A Survey of the Microbial World Part II

Universal Blueprint and the Flow of Genetic Information

The microbial world operates under a universal blueprint where genetic information flows through a shared heritage defined by common ancestry and a universal code. This genetic material is heritable and possesses specific characteristics that ensure biological continuity:

Information Storage: Highly stable storage of biological instructions.
Replication Fidelity: Mechanisms ensure accuracy during copying.
Adaptability: The genome remains flexible to environmental pressures.
Genetic Redundancy: Multiple copies or similar sequences provide a buffer against damage.

Gene Expression Pathways

The flow of genetic information involves three primary processes:

Replication: Doubling the DNA for inheritance.
Transcription: Synthesizing RNA from a DNA template.
Translation: Synthesizing proteins from mRNA transcripts.

Genetic Mutations serve as the raw material for evolution, allowing for beneficial, harmful, or neutral changes in the genetic code.

DNA Replication: Mechanisms and Comparison

DNA replication is defined as the process of producing two identical replicas of DNA from one original DNA molecule. It is essential for growth, repair, reproduction, and genetic diversity in all living organisms.

Comparison of Replication between Prokaryotes and Eukaryotes

Feature	Prokaryotes	Eukaryotes
Chromosome Structure	Single Circular Chromosome	Multiple Linear Chromosomes
Directionality	Bidirectional	Unidirectional
Origin of Replication	Single Origin	Multiple Origins
Speed	$1000\,\text{nucleotides per second}$	$100\,\text{nucleotides per second}$

Prokaryotic Replication Components

This process requires significant energy and specific enzymes:

Origin of Replication: The starting point.
Replication Fork: Created by the unwinding of the helix.
Single-Stranded Binding Proteins: Stabilize unwound DNA.
Leading Strand: Synthesized continuously in the $5'$ to $3'$ direction.
Lagging Strand: Synthesized discontinuously.
DNA Helicase: Unwinds the double helix.
RNA Primase: Lays down an RNA primer for DNA polymerase.
DNA Polymerase III: Main enzyme for adding nucleotides.
DNA Polymerase I: Removes RNA primers and fills gaps.
DNA Ligase: Seals the fragments together.
DNA Gyrase: Relieves torsional strain.

Post-Replication Mechanisms for Fidelity

To ensure accuracy and stability, several repair and maintenance processes occur:

Endonucleases & Exonucleases: Enzymes that cleave phosphodiester bonds and remove nucleotides.
Ribozymes: RNA molecules with catalytic activity.
Methylase: Adds methyl groups to DNA for protection and regulation.
Mismatch Repair: Proteins scan newly synthesized strands for errors.
Base Excision Repair: Repairs specific damaged or modified bases.
Nucleotide Excision Repair: Fixes bulky DNA damage that distorts the helix.
Telomere Maintenance: In eukaryotes, Telomerase maintains chromosomal ends using the specialized sequence $TTAGGG$ , repeated $100$ to $1000$ times to prevent loss of genetic material.

RNA Transcription and Processing

Transcription is the process of making an RNA copy of a gene’s DNA sequence. The resulting messenger RNA (mRNA) carries encoded genes to the ribosome.

Comparison of Transcription

Prokaryotes:
- Architecture: Polycistronic (codes for multiple proteins).
- Promoter: Short and simple. Contains the $-35\,\text{Element (TTGACA)}$ for binding and the $-10\,\text{Element (TATAAT)}$ for initiation.
- RNA Polymerase: Single type.
- Location: Cytoplasm (highly accessible).
- Processing: Not required.
Eukaryotes:
- Architecture: Monocistronic (codes for one protein).
- Promoter: Long and complex. Contains a TATA Box ( $-35$ to $-25$ ) and a $+1\,\text{Element}$ for initiation.
- RNA Polymerase: Uses types I, II, and III.
- Location: Nucleus (less accessible).
- Processing: Extensive (splicing, capping, tailing).

Transcriptional Steps and Strand Identification

Initiation: RNA polymerase binds to the promoter. The Antisense (template) strand runs $3'$ to $5'$ , while the Sense (coding) strand runs $5'$ to $3'$ .
Elongation: Nucleotides are added to the mRNA in the $5'$ to $3'$ direction.
Termination: The process stops and the transcript is released.

Genetic Code: Every three nucleotides on the mRNA form a codon (triplet) which corresponds to an amino acid.

Post-Transcriptional Modifications

Prokaryotes: RNases degrade RNA, while RNA-binding proteins stabilize it.
Eukaryotes: Involves Ribonucleoproteins (snRNPs) and the Spliceosome. Introns (non-coding) are removed, and Exons (coding) are spliced together. A $5'\,\text{Cap}$ and a $3'\,\text{poly-A tail}$ are added.

Protein Translation and Regulation

Translation is the process where ribosomes synthesize proteins from mRNA transcripts in the cytoplasm or endoplasmic reticulum.

Translational Comparison

Prokaryotic Architecture: Uses $70S$ ribosomes. mRNA contains the Shine-Dalgarno Sequence. The start codon is $AUG$ : fMethionine.
Eukaryotic Architecture: Uses $80S$ ribosomes. mRNA contains the Kozak Sequence. The start codon is $AUG$ : Methionine.

Prokaryotic Translation Steps

Initiation: mRNA start codon $AUG$ pairs with tRNA anticodon $UAC$ , carrying fMethionine.
Elongation: Involves three ribosomal sites—Aminoacyl (A) site, Peptidyl (P) site, and Exit (E) site.
Termination: Occurs when the ribosome hits Stop (Nonsense) codons.

Genetic Codon Chart Details

Phe (UUU, UUC), Leu (UUA, UUG, CUU, CUC, CUA, CUG), Ser (UCU, UCC, UCA, UCG, AGU, AGC).
Tyr (UAU, UAC), Cys (UGU, UGC), Trp (UGG).
Pro (CCU, CCC, CCA, CCG), His (CAU, CAC), Gln (CAA, CAG), Arg (CGU, CGC, CGA, CGG, AGA, AGG).
Ile (AUU, AUC, AUA), Met (AUG - Start), Thr (ACU, ACC, ACA, ACG), Asn (AAU, AAC), Lys (AAA, AAG).
Val (GUU, GUC, GUA, GUG), Ala (GCU, GCC, GCA, GCG), Asp (GAU, GAC), Glu (GAA, GAG), Gly (GGU, GGC, GGA, GGG).
Stop Codons: $UAA$ , $UAG$ , $UGA$ .

Post-Translational Regulation

Includes protein modification through phosphorylation, methylation, and acetylation. Eukaryotes specifically utilize glycosylation, prenylation, and myristoylation. Misfolded proteins are degraded by proteases.

Mutations and Mutagens

Mutations can be beneficial, harmful, or neutral, resulting in abnormal or absent proteins.

Types of Mutations

Gene (Point) Mutations:
- Silent: No change in amino acid.
- Missense: Changes one amino acid.
- Nonsense: Creates a premature stop codon.
Chromosomal Mutations:
- Frameshift: Insertions or Deletions that shift the reading frame.

Mutagens

Biological: Viruses, replication errors, transposons.
Chemical:
- Alkylating Agents (shifts purines or pyrimidines).
- Nucleoside Analogs (modified bases).
- Intercalating Agents (cause frameshifts).
Physical: Ionizing radiation and Non-ionizing radiation (causes Thymine Dimers).

Prokaryotic Diversity: Domain Bacteria

Bacteria are ubiquitous, single-celled organisms with peptidoglycan cell walls. Classification is often based on the G+C content (baseline of $50\%$ ) and Gram stain properties.

Deeply Branching Bacteria (Extremophiles)

Genus Aquifex: A. pyrophilus found in underwater volcanoes.
Genus Thermotoga: T. maritima (vents) and T. subterranea (oil reservoirs).
Genus Deinococcus: D. radiodurans (nicknamed ‘Conan the Bacterium’), a polyextremophile.

Atypical Bacteria

Phylum Tenericutes: Includes Mycoplasma pneumoniae (Walking Pneumonia). These lack a cell wall (pleomorphic) and are the smallest self-replicating organisms.
Phylum Chlamidiae: Obligate intracellular parasites. Chlamydia trachomatis is the most common bacterial STI.
Phylum Planctomycetes: Lack peptidoglycan; show compartmentalization.

Cell Envelope: Gram-Positive vs. Gram-Negative

Gram-Positive: Thick peptidoglycan ( $20-80\,\text{nm}$ , $+40$ layers). Contains Teichoic acid and Lipoteichoic acid. Stains purple.
Gram-Negative: Thin peptidoglycan ( $8-11\,\text{nm}$ , $3$ layers). Contains an Outer Membrane with Lipopolysaccharide (LPS) and Porins. Stains pink.

Phylum Actinobacteria (High G+C, +70%)

Streptomyces griseus: Source of antibiotics.
Bifidobacterium spp.: Found in intestines (probiotic).
Gardnerella vaginalis: Causes Vaginosis.
Corynebacterium diphtheria: Causes Diphtheria.
Mycobacterium: M. tuberculosis (Tuberculosis) and M. leprae (Leprosy).

Phylum Firmicutes (Low G+C, <30%)

Staphylococcus aureus: Causes pneumonia/septicemia; includes MRSA.
Streptococcus pyogenes: Causes Strep Throat/Scarlet Fever.
Bacillus: B. anthracis (Anthrax) and B. cereus (food poisoning).
Clostridium: C. botulinum (Botulism - most potent neurotoxin), C. tetani (Tetanus/Lockjaw), and C. difficile.

Gram-Negative Diversity: Proteobacteria and Others

Photosynthetic Bacteria:
- Phylum Cyanobacteria: Pioneers of the oxygen atmosphere ( $20-30\%$ of global oxygen).
- Phylum Chlorobi: Green sulfur bacteria (anoxygenic).
Phylum Spirochaetes: Helical with an axial filament. Includes Borrelia burgdorferi (Lyme Disease via ticks) and Treponema pallidum (Syphilis).
Phylum Proteobacteria: Divided into classes:
- Alpha: Low-nutrient specialists (Oligotrophs). Rickettsia (Typhus), Brucella (Brucellosis), Bartonella henselae (Cat Scratch Disease).
- Beta: Bordetella pertussis (Whooping Cough), Neisseria gonorrhoeae (Gonorrhea).
- Gamma: Largest group. Pseudomonas aeruginosa (antibiotic resistant), Vibrio cholerae (Cholera), Yersinia pestis (Plague).
- Delta: Bdellovibrio (predatory) and Myxobacteria (fruiting bodies).
- Epsilon: Smallest group. Helicobacter pylori (ulcers) and Campylobacter jejuni (gastroenteritis).

Domain Archaea

Archaea are extremophiles distinct from bacteria, recognized by Carl Woese via rRNA sequencing.

Characteristics: Single circular chromosome with histones, unique cell membranes (bilayers or monolayers), and archaealla for motility.
Extreme Habitats: Hot springs ( $122^\circ\text{C}$ ), hydrothermal vents ( $+400^\circ\text{C}$ ), salt lakes (<35\%), and high acidity (p\text{H} < 0) or alkalinity (p\text{H} > 9).
Phyla:
- Euryarchaeota: Includes Halophiles (Halobacterium) and Methanogens (Methanobacterium).
- Crenarchaeota: Primarily aquatic extremophiles (Sulfolobus at p\text{H} < 0, Thermoproteus at $80^\circ\text{C}$ ).
- Thaumarchaeota: Involved in aquatic nitrogen cycling (Nitrosopumilus).

Eukaryotic Diversity: Algae, Protozoa, and Others

Algae

Autotrophic protists that lack true stems/roots/leaves. Categorized into Phaeophyta (brown), Chrysophyta (golden), Bacillariophyta (diatoms - provide $20\%$ of oxygen), Chlorophyta (green), and Rhodophyta (red). They contribute $80\%$ of Earth's $O_2$ .

Protozoa (Animal-like Protists)

Unicellular chemoheterotrophs classified by movement:

Supergroup Excavata:
- Flagellates: Trypanosoma cruzi (Chagas Disease via Triatomine bug), Trypanosoma brucei (African Sleeping Sickness via Tsetse fly), Giardia lamblia (Giardiasis via contaminated water).
- Naegleria fowleri: Brain-eating amoeba causing PAM.
- Trichomonas vaginalis: Most common parasitic STI.
Supergroup SAR:
- Ciliates: Balantidium coli (intestinal parasite).
- Apicomplexans: Obligate intracellular parasites with complex life cycles. Includes Plasmodium falciparum (Malaria) and Toxoplasma gondii (Toxoplasmosis via cat feces).
- Dinoflagellates: Cause harmful algal blooms (red tides) and Paralytic Shellfish Poisoning.
Supergroup Amoebozoa: Use pseudopods. Entamoeba histolytica (Amebiasis) and Acanthamoeba (keratitis).

Lichens

A symbiotic relationship between a fungus (typically Ascomycota) and a photosynthetic partner (Algae or Cyanobacteria). Forms include Crustose, Foliose, and Fruticose.

Fungi (Mycology)

Heterotrophic decomposers with chitin cell walls and ergosterol membranes.

Phylum Microsporidia: Smallest eukaryotes; obligate intracellular parasites ( $Enterocytozoon bieneusi$ ).
Phylum Zygomycota: Filamentous molds like Rhizopus stolonifera (bread mold).
Phylum Basidiomycota: Club fungi (mushrooms). Includes Cryptococcus neoformans (meningitis) and Amanita phalloides (Death Cap).
Phylum Ascomycota: Sac fungi. Includes Penicillium, Candida albicans (yeast infections), and Saccharomyces cerevisiae (baker's yeast).

Parasitic Helminths

Multicellular invertebrates often with complex life cycles involving primary and intermediate hosts.

Phylum Nematoda (Roundworms)

Enterobius vermicularis (Pinworm): Most common in the USA.
Trichinella spiralis: Causes trichinosis from undercooked meat.
Wuchereria bancrofti: Causes Elephantiasis via mosquitoes.
Ascaris lumbricoides: Most common worldwide.
Necator americanus & Ancylostoma duodenale: Hookworms that penetrate skin.

Phylum Platyhelminthes (Flatworms)

Class Trematoda (Flukes): Leaf-shaped. Includes Schistosoma (Blood flukes) and Clonorchis sinensis (Liver fluke).
Class Cestoda (Tapeworms): Segmented (proglottids) with a scolex (head). Includes Taenia saginata (beef) and Taenia solium (pork; causes cysticercosis).

Acellular Pathogens: Viruses, Viroids, and Prions

Viruses are obligate intracellular parasites lacking metabolism.

Viral Classification

DNA Viruses: Replicate in the nucleus. Enveloped examples: Herpesviridae, Poxviridae (Smallpox). Non-enveloped: Adenoviridae, Papillomaviridae (HPV).
RNA Viruses: High mutation rates.
- +ssRNA: Directly translated (e.g., Coronavirus, Rhinovirus, Polio).
- -ssRNA: Must synthesize +ssRNA (e.g., Rabies, Ebola, Influenza).
- Retroviruses: Use Reverse Transcriptase to integrate into host DNA (e.g., HIV).

Viroids and Virusoids

Viroids: Short, circular ssRNA plant pathogens without a protein coat.
Virusoids: Non-self-replicating ssRNAs requiring a helper virus (e.g., Sobemovirus).

Prions

Misfolded infectious proteins ( $200-250\,\text{AA}$ ) that cause fatal neurodegenerative diseases like Creutzfeldt-Jakob Disease and Bovine Spongiform Encephalopathy (Mad Cow Disease). They cause "spongy holes" in the brain and are extremely resistant to destruction.