temperatures favor shorter, more unsaturated fatty acids.

• Higher growth temperatures favor longer, more saturated fatty acids.

• Common fatty acids in bacterial lipids have C12-C20 lengths.

• Fatty acids can be saturated, unsaturated, branched, or contain odd numbers of carbon atoms.

• Unsaturated fatty acids contain one or more double bonds, formed by desaturation of saturated fatty acids.

Example: Escherichia coli adjusts its membrane fatty acid composition in response to temperature changes.

Lipid Assembly in Bacteria, Eukarya, and Archaea

Lipid assembly differs between domains, especially in the nature of hydrophobic chains and polar groups.

• In Bacteria and Eukarya, fatty acids are added to glycerol to form triglycerides or complex lipids.

• Complex lipids have one glycerol carbon modified with phosphate, ethanolamine, carbohydrate, or other polar substances.

• In Archaea, membrane lipids are constructed from isoprene units (phytanyl or biphytanyl side chains) instead of fatty acids.

• All domains require polar groups for proper membrane architecture (hydrophobic interior, hydrophilic surfaces).

Example: Archaeal membranes are more stable at extreme temperatures due to their unique lipid structure.

Comparison Table: Bacterial vs. Archaeal Lipids

Feature	Bacteria/Eukarya	Archaea
Hydrophobic Chain	Fatty acids	Isoprene units (phytanyl/biphytanyl)
Linkage to Glycerol	Ester linkage	Ether linkage
Membrane Stability	Less stable at extremes	More stable at extremes
Polar Groups	Phosphate, ethanolamine, carbohydrate	Phosphate, sulfate, organic compounds

Additional info: Archaeal lipids contribute to the ability of these organisms to thrive in extreme environments.