MICRB 265 MIDTERM 1

Who is the first person to depict microorganisms?

Robert Hooke

Who is considered the Father of microbiology?

Antoni van Leeuwenhoek

Spontaneous generation

Life can emerge spontaneously from non-living materials

Who disproved spontaneous generation?

Loius Pasteur

What are the major accomplishments of Louis Pasteur? (5)

1. Sterilization techniques (pasteurization)

2. Fermentation by microbes

3. Important contributions to the advancement of vaccine development

4. Germ theory of disease with others

5. Disproved spontaneous generation

Who provided evidence for germ theory of disease?

Robert Koch

What are some significant limitations to Koch's postulates? (2)

- Not all pathogens can be cultured in isolation

- Some disease-causing microbes can be present in healthy people, only cause disease in certain people/conditions

What did Robert Koch discover?

The cause of tuberculosis and of cholera

Who developed the first vaccine for smallpox?

Edward Jenner

Who discovered the spore formation (bacterial cell differentiation)?

Ferdinand Cohn

Who discovered enrichment culturing for growing the desired microbes?

Martinus Bejerinck

Who developed antibiotics?

Alexander Fleming (Penicillin)

Gerhard Domagk and others (Sulfonamides)

Selman Waksman (Albert Schatz) (Streptomycin)

Who discovered archaea and reworked the tree of life?

Carl Woese and George Fox

Who was the first to complete sequence of a bacterial genome?

Craig Venter and Hamilton Smith

What are the 3 domains of life?

Bacteria, Archaea, Eukarya

What are Archea known as?

Extremophiles

Virus

Genetic elements (DNA/RNA) that can only multply within a living cell

Explain the RNA world hypothesis

Life on earth started with lifeforms that used RNA only

- Because RNA can catalyze reactions just like proteins and can store genetics

What were some evolutionary forces that supposedly kicked in in RNA world hypothesis? (3)

Improved replication

Simple functions

More complex functions

What is the evidence of RNA world hypothesis?

RNA can form intricate, stable structures

Proteins are still made today using RNA components

Many apparent "relics" from RNA world

- Common biological molecules with ribonucleotide components

When and where did the first microbe evolve?

4 billion years ago

Not known where, but one hypothesis is that it happened in hydrothermal systems on ocean floor

- Stable environment, low UV light, compartments (cells) energy, organic molecules

LUCA - explain the abbreviation

Last Universal Common Ancestor

What are the presumed features of LUCA? (4)

DNA replication, transcription, translation, cell division

ATP served as energy intermidiate

Lipid bilayer membrane

Anaerobic metabolism (no oxygen) - likely used H2 as energy source and CO2 as carbon source

When did bacteria and archaea diverge?

More than 3,5 billion years ago

What was thought to have evolved from one another: Eukarya or Archaea? When?

Eukarya thought to have evolved from Archaea approx. 2 billion years ago

Chemotroph

Derive energy from releasing bond energy from chemical compounds

Phototroph

Absorbs light, transforms it into chemical energy

Anoxic

No oxygen

Cyanobacteria

Bacteria that can carry out photosynthesis

- Oxygenic photosynthesis

Oxygenic photosynthesis

Photosynthesis that produces oxygen as a by product

What did oxygen in the atmosphere cause?

It made ideal electron acceptor - gave rise to aerobic organisms

Ozone (O3 layer) - protects against UV (lethal to cells, damages DNA)

Explain the endosymbiotic theory

Eukaryotes emerged when an archaea-like ancestor engulfed a bacterium that became endosymbiont (organism living within another organism in symbiotic relationship)

Eventually this bacterium became the mitochondria

Plants emerged in a second event when an engulfed photosynthetic bacteria became basis for chloroplast

Explain the serial endosymbiosis theory

Mitochondria: Stable engulfing of an aerobic respiring bacterium from Alphaproteobacteria into early eukaryotic cell organism

Chloroplasts: Stable engulfing of a photosynthetic cyanobacterium-like cell into cytoplasm of a eukaryotic cell

What are the evidences of endosymbiotic theory?

