Term
What do Pre-killing "S" strains of Streptococcus pneumoniae do to the host? |
|
Definition
|
|
Term
|
Definition
|
|
Term
|
Definition
|
|
Term
|
Definition
R and S colonies isolated from tissue of dead mouse |
|
|
Term
difference between conjugation and transformation |
|
Definition
Transformation is movement of “free DNA” into a live cell. Conjugation requires two live cells physically contacting each other. |
|
|
Term
|
Definition
an enzyme that nicks DNA to relax it to allow for its movement from one bacterium to another in the conjugation process. One DNA strand is transferred. The donor also keeps a strand for itself so it doesn’t lose the genetic information. |
|
|
Term
size of PROKARYOTIC GENOMES |
|
Definition
|
|
Term
|
Definition
|
|
Term
|
Definition
1: The two cells are brought together by the pilus on the donor. 2: The two cells are brought closer together by the pilus on the donor. 3: Relaxase assists in the DNA transfer by nicking one DNA strand to relax it to allow for its movement from one bacterium to another. 4: the recipient bacteria now becomes a donor. [image] |
|
|
Term
|
Definition
|
|
Term
|
Definition
|
|
Term
|
Definition
a group of genes that exist in tandem with each other, situated from head to tail. The entire operon is controlled by a single regulatory sequence located in front of the first gene. |
|
|
Term
The entire operon is controlled by... |
|
Definition
a single regulatory sequence located in front of the first gene. |
|
|
Term
|
Definition
a collection of genes or operons with a unified biochemical purpose. They can occur on different parts of the chromosome, but they're regulated by the same regulatory protein. [image] |
|
|
Term
|
Definition
-Usually single proteins -Cleave one strand of DNA |
|
|
Term
|
Definition
-Have multiple subunits -Cleave both strands of DNA (“ds break”) |
|
|
Term
______ is targeted by quinolone antibiotics |
|
Definition
|
|
Term
how type I topoisomerase supercoils DNA |
|
Definition
1: Topoisomerase I cleaves one strand of a double helix, holds on to both ends, and . . . 2: . . . passes the other, intact strand through the break and re-ligates the strand. 3: The helix winds in this region, resulting in one less negative supercoil. [image] |
|
|
Term
how type II topoisomerase supercoils DNA |
|
Definition
1: GyrB grabs one section of double-stranded DNA (represented by cylinder). 2: GyrA introduces double-strand break in this section (cylinder) and holds the two ends apart while remaining covalently attached to the DNA. 3: GyrA ATPase passes the intact double-stranded section through the double-strand break. 4: GyrA re-joins the cleaved DNA and opens at the other end to allow the strand that has passed through to exit. [image] |
|
|
Term
how bacterial DNA replicates |
|
Definition
1. Replication begins at origin.
2. Replication bubble forms. Replication forks progress in opposite directions.
3. One strand at each fork is synthesized continuously 5′ to 3′.
4. Second strand at each fork is synthesized discontinuously in Okazaki fragments 5′ to 3′.
5. Replication ends at terminus.
[image] |
|
|
Term
2 molecules that regulate DNA replication in E. coli |
|
Definition
|
|
Term
|
Definition
initiates replication in E. coli |
|
|
Term
|
Definition
inhibits replication in E. coli |
|
|
Term
SeqA has an affinity for... |
|
Definition
|
|
Term
______ bind to 9-bp repeats upstream of the origin (oriC). |
|
Definition
|
|
Term
DnaA-ATP complexes bind to ______ upstream of the origin (oriC). |
|
Definition
|
|
Term
Binding of DnaA-ATP complexes causes DNA to... |
|
Definition
prepare for being melted open by the helicase (DnaB). |
|
|
Term
|
Definition
the helicase that melts open DNA in E. coli |
|
|
Term
|
Definition
The main replication polymerase in E. coli |
|
|
Term
DNA Pol III can also scan for... |
|
Definition
|
|
Term
Mismatching of bases causes... |
|
Definition
cleavage of the phosphodiester bond on the mismatched base (exonuclease activity). |
|
|
Term
|
Definition
cleavage of the phosphodiester bond on the mismatched base Once removed, elongation resumes. |
|
|
Term
|
Definition
cells use this to remove RNA primers |
|
|
Term
WHAT HAPPENS TO THE RNA PRIMERS in bacteria? |
|
Definition
1: To remove RNA primers, cells use RNase H. 2: A DNA Pol I enzyme then synthesizes a DNA patch using the 3′ OH end of the preexisting DNA fragment as a priming site. 3: Finally, DNA ligase repairs the phosphodiester nick using energy from NAD (in bacteria) or ATP (in eukaryotes). |
|
|
Term
|
Definition
In terminating DNA replication, this catalyzes a breaking and re-joining event that resolves the link. |
|
|
Term
how DNA replication in bacteria is terminated |
|
Definition
1: Replication forms a linked catenane of sister chromosomes. 2: XerCD passes linked chromosomes through each other, forming a catenane. 3: Topoisomerase IV catalyzes a breaking and re-joining event that resolves the link. [image] |
|
|
Term
some characteristics of plasmids |
|
Definition
-smaller than chromosomes -Found in bacteria, archaea, and eukaryotic microbes -Circular -Separate Ori -Primarily encode genes for survival |
|
|
Term
What are some examples of genes that plasmids might carry? |
|
Definition
-antibiotic resistance -pathogenesis -environmental survival |
|
|
Term
advantage of plasmid conferring antibiotic resistance |
|
Definition
with this being on a plasmid, bacteria can quickly replicate and produce this as needed |
|
|
Term
advantage of plasmid conferring environmental survival |
|
Definition
this helps it survive in environments it’s usually not in |
|
|
Term
tricks plasmids have to ensure their inheritance |
|
Definition
-Low-copy-number plasmids segregate equally to daughter cells. -High-copy-number plasmids segregate randomly to daughter cells. |
|
|
Term
some conditions plasmids are advantageous under |
|
Definition
-Resistance to antibiotics and toxic metals -Pathogenesis -Symbiosis |
|
|
Term
how restriction enzymes are named |
|
Definition
their names reflect the genus and species of the source organism |
|
|
Term
how recombinant DNA molecules are formed |
|
Definition
1. Plasmid and foreign DNA are cut with a restriction endonuclease (EcoRI) to produce identical cohesive ends. 2. Cut vector and foreign DNA fragments are mixed. Cohesive ends anneal. 3. DNA ligase seals the nicks. [image] |
|
|
Term
how bacteria are artificially manipulated to undergo transformation |
|
Definition
by perturbing the membrane by chemical (CaCl2) or electrical (electroporation) methods |
|
|
Term
|
Definition
subject (a system, moving object, or process) to an influence tending to alter its normal or regular state or path |
|
|
Term
how CaCl2 enables a bacterium to undergo transformation |
|
Definition
it alters the membrane, making these cells chemically competent so that DNA can pass |
|
|
Term
In a natural environment, what would be the advantage of a bacteria being competent? |
|
Definition
enhances survival by being able to acquire the necessary genes |
|
|
Term
the DNA taken in by the transformasome complex |
|
Definition
ssDNA; it takes in one strand while degrading the other |
|
|
Term
The process of transformation in competent bacteria begins with... |
|
Definition
the synthesis of a signaling molecule (competence factor, CF) |
|
|
Term
The process of transformation in competent bacteria concludes with... |
|
Definition
the import of a single-stranded DNA strand through a transformasome complex |
|
|
Term
how Gram positive bacteria undergo transformation |
|
Definition
1. Precursor to competence factor (CF) is made and cleaved, and active CF is secreted. 2. As cell numbers rise, external CF level increases and activates ComD sensor kinase. 3. Phosphate from ComD is transferred to ComE. ComE-P stimulates sigma factor H (SigH) transcription. 4. SigH directs transcription of transformasome components. 5. Transformasome binds extracellular DNA. One strand is transported; one strand is degraded. [image] |
|
|
Term
Competence in Gram positive bacteria is generated by... |
|
Definition
|
|
Term
when Gram-negative bacteria are competent |
|
Definition
Either they are always competent or they become competent when starved. |
|
|
Term
Why is gene exchange limited between genera of Gram-negative bacteria? |
|
Definition
because transformation in most Gram-negative species is sequence specific |
|
|
Term
2 ways genes can be transferred between bacteria |
|
Definition
-transformation -conjugation |
|
|
Term
GENE TRANSFER BY CONJUGATION requires... |
|
Definition
the presence of special transferable plasmids |
|
|
Term
transferrable plasmids that are transferred by conjugation usually contain... |
|
Definition
all the genes needed for pilus formation and DNA export |
|
|
Term
example of a gene needed for pilus formation and DNA export |
|
Definition
E. coli fertility factor (F) |
|
|
Term
The relaxosome complex is composed of... |
|
Definition
TraH, TraI (the helicase/ endonuclease), TraJ, and TraK |
|
|
Term
the helicase in gene transfer by conjugation |
|
Definition
|
|
Term
the endonuclease in gene transfer by conjugation |
|
Definition
|
|
Term
|
Definition
|
|
Term
|
Definition
|
|
Term
|
Definition
|
|
Term
|
Definition
|
|
Term
|
Definition
Relaxase nicks DNA at oriT (nic site) |
|
|
Term
|
Definition
|
|
Term
|
Definition
|
|
Term
|
Definition
|
|
Term
how the ssDNA moves through the pore into the recipient |
|
Definition
The 5′ end of the nick will move through the pore and remain attached to the membrane while the rest of the single-stranded DNA passes into the recipient. |
|
|
Term
example of DNA transfer From Human to Bacteria |
|
Definition
Neisseria gonorrhoeae contain human-derived sequences. |
|
|
Term
what Agrobacterium tumefaciens does to host plants |
|
Definition
-Invades crown, stems, sometimes roots of many plants. -Transform infected plant cells into tumors. |
|
|
Term
how Agrobacterium tumefaciens causes crown gall disease in plants |
|
Definition
-Bacteria enter plants through wound/injured plant cells. They detect signals from “wound compounds” -Transfers Ti plasmid to plant. -Gene stimulates plant hormone production and cell division |
|
|
Term
treatments for CROWN GALL DISEASE |
|
Definition
-Destroy infected plant -Prune infected stem(s) -Treat roots with control bacteria |
|
|
Term
|
Definition
the process in which bacteriophages carry host DNA from one cell to another |
|
|
Term
2 basic types of transduction |
|
Definition
-Generalized transduction -Specialized transduction |
|
|
Term
|
Definition
can transfer any gene from a donor to a recipient cell |
|
|
Term
|
Definition
can transfer only a few closely linked genes between cells |
|
|
Term
how generalized transduction occurs |
|
Definition
1. P22 phage DNA infects a host cell and makes subunit components for more phage. 2. DNA is packaged into capsid heads. Some capsids packages host DNA. 3. New phage assembly is completed. 4. Cell lyses; phage is released. 5. Transducing phage particle injects host DNA into new cell, where it may recombine into the chromosome. [image] |
|
|
Term
examples of mutagenic agents |
|
Definition
|
|
Term
|
Definition
Salmonella defective in hisG |
|
|
Term
|
Definition
-Chief detoxifying organ of the human body -Chemically modify foreign substances |
|
|
Term
how the modified Ames test is conducted |
|
Definition
1: The potential mutagen, his-mutant bacteria, and liver homogenate are combined and mixed with agar.
2: The combination is poured into a petri plate.
3: If the liver extract enzymes act on the test compound and the metabolites produced are mutagenic, then increasing numbers of His+ revertants will be observed with increasing doses of mutagen. If the compound is not mutagenic, few relevant colonies will be seen on any plate. [image] |
|
|
Term
|
Definition
|
|
Term
|
Definition
The methyl-directed mismatch repair proteins (and genes) |
|
|
Term
A high mutation rate results in... |
|
Definition
strains that are defective in certain Mut proteins. |
|
|
Term
how methyl mismatch repair works |
|
Definition
1. MutS binds DNA mismatch. 2. MutS draws MutHL to the site to form MutHLS complex. 3. MutHLS complex causes looping 4. MutH cleaves the unmethylated strand [image] |
|
|
Term
NUCLEOTIDE EXCISION REPAIR |
|
Definition
An endonuclease removes a patch of single-stranded DNA containing damaged bases. New, correctly base-paired DNA is synthesized by DNA polymerase I. |
|
|
Term
|
Definition
The nucleotide excision repair proteins (and genes) |
|
|
Term
how nucleotide excision repair works |
|
Definition
1: UvrA & B form a complex that binds to damaged DNA
2: UvrA bends the DNA.
3: UvrA gets ejected.
4: UvrB recruits UvrC
5: UvrC cleaves at sites that flank the damage
6: UvrD has helicase activity that strips away the damaged DNA
7: DNA Pol I fills the gap.
8: DNA ligase seals the new DNA to the 5′ end of the preexisting strand.
[image] |
|
|
Term
transcription coupled repair |
|
Definition
mechanism by which polymerases that stall during transcription can recruit Uvr proteins |
|
|
Term
when Error-prone repair pathways operate |
|
Definition
only when damage is so severe that the cell has no other choice but to mutate or die |
|
|
Term
SOS (“SAVE OUR SHIP”) REPAIR |
|
Definition
I think this is another name for Error-prone repair pathways
-Induced by extensive DNA damage. -Polymerase actions are “sloppy” because they lack the capacity for proofreading. -However, they will replicate “through anything” to have a chance at survival. -This is not a single mechanism but a collaborative effort. |
|
|
Term
Polymerase actions in SOS (“SAVE OUR SHIP”) REPAIR are “sloppy” because... |
|
Definition
they lack the capacity for proofreading. |
|
|
Term
|
Definition
a protein that will regularly monitor the level of single stranded DNA. |
|
|
Term
|
Definition
a protein that prevents DNA repair gene transcription (repressor) |
|
|
Term
|
Definition
During extensive DNA damage |
|
|
Term
During extensive DNA damage,... |
|
Definition
|
|
Term
some SOS proteins that are synthesized |
|
Definition
-Pol IV -Pol V -these are both “sloppy” polymerases |
|
|
Term
a side effect that may occur as a result of SOS repair |
|
Definition
|
|
Term
example of a stress pathway triggering SOS repair and resulting in something bad |
|
Definition
-Many humans carry Staphylococcus aureus in their nasopharynx.
-Competing bacteria (Streptococcus pneumoniae) can destroy Staph. aureus DNA, evidently by way of toxic compounds.
-SOS response is triggered.
