Module 1: The Microbial World Flashcards
What are microorganisms?
Microscopic forms of life (organisms too small to see with the naked eye)
What ARENT microorganisms?
WHY?
Viruses
–> Because they technically aren’t living, they can’t be considered organisms
What organisms are considered microorganisms? (5)
1) Bacteria
2) Protozoa
3) Archaea
4) Fungi
5) Algae
What are microbes?
Refers to microorganisms AND viruses
What is microbiology?
The study of microbes
Ways in which microbes HELP humans: (6)
1) Food digestion
2) Protect from harmful microbial invaders
3) Used to advance understanding of molecular machinery (research models)
4) Provide nitrogen to plant roots (nitrogen fixing bacteria)
5) Carry out fermentation (Ex: yogurt/alcohol,etc.)
6) Medicine production (Ex: Insulin)
Ways in which microbes DONT help humans: (3)
1) Infectious diseases
2) Crop failure
3) Food rot
What are the characteristics of life?
1) Made up of cells
2) Capable of:
a) Growth
b) Reproduction
c) Metabolism
3) Contain Genetic Information (+ variation)
4) Respond to external stimuli and ADAPT to external environ.
5) Homeostasis
What is the working definition of life?
A set of characteristics specific to a self-organizing, self replicating, non-equilibrium system that preserves and reinforces its existence in a given environment
Growth
Increase in mass of biological material
Reproduction
Production of new copies of an organism
Metabolism
A controlled set of chemical reactions within cells that extract energy + nutrients from the environment and transform them into new biological materials
Homeostasis
Active regulation of internal environment to maintain relative constancy despite external changes
Homeostasis vs Equilibrium
Homeostasis = an active process
Equilibrium = a passive state of being
–> Homeostasis attempts to achieve an equilibrium state in different systems
Why is homeostasis a condition of life but equilibrium is not?
Equilibrium implies a static state where no net change occurs:
–> essentially, a living organism at equilibrium is considered “dead” as it cannot respond to environmental fluctuations
Whereas an organism in homeostasis is “alive” as it is constantly responding to the environment rather than existing in a static state
All cells are foundationally made up of…
Macromolecules
What are macromolecules?
Large, complex organic molecules made up of (polymerized) simple subunits
Dry Weight
Weight obtained after removing all water from something (like a cell)
Macromolecules account for _________% of cellular dry weight
> 90% of cellular dry weight
4 major macromolecules
1) Polypeptides (proteins)
2) Nucleic Acids
3) Polysaccharides
4) Lipids
Polypeptides
AKA proteins
–> Polymers of amino acids joined together by peptide bonds
(often fold into highly specific structures which determine their function)
Polypeptide Functions
1) Enzymes –> Catalysis of chemical reactions
2) Structural Support/Cell Motility –> Cytoskeleton
3) Material Movement –> Membrane protein channels and pumps
What % of cellular dry weight do polypeptides make up?
~50-55% of cellular dry weight
What is the most abundant macromolecule?
Proteins (~50-55%)
FtsZ
Protein associated with bacterial cell membrane that is needed for bacterial reproduction
Flagellin
Protein that makes up bacterial flagellum (needed for bacterial motility)
Nucleic Acids
Polymers of nucleotides
What are nucleotides made up of?
1) Sugar
2) Phosphate group/s
3) Nitrogenous Base
Function of Deoxyribonucleotide Polymers
Information storage
(Ex: DNA)
Function of Ribonucleotide Polymers
Many functions, 2 main ones:
1) Protein Synthesis
2) Enzymatic Activity
Ex: RNA
% of cellular dry weight taken up by 1) deoxyribo- and 2) ribo- nucleotide polymers
1) Deoxyribonucleotides = 2-5% cellular dry weight
2) Ribonucleotides = 15-20% cellular dry weight
What is the second most abundant macromolecule?
Nucleic Acids
(~2-5% DNAs and ~15-20%RNAs)
Lipids
Hydrophobic hydrocarbon molecules
Lipid Functions
Main function =
structural –> Forms the foundation of plasma membranes which separate inside from outside
Why is a semi-permeable membrane beneficial/necessary?
To restrict the movement in and out of cells
–> Allows cells to capture and concentrate materials needed for metabolism and growth
–> Prevents the escape of metabolic products
–> Prevents (some) of the invasion of unwanted, foreign, and toxic materials
What % of cellular dry weight is lipids?
10%
What is the third most abundant macromolecule?
Lipids (10%)
Rank the macromolecules in terms of abundance
1) Proteins (most abundant) –> ~50-55%
2) Nucleic acids (RNA = ~15-20%, DNA = ~2-5%)
3) Lipids (~10%)
4) Polysaccharides (least abundant) (~6-7%)
Polysaccharides
Polymers of monosaccharides (sugars)
What is the general composition of polysaccharides (chemical equation)?
Made up entirely of C, H, O
–> General formula = C(n) (H2O)(n)
Polysaccharide Functions
1) Energy storage –> Ex: starch and glycogen
2) Structural –> Ex: Chitin and cellulose
What % of cellular dry weight is polysaccharides?
6-7%
What is the fourth most abundant macromolecule?
Polysaccharides
(~6-7% of dry weight)
Old classification for domains of life
1) Prokaryotes
2) Eukaryotes
What distinguished prokaryotes from eukaryotes?
The presence of a membrane bound nucleus (and membrane bound organelles as well)
Eukaryotes = Had a defined nucleus
Prokaryotes = LACKED a defined nucleus
How do prokaryotes and eukaryotes differ in terms of genetic material?
Prokaryotes = Singular circular chromosome
Eukaryotes = Multiple linear DNA molecules
New classification for domains of life
1) Bacteria
2) Archaea
3) Eukarya
Why did we switch away from the old classification for the domains of life?
Due to new research that found certain prokaryotes to have seem cellular machinery as eukaryotes
Who conducted the preliminary research that was responsible for changing the classifications of life?
CARL WOESE (1970)
What did Carl Woese investigate?
Investigated prokaryotes and eukaryotes
–> Observed similarities in the protein synthesis machinery between some prokaryotes and eukaryotes
–> He then investigated further by analyzing differences and similarities in the SMALL SUBUNIT RIBOSOMAL RNA
What is SSU rRNA?
–> Function?
Small Subunit Ribosomal RNA
–> Functions as a scaffold for ribosomal assembly AND interacts with mRNA during translation
What molecular structure did Carl Woese mainly study?
WHY?
SSU rRNA
–> Because it is present in all living organisms (necessary for protein synthesis) yet it contains enough variable regions to allow for accurate identification and comparison between different taxa
What were the impacts of Carl Woese’s work?
1) Led to major revisions of the taxonomy of life
2) Started a revolution about the phylogeny of organisms
What did Carl Woese find when studying SSU rRNA?
He found that the SSU rRNA sequences of some prokaryotes resembled that of eukaryotes
Phylogeny
Evolutionary History
What is this? What are the different taxa shown?
The revised phylogenetic tree of life
What does the dashed line and yellow circles mean?
Dashed line distance is proportional to evolutionary distance (represented by SSU rRNA similarity)
Yellow circles denoting the endpoints = individual species or organisms
In a phylogenetic tree, linear distance between any 2 endpoints is…
Proportional to evolutionary distance (and similarity of the SSU rRNA)
–> Closer together (small line distance) = closer evolutionarily (more similar SSU rRNA sequence
Archaea, bacteria, eukarya:
Nuclear Membrane
Archaea = NO
Bacteria = NO
Eukarya = YES
Archaea, bacteria, eukarya:
Membrane-Bound Organelles
Archaea = Rare (select species)
Bacteria = Rare (select species)
Eukarya = YES (all species and many types of organelles)
Archaea, bacteria, eukarya:
Plasma Membrane
Archaea = UNIQUE
Bacteria and Eukarya = SIMILAR
Archaea, bacteria, eukarya:
Cell Wall
Archaea = YES (all species) –> Varied composition
Bacteria = YES (all species) –> Made of peptidoglycan
Eukarya = ~ (some species) –> Varied composition
Archaea, bacteria, eukarya:
RNA Polymerase
Archaea = 1 type (like eukarya RNA Polym. II)
Bacteria = 1 type
Eukarya = 3 types
Archaea, bacteria, eukarya:
Histones
Archaea = YES
Bacteria = NO (Histone-like proteins; topoisomerases)
Eukarya = YES
What technique further aided in developing the phylogenetic tree of life?
