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Exam 2
Modules 3 and 4
528
Microbiology
Undergraduate 3
06/20/2020

Additional Microbiology Flashcards

 


 

Cards

Term
What do Pre-killing "S" strains of Streptococcus pneumoniae do to the host?
Definition
prevent illness
Term
what's number 4? [image]
Definition
living R cells
Term
what's number 7?
[image]
Definition
Heat-killed S cells
Term
what's number 12?
[image]
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
Relaxase
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
~ 130-14,000 kb
Term
size of human genome
Definition
over 3 million kb
Term
the steps of conjugation
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
what's number 2?
[image]
Definition
mobile DNA
Term
what's number 6?
[image]
Definition
relaxase
Term
operon
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
Regulons
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
Type I topoisomerases
Definition
-Usually single proteins
-Cleave one strand of DNA
Term
Type II topoisomerases
Definition
-Have multiple subunits
-Cleave both strands of DNA (“ds break”)
Term
______ is targeted by quinolone antibiotics
Definition
DNA gyrase
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
-DnaA
-SeqA
Term
DnaA
Definition
initiates replication in E. coli
Term
SeqA
Definition
inhibits replication in E. coli
Term
SeqA has an affinity for...
Definition
partially methylated DNA
Term
______ bind to 9-bp repeats upstream of the origin (oriC).
Definition
DnaA-ATP complexes
Term
DnaA-ATP complexes bind to ______ upstream of the origin (oriC).
Definition
9-bp repeats
Term
Binding of DnaA-ATP complexes causes DNA to...
Definition
prepare for being melted open by the helicase (DnaB).
Term
DnaB
Definition
the helicase that melts open DNA in E. coli
Term
DNA Pol III
Definition
The main replication polymerase in E. coli
Term
DNA Pol III can also scan for...
Definition
mismatched bases
Term
Mismatching of bases causes...
Definition
cleavage of the phosphodiester bond on the mismatched base (exonuclease activity).
Term
exonuclease activity
Definition
cleavage of the phosphodiester bond on the mismatched base
Once removed, elongation resumes.
Term
RNase H
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
Topoisomerase IV
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
Perturbing
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
quorum sensing
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
TraH
Term
the endonuclease in gene transfer by conjugation
Definition
TraI
Term
what's number 1?
[image]
Definition
relaxosome complex
Term
what's number 4?
[image]
Definition
TraJ
Term
what's number 5?
[image]
Definition
TraH
Term
what's number 6?
[image]
Definition
TraI
Term
what's number 7?
[image]
Definition
Relaxase nicks DNA at oriT (nic site)
Term
what's number 8?
[image]
Definition
TraK
Term
what's number 10?
[image]
Definition
TraG
Term
what's number 12?
[image]
Definition
cell membrane pore
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
Transduction
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
Generalized transduction
Definition
can transfer any gene from a donor to a recipient cell
Term
Specialized transduction
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
-Nitrates
-5-Bromouracil
Term
what the Ames test uses
Definition
Salmonella defective in hisG
Term
the role of the liver
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
Error-proof pathways
Definition
prevent/repair mutations
Term
Mut
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
Uvr
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
RecA
Definition
a protein that will regularly monitor the level of single stranded DNA.
Term
LexA
Definition
a protein that prevents DNA repair gene transcription (repressor)
Term
when RecA degrades LexA
Definition
During extensive DNA damage
Term
During extensive DNA damage,...
Definition
RecA degrades LexA
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
phage activation
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
QUORUM SENSING requires
Definition
the accumulation of a secreted small molecule called an autoinducer.
Term
autoinducer
Definition
A secreted molecule that induces quorum-sensing behavior in bacteria
Term
the regulatory molecule the autoinducer binds to in Alliivibrio fischeri
Definition
LuxR
Term
LuxR autoinducer
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
lux
Term
induction
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
cyclic AMP
Term
Diauxic growth results when...
Definition
both carbon sources, lactose and glucose, are present
Term
diauxic growth
Definition
A biphasic cell growth curve caused by depletion of the favored carbon source and a metabolic switch to the second carbon source
Term
catabolite repression
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
beta-galactosidase
Term
what removes the repressor from the lac operon?
Definition
allolactose
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
Inducer Exclusion
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
-catabolism
-anabolism
Term
some complex carbon sources for catabolism in microbes
Definition
-polysacs
-lipids
-peptides
-complex aromatic molecules
Term
some examples of polysacs
Definition
-starch
-cellulose
-pectin
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
Carbohydrates
Term
______ are converted to pyruvate, which releases acetyl groups.
Definition
Glucose and sugar acids
Term
Glucose and sugar acids are converted to ______, which releases acetyl groups.
Definition
pyruvate
Term
Glucose and sugar acids are converted to pyruvate, which releases ______.
Definition
acetyl groups
Term
______ are also the breakdown products of fatty acids, amino acids, and complex aromatic plant materials such as lignin.
Definition
Acetyl groups or acetate
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
what's number 1?
[image]
Definition
polysaccharide
Term
what's number 2?
[image]
Definition
disaccharide
Term
what's number 3?
[image]
Definition
glucose (6C)
Term
what's number 4?
[image]
Definition
carbohydrates
Term
what's number 6?
[image]
Definition
Entner-Doudoroff
Term
what's number 7?
[image]
Definition
glycolysis
Term
what's number 8?
[image]
Definition
lipids
Term
what's number 9?
[image]
Definition
glycerol
Term
what's number 10?
[image]
Definition
fatty acid
Term
what's number 11?
[image]
Definition
lignin
Term
what's number 12?
[image]
Definition
aromatics
Term
what's number 13?
[image]
Definition
vanillin
Term
what's number 14?
[image]
Definition
benzoate
Term
what's number 15?
[image]
Definition
peptides
Term
what's number 16?
[image]
Definition
amino acids
Term
what's number 17?
[image]
Definition
2 pyruvate (3C)
Term
what's number 18?
[image]
Definition
fermentation products: acetate, ethanol, lactate, CO2, H2
Term
what's number 19?
[image]
Definition
acetyl-CoA (2C)
Term
what's number 20?
[image]
Definition
syntrophy
Term
what's number 21?
[image]
Definition
CO2, CH4
Term
what's number 22?
[image]
Definition
CO2
Term
what's number 24?
[image]
Definition
TCA cycle
Term
what's number 25?
[image]
Definition
CO2
Term
The major polysaccharide of lettuce and tomatoes is ______.
Definition
xyloglucans
Term
polysaccharide utilization locus (PUL)
Definition
set of genes used to digest xyloglucan
Term
what's number 1?
[image]
Definition
starch
Term
what's number 2?
[image]
Definition
SusG
Term
what's number 3?
[image]
Definition
oligocaccharides
Term
what's number 4?
[image]
Definition
SusC
Term
what's number 5?
[image]
Definition
monosaccharide import
Term
what's number 6?
[image]
Definition
outer membrane
Term
what's number 7?
[image]
Definition
periplasm
Term
what's number 8?
[image]
Definition
inner membrane
Term
what's number 9?
[image]
Definition
TonB
Term
what's number 10?
[image]
Definition
SusR
Term
what's number 11?
[image]
Definition
Maltose sensor and regulator: transcriptional activation of the sus operon.
Term
what's number 12?
[image]
Definition
glycosidases
Term
what's number 13?
[image]
Definition
SusA
Term
what's number 14?
[image]
Definition
SusB
Term
what's number 15?
[image]
Definition
SusD
Term
what's number 16?
[image]
Definition
SusE
Term
what's number 17?
[image]
Definition
SusE
Term
what's number 18?
[image]
Definition
SusD
Term
what's number 19?
[image]
Definition
glycosidase
Term
what's number 20?
[image]
Definition
lipase
Term
what's number 21?
[image]
Definition
peptidase
Term
the most common form of glycolysis
Definition
the EMP pathway
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
Fructose 6-phosphate
Term
Protein precursor (cysteine, glycine, serine) in EMP pathway
Definition
3-Phosphoglycerate
Term
______ connects with the TCA cycle through pyruvate breakdown to acetyl-CoA and CO2.
Definition
Glucose catabolism
Term
Glucose catabolism connects with the TCA cycle through ______ to acetyl-CoA and CO2.
Definition
pyruvate breakdown
Term
Glucose catabolism connects with the TCA cycle through pyruvate breakdown to ______.
Definition
acetyl-CoA and CO2
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
what's number 1?
[image]
Definition
glycolysis
glucose --> 2 pyruvate
Term
what's number 2?
[image]
Definition
2 ATP
Term
what's number 3?