-The SOS response activates resident phages (viruses) of Staph. aureus! Staph. aureus is killed…but Strep. pneumoniae survive… |
|
|
Term
the light source in the Hawaiian Bobtailed Squid |
|
Definition
The bacteria Aliivibrio fischeri living within the squid produce the light. |
|
|
Term
|
Definition
the accumulation of a secreted small molecule called an autoinducer. |
|
|
Term
|
Definition
A secreted molecule that induces quorum-sensing behavior in bacteria |
|
|
Term
the regulatory molecule the autoinducer binds to in Alliivibrio fischeri |
|
Definition
|
|
Term
|
Definition
binds to LuxR in Alliivibrio fischeri to activate transcription of luciferase (bioluminescence) |
|
|
Term
how quorum sensing works in Alliivibrio fischeri |
|
Definition
1. The LuxI protein synthesizes an acyl homoserine lactone autoinducer (AI). 2. AI diffuses into medium and accumulates. 3. At threshold concentration, AI diffuses into cell and binds LuxR, which activates lux + transcription. [image] |
|
|
Term
The ______ system of Alliivibrio fischeri mediates that organism’s bioluminescence. |
|
Definition
|
|
Term
|
Definition
Increased transcription of target genes caused by an inducer binding to a repressor and preventing repressor-operator binding |
|
|
Term
Activators bind to specific ligand and touch... |
|
Definition
RNA polymerases sitting near promoters |
|
|
Term
sensor kinases in the cell membrane |
|
Definition
-Bind to environmental signals -Regulate cytoplasmic events via phosphorylation |
|
|
Term
how two-component signal transduction systems sense the external environment |
|
Definition
1. Sensor kinase detects condition outside the cell. 2. Signal triggers (or prevents) autophosphorylation. 3. Phosphate is transferred to a response regulator in the cytoplasm. Regulator binds DNA and either stimulates or represses the target genes. 4. A phosphatase removes the phosphate and down-regulates the system. [image] |
|
|
Term
Response regulator in the cytoplasm |
|
Definition
-Takes phosphate from sensor -Binds chromosome, which alters transcription rate for gene(s) |
|
|
Term
how a cell absorbs and processes lactose |
|
Definition
1: A dedicated lactose permease uses proton motive force to move lactose (and a proton) into the cell.
2: The enzyme beta-galactosidase (LacZ) cleaves the disaccharide into its component parts (galactose and glucose) or alters the linkage between the monosaccharides to produce allolactose, an important chemical needed to induce the genes that encode the pathway associated with the lac operon.
[image] |
|
|
Term
how the LacZYA OPERON is organized |
|
Definition
lacI and lacZYA are separate transcriptional units, each with its own promoter.
[image] |
|
|
Term
how the LacZYA OPERON is repressed in the absence of lactose |
|
Definition
The Lacl tetrameric repressor binds to specific DNA sites (the operator: lacO).
[image] |
|
|
Term
how the LacZYA OPERON is induced in the presence of lactose |
|
Definition
Inducer (lactose converted to allolactose) binds LacI repressor. This reduces LacI affinity for lacO, and transcription of the operon occurs. [image] |
|
|
Term
induction of the the LacZYA OPERON can be enhanced by... |
|
Definition
|
|
Term
Diauxic growth results when... |
|
Definition
both carbon sources, lactose and glucose, are present |
|
|
Term
|
Definition
A biphasic cell growth curve caused by depletion of the favored carbon source and a metabolic switch to the second carbon source |
|
|
Term
|
Definition
when an operon enabling the catabolism of one nutrient is repressed by the presence of a more favorable nutrient |
|
|
Term
the protein yielded by LacZ |
|
Definition
|
|
Term
what removes the repressor from the lac operon? |
|
Definition
|
|
Term
What is happening at the time point circled in red? [image] |
|
Definition
-this is when the repressor gets removed, so it takes time
-this is basically where E. coli is switching gears |
|
|
Term
|
Definition
The ability of glucose to cause metabolic changes that prevent the cellular uptake of less favorable carbon sources that could cause unnecessary induction. |
|
|
Term
how lactose import is inhibited in the presence of glucose |
|
Definition
-Phosphoenolpyruvate (PEP) “feeds” phosphate into the PTS, which relays the phosphate to glucose during transport.
-Glucose moves from protein IIC to IIB, which transfers a phosphate from IIA to glucose.
-Unphosphorylated IIAGlc inhibits LacY (lactose permease). [image] |
|
|
Term
how the absence of glucose allows the cell to take in lactose |
|
Definition
-In the absence of glucose, phosphorylated IIA accumulates and LacY is free to transport lactose.
-In the absence of glucose, the phosphorylated forms of glucose-specific IIAGlc and IIBCGlc accumulate and cannot inhibit LacY, which transports lactose
-LacY transports lactose, and the lac operon is induced. |
|
|
Term
The energy to build cells comes from chemical reactions such as... |
|
Definition
|
|
Term
some complex carbon sources for catabolism in microbes |
|
Definition
-polysacs -lipids -peptides -complex aromatic molecules |
|
|
Term
some examples of polysacs |
|
Definition
|
|
Term
Peptides are hydrolyzed to amino acids and then broken down to ______. |
|
Definition
acetate, amines, and other molecules |
|
|
Term
______ are broken down to acetate and other molecules. |
|
Definition
Complex aromatic molecules |
|
|
Term
Complex aromatic molecules are broken down to ______. |
|
Definition
acetate and other molecules |
|
|
Term
______ are broken down by specific enzymes to disaccharides and then to monosaccharides such as glucose. |
|
Definition
|
|
Term
______ are converted to pyruvate, which releases acetyl groups. |
|
Definition
|
|
Term
Glucose and sugar acids are converted to ______, which releases acetyl groups. |
|
Definition
|
|
Term
Glucose and sugar acids are converted to pyruvate, which releases ______. |
|
Definition
|
|
Term
______ are also the breakdown products of fatty acids, amino acids, and complex aromatic plant materials such as lignin. |
|
Definition
|
|
Term
Acetyl groups or acetate are also the breakdown products of ______. |
|
Definition
fatty acids, amino acids, and complex aromatic plant materials such as lignin |
|
|
Term
|
Definition
|
|
Term
|
Definition
|
|
Term
|
Definition
|
|
Term
|
Definition
|
|
Term
|
Definition
|
|
Term
|
Definition
|
|
Term
|
Definition
|
|
Term
|
Definition
|
|
Term
|
Definition
|
|
Term
|
Definition
|
|
Term
|
Definition
|
|
Term
|
Definition
|
|
Term
|
Definition
|
|
Term
|
Definition
|
|
Term
|
Definition
|
|
Term
|
Definition
|
|
Term
|
Definition
fermentation products: acetate, ethanol, lactate, CO2, H2 |
|
|
Term
|
Definition
|
|
Term
|
Definition