PCR –> Allowed for large scale DNA sequencing and comparison between organisms
Advantages of using microbes in research:
1) Easily cultivated (Cheap to grow, FAST to grow/reproduce)
2) Small # of genes –> Easier to genetically manipulate
3) Industrial Production
–> Used to facilitate the production of enzymes, proteins, and other biomolecules for industrial or medical uses
Popular microbial research models:
1) Escherichia coli (E. Coli)
2) Saccharomyces cerevisiae (eukaryal yeast)
What was Paul Ehrlich the first to recognize?
First to recognize:
–> That differences in structures between human and bacterial cells could be targeted to selectively attack bacterial cells
What was Paul Ehrlich studying initially that led him to begin his work on antimicrobials?
Was studying dyes that differentially stained bacteria and human cells
What did Paul Ehrlich propose after noticing dying differences between bacteria and human cells?
Proposed the possibility of “Magic Molecular Bullets” that could specifically target and attack microbial invaders
In 1910, what did Paul Ehrlich discover?
Arsphenamine (Salvarsan)
–> An antimicrobial drug for syphilis
What is arsphenamine?
AKA Salvarsan (Commercial Name)
–> An arsenic containing organic compound that acted as a antimicrobial drug for the bacteria causing syphilis
–> FIRST commercial antimicrobial drug!
What bacteria did Salvarsan target?
Treponema pallidum
When was Salvarsan abandoned?
In 1940 (penicillin became popular)
What led to the discontinuation of Salvarsan?
1) Safety Issues –> Salvarsan did kill the syphilis bacteria but it was also toxic to healthy human cells
2) Better Alternative –> PENICILLIN was found!
When was Penicillin discovered?
Who discovered it?
In 1928
By Alexander Fleming
What was the larger impact of Paul Ehrlich’s work?
Established that lethal agents could be developed to selectively target microbial cells
–> Led to the modern antibiotics we know today
When was Earth formed?
~4.5B years before present
When is the theorized origin of life?
~3.8B years before present
Between the formation of Earth and the first signs of life, what was occurring on Earth?
CHEMICAL EVOLUTION
–> Believed that the synthesis of biomolecules was occurring
What was prebiotic Earth like?
Hot, sterile, and anoxic
What was the Miller-Urey experiment investigating?
Investigated whether or not the synthesis of organic molecules from inorganic starting materials was possible under the potential conditions of primordial Earth
Procedure/Set Up for the Miller-Urey Experiment:
1) Water-filled flask (simulating Earth’s oceans) was heated to boil
–> The Water flask was connected to a “primitive atmosphere” (NH3, CH4, H2)
2) Water vapor from the boiling water moved up the flask and into the atmosphere chamber
3) Electrical sparks were dispersed into the atmosphere chamber
4) A condenser column allowed vapors in the atmosphere to condense and flow out of the atmosphere chamber and BACK into the original water flask (ocean)
What was the purpose of the electrical sparks in the Miller-Urey experiment?
To mimic potential energy inputs on early Earth:
1) Lightning (which was rampant on early Earth)
2) Heat from the Sun + Earth’s crust
–> This energy possibly helped certain chemical reaction occur!
What was the primitive atmosphere composed of in the Miller-Urey experiment?
1) Ammonia (NH3)
2) Methane (CH4)
3) Hydrogen (H2)
What was a criticism of the Miller-Urey Experiment?
That the primitive atmosphere composition they utilized was not representative of the actual atmospheric composition of early Earth
What was observed in the Miller-Urey experiment? (specific molecules)
After a few days of continuously operating the reactor, the water in the flask had turned a deep red color
–> The water was analyzed and the following AMINO ACIDS were found:
1) GLYCINE
2) ANALINE
3) ASPARTIC ACID
What were the conclusions drawn from the Miller-Urey Experiment?
