Genetics in Prokaryotes and Eukaryotes

Genome Organization and Size

Prokaryotic and eukaryotic organisms differ significantly in the size and organization of their genomes, which impacts their genetic complexity and regulatory mechanisms.

• Prokaryotic Genomes: Typically consist of a single, circular chromosome located in the nucleoid region. Plasmids (small, circular DNA molecules) may also be present.

• Eukaryotic Genomes: Composed of multiple, linear chromosomes contained within a membrane-bound nucleus. Eukaryotes often have more non-coding DNA and complex regulatory sequences.

• Genome Size: Eukaryotic genomes are generally much larger than prokaryotic genomes.

• Example: Escherichia coli (prokaryote) has ~4.6 million base pairs; humans (eukaryote) have ~3 billion base pairs.

DNA Structure and Function

DNA (deoxyribonucleic acid) is the hereditary material in all living organisms, encoding genetic information.

• Structure: Double helix composed of two antiparallel strands of nucleotides (adenine, thymine, cytosine, guanine).

• Base Pairing: Adenine pairs with thymine; cytosine pairs with guanine.

• Function: Stores genetic information, directs synthesis of RNA and proteins.

• Equation:

RNA Structure and Function

RNA (ribonucleic acid) is a single-stranded nucleic acid involved in protein synthesis and gene regulation.

• Types: mRNA (messenger), tRNA (transfer), rRNA (ribosomal).

• Base Pairing: Adenine pairs with uracil (instead of thymine); cytosine pairs with guanine.

• Function: mRNA carries genetic code from DNA to ribosomes; tRNA brings amino acids; rRNA forms part of ribosome structure.

Central Dogma: Flow of Genetic Information

Genetic information typically flows from DNA to RNA to protein, a process known as the central dogma of molecular biology.

• Transcription: DNA is transcribed into mRNA.

• Translation: mRNA is translated into a polypeptide (protein).

• Equation:

DNA Replication

DNA replication is the process by which a cell duplicates its DNA before cell division.

• Initiation: Begins at specific origins of replication.

• Enzymes: DNA helicase unwinds the helix; DNA polymerase synthesizes new strands.

• Direction: New DNA is synthesized in the 5' to 3' direction.

The Genetic Code and Amino Acids

The genetic code is a set of rules by which information encoded in mRNA is translated into proteins.

• Codons: Triplets of nucleotides in mRNA specify amino acids.

• Start Codon: AUG (methionine).

• Stop Codons: UAA, UAG, UGA.

• Redundancy: Multiple codons can code for the same amino acid.

Mutations, Mutagens, and Carcinogens

Mutations are changes in the DNA sequence. They can be spontaneous or induced by external agents.

• Induced Mutations: Caused by mutagens (chemicals, radiation).

• Carcinogens: Mutagens that cause cancer.

• Types: Point mutations, insertions, deletions.

• Example: UV light induces thymine dimers in DNA.

Horizontal Gene Transfer in Bacteria

Bacteria can acquire new genetic material from other organisms without cell division, increasing genetic diversity.

• Transformation: Uptake of free DNA from the environment.

• Other Methods: Conjugation (direct transfer via pilus), transduction (via bacteriophages).

• Significance: Can spread antibiotic resistance genes.

Viruses and Prions

Nature of Viruses

Viruses are nonliving infectious agents that require a host cell to replicate.

• Structure: Nucleic acid (DNA or RNA) surrounded by a protein coat (capsid); some have a lipid envelope.

• Obligate Intracellular Parasites: Cannot reproduce outside host cells.

Comparing Viruses, Prokaryotes, and Eukaryotes

The following table summarizes key differences among viruses, prokaryotes, and eukaryotes.

Viral Envelopes

Some viruses possess a lipid envelope derived from the host cell membrane, which aids in host cell entry and immune evasion.

• Enveloped Viruses: More sensitive to desiccation and disinfectants.

• Naked Viruses: Lack an envelope; generally more resistant to harsh conditions.

Medically Important Virus Families

Several virus families are significant in human disease. Key examples include:

• Hepadnaviridae: DNA viruses (e.g., Hepatitis B virus).

• Coronaviridae: RNA viruses (e.g., SARS-CoV-2).

• Retroviridae: RNA viruses that use reverse transcriptase (e.g., HIV).

Bacteriophage Replication

Bacteriophages (viruses that infect bacteria) replicate via two main cycles:

• Lytic Cycle: Virus replicates and lyses the host cell.

• Lysogenic Cycle: Viral DNA integrates into host genome and replicates with it.

Animal Virus Replication

Animal viruses follow a general replication cycle:

• Attachment to host cell

• Entry (fusion or endocytosis)

• Uncoating of viral genome

• Replication and synthesis of viral components

• Assembly of new virions

• Release (budding or lysis)

Persistent Infections and Cancer

Some viruses establish persistent infections that can lead to cancer (oncogenic viruses).

