Brainscape's Knowledge GenomeTM

Browse over 1 million classes created by top students, professors, publishers, and experts.


See full index

BIOL 240 Microbiology > Topic 8 - Regulation > Flashcards

Topic 8 - Regulation Flashcards

You may prefer our related Brainscape-certified flashcards:
Biology 101 flashcards
1
Q

role of DNA (4 - replication, transcription, translation, repair)

A

replication - DNA must be retained intact and copied to make new cells

transcription - DNA must be turned into multiple “working copies” to provide instructions for enzymes/structural proteins production

translation - RNA must be read and decoded to form the enzymes/structural proteins of cell

DNA repair - systems need to be able to deal w/ dmg

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
2
Q

transcription in bacteria! (sigma factor details)

A
  • sigma factors bound to RNA pol core enzyme direct it to a promoter
  • transcription proceeds
  • diff sigma factors can direct core RNA pol enzyme to diff genes (as needed)
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
3
Q

rho-dep/indep transcription in bacteria

A

rho-dependent:
- rho protein follows RNA pol and removes it from DNA when it reaches a termination sequence

rho-independent
- RNA hairpin loop forms, causing RNA pol to dissociate from DNA (terminator loop)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
4
Q

translation in bacteria

A
  • the small ribosome subunit and Shine-Dalgarno seq help align all machinery to correct starting location
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
5
Q

multiple Shine-Dalgarno seq allow bacterial mRNA to be ________

A

polycistronic

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
6
Q

polycistronic meaning

A

multiple separate proteins are encoded on one mRNA (common in prok)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
7
Q

why we need regulation?

A

diff env conditions
- changes in nutrients/availability
- changes in competition

permits condition-specific responses
- substrate specificity
- metabolism and transport
- sporulation

excess protein production wastes energy

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
8
Q

key cellular enzymes are _____, AKA ____ ____

A

constitutive
housekeeping genes

e.g., TCA cycle, ATP synthases

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
9
Q

constitutive vs inducible?

A

constitutive genes - always need to be on
inducible genes - only needed at certain times

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
10
Q

basic control of gene expression can take place on the level of? (3)

A

transcription
translation
post-translation (enzyme activity)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
11
Q

ways to regulate protein activity (2)

A
  • covalent modifications: may alter enzyme conformations
  • allosteric regulation
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
12
Q

allosteric meaning, details

A

“other site”
- activity inhibition/activation from binding of an allosteric effector molecule
- binding of a non-substrate molecule at a site away from active site

  • conformation altered (inhibition - substrate no longer binds; activation - substrate is able to bind)
  • allosteric inhibitor often end product of multi-step pathway
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
13
Q

the operon

A

transcriptional unit with a series of structural genes and their transcriptional regulatory elements (e.g., lac operon)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
14
Q

where are operator, promoter, activator binding site, and structural genes in relation to each other?

which parts use positive / negative control of transcription?

A

order of left to right:
activator binding site (positive control), promoter, operator (negative control), structural genes

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
15
Q

regulatory elements vs operon?

A

regulatory elements:
- activator binding site, promoter, operator

operon (regulatory elements + structural genes):
- activator binding site, promoter, operator, structural genes

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
16
Q

positive control is ______ of promoter
negative control is ______ of promoter

A

upstream
downstream

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
17
Q

can operons have more than one promoter?

A

yes, each with their own control system

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
18
Q

negative control of transcription (2 types)

A

both involve a repressor protein

repression:
- inhibit transcription in response to signal
- minority of enzymes are controlled by repression
- typically affects anabolic (biosynthetic) enzymes

induction:
- DErepression of enzyme production in response to signal
- typically affects catabolic enzymes
- enzymes synthesized only when substrates available

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
19
Q

default mode of induction-controlled site

A

gene is off (negative control);
co-inducer molecule removing repressor protein turns gene on

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
20
Q

positive control of transcription

A
  • allosteric regulator proteins activate binding of RNA pol to DNA
    – activator proteins bind specifically to ACTIVATOR BINDING SITE of promoter
  • positively controlled promoters WEAKLY bind RNA pol
    – activator protein recruits polymerase to promoter
    – may cause DNA structural change
    – may interact directly w/ pol
    – can be close to promoter or 100s bp away
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
21
Q

maltose catabolism in E.coli is an example of?

A

positive control of transcription
- maltose activator protein only binds DNA in presence of maltose

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
22
Q

effectors (effector molecules) meaning, types/examples

A

collective term for molecules that affect protein production in association with allosteric protein regulators
- co-inducers or co-activator: substance that turns on enzyme production (induction, activator binding/positive)
- co-repressor: substance that binds and activates a repressor (repression)

  • effectors interact with DNA-binding proteins
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
23
Q

glucose is easier to eat than lactose, so
the lac operon is not expressed until ______________________, AKA?

A

until all glucose is consumed
- diauxic growth (2 growth phases; glucose easier, eat lactose later)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
24
Q

functions of beta-galactosidase and permease

A

beta-galactosidase - cuts lactose into 2
permease - brings it into cell

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
25
Q

what structural genes does the lac operon have (3)? what proteins do they code for?

(upstream of promoter) what does lacI (lac-i) code for?

A

lacZ - beta-galactosidase
lacY - permease
lacA - beta-galactosidase transacetylase

lacI - LacI repressor

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
26
Q

lac operon uses ____ regulated expression

A

inducible (catabolism)
- system only turned on when needed

27
Q

lac operon (turned on) allows use of ____ sugar

A

lactose

28
Q

how does the repressor protein get removed in the lac operon? (details)

A
  • permease brings lactose into cell
  • beta-galactosidase cuts lactose into 2 (producing glucose-galactose & allolactose)
  • allolactose = co-inducer, lets cell know there is lactose, REMOVING REPRESSOR PROTEIN!
29
Q

negative control in lac operon (repressor protein + effector molecule)?

A

repressor protein: LacI
- binds to operator, blocking RNA pol and inhibiting transcription

effector molecule: allolactose (co-inducer)
- induces transcription by inhibiting binding of repressor (LacI) to operator

30
Q

positive control of lac operon (activator protein + effector molecule)

A

activator protein: cyclic AMP receptor protein; CRP
- binds and increases transcription rates when effector molecule (cAMP) present (low glucose)

cAMP (coactivator) binds to CRP, active CRP-cAMP binds to activator binding site (of promoter) (transcription proceeds)

effector molecule - induces conformational change in activator protein, which increases affinity for binding site, INCREASING RNA pol AFFINITY for Lac operon promoter

31
Q

operon status?
level of lacZ, lacY, lacA transcription?
is lactose metabolized?

glucose conc: low
lactose conc: high
cAMP conc: high

A

operon status:
- cAMP (coactivator) bound to CRP (activator) bound to activator binding of promoter
- allolactose (inducer) bound to LacI (repressor) not bