Week 1 - The Microbial World

Microbiology

The study of microorganisms/microbes and how they interact with humans

Microbes

Forms of life too small to be seen by the naked eye, including viruses

The 7 bases of life

1. Cellular composition

2. Metabolism

3. Growth

4. Reproduction

5. Genetic variation/evolution

6. Response/adaptation to external environment

7. Homeostasis

Proteins/polypeptides (subunits, functions, dry weight of cell %)

• Amino acids

• Enzymes catalyze biochemical reactions, while other proteins are structural components

• 50-55% of cell

Nucleic acids (subunits, functions, dry weight of cell %)

• DNA: provides the instructions for the assembly and reproduction of the cell (2-5%)

• RNA: produces proteins and has structural or catalytic functions (15-20%)

Lipids (subunits, functions, dry weight of cell %)

• Diverse structures as subunits

• Structural functions, make up cell membranes and the membranes of internal organelles

• 10%

Polysaccharides (subunits, functions, dry weight of cell %)

• Sugars

• Structural functions (ex. cellulose and chitin) and energy storage (ex. glycogen and glucose)

• 6-7%

Most important purpose of polypeptides

Enzymes as catalysts of chemical reactions

RNA polymerase (location + function)

• Bacteria/archaea cytoplasm, eukarya nucleus

• Produces RNA from DNA template

Glycogen phosphorylase (location + function)

• Cytoplasm

• Converts glycogen to glucose

K+ channel (location + function)

• Plasma membrane

• Passive transport of K+ across the cell membrane

Na+/K+ ATPase (location + function)

• Plasma membrane

• Active transport of Na and K across the membrane

Flagelin (location + function)

• Bacterial flagellum

• Helps bacterial mobility

FtsZ (location + function)

• Plasma membrane of bacteria

• Component of cell division machinery

Plasma membrane

The lipid bilayer of a cell, can have embedded sugars and proteins

How were organisms categorized before the 3 domains?

Prokaryote or eukaryote based on the presence of membrane-bound organelles

How did Carl Woese establish the 3 domains of life?

Compared the rRNA genes in difference organisms to establish bacteria, archaea, and eukarya

Nuclear membrane in the 3 domains

• Bacteria: none

• Archaea: none

• Eukarya: yes

Membrane-bound organelles in the 3 domains

• Bacteria: rare

• Archaea: rare

• Eukarya: yes

Plasma membrane in the 3 domains

• Bacteria: similar to eukarya

• Archaea: different

• Eukarya: similar to bacteria

Cell wall in the 3 domains

• Bacteria: made of peptidoglycan

• Archaea: made of various materials

• Eukarya: only in some species, made of various materials

RNAP in the 3 domains

• Bacteria: single polymerase

• Archaea: single polymerase

• Eukarya: 3 polymerases

Histones in the 3 domains

• Bacteria: histone-like proteins

• Archaea: yes

• Eukarya: yes

Why is there debate of whether or not viruses are alive?

Needs a host cell to carry out functions of life, but it possesses DNA that can evolve

What makes microbes good model organisms?

• Cheap, fast, and easy to grow

• Can produce enzymes and other molecules for industrial/medical uses

• Genetically simple

• Easy to manipulate (unicellular)

Examples of model microbes

E. coli, Saccharomyces cerevisiae (baker’s yeast)

Order of the origin of life

Primordial soup > macromolecules > RNA and micelles > primitive cell using RNA > DNA > prokaryotes > eukaryotes

Conditions of early Earth

• Little oxygen in the atmosphere

• Soup of chemicals on the surface

How long have microbes been on Earth?

3.8 bya

Microbial fossil record

Not very well-documented since fossil formation is so particular and microbes are so small

Stromatollites

Fossilized mats of microbes (cyanobacteria)

What did Stanley Miller and Harold Urey prove?

Organic molecules can arise from inorganic primordial soup

RNA world hypothesis

Since RNA can catalyze reactions (ribozymes), early life on Earth was probably based on RNA

Micelle

A single lipid layer that may have been an early form of a plasma membrane

Endosymbiotic theory + who proposed it

Proposed by Lynn Margulis. Primitive prokaryotic microbes ate other microbes (mitochondria or chloroplasts), starting a symbiotic relationship and forming the first basic eukaryotes

Heterotroph vs autotroph

Use organic compounds as a carbon source, vs. use carbon dioxide as a carbon source and create organic compounds

Fermentation vs aerobic respiration

Doesn’t need oxygen but doesn’t yield much energy vs needs oxygen and yields much more energy

Why is DNA better than RNA for storing genetic info?

1. 2 strands provides a backup copy of information

2. DNA is more stable than RNA

Central dogma

DNA >(transcription)> mRNA > (translation)> proteins + tRNA and rRNA are important too, showing the versatility of RNA

Glycolysis

Converting glucose to pyruvate for the Krebs Cycle/fermentation anaerobically

Biogeochemical cycling

Process where inorganic molecules are cycled to organic molecules and back again

Microbial communities

Microbes do not exist individually and instead in colonies (ex. dental plaque, mold growths, intestinal microbes)

Biotechnology

Use of biological processes/organisms to produce goods (ex. producing human insulin by inserting the gene into E.coli cells)

The nitrogen cycle

1. Nitrogen fixation: N2 gas > ammonia

2. Nitrification: ammonia > nitrate

3. Ammonification: nitrogen from organic matter > ammonia

4. Denitrification: nitrate > N2 gas

Recombinant DNA

DNA containing a new gene of interest by splicing it into a plasmid using sticky ends, then inserting it back into bacteria

Spontaneous generation theory

Life can spontaneously form from nonliving matter

Louis Pasteur’s experiment

Used an S-shaped beaker to show that bacterial growth did not occur in sterile broth but did when it had contact with the dust with bacteria, disproving spontaneous generation theory

Robert Koch

Determined the causes of anthrax and tuberculosis, established Koch’s postulates to determine which microbes cause which diseases

Factors reducing disease mortality

• Antiseptics

• Sanitation improvements

• Food/water safety (pasteurization)

• Vaccination

• Personal hygiene improvements

• Antibiotics

Evidence of the endosymbiotic theory

• Mitochondria/chloroplasts have their own DNA and protein synthesis machinery

• Similar 16S rRNA gene sequences as bacteria

Phylogeny

History of an organism’s evolution

Anton van Leeuwenhoek

First person to provide a written description of bacteria by designing microscopes