Prokaryotes vs Eukaryotes: Taxonomy and Morphology

Taxonomy

• It is the science of classifying living organisms.

Prokaryotes Vs Eukaryotes

• Prokaryotes are organisms that lack a nucleus, for example, bacteria.
• Eukaryotes are organisms with a nucleus.

Differences Between Prokaryotes and Eukaryotes

• Prokaryotes have genetic material distributed in the cytoplasm because they do not have a nucleus.
• Eukaryotes have genetic material located inside the nucleus.
• Prokaryotes reproduce via binary fission.
• Eukaryotes reproduce using mitosis and meiosis.
• Prokaryotes may possess extrachromosomal elements like plasmids, located outside the chromosome.
• Eukaryotes do not have extrachromosomal elements.
• Prokaryotes lack membrane-bound organelles.
• Eukaryotes have membrane-bound organelles.

Morphology

• Morphology is study of shapes and structures.
• Bacteria are categorized into three groups based on shape.
• Cocci are spherical.
• Bacilli are rod-shaped.
• Spirochetes are spiral shaped.
• Bacteria may occur in clusters, chains, pairs, or as single cells.
• Bacteria classification falls into two main categories based on Gram stain results.
• Gram-negative bacteria stain pink and are more resistant to antibiotics.
• Gram-positive bacteria stain purple.

Structures of Bacteria

• Bacteria structures include flagella, pili, glycocalyx and capsule.
• Flagella mediate bacterial movement, and some bacteria lack these.
• Flagella types are mono, lopho and peri.
• Pili (or fimbriae) facilitate attachment to host cells and control gene transfer.
• Glycocalyx mediates bacterial attachment.
• Capsule is important for adhesion and inhibiting phagocytosis, and lab identification and vaccine production.

Gram Positive & Gram Negative Bacteria

• Gram-positive bacteria cell walls are composed mainly of a thick peptidoglycan layer.
• Gram-negative bacteria cell walls are complex, including lipopolysaccharide, lipoprotein, phospholipid, and peptidoglycan.

Bacteria lacking cell walls

• Mycoplasmas do not have a cell wall.

Cell Membrane Functions in Bacteria

• Selectively diffuses molecules inside membrane.
• Undergoes aerobic respiration.
• Incorporates bacterial receptors to detect environmental signals.

Cytoplasm

• Cytoplasm of bacterial cell consists of ribosomes and genetic material.

Spores

• Formed in response to unfavorable conditions.
• Bacillus and Clostridium are two bacteria that produce spores.
• Spores can be located centrally, subterminally, or terminally within the cell.

Classification Between Bacteria

• Bacteria is phenotypically classified based on observable traits.
• Bacteria is genotypically classified based on DNA similarity.

Necessity for Bacteria

• Water is essential for bacterial growth.
• Some bacteria are aerobic or anaerobic.
• Oxygen is essential for aerobic bacteria and an inhibitor for anaerobic bacteria.
• Autotrophs use CO₂ directly.
• Heterotrophs cannot directly use CO₂ and must obtain carbon from organic forms.

Growth Cycle

• Four main phases in the bacterial growth cycle include lag, log, stationary, and decline (death).
• Lag phase is period where bacteria adjust to the environment without significant reproduction.
• Log phase is period of exponential growth.
• Stationary phase is where bacteria reproduction slows due to nutrient depletion and toxic product accumulation.
• Decline (Death) phase is where viable cell numbers decline.

External Factors Required for Bacterial Growth

• Temperature influences bacterial growth.
• Mesophilic bacteria require moderate temperatures; most human bacteria are mesophilic.
• Thermophilic bacteria require high temperatures.
• Psychrophilic bacteria require cold temperatures.
• Neutrophilic bacteria survive in neutral pH.
• Acidophilic bacteria survive in acidic environments.
• Oxygen is either a requirement or is toxic.
• Obligate aerobic bacteria require oxygen to survive.
• Strict anaerobic bacteria die with oxygen.
• Facultative anaerobic/aerobic bacteria can live with and without oxygen.
• Microaerophilic bacteria require low oxygen amounts and die with high amounts.
• Capnophilic bacteria require carbon dioxide to survive.

Plasmids in Bacteria

• F plasmids facilitate conjugation with extrachromosomal genetic material replication, independent of the regular chromosome.
• R plasmids confer resistance to antibiotics.

Genetics of Bacteria

• Bacteria are haploid, having one copy of chromosomes (genes).
• A gene is a specific DNA segment coding for a protein.
• Mutation is a permanent change in nucleotide sequence of the genome.
• Types of Mutation are substitution or frameshift.
• Substitution preserves nucleotide sequence length.
• Frameshift (insertion or deletion) alters sequence length.
• Gene transfer involves genetic material transfer.
• Conjugation is gene transfer by F plasmid.