• Examples: Human papillomavirus (HPV), Hepatitis B and C viruses.

• Mechanism: Integration of viral DNA can disrupt host cell cycle regulation.

Detecting Viral Genetic Material

Laboratory techniques can detect viral nucleic acids for diagnosis.

• PCR (Polymerase Chain Reaction): Amplifies viral DNA/RNA.

• RT-PCR: Used for RNA viruses (reverse transcription step).

Prions

Prions are infectious proteins that cause neurodegenerative diseases.

• Characteristics: Lack nucleic acids; induce abnormal folding of normal proteins.

• Diseases: Creutzfeldt-Jakob disease, mad cow disease.

Microbial Growth and Control

Bacterial Growth Phases

Bacteria grown in a closed batch system exhibit four distinct growth phases:

• Lag Phase: Adaptation, no cell division.

• Log (Exponential) Phase: Rapid cell division.

• Stationary Phase: Nutrient depletion slows growth; cell death equals cell division.

• Death Phase: Cell death exceeds division.

Environmental Factors Affecting Growth

• Temperature: Psychrophiles (cold), mesophiles (moderate), thermophiles (hot).

• pH: Acidophiles, neutrophiles, alkaliphiles.

• Essential Nutrients: Carbon, nitrogen, sulfur, phosphorus, trace elements.

• Energy Sources: Phototrophs (light), chemotrophs (chemicals).

Culture Media

• Complex Media: Contains unknown exact composition (e.g., nutrient broth).

• Defined Media: Exact chemical composition is known.

• Selective Media: Inhibits growth of some microbes while allowing others.

Counting Microbes

• Direct Methods: Microscopic count, plate count (CFU).

• Indirect Methods: Turbidity (optical density), metabolic activity.

Microbial Control Strategies

Various methods are used to reduce or eliminate microbial contamination.

• Physical Methods: Heat (autoclaving, pasteurization), filtration, radiation.

• Chemical Methods: Disinfectants, antiseptics, antibiotics.

• Effectiveness: Depends on type of microbe and method used.

Microbial Metabolism

Catabolic and Anabolic Reactions

Metabolism consists of catabolic (breakdown) and anabolic (biosynthesis) reactions.

• Catabolism: Breaks down molecules to release energy.

• Anabolism: Uses energy to build complex molecules.

Enzyme-Substrate Interactions

Enzymes are biological catalysts that speed up metabolic reactions by lowering activation energy.

• Mechanism: Substrate binds to enzyme's active site, forming enzyme-substrate complex.

• Cofactors: Non-protein helpers (metal ions, coenzymes) required for enzyme activity.

Redox Reactions and ATP Production

Redox (reduction-oxidation) reactions transfer electrons, fueling ATP synthesis.

• ADP to ATP: Energy from redox reactions is used to add a phosphate to ADP, forming ATP.

• Equation:

Glycolysis

Glycolysis is the first step in cellular respiration, breaking down glucose into pyruvate.

• Location: Cytoplasm

• Net Yield: 2 ATP, 2 NADH per glucose

• Equation:

Cellular Respiration: Intermediate Step and Krebs Cycle

• Intermediate Step: Pyruvate is converted to acetyl-CoA, producing NADH and CO2.

• Krebs Cycle: Acetyl-CoA enters the cycle, generating NADH, FADH2, ATP, and CO2.

Electron Transport Chain (ETC)

The ETC uses electrons from NADH and FADH2 to generate a proton gradient, driving ATP synthesis.

• Location: Prokaryotes (plasma membrane), eukaryotes (mitochondrial inner membrane).

• Final Electron Acceptor: Oxygen (aerobic), other molecules (anaerobic).

ATP Yield: Aerobes vs. Anaerobes

• Aerobic Respiration: Up to 38 ATP per glucose (prokaryotes).

• Anaerobic Respiration: Less ATP, varies with electron acceptor.

Fermentation

Fermentation allows ATP production without a respiratory chain, using organic molecules as final electron acceptors.

• Alcohol Fermentation: Produces ethanol and CO2 (e.g., yeast).

• Lactic Acid Fermentation: Produces lactic acid (e.g., muscle cells, some bacteria).

Amphibolic Pathways

Amphibolic pathways function in both catabolism and anabolism, providing metabolic flexibility.

• Example: Krebs cycle intermediates used for amino acid synthesis.

Biochemical Tests for Bacterial Identification

• Oxidase Test: Detects presence of cytochrome c oxidase enzyme.

• Catalase Test: Detects catalase enzyme, which breaks down hydrogen peroxide.

• Application: Used to differentiate bacterial species in clinical microbiology.