Chapter 1-8: Introduction to Microbiology and Biochemistry
Benefits and applications of microorganisms
Bioremediation: microorganisms help clean toxins and pollutants; many are naturally occurring.
Mention of organisms that can degrade plastics; potential application in landfills and the environment.
Microorganisms as pesticides: an example given is Bacillus anthracis used in crop dusting to control insects.
It produces spores; when ingested by insects, the bacteria produce protein crystals that are toxic to the insects.
Note: in practice, Bacillus thuringiensis is the well-known microbial insecticide; the transcript references Bacillus anthracis, which is a pathogen. This distinction is important in real-world contexts.
Infectious diseases and the host microbiome
Humans are covered with bacteria; the immune system interacts with these microorganisms.
Skin as a barrier:
Skin is described as being 90% covered with a scaph epidermis (likely intended: epidermis); space and nutrients on the skin affect microbial colonization.
Routine use of sanitizers (e.g., Purell) can reduce resident organisms; this may influence subsequent exposure to new microbes.
Skin is dry, which limits most organisms; Staphylococcus thrives in dry, salty skin environments due to sweating and saltiness.
Opportunistic infections:
Disruption of normal microflora, especially in the gut, can permit infections such as Clostridium difficile (C. diff) when broad-spectrum antibiotics are used for a long period.
Biofilms:
Biofilms are communities of microorganisms that can include different species, embedded in a slimy extracellular matrix.
They can form on many surfaces: teeth (dental plaque), contact lenses, catheters, showers, pipes, rocks in rivers, etc.
The NIH estimates that 60–80% of infectious diseases in humans are associated with biofilms.
Biofilms provide protection against antibiotics and immune responses due to the slime layer, making infections harder to eradicate.
Examples of biofilm-related infections: chronic lung infections in cystic fibrosis patients, inner ear infections, urinary tract infections, and infections on medical devices like pacemakers.
Emergent infectious diseases and surveillance:
Infectious diseases can be categorized as emerging, reemerging, or deliberately emerging (bioterrorism).
Newly emerging diseases (red in schematic): e.g., malaria, measles, diphtheria, cholera.
Reemerging diseases (blue) are returning after a period of decline.
Deliberately emerging (black) refers to bioterrorism (e.g., anthrax mail incidents in 2001).
Notable emerging or reemerging pathogens and concepts discussed:
Influenza A (H5N1, H1N1 swine flu): the flu virus mutates annually; vaccines are updated to match circulating strains.
MRSA (methicillin-resistant Staphylococcus aureus): resistant to many antibiotics; vancomycin used as a last resort; emergence of vancomycin-resistant strains.
West Nile virus: viral encephalitis transmitted by birds and vectors (mosquitoes).
Prions: infectious proteins (e.g., BSE/mad cow disease) causing neurodegenerative diseases; extremely difficult to sterilize; prion sterilization requires extended and specialized procedures; incubation can be years.
E. coli O157:H7: causes food poisoning and can lead to hemolytic uremic syndrome (kidney failure) if not treated promptly.
Group A Streptococcus (flesh-eating bacteria) and Vibrio species: cause severe soft-tissue infections and are associated with severe outcomes in some cases.
Ebola and Marburg viruses: highly infectious viral hemorrhagic fevers (primarily in Africa).
Cryptosporidiosis: protozoan causing diarrhea, found in contaminated water and pools.
AIDS and COVID-19: long-standing and ongoing public-health challenges.
The takeaway: most microorganisms are beneficial, but a subset causes disease; ongoing vigilance and research are essential.
Basic chemistry and biology foundations (essential ideas)
Major elements and composition of life:
The four elements that make up about 96% of living matter: ext{C}, ext{N}, ext{O}, ext{H}
The remaining ~4% includes: ext{P}, ext{S}, ext{Ca}, ext{K} and other trace elements.
Biological significance: carbon, hydrogen, nitrogen, and oxygen form the backbone of organic molecules; phosphorus, sulfur, calcium, potassium contribute to functional groups and biochemical processes.
Organic vs inorganic compounds:
Inorganic: typically do not contain carbon-hydrogen (C-H) backbones (with some exceptions like CO2, CO).
Organic: always contain carbon and hydrogen (C–H) and tend to be larger and more complex (including macromolecules).
Hydrocarbons: compounds consisting only of carbon and hydrogen (e.g., propane, butane).
Macromolecules and monomers/polymers:
Macromolecules are large molecules built from repeating units called monomers.
Examples of monomers: glucose (carbohydrates), amino acids (proteins), nucleotides (nucleic acids), glycerol and fatty acids (lipids).
Polymers are long chains of monomers (e.g., glycogen, starch, cellulose, chitin, proteins, nucleic acids).
Important concept: inclusion bodies in bacteria store glycogen and other materials; bacteria are composed of macromolecules like other organisms, but lack membrane-bound organelles.
Covalent bonds and molecule architecture:
Most organic molecules are held together by covalent bonds (strong bonds) between atoms like C–H, C–C, C–O, etc.
Functional groups, not just the carbon-hydrogen backbone, determine the chemical behavior and classification of macromolecules.
Functional groups (six biologically important ones discussed):
Hydroxyl group: ext{-OH}; hydrophilic and increases polarity; common in carbohydrates.
Carbonyl group: ext{C}= ext{O}; part of aldehydes or ketones depending on position; in carbohydrates, carbonyl location differentiates aldose vs ketose.
Carboxyl group: ext{-COOH}; acidic; found in amino acids and fatty acids.
Sulfhydryl group: ext{-SH}; occurs in cysteine; can form disulfide bonds crucial for protein structure.
Amino group: ext{-NH}_2; acts as a base; found in amino acids.
Phosphate group: ext{-PO}_4^{3-} (in phospholipids and nucleic acids); contributes to polarity and energy transfer in metabolism.
Functional groups as determinants of molecular behavior:
A carbon-hydrogen backbone by itself is relatively inert; functional groups enable chemical reactivity and define macromolecule class (carbohydrate, lipid, protein, nucleic acid).
A carbon atom can form four covalent bonds, enabling vast molecular diversity.
A compound may contain multiple functional groups, enabling complex chemistry (e.g., amino acids have both an amino and a carboxyl group).
Monomers and polymers terminology:
Monomer: a single subunit (e.g., glucose, nucleotides, amino acids).
Polymer: a long chain of monomers (e.g., starch, glycogen, cellulose, chitin, nucleic acids, proteins).
Nucleotides form nucleic acids (DNA, RNA); amino acids form proteins; monosaccharides form polysaccharides.
Reactions: polymer formation and breakdown
Dehydration (condensation) synthesis: joining two monomers with release of a water molecule.
Generic form: ext{Monomer}1 + ext{Monomer}2
ightarrow ext{Polymer} + H_2OHydrolysis (breakdown) reactions: splitting polymers by adding water.
Generic form: ext{Polymer} + H2O ightarrow ext{Monomer}1 + ext{Monomer}_2
Carbohydrates: structure, function, and examples
Definition and roles:
Carbohydrates are large and diverse; they serve as energy sources and structural components in cells.
Primary energy source for many organisms is glucose; glucose is also the backbone of many polysaccharides.
Simple vs complex carbohydrates:
Simple carbohydrates: monosaccharides and disaccharides.
Complex carbohydrates: polysaccharides.
Monosaccharides (simple sugars):
Range from 3 to 7 carbon atoms per molecule; prefixes indicate carbon count: triose (3C), tetrose (4C), pentose (5C), hexose (6C), heptose (7C).
Pentoses: ribose and deoxyribose are the sugars of RNA and DNA, respectively.
Hexoses: glucose, fructose, and galactose are common hexoses.
They can exist in linear or cyclic forms; cyclic forms are more common in solution.
Common formula: C6H{12}O_6 for many hexoses like glucose and fructose; glucose and fructose share this formula but differ in the position of the carbonyl group (aldose vs ketose).
Disaccharides:
Formed by dehydration synthesis of two monosaccharides.
Common examples: sucrose (glucose + fructose), lactose (glucose + galactose), maltose (glucose + glucose).
Polysaccharides (complex carbohydrates):
Glycogen: glucose polymer used for short-term energy storage in animals (liver and muscle); also stored in bacterial inclusion bodies; highly branched with α-1,4 and α-1,6 linkages.
Starch: glucose polymer used by plants for energy storage; two components include amylose (unbranched, α-1,4) and amylopectin (branched, α-1,6).