Biomolecules could be synthesized from inorganic precursors under conditions thought to mimic primordial Earth
–> FIRST evidence of this!
From the Miller-Urey experiment, what did other scientists do?
Attempted to repeat the Miller-Urey experiment with different hypothesized early Earth atmosphere compositions
Under what atmospheric conditions was no biomolecule synthesis observed?
CO2 + N2 rich atmosphere
–> Yielded few to NO organic molecules
(refuted the Miller-Urey experiment)
In further tested Hydrogen rich atmospheric conditions, what was found?
Abiotic production of MANY amino acids, nitrogenous bases, and organic molecules was observed!
(supported the Miller-Urey experiment)
Regardless of whether or not biomolecules came from abiotic synthesis,
what critical info did the Miller-Urey experiment provide?
Showed that organic molecule synthesis REQUIRED WATER
What other evidence contradicted the theory of abiotic synthesis of biomolecules on Earth?
Some evidence exists that organic molecules may have been BROUGHT to Earth by comets and asteroids that crashed into the planet
(Some organic molecules have been found on comets and asteroids)
According to the the Miller-Urey duo and their results, where did they hypothesize life originated from?
“Prebiotic Soup”
–> Believed that organic molecules accumulated within the early oceans creating a “prebiotic soup” that organized cellular life eventually arose from
When was the Miller-Urey experiment done?
(Scientists names?)
1953
Harold Urey and Stanley Miller
What did Gunter Wachterhauser hypothesize?
Hypothesized that maybe instead of the organic molecules floating in the oceans that they adhered to and accumulated on some metallic surfaces of the Earth’s crust
–> Specifically stated IRON surfaces
What was Gunter Wachterhauser’s proposed theory for the formation of life?
Life evolved on iron containing surfaces
–> Adherence to the iron surfaces possibly allowed for proper positioning of molecules to then react with each other leading to many of the cellular reactions needed for life
Evidence for Gunter Wachterhauser’s theory
1) Many modern proteins must bind iron to function properly (hemes, cytochromes)
2) Many enzymes require binding to metals for activity (RNA polymerase)
What hypothesis did Carl Woese propose?
the “RNA WORLD” hypothesis
What was the RNA WORLD hypothesis?
In the early stages of life on Earth, RNA molecules acted as both the genetic material and the catalysts for chemical reaction (dual function)
–> Proposed that cellular life was maintained by RNA systems before DNA and further proteins were created
Ribozymes
RNA molecule that acts as a catalyst
What is the theory of how the first cells formed?
1) Polar lipids formed
2) Spontaneous micelle and bilayer formation
(perhaps around other biomolecules, enclosing them inside! )
–> If a ribozyme got encapsulated by this spontaneous vesicle formation, a cell could have formed
Progenote
A cell hypothesized to store info in genes not yet linked together on chromosomes
Who proposed the idea of a progenote?
Carl Woese (his proposed “first organism”)
Why was there an increase in genetic variation among progeny?
Because there was probably a high rate of mutation (due to no machinery being present for effective gene repair)
–> High mutation rates probably led to lots of genetic variation among progeny
How did Darwinian Evolution impact progeny?
The progeny that survived and reproduced the most would have spread most rapidly
Darwinian Evolution Criteria
1) Genetic variation
2) Environmental selective pressure
3) Differential survival and reproductive success
Current theory on the evolution of life (full)
1) Sterile Earth
2) Abiotic biomolecule synthesis (primarily RNA)
3) Self-replicating RNAs enclosed in an early membrane
4) RNA acted as catalysyts and info storage
5) RNA info synthesized proteins which took over catalytic activity
6) Development of DNA from RNA occurred; DNA took over genetic storage
–> This series of events would explain how the central dogma formed
Who was a significant pusher of the endosymbiotic theory?
Lynn Margulis
What is the endosymbiotic theory?
A theory of how eukaryotic cells evolved to contain mitochondria and chloroplasts through a process of endosymbiosis
Endosymbiosis
A symbiotic relationship (mutually beneficial) in which one organisms lives INISDE the other one
What is the suggested endosymbiotic theory process?
Believed to have been 2 endosymbiotic events:
First Event –> Primitive cell engulfed an aerobically respiring bacteria that eventually became a permanent part of the cell, developing into the mitochondrion
Second Event –> Some of the aerobic cells also engulfed smaller photosynthesizing bacteria (mainly cyanobacteria) which also became permanent structures in the cell leading to the formation of chloroplasts
Relationship between aerobic bacteria and host cell:
Host cell provided:
safe environment and access to nutrients
Aerobic bacteria provided:
Extra ATP access!
What did the development of mitochondria lead to?
Allowed for cells to increase in size (as they had enough energy to support larger structures)
Allowed for cells to form complex multicellular systems
Relationship between photosynthetic bacteria and host cell:
Host cell provided:
Safe environment and access to nutrients
Photosynthetic bacteria provided:
New energy sources and the ability to expand into new habitats (didn’t need to follow a food source)
What gene was primarily used as evidence of the endosymbiotic theory?
16S rRNA Gene
16S rRNA gene
Encodes for the SSU rRNA molecule found in bacteria
What evidence supports the endosymbiotic theory?
1) Mitochondria and chloroplasts have their own (circular) genome
2)) The 16S rRNA gene of mitochondria and chloroplasts have been found to be similar to specific groups of bacteria
What is dsDNA?
Double-stranded DNA
Why was DNA favored over RNA for genetic storage?
1) 100x more stable than RNA (safer from degradation)
2) Complementary strands offer a “backup” copy in case one strand is damaged
–> Overall, reproduces and transmits genetic info more faithfully (less risk of the genetic info being changed)
Types of RNA
mRNA –> Transcribed from DNA and directs AA sequence of protein synthesis
tRNA –> Brings AAs to ribosomes during translation
rRNA –> Structural scaffold of ribosome and catalyzes peptide bond formation during protein synthesis
Mutation
Heritable changes in the base sequence of a genome
–> The ultimate source of genetic variation
Horizontal Gene Transfer
How bacteria are able to exchange genes between different cells
Contributions of Anton Van Leeuwenhoek
First to observe microbes
1) Achieved up to 300x magnification using a single lens microscope
2) Demonstrated the use of microscopes to view biological ultrastructures
When were the first microbes observed?
1623-1673
By Anton Van Leeuwenhoek
Who was the “Father of Microbiology”?
Anton Van Leeuwenhoek
Contribution of Robert Hooke
Developed CELL THEORY
(the guy who looked at cork under a microscope)
–> First to observe and name the basic unit of life “cells”
What is Cell Theory?
All living organisms are made up of cells
What were the two competing theories about how microbes arise?
1) Spontaneous Generation Theory
2) Biogenesis Theory
Spontaneous Generation Theory
Hypothesis that life arises spontaneously from non-living matter
(and that a “vital force” is needed for life)
Biogenesis Theory
The hypothesis that all living cells arise only from PRE-EXISTING living cells
Evidence supporting the spontaneous generation theory
Experiment conducted by John Needham (1745)
John Needham’s Experiment Procedure
1) Placed nutrient broth into an OPEN flask
2) Heated the broth to boil and then let cool in the OPEN flask
3) Once cooled, sealed the flask with a stopper
4) Left for a while and then noted any observations of microbial growth
John Neeham’s Study
Results + Conclusion
Results:
Microbial growth was found in the flask after boiling, a process that should have killed any present microbes
Conclusion:
The microbes must have spontaneously generated from the broth
Flaws in the John Needham Study
1) Did not boil for long enough to kill all microbes present in the broth
2) Had an open system; did not account for contamination by microbes in the air
What was the FIRST evidence supporting the theory of biogenesis?
Lazzaro Spallanzani’s Experiment (1765)
Lazzaro Spallanzani’s Experiment Procedure
Repeated Needham’s study but with a change:
One run of the experiment had a sealed flask and the other did not
1) Put nutrient broth into sealed and unsealed flasks
2) Boiled the broth in both flasks
3) Waited and observed if any microbial growth occurred
Lazzaro Spallanzani’s Experiment
Results + Conclusion
Unsealed Flask (open) = Microbial growth
Sealed Flask (closed) = NO microbial growth
Conclusion –> life arose from pre-existing microorganisms in the air and not spontaneously from the broth itself
Why was there pushback on Spallanzani’s experiment?
People believed that sealing the flask deprived the medium of oxygen or some vital force necessary for microbial growth, resulting in the lack of microbial growth
What experiment definitively refuted the spontaneous generation theory?
WHEN was it?
Louis Pasteur’s Experiment (1858)
Louis Pasteur Experimental Setup/Procedure
1) Placed nutrient broth into an S-Shaped Flask
2) Boiled the broth
3) Left it to cool and observed for any microbial growth
4) Then tipped the flask so that the broth came into contact with the neck area
5) Tipped it back upright and waited to observe for any microbial growth
Louis Pasteur Experiment:
Results
Flask left upright (not coming into contact with the air microbes) =
NO microbial growth
Flask tilted (coming into contact with the air microbes) =
MICROBIAL GROWTH
Why did Pasteur use an S-Shaped flask?
To allow for an open system (addressing the issues people had with spallanzani’s experiment
BUT also preventing air microbes on dust particles from getting to the nutrient broth (preventing contamination)
–> The microbes got trapped in the neck of the flask and therefore never reached the broth unless the flask was tipped
What was the conclusion from the Pasteur experiment?
Microbial life in the broth could only result from microbial life in the neck of the flask
–> Life did NOT spontaneously generate!
Germ Theory
The theory that diseases are caused by the action of microorganisms
Who FIRST coined/proposed germ theory?
Robert Koch
What was the first piece of evidence leading to the development of germ theory?
Robert Koch’s finding of Anthrax being caused by bacteria!
–> Found that Anthrax is caused by Bacillus anthracis
When did Robert Koch discover the bacterial cause of Anthrax?
1876
What were some other contributions of Robert Koch (other than Anthrax work)?
1) Koch’s Postulates
2) Identification of bacteria causing TB (Mycobacterium tuberculosis)
3) Lab technique of solidifying media with agar to isolate bacteria
How much of the population died due to the plague?
up to 60%
What bacteria causes the plague?
Yersinia pestis
What is the source of the plague?
How does this differ from the main mode of disease TRANSMISSION?
Bacterial Source = Rats
Main Transmitter = FLEAS
How was the plague transmitted?
1) Fleas bite infected rats (consume the infected blood)
2) Fleas carrying the infected blood bite humans and regurgitate the infected blood into the wound
3) Humans contract the infection and begin spreading it to other humans
How is infectious disease controlled?
1) Treatment
2) Prevention
What was the first antimicrobial drug?
Who made it?
SALVARSAN (arsphenamine)
Paul Ehrlich (1910)
What was the first SAFE antibiotic?
Penicillin
(Alexander Flemming in 1928)
What practices aid in preventing infectious disease? (5)
1) Disinfecting practices
2) Sanitation procedures (indoor plumbing, sewage disposal/treatment)
3) Personal hygiene
4) Food and water safety (Pasteurization, refrigeration, water treatment)
5) Vaccination
What were the contributions of Joseph Lister?
In 1860 he observed increased infection rates after surgery
(Hypothesized it was due to microbes on the tools and surgical environment)
Introduced the use of antiseptics (carbolic acid) to clean surgical tools
Pasteurization
Technique using mild heating, irradiation, or high pressure to destroy pathogenic microbes while maintaining the quality of food
–> Increases shelf-life and prevents infection
Vaccination
Exposing a person to an inactivated or weakened version of a microbe to create immunity to a disease
Who popularized the first vaccine?
Edward Jenner (1796)
–> Inoculated a boy with material from a milkmaid with cowpox and found that the boy was later immune to smallpox