Viruses

• These are among the tiniest microorganisms capable of infecting bacteria, animals, and plants.

Typical Characteristics of Viruses

• They are small and range from 1/10th of the size of bacteria.
• Viruses are metabolically inactive and cannot carry out metabolic processes on their own outside a host cell; for that reason they are intracellular parasites.
• Consist of a specific genome.

Virus Structure

• Viruses contain a genome, capsid and sometimes an envelope.
• Genomes consist of either DNA, RNA, or both.
• Capsid is a protein shell that protects the genome.
• It helps attach a virus to host cells.
• Capsids are made of subunits called capsomeres.
• Some viruses have an extra layer called an envelope (lipoprotein sheath).
• Glycoprotein units in enveloped viruses are called peplomeres or spikes.

Types of DNA Viruses

• Common types include Papoviruses, Poxviruses, Adenoviruses, parvoviruses, Hepadnaviruses and Herpes viruses.
• Papillomaviruses cause both benign growths (papillomas, warts) and cancers, especially in genital or oral areas.
• Poxviruses are the largest animal viruses.
• Adenoviruses cause eye, respiratory, and digestive infections.
• Parvovirus B19 is found in asymptomatic blood donors.
• Fifth disease (Slapped-cheek syndrome) is a common childhood infection caused by B19. The symptoms are fever and flu.
• Hepadnaviruses are causative agents of hepatitis B, chronic liver infections, and liver cancer.
• Herpesviruses are sensitive at room temperature and easily inactivated by lipid solvents.
• These viruses can cause cells to fuse together and form giant cells (Tzanck cells/Lipschütz bodies).
• Herpesviruses can stay dormant.

Types of RNA Viruses

• Includes, Picornavirus, Togaviruses, Orthomyxoviruses, Paramyxoviruses and Corona Viruses.
• Picornaviruses are the smallest RNA viruses.
• Important Picornavirus types are: Rhinoviruses cause respiratory infections, Enteroviruses cause digestive system infections.
• Human enteroviruses include Poliovirus, Echovirus, and Coxsackievirus.
• Togaviruses are the causative agent of Rubella.
• Orthomyxoviruses include influenza virus.
• Orthomyxoviruses influenza types A and B can affect both humans and animals.
• Paramyxoviruses is a family of viruses that cause diseases such as parainfluenza, mumps, measles, RSV, and croup.
• Corona Viruses can cause infections ranging from mild (common cold) to severe (SARS, COVID-19).
• In infants Corona viruses can cause gastroenteritis.
• Those with COVID-19 (SARS-CoV-2) can experience fever, dry cough, loss of taste/smell and a runny nose.
• In severe COVID-19 cases symptoms include shortness of breath.

Retroviruses

• Are tumor viruses with a diploid genome (two copies of RNA).
• Use reverse transcriptase (RT) enzyme to convert RNA to DNA.
• RNA → DNA → mRNA → Protein is a unique retrovirus replication strategy.

Viral Replication

• Replication is the process by which a copies itself inside the host cell.
• Replication occurs in the cytoplasm or nucleus.
• The latent or eclipse period is the time between virus entry and new virus production.

Stages of Replication

• Attachment - virus binds to host cell receptors.
• Penetration - virus enters host cell.
• Uncoating - capsid and envelope are removed, exposing genetic material.
• Transcription - viral RNA or DNA is used to produce mRNA.
• Translation - viral protein is made from mRNA.
• Assembly - new viruses are put together inside the cell.
• Release - new viruses leave the host cell to infect other cells.

Prions

• They are unique infectious agents composed solely of proteins.
• They infect the central nervous system (CNS), causing brain damage.
• They have long incubation periods before symptoms appear.
• Prions cause TSE (Transmissible Spongiform Encephalopathy).
• They make the brain have holes appearing like a sponge causing brain damage.

Prion Diseases

• Common types are: Scrapie which is a prion disease in sheep.
• Kuru occurs because of cannibalism.
• Creutzfeldt-Jakob Disease (CJD) runs in families, mostly occurring at 40-60 years
• Variant Creutzfeldt-Jakob Disease (vCJD): related to mad cow disease, typically affecting young adults.

Pathogenesis and Microbial Diseases

• Pathogenesis describes a microbe's ability to cause disease or infection.

Key Terms

• Pathogen is a microorganism that can cause disease.
• Opportunistic microorganisms can cause disease only in people with a weakened immune system.
• Virulent microorganisms cause disease even with a small number of organisms.

