Term
| Difference between proks and euks |
|
Definition
| Euks have a membrane enclosed nucleus |
|
|
Term
|
Definition
| Oxygenic photosynthesis, responsible for conversion of atmosphere from anoxic to oxic |
|
|
Term
|
Definition
| Form methane, strict anaerobe, |
|
|
Term
|
Definition
| Largest in number and types, extreme morphological diversity, predominant in many environments |
|
|
Term
SSU rRNA-What are the properties of a good evolutionary
chronometer? |
|
Definition
| present in all cell, same fxn, conserved, intermediate size, rapidly/slow evolving regions, no horizontal transfer |
|
|
Term
|
Definition
| Sm. organisms, single cell/prokaryotic |
|
|
Term
| What are the steps in a molecular phylogenetic analysis? |
|
Definition
1) Determine seq of SSU rRNA
2) Count # of diffs at each position
3) compute corrected ED
4) use distance/parsimony to make evol tree |
|
|
Term
| What are the three domains of life? |
|
Definition
| Archaea, Bacteria, Eukarya |
|
|
Term
Why aren't viruses included in most molecular
phylogenetic trees? |
|
Definition
| The use host rRNA because they don't have their own |
|
|
Term
What is the endosymbiont hypothesis and how would
you prove it? |
|
Definition
| Mitochondria and chloroplasts were once proks. They developed an intracellular symbiosis and became organelles. It can be proven because both mitochondria and plastids contain DNA that is different from that of the cell nucleus and that is similar to that of bacteria (in being circular in shape and in its size). Look at SSU rRNA |
|
|
Term
| What are the components of all bacterial cytoplasmic membrane and what is the fxn of the cytoplasmic membrane? |
|
Definition
| Proteins, polysacch, hydrophilic moieties, hydrophobic tails. The fxns are permeability barrier, protein anchor, energy conserv. |
|
|
Term
| What is the chief component of bacterial cell walls? |
|
Definition
|
|
Term
| What are the components of peptidoglycan? |
|
Definition
| protein, polysacch, NAM/NAG, crosslinked polypeptides |
|
|
Term
|
Definition
This classification could be used to identify organisms that
had already been characterized.
– clinical microbiology
It does not allow study of the origin and evolution of
cellular functions
– Replication, transcription, translation
It does not allow study of organisms that have not been
cultivated in the laboratory
– Predict properties of the organisms based on its
relatives |
|
|
Term
| Phylogenetic classification |
|
Definition
A natural scheme of classification based on
phylogenetic/evolutionary relatedness |
|
|
Term
| Molecular phylogenetic analysis |
|
Definition
| Use of macromolecular sequences to reconstruct phylogenetic relationships btwn orgs. Also the diff btwn homologous DNA/RNA is used to measure divergence |
|
|
Term
| Steps to make a phylogenetic tree |
|
Definition
| Isolate DNA from cells, PCR of gene encoding rRNA, DNA seq, seq analysis, generate tree! |
|
|
Term
|
Definition
| Mostly water (macro molecules, precursors),site of metabolism, Nucleoid(DNA), ribosomes, inclusion bodies (storage) |
|
|
Term
|
Definition
| area of cell immediately surrounding cytoplasm. Most conserved structure in living cells |
|
|
Term
| Major functions of the cytoplasmic membrane |
|
Definition
| permeability barrier, protein anchor, Energy conservation |
|
|
Term
| 3 features of phospholipids |
|
Definition
| Ester linkages, glycerol, R group |
|
|
Term
|
Definition
| Stabilize the membrane, Sterols not present in Proks, Hopanoid not in Archaea (similar role) |
|
|
Term
|
Definition
Isoprenoids in place of fatty acids
Bilayer and monolayer
Ether linked glycerides in place of ester linked |
|
|
Term
|
Definition
| provide cell shape, withstand turgor pressure, composed of peptidoglycan (NAG/NAM), crosslinked w/ peptides |
|
|
Term
|
Definition
| gram- has a periplasm and outer membrane. Gram- has 1-3 layers of peptidoglycan whereas gram+ has 25. |
|
|
Term
|
Definition
The two sugars constitute the backbone and
are β (1,4) linked. This linkage can be hydrolyzed by
lysozyme. NAM is only found in bateria |
|
|
Term
| Lysozyme is effective only against: |
|
Definition
|
|
Term
| What are the components of all bacterial cytoplasmic membranes and what are the functions of the cyt. membrane? |
|
Definition
| Proteins, polysaccharides,hydrophilic moieties, hydrophobic tails. Functions are permeability barrier, protein anchor and energy conservation |
|
|
Term
| What is the chief component of bacterial cell walls? |
|
Definition
|
|
Term
| What are the components of peptidoglycan? |
|
Definition
| proteins, polysaccharides, NAM/NAG, crosslinked polypeptides |
|
|
Term
| How does the lysozyme experiment demonstrate that cell walls confer shape? |
|
Definition
| In an isotonic soln, if lysozyme is added, the cell wall is removed. If the shape of the cell changes, you will know that it is responsible for cell shape. |
|
|
Term
| Do all bacteria have an outer membrane? |
|
Definition
| No, gram+ bacteria do not have one |
|
|
Term
| Do bacteria have functional/structural homologs of eukaryotic cytoskeleton? |
|
Definition
| Yes, Mre proteins are actin-like, form helical structures |
|
|
Term
| How is bacterial cell shape determined? |
|
Definition
| peptidoglycan, bacterial cytoskeleton proteins |
|
|
Term
| What are the major parts of bacterial flagellum? |
|
Definition
| Filaments, hooks, basal structures |
|
|
Term
| How do the major parts of the flagellum differ btwn gram+/gram-? |
|
Definition
| gram- had L and P rings, gram+ doesn't have L ring |
|
|
Term
| What makes flagella turn? |
|
Definition
| Energy from PMF, takes 1000 protons |
|
|
Term
|
Definition
| an innate behavioural response by an organism to a directional stimulus |
|
|
Term
| How does chemotaxis work? |
|
Definition
physical or chemical gradients
& motility machinery responds in positive or negative manner
Directing movement of bacteria toward or away from the signal
CHEMOTAXIS….is to chemicals |
|
|
Term
| What are the types of taxis that affect bacteria? |
|
Definition
| Chemo, photo, osmo, aero, magneto |
|
|
Term
| What are the functions of pili? |
|
Definition
| motility, attachment of bacteria to host cells, transfer of proteins,N.A.s |
|
|
Term
| What are the functions of slime layers and capsules? |
|
Definition
| Protection against phagocytotic attack, attach pathogen to host, resistance to desiccation, motility aid |
|
|
Term
| If you were going to grow a bacterium for the first time, what type of media would you use? |
|
Definition
|
|
Term
|
Definition
| Specific, low MW compounds that can't be made by cell (vitamins, AAs, pur/pyr) |
|
|
Term
|
Definition
| Results in chemical alteration of the compound transported into cell |
|
|
Term
Why is diamino acid or Lysine are
important in peptidoglycan? |
|
Definition
| Lysine is a component of diamino acid, which is a part of the amino acid sequences that makes up the peptidoglycan |
|
|
Term
| Peptidoglycan is unique to: |
|
Definition
|
|
Term
|
Definition
|
|
Term
With such a rigid molecule around, how does a
bacterium grow? |
|
Definition
• It has to enlarge its peptidoglycan
shell.
• Bacteria produces enzymes:
– autolysins… breaks cross-linking bonds
– transpeptidases… reseal the breakes by
adding new peptidoglycan monomers
• It has to be highly regulated
• Cell would burst |
|
|
Term
| Penicillin kills growing bacteria…..why? |
|
Definition
Penicillin and related antibiotics inactivate
transpeptidases by binding to them |
|
|
Term
Which prokaryotes are not sensitive to
penicillin? Why? |
|
Definition
| Those that don't have peptidoglycan (Archaea) |
|
|
Term
|
Definition
polyhydryl alcohols that are imbedded and
covalently linked to the peptidoglycan layer of Gram+ bacteria |
|
|
Term
|
Definition
| Lipopolysaccharides,3-5 sugars repeated 25 times, sugar polymer and fatty acids ester bonded to Glu. Is an endotoxin |
|
|
Term
| Why are we concerned about the outer membrane? |
|
Definition
• Lipid A is toxic to animals and humans
= endotoxin
• endotoxins are bound to the cell (in contrast to
exotoxins, which are secreted)
cause endotoxic shock |
|
|
Term
| OMPs (Outer Membrane Proteins) |
|
Definition
OMPs allow the outer membrane to serve as
a molecular sieve or permeability barrier
• Some OMPs are specific for certain
substrates |
|
|
Term
| The periplasmic space in Gram- bacteria |
|
Definition
• space between the cytoplasmic and outer membrane
• filled with proteins:
•specialized nutrient-binding proteins,
For amino acids (e.g. histidine, arginine)
For sugars (e.g. glucose, maltose)
For vitamins (e.g. thiamine, vitamin B12)
For ions (e.g. phosphate, sulfate)
•hydrolytic enzymes, phosphatases , proteases
• and others.. Biosynthetic enzymes
For murein assembly (e.g. transglycosylases, transpeptidases)
•gel-like consistency (highly hydrated) |
|
|
Term
|
Definition
In cell wall of Archaea. • composed of a ordered layer of
protein or glycoprotein
Examples: Many thermophiles,
halophiles, methanogens |
|
|
Term
| The eukaryotic cytoskeleton |
|
Definition
– Microtubules, tubulin
– actin microfilaments
– intermediate filaments
Play a major role in maintaining the various cell
shapes in eukaryotes . |
|
|
Term
Eukaryotic cytoskeletal proteins have homologues
in bacteria |
|
Definition
– actin : MreB and relatives
– intermediate filament-like cytoskeleton: crescentin
– tubulin-like proteins: the cell division protein, FtsZ |
|
|
Term
| Mre proteins--actin-like cytoskeleton |
|
Definition
Mre proteins form helical structures along the
long axis of the cell underneath the cytoplasmic
membrane.
