Term
|
Definition
| an increase in cell numbers |
|
|
Term
|
Definition
| The formation of two cells from one |
|
|
Term
|
Definition
| Time required for the cell number to double (also called doubling time) |
|
|
Term
|
Definition
time required for the cell number to double This is a convenient growth parameter when you compare growths
among bacteria or in different conditions.(also called generation time) |
|
|
Term
|
Definition
| Process by which most bacteria divide by |
|
|
Term
|
Definition
| In the proces of binary Fission, a septum is a partition or division formed by divisome |
|
|
Term
|
Definition
| Cell division apparatus at septum |
|
|
Term
|
Definition
| After the DNA is duplicated in a cell undergoing Binary Fission, these Protiens form a ring and begin the dividing process. |
|
|
Term
|
Definition
| The protien that determines the FtsZ ring assembly. |
|
|
Term
|
Definition
| Localizes synthesis of new peptidoglycan |
|
|
Term
|
Definition
| Creates small openings in peptidoglycan to which peptidoglycan can be added |
|
|
Term
|
Definition
| If there are Autolysins and new peptidoglycan is not added the cell with lyse because it has a hole in the wall. Also called Self Breaking. |
|
|
Term
| Peptidoglycan Synthesis Step 1 of 8 |
|
Definition
| Sequential addition of L-Ala, D-Glu and L-Lys (or DAP in Gram[-]) to UDP-NAM |
|
|
Term
| Peptidoglycan Systhesis step 2 of 8 |
|
Definition
| Attachment of a dipeptode D-Ala-D-Ala |
|
|
Term
| Peptidoglycan Synthesis Step 3 of 8 |
|
Definition
| Transfer of NAM-pentapeptide to a membrane-bound lipid bactoprenol. UMP is released. |
|
|
Term
| Peptidoglycan Synthesis Step 4 of 8 |
|
Definition
| NAG from UDP-NAG is linked to NAM |
|
|
Term
| Peptidoglycan Synthesis Step 5 of 8 |
|
Definition
| Bactoprenol carrying NAM-NAG moves to the outer side of the membrane where transpeptodases and transglycosylases (two so-called penicillin-binding proteins) bind to D-Ala-D-Ala part. |
|
|
Term
| Peptidoglycan Synthesis Step 6 of 8 |
|
Definition
| Transglycosylase attaches the new disaccharide unit to an existing peptidoglycan chain. |
|
|
Term
| Peptidoglycan Synthesis Step 7 of 8 |
|
Definition
| Transpeptidase then links two peptide side chains with the pentiglycine cross link (Staphlococcus aureus). The terminal D-Ala is removed in the process. Other bacteria (eg.E.coli) directly form a peptide bond without pentaglycine. |
|
|
Term
| Peptidolycan Synthesis Step 8 of 8 |
|
Definition
| One phosphate is removed from bactoprenol, which then moves back to the cytoplasmic side for recycle. |
|
|
Term
|
Definition
| Enzymes that interact with bactoprenol to insert cell wall precursors into growing points of cell wall and to catalyze glycosidic bond formation |
|
|
Term
|
Definition
| Enzymes that catalyze the final step in cell wall synthesis to form the peptide cross links between muramic acid residues in adjacent glycan chains (inhibited by the antibiotic penicillin and others) |
|
|
Term
| How many D-Ala are removed during Transpeptidation and why |
|
Definition
| One is removed, which drives the reaction forward (no ATP needed) |
|
|
Term
| β-lactam antibiotics (eg. Penicillin) |
|
Definition
| block transpeptidation by directly binding and preventing the activity of transpeptidase |
|
|
Term
|
Definition
inhibits two enzymes
that make D-Ala-D-Ala dipeptide. |
|
|
Term
|
Definition
binds to and inhibits
dephosphorylation of bactoprenol,
blocking its recycle. |
|
|
Term
|
Definition
blocks transpeptidation
but by binding to D-Ala-D-Ala and
preventing cross-linking. |
|
|
Term
|
Definition
growth of a microbial population in which cell
numbers double within a specific time interval |
|
|
Term
|
Definition
a closed-system microbial culture of fixed volume (no extra
nutrients except the ones to start with and no waste removal) |
|
|
Term
|
Definition
| required to adapt to a new growth condition |
|
|
Term
|
Definition
| log phase (number of cells doubles regularly) |
|
|
Term
|
Definition
run out of food or produce waste products. Equilibrium
between new cell division & cell death (cryptic growth) |
|
|
Term
|
Definition
metabolic balance is affected and cells begin to die. Sometimes
they lyse and other times they don't |
|
|
Term
|
Definition
| Includes both viable and dead cells |
|
|
Term
|
Definition
| Measures number of living cells (Colony Forming Units, CFU) Complex and slow, but provide info about viable cells |
|
|
Term
|
Definition
an indirect
but very rapid and useful method of
measuring microbial growth |
|
|
Term
|
Definition
The higher OD
value, the more turbid the cell
suspension |
|
|
Term
| What must be done to keep a culture in a constant enviroment? |
|
Definition
| You must continually feed it and remove wastes. |
|
|
Term
|
Definition
| keeping a culture in a constant enviroment. Done in a Chemostat |
|
|
Term
|
Definition
| Where a Continuous Culture is kept. |
|
|
Term
|
Definition
| Used to control the culture in a chemostat by limiting the amount of a nutrient such as glucose or phosphate. Can be used to adjust the population density |
|
|
Term
|
Definition
| change in cell number per unit time |
|
|
Term
|
Definition
amount of biomass produced during bacterial
growth on a given substrate. YATP= Grams of dry cell material
produced per mole of ATP. |
|
|
Term
|
Definition
When a cell has to
make everything from scratch this requires more energy and more time |
|
|
Term
| Factors affecting Growth Rate |
|
Definition
| growth medium, temperature, water availability, osmolarity, and pH |
|
|
Term
|
Definition
| a major environmental factor controlling microbial growth |
|
|
Term
|
Definition
Minimum,
Optimum, and Maximum temperatures
characteristic of each microorganism |
|
|
Term
|
Definition
| cold loving. Cellular macromolecules function at low temps, Membranes contain unsaturated fatty acids that keep it fluid at low temperature. Enzymes have more α-helices and fewer β-sheets, Proteins contain more polar amino acids and fewer hydrophobic amino acids. |
|
|
Term
|
Definition
Organisms that live at the temperature range of warm blooded
mammals. |
|
|
Term
|
Definition
| Optimum temperature is above between 45 and 80 °C. Bacteria have lipids rich in saturated fatty acids. Archaea have lipid monolayer rather than bilayer. |
|
|
Term
|
Definition
Temp optimum above 80 °C There are several habitats on earth where things live at temperatures near or above the
boiling point of water. Hot springs, deep sea vents. |
|
|
Term
| 4 groups of microbes based on temp optima |
|
Definition
| psychrophilies, mesophiles, thermophiles, hyperthermophiles |
|
|
Term
|
Definition
Organisms that grow at 0 °C (not well but do grow) but have optima of 20 - 40 °C. These are a problem for the food industry and in your refrigerator. Just
because cells aren't able to grow doesn't mean that they are dead. |
|
|
Term
|
Definition
-Organisms that prefer low pH.
- Many fungi prefer this. Also many bacteria are acidophiles.
- In these organisms, the plasma membrane is stabilized by high H+ concentration and when shifted to more neutral pH the membrane dissolves and the bacteria lyse. |
|
|
Term
|
Definition
- Prefer high pH.
- Usually found in regions with high carbonate deposits (soda lakes). |
|
|
Term
|
Definition
|
|
Term
|
Definition
Grow optimally at
normal salt concentrations
(0.85%) but are able to grow well
at high salt concentrations
(reduced water activity) (7.5%) |
|
|
Term
|
Definition
Organisms which
grow optimally in salt
concentrations equal to sea
water. (3% NaCl + many other
minerals) |
|
|
Term
|
Definition
Organisms that live in extremely salty environments
(15 - 30% NaCl). Some actually grow on salt crystals |
|
|
Term
|
Definition
| Organisms that live in high sugar concentrations |
|
|
Term
|
Definition
| Organisms that live in very dry environments |
|
|
Term
| The higher the water activity |
|
Definition
the more
water is available for
microbes to use |
|
|
Term
| Synthesis of compatible solutes |
|
Definition
increase the concentration of a solute inside
the cell which is compatible with the cell (non-inhibitory to biochemical processes)
so the water does not move out of the cell |
|
|
Term
| Examples of compatible solutes used by microbes |
|
Definition
| Glycine betaine, proline, glutamate, trehalose, glycerol |
|
|
Term
| Staphylococcus epidermidis |
|
Definition
| Halotolerant, grows on your skin |
|
|
Term
|
Definition
| need oxygen, includes Obligate, Facultative, Microaerophilic. |
|
|
Term
|
Definition
| don't need oxygen, includes Aerotolerant and Obligate |
|
|
Term
|
Definition
Add 30% hydrogen peroxide to bacterial cells and look for bubbles. Cells of the immune system (Phagocytes) produce hydrogen peroxide to
kill bacteria. Bacteria that produce catalase are able to survive this
chemical attack from the immune system. Catalase is therefore a virulence
factor. |
|
|
Term
|
Definition
| How well a bacteria will stand up to an immune system. |
|
|
Term
|
Definition
| One of the best known genera of anaerobic bacteria, |
|
|
Term
|
Definition
|
|
Term
|
Definition
| causes tetanus after a deep puncture wound |
|
|
Term
| green fluorescent protein |
|
Definition
Found in Jellyfish. This protien absorbs ultraviolet light from the sunlight, and then emits it as lower energy green light.
-This protien can be used to look directly at the inner workings of cells, by attaching the protien to any object you are interested in watching, i.e. a virus and see how it spreads through a host by shining ultraviolet light on it. |
|
|
Term
|
Definition
| All living things must have an energy source to maintain this. NOT Equilibruim because there is no reverse reaction, the system is not closed, and there is a constant input of reactants and outflow of products |
|
|
Term
|
Definition
| lower the energy of activation (a.k.a. enzymes) Typically protiens. Increase the rate of reaction by 10 to the 8th - 10 to the 20th times. |
|
|
Term
|
Definition
| Will tell you what the concentration of reactants and products are at the end of a reaction (equilibrium) but won't tell you hohw long the reaction will take. |
|
|
Term
|
Definition
| Required to bring all molecules ina chemical reaction into the reactive state |
|
|
Term
|
Definition
| usually required to breach activiation energy barrier. |
|
|
Term
|
Definition
| an Enzyme must bind it's subtrate here |
|
|
Term
|
Definition
|
|
Term
| Enzyme-substrate specificity (4) |
|
Definition
| The shape of the enzyme is very important because it ust be just the right shape to bind it's substrates and carry out its reaction. |
|
|
Term
| Physical conditions that affect Enzyme shape (4) |
|
Definition
|
|
Term
| Cofactors and the two types (4) |
|
Definition
| Small non-protien molecules that participate in catalysis but are not substrates. Prosthetic groups and Coenzymes |
|
|
Term
|
Definition
| Tightly (covalently) bound cofactors |
|
|
Term
|
Definition
| Loosely bound cofactors that are used to carry small molecules (functional groups) or electrons from one enzyme to another. |
|
|
Term
|
Definition
| The tendency to be reduced of a compound |
|
|
Term
|
Definition
| Prothetic groups or Coenzymes |
|
|
Term
|
Definition
Oxidation of organic compounds in the
absence of an external electron acceptor. Organisms that
ferment actually use an internal electron acceptor, substrate-level phosphorylation. |
|
|
Term
|
Definition
Oxidation of organic compounds in the
presence of an external electron acceptor, oxidative phosphorylation. |
|
|
Term
|
Definition
| Conversion of glucose to pyruvate |
|
|
Term
| Production of fermentation products (4) |
|
Definition
conversion of pyruvate to
various fermentation products |
|
|
Term
|
Definition
| See Slides 30-34 in chapter 4 |
|
|
Term
|
Definition
External electron acceptor is
oxygen |
|
|
Term
| Anaerobic respiration (4) |
|
Definition
External electron acceptor is
something other than oxygen |
|
|
Term
| Electron Transport System (4) |
|
Definition
Part of Aerobic Respiration. Electron carriers are oriented in the membrane in such a way that, as
electrons are transported, protons are separated from electrons.During this process, several protons are released outside of the membrane,
resulting in the generation of proton motive force. |
|
|
Term
electrochemical gradient of
protons (4) |
|
Definition
proton motive force, drives conversion of ADP to ATP through ATP
synthase |
|
|
Term
|
Definition
cyanide (CN-) & CO binds to the Fe of the porphyrin ring (in a-type
chytochromes) and prevents it from accepting electrons. |
|
|
Term
|
Definition
- prevent ATP synthesis without affecting electron transport (uncoupling
PMF and ATP synthesis) |
|
|
Term
|
Definition
Some of energy conserved as
ATP during catabolism is used for
biosynthesis of cell material |
|
|
Term
|
Definition
essentially running
glycolysis backwards. |
|
|
Term
| Primary Structure of nucleic acids (6) |
|
Definition
Sequence
of nucleotides in a DNA or RNA molecule |
|
|
Term
|
Definition
folding structure in a
DNA or RNA molecule. |
|
|
Term
|
Definition
| Enzymes that do the replication or copying of DNA in a cell. |
|
|
Term
|
Definition
| Enzyme that makes an RNA copy of the gene. mRNA. |
|
|
Term
|
Definition
| Converts the mRNA into protien by reading the three letter at a time and hooking the correct amino acids together to make a protien. |
|
|
Term
|
Definition
| The way that information is stored in DNA or RNA is the sequence of the nucleotides taken 3 at a time. |
|
|
Term
|
Definition
| Three letter sequence that codes for an amino acid in mRNA |
|
|
Term
|
Definition
Not all genes are active at the same time. If they were it would
constitute a tremendous waste of energy. Instead they are turned on
(transcribed) only when they are needed. |
|
|
Term
|
Definition
| Genes that are not on all of the time, turned on by inducers |
|
|
Term
|
Definition
| Genes that are always turned on |
|
|
Term
|
Definition
|
|
Term
|
Definition
|
|
Term
|
Definition
| the actual coding part or a gene |
|
|
Term
|
Definition
|
|
Term
|
Definition
|
|
Term
|
Definition
bind DNA by interacting with regions of DNA
containing repeated sequences that are arranged in inverse orientation (inverted
repeats) |
|
|
Term
|
Definition
melting of doublestranded
DNA into single-stranded DNA |
|
|
Term
|
Definition
Single-stranded DNA
(ssDNA) absorbs more UV light than doublestranded
DNA (dsDNA) so when dsDNA melts
(denatures) you get an increase in absorbance |
|
|
Term
|
Definition
Since the ability of two strands of DNA to base pair depends on them having
complementary antiparallel sequences, denatured DNA strands in solution can
find each other and reform the double helix if they are cooled slowly in the same
solution. |
|
|
Term
|
Definition
is when the DNA is
twisted in the opposite direction of the
helix and positive supercoiling is when
the DNA is twisted in the same direction
as the helical turns.
2. Positive supercoiling have been discovered in extreme thermophiles. This may
stabilize their DNA in hot environments. Reverse gyrase is an enzyme that catalyzes
positive supercoiling in some extreme thermophiles.
DNA Supercoiling
- Negative supercoiling is
most common in nature.
Gyrase (topoisomerase II is the enzyme that introduces it. |
|
|
Term
|
Definition
discovered in extreme thermophiles. This may
stabilize their DNA in hot environments. Reverse gyrase is an enzyme that catalyzes
it in some extreme thermophiles |
|
|
Term
|
Definition
an enzyme that cleaves the
phosphodiester bond in a single strand in the DNA and
causes the tension to relax. This removes the supercoiling |
|
|
Term
|
Definition
nucleic acids that:
1. Have genes.
2. Replicate themselves |
|
|
Term
|
Definition
No nucleus so transcription and translation
are coupled - as soon as the mRNA has begun
being made translation begins |
|
|
Term
|
Definition
Transcription and translation are not coupled
since mRNA must be transported out of
nucleus. |
|
|
Term
|
Definition
| Semiconsevative & Bi-directional |
|
|
Term
|
Definition
| small pieces of a DNA strand are about 1000 nucleotides long |
|
|
Term
| Requrements for DNA Replication |
|
Definition
| Template, Primer, Primase, DNA Polyerase III, neucleotide Triphosphates, DNA polymerase, DNA helicase, Single-stranded binding protien, DNA Ligase |
|
|
Term
|
Definition
| must have something to copy. The strand that is copied is called the template |
|
|
Term
|
Definition
Must have a starting place. You must have something to hook the nucleotides to (-
OH group) as they are brought in place. This is a short strand of RNA. Remember that
the nucleotides are added in a 5' to 3' direction |
|
|
Term
|
Definition
A specific type of RNA polymerase that copies the first 11 nucleotides by making
an RNA chain 11 ribonucleotides long |
|
|
Term
|
Definition
Enzyme that catalyzes the addition of the nucleotides to the primer
and then to the growing DNA strand |
|
|
Term
|
Definition
dATP, dTTP, dCTP,
dGTP. Precursors for the growing chain |
|
|
Term
|
Definition
When replication is well
under way this enzyme chews up the RNA
primer (RNase H) and replaces it with DNA. |
|
|
Term
|
Definition
| This is a DNA unwinding protein. |
|
|
Term
| Single-stranded binding protein |
|
Definition
Proteins that
bind to the unwound (ss)DNA and prevent it
from re-base pairing |
|
|
Term
|
Definition
Attaches the ends of two DNA
strands |
|
|
Term
|
Definition
DNA polymerase III reads the template nucleotides accurately
and usually inserts the correct complementary nucleotide, way of DNA replicaton fidelity |
|
|
Term
|
Definition
DNA polymerase III is able to detect incorrect nucleotides that
are not complementary and remove them by chewing back the new strand
from the 3' end (3 |
|
|
Term
|
Definition
Making an RNA copy of a
gene. Messenger RNA (mRNA). This
carries the information in the DNA for
protein synthesis. The enzyme that does
this is called an RNA polymerase |
|
|
Term
|
Definition
|
|
Term
| Three steps of Transcription |
|
Definition
| Initiation, Elongation, termination |
|
|
Term
|
Definition
|
|
Term
|
Definition
Inverted repeats (GC-rich
region of RNA roughly 20 bp upstream
from the 3 |
|
|
Term
|
Definition
prokaryotic transcriptional units whose expression is controlled by a
single regulator sequence |
|
|
Term
|
Definition
Converting the mRNA into
protein by reading the three letters at a time
and hooking together the correct amino
acids to make a protein. Ribosomes do
this. |
|
|
Term
| Components of Translation |
|
Definition
1. Aminoacyl-tRNA - tRNAs carrying the amino acids
2. mRNA - carries the genetic instructions from the DNA
3. Ribosomes - catalyze assembly of the amino acids into
peptides
4. Translation Factors - proteins that are not part of the
ribosome but are required for proper protein synthesis. |
|
|
Term
| Codon-anticodon interaction |
|
Definition
Note that codon-anticodon recognition by
base-pairing is also anti-parallel. The first two positions in codon should form
standard base pairing but the third one can form irregular base pairing (Wobble
base pairing) |
|
|
Term
|
Definition
no one-to-one correspondence between the
amino acid and the codon |
|
|
Term
|
Definition
a
start codon (mostly AUG, sometimes GUG) followed by some number of
codons and then a stop codon in the same reading frame. |
|
|
Term
|
Definition
| A single mRNA with several rbosomes translating at the same time. |
|
|
Term
coupled transcription and
translation |
|
Definition
Done when there is no nucleus, ribosomes can bind to the mRNA before
it is finished being transcribed |
|
|
Term
|
Definition
| the sequence of amino acids in a peptide or protein |
|
|
Term
|
Definition
the repeating conformational patterns
formed by twist and fold in a polypeptide |
|
|
Term
|
Definition
a unique 3-dimensional shape formed
by combinations of secondary structures of a polypeptide |
|
|
Term
|
Definition
a unique 3-dimensional shape formed by
more than two polypeptides |
|
|
Term
|
Definition
occur intramolecularly (i.e within a single polypeptide chain) and
intermolecularly (i.e. between two polypeptide chains) |
|
|
Term
|
Definition
an assembly or complex formed by
more than two proteins |
|
|
Term
|
Definition
| unfolding of polypeptide chain |
|
|
Term
|
Definition
| restoring proper folding upon removal of denaturing agents |
|
|