|
|
Term
|
Definition
|
|
Term
|
Definition
|
|
Term
|
Definition
|
|
Term
|
Definition
|
|
Term
The major polysaccharide of lettuce and tomatoes is ______. |
|
Definition
|
|
Term
polysaccharide utilization locus (PUL) |
|
Definition
set of genes used to digest xyloglucan |
|
|
Term
|
Definition
|
|
Term
|
Definition
|
|
Term
|
Definition
|
|
Term
|
Definition
|
|
Term
|
Definition
|
|
Term
|
Definition
|
|
Term
|
Definition
|
|
Term
|
Definition
|
|
Term
|
Definition
|
|
Term
|
Definition
|
|
Term
|
Definition
Maltose sensor and regulator: transcriptional activation of the sus operon. |
|
|
Term
|
Definition
|
|
Term
|
Definition
|
|
Term
|
Definition
|
|
Term
|
Definition
|
|
Term
|
Definition
|
|
Term
|
Definition
|
|
Term
|
Definition
|
|
Term
|
Definition
|
|
Term
|
Definition
|
|
Term
|
Definition
|
|
Term
the most common form of glycolysis |
|
Definition
|
|
Term
the 2 stages of the 10 distinct reactions in the EMP pathway |
|
Definition
1: Glucose Activation Stage 2: Energy Yielding Stage |
|
|
Term
Peptidoglycan precursor in the EMP pathway |
|
Definition
|
|
Term
Protein precursor (cysteine, glycine, serine) in EMP pathway |
|
Definition
|
|
Term
______ connects with the TCA cycle through pyruvate breakdown to acetyl-CoA and CO2. |
|
Definition
|
|
Term
Glucose catabolism connects with the TCA cycle through ______ to acetyl-CoA and CO2. |
|
Definition
|
|
Term
Glucose catabolism connects with the TCA cycle through pyruvate breakdown to ______. |
|
Definition
|
|
Term
In the TCA cycle, ______ can be catabolized to CO2 and H2O. |
|
Definition
products of sugar breakdown |
|
|
Term
the TCA cycle generates... |
|
Definition
electron carriers NADH & FADH2 |
|
|
Term
Glucose catabolism generates ATP through... |
|
Definition
substrate-level phosphorylation and the electron transport system’s pumping of H+ ions to drive the ATP synthase. |
|
|
Term
|
Definition
glycolysis glucose --> 2 pyruvate |
|
|
Term
|
Definition
|
|
Term
|
Definition
4 e- carried via 2 NADH + 2H+ |
|
|
Term
|
Definition
2 pyruvate --> 2 acetyl-CoA |
|
|
Term
|
Definition
|
|
Term
|
Definition
4 e- carried via 2 NADH + 2H+ |
|
|
Term
|
Definition
|
|
Term
|
Definition
|
|
Term
|
Definition
|
|
Term
|
Definition
16 e- carried via 6 NADH + 6H+ and 2 FADH2 |
|
|
Term
|
Definition
|
|
Term
|
Definition
oxidative phosphorylation |
|
|
Term
|
Definition
|
|
Term
|
Definition
|
|
Term
|
Definition
|
|
Term
|
Definition
|
|
Term
The ED pathway enables intestinal bacteria to... |
|
Definition
|
|
Term
the ED pathway starts off with... |
|
Definition
|
|
Term
|
Definition
sugars with acidic side chains |
|
|
Term
the ED pathway starts off with glucose or sugar acids and forms... |
|
Definition
|
|
Term
|
Definition
a sugar acid found in intestinal mucus |
|
|
Term
|
Definition
gluconate from mucus secretions. |
|
|
Term
______ actually induces colonic production of the mucus. |
|
Definition
Bacteroides thetaiotaomicron |
|
|
Term
Bacteroides thetaiotaomicron actually induces... |
|
Definition
colonic production of the mucus. |
|
|
Term
what happens to 6-phosphogluconate in the ED pathway? |
|
Definition
it gets dehydrated and cleaved into Pyruvate and Glyceraldedyde-3-P |
|
|
Term
Glyceraldedyde-3-P can enter the EMP pathway to form... |
|
Definition
|
|
Term
|
Definition
-NADH transfers electrons to the electron transport chain -NADPH is used for biosynthesis; Enzymes for amino acid biosynthesis use NADPH |
|
|
Term
|
Definition
it transfers electrons to the electron transport chain |
|
|
Term
The PPP pathway, like the ______, involves glucose 6-phosphate losing electrons to form NADPH. |
|
Definition
|
|
Term
The PPP pathway, like the ED pathway, involves ______ losing electrons to form NADPH. |
|
Definition
|
|
Term
The PPP pathway, like the ED pathway, involves glucose 6-phosphate losing electrons to form ______. |
|
Definition
|
|
Term
______, w/loss of C as CO2 generates ribulose-5-phosphate, which in turn produces a series of sugars, which are precursor metabolites. |
|
Definition
|
|
Term
Oxidation by NADP+, w/loss of ______ generates ribulose-5-phosphate, which in turn produces a series of sugars, which are precursor metabolites. |
|
Definition
|
|
Term
Oxidation by NADP+, w/loss of C as CO2 generates ______, which in turn produces a series of sugars, which are precursor metabolites. |
|
Definition
|
|
Term
Oxidation by NADP+, w/loss of C as CO2 generates ribulose-5-phosphate, which in turn produces... |
|
Definition
a series of sugars (precursor metabolites) |
|
|
Term
how the electron transport chain generates proton motive force |
|
Definition
It accept electrons from NADH and FADH2 and passes electrons from one carrier to the next. |
|
|
Term
In the electron transport chain, energy is released as... |
|
Definition
|
|
Term
The three important uses of the PMF for a prokaryote |
|
Definition
-ATP synthesis -active transport -flagella rotation |
|
|
Term
|
Definition
|
|
Term
|
Definition
|
|
Term
|
Definition
|
|
Term
|
Definition
|
|
Term
|
Definition
|
|
Term
|
Definition
|
|
Term
|
Definition
terminal electron acceptor |
|
|
Term
|
Definition
uses of proton motive force |
|
|
Term
|
Definition
ATP synthase (ATP synthesis) |
|
|
Term
|
Definition
active transport (one mechanism) |
|
|
Term
|
Definition
|
|
Term
|
Definition
a form of anaerobic catabolism that uses endogenous, organic electron acceptors
it produces ATP |
|
|
Term
how fermentation helps produce Swiss cheese |
|
Definition
1: Lactobacillus ferments the milk sugar, lactose, into lactic acid.
2: Propionibacterium freudenreichii converts lactate to propionate, acetate, and CO2.
Concurrent fermentation of lactate and aspartate generates additional CO2, increasing the size and number of eyes. |
|
|
Term
how the Phenol red broth test detects fermentation |
|
Definition
Phenol red turns yellow at low pH (acidic products from fermentation). Durham tube collects gas. [image] |
|
|
Term
how Geobacter helps remove uranium from water |
|
Definition
It oxidizes acetate into CO2, reducing uranium in the process. The reduced uranium precipitates out of the water. |
|
|
Term
Sulfolobus is found in... |
|
Definition
|
|
Term
|
Definition
the harnessing of photo-excited electrons to power cell growth |
|
|
Term
composition of Bacteriorhodopsin |
|
Definition
-seven alpha helices that span the membrane in alternating directions and... -surround a molecule of retinal, which is linked to... -a lysine residue [image] |
|
|
Term
|
Definition
|
|
Term
|
Definition
|
|
Term
what happens when BACTERIORHODOPSIN absorbs light? |
|
Definition
1: A photon is absorbed by retinal, which shifts its configuration from trans to cis.
2: Change causes proton pick-up.
