Microbes and Their Building Blocks

Introduction to Microbes and Their Building Blocks

Learning Outcomes Section 1.1

  • List the various types of microorganisms that can colonize humans.

  • Describe the role and impact of microbes on the earth.

  • Explain the theory of evolution and why it is called a theory.

  • Explain the ways that humans manipulate organisms for their own uses.

  • Summarize the relative burden of human disease caused by microbes.

  • Differentiate among bacteria, archaea, and eukaryotic microorganisms.

  • Identify two acellular infectious agents that are studied in microbiology.

  • Compare and contrast the relative sizes of the different microbes.

Microbes: Tiny but Mighty

  • Microbiology is a specialized area of biology that deals with living things ordinarily too small to be seen without magnification.

  • Microorganisms include:

    • Bacteria

    • Archaea

    • Protozoa

    • Fungi

    • Helminths

    • Algae

    • Viruses

    • Prions

The Nature of Microorganisms

  • Microbes are very easy and very difficult to study:

    • Reproduce rapidly

    • Can be grown quickly in large populations in the laboratory

    • Cannot be seen directly

    • Analyzed through indirect means

    • Viewed through microscopes

Microbes and the Planet

  • Microbes have shaped the development of earth’s habitat for billions of years

  • Single-celled organisms appeared on this planet about 3.8 billion years ago

  • Cell types arose from a single (extinct) common ancestor:

    • Eukaryotes: “true nucleus”

    • Bacteria: single-celled, no true nucleus

    • Archaea: single-celled, no true nucleus, distinct from bacteria

    • Prokaryotes: bacteria and archaea “pre-nucleus”

    • Akaryotes: “no nucleus” (alternate term used for prokaryotes)

Bacteria and Archaea versus Eukaryotes

  • Bacteria and archaea are predominantly single-celled

  • Eukaryotes:

    • Many are single-celled

    • Developed into highly complex multicellular organisms

    • Larger size

    • A small minority compared to bacteria and archaea

Microbes Are Ubiquitous

  • Microbes are ubiquitous and are found:

    • Deep in the earth’s crust

    • In polar ice caps and oceans

    • Inside the bodies of plants and animals

    • In the earth’s landscape

    • Essential to life

Theories of Evolution and Science

  • Theory of evolution:

    • The accumulation of changes that occur in organisms as they adapt to their environments

    • Documented every day in all corners of the planet

    • Testable by science

  • Theories in science:

    • Have undergone years and years of testing and have not been disproved

    • A well-studied and well-established natural phenomenon.

    • Not just a random guess

Photosynthesis

  • Photosynthesis:

    • Light-fueled conversion of carbon dioxide to organic material

    • Accompanied by the formation of oxygen

  • Anoxygenic photosynthesis:

    • Occurred in bacteria before plants evolved

    • Did not produce oxygen

    • More efficient in extracting energy from sunlight

  • Oxygenic photosynthesis:

    • Evolved from anoxygenic photosynthesis

    • Photosynthetic microorganisms are responsible for 70% of the earth’s photosynthesis.

How Microbes Shape Our Planet

  • Microorganisms are the main forces that drive the structure and content of the soil, water, and atmosphere:

    • Microbes produce CO<em>2CO<em>2, NONO, and CH</em>3CH</em>3 that insulate the earth’s atmosphere

    • Bacteria are the most abundant cellular organisms in the oceans.

    • Viruses are the most abundant inhabitants of the oceans

    • Bacteria and fungi live in close associations with plants and assist them in obtaining nutrients and water and may protect them against disease

Microbes and Humans

  • Historical uses of microbes by humans:

    • Bread production

    • Alcohol production

    • Cheese production

    • Treatment of wounds and lesions

    • Mining precious metals

    • Cleaning up human-created contamination

Biotechnology

  • Genetic engineering:

    • Manipulates the genetics of microbes, plants, and animals for the purpose of creating new products and genetically modified organisms (GMOs)

  • Recombinant DNA technology:

    • Makes it possible to transfer genetic material from one organism to another and deliberately alter DNA

  • Bioremediation:

    • Uses microbes already present or introduced intentionally to restore stability or clean up toxic pollutants

Microbes Harming Humans

  • The vast majority of microorganisms that associate with humans are harmless or beneficial

  • Pathogens: microbes that cause disease:

    • Over 2,000 different microbes cause disease

    • Ten billion infections occur across the world every year

    • Infectious diseases are important common causes of death worldwide

Microbes and Disease

  • Emerging and reemerging diseases:

    • AIDS

    • Hepatitis C

    • Zika virus

    • West Nile virus

    • Tuberculosis

  • Associations between noninfectious diseases and microbes:

    • Gastric ulcers are caused by Helicobacter pylori.

    • Multiple sclerosis, OCD, coronary artery disease, and obesity have been linked to chronic infections with microbes.

Infectious Disease Trends

  • Increasing number of patients with weakened defenses:

    • Subject to infections by common microbes that are not pathogenic to healthy people

  • Increase in microbes that are resistant to drugs

Cellular Organization

  • Eukaryotes:

    • Organelles: small, double-membrane-bound structures that perform specific functions:

      • Examples: nucleus, mitochondria, chloroplasts

    • Some are microorganisms; some are macroscopic

  • Bacteria and Archaea:

    • Ten times smaller than eukaryotes

    • Lack organelles

    • All are microorganisms

Viruses

  • Viruses:

    • Not independently living cellular organisms

    • Exist at the level of complexity somewhere between large molecules and cells

    • Composed of a small amount of hereditary material (DNA or RNA) surrounded by a protein coat and sometimes a membrane

  • Prions:

    • Simpler than viruses

    • No nucleic acid, only protein act like infectious microorganisms

Learning Outcomes Section 1.2

  • Make a time line of the development of microbiology from the 1600s to today.

  • List some recent microbiology discoveries of great impact.

  • Identify the important features of the scientific method.

Microbes in History

  • Spontaneous generation:

    • The belief that invisible vital forces present in matter led to the creation of life

  • Even after the discovery of microbes, the belief in abiogenesis, which embraced spontaneous generation, was still embraced by some scientists

  • Other scientists advocated biogenesis, saying that living things arise only from others of their same kind

Louis Pasteur

  • Studied the roles of microorganisms in the fermentation of beer and wine

  • Swan-necked flask experiments used to disprove spontaneous generation:

    • Filled flasks with broth and shaped the openings into long, swan-necked tubes

    • Heated the flasks to sterilize the broth

    • Flasks that were exposed to dust from the air showed microbial growth

    • Flasks exposed to air but not to dust showed no microbial growth

The Role of the Microscope

  • Robert Hooke:

    • Studied household objects, plants, and trees

    • Described cellular structures and drew sketches of “little structures” that seemed alive

  • Antonie van Leeuwenhoek:

    • Manufactured simple microscopes to study fabrics

    • Observed “animals” in a drop of water

    • Observed “animacules” scraped from teeth

    • Constructed over 250 small microscopes that could magnify objects up to 300 times

The Beginnings of Medical Microbiology

  • Ferdinand Cohn: discovered and described heat-resistant endospores

  • Oliver Wendell Holmes and Ignaz Semmelweis: described the importance of hand washing in preventing disease in the hospital setting

  • Joseph Lister: used aseptic techniques in surgery

The Germ Theory of Disease

  • Louis Pasteur:

    • Invented pasteurization

    • Conducted the first studies linking human disease to infection

  • Robert Koch:

    • Koch’s postulates are a series of logical steps that establish whether or not an organism is pathogenic and which disease it caused

    • Showed that anthrax was caused by Bacillus anthracis in 1875

Discovery of Restriction Enzymes – 1970s

  • Three scientists, Daniel Nathans, Werner Arber, and Hamilton Smith, discovered these little molecular “scissors” inside bacteria

  • They chop up DNA in specific ways

  • This allows scientists to use these enzymes to cut DNA in tailor-made ways

  • This opened the floodgates to genetic engineering and all that has meant for the treatment of diseases, the investigation into biological processes, and the biological “revolution” of the 21st century

The Invention of the PCR Technique – 1980s

  • The polymerase chain reaction (PCR) was a breakthrough in our ability to detect tiny amounts of DNA and then amplify them into quantities sufficient for studying

  • It has provided a new and powerful method for discovering new organisms, diagnosing infectious diseases, and for forensic work such as crime scene investigation

The Importance of Small RNAs – 2000s

  • Genome sequencing has revealed that perhaps only 2% of DNA actually codes for a protein

  • Much RNA doesn’t end up with a protein counterpart

  • These pieces of RNA are usually small

  • It now appears that they have critical roles in regulating what happens in the cell

  • It has led to new approaches to how diseases are treated

  • For example, if the small RNAs are important in bacteria that infect humans, they can be new targets for antimicrobial therapy

Genetic Identification of the Human Microbiome – 2010s and Beyond

  • The first detailed information produced by the Human Microbiome Project (HMP) was astounding: Even though the exact types of microbes found in and on different people are highly diverse, the overall set of metabolic capabilities the bacterial communities possess is remarkably similar among people

  • This and other groundbreaking discoveries have set the stage for new knowledge of our microbial guests and their role in our overall health and disease

Learning Outcomes Section 1.3

  • Name the four main families of biochemicals.

