Exam 1 Flashcards
Microbe
Microscopic organism (microorganism)
Requires microscope to see, invisible to the naked eye
Single celled organisms
For a long time, were the only lifeforms on Earth
Microbes include…
Bacteria
Archaea
Protozoa
Fungi (yeast and mold)
Algae
Viruses (simple, non-cellular)
(BAPFAV)
Disease
A condition that prevents the body from functioning normally
Exhibits signs and symptoms (e.g. nausea)
Pathogen
a disease-causing microbe
Goal: survival and reproduction (NOT disease)
Want to find a way to spread to new hosts; therefore, they cause symptoms that will increase their chances of spreading to a new host
The human body contains ~ _ ____ body cells and ~
_ ____ bacterial cells
30 trillion
Bacterial cells are much smaller so it doesn’t look like we’re covered in germs
Most human bacteria live in …
the gut/GI tract
Human microbiota
the microbes that stably live in/on the human body
The microbiota contributes to human health
Bacteria in our intestines (e.g. E. coli) aid digestion and synthesize vitamins
Prevent pathogenic bacteria from colonizing; Good bacteria is there first and blocks bad bacteria
Our bodies become populated by microbes at birth; c-section vs vaginal birth affects microbes
The Human Microbiome Initiative
Launched in 2016
Research funding to expand our understanding of the role of microbes in ecosystems such as the human body
Nomenclature
System of naming organisms still in use today
Developed in 1735 by Carolus Linnaeus
Assigns each organism two names, both italicized (underlined when written)
Names often describe the organism, honor a researcher, or identify the habitat
Genus
First name in nomenclature
Capitalized + Italicized
Can be abbreviated by initial
Species
Second name in nomenclature
Lowercase
Italicized
Bacteria
Unicellular
Prokaryotes – lack a nucleus (DNA not contained within membrane-bound organelle, floating around)
3 common cell shapes: bacillus rods, cocci spheres, spiral
Surrounded by a cell wall composed of peptidoglycan
Reproduce asexually through binary fission
Peptidoglycan
Chains of sugars (glycans) linked together by amino acids (peptide)
Archea
Unicellular
Prokaryotes
Cell wall, but not composed of peptidoglycan
Extremophiles, so not encountered a bunch in our lives
Not known to cause disease
Asexual reproduction (Often binary fission or similar process)
Extremophile
found in extreme environments
Methanogens
produce methane, in GI tract
Halophiles
live in extremely salty environments (salt lakes, not just oceans)
Thermophiles
live in extremely hot environments (thermal vents in ocean, hot springs)
Fungi
Eukaryotes (DNA contained within a nuclear membrane)
Can be multi or unicellular
Cell wall, composed of chitin (polysaccharide; sugars linked together)
Include yeast and mold
Dimorphic fungi flip back and forth between existing as mold and yeast
Yeast
unicellular fungi, larger than bacteria
Mold
form multicellular structures (mycelia – network of hyphae)
Protozoa
Eukaryotes
No cell wall
Very diverse
Many move through using pseudopods, flagella, or cilia
Can be free-living or parasitic
Algae
Eukaryotes
Cell wall composed of cellulose (polysaccharide)
Photosynthetic
Require sunlight, carbon dioxide, and water
Produce energy, oxygen, and carbohydrates
Viruses
Acellular (lack cellular structure)
Very small (requires electron microscope, light microscope not sufficient)
Simple structure
Reproduce by using machinery of other organisms/cells; Don’t possess their own cellular machinery
Strictly parasites
Often considered not alive
What 2 things does it take to be a virus?
- Nucleic acid genome (either DNA or RNA)
- Protein coat – capsid (encloses genetic material)
Optional: lipid membrane – envelope
Why are viruses often not considered to be alive?
No metabolism or cellular reactions
Host cell required for reproduction
Before microbes were discovered, all organisms were classified as….
plants or animals
Organic compounds
Compounds that contain at least 1 carbon-hydrogen bond (C-H)
Life wouldn’t be possible without organic compounds
Are vital to cells; Provide structure and perform functions
Inorganic compounds
compounds that lack C-H bonds
4 Types of Macromolecules
Carbohydrates (polysaccharide)
Lipids
Nucleic acids (DNA, RNA)
Proteins
What is the defining characteristic of prokaryotic cells compared to eukaryotic cells?
lack of a nucleus
Which organisms have a cell wall composed of peptidoglycan? Select all that apply.
Bacteria
The three domain model developed by Carl Woese in 1978 is widely accepted today. According to this model, what are the three domains?
Bacteria, Archaea, Eukaryotes
Who was the first to describe “cells” in dead cork tissue?
Robert Hooke
What was the purpose of Pasteur’s swan-neck flask?
To prevent microbes in the air from reaching the sterile broth in the flask & To allow gases in the air to reach the sterile broth in the flask
Which of the following developed a set of postulates for determining whether a particular disease is caused by a particular pathogen?
Robert Koch
What observation prompted Edward Jenner to use cowpox lesions to vaccinate against smallpox?
Individuals that had developed cowpox rarely developed smallpox later in life
Alexander Fleming noticed that bacteria did not grow near mold that had contaminated an agar plate. What did the mold secrete into the media that inhibited bacterial growth?
antibiotic
Studying bacterial genomes:
Involves studying all genes found within a bacterial cell
Allows us to determine what a microbe is capable of without having to observe it directly
Shows us how microbes are related evolutionarily.
Which of the following is an infectious disease?
malaria
Which of the following molecules is classified as an organic compound?
Glucose (C6H1206)
What portion of a phospholipid is oriented toward the interior of a biological membrane?
The fatty acid chains
The primary structure of a protein refers to the sequence of amino acids linked together through __ bonds
Peptide
Which of the following macromolecules are encoded directly within DNA? (select all that apply)
Proteins
_______ are responsible for the base pairing between two strands of DNA.
Hydrogen bonds
The backbone of DNA is composed of (select all that apply)
Phosphate, Sugar
Why does the orientation of a DNA strand involve using the 3’ and 5’ designations?
To indicate the position of the carbons in the deoxyribose sugar of the nucleotide
Enzymes
proteins that catalyze reactions
____ is the genetic material for all cellular organisms
DNA
Koch’s Postulates
a set of 4 steps for linking a disease (i.e. illness) with the microbe responsible
Koch’s Postulate #1
The same microbe must be present in every individual with the disease (illness) and absent in healthy individuals
Koch’s Postulate #2
The microbe must be isolated from the diseased host and grown in pure culture
Koch’s Postulate #3
The microbe from the pure culture must cause disease when it’s inoculated into a healthy, susceptible laboratory animal
Koch’s Postulate #4
The microbe must be isolated from the inoculated animal and be shown to be the original microbe
Bacteria is not a disease, it _____ the disease
causes
Significance of Koch’s Postulate #1
Ensures that the suspected microbe is consistently associated with the disease, implying that it plays a role in causing it
Rules out other potential causes
Significance of Koch’s Postulate #2
Isolating the microbe ensures that you’re studying the actual organism responsible for the disease, not a contaminant or something unrelated
Significance of Koch’s Postulate #3
Tests if the isolated microbe is indeed the cause of the disease, as it should reproduce the disease symptoms in a new, healthy host.
Strengthens the causal link between the microbe and the disease
Significance of Koch’s Postulate #4
Recovering the same microbe from the experimentally infected host confirms that the microorganism was responsible for the disease
The Germ Theory of Disease
microbes cause infectious disease
Infectious diseases
Develop when an individual acquires a disease-causing microbe
Diseases can also have genetic or environmental causes (or a combination)
Denature
Refers to the breaking of hydrogen bonds
Hydrogen bonds are much weaker than covalent bonds
microbial ecology
how microbes interact with the world around them
Today, we can learn about microbes by ….
Reading their genome
Allows us to see what a microbe is capable of without having to observe/culture it directly; we look at its sequence
Ex. A microbe with a gene for the lactase can break down lactose
We can learn how microbes are related (evolutionarily)
Similar genome = closely-related
Genome
all the genes (DNA) that make up the microbe
In the late 18th century, a physician named _____ ______ was responsible for developing the first vaccine
Edward Jenner
What was the first vaccine against?
smallpox
_____ were the first organisms to appear on Earth
Prokaryotes
spontaneous generation
microbes could arise spontaneously from non-living matter
biogenesis
living cells only arise from other living cells
acute
short-term infection
Ex. cold, flu, COVID
chronic
long-term infection (e.g. for life)
Ex. HIV
Lipids
Essential component of biological membranes
What are phospholipids composed of?