DNA replication, transcription, translation machinery of eukaryotes more similar to archaea than bacteria

Mitochondria and chloroplasts:

- Have their own genomes, ribosomes, tRNA

- This machinery is bacterial

- Mitochondria related to Proteobacteria, chloropolasts related to Cyanobacteria

Ubiquitous

Present or existing everywhere

Taxonomy

Science of classifying/naming biological organisms

Phylogeny

Study of the evolutionary relationships between different organisms

Taxonomists use a combination of _______, ________ and _____________- information to make classifications

Genotype, phenotype and phylogenetic

Each organism has 2 names in taxonomy: what are the 2 names and give an example

Genus (more broad) and species (more specific)

Homo sapiens

What are the rules for writing scientific names?

Species names italicized or underlined (if handwriting)

The genus is capitalized and species is lower case

Higher taxa are NOT italicized. They are capitalized, through

After the first use in a manuscript, paper, or report, scientific names are abbreviated with the 1st letter of the genus plus the species name

Subspecies

Essentially just the next finer classification after species

Biovar or biotype

Grouping based on physiological or biochemical difference from other members of the species

Serovar or serotype

Grouping based on surface antigens

Other naming systems

Sometimes strains can be lumped together based on an important feature

Ex. STEC (Shiga toxin-producing E. coli)

Certain DNA sequences are better choices than others. Which ones?

Typically looking for highly conserved genes with a highly conserved function that slowly accumulates mutations over time

The most common DNA sequence that gets used for determining phyogenetic relationship is ______

ribosomal RNA of the small subunit (SSU) of the ribosome

What regions of rRNA are useful for identifying relationships?

Variable regions

What regions of rRNA are useful for PCR?

Conserved regions

How do we use sequences to build phylogenetic tree?

1. The 1st step in making a tree is to align sequences

2. A distance matrix is calculated from the number of sequence differences

3. The tree is constructed by adding nodes to join lineages that have the fewest differences

HGT abbreviation - translate it

Horizontal gene transfer

What are the 2 basic differences between prokaryotes and eukaryoes?

1. Eukaryotes contain numerous compartments (organelles) and prokaryotes generally lack organelles

2. Prokaryotes are generally much smaller in size: equivalent to a mitochondrion

How does surface area to volume ration affect in the cell?

Affects how quickly cells exchang nutrients and waste with their environment (how quickly they grow)

Small cells can generally grow (reproduce) _______ _____

More quickly

Smaller size/less complexity also means ______ time/energy to replicate cell

Less

Nucleus

Defining charasteristic of eukaryotic cells

What does nucleus do?

Separates genetic material (DNA) from the rest of the cell

Transcription/translation uncoupled - ribosomes outside of the nucleus

Proteins related to DNA replication, transcription, etc must be translocated into nucleus

Mitochondria

Energy center of the cell - site of respiration, ATP production

What does mitochondria contain?

Contain own genomes, ribosomes

What is Golgi complex & endoplasmic reticulum primary function?

Involved in modifying and sotring proteins (and other molecules) to be translocated to other parts of the cell or secreted from the cell

Glycosylation

Glycosylation

Many eukaryotic proteins have glycans (sugars) added

What are proteins & other molecules packaged into by golgi complex and endoplasmic reticulum?

Into vesicles and trafficked around the cell (and secreted from the cell)

What is the analogy to golgi complex and endoplasmic reticulum?

That they are like post office, they package stuff and ship them to very specific places in the cell

Cytoskeletion

Dynamic protein filament network involved in cell shape, transport within cell, cell movement and more

Vacuoles

Membrane bound compartment, often for storing nutrients and/or waste

Lysosomes

Specialized vacuoles found in many cells that contain enzymes to break down incoming nutrients

Chloroplasts

Found in phototrophs - contain the marchinery for photosynthesis

Vesicles

Small, membrane bound compartments used extensively to traffic materials around the cell, into/out of cells and between organelles

Cell wall

Some eukaryotes have one (plants, fungi), others dont (animals). Much diversity in structure

Tell everything we should know about Staphylococcus auerus

Cocci: Spheres

Common component of human microbiota

Opportunistic pathogen (through wounds)

Can enter bloodstream and cause life-threatening infections

Tell everything we should know about Neisseria gonorrhoeae

Cocci: spheres

Gram negative coccus

Etiological agent of the common STD gonorrhea

Streptococci - what does the word mean?