  • Provide examples of cell components made from each of the families of biochemicals.

  • Differentiate among primary, secondary, tertiary, and quaternary levels of protein structure.

  • List the three components of a nucleotide.

  • Name the nitrogen bases of DNA and RNA.

  • List the three components of ATP.

  • Recall three characteristics common to all cells.

Macromolecules: Superstructures of Life

  • Macromolecules:

    • Very large

    • Four main types:

      • Carbohydrates

      • Lipids

      • Proteins

      • Nucleic acids

    • Monomers: subunits of macromolecules

    • Polymers: chains of various lengths of monomers

Carbohydrates

  • Combinations of carbon and water:

    • Represented by the formula (CH<em>2O)</em>n(CH<em>2O)</em>n

    • End with the suffix –ose:

      • Hexose: 6-carbon sugar

      • Pentose: 5-carbon sugar

    • Glucose: the most common and universally important hexose

    • Fructose: named for fruit

    • Xylose: from the Greek word for “wood”

    • Lactose: important component of milk

    • Maltose: malt sugar

    • Sucrose: table sugar or cane sugar

Polysaccharides

  • Contribute to structural support and protection; serve as nutrient and energy stores:

    • Cellulose: cell wall of plants and many microscopic algae

    • Agar: important component of culture media

    • Chitin: cell wall found in fungi

    • Peptidoglycan: component of bacterial cell wall

    • Lipopolysaccharide: component of gram-negative cell wall

    • Glycocalyx: protective outer layer; role in the attachment of cells to other cells or surfaces

Lipids

  • Triglycerides:

    • Important storage lipid

    • Composed of a single molecule of glycerol bound to three fatty acids

    • Fatty acids can be saturated or unsaturated

    • Stored in long-term concentrated form as droplets or globules

    • Yield twice as much energy per gram as other storage molecules (carbohydrates)

Phospholipids in Membranes

  • Membrane lipids:

    • Hydrophilic (“water-loving”) head; negative charge

    • Hydrophobic (“water-fearing”) tail; uncharged

    • When exposed to an aqueous solution:

      • Charged heads are attracted to the water phase

      • Nonpolar tails are repelled from the water

      • They naturally assume a single or double layer (bilayer)

    • This behavior allows them to be the main constituent of all cell membranes

Steroids and Waxes

  • Steroids:

    • Complex ringed compounds found in cell membranes and as animal hormones

    • Cholesterol reinforces the cell membrane in animal cells and cell-wall-deficient bacteria

  • Waxes:

    • Ester formed between a long-chain alcohol and a saturated fatty acid

    • Waterproofing in fur, feathers, fruits, leaves, human skin, insect exoskeletons, etc.

    • Found in the cell wall of bacteria that cause tuberculosis and leprosy, contributing to their disease-causing potential

Proteins: Shapers of Life

  • Proteins:

    • Predominant organic molecules in cells

    • Composed of 20 different amino acids

    • Peptide: a molecule composed of short chains of amino acids

    • Polypeptide: usually has more than 20 amino acids and is often a smaller subunit of a protein

    • Protein: usually contains a minimum of 50 amino acids

Primary and Secondary Protein Structure

  • Primary (1°) structure: type, number, and order of amino acids in the chain

  • Secondary (2°) structure: arises when various functional groups (called R groups) interact by forming hydrogen bonds:

    • Alpha helix

    • Beta pleated sheet

Tertiary and Quaternary Protein Structure

  • Tertiary (3°) structure: created by additional bonds between functional groups:

    • Amino acids containing cysteine form disulfide bonds

  • Quaternary (4°) structure: when more than one polypeptide forms a large, multiunit protein

More Protein Structure and Diversity

  • Each protein develops a unique shape, and its surface displays a distinct pattern of pockets and bulges

  • Proteins can only interact with molecules that fit its particular surface features, like a lock and key

  • Enzymes: catalysts for all chemical reactions in cells

  • Antibodies: glycoproteins with specific regions of attachment for bacteria, viruses, and other microorganisms

Native versus Denatured Protein

  • Native state: the functional three-dimensional form of a protein

  • Denatured: disruption of the native state of a protein through the application of various agents:

    • Heat

    • Acid

    • Alcohol

    • Some disinfectants

The Nucleic Acid: A Cell Computer and Its Programs

  • DNA: contains a special coded genetic program with detailed and specific instructions for each organism’s heredity

  • RNA: “helper” molecules responsible for carrying out DNA’s instructions and translating the DNA program into proteins that can perform life functions

The Double Helix of DNA

  • Formed by two very long nucleotide strands linked along their length by hydrogen bonds between nitrogen bases

  • Pairing of nitrogen bases occurs according to a predictable pattern:

    • Adenine always pairs with thymine.

    • Guanine always pairs with cytosine.

RNA: Organizers of Protein Synthesis

  • Long chains of nucleotides, usually in a single strand:

    • mRNA: copy of a gene that provides the information for the order and type of amino acids in a protein

    • tRNA: carrier that delivers the correct amino acids for protein assembly

    • rRNA: major component of ribosomes

    • Fourth type of RNA acts to regulate the genes and gene expression

ATP: The Energy Molecule of Cells

  • Adenosine triphosphate:

    • Adenine

    • Ribose

    • Three high-energy phosphate molecules

  • Give off energy when the bond is broken between the second and third phosphate

  • Energy is released and stored for chemical reactions

Fundamental Characteristics of Cells

  • Bacteria and protozoa: single cell

  • Animals and plants: trillions of cells

  • Characteristics:

    • Spherical, polygonal, cuboidal, or cylindrical

    • Contain a protoplasm encased in a cell membrane

    • Have chromosomes containing DNA

    • Ribosomes for protein synthesis

    • Exceedingly complex in function

Eukaryotic versus Bacteria and Archaea Cells

  • Eukaryotic cells:

    • Animals, plants, fungi, protozoa

    • Contain organelles that are encased by membranes and perform specific functions

  • Bacteria and Archaea:

    • No nucleus or other organelles

    • Complex fine structure

    • Can engage in same activities as eukaryotic cells

Learning Outcomes Section 1.4

  • Differentiate among the terms nomenclature, taxonomy, and classification.

  • Create a mnemonic device for remembering the taxonomic categories.

  • Correctly write the binomial name for a microorganism.

  • Draw a diagram of the three major domains.

  • Explain the difference between traditional and molecular approaches to taxonomy.

Naming, Classifying, and Identifying Microorganisms

  • Taxonomy: the science of classifying living things:

    • Developed by Carl Von Linné (1701 to 1778)

    • Nomenclature: the assignment of scientific names to the various taxonomic categories and to individual organisms

    • Classification: the orderly arrangement of organisms into a hierarchy

    • Identification: the process of discovering and recording the traits of organisms so that they may be recognized or named and then classified

Nomenclature

  • The assignment of scientific names to various taxonomic categories and to individual organisms

  • Binomial system of nomenclature:

    • Scientific name is a combination of the genus and species names

    • Scientific names are italicized when they are written in print and underlined when they are written by hand

    • When the name is abbreviated, the genus name is abbreviated to the first initial followed by a period and the full species name is written

Classification

  • Organized into several descending ranks, beginning with the most general and ending with the smallest and most specific:

    • Domain

    • Kingdom

    • Phylum or division

    • Class

    • Order

    • Family

    • Genus

    • Species

The Origin and Evolution of Microorganisms

  • Phylogeny: the taxonomic scheme that represents the natural relatedness between groups of living beings

  • Evolution:

    • Hereditary information of living beings gradually changes through time

    • Changes result in various structural and functional changes through many generations

    • Selective for those changes that favor survival and reproduction, also known as natural selection

  • COVID-19: During the COVID-19 pandemic, it was declared that the virus had evolved from being able to infect non-human animals to being able to infect humans. This is an example of small (random) changes in the genetic information that happened to provide the virus a new “skill”: the ability to infect a new species.

A Universal Web of Life

  • Charles Darwin and Ernest Haeckel proposed two kingdoms: plants and animals:

    • Haeckel later added Protista (or Protozoa)

    • Haeckel then added Monera in 1870

  • Whittaker Model:

    • Added fungi in the period from 1959 to 1969

    • Based on structural similarities and differences

Woese-Fox System of Taxonomy

  • Based on conserved small subunit ribosomal RNA sequences (ssu 16S rRNA)

  • Analysis of these sequences revealed a separate group for the archaeabacteria called Archaea

  • An entirely new system was proposed based on domains:

    • Bacteria

    • Archaea

    • Eukarya