A glycerol
2 fatty acids that are nonpolar (uniform neutral charge) and hydrophobic
A phosphate group bonded to one of several organic groups that imparts an inherent negative charge to membranes
Kingdoms of Eukaryotes
Protists
Fungi
Plants
Animals
What is the highest-powered objective lens on a standard light microscope? (hint: the oil immersion lens)
100x
Which of the following is limited by the wavelength of light and cannot be adjusted on a light microscope?
Resolution
Magnification
Enlarging the appearance of an object
CAN be changed by rotating the nosepiece
Resolution
The ability to distinguish between two objects
Limited by the wavelength of light
Is lost if magnification increases beyond 1,000x
Even if lenses allowed magnification beyond 1,000x, the image would be blurry due to lack of resolution
CANNOT be adjusted/changed
Focus
Adjusting the plane of the specimen so the image can be clearly resolved
Accomplished by raising/lowering the stage (bring specimen closer/further)
CAN be adjusted using the coarse and fine focus adjustment knobs
Simple Stain
Involves a single dye so that all cells, despite differences in physiology, all stain the same color
Enables observation of cell morphology (cell shape and arrangement)
Methylene blue is commonly used
E. coli, S. aureus, and P. aeruginosa stains blue
Cell Morphology
The appearance of cells under the microscope
Don’t confuse cell morphology with colony morphology
2 Main Attributes: Cell Shape & Arrangement
Spherical Cell Shape
Coccus/cocci
Rod-Shaped Cell Shape
Bacillus/Bacilli
Other shapes (e.g. curved, spiral)
Cell Arrangements
Single cells
Chains → strepto-
Clusters → staphylo-
Others arrangements (e.g. diplo-)
Cell Chain Arrangement
Strepto
Cell Cluster Arrangements
Staphylo-
Gram Stain
Differential bacteria that stains different colors based on their physiology
Named after Hans Christian Gram, who developed the technique
Based on cell wall composition (thickness of peptidoglycan)
Gram Stain Process
- All cells are stained purple (crystal violet → primary stain)
- The purple color is ‘locked’ into a thick cell wall with iodine, the mordant
- The purple color is washed out of cell with a thin cell wall with alcohol, the decolorizer
- All cells receive a pink stain (safranin – counterstain); The cells with a thick cell wall are already purple so the pink color is masked
In a Gram Stain, bacteria with a ___ cell wall composed of a single layer of peptidoglycan are called _____ and stained _____
Thin
Gram negative
Stain pink
In a Gram Stain, bacteria with a ___ cell wall composed of multiple layers of peptidoglycan are called _____ and stained _____
Thick
Gram positive
Stain purple
Proteins
Make up 50% of cell (by dry weight)
Essential to cell structure and function
Composed of amino acids linked together by peptide bonds (covalent)
Are encoded by genes (no gene for glucose; there are genes for enzymes that make glucose)
Different proteins have different lengths and amino acid sequences → different shapes → different functions
Amino Acids
The building blocks of proteins
Has Carboxyl (C terminus) and amino (N terminus) ends
20 different amino acids, each with a different R group → each with different properties (e.g. charge, size)
Refractive Index
How light bends as it moves through the material
Allows us to see a specimen
The specimen (e.g. cells) is made of a different material than the surrounding
Glass and air have different refractive indexes so light moves through the glass slide, then to air, then into the glass objective lens
Results in light being lost, leading to lost resolution
Immersion oil is used with the 1,000x objective to minimize refraction
Oil has the same refractive index as glass so it behaves as an extension of the glass; Fills in the gap
Acid-Fast Stain
For bacteria with a waxy cell wall that does not stain well/consistently by Gram stain
The waxy character is due to mycolic acid in the cell wall
E.g. Mycobacteria spp
Steps to an Acid-Fast Stain
- Primary stain – carbolfuchsin (with heat); wax stains pink
- Decolorizer – acid alcohol
- Counterstain – methylene blue
Endospore Stain
a differential stain
Steps to an Endospore Stain
- Primary stain – malachite green (with heat); stains endospores green
- Decolorizer – water
- Counterstain – safranin; everything else is stained pink
3 major types of Carbohydrates
- Monosaccharide
- Disaccharide
- Polysaccharide
Monosaccharide
a single monomer (e.g. glucose)
Disaccharide
2 monosaccharides joined by a glycosidic bond – special type of covalent bond
Ex. sucrose, lactose
Polysaccharide
tens-hundreds of monosaccharides joined by glycosidic bonds
Ex. glycogen, cellulose, chitin, starch
Bacteria’s cell wall made of peptidoglycan is polysaccharide chains linked together
Carbohydrates
Made of carbon (C), hydrogen (H), and oxygen (O) → CHO
Used by many microbes as carbon and energy/food sources
Bioremediation
Pollutants and toxic waste can be broken down by microbes
Helped to clean up the Deepwater Horizon oil spill in 2010 (210 million gallons of oil leaked into the Gulf of Mexico, microbes learned how (evolved) to use the oil as a food source)
Similarly, microbes can break down plastic
Archaea seem similar to bacteria but…
are genetically distant (rRNA)
Water
Inorganic compound
Most abundant compound in cells (65-75%)
The nonpolar fatty acid tails (nonpolar, hydrophobic) in lipids repel from water, forming a…
Lipid bilayer consisting of 2 leaflets
Water in and outside of cell → why the fatty acids are oriented this way
No membrane is made up of one leaflet
The conformation of DNA (double helix) forms due to ________ bonds between the base pairs (A, T, G, C)
hydrogen
The conformation of DNA is essential for storing genetic material in an accessible manner
In contrast, adjacent nucleotides are linked by covalent bonds
When DNA denatures by heat, it separates into….
single strains
The conformation of proteins is also due to ______ bonding
Hydrogen
H bonds are responsible for protein folding
Adjacent amino acids are held together by covalent bonds but distant amino acids interact through hydrogen bonds
If a protein denatures, it is no longer functional
This is why boiling water kills microbes
Endospores
A hardy structure some bacteria form
Allows them to survive harsh conditions
The cell surrounds its DNA with several protective layers
Endospore is initially formed within the bacterial cell, eventually the cell breaks down leaving only the endospore behind
Once conditions improve, the endospore can reactivate and transition back into a vegetative cell
Capsule
A gelatinous polysaccharide that some bacteria material (polysaccharide) are covered in
Common to bacterial pathogens as they function in immune evasion
Capsule isn’t recognized as ‘foreign’ so the immune system doesn’t respond
Allows the bacteria to ‘hide’ from phagocytes that are looking for threats within the body
It’s so good at hiding that the capsule doesn’t stain well
Capsule Stain
A negative stain
Everything is stained but the capsule
1. India ink – provides color to the background
2. Counterstain – stains the cell
3. Capsule, the feature we’re interested in, is left unstained
Anton von Leeuwenhoek
First person to observe microbial cells (late 17th century)
Lens-maker; created a lens with minimal imperfections, allowing him to see cells with 300x magnification
At the time, other scientists (like Robert Hooke) used compound microscopes (two lenses in sequence) but due to their imperfections, were not powerful enough to see microbes
Macromolecules
Polymers made up of many monomers linked together by strong covalent bonds
Large biological molecules
Are unique to living organisms
Provide structure and perform functions:
DNA store genetic information
Proteins catalyze enzymatic reaction, also structural
Lipids form membranes
Monosaccharides are the monomer that make up
Carbohydrates
Fatty acids are the monomer that make up
Lipids
Nucleotides are the monomer that make up
Nucleic Acids
Amino acids are the monomer that make up
Proteins
Preparing a Bacterial Smear
Before staining: bacteria must be attached the slide → bacterial smear
Heat fix: Add bacteria to a slide and pass it briefly over a flame to kill the bacteria in the process (cells won’t be moving under the microscope)
Dead bacteria take to stain better than live bacteria
Heat fix is not about sterilizing the slide
Spread culture → air dry → heat fix