Cellulose: glucose polymer used for structural support in plants and some algae; β-1,4 linkages (cellulose is rigid and not digestible by humans).
Chitin: glucose derivative (N-acetylglucosamine) polymer; structural component in fungal cell walls and arthropod exoskeletons.
Bacterial cell walls and polysaccharides:
The bacterial cell wall includes peptidoglycan, a disaccharide composed of N-acetylglucosamine (NAG) and N-acetylmuramic acid (NAM) linked together, with cross-linking peptides.
This organization allows antibiotics to target cell wall synthesis (e.g., penicillin and cephalosporins) and vancomycin, which disrupts peptidoglycan formation.
Archaea and some bacteria have cell walls that differ from peptidoglycan.
Important examples and linkage details:
Fructose and glucose share the formula C6H{12}O_6; glucose has an aldehyde carbonyl at the end (aldose), fructose has an internal carbonyl (ketose).
Cell walls in bacteria contain peptidoglycan made from modified glucose units: N-acetylglucosamine (NAG) and N-acetylmuramic acid (NAM).
The sugar components and the peptide cross-links give structural integrity to bacterial cells and are targets for antibiotics.
Biological relevance of polysaccharides:
Glycogen and starch store energy (short-term in animals and plants, respectively).
Cellulose provides structural support in plants and some algae.
Chitin serves as a major structural polysaccharide in fungi and arthropods.
The edible and clinical implications of biofilms and disease control
Biofilms in everyday life and medicine:
Biofilms form on medical devices (catheters, implants) and in everyday settings (dental plaque, shower biofilms, contact lenses).
Biofilms contribute to persistent infections and increased resistance to antibiotics and immune clearance.
Notable clinical implications:
Biofilms are implicated in a large fraction of infectious diseases; they complicate treatment and may require device removal or alternative therapies.
Dental plaque is a natural example of a biofilm, explaining why oral hygiene (flossing) disrupts a biofilm layer.
Practical considerations:
Overuse of antiseptics like hand sanitizers can disrupt the normal skin microbiota, potentially changing susceptibility to certain infections.
Public health strategies must consider biofilms in device design, cleaning protocols, and antibiotic stewardship to mitigate resistance.
Quick reference: notable pathogens, diseases, and concepts mentioned
MRSA: Methicillin-resistant Staphylococcus aureus; resistant to many antibiotics; vancomycin is a last-resort treatment, with emerging resistance.
West Nile virus: Causes encephalitis; transmitted via vectors (mosquitoes) from birds.
Prions: Infectious proteins causing neurodegenerative diseases (e.g., BSE/mad cow disease); difficult to sterilize; long incubation periods.
E. coli O157:H7: Causes foodborne illness and can lead to hemolytic uremic syndrome in severe cases.
Group A Streptococcus: Flesh-eating bacteria; severe infections.
Vibrio species: Flesh-eating bacteria associated with seawater exposure; potential for severe infections.
Ebola and Marburg: Filoviruses causing hemorrhagic fevers, with high mortality.
Cryptosporidiosis: Protozoan diarrhea from contaminated water.
AIDS and COVID-19: Ongoing global health concerns.
Concept recap: key terminology and concepts to remember
Monomer vs. Polymer: building block vs. long-chain molecule (e.g., glucose → glycogen).
Dehydration (condensation) synthesis: Monomer-Monomer linkage with release of water: ext{Monomer}1 + ext{Monomer}2
ightarrow ext{Polymer} + H_2OHydrolysis: Polymer breakdown by adding water: ext{Polymer} + H2O ightarrow ext{Monomer}1 + ext{Monomer}_2
Functional groups determine molecule behavior and classification (carbohydrates, lipids, proteins, nucleic acids).
Carbon’s tetravalence (four covalent bonds) enables vast structural diversity in biomolecules.
Carbohydrate chemistry basics: hexoses (6C) like glucose/fructose; pentoses (5C) like ribose/deoxyribose; aldehyde vs ketone distinction hinges on carbonyl placement.
Peptidoglycan in bacterial cell walls vs other organisms’ walls (e.g., cellulose in plants, chitin in fungi) and implications for antibiotic targeting.
Biofilm biology: protective matrix, surface colonization, antibiotic resistance, and clinical burden; ubiquity from teeth to devices.