microbio Flashcards

(124 cards)

1
Q

Some proteins are needed under all growth conditions
Proteins that are always being expressed are ____________

A

constitutive

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2
Q

Cells use two approaches to regulate protein function
Control the _______ of a protein
Control the ________of a protein

A

-amount
-activity

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3
Q

Primary form of regulation in Bacteria and Archaea

A

Transcriptional control

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4
Q

Small molecules influence the binding of _________ _______ to DNA
-Turns transcription on or off

A

Regulatory Proteins

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5
Q

Bacterial gene arrangement differs from eukaryotes.
-Lack _______
Can be arranged in operons:
two or more genes transcribed under the control of a _________region (single regulatory site) located upstream of where R N A polymerase initiates transcription

A

-introns
-promoters

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5
Q

Bacterial promoters characterized by distinct nucleotide sequences recognized and bound by ____-binding proteins
-Allows _____ polymerase to bind, transcription to occur

A

-DNA
-RNA

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6
Q

DNA-Binding Proteins
Interaction of Proteins with Nucleic Acids
Small molecules influence the binding of _________ ________ to DNA
-turns transcription up or down

may be _________-specific or ___________

A

-regulatory proteins
-squence
-nonspecific

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7
Q

Major ________ of DNA is the main site of protein binding

A

groove

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8
Q

DNA Binding Proteins

_________ ________frequently are specific binding sites for regulatory proteins.
Homodimeric proteins: proteins composed of two identical _____________
Each __________ has a _______ that binds to one inverted repeat.
Domain: region of a polypeptide with specific structure and function

A

-Inverted repeats
-polypeptide
-polypeptide
-domain

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9
Q

region of a polypeptide with specific structure and function

A

domain

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10
Q

Structure of DNA-Binding Proteins

helix-turn-helix
two α-helices connected by a short “turn” sequence
first helix the ________ helix
interacts specifically with ____

second helix the stabilizing helix
interacts with first helix through______________ interactions

A

-recognition
-DNA
-stabilizing
-hydrophobic

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11
Q

Many different DNA-binding proteins from Bacteria contain ____-____-_____
____and ___ repressors of E. coli

A

-helix-turn-helix
- lac
-trp

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12
Q

Structure of DNA-Binding Proteins

Eukaryotic regulatory protein structure that binds a zinc ion

A

Zinc finger domains

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13
Q

Structure of DNA-Binding Proteins

-Contains regularly spaced leucine residues
-Function to hold two recognition helices in the correct orientation

A

Leucine zipper domain

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14
Q

DNA Binding Proteins
Multiple outcomes after DNA binding are possible.

DNA-binding protein may catalyze a specific reaction on the DNA molecule (e.g., transcription by ___ polymerase)
The binding event can block transcription - ________ regulation
The binding event can activate transcription ________ regulation

A

-RNA
-negative
-positive

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15
Q

Proteins that control the rate of transcription by binding to specific DNA

A

Transcription factors

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16
Q

-turns on transcription
-Binds DNA and recruits RNA polymerase or sigma factor to promoter region

A

Activator protein

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17
Q

-turns off expression
-Binds operator region of DNA downstream of promoter

A

Repressor protein

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18
Q

_________ _______: Conformation altered when effector molecule binds

-Since transcription factors are allosteric, conformational change determines whether transcription factor can bind _____

A

-Allosteric proteins
-DNA

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19
Q

Transcription factors
Inducers turn ___ transcription, corepressors turn ____ transcription

A

-on
-off

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20
Q

Repression and Activation

:preventing the synthesis of an enzyme unless product is absent from culture medium; excess of product decreases enzyme synthesis

A

Enzyme repression

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21
Q

Enzyme repression

-Specific effect (synthesis of all other enzymes continues normally)
-Widespread as control for production of _____ _____ and nucleotide precursors
-Usually, final product of a biosynthetic pathway is the ___________ effector molecule
- Typically affects biosynthetic/anabolic enzymes

A

-amino acid
-corepressor

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22
Q

Repression and Activation

Enzyme induction:
-opposite of ___________
-production of an enzyme in response to presence of __________
-typically affects degradative/catabolic enzymes (e.g., ____ operon)
-ensures enzymes are ____________ only when needed

A

-repression
- substrate
-lac
-synthesized

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23
Q

Mechanisms of Repression and Derepression

Repressors turn off ___________
Corepressors only bind ____ in presence of its ________.

Example: Arginine becomes ___________when plentiful
Binds _______ repressor (Arg R)
Results in _______ change and ________ binding
Since arg mRNA is ___________, all peptides encoded are repressed

A

-transcription
-DNA,
-effector
-corepressor
-arginine
-allosteric
-operator
-polycistronic

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24
Mechanisms of Repression and Derepression Some repressors bind in absence of effector, e.g., ____ operon (____________) Lac __(lactose repressor) binds to________, blocks transcription If Lac __ _____ present, combines with repressor, causing ______ change that prevents Lac ___ from binding ____ ___________ can proceed Corepressor = _______ (inactivates repressor) Allolactose and isopropylthiogalactosie (IPTG) are ___ inducers
-lac, derepression; -I, operator -I, effector -allosetric, I, DNA -Transcription\ -inducer, lac
25
Mechanisms of Repression and Derepression Repressor’s role is _______ (preventing mRNA synthesis), so it is called _______ control Genes are not turned on and off completely; often very low level of basal ___________ when “fully repressed”
-inhibitory, negative -transcription
26
Mechanisms of Activation Some operons transcribed only if _____protein first bound to _____ ________ sequences are poor matches to consensus ________ sequences, thus only _______ bind ____ polymerase Positive control: regulator protein facilitates transcription
-activator, DNA -promoter, promoter, weakly, RNA
27
:regulator protein facilitates transcription
Positive control
28
Mechanisms of Activation ____________ proteins help R N A ______________ recognize promoter. May bend _________ structure May interact directly with R N A polymerase
-polymerase -polymerase -DNA
29
Mehcanisms of Activation Example: maltose _________ in E. coli Maltose activator protein (Mal T) cannot bind to DNA unless it first binds _________(effector/inducer) Binding of Mal T allows ____ polymerase to __________ Activator proteins bind specifically to ________-binding site (specific D N A sequence, not called an operator)
-catabolism -maltose -RNA, transcribe -activator
30
Positive Regulation - Activation Genes for ______ are spread out over the chromosome in several _______. -Each operon has an _______-binding site. -Multiple operons controlled by the same regulatory protein are called a ________. ________ also exist for _________ controlled systems (e.g., ________ regulon).
-maltose; operons -activator -regulon -regulons, negatively, arginine
31
Two-Component Regulatory Systems Prokaryotes regulate cellular __________ in response to environmental fluctuations -External signal may be transmitted _______ to the target -External signal may be detected by sensor and transmitted to ___________machinery (signal ____________)
-metabolism -directly -regulatory, trasnduction
32
Two-Component Regulatory Systems Most signal ____________ systems are two-component regulatory systems containing two parts -______ kinase (in cytoplasmic membrane): detects environmental signal and autophosphorylates at specific -_______ residue (________ kinase) -________ regulator (in cytoplasm): _____-binding protein that regulates ____________, receives phosphate from ______ kinase
-transduction -senor -histidine, histidine -response, DNA, transcription, sensor
33
Two-Component Regulatory Systems Most signal transduction systems are two-component regulatory systems containing two parts Also has __________ loop -__________ response uses _____________ that removes phosphate from _________ regulator
-feedback -terminates -phosphatase, repsonse
34
Examples of Two-Component Regulatory Systems Almost 50 different two-component systems in _______ -examples include phosphate assimilation, nitrogen metabolism, and osmotic pressure response -e.g., OmpC and OmpF controlled by environment ________; EnvZ sensor __________ kinase detects osmotic pressure changes
-Ecoli -osmolarity; histidine
35
_________: Moving toward attractants, away from repellents respond to temporal gradients (change in concentration over time)
-Chemotaxis -temporal
36
Regulation of Chemotaxis Bacteria use modified two-component system to sense _________ changes in attractants or repellents and regulate________ rotation thus regulate activity of ___________ proteins instead of modifying transcription of genes
-temporal, flagellar -preexisiting
37
Regulation of Chemotaxis Response to Signal Depends upon signal cascade of multiple proteins :Sensory proteins that sense attractants and repellents and interact with cytoplasmic sensor kinases Chemoreceptors: clusters of thousands of MCPs
-Methyl -accepting chemotaxis proteins (MCPs)
38
Regulation of Chemotaxis Response to Signal _______ has four transmembrance chemoreceptors, each containing ____ different MCPs MCP binding of attractant or repellent triggers interactions with Che__ (sensor kinase) and Che__ -Increase in ________, increases Che__ autophosphorylation -Phosphate transferred to Che__(response regulator) - controls _______ rotation
-E.coli, five -A, W -repellant, A -Y, flagellar
39
CheA is the what in regulation of chemotaxis?
sensor kinase
40
CheY is the what in regualation of chemotaxis
-response regulator -governs direction of rotation
41
Regulation of Chemotaxis Controlling Flagellar Rotation -Che __ governs direction of rotation Counterclockwise: ____ (swim smoothly) Clockwise: _____ (move randomly) When ________ bind _______ or release attractant, Che__-__ (phosphorylated) interacts with flagellar motor to induce _______ rotation and tumbling When M C P s bind ______ or release repellent, _____________ Che Y does not bind to flagellar motor, resulting in ________________ rotation and running
-Y -run - tumble -MCPs, repellants, Che Y-P, clockwise -attractant, unphosphorylated, counterclockwise
42
Regulation of Chemotaxis ___________: Stop responding and reset sensory system -_________ loop resets system -relies on response regulator Che__ -involves methylation of MCPs Methylation stops response to _____ and ________ response to repellents When unmethylated, respond ______ to attractants, __________ to repellents Che__ methytlates, phosphorylated Che__ (Che__-P) demethylates
-adaptaion -feedback -B -attractansts, increases -strongly, insensitive -R, B, B -
43
Regulation of Chemotaxis ____ proteins also play a role in other taxes _____taxis: movement toward ____ -Light sensor replaces _____ _____taxis: movement toward _____ -_____ protein monitors oxygen level _______ interact with cytoplasmic ____ proteins, leading to runs/tumbles
-Che -photo, light, MCPs -aero, oxygen, redox -sensors, Che
44
Cell-to-Cell Signaling ___________ can communicate through production of small extracellular molecules Small peptides or nonpeptide organics Accumulation leads to coordinated group behaviors, e.g., _______ ___________
-prokayotes -biofilm formation
45
Cell-to-Cell Signaling ______ _________:regulatory mechanism by which Bacteria and some Archaea assess their population density
quorum sensing
46
Cell-to-Cell Signaling Mechanism of Quorum Sensing Ensures a sufficient number of cells are present before initiating activities that require a certain cell density to be effective (e.g., _____ production by a _________ bacterium) Each species produces a specific ___________ signaling molecule -diffuses freely across the ____ envelope -reaches ____ concentrations only if many cells are nearby and making the same _____________ -binds to specific _______ protein or sensor kinase, triggering transcription of specific genes
-toxin, pathogenic -autoinducer -cell -high, autoinducer -activator
47
Cell-to-Cell Signaling Mechanism of Quorum Sensing Several different classes of _____________ -acyl __________ lactone (AHL): _____ to be identified, several types found in different gram-________ -____________ 2 (AI-2): a common autoinducer among many gram-_________ species, allowing interspecies _____________ -short peptides used as autoinducers by gram-positives and _________
-autoinducer -homoserine, first -negatives -autoinducer, negative, communication peptides, positives, Archaea
48
Cell-to-Cell Signaling Mechanism of Quorum Sensing Quorum sensing first discovered as mechanism regulating ____production in bacteria including Aliivibrio _________. -_____ operon encodes bioluminescence/luciferase also occurs in microbial eukaryotes (Saccharomyces __________ and ________)
-light, fischeri, lux -eukaryotes -cerevisiae,Candida
49
Cell-to-Cell Signaling Virulence factors example: )______ O157:H7 Shiga toxin–producing strain Produces AHL A I-2 that induces ______ genes Epinephrine plus norepinephrine (both produced by ____) + A I-3 bind to _____ _______ in cytoplasmic membrane. -activates two transcriptional _______, thus activating motility, toxin secretion, and production of ______-forming proteins
-E.coli -AHL, virulence -host -sensor kinases -activators, lesion
50
Cell-to-Cell Signaling Virulence factors example: Staphylococcus aureus secretes small ______that damage _____ cells or interfere with _______immune system under control of ______________ peptide (AIP) -activates several proteins that lead to production of ___________ proteins _________-sensing disruptors could be potential drugs for dispersing _______ and preventing virulence gene expression
-small, host's, host's -autoinducing, virulence -Quorum, biofilm, virulence
51
- regulate expression of many different genes simultaneously - lactose operon and maltose regulon
Global control systems
52
Catabolite repression is an example of _____ control. -Controls use of ______ sources if more than one present -Synthesis of unrelated catabolic enzymes (e.g., _______ operon and ________ regulon) is repressed if _______ is present in growth medium. -Ensures that the "best" carbon and energy source is used _____
-global -carbon -lactose, maltose, glucose -first
53
Global control and lac operon _______ _________:two exponential growth phases if two energy sources available -Better energy source consumed first, growth _____ -After ___, growth resumes with second energy source.
-Diauxic growth -stops -lag
54
Global control and lac operon Cyclic AMP and cyclic AMP receptor protein -In _________ repression, transcription is controlled by the _____ ____ receptor protein (CRP), an activator protein, and is a form of ________ control. -CRP binds to ____ only if it has bound cyclic adenosine monophosphate (cyclic AMP or cAMP)
-catabolite, cyclic AMP, positive -DNA, adenosine
55
Global Control and lac operon For ___ genes to be transcribed -_____ level must be high enough for CRP protein to bind to ____-binding site. -_______ or another inducer must be present to prevent ________ repressor (LacI) binding.
-lac - cAMP, CRP -lactose, lactose
56
- counteract damage of denatured proteins and help cell recover from temperature stres
Heat shock proteins
57
Heat Shock Response Heat shock proteins - counteract damage of denatured proteins and help cell recover from temperature stress -Very ancient proteins -Induced by ____, exposure to ____ or ___ radiation Three major classes: Hsp___ (DnaK in E. coli), Hsp___ (GroEL in E. coli), and Hsp___ (GroES in E. coli) Largely controlled by alternative _____ factor ____
-heat, ethanol, UV -70, 60, 10
58
The general _____ response – RpoS regulon -Allows cells to withstand harsh conditions (e.g., extreme pH, oxidative stress) -Controlled by alternative sigma factor _____ (stationary phase sigma factor) ______ regulon includes 400+ genes: nutrient limitation, resistance to DNA damage, biofilm formation, responses to osmotic, oxidative, and acid stress
-stress -RpoS -RpoS
59
RNA-Based Regulation Noncoding RNA (ncRNA): RNA that is not translated to _____ _____ RNAs (sRNAs): 40–400 nucleotides that regulate gene expression in prokaryotes and eukaryotes
-proteins -small
60
Regulatory RNAs sRNAs exert regulatory effects by ____ _______ with other ____ with complementary sequence (usually mRNA) -Block a _________-binding site (RBS), decreasing __________ -Open up a ______ RBS, increasing _______ -Increase degradation of mRNA, ____________ synthesis -Decrease degradation of mRNA, __________ synthesis
base pairing, RNA -ribosome, expression -blocked, expression -preventing -incresasing
61
Regulatory RNAs Types of _____ RNA -______-sRNAs are encoded in the __________ region -Limited ______________ to target molecule, may only base-pair with 5–11 nucleotides -Binding of _____-sRNA to targets depends on Hfq - binds to both RNA molecules to facilitate interaction. Hfq is an RNA ____________
-small -trans, intergenic -complementarity -trans -chaperon
62
Riboswitches ______ can carry out many roles similar to proteins -Binding results from the folding of the RNA into a 3D structure -Catalytically active RNAs are called _______ Riboswitches - RNA molecules that resemble repressors and activators in binding small metabolites and regulating gene expression
-RNA - ribozymes
63
:RNA molecules that resemble repressors and activators in binding small metabolites and regulating gene expression
riboswitches
64
65
Mechanisms of riboswitches -Metabolite binds ______ to _______ -Control __________ of mRNA instead of transcription; Prevents __________ binding -______ molecule binding domain at ___ end of mRNA ____ alternative structures, one with small molecule bound and other without
-directly, mRNA -translation, Ribosomal -small, 5', two
66
Riboswitches and evolution -found in some bacteria, fungi, and plants -likely in _______ -believed to be remnants of ____world (before cells, DNA, and protein were present)
-Archea -RNA
67
Regulation of Proteins Previous activities ( start of ch 7 pptx) regulated the _______ of a protein Here we focus on mechanisms that control the _______ of proteins Feedback inhibition Post-translational __________
-amount -activity -Feedback , regulation
68
Feedback inhibition: mechanism for temporarily turning off the reactions in a biosynthetic pathway -End product of the pathway binds to the first _______ in the pathway, thus _________- its activity. -_________ reaction -Inhibited enzyme is an ________ enzyme. 2 binding sites: ______ (substrate-binding) and ________ (end product binds) Binding at allosteric site changes _____________ , __________ substrate binding.
-enzyme, inhibiting -reversible -allosteric -active, allosteric -conformation, preventing
69
: mechanism for temporarily turning off the reactions in a biosynthetic pathway
Feedback inhibition
70
Feedback inhibition :different enzymes that catalyze the same reaction but are subject to different regulatory controls. example: DAHP synthase for aromatic amino acids
isoenzymes
71
Post-translational Regulation Biosynthetic enzymes can also be regulated by_______ modifications. Regulation involves a _____molecule attached to or removed from the ______ that affects activity. Common modifiers include _________ monophosphate (AMP), adenosine diphosphate (ADP), inorganic phosphate (PO43–), and ______ groups (CH3).
-covalent, protein -small -adenosine, methyl
72
Post-translational Regulation Regulation of PII signal transduction proteins -Widespread family found in Bacteria, Archaea, and ________. -regulate ________ metabolism -Modifications like (addition of UMP, uridine monophosphate), _______ (addition of AMP), and phosphorylation affect activity. -Uridylylation by GlnD affects ________ assimilation.
-plastids -nitrogen -uridylylation, adenylylation, phosphorylation -ammonia
73
:addition of UMP, uridine monophosphate
uridylylation
74
:addition of AMP
adenylylation
75
Post-translational Regulation Inactivation of sigma factors _____-sigma factors can inactivate sigma factors. example: RpoE and anti-sigma factor _____ under __________ stress example: σF and anti-sigma factor SpoIIAB during Bacillus ________ formation
-anti -RseA, membrane -endospore
76
________-___________ _______________:powerful new form of light microscopy using fluorescent molecules
-Super-resolution microscopy
77
Fluorescent Tagging _________ _______:encode proteins easy to detect or assay and fused to genes of interest -can resolve different genetic elements (e.g., chromosome and plasmid)
reporter genes
78
:maps movement of individual molecules (e.g., Muk B in ______)
photoactivated localization microscopy -E. coli
79