Most bacteria are colorless, so…
There is poor contrast under the microscope
Bacteria are stained to improve contrast
Most stains are positively charged to bind to the bacterial cell surface which has an inherent negative charge
miasma theory
Blaming “bad air” for the cause of infectious diseases
Common for malaria
Robert Koch
While dissecting an animal with anthrax, observed some rod-shaped bacteria in its blood, which is usually sterile with no bacteria
He collected some cells, grew them in the lab, and used them to inoculate a healthy animal
He followed these animals and saw they developed anthrax as well
He found the same rod-shaped bacterium in the blood of these animals
Exceptions to Koch’s postulate #1
E.coli: lives in our gut and is apart of our normal microbiota, certain strains of E.coli cause disease
If it leaves our gut, it can cause disease (ex. UTI)
COVID: SARS-COV 2 virus still found in asymptomatic “healthy”-looking people
Common cold: Caused by hundreds of different viruses
Stomach bug: Caused by different pathogens
Exceptions to Koch’s postulate #2
All viruses
Exceptions to Koch’s postulate #3
Pathogen may only infect humans, not animals like HIV or HPV
Robert Hooke
In 1665, using a simple compound microscope (2 microscopic lens’) first saw cells
Started the cell theory
Hooke’s microscope was not powerful enough to see microbes (bacterial cells)
cell theory
all organisms are composed of cells
RNA
Serves as a transcript; an intermediate between DNA and protein
Take info in DNA, transcript it into RNA, form protein
DNA and RNA nucleotides are the same except for the presence of a single -OH group in RNA
Some viruses use RNA as their genetic material (ex. SARS COV-2 and Influenza are RNA viruses)
Edward Jenner
Responsible for developing the first vaccine – a vaccine against smallpox
Late 18th century physician
At the time, the Germ Theory of Disease was not widely accepted
The first vaccine was developed before it was known that microbes caused infectious diseases; Discovered the solution before the problem
Jenner hypothesized that the development of cowpox somehow prevented the development of smallpox
To test his hypothesis….
Jenner scraped puss from a cowpox lesion and used it to inoculate a young boy (not ethical)
The boy developed symptoms of cowpox but was protected (immune) from deadly smallpox
Later, it was discovered that cowpox is caused by a virus that is very similar to the virus that causes smallpox.
The similarity between the two viruses is sufficient to train the immune system; Immune response to cowpox works to prevent smallpox
Milkmaids got cowpox b/c the cows had cowpox
Vaccination
Primary purpose: to prevent the development of an infectious disease
Based on the idea that exposure to a substance (i.e. vaccine) can prevent disease upon future exposure to the pathogen
Biogeochemical Cycling
Microbes play a crucial role in converting chemical elements into various forms; Nitrogen, carbon, oxygen
Many organisms (including humans) can only access elements if they’re in the proper form
Animals require N but can’t use N2 (atmospheric nitrogen), microbes can (nitrogen fixation)
Antibiotics
Primary purpose: to treat an infectious disease
Discovered in 1928 by microbiologist Alexander Fleming
Have saved countless lives since their discovery
Are effective against bacteria, not viruses
(viruses lack cellular structure)
Antibiotics effectiveness has been compromised due to…
The development of antibiotic resistant bacteria
Antibiotic resistant bacteria have mutations that allow them to survive in the presence of the antibiotic
Antibiotic resistance is inevitable but we can slow it down
What 3 things are nucleotides comprised of?
- Phosphate
- 5-Carbon Sugar
- Base (A,T,G,C)
Which carbon on the 5-carbon sugar does the phosphate attach to?
5
Which carbon on the 5-carbon sugar does the base attach to?
1
Amino acids are linked together by _____ bonds
peptide
2 monosaccharides are linked together by a _______ bond
glycosidic
Why are A-T bonds weaker than G-C bonds?
They have 2 H bonds, G-C has 3
Which # carbon of the sugar does the phosphate come off of?
5
Which # carbon of the sugar does the base come off of?
1
