microbiology exam 1 study guide

what is inoculation in the 5 I’s?

• Introduction of microorganisms into or onto a culture medium

• Begins the process of growing a microorganism

mitosis

Mitosis creates two identical body cells for growth and repair

meiosis

meiosis creates four unique sex cells for sexual reproduction

conjugation

the direct transfer of genetic material between two bacterial cells through physical contact

type of appendages: flagella and axial filaments

provides motility

type of appendages: fimbriae, pili, and nanowires

provide attachment points or channels

turbidity

the cloudiness or haziness of a liquid culture caused by a large number of individual suspended microbial cells

serial dilution

a stepwise process of reducing the concentration of a microbial sample using a consistent dilution factor to achieve a countable number of colonies

direct cell count

a method used to physically observe and count all micro-organisms in a known volume of a liquid sample

what is incubation in the 5 I’s?

• Providing appropriate conditions for microbial growth

• Temperature and atmospheric gases such as oxygen and carbon dioxide can be controlled

• Typical laboratory temperatures: 20–45°C

what is isolation in the 5 I’s?

• Separating microorganisms from one another

• Goal: obtain a pure culture

• Solid media allows individual colonies to form

what is inspection in the 5 I’s

• Examining microorganisms

• Includes:

  • Macroscopic analysis

  • Microscopic analysis

  • Phenotypic testing

  • Genotypic testing

  • Immunologic testing

what is identification in the 5 I’s?

• Determining what microorganism is present

• Uses characteristics obtained during inspection and testing

order in which the 5 I’s take place

Inoculation → Incubation → Isolation → Inspection → Identification

robert hooke

made early observations of microbes in the 1600s

Antonie van Leeuwenhoek - 1670s

observes microorganisms; first to see and describe bacteria and protozoa using handcrafted microscopes

Edward Jenner - 1796

develops first vaccine; used cowpox to protect againsit smallpox

Louis Pasteur - 1860s

establishes germ theory; demonstrated that microorganisms cause fermantation and disease; developed pasteurization

John Tyndall - 1870s

confirms germ theory; showed that dust carries microorganisms and developed tyndallization (a method used to sterilize using intermittent boiling)

Joseph Lister - 1867

introduces antiseptic surgery; used carbolic acid to sterilize surgical tools and wounds, dramatically reducing infections

Robert Koch - 1876

indentifies bacillus anthracis; introduced koch’s postulates for linking microbes to certain diseases

1880s-1890s

discovery of major pathogens; bacteria responsible for TB, chokra, and plague were isolated

Alexander Pleming - 1928

discovers penicillin; marks the beginning of the antibiotic era

Avery MacLeod and McCarthy - 1944

show DNA is hereditary material; found that DNA, not protein, carries genetic info

Watson and Crick - 1953

describes DNA’s double helix structure

Carl Woese - 1977

indentifies archaea; reclassified the tree of life using RNA sequencing

Kary Mullis - 1983

invents PCR (polymerase chain reaction); allowed scientists to amplify DNA rapidly and revolutionized molecular biology and diagnostics

discovery of HIV - 1983

identification of the virus responsible for AIDS

1995

first bacterial genome sequenced (Hacmophilus influenzae)

2000s - present - CRISPR - Cas Gene Editing and Microphone Research

CRISPR, derived from bacterial immune systems, revolutionized genetic engineering; expanded understanding of human health through gut biome research

2020 - Microbiologists lead global response to COVID

rapid identification, genome sequencing, testing and vaccine development for SARS-Cov-2

fastidious organisms

requires specific, complex nutrients that must be applied in enriched

e. coli

salmonella

methanogens

• covert CO2 and H2 into methane gas

• produces methane

• common inhabitabts of anaerobic swamp mud, bottom sediments of lakes and oceans, and the digestive systems of animals

• may contribute to greenhouse gases and global warming

extreme halophiles

• require salt to grow

• exist in inland seas, salt lakes, salt mines, and salted fish

• use a red pigment to synthesize ATP in the presence of light - unique to halophiles

hyperthermophiles and psychrophiles

• hyper - grow at very high temps

• psych - grow at very low temps

• often salt and acid tolerant

• live in volcanic waters and soils submarine vents

sulfer reducers

• use sulfer instead of oxygen during metabolism

• typically hyperthermophiles, living in hot, oxygen-free environments such as volcanic vents and hot springs, where they reduce sulfer to hydrogen sulfide (H2S)

bacteria

cellular microorganisms; single celled prokaryotes found almost everywhere

archaea

cellular microorganisms; single celled prokaryotes, often in extreme environments

