Microbial Genetics and Metabolic Pathways: Structured Study Notes

Microbial Metabolism

Biosynthesis of Polysaccharides

Polysaccharides are essential macromolecules in microbial cells, serving as energy storage and structural components.

• Glucose-6-phosphate can be used to synthesize glycogen (in bacteria) and glycogen (in animals).

• Bacteria also produce peptidoglycan using glucose derivatives.

• Excess glucose is converted into glycogen; if storage capacity is exceeded, it is stored as fats.

• Glycogen is stored in the liver and muscle in animals.

Biosynthesis of Simple Lipids

Lipids are synthesized from excess glucose, which is converted into glycerol and fatty acids via glycolysis.

• Simple lipids are the main fat molecules in the body.

• Fatty acids and glycerol combine to form simple lipids.

Biosynthesis of Amino Acids

Amino acids are the building blocks of proteins, and their biosynthesis is crucial for microbial growth and function.

• There are 20 total natural amino acids:

  • 8 essential amino acids: Cannot be synthesized by the body and must be obtained from the diet.

  • 12 non-essential amino acids: Can be synthesized by the body via amination or transamination reactions.

• Precursors for amino acid synthesis include intermediates from the pentose phosphate pathway and Krebs cycle.

Biosynthesis of Purine and Pyrimidine Nucleotides

Purines and pyrimidines are nitrogenous bases required for nucleic acid synthesis.

• Purine bases: Adenine (A) and Guanine (G)

• Pyrimidine bases: Cytosine (C), Thymine (T), and Uracil (U)

• These bases are synthesized from amino acids and other metabolic intermediates.

Amphibolic Pathways

Amphibolic pathways are metabolic routes that function in both anabolism and catabolism, allowing cells to efficiently manage resources.

• Many metabolic pathways share common intermediates and operate simultaneously.

Energy-Producing Pathways in Microorganisms

Microorganisms utilize various energy-producing pathways depending on their environment and available resources.

Pathway	Growth Condition	Final Electron Acceptor	ATP Yield
Aerobic Respiration	Aerobic	O2	High (38 ATP per glucose)
Anaerobic Respiration	Anaerobic	Inorganic molecule (not O2)	Variable (less than aerobic)
Fermentation	Aerobic or Anaerobic	Organic molecule	Low (2 ATP per glucose)

Microbial Genetics

Genetics Overview

Genetics is the science of heredity, focusing on how traits are passed from parent to offspring in microorganisms.

• The central dogma of molecular biology: DNA → RNA → Protein

• Retroviruses can reverse this flow using reverse transcriptase (RNA → DNA).

Mutation

Mutations are changes in the DNA sequence that can affect microbial traits and evolution.

• Base substitution: A single DNA base pair is altered.

• Frameshift mutation: DNA base pairs are added or removed, shifting the reading frame.

• Mutations provide genetic diversity and the raw material for evolution.

Gene Expression and Operons

Gene expression in bacteria is often controlled by operons, which are clusters of genes regulated together.

• Inducible operon: Genes are "off" until an inducer inactivates the repressor, turning them "on" (e.g., lac operon).

• Repressible operon: Genes are "on" until a corepressor activates the repressor, turning them "off" (e.g., trp operon).

Alteration of Bacterial Genes and Gene Expression

Changes in gene expression can cause disease, affect treatment, and be manipulated for human benefit.

Key Genetic Terms

• Genetics: Study of genes, heredity, and gene replication.

• Chromosomes: Structures containing DNA and hereditary information.

• Genes: Segments of DNA encoding functional products, usually proteins.

• Genetic code: Rules for converting nucleotide sequences into amino acid sequences.

• Genotype: Genetic makeup of an organism.

• Phenotype: Observable traits of an organism.

• Short tandem repeats (STRs): Repeating sequences of noncoding DNA.

Flow of Genetic Information

• Vertical gene transfer: Transfer of genetic information from parent to offspring (replication).

• Horizontal gene transfer: Transfer of genetic information between members of the same generation (transformation, transduction, conjugation).

DNA and Chromosomes

Bacterial chromosomes are usually single, circular DNA molecules associated with proteins.

DNA Replication

DNA replication is the process by which DNA is copied before cell division.

• DNA forms a double helix structure.

• Base pairing: Adenine (A) pairs with Thymine (T), Guanine (G) pairs with Cytosine (C).

• Semiconservative replication: Each new DNA molecule consists of one old (template) strand and one new strand.

Steps in DNA Replication

1. Enzymes unwind the double helix (topoisomerase and gyrase).

2. Proteins stabilize the unwound DNA.

3. DNA polymerase synthesizes new DNA strands in the 5' → 3' direction.

4. Leading strand is synthesized continuously; lagging strand is synthesized discontinuously, forming Okazaki fragments.

5. RNA primers are replaced with DNA; DNA ligase joins Okazaki fragments.

DNA Replication Fork Summary

• Energy for replication is supplied by nucleotides (hydrolysis of ATP).

• Most bacterial DNA replication is bidirectional.

• Each offspring cell receives one copy of the DNA molecule.

• DNA polymerase has proofreading capability for high accuracy.

RNA and Protein Synthesis

Types of RNA

• Messenger RNA (mRNA): Carries genetic information from DNA to ribosomes.

• Ribosomal RNA (rRNA): Integral part of ribosomes.

• Transfer RNA (tRNA): Transfers amino acids to ribosomes during protein synthesis.

Transcription

Transcription is the process of making an RNA copy from a DNA template.

• Occurs in the 5' → 3' direction.

• Only one of the two DNA strands is transcribed.

• Transcription stops at the terminator sequence on DNA.

Translation

Translation is the process by which mRNA is decoded to synthesize proteins.

• Occurs at the ribosome, where mRNA codons are matched with tRNA anticodons.

• Each codon specifies an amino acid; translation begins at the start codon (AUG) and ends at a stop codon.

Transcription in Prokaryotes

• Synthesis of a complementary mRNA strand from a DNA template.

• Transcription begins when RNA polymerase binds to the promoter sequence on DNA.

• mRNA is released and can be translated into protein.

Additional info:

• Equations for DNA replication: $\text{DNA}_{\text{parent}} \rightarrow \text{DNA}_{\text{daughter}}$

• Central dogma: $\text{DNA} \rightarrow \text{RNA} \rightarrow \text{Protein}$

• Okazaki fragments: Short DNA fragments synthesized on the lagging strand during DNA replication.

• Operons are a key regulatory feature in prokaryotic gene expression.