• Play a major role in determining the rod shape of
Escherichia coli, Bacillus subtilis, C. crescentus,
and presumably all non- spherical bacteria. |
|
|
Term
|
Definition
an intermediate filament-like protein. is essential for the
vibroid (curved rod) and helical shapes of C.
crescentus.
• creS mutant, unable to produce crescentin, has a
straight-rod morphology . |
|
|
Term
| Bacterial cell shape is determined by |
|
Definition
– Peptidoglycan
– Bacterial cytoskeletal proteins |
|
|
Term
| Methods to detect bacterial motility |
|
Definition
• flagellar stains
– outline flagella and show their pattern of
distribution.
– If a bacterium possesses flagella, it is
presumed to be motile
-direct microscopic observation
Bacterial flagellum as
observed by negative staining
in the TEM
-• motility test medium
– demonstrates if cells can
swim in a semisolid
medium.
• A semisolid medium is
inoculated with the bacteria
in a straight-line stab with a
needle.
• After incubation, if bacterial
growth can be observed
away from the line of the
stab, it is evidence that the
bacteria were able to swim
through the medium. |
|
|
Term
| Energy required for flagellar rotation comes from |
|
Definition
|
|
Term
| Two Types of Motile Behavior |
|
Definition
|
|
Term
How do microbial cells seek out favorable
environments and avoid harmful ones? |
|
Definition
TAXES
physical or chemical gradients
& motility machinery responds in positive or negative manner
Directing movement of bacteria toward or away from the signal
CHEMOTAXIS….is to chemicals |
|
|
Term
|
Definition
| Added attractant. When no attractant present, movement was random. Presence of it caused longer runs and less tumbles |
|
|
Term
| How do bacteria sense the signal? |
|
Definition
|
|
Term
How do they measure bacteria change of signal
per time (signal gradient)? |
|
Definition
|
|
Term
|
Definition
•protein filaments that extend from the surface of a cell
•Grow from inside of the cell outward
•Occurs mostly in Gram- (possibly also in other microbes)
• most Gram- bacteria have both flagella and pili
• Thinner and shorter than flagella
• Function in:
•Motility
•Attachment of bacteria to host cells and surfaces
•Transfer of proteins and nucleic acids
Protein subunits form a helix with with a pore
in the center.
Some have a glycoprotein tip called adhesin,
which aids in adhesion. |
|
|
Term
| Capsules and Slime layers |
|
Definition
Secreted material consisting of polysaccharides or protein
•Remains attached to the cells… CAPSULE
•Loose… SLIME LAYER
•The consistency and constituents may vary
•May have several functions: protection against phagocytotic
attack, attachment of pathogen to host,
may provide resistance to desiccation, aids in motility |
|
|
Term
|
Definition
| CO2 carbon source/organic source |
|
|
Term
|
Definition
| Inorganic/organic sources |
|
|
Term
|
Definition
| CO2, constituent of cell materials |
|
|
Term
|
Definition
H2O, organic
compounds, CO2,
and O2
Constituent of cell material and cell water; O2 is electron
acceptor in aerobic respiration |
|
|
Term
| Nitrogen: source/function |
|
Definition
NH3, NO3, organic
compounds, N2
Constituent of amino acids, nucleic acids nucleotides,
and coenzymes |
|
|
Term
| Hydrogen: source/ function |
|
Definition
H2O, organic
compounds, H2
Constituent of organic compounds and cell water. Also
important in energy generation as protons. |
|
|
Term
| Phosphorus: source/function |
|
Definition
inorganic phosphates(PO4)
Constituent of nucleic acids, nucleotides, phospholipids,
LPS, teichoic acids |
|
|
Term
|
Definition
SO4, H2S, So, organic
sulfur compounds
Constituent of cysteine, methionine, glutathione, several
coenzymes |
|
|
Term
| Potassium: source/function |
|
Definition
Potassium salts Main cellular inorganic cation and cofactor for certain
enzymes |
|
|
Term
| Magnesium: source/function |
|
Definition
Magnesium salts Inorganic cellular cation, cofactor for certain enzymatic
reactions |
|
|
Term
|
Definition
Calcium salts
Inorganic cellular cation, cofactor for certain enzymes
and a component of endospores |
|
|
Term
|
Definition
Iron salts Component of cytochromes and other proteins and a
cofactor for some enzymatic reactions |
|
|
Term
|
Definition
|
|
Term
|
Definition
|
|
Term
|
Definition
| A pure culture used in a technique to isolate a species |
|
|
Term
| Examples of complex culture media: |
|
Definition
Luria broth
Tryptone Yeast extract •contains carbon and energy source
Tryptone-broth
Meat extract broth
Brain-heart infusion broth
Tomato juice broth |
|
|
Term
| Examples of Synthetic culture media: |
|
Definition
• inorganic salts
• carbon source
• energy source
• growth factors (vitamins, amino acids)
• buffer system |
|
|
Term
| How do bacteria obtain nutrients? |
|
Definition
– Fast Entry
• Food must enter at high rates
– Selective Admission
• Exclude substances that are harmful
– Need to concentrate food inside the cells
• microbes grow in dilute nutrient solutions |
|
|
Term
Several transport mechanisms are
utilized: |
|
Definition
• Facilitated diffusion
• Active transport
• Group translocation |
|
|
Term
|
Definition
no membrane
proteins are required—gasses, water,
and fat-soluble compounds |
|
|
Term
|
Definition
transmembrane
proteins called permeases transport the
molecules.
• Energy input is not required. The solute
binds to external portion of the
permease, a change in conformation
moves the solute inward.
• The solute is generally metabolized on
entry, keeping the concentration inside
the cell low. |
|
|
Term
|
Definition
uses cell energy to
move solutes against a concentration
gradient.
• Solute-specific transmembrane proteins
are used.
•Most organic and inorganic nutrients are
taken into cells by active transport
mechanisms.
• Energy is from ATP or proton gradients. |
|
|
Term
ATP-Binding Cassette transporters
(ABC transporters) |
|
Definition
consist of 3 kinds
of proteins:
• Hydrophobic transmembrane protein
• ATP hydrolyzing protein – attached to
the inner side of the transmembrane
protein
• Periplasmic solute-binding protein – in
the periplasmic space or anchored to
the membrane |
|
|
Term
|
Definition
carry one solute in one
direction. |
|
|
Term
|
Definition
carry amino acids, sugars,
or anions that are accompanied by a
proton or sodium ion.
Binding of proton to transport protein
drives conformational change that
transports the solute across the
membrane. |
|
|
Term
|
Definition
energy from a proton
gradient is used to move a proton
inward and a cation such as Na+
outward, creating a Na+ gradient. |
|
|
Term
|
Definition
|
|
Term
|
Definition
the transported
compound is chemically altered upon
entry into the cell. |
|
|
Term
Phosphotransferase system
(PTS) |
|
Definition
is involved in transporting sugars
into the cell. It uses energy from
phosphoenolpyruvate (PEP) and 5
different enzymes. |
|
|
Term
|
Definition
| in the cytoplasm, beginning of PTS |
|
|
Term
|
Definition
| attached to the inner surface of the cell membrane |
|
|
Term
|
Definition
is an integral
transmembrane protein. It forms a pore
across membrane and is the final
recipient of the high energy phosphate
which is used to phophorylate the sugar |
|
|
Term
|
Definition
| a category of enzymes which catalyze phosphorylation reactions. used by, for example, bacterias, to transport sugar (Glucose) into the cell |
|
|
Term
|
Definition
a siderophore produced
by E. coli. It chelates Fe3+ through
oxygen molecules on the catechol rings.
• The complex is bound by a binding
protein, transferred to a specific receptor
on the cell envelope, and transported
across the membrane by an ABC
system. |
|
|
Term
|
Definition
| cell division protein, tubulin-like |
|
|
Term
|
Definition
| appears to be necessary for their shape, as mutants lacking the protein form rod-shaped cells |
|
|
Term
| Why does group translocation cost no extra energy? |
|
Definition
| Because it involves phosphorylating glucose, which is a process that normally occurs in gylcolysis |
|
|