fungi

cellular microorganisms; eukaryotes such as yeasts (unicellular) and molds (multicellular)

protozoa

cellular microorganisms; single celled eukaryotes, often mobile

algae

cellular microorganisms; photosynthetic eukaryotes, can be uni or multi cellular

viruses

acellular microorganisms; DNA or RNA in a protein coat; must infect a host cell to reproduce

viroids

acellular microorganisms; small infectious RNA molecules (mainly plant pathogens)

prions

acellular microorganisms; misfolded proteins with no RNA or DNA

pasteur’s experiment

showed that microorganisms do not arise spontaneously. he used swan - neck fasks filled with broth and boiled them to kill any members, the curved neck let air in but trapped dust and microorganisms. the broth stayed sterile as long as the flask was upright. when the neck was broken, microbes entered and broth became contaminated

koch’s contribution - koch’s postulates

• created a set of criteria to prove that a specific microorganism causes a specific disease

• 1. the organism must be found in all cases of the disease but not in healthy individuals

• 2. organism must be isolated and grown in pure culture

• 3. cultured microorganism should cause the same disease whe introduced to a healthy host

• 4. microorganism must then be reisolated from the newly infected host and shown to be the same as the original microbe

• these postulates formed the foundation of germ theory of disease

koch’s contribution - identification of disease

• first to definitively link certain bacteria to certain diseases: bacillus anthracis - anthrax, microbacterium tuberculosis - tuberculosis, vibrio cholerae - cholera

liquid media

water based solutions that do not solidify at temps above freezing and flow freely in a tilted container. ex: broths, milk, infusions

semisolid media

clot like consistency at room temp, contains enough gelatin or agar to thicken but not produce a firm surface, used to determine motility of bacteria or localize a reaction to a specific site

solid media

provided a firm surface upon which cells can form discrete colonies; used to isolate bacteria and fungi

ex: agar

agar

complex polysaccharide isolated from the red alga gelidium; solid at room temp, liquifies at 100 C; any medium containing 1%-5% agar usually has the word “agar” in its name

synthetic media

media whose exact chemical compositions are know

• may contain pure organic and inorganic compounds that vary little from one source to another

• have a molecular content defined by means of an exact formula

• useful in research

complex media

• contains at least one component that is not chemically definable

• contains extracts of animals, plants, or yeasts

• may contain group up cells, tissues, or secretions

ex: blood, serum, milk

general purpose media

• grow as many microbes as possible

• complex media that contains a mixture of ingredients that support a wide variety of microbial life

enriched media

contains complex organic substances that fastidious bacteria require for growth

selective media

contains one or more agents that inhibit the growth of certain microbes; encourage a select microbe to grow; important in the inital isolation of a specific type of microorganism from a mixed sample

differential media

• allow multiple types of microorganisms to grow, but display visible differences between colonies

• differences in colony size/color, media color changes, or formation of gas bubbles/precipitates

• variations may be due to metabolism of certain ingredients that cause a color change

blood agar

used as an enrichment medium for fastidious microbes

• hemolysins - enzymes that break down red blood cells to release hemoglobin

• beta-homolysis - complete lysis of red blood cells

• alpha-homolysis - incomplete lysis of red blood cells

• gamma-homolysis - no hemolysis

reducing media

grow anaerobic bacteria

carbohydrate fermentation media

contain sugars that can be fermented and a pH indicator to show this reaction

how do we determine evolutionary relatedness?

• determined by comparing genetic material, usually DNA or RNA sequences. The more similar the sequences, the more closely related the organisms are.

• 16S RNAs gene is usually compared

how did carl woes distinguish between the domains?

• used 16s rRNA sequencing to compare microbes

• discovered that some prokaryotes previosuly grouped as bacteria were actually very different

• based on these genetic differences, he proped 3 domains of life: bacteria, archaea, eukarya

what is serological analysis?

it is a method used to identofy microorganisms based on their antigens and antibodies

• antigens - molecules that trigger an immune response

• antibodies - proteins produced by the immune system that specifically bind to antigens

how is serological analysis determined?

1. a sample containing the microorganism is mixed with a specific antibody

2. if the antibody binds to the antigen, a visible reaction occurs. this reaction can be

• agglutination - clumping of cells or particles

• precipitation - formation of a visible precipitate

• color change - using enzyme linked antibodies

3. the reaction confirms the identity of the molecule or detects specific strains

parts of bacteria

1. ribosome: tiny particles composed of proteins and RNA that are the sites of protein synthesis

2. flagella: specialized appendage attached to the cell by a basal body that holds a long, rotating filament (the movement pushes the cell forward and provides motility)

3. capsule: a coating or layer of molecules external to cell wall; serves protective, adhesive, and receptor functions

4. cell wall: semi rigid casing that provides structural support and shape for the cell

5. chromosome (nucleoid): composed of condensed DNA molecules

6. cytoplasm: water based solutoon filling the entire cell

parts of eukaryotic cell

1. ER: rough-studded with ribosomes; synthesizes and modifies proteins for secretion; smooth-synthesizes lipids and steroids, detoxifies drugs, stores calcium

gram positive

• Thick peptidoglycan layer

• About 20-80 nm

• Contains teichoic and lipoteichoic acids

• Gram-positive = thick wall = purple

gram negative

• Thin peptidoglycan layer

• About 1–3 nm

• Has an outer membrane

• Contains lipopolysaccharide (LPS)

• Gram-negative = thin wall + outer membrane = pink

steps of gram stain

1. Crystal Violet

• Primary stain

• All cells initially become purple

2. Iodine

• Mordant

• Helps retain crystal violet

3. Decolorizer

• Alcohol/acetone

• Removes crystal violet from Gram-negative cells

• Critical differentiating step

4. Safranin

• Counterstain

• Gram-negative cells become pink/red

C → I → D → S

Crystal Violet → Iodine → Decolorizer → Safranin Gram-positive = Purple

Gram-negative = Pink

arrangement of flagella

Polar- flagella attached at one or both ends of the cell

Monotrichous- One flagellum

Lophotrichous- Tuft/bunch of flagella

Amphitrichous- Flagella at both poles

Peritrichous- Flagella distributed over the entire surface

MONO = one

LOPHO = tuft

AMPHI = both ends

PERI = everywhere

ER (Endoplasmic Reticulum)

Makes and transports proteins and lipids; rough ER makes proteins, smooth ER makes lipids

Lysosome

Breaks down waste, damaged cell parts, and foreign materials using digestive enzymes

histones

Proteins that package and organize DNA into chromatin

nucleus

Stores DNA and controls gene expression and cell activities

mitochondria

Produces ATP (energy) through cellular respiration

chloroplast

Performs photosynthesis, converting light energy into chemical energy (found in plants and algae)

what are the major differences between Bacteria, Archaea, and Eukarya?

Bacteria:
Prokaryotic → 70S ribosomes → circular DNA → peptidoglycan cell wall → ester-linked fatty acids

Archaea:
Prokaryotic → 70S ribosomes → circular DNA → NO peptidoglycan → ether-linked branched hydrocarbons

Eukarya:
Eukaryotic → 80S ribosomes → linear DNA → nucleus + membrane-bound organelles → ester-linked fatty acids

what is the function of the cytoskeleton?

• Helps maintain cell shape

• Provides structural organization

• Located just beneath the cytoplasmic membrane

what is a nucleolus

makes ribosomes! The nucleolus is a region inside the nucleus responsible for producing rRNA and assembling ribosomal subunits

decomposer

Organism that breaks down dead matter and wastes.

pathogen

An agent capable of causing diseases. ex:

• Viruses

• Bacteria

• Fungi

• Protozoa

• Helminths

sterile

Free of all life forms, including spores and viruses.

eukaryotes

Cell containing a true nucleus

biotechnology

Manipulation of microorganisms to make useful products in an industrial setting.

media

A nutrient-containing environment in which microorganisms can multiply.

prokaryotes

Cell without a true nucleus.

Bacteria and Archaea are prokaryotes.

bioremediation

Introduction/use of microorganisms to restore environmental stability or clean up toxic pollutants.

Bioremediation = microbes clean up pollution

endospore

Dormant, resistant structure that allows certain bacteria to survive unfavorable conditions.

fermenter

a controlled vessel used to grow microorganisms and produce useful products.

prion

Small protein that can behave as an infectious agent; noncellular microorganism

plasmid

Small, separate, double-stranded circular DNA molecule in bacteria.

• Nonessential DNA

• Can provide protective traits

• Important in genetic engineering

capsomere

a protein subunit that makes up the capsid of a virus.

Capsomeres = building blocks → Capsid = protective shell → DNA/RNA = genetic material

microorganisms

an organism or biological agent too small to be seen with the naked eye

chemotaxis

Movement in response to chemical signals.

• Positive = toward favorable chemical

• Negative = away from harmful chemical

epidemiology

Study of disease distribution and control in population

reverse transciptase

Reverse transcriptase is an enzyme that makes DNA from an RNA template.

Reverse transcriptase = RNA → DNA

lysogeny

virus hides in the host DNA without killing the cell right away.

CFU calculation

• CFU/mL = CFU ÷ (Dilution × Volume)