3: The relaxation back to the trans form is coupled to pumping 1H+ across the membrane. |
|
|
Term
|
Definition
polysaccharide utilization locus |
|
|
Term
|
Definition
starch utilization system |
|
|
Term
|
Definition
Metabolic cooperation between two different species |
|
|
Term
types of GENETIC MATERIAL TRANSFER |
|
Definition
-vertical transmission
-horizontal transmission |
|
|
Term
|
Definition
genetic material transfer from parent to offspring |
|
|
Term
|
Definition
Transfer of small pieces of DNA from one cell to another |
|
|
Term
Bacterial Chromosomes Are Compacted into a... |
|
Definition
|
|
Term
the normal pH of the E. coli cell |
|
Definition
|
|
Term
DNA is the second-largest molecule in the bacterial cell (only ______ is larger) |
|
Definition
|
|
Term
|
Definition
series of protein-bound domains that bacteria pack their DNA into |
|
|
Term
Studied Streptococcus pneumoniae in mice |
|
Definition
|
|
Term
Hypothesized that the bacteria Streptococcus pneumoniae could “transfer information” to each other. |
|
Definition
|
|
Term
What does the "Smooth (S)" strain of Streptococcus pneumoniae do to the host? |
|
Definition
|
|
Term
What does the "Rough (R)" strain of Streptococcus pneumoniae do to the host? |
|
Definition
|
|
Term
What does the combination of killed "(S)" and live (R) strains of Streptococcus pneumoniae do to the host? |
|
Definition
|
|
Term
|
Definition
|
|
Term
|
Definition
|
|
Term
|
Definition
mouse contracts pneumonia |
|
|
Term
|
Definition
S colonies isolated from tissue of dead mouse |
|
|
Term
|
Definition
|
|
Term
|
Definition
R colonies isolated from tissue |
|
|
Term
|
Definition
|
|
Term
|
Definition
no colonies isolated from tissue |
|
|
Term
|
Definition
living R cells plus heat-killed S cells |
|
|
Term
|
Definition
mouse contracts pneumonia |
|
|
Term
shape of most bacterial genomes |
|
Definition
|
|
Term
|
Definition
Horizontal gene transfer requiring cell contact. Genes transferred sequentially. |
|
|
Term
|
Definition
movement of “free DNA” into a live cell |
|
|
Term
how bacteria come together to begin conjugation |
|
Definition
-The two cells are brought together by the pilus on the donor. -The two cells then come closer together by the pilus on the donor. |
|
|
Term
what happens at the completion of conjugation? |
|
Definition
the recipient bacteria now becomes a donor |
|
|
Term
amount of non-coding DNA in prokaryotic genomes |
|
Definition
|
|
Term
amount of non-coding DNA in human genome |
|
Definition
|
|
Term
|
Definition
|
|
Term
|
Definition
|
|
Term
|
Definition
|
|
Term
|
Definition
|
|
Term
|
Definition
|
|
Term
|
Definition
|
|
Term
|
Definition
units of information composed of a sequence of DNA nucleotides |
|
|
Term
|
Definition
[image] the yellow is a single gene, but the green is an operon |
|
|
Term
|
Definition
RNA that codes for one protein |
|
|
Term
|
Definition
RNA that codes for more than one protein |
|
|
Term
single gene produces monocistronic or polycistronic RNA? |
|
Definition
|
|
Term
operon produces monocistronic or polycistronic RNA? |
|
Definition
|
|
Term
A supercoil can be introduced into a double-stranded, circular DNA molecule by... |
|
Definition
(1) cleaving both strands at one site in the molecule (2) passing an intact part of the molecule between ends of the cut site (3) reconnecting the free ends. [image] |
|
|
Term
the 2 types of supercoils |
|
Definition
|
|
Term
|
Definition
|
|
Term
|
Definition
|
|
Term
organisms that positively supercoil their DNA |
|
Definition
archaeans living in acid at high temperature |
|
|
Term
why archaeans living in acid at high temperature have positively supercoiled DNA |
|
Definition
to make it harder to denature, because it takes excess energy to separate overwound DNA |
|
|
Term
organisms that negatively supercoil their DNA |
|
Definition
-bacteria -archaea -eukaryotes |
|
|
Term
|
Definition
|
|
Term
the 2 types of topoisomerases |
|
Definition
|
|
Term
example of type II topoisomerase |
|
Definition
|
|
Term
DNA gyrase is targeted by ______ antibiotics |
|
Definition
|
|
Term
Topoisomerase I relaxes a negatively supercoiled DNA molecule by... |
|
Definition
introducing a single-strand nick. |
|
|
Term
|
Definition
how spatial features of an object are connected to each other |
|
|
Term
where topoisomerases get their name |
|
Definition
they change the topology of DNA |
|
|
Term
how gyrase supercoils DNA |
|
Definition
1: Gyrase grabs one section and introduces a ds break. 2: It then passes the intact strand through the ds break. |
|
|
Term
|
Definition
where DNA replication begins |
|
|
Term
does E. coli methylate its own DNA? |
|
Definition
|
|
Term
does freshly made E. coli DNA have methyl groups? |
|
Definition
just after replication, there is a short period before methyl groups can be added to new strand. |
|
|
Term
As the cell grows, DnaA levels ______. |
|
Definition
|
|
Term
DnaA-ATP complexes bind to 9-bp repeats upstream of the ______. |
|
Definition
|
|
Term
E. coli has how many DNA polymerases? |
|
Definition
|
|
Term
all the DNA polymerases in E. coli catalyze DNA synthesis in what direction? |
|
Definition
|
|
Term
The main replication polymerase in E. coli |
|
Definition
|
|
Term
this DNA polymerase can scan for mismatched bases in E. coli |
|
Definition
|
|
Term
|
Definition
After the removal of RNA primers, this repairs the phosphodiester nick using energy from NAD (in bacteria) or ATP (in eukaryotes). |
|
|
Term
DNA ligase repairs the phosphodiester nick using energy from ______ (in bacteria) or ______ (in eukaryotes). |
|
Definition
|
|
Term
DNA ligase repairs the phosphodiester nick using energy from NAD (in ______) or ATP (in ______). |
|
Definition
|
|
Term
|
Definition
An extrachromosomal genetic element that may be present in some cells. |
|
|
Term
|
Definition
-bacteria -archaea -eukaryotic microbes |
|
|
Term
plasmids primarily encode... |
|
Definition
|
|
Term
|
Definition
|
|
Term
why bacteria can cause sickness |
|
Definition
because some genes they use just happen to make the host sick |
|
|
Term
|
Definition
segregate equally to daughter cells |
|
|
Term
High-copy-number plasmids |
|
Definition
segregate randomly to daughter cells |
|
|
Term
Plasmids are useful for... |
|
Definition
genetic engineering applications. |
|
|
Term
one way bacteria rid themselves of foreign DNA |
|
Definition
restriction endonucleases |
|
|
Term
restriction endonucleases |
|
Definition
“Molecular scissors” that cleave unfamiliar DNA molecules at specific palindromic sequences called restriction sites |
|
|
Term
restriction endonucleases aka... |
|
Definition
|
|
Term
|
Definition
specific palindromic sites where restriction endonucleases cleave unfamiliar DNA molecules |
|
|
Term
what humens use restriction endonucleases for |
|
Definition
|
|
Term
scenario in which a bacteria would want to use restriction enzymes to cut foreign DNA |
|
Definition
protection, often against viral DNA (bacteriophages) |
|
|
Term
how bacteria avoid cutting their own DNA |
|
Definition
they methylate their DNA at specific sequences where they would otherwise be cut |
|
|
Term
|
Definition
sequence where both strands read the same in the 5’-3’ direction |
|
|
Term
2 types of ends that can be caused by restriction endonucleases |
|
Definition
-blunt (no overhang) -sticky (has overhang) |
|
|
Term
______ can be used to analyze fragments of DNA cut after cleavage with restriction endonucleases. |
|
Definition
|
|
Term
|
Definition
the process of importing free DNA into bacterial cells |
|
|
Term
|
Definition
Able to take up DNA from the environment (capable of natural transformation) |
|
|
Term
|
Definition
A bacterial cell membrane protein complex that imports external DNA during transformation in Gram positive bacteria. It facilitates uptake of DNA. |
|
|
Term
As the Gram positive bacteria grow, the competence factor (CF)... |
|
Definition
|
|
Term
In Gram positive bacteria, at specific levels, CF will induce... |
|
Definition
a genetic program that induces the transformasome |
|
|
Term
Gram-negative bacteria transform DNA without... |
|
Definition
the use of competence factors (CF) |
|
|
Term
Do Gram-negative bacteria use transformasomes? |
|
Definition
|
|
Term
specificity of transformation in most Gram-negative species |
|
Definition
|
|
Term
|
Definition
|
|
Term
|
Definition
|
|
Term
Membrane proteins encoded by F+ bacteria prevent... |
|
Definition
conjugation with other F+ |
|
|
Term
how gene transfer by conjugation occurs |
|
Definition
1. Sex pilus from the F+ plasmid donor (left) attaches to receptors on the recipient cell (right).
2. Contraction of the pilus draws the two cells together and forms a relaxosome bridge.
3. The F factor is nicked at oriT, and the 5′ end begins transfer through the bridge.
4. The strand remaining in the donor is replicated.
5. Once in the recipient, the transferred strand circularizes and replicates.
6. The recipient has been converted to a donor.
[image] |
|
|
Term
|
Definition
|
|
Term
|
Definition
|
|
Term
|
Definition
|
|
Term
|
Definition
|
|
Term
|
Definition
|
|
Term
example of DNA transfer From Bacteria to Plants |
|
Definition
Agrobacterium tumefaciens transfers DNA to plants. |
|
|
Term
Does Agrobacterium tumefaciens stimulate nodule formation or fix nitrogen? |
|
Definition
|
|
Term
why Agrobacterium tumefaciens causes tumors |
|
Definition
because it contains a tumor-inducing plasmid (Ti) that can be transferred via conjugation to plants |
|
|
Term
|
Definition
tumor-inducing plasmid that Agrobacterium tumefaciens can transfer to plants via conjugation |
|
|
Term
Agrobacterium tumefaciens causes... |
|
Definition
Crown gall disease tumor [image] |
|
|
Term
characteristics of CROWN GALL DISEASE |
|
Definition
-Round tumor growths on stems or roots. -Interferes with plants ability to move nutrients and water. -Plant severely growth impaired. |
|
|
Term
how Agrobacterium tumefaciens knows plant is wounded |
|
Definition
it detects “wound compounds” |
|
|
Term
Agrobacterium tumefaciens metabolizes... |
|
Definition
|
|
Term
|
Definition
CROWN GALL DISEASE caused by Agrobacterium tumefaciens |
|
|
Term
the control bacteria used to treat roots with crown gall disease |
|
Definition
Agrobacterium radiobacter |
|
|
Term
Agrobacterium radiobacter |
|
Definition
a non-pathogenic competitor of Agrobacterium tumefaciens
-it is the control bacteria used to treat roots with crown gall disease |
|
|
Term
how Agrobacterium radiobacter counteracts Agrobacterium tumefaciens |
|
Definition
Agrobacterium radiobacter outcompetes Agrobacterium tumefaciens for space and nutrients and eventually limits the growth of A. tumefaciens. |
|
|
Term
The number of genes transferred in any one phage capsid is limited to... |
|
Definition
what can fit in the phage head. |
|
|
Term
|
Definition
a heritable change in DNA |
|
|
Term
|
Definition
A substances that causes DNA mutations |
|
|
Term
|
Definition
A test of the mutagenicity of a substance |
|
|
Term
what does it mean when Salmonella is defective in hisG? |
|
Definition
it means it's a mutant of wild-type Salmonella that cannot grow on media lacking histidine |
|
|
Term
If Salmonella hisG suddenly grows on this histidine-free media, it means... |
|
Definition
they acquired changes to their DNA such that it reverted the gene back to normal. This is called reversion. |
|
|
Term
|
Definition
A mutation that changes a previous mutation back to its original state |
|
|
Term
|
Definition
bacteria that has undergone reversion, which is the change of a previous mutation back to its original state |
|
|
Term
|
Definition
-A hisG auxotrophic mutant of Salmonella enterica will not grow on histidine-free medium.
-A disk containing a possible mutagen is placed at the center of the plate.
-Prototrophic hisG+ revertants form around the disk as the mutagen diffuses into the medium. [image] |
|
|
Term
the purpose of the Ames test |
|
Definition
to screen for mutagenesis |
|
|
Term
why screening for mutagenesis is important |
|
Definition
because mutagenesis is an uderlying factor in tumor and cancer development |
|
|
Term
why the Ames test uses histidine-free media with Salmonella hisG (unable to produce histidine) |
|
Definition
screens for revertants that mutate back to Salmonella WT |
|
|
Term
|
Definition
Ames test where liver enzymes are added to the media to determine whether or not they promote mutations |
|
|
Term
A mutagen-containing disk is placed on an agar plate with the mutant. Mutagen causes reversion mutations, and colonies start to appear around the disk. Q- What does this tell you about the test mutagen? |
|
Definition
it causes a significant amount of DNA damage |
|
|
Term
modified Ames tests for... |
|
Definition
the mutagenic properties of chemicals processed through the liver |
|
|
Term
2 types of Error-proof pathways |
|
Definition
-Methyl mismatch repair -Nucleotide excision repair |
|
|
Term
|
Definition
corrects unmethylated daughter strand based on the methylated parental strand so that the unmethylated daughter strand complements the methylated parental strand |
|
|
Term
how methyl mismatch repair differentiates between parent and daughter strands of DNA |
|
Definition
it uses methylation of the parental strand to discriminate from newly replicated DNA |
|
|
Term
the premise of Methyl mismatch repair |
|
Definition
The premise is that the parental strand will contain the proper DNA sequence. |
|
|
Term
does nucleotide excision repair distinguish between parental/daughter strands? |
|
Definition
|
|
Term
Error-prone repair pathways |
|
Definition
Risk introducing mutations |
|
|
Term
SOS (“SAVE OUR SHIP”) REPAIR is induced by... |
|
Definition
|
|
Term
______ can introduce many single stranded “gaps”. |
|
Definition
Extensive UV light exposure |
|
|
Term
Extensive UV light exposure can introduce many ______. |
|
Definition
|
|
Term
|
Definition
A regulatory protein that can bind to a specific DNA sequence and inhibit transcription of genes |
|
|
Term
what happens to cell division in SOS repair? |
|
Definition
|
|
Term
Cell will live after SOS repair if... |
|
Definition
it can tolerate any mutations caused by PolIV and Pol V…and any other side effects of the cellular stress (ie. phage activation) |
|
|
Term
why SOS repair may not always lead to survival and DNA repair |
|
Definition
because it activates multiple pathways
Some stress pathways may be activated and inadvertently harm the cell |
|
|
Term
example of SOS repair leading to harming the cell |
|
Definition
Some stress pathways may be activated and inadvertently harm the cell |
|
|
Term
Many humans carry ______ in their nasopharynx. |
|
Definition
|
|
Term
Many humans carry Staphylococcus aureus in their ______. |
|
Definition
|
|
Term
When it swims, it projects light downward. |
|
Definition
|
|
Term
some details about the Hawaiian Bobtailed Squid |
|
Definition
-found in the warm waters of Hawaiian coast.