Important Measurements

• LD50 (Lethal Dose 50) specifies the number of organisms to kill 50% of hosts.
• ID50 (Infectious Dose 50) specifies the number of organisms to infect 50% of hosts.

Disease Terms

• Communicable diseases pass from one person (host) to another.
• Contagious diseases are highly communicable/spread very easily.
• Endemic diseases are found at low/stable levels in specific areas/communities.
• Epidemic diseases are more frequent than usual in specific areas or in specified populations.
• Pandemic diseases spread worldwide.
• Subclinical (Inapparent) infections do not show symptoms, so patients do not know that they have it.
• Chronic diseases remain in the body long-term, even after recovery.
• Latent infections are caused when pathogens stay in your body without causing symptoms then reactivate later to cause illness.

Stages of Infection

• Incubation Period is when pathogen enters body, but no symptoms or signs appear.
• Prodromal Period is a period of early/non-specific symptoms may appear that do not clearly point to a diagnosis.
• Acute Specific Illness Period is when specific symptoms of infection manifest.
• Recovery Period is when the body beings healing the infection.

Pathogenesis of Bacteria

• Transmission: Bacteria can enter the body through exogenous sources (from the environment) and endogenous sources (from within the body).
• Main entry routes: Skin (cuts/wounds), respiratory tract (breathing), gastrointestinal tract (food/water), genitourinary tract (sexual contact/urinary tract), and blood (direct entry).
• Adherence: After entering a host, bacteria must attach to host cells' surfaces/prostheses to initiate infection.
• Biofilm formation: Bacteria form biofilms which are communities of bacteria that live together. The structure is composed of extracellular polysaccharides (sugar) and has a protective "shield" protecting the bacteria.
• Quorum sensing: In a biofilm, bacteria can communicate and reject new bacteria from surrounding populations.
• Sessile organisms (bacteria in a biofilm) are highly resistant to treatments. This is because they are antibodies and have an immune response.
• Invasiveness: Some bacteria produces an enzyme to break into tissues.
• Collagenase/Hyaluronidase breakdown collagen/Hyaluronic acid.
• Coagulase is an enzyme that creates blood clot.
• IgA protease breakdown Immune defense (white blood cell).

Toxigenicity (Toxin Production)

• Endotoxins are exclusively found in gram-negative bacteria and are not actively released. Example effects are fever, hypotension/shock, inflammation, and DIC (disseminated intravascular coagulation).
• Exotoxins are found in both gram-negative and gram-positive bacteria and can damage and harm tissue to cause illness. When an body encounters exotoxin, the immune system create creating antitoxins. Antitoxins helps neutralize toxin effects.
• A toxoid is an inactivated exotoxin that does not stimulate response. Since there are no longer any harmful substances, a treated form of an endotoxin is commonly used as a vaccine to train them.

Medically Important Exotoxins

• Neurotoxins affect nerve cells. They are tetanus toxin, botulism toxin and diphtheria toxin.
• Tetanus toxin: prevent inhibitory neurotransmitter to release causing muscle spasm.
• Botulism toxin: prevents release of stimulatory neurotransmitter causing muscle paralysis.
• Diphtheria toxin: inhibits protein synthesis in cells.
• Enterotoxins affect the digestive system/intestimes .
• E. Coli enterotoxin can produce a toxin that causes diarrhea/gastrointestinal symptoms.

Virus Entry

• Skin & Mucosa.
• Intestinal tract.
• Respiratory tract.
• Genitourinary tract.

Viral Spread

• Local Spread: Occurs when a virus infects epithelial cells causing an infection to stay in one spot.
• Lymphatic Spread: Occurs when a virus travels through the lymphatic system and reaches lymph.
• Blood Spread (viremia) is the process of a virus spreading through the bloodstream.
• Primary Viremia is when a virus enters the bloodstream from the lymph nodes.
• Secondary Viremia occurs when a virus re-enters the blood stream after spreading in tissue.
• CNS & PNS Spread: A virus can spread through the CNS and PNS.

Virus and Host Cell Interaction

• Permissive Infection which causes lytic or cyctocidal infection. Can kill as well.
• Non-permissive Infection, a virus can replicate inside host but no kill
• Latent Infection occurs when viral nucleic present, as provirus like: HSV, VZV, HIV
• Chronic Infection a virus can appear for a long time, and the infected person is a carrier. -Ex: Hepatitis B and C
• Oncogenic Infection that cancer ex HIV
• Slow virus infection and long incubation period occurs (long period before symptoms appear).

Koch's Postulates.

1. Isolate from the infected host tissue of the infected to be in the same location that disease symptom show (especially where the infection is)
2. Must exist in lab or outside the tissue itself.
3. Ability to cause disease in animals
4. Re-isolate from the animal (animal to confirm)