[image]
Definition
4 e- carried via 2 NADH + 2H+
Term
what's number 4?
[image]
Definition
2 pyruvate --> 2 acetyl-CoA
Term
what's number 5?
[image]
Definition
2 CO2
Term
what's number 6?
[image]
Definition
4 e- carried via 2 NADH + 2H+
Term
what's number 7?
[image]
Definition
TCA cycle
Term
what's number 8?
[image]
Definition
2 ATP
Term
what's number 9?
[image]
Definition
4 CO2
Term
what's number 10?
[image]
Definition
16 e- carried via 6 NADH + 6H+ and 2 FADH2
Term
what's number 11?
[image]
Definition
ETS
Term
what's number 12?
[image]
Definition
oxidative phosphorylation
Term
what's number 13?
[image]
Definition
ATP synthase
Term
what's number 14?
[image]
Definition
F0
Term
what's number 15?
[image]
Definition
F1
Term
what's number 16?
[image]
Definition
34 ATP
Term
The ED pathway enables intestinal bacteria to...
Definition
feed on mucus.
Term
the ED pathway starts off with...
Definition
glucose or sugar acids
Term
sugar acids
Definition
sugars with acidic side chains
Term
the ED pathway starts off with glucose or sugar acids and forms...
Definition
6-phosphogluconate
Term
Gluconate
Definition
a sugar acid found in intestinal mucus
Term
E. coli feeds on...
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
pyruvate.
Term
NADH VS. NADPH
Definition
-NADH transfers electrons to the electron transport chain
-NADPH is used for biosynthesis; Enzymes for amino acid biosynthesis use NADPH
Term
the role of NADH
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
ED pathway
Term
The PPP pathway, like the ED pathway, involves ______ losing electrons to form NADPH.
Definition
glucose 6-phosphate
Term
The PPP pathway, like the ED pathway, involves glucose 6-phosphate losing electrons to form ______.
Definition
NADPH
Term
______, w/loss of C as CO2 generates ribulose-5-phosphate, which in turn produces a series of sugars, which are precursor metabolites.
Definition
Oxidation by NADP+
Term
Oxidation by NADP+, w/loss of ______ generates ribulose-5-phosphate, which in turn produces a series of sugars, which are precursor metabolites.
Definition
C as CO2
Term
Oxidation by NADP+, w/loss of C as CO2 generates ______, which in turn produces a series of sugars, which are precursor metabolites.
Definition
ribulose-5-phosphate
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
electrons are passed.
Term
The three important uses of the PMF for a prokaryote
Definition
-ATP synthesis
-active transport
-flagella rotation
Term
what's number 1?
[image]
Definition
electron transport chain
Term
what's number 2?
[image]
Definition
NADH dehydrohenase
Term
what's number 3?
[image]
Definition
path of electrons
Term
what's number 4?
[image]
Definition
ubiquinone
Term
what's number 5?
[image]
Definition
succinate dehydrogenase
Term
what's number 6?
[image]
Definition
ubiquinol oxidase
Term
what's number 7?
[image]
Definition
terminal electron acceptor
Term
what's number 8?
[image]
Definition
uses of proton motive force
Term
what's number 9?
[image]
Definition
ATP synthase
(ATP synthesis)
Term
what's number 10?
[image]
Definition
active transport
(one mechanism)
Term
what's number 11?
[image]
Definition
rotation of flagella
Term
fermentation
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
volcanic hot springs
Term
Phototrophy
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
what's number 1?
[image]
Definition
retinal
Term
what's number 2?
[image]
Definition
lysine
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
PUL
Definition
polysaccharide utilization locus
Term
SUS
Definition
starch utilization system
Term
syntrophy
Definition
Metabolic cooperation between two different species
Term
types of GENETIC MATERIAL TRANSFER
Definition

-vertical transmission

-horizontal transmission

Term
Vertical transmission
Definition
genetic material transfer from parent to offspring
Term
Horizontal transmission
Definition
Transfer of small pieces of DNA from one cell to another
Term
Bacterial Chromosomes Are Compacted into a...
Definition
Nucleoid
Term
the normal pH of the E. coli cell
Definition
7.8
Term
DNA is the second-largest molecule in the bacterial cell (only ______ is larger)
Definition
peptidoglycan
Term
nucleoid
Definition
series of protein-bound domains that bacteria pack their DNA into
Term
Studied Streptococcus pneumoniae in mice
Definition
Frederick Griffith
Term
Hypothesized that the bacteria Streptococcus pneumoniae could “transfer information” to each other.
Definition
Frederick Griffith
Term
What does the "Smooth (S)" strain of Streptococcus pneumoniae do to the host?
Definition
kills it
Term
What does the "Rough (R)" strain of Streptococcus pneumoniae do to the host?
Definition
nothing
Term
What does the combination of killed "(S)" and live (R) strains of Streptococcus pneumoniae do to the host?
Definition
kills it
Term
which scientist? [image]
Definition
Frederick Griffith
Term
what's number 1? [image]
Definition
living S cells
Term
what's number 2? [image]
Definition
mouse contracts pneumonia
Term
what's number 3? [image]
Definition
S colonies isolated from tissue of dead mouse
Term
what's number 5? [image]
Definition
mouse remains healthy
Term
what's number 6?
[image]
Definition
R colonies isolated from tissue
Term
what's number 8?
[image]
Definition
mouse remains healthy
Term
what's number 9?
[image]
Definition
no colonies isolated from tissue
Term
what's number 10?
[image]
Definition
living R cells plus heat-killed S cells
Term
what's number 11?
[image]
Definition
mouse contracts pneumonia
Term
shape of most bacterial genomes
Definition
circular
Term
Conjugation
Definition
Horizontal gene transfer requiring cell contact. Genes transferred sequentially.
Term
Transformation
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
less than 15%
Term
amount of non-coding DNA in human genome
Definition
over 90% non-coding
Term
what's number 1?
[image]
Definition
chromosome
Term
what's number 3?
[image]
Definition
pilus
Term
what's number 4?
[image]
Definition
donor bacterium
Term
what's number 5?
[image]
Definition
recipient bacterium
Term
what's number 7?
[image]
Definition
donor bacterium
Term
what's number 8?
[image]
Definition
donor bacterium
Term
Genes
Definition
units of information composed of a sequence of DNA nucleotides
Term
single gene vs. operon
Definition
[image]
the yellow is a single gene, but the green is an operon
Term
monocistronic RNA
Definition
RNA that codes for one protein
Term
polycistronic RNA
Definition
RNA that codes for more than one protein
Term
single gene produces monocistronic or polycistronic RNA?
Definition
monocistronic
Term
operon produces monocistronic or polycistronic RNA?
Definition
polycistronic
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
-positive
-negative
Term
Positive supercoils
Definition
DNA is overwound
Term
Negative supercoils
Definition
DNA is underwound
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
TOPOISOMERASE
Definition
SUPERCOILS DNA
Term
the 2 types of topoisomerases
Definition
-Type I
-Type II
Term
example of type II topoisomerase
Definition
DNA gyrase
Term
DNA gyrase is targeted by ______ antibiotics
Definition
quinolone
Term
Topoisomerase I relaxes a negatively supercoiled DNA molecule by...
Definition
introducing a single-strand nick.
Term
Topology
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
origin (oriC)
Definition
where DNA replication begins
Term
does E. coli methylate its own DNA?
Definition
yes
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
rise
Term
DnaA-ATP complexes bind to 9-bp repeats upstream of the ______.
Definition
origin (oriC)
Term
E. coli has how many DNA polymerases?
Definition
5
Term
all the DNA polymerases in E. coli catalyze DNA synthesis in what direction?
Definition
5’ --> 3'
Term
The main replication polymerase in E. coli
Definition
DNA Pol III
Term
this DNA polymerase can scan for mismatched bases in E. coli
Definition
DNA Pol III
Term
DNA ligase
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
NAD
ATP
Term
DNA ligase repairs the phosphodiester nick using energy from NAD (in ______) or ATP (in ______).
Definition
bacteria
eukaryotes
Term
plasmid
Definition
An extrachromosomal genetic element that may be present in some cells.
Term
plasmids are found in...
Definition
-bacteria
-archaea
-eukaryotic microbes
Term
plasmids primarily encode...
Definition
genes for survival
Term
pathogenesis
Definition
causing illness
Term
why bacteria can cause sickness
Definition
because some genes they use just happen to make the host sick
Term
Low-copy-number plasmids
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
restriction enzymes
Term
restriction sites
Definition
specific palindromic sites where restriction endonucleases cleave unfamiliar DNA molecules
Term
what humens use restriction endonucleases for
Definition
biotechnology
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
palindromic DNA sequence
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
DNA gel electrophoresis
Term
Transformation
Definition
the process of importing free DNA into bacterial cells
Term
competent
Definition
Able to take up DNA from the environment (capable of natural transformation)
Term
transformasome complex
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
accumulates
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
no
Term
specificity of transformation in most Gram-negative species
Definition
sequence specific
Term
F+ cells
Definition
the genetic donors
Term
F- cells
Definition
the recipients
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
what's number 2?
[image]
Definition
donor
Term
what's number 3?
[image]
Definition
recipient
Term
what's number 9?
[image]
Definition
DNA
Term
what's number 11?
[image]
Definition
cell membrane pore
Term
what's number 13?
[image]
Definition
nic
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
no
Term
why Agrobacterium tumefaciens causes tumors
Definition
because it contains a tumor-inducing plasmid (Ti) that can be transferred via conjugation to plants
Term
Ti plasmid
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
plant hormones
Term
what is this?
[image]
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
mutation
Definition
a heritable change in DNA
Term
mutagenic agent
Definition
A substances that causes DNA mutations
Term
AMES TEST
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
reversion
Definition
A mutation that changes a previous mutation back to its original state
Term
revertant
Definition
bacteria that has undergone reversion, which is the change of a previous mutation back to its original state
Term
how the Ames test works
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
modified Ames test
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
Methyl mismatch repair
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
no
Term
Error-prone repair pathways
Definition
Risk introducing mutations
Term
SOS (“SAVE OUR SHIP”) REPAIR is induced by...
Definition
extensive DNA damage.
Term
______ can introduce many single stranded “gaps”.
Definition
Extensive UV light exposure
Term
Extensive UV light exposure can introduce many ______.
Definition
single stranded “gaps”
Term
repressor
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
it gets halted
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
Staphylococcus aureus
Term
Many humans carry Staphylococcus aureus in their ______.
Definition
nasopharynx
Term
When it swims, it projects light downward.
Definition
Hawaiian Bobtailed Squid
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
[image]
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
Alliivibrio fischeri
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
Repressors
Definition
bind to regulatory sequences in the DNA and prevent transcription of target genes
Term
repressor requires ligand (______) to release
Definition
inducer
Term
corepressor
Definition
A small molecule that must bind to a repressor to allow the repressor to bind operator DNA
Term
derepression
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
induction
Term
induction or derepression?
[image]
Definition
derepression
Term
Activators
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
bind a small ligand.
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
lactose permease
Definition
uses proton motive force to move lactose (and a proton) into the cell
Term
β-galactosidase
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
very low
Term
levels of Beta-galactosidase in the absence of lactose
Definition
very low
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
constitutive
Definition
produced all the time
Term
In E.coli, ______ is the preferred carbon source.
Definition
glucose
Term
depiction of a diauxic growth curve
Definition
[image]
Term
what does this represent?
[image]
Definition
diauxic growth
Term
the protein yielded by LacY
Definition
permease
Term
Glucose ______ β-galactosidase production.
Definition
represses
Term
Glucose transport into the cell ______ lactose import.
Definition
inhibits
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
inhibits
Term
In the ______ of glucose the lactose transporter is fully functional to move lactose into the cell.
Definition
absence
Term
In the absence of glucose the lactose transporter is ______ to move lactose into the cell.
Definition
fully functional
Term
Absence of glucose ______ free lactose transport into the cell.
Definition
allows
Term
______ of glucose allows free lactose transport into the cell.
Definition
Absence
Term
Catabolism
Definition
breakdown of complex molecules into smaller ones, releasing energy
Term
Anabolism
Definition
building up of complex biomolecules from smaller precursors
Term
anabolism aka...
Definition
biosynthesis
Term
______ are hydrolyzed to glucose
Definition
polysacs
Term
polysacs are ______ to glucose
Definition
hydrolyzed
Term
polysacs are hydrolyzed to ______
Definition
glucose
Term
______ are broken down to acetate.
Definition
Lipids
Term
Lipids are broken down to ______.
Definition
acetate
Term
______ are hydrolyzed to amino acids and then broken down to acetate, amines, and other molecules.
Definition
Peptides
Term
Peptides are ______ to amino acids and then broken down to acetate, amines, and other molecules.
Definition
hydrolyzed
Term
Peptides are hydrolyzed to ______ and then broken down to acetate, amines, and other molecules.
Definition
amino acids
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
disaccharides
Term
Carbohydrates are broken down by specific enzymes to disaccharides and then to ______.
Definition
monosaccharides such as glucose
Term
what's number 5?
[image]
Definition
sugar acid
Term
what's number 23?
[image]
Definition
citrate
Term
Humans can’t digest xyloglucans without...
Definition
help from gut bacteria.
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
beta-linked
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
D-glucose (Glc)
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
tomatoes
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
arabinose (Ara)
Term
Each type of xyloglucan requires a slightly different set of genes, called a...
Definition
polysaccharide utilization locus (PUL).
Term
The PULs evolved from...
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
The PULs show...
Definition
synteny, evidence of descent from a common ancestor.
Term
synteny
Definition
evidence of descent from a common ancestor
Term
Bacteroides share ______ with their community.
Definition
catabolic enzymes
Term
Bacteroides share catabolic enzymes with their ______.
Definition
community
Term
Some of the outer membrane of Bacteroides can pinch off to form ______.
Definition
vesicles
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
cytoplasm
Term
the EMP pathway functions in the presence or absence of O2?
Definition
both
Term
Glucose catabolism connects with the ______ through pyruvate breakdown to acetyl-CoA and CO2.
Definition
TCA cycle
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
cytoplasm.
Term
In eukaryotes, the TCA cycle occurs in the...
Definition
mitochondria.
Term
In the ______, products of sugar breakdown can be catabolized to CO2 and H2O.
Definition
TCA cycle
Term
In the TCA cycle, products of sugar breakdown can be ______ to CO2 and H2O.
Definition
catabolized
Term
In the TCA cycle, products of sugar breakdown can be catabolized to ______.
Definition
CO2 and H2O
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
prokaryotes
Term
the ED pathway occurs in the...
Definition
cytoplasm
Term
The ED pathway functions in the presence or absence of O2?
Definition
both
Term
the role of NADPH
Definition
it is used for biosynthesis; Enzymes for amino acid biosynthesis use NADPH
Term
PPP PATHWAY occurs in the ______ of the cell.
Definition
cytosol
Term
Can the PPP PATHWAY operate independently or at the same time as other pathways?
Definition
it can do either
Term
Does the PPP PATHWAY function in the presence or absence of O2?
Definition
both
Term
The ______, like the ED pathway, involves glucose 6-phosphate losing electrons to form NADPH.
Definition
PPP pathway
Term
The PPP pathway, like the ED pathway, involves glucose 6-phosphate ______ to form NADPH.
Definition
losing electrons
Term
the electron transport chain generates...
Definition
proton motive force
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
fermentation
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
beef & vegetables.
Term
E. COLI 0157: H7 contains ______ genes.
Definition
pathogenic
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
anaerobic
Term
Geobacter is “______-breathing”
Definition
Iron
Term
______ oxidizes organic compounds to CO2, with iron being the final electron acceptor.
Definition
Geobacter
Term
Geobacter oxidizes organic compounds to CO2, with ______ being the final electron acceptor.
Definition
iron
Term
______ is also said to “produce electricity”.
Definition
Geobacter
Term
Bioremediation
Definition
using microorganisms to reduce pollution.
Term
______ used for removal of Uranium from water in Colorado.
Definition
Geobacter
Term
Geobacter used for removal of ______ from water in Colorado.
Definition
Uranium
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
archaea
Term
example of a Thermoacidophile
Definition
Sulfolobus
Term
Sulfolobus has biotechnology applications due to ______ at high temp & low pH.
Definition
enzyme stability
Term
Sulfolobus has biotechnology applications due to enzyme stability at ______.
Definition
high temp & low pH
Term
Sulfur oxidation
Definition
Hydrogen sulfide oxidized to sulfuric acid
Term
example of an organism that does sulfur oxidation
Definition
Sulfolobus
Term
Microbial sulfur oxidation can cause...
Definition
severe environmental acidification
Term
Most of Earth’s photosynthetic production, especially in the oceans, comes from...
Definition
microbes
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
bacteriorhodopsin
Term
composition of the "purple membrane" of bacteriorhodopsin
Definition
trimers of bacteriorhodopsin packed in hexagonal arrays
[image]
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