Chain of the cells

Tell everything we should know about Streptococcus pyogenes

Cocci: spheres

Can cause a range of diseases, including "step throat". Can also be carried by healthy individuals

Tell everything we should know about Salmonella enterica

Bacilli: rods

Common cause of "food posinoning" worldwide. Also causes of Typhoid fever"

Tell everything we should know about Vibrio cholerae

Vibrio: comma shaped or bent rod

Important human pathogen, especially in developing world, that causes profuse diarrhea and dehydration

Tell everything we should know about Helicobacter pylori

Helical

Commonly found in human stomach, often innocuous

Cause of vast majority of stomach ulcers, stomach cancers

Tell everything we should know about Borrelia burgdorferi

Spirochetes

Pathogen that causes Lyme disease, transmitted by ticks

Tell everything we should know about Caulobacter crescentus

Appendaged/budding

Used as a model system to study bacterial cell cycle, assymetric cell division

Cell cycle can be synchronized, facilitating its characterization

Tell everything we should know about Chloroflexus aurantiacus

Filamentous

Photosynthetic bacterium that does not produce O2

Studied to understand the evolutionary origins of photosynthesis

What can cell shape affect? (at least 5)

Nutrient access/uptake

Motility

Attachment to surfaces

Formation of biofilms

Interactions with other microbes and/or eukaryotic host cells

Etc

Monomorphic

One shape; observed in most pure cultures of bacteria

Pleomorphic

Multiple different morphologies for same bacterium

What causes different morphologies/changes of morphology? (3)

1. Differentiation into different cell types or spore formation

2. Altered morphology in response to environmental cues

3. Altered morphology due to mutation

What are the major structures of cell envelope? (4)

Cytoplasmic membrane,

Cell wall,

Outer membrane,

S-layers

Name at least 4 roles of cell envelope

Maintains barrier with environment

Protects cell from stress

Allows transport of nutrients into cell and waste out of cell

Energy conservation/production

And much much more (this is where much of the action takes place in a bacterium)

Cytoplasmic membrane

Primary barrier between the inner workings of the cell & its environment

What are the functions of the cytoplasmic membrane?

1. Permeability barrier: prevents ;eakage and functions as a gateway for transport of nutrients into, and wastes out of, the cell

2. Protein anchor: site of proteins that participate in trasnport, bioenergetics, and chemotaxis

3. Energy conservation: site of generation and dissipation of the proton motive force

What is the cytoplasmic membrane composed of?

Lipid bilayer: 2 sheets of phospholipids together tail to tail

What kind of backbone is conserved in bacteria?

Glycerol phosphate backbone

What kinds of membrane proteins exist in cytoplasmic membrane? (3) (!)

Peripheral membrane proteins (loosely attached)

Integral membrane proteins (embedded in membrane)

Transmembrane proteins (pass all the way through membrane)

What are the 2 faces of the cytoplasmic membrane?

Cytoplasmic face (faces the cytoplasm)

Periplasmic face (faces outwards)

Amino acids that reside within the membrance are typically hydrophillic or hydrophobic?

Hydrophobic

Hydrophillic side chains of amino acids often do what in cytoplasmic membranes?

Often surface exposed in cytoplasm or periplasm

What is the primary function of cell wall?

Prevent cells from bursting due to osmotic pressure

Also provides cell shape, rigidity

Explain what is the difference in cell wall between Gram + & gram - (!)

Gram + bacteria: Thick cell wall, no outer membrane

Gram - bacteria: Thin cell wall, have an outer membrane

What are the bacterial cell walls made of? (primary component)

Peptidoglycan

Peptidoglycan (!)

A lattice-like structure formed from chains of glycans llinked together by peptide bridges

Peptido (short peptides) glycan (sugars)

- Sugar backbone and peptide crosslinks

Which bacteria (gram +/-) has interbridges? Explain its function (!)

Gram +

Helps connect different peptidoglycan layers. These are also peptide crosslinks, extended by a few amino acids

(This way provides additional strength)

Which bacteria (gram +/-) has teichoic acids? Explain its function (!)

Gram +

Provide cell strength

Help trap divalent metal ions such as Mg2+

Barrier & attachment functions

Teichoic acids

Long polymers comprised of glycerol phosphate or ribitol phosphate with attached D-glucose and/or D-alanine

What are teichoic acids attached to?

Covalently attached to peptidoglycan or cytoplasmic membranes