Regulation of Chromosome Replication Initiation -Several proteins initiate and inhibit ____________ replication in _______ -DnaA binding to specific sequences within _____ region leads to unwinding and loading of __________ most active when linked to ____ (____–ATP) -Mechanisms to inactivate DnaA–ATP include competition for ____binding, repression of _____ expression, titration of DnaA–ATP away from oriC, and ___________ of DnaA–ATP -After replication initiation, only parental strand is ___________, yielding ______________ DNA, facilitates competition for origin binding between DnaA–ATP and SeqA protein hemimethylated_____ strongly bound by ____, blocking DnaA–ATP
-chromosome, E.coli -oriC, replisome, DnaA, ATP, -oriC, dnaA, oriC, inactivation -methylated, hemimethylated, competition -competition, SeqA
80
Binding of the Escherichia coli Ori C by D n a A and Seq A Proteins SeqA and DnaA both compete for binding at the ____ -When DNA is methylated, _____ binds -When DNA is ______________, SeqA binds -DNA is methylated when __________ is supposed to occur -Newly ____________ DNA not yet ready for replication is _______________ -_______ binding inhibits transcription of DnaA -DnaA activates its own ______________
-OriC -DnaA -hemimethylated -replication -synthesized, hemimethylated -SeqA, transcription
81
Regulation of Chromosome Replication Initiation -Binding of Seq A represses _______ expression through _______________ -DnaA expression also ______________ by DnaA binding to _______ boxes in its promoter region (When DnaA is _______ more DnaA is made) -ATPase ______ targets and __________ Dna A–A T P This removes the _____from DnaA and reduces its _______ affinity for the OriC -Overall, Dna A–ATP concentration oscillates during cell cycle, reaching _________ when _________ needed and waning after
-dnaA, hemimethylation -autogreulated, DnaA, bound -HdaA, hydrolyzes, ATP, binding -oscillates, maximum, initiation -
82
Genome Replication in Fast-Growing Cells -Circular genome replication ___________ from origin -________ genome replication takes 40 minutes but generation time can be as little as ___ minutes -Multiple ____ __________ forks present in each cell if doubling time _______ than genome replication time, so a new round begins before the previous round completed some genes present in multiple copies
-bidirectional -E. coli’s, 20 -DNA replication, shorter
83
Cell Division and F t s Proteins The _______– Cell division apparatus -Several essential proteins called ____ proteins -FtsZ protein crucial in ______ fission related to _______ (eukaryotic cell-division protein) also found in virtually all _______ Other Fts proteins found only in ________
-divisome -Fts -binary, tubulin, archaea -bacteria
84
Cell Division and Fts Proteins -Fts proteins interact to form the _________(cell division apparatus) -In ____-shaped cells, begins with attachment of _____ molecules around center of cell in a ring that becomes ______-_________ plane -Ring attracts other divisome proteins including F t s3A and Zip A
-divisome -rod, FtsZ, cell-division -
85
Cell Division and F t s Proteins : anchor that connects F t s Z ring to cytoplasmic membrane
Zip A
85
Determinants of Cell Morphology Prokaryotes contain a protein ________ that is dynamic and multifaceted ______ (Shape, elongation, division, and sporulation) Shape determining proteins are homologous to eukaryotic cytoskeletal proteins
cytoskeleton, SEDS
85
Cell Division and Fts Proteins : related to actin; recruits FtsZ and helps connect FtsZ ring to membrane
FtsA
85
The Divisome -Divisome forms about _____-quarters of the way into cell division -Also contains Fts proteins needed for peptidoglycan synthesis ____: penicillin-binding protein (inhibited by penicillin antibiotic) -Orchestrates synthesis of new ___________ membrane and cell ____ material (division septum), then cell divides
-three -peptidoglycan -FtsI -cytoplasmic, wall
85
Cell Division and Fts Proteins Min Proteins and Cell Division -DNA replicates before the ____ ring forms because ring forms between ________ Before nucleoids _________, they block formation of FtsZ ring (nucleoid __________) -Min__, Min__, and Min__ proteins guide FtsZ to cell midpoint -FtsK and other proteins mediate __________ of chromosomes to daughter cells -FtsZ ____________, triggering _______ growth of wall materials to form _______ -FtsZ also hydrolyzes ____ to provide energy for polymerization and depolymerization of ____ ring
-Fstz, nucleoids, segregate, occulsion - C, D,E - separation -depolymerizes, inward, septum -GTP, FtsZ
86
Cell shape _______: major shape-determining factor in Bacteria and a few Archaea -Forms simple cytoskeleton with patchlike filaments around inside of cell just _____ cytoplasmic membrane -Recruits other proteins for cell wall growth to form the ____________ -MreB _________ causes bacilli to become ____ -Mos _______ bacteria lack MreB and RodZ -Filaments move from one side to another, directing __---____________ synthesis and allowing new ____ _____ to form at several points (____) instead of a single location (cocci)
-MreB -below -elongasome -inactivation, cocci -coccoid -peptidoglycan, cell wall, rods
87
Crescentin shape-determining protein found in ______-shaped ___________ organizes into filaments ~10 n m wide that localize on concave face of the curved cells impart curved morphology similar proteins found in other curved cells (e.g., ___________ pylori)
-vibrio, Caulobacter -Helicobacter
88
Evolution of Cell Division and Cell Shape -MreB functions similarly to eukaryotic _____ Actin forms ______________ that function as scaffolding in cytoskeleton and cell division -FtsZ structurally and functionally related to tubulin Tubulin forms _____________ important in ________ and other processes -____________ is related to keratin proteins that make up intermediate ___________ in eukaryotic cells
-actin,microfilaments -mircotubules, mitosis -crescentin
89
Determinants of Cell Morphology -Except for FtsZ, cell division/cytoskeleton protein homologs missing from most ________ Diversity of morphologies exists, especially in gram-negative __________________ Some can synthesize _______________ at poles (polar elongation or unipolar elongation) Some grow by ________ Morphology and phylogeny are typically unrelated
-archaea -alphaproteobacteria, peptidoglycan, budding
90
Peptidoglycan Biosynthesis Preexisting peptidoglycan needs to be temporarily _______ to allow newly synthesized peptidoglycan to be inserted In ______-shaped cells, cell wall growth occurs at ______ points along length of the cell In ______, cell walls grow in opposite directions _______ from the FtsZ ring All bacterial cells must synthesize new peptidoglycan and export it ________ the cytoplasmic membrane
-severed -rod, several -cocci, outward -outside
91
Regulation of Endospore Formation -Response to adverse conditions: conversion of growing (vegetative) cells into _______ -____________ occurs when favorable conditions return -__________ division results in endospore (smaller cell) surrounded by larger ________ cell
-spores -Germination -Asymmetric, endospore, mother
92
Endospore Formation: Sporulation Factors -triggered by adverse external conditions (e.g., ________, desiccation, _________temperatures) -monitors environment through ____ sensor kinases functioning through phosphotransfer relay system that resembles a ___-___________ regulatory system but is more complex -results in successive phosphorylation of ______________factors, culminating with Spo0A -when Spo0 A highly___________, sporulation proceeds
-starvation, inhibitory -five, phosphotransfer, two-component -sporulation -phosphorylated
93
Endospore Formation: Alternative Sigma Factors -development controlled by four sigma factors two (σ__ and σ __) activate genes needed in the _________ (developing endospore) two (σ __and σ __) activate genes needed in the ______ cell
-F,G -E,K -forespore -mother
94
Endospore Formation: Alternative Sigma Factors -sporulation signal transmitted by Spo0A activates σ__ in _________ -σ __ binds RNA polymerase and promotes transcription of genes including σ__ and proteins that activate σ__ -σ E required for _________ of _______ cell genes including σ__ -σ __ and σ ___ needed for even more ____________ eventually spore coats formed and mature _________ released
-F, forespore - F, G, E - transcription, mother, K -G,K, transcrption, endospore
95
Nutrients for Endospore Formation -Sporulating cells ___________others -Cells in which Spo0A has become activated secrete toxic protein that _____ nearby _______ whose Spo0A has not yet been activated -Second protein that delays __________ is also released -Cells committed to sporulation make an ________ to protect themselves -______ cells are used as a source of nutrients for developing endospores -Shortage of phosphate increases transcription of toxic protein gene
-cannibalize -lyses, bacillus -sporulation -antitoxin -lyses -phosphate, transcription
96
Endospores are: Not ____________active Can remain ________ for years Still able to sense and respond to nutrients and favorable conditions Allow germination: conversion back to vegetative cells Three consecutive stages: __________, germination, ____________
- metabolically -dormant -germination -activation, outgrowth
97
Triggers for Activating Endospore Germination -_____________ receptors (G R) within inner membrane surrounding ___________ core exist in clusters called the “___________” (senses and binds nutrients) -Germinants trigger stage I: _________ GerA binds ________, Ger __ and Ger __ binds asparagine, glucose, fructose, potassium ions Increased temperatures helps trigger germination How does germinant binding trigger activation? -Cascade results in release of monovalent cations and ________-dipicolinic acid (DPA) from spore core -Sporulation factor activity _________, partially rehydrating core -Transcription and translation, and __________ gene expression increases
Germinant , endospore, germisome -actiavtion -alanine -B, K -calcium -reversed -chaperone, increases
98
Germination and Outgrowth Stages ______ lytic enzymes (CLE) triggered to degrade endospore cortex _____________. _____________ (Stage II): Removal of cortex is a major event Completely Hydrated; can be metabolically active
-Cortic, peptidoglycan -Germination, cortex -metabolically
99
Germination and Outgrowth Stages __________ (stage III) -Near-rates of metabolism, start cell cycle and ______ _______ -Cell __________ allows escape of vegetative cell from ______ coats -Requires increased ____ for energy-generating processes -Also triggered by increased expression of _____________ and teichoic and lipoteichoic acid biosynthetic enzymes and FtsZ
-elongation, spore -genes -peptidoglycan
100
Caulobacter: gram-_______ aquatic genus in _______________ -Divides into two genetically identical ________ cells that are structurally and functionally distinct -Common in __________ (nutrient-poor) ______ environments -In life cycle, free-swimming _________ cells alternate with cells lacking _______and are attached to surfaces by a stalk with a _______ -Swarmer cells ________; cannot divide or replicate D N A -Stalked cells strictly ________ -To divide, swarmer cells must differentiate into _______ cells or stalked cells must produce swarmer
-negative, alphaproteobacteria -daughter - oligotrophic, aquatic -swarmer, flagella, holdfast -disperse -reproduce -stalked
101
Regulatory Features three major regulatory proteins whose concentrations oscillate in succession: transcriptional regulators _____ and _____ and _____ (initiates DNA replication and regulates transcription)
GcrA, CtrA, DnaA
102
Caulobacter Differentiation CtrA activated by _____________ (____-P) in emerging swarmer cells in response to cell cycle signals CtrA-P activates genes encoding ________ synthesis and other swarmer-specific functions. CtrA-P _________ synthesis of _____ and inhibits DNA __________ initiation in swarmer cells by binding and blocking origin of ___________ As cell cycle proceeds, _____ is degraded and _____ levels rise, triggering DNA replication and activating other genes for ___________ replication DnaA level falls due to degradation; _____ level rises GcrA promotes __________ of chromosome replication, cell division, and _____ growth on _________ daughter cell GcrA levels _____ and CtrA _______, cycle repeats
-phosphorylation,CtrA -flagellum -represses, GcrA, replication, replication -ctrA, DnaA, chromosomal -degradation, GcrA -elongation, stalk, immobile -fall, reappears
103
Caulobacter and the Eukaryotic Cell Cycle External stimuli and _______ factors (nutrient and metabolite levels) coordinate cell cycle Used as a model for studying cell developmental processes in other organisms Cell cycle resembles ___________ cells in many respects In __________, phase ____ is growth and normal metabolism; ___ phase is when D N A replication occurs; ___ is preparation for subsequent mitotic events in the ___ phase In ____________, no mitosis, but analogs of G1, G2, and S apparent
-internal -eukaryotic -eukaryotes, G1, S, G2, M -Caulobacter
104
What formation contain the four basic stages: Attachment, colonization, development, and dispersal
Biofilm formation
105
Cyclic D i-G M P and Biofilm Formation -_______ guide bacteria in transitioning from _________ growth to life in a _________ matrix Switch to biofilm growth triggered by accumulation of regulatory molecule cyclic __-__________ monophosphate (c-di-GMP) -Widely distributed only in ________ -Synthesis and _________ depend on environmental and cellular cues -Synthesis either promotes or _________ physiological events (e.g., differentiation, development, biofilm-relevant functions)
-Signals, planktonic, semisolid -di-guanosine - bacteria -degradation -inhibits
105
Four basic stages: Attachment, colonization, development, and dispersal -Random ________accounts for ______ attachment -Facilitated by structures such as ________ and pili or by cell surface proteins -____________ is a signal for expression of _______-specific genes (encoding proteins that produce intercellular ________ molecules and extracellular ____________) Once committed to biofilm formation, cell loses ________and becomes __________ Cells can be released through ______ dispersal
-collision, initial -flagella -Attachment, biofilm, signaling, polysaccharides -flagella, nonmotile -active
106
Cyclic D i-G M P and Biofilm Formation __________ cyclases synthesize c-di-GMP. -often have ________ binding site for c-d i-G M P -sensitive to __________ inhibition -Elevated c-di-GMP levels reduce __________ Phosphodiesterases _________ c-di-GMP to _________ derivatives (pGpG and GMP) c-d i-G M P binds ________ that reduce ________ motor activity, regulates attachment proteins, and mediates biosynthesis of extracellular matrix polysaccharide
-Diguanylate, allosteric, feedback, production -degrade, guanine -proteins, flagellar,attachment, biosynthesis
107
Pseudomonas aeruginosa and Biofilms -forms a ________ biofilm containing ______________ that increase ____________ and prevent antibiotic penetration -classic ___________pathogen -primary reservoir: _____ -______ blood, lungs, urinary tract, ears, skin, other tissues -cystic fibrosis symptoms caused by ______ biofilms in lungs -significant ___________ (hospital-acquired) pathogen
- tenacious, polysaccharides, pathogenicity -opportunistic -soil -infects -thick -nosocomial
108
Pseudomonas aeruginosa and Biofilms ____________ communication by _______ sensing critical for biofilm development and maintenance Accumulation of acyl ________ lactones (AHLs) signal population is growing also triggers genes for __________ polysaccharide and c-d i-G M P synthesis Elevated c-di-GMP initiates extracellular polysaccharide production (e.g., ___) and leads to decreased ________ function
-Intercellular, quorum - homoserine -extracellular -Pel, flagellar
109
Pseudomonas aeruginosa and Biofilms DNA release by ______ cells also promotes ________formation. “Explosive death” in a subpopulation Caused by _____ protein expression by _______ prophage in response to stress Explains why antibiotic treatment enhances _______ formation
-lysed, biofilm -"Explosive" -lysis, inactive -biolfilm
110
Pseudomonas aeruginosa and Biofilms -Formation strategies differ among species within same genus -e.g., ____________ fluorescens: increase in c-di-GMP promotes formation but machinery differs greatly -Changes in c-di-GMP affect _________and cell surface ___________ of LapA adhesion protein that helps cell ______to surface -If nutrient (e.g., _________) levels high, LapA localizes to membrane, promoting biofilm synthesis -With ____ phosphate, cells maintain low c-di-GMP preventing ________ of LapA to outer membrane, disabling _________ mechanism -If phosphate levels continue to fall, a ________ is activated to cleave LapA, _______ cells
-Pseudomonas -secretion, localization, sticks -phosphate -low, localization, attachment -protease, cleave
111
Vibrio cholerae and Biofilms -quorum _______ acts opposite of P.__________ -Biofilm formation triggered by low ________, repressed by _____ cell densities -Accumulation of _______ signaling molecules represses biofilm formation genes and activates _______ genes -More likely to occur when V. ________ is found in natural marine environment compared with _________ cells where nutrients are more plentiful -Biofilm formation allows cell to attach to ______ surfaces (e.g., plankton, __________, sediments) for better access to nutrients and protection from perturbations -Dispersal aids in _____________ to new host cells
-sensing, aeruginosa -densities, high -quorum, flagellar -cholerae, intestinal -marine, crusteceans - transmission
112
Antibiotics are anti________ naturally produced by microbes kill or inhibit _______growth target essential molecular processes
-microbials -bacterial
113
Antibiotics That Target Major Molecular Processes Many antibiotics target DNA replication, RNA synthesis, and translation _________ target DNA gyrase and topoisomerase IV by interfering with DNA unwinding and replication __________ and actinomycin prevent ____ synthesis by blocking RNA polymerase active site or RNA __________ Inhibition of protein synthesis -Ribosomes in Bacteria are __S; eukaryotic are __S -Puromycin binds to __ site in ___S ribosome, inducing chain __________ and __________ protein synthesis -Aminoglycoside antibiotics (e.g., _______mycin) target 16S _____ of 30S ribosome, leading to ______-filled proteins that inhibit growth
-Quinolones -Rifampin, RNA, elongation -70, 80 -A, 70, termination, inhibiting -strepo, RNA, error
114
Antibiotics That Target the Cell Membrane and Wall Daptomycin specifically binds to _________________ residues of bacterial cytoplasmic membrane, leading to ____ formation, depolarization, and death __________ are cyclic peptides whose long _____________ tails target ____ layer, disrupting membrane and causing leakage and death
-phosphatidylglycerol, pore -Polymyxins, hydrophobic, LPS
115
Antibiotics That Target the Cell Membrane and Wall -targeting _____________ synthesis -β-_______ (penicillin, cephalosporin, derivatives) interfere with ____________ (formation of cross-links) between muramic acid residues -Vancomycin binds to ___________ precursor and prevents ___________ formation -Bacitracin binds to ______________ and prevents new peptidoglycan precursors from reaching site of synthesis
-peptidoglycan -lactams, transpeptidation -pentapeptide, interbridge -bactoprenol, synthesis
116
Antibiotic Resistance: Spontaneous Mutations and Antibiotic Modification Resistance mechanisms genetically encoded in four classes: modification of ____ target, enzymatic inactivation, removal via _____ pumps, metabolic _________ Random chromosomal mutations can lead to __________ e.g., Spontaneous mutants resistant to _________ can be obtained by exposing a _____ population and selection Resistance genes can exist on mobile _______ elements and be transferred by ___________ gene flow Many mobile __________ genes encode enzymes that __________ antibiotic (e.g., β-_________ cleaves a ring structure; an ____________ enzyme adds acetyl groups to _______mphenicol)
-drug, inactivation, efflux, bypasses -resistance, rifampin, large, selection. -genetic, horizontal -resistance, inactivate, lactamase, acetylating, chlora
117
Antibiotic Resistance: Efflux Pumps and Metabolic Bypasses Efflux pumps are _________ and transport various molecules, including __________, out of the cell -Lowers __________concentration, allowing cell to survive at higher _________ concentrations -Many act promiscuously and transport different ___________ classes, contributing to multidrug resistance -AcrAB-Tol C of ________ is one of the best characterized; pumps out rifampicin, chloramphenicol, fluoroquinolones Biofilm growth leads to _______ resistance Makes infections difficult to treat Acr A B-Tol C efflux pumps genes __________ when cells enter _______ growth mode __________ aeruginosa encodes several multidrug efflux pumps that are more active when cells grow in an _________ state
-ubiquitous, antibiotics -intracellular, external -resistance, antibiotic, -ecoli -resistence -upregulated, biofilm -Pseudomonas, attached
118
Antibiotic Resistance: Efflux Pumps and Metabolic Bypasses Antibiotic target is no longer _________ example: Methicillin-resistant Staphylococcus aureus (MRSA) Methicillin is a β-lactam resistant to β-lactamase ________ MRSA strains contain a chromosomal island called ______________ chromosomal cassette for _________ resistance (SCCmec) that encodes MecA, an alternative _________-binding protein that is not recognized by β-lactams MRSA synthesize _____only in the presence of β-lactams due to repressor _____ and β-lactam sensor MecR1 Island encodes _________ (erythromycin and spectinomycin) resistance
- essential -β-lactam, cleavage -Staphylococcus, methicillin, MecA, penicillin -MecA, MecI, multidrug