-nocturnal
-When it is active at night it projects light produced by the bacteria Aliivibrio fischeri downward so its predators can't see it. That is, it projects light of the same intensity as moonlight. Doing so means it won’t cast a shadow as it swims. Its predators (such as sharks) don’t see its shadow and thus, don’t notice it. It’s a survival mechanism. |
|
|
Term
the Hawaiian Bobtailed Squid's survival mechanism |
|
Definition
-When it swims it projects downward light about the same light of the same intensity as moonlight so that it won’t cast a shadow as it swims, making its predators (such as sharks) unable to see it. |
|
|
Term
how the bacteria Aliivibrio fischeri grows inside the Hawaiian Bobtailed Squid |
|
Definition
-During the day as the squid is buried in the sand the bacteria grow to high numbers in the squid light organ. This is so at night the levels of bacteria are high enough to produce the light needed for camouflage. -At dawn (morning) the squid will flush most of the bacteria out of the light organ (note the levels of bacteria drop). As it rests in the sand during the day the few bacteria that were not flushed out reproduce and repopulate the light organ and the cycle repeats. |
|
|
Term
depiction of how molecular regulation in the Hawaiian Bobtailed Squid works |
|
Definition
|
|
Term
when the secreted autoinducer reenters cells |
|
Definition
when it is at a certain extracellular concentration |
|
|
Term
what the autoinducer does when it reenters the cell |
|
Definition
It binds to a regulatory molecule |
|
|
Term
|
Definition
the light-producing bacteria in the Hawaiian Bobtailed Squid |
|
|
Term
Light production by Alliivibrio fischeri requires... |
|
Definition
quorum sensing
That is, the bacteria can sense when the population is at high density and communicate with each other to produce the light (at night in this case). |
|
|
Term
|
Definition
bind to regulatory sequences in the DNA and prevent transcription of target genes |
|
|
Term
repressor requires ligand (______) to release |
|
Definition
|
|
Term
|
Definition
A small molecule that must bind to a repressor to allow the repressor to bind operator DNA |
|
|
Term
|
Definition
An increase in gene expression caused by the decrease in concentration of a corepressor |
|
|
Term
difference between induction and derepression |
|
Definition
induction is caused by increased concentration of a ligand (inducer) while derepression is caused by decreased concentration of a ligand (corepressor) [image] |
|
|
Term
induction or derepression? [image] |
|
Definition
|
|
Term
induction or derepression? [image] |
|
Definition
|
|
Term
|
Definition
bind to regulatory sequences in the DNA and stimulate transcription of target genes
Most must first bind a small ligand. |
|
|
Term
Most activators must first... |
|
Definition
|
|
Term
can inducers be involved in activation? |
|
Definition
yes
inducers bind to activator proteins
[image] |
|
|
Term
Jacques Monod and François Jacob |
|
Definition
-1961
-proposed the revolutionary idea that genes could be regulated.
-They noticed that, in E. coli, enzymes used to metabolize lactose were inducible. These enzymes were produced only when lactose was added to media.
-noted glucose enzymes were different from that of lactose
-noticed that, in E. coli, enzymes used to metabolize glucose were constitutive, which means it's produced all the time |
|
|
Term
-proposed the revolutionary idea that genes could be regulated |
|
Definition
Jacques Monod and François Jacob |
|
|
Term
-noticed that, in E. coli, enzymes used to metabolize lactose were inducible. These enzymes were produced only when lactose was added to media. |
|
Definition
Jacques Monod and François Jacob |
|
|
Term
how lactose is moved into an E. coli cell |
|
Definition
A lactose permease uses PMF to move lactose into cell. |
|
|
Term
|
Definition
uses proton motive force to move lactose (and a proton) into the cell |
|
|
Term
|
Definition
cleaves lactose into galactose and glucose at high β–galactosidase levels or... modifies linkage producing allolactose at low β–galactosidase levels |
|
|
Term
when β-galactosidase cleaves lactose into galactose and glucose |
|
Definition
Only at high β–galactosidase levels |
|
|
Term
when β-galactosidase modifies linkage in lactose to produce allolactose |
|
Definition
Only at low β–galactosidase levels |
|
|
Term
does the bacterium transcribe and translate the genes for lactose utilization when it doesn’t need to? |
|
Definition
yes, but to a very small extent |
|
|
Term
When there is no lactose, LacZYA operon is transcribed at ______ levels. |
|
Definition
very low
Thus, levels of Lactose permease and Beta-galactosidase will be very low. |
|
|
Term
levels of Lactose permease in the absence of lactose |
|
Definition
|
|
Term
levels of Beta-galactosidase in the absence of lactose |
|
Definition
|
|
Term
noted glucose enzymes were different from that of lactose |
|
Definition
Jacques Monod and François Jacob |
|
|
Term
noticed that, in E. coli, enzymes used to metabolize glucose were constitutive, which means it's produced all the time |
|
Definition
Jacques Monod and François Jacob |
|
|
Term
|
Definition
|
|
Term
In E.coli, ______ is the preferred carbon source. |
|
Definition
|
|
Term
depiction of a diauxic growth curve |
|
Definition
|
|
Term
what does this represent? [image] |
|
Definition
|
|
Term
the protein yielded by LacY |
|
Definition
|
|
Term
Glucose ______ β-galactosidase production. |
|
Definition
|
|
Term
Glucose transport into the cell ______ lactose import. |
|
Definition
|
|
Term
example of Inducer Exclusion |
|
Definition
Glucose transport into the cell inhibits lactose import. [image] |
|
|
Term
Glucose transport via the phosphotransferase system ______ LacY (lactose permease) |
|
Definition
|
|
Term
In the ______ of glucose the lactose transporter is fully functional to move lactose into the cell. |
|
Definition
|
|
Term
In the absence of glucose the lactose transporter is ______ to move lactose into the cell. |
|
Definition
|
|
Term
Absence of glucose ______ free lactose transport into the cell. |
|
Definition
|
|
Term
______ of glucose allows free lactose transport into the cell. |
|
Definition
|
|
Term
|
Definition
breakdown of complex molecules into smaller ones, releasing energy |
|
|
Term
|
Definition
building up of complex biomolecules from smaller precursors |
|
|
Term
|
Definition
|
|
Term
______ are hydrolyzed to glucose |
|
Definition
|
|
Term
polysacs are ______ to glucose |
|
Definition
|
|
Term
polysacs are hydrolyzed to ______ |
|
Definition
|
|
Term
______ are broken down to acetate. |
|
Definition
|
|
Term
Lipids are broken down to ______. |
|
Definition
|
|
Term
______ are hydrolyzed to amino acids and then broken down to acetate, amines, and other molecules. |
|
Definition
|
|
Term
Peptides are ______ to amino acids and then broken down to acetate, amines, and other molecules. |
|
Definition
|
|
Term
Peptides are hydrolyzed to ______ and then broken down to acetate, amines, and other molecules. |
|
Definition
|
|
Term
some examples of a complex aromatic molecules |
|
Definition
-lignins -halogenated aromatic pollutants |
|
|
Term
Carbohydrates are broken down by specific enzymes to ______ and then to monosaccharides such as glucose. |
|
Definition
|
|
Term
Carbohydrates are broken down by specific enzymes to disaccharides and then to ______. |
|
Definition
monosaccharides such as glucose |
|
|
Term
|
Definition
|
|
Term
|
Definition
|
|
Term
Humans can’t digest xyloglucans without... |
|
Definition
|
|
Term
Lettuce xyloglucans are ______ polymers of D-glucose (Glc) with side chains of xylose (Xyl), galactose (Gal), and fucose (Fuc). In tomatoes, xyloglucan side chains also have arabinose (Ara). |
|
Definition
|
|
Term
Lettuce xyloglucans are beta-linked polymers of ______ with side chains of xylose (Xyl), galactose (Gal), and fucose (Fuc). In tomatoes, xyloglucan side chains also have arabinose (Ara). |
|
Definition
|
|
Term
Lettuce xyloglucans are beta-linked polymers of D-glucose (Glc) with side chains of ______. In tomatoes, xyloglucan side chains also have arabinose (Ara). |
|
Definition
xylose (Xyl), galactose (Gal), and fucose (Fuc) |
|
|
Term
Lettuce xyloglucans are beta-linked polymers of D-glucose (Glc) with side chains of xylose (Xyl), galactose (Gal), and fucose (Fuc). In ______, xyloglucan side chains also have arabinose (Ara). |
|
Definition
|
|
Term
Lettuce xyloglucans are beta-linked polymers of D-glucose (Glc) with side chains of xylose (Xyl), galactose (Gal), and fucose (Fuc). In tomatoes, xyloglucan side chains also have ______. |
|
Definition
|
|
Term
Each type of xyloglucan requires a slightly different set of genes, called a... |
|
Definition
polysaccharide utilization locus (PUL). |
|
|
Term
|
Definition
a common ancestral starch utilization system (SUS). |
|
|
Term
Most gut bacteria possess a number of PULs distributed around their genomes, showing evidence of... |
|
Definition
horizontal gene transfer. |
|
|
Term
|
Definition
synteny, evidence of descent from a common ancestor. |
|
|
Term
|
Definition
evidence of descent from a common ancestor |
|
|
Term
Bacteroides share ______ with their community. |
|
Definition
|
|
Term
Bacteroides share catabolic enzymes with their ______. |
|
Definition
|
|
Term
Some of the outer membrane of Bacteroides can pinch off to form ______. |
|
Definition
|
|
Term
Why would it be advantageous for Bacteroides to share catabolism genes with other bacteria in the gut (ie. its competitors)? |
|
Definition
possible reasons
1: more small molecules available for Bacteroides, increasing the efficiency with which the xyloglucans are digested
2: host health; the bacteria want their host to remain healthy, because that's their envirinment |
|
|
Term
the 3 main routes by which Bacteria & Archaea catabolism of glucose occurs |
|
Definition
1. Glycolysis or Embden-Meyerhof-Parnas Pathway (EMP) 2. Entner-Doudoroff Pathway (ED) 3. Pentose phosphate pathway (PPP) |
|
|
Term
where the EMP pathway occurs |
|
Definition
|
|
Term
the EMP pathway functions in the presence or absence of O2? |
|
Definition
|
|
Term
Glucose catabolism connects with the ______ through pyruvate breakdown to acetyl-CoA and CO2. |
|
Definition
|
|
Term
The tricarboxylic acid (TCA) cycle is also known as... |
|
Definition
the Krebs cycle, or citric acid cycle. |
|
|
Term
In prokaryotes, the TCA cycle occurs in the... |
|
Definition
|
|
Term
In eukaryotes, the TCA cycle occurs in the... |
|
Definition
|
|
Term
In the ______, products of sugar breakdown can be catabolized to CO2 and H2O. |
|
Definition
|
|
Term
In the TCA cycle, products of sugar breakdown can be ______ to CO2 and H2O. |
|
Definition
|
|
Term
In the TCA cycle, products of sugar breakdown can be catabolized to ______. |
|
Definition
|
|
Term
The complete oxidative breakdown of glucose to CO2 and H2O could theoretically generate up to ______ ATP. |
|
Definition
38
Under actual conditions, the number is smaller. |
|
|
Term
the ED pathway is studied mostly in... |
|
Definition
|
|
Term
the ED pathway occurs in the... |
|
Definition
|
|
Term
The ED pathway functions in the presence or absence of O2? |
|
Definition
|
|
Term
|
Definition
it is used for biosynthesis; Enzymes for amino acid biosynthesis use NADPH |
|
|
Term
PPP PATHWAY occurs in the ______ of the cell. |
|
Definition
|
|
Term
Can the PPP PATHWAY operate independently or at the same time as other pathways? |
|
Definition
|
|
Term
Does the PPP PATHWAY function in the presence or absence of O2? |
|
Definition
|
|
Term
The ______, like the ED pathway, involves glucose 6-phosphate losing electrons to form NADPH. |
|
Definition
|
|
Term
The PPP pathway, like the ED pathway, involves glucose 6-phosphate ______ to form NADPH. |
|
Definition
|
|
Term
the electron transport chain generates... |
|
Definition
|
|
Term
the electron transport chain is composed of... |
|
Definition
a series of membrane embedded electron carriers |
|
|
Term
A place for electron carriers to drop off electrons other than the electron transport chain |
|
Definition
|
|
Term
a way to use fermentation to detect pathogenic E. coli |
|
Definition
Sorbitol fermentation test for pathogen E. coli O157:H7. White colonies (strain O157:H7) fail to ferment sorbitol, unlike red colonies (nonpathogenic E. coli). It uses McConkey agar.
[image] |
|
|
Term
E. COLI 0157: H7 is a lethal contaminant of... |
|
Definition
|
|
Term
E. COLI 0157: H7 contains ______ genes. |
|
Definition
|
|
Term
the genes "normal" E. coli has that pathogenic E. coli doesnt |
|
Definition
those for the enzymes to ferment sorbitol |
|
|
Term
is Geobacter aerobic or anaerobic? |
|
Definition
|
|
Term
Geobacter is “______-breathing” |
|
Definition
|
|
Term
______ oxidizes organic compounds to CO2, with iron being the final electron acceptor. |
|
Definition
|
|
Term
Geobacter oxidizes organic compounds to CO2, with ______ being the final electron acceptor. |
|
Definition
|
|
Term
______ is also said to “produce electricity”. |
|
Definition
|
|
Term
|
Definition
using microorganisms to reduce pollution. |
|
|
Term
______ used for removal of Uranium from water in Colorado. |
|
Definition
|
|
Term
Geobacter used for removal of ______ from water in Colorado. |
|
Definition
|
|
Term
Many bacteria that are utilized in bioremediation form biofilms. Why would that be important? |
|
Definition
If you can get bacteria to stay at the site and get them to flourish there, you increase the chances of them staying there and removing the toxin from the environment. |
|
|
Term
is Sulfolobus bacteria or archaea? |
|
Definition
|
|
Term
example of a Thermoacidophile |
|
Definition
|
|
Term
Sulfolobus has biotechnology applications due to ______ at high temp & low pH. |
|
Definition
|
|
Term
Sulfolobus has biotechnology applications due to enzyme stability at ______. |
|
Definition
|
|
Term
|
Definition
Hydrogen sulfide oxidized to sulfuric acid |
|
|
Term
example of an organism that does sulfur oxidation |
|
Definition
|
|
Term
Microbial sulfur oxidation can cause... |
|
Definition
severe environmental acidification |
|
|
Term
Most of Earth’s photosynthetic production, especially in the oceans, comes from... |
|
Definition
|
|
Term
The proton gradient generated using bacteriorhodopsin drives... |
|
Definition
ATP synthesis by a typical F1Fo ATP synthase |
|
|
Term
To maximize light absorption organisms may pack their entire cell membrane with ______. |
|
Definition
|
|
Term
composition of the "purple membrane" of bacteriorhodopsin |
|
Definition
trimers of bacteriorhodopsin packed in hexagonal arrays [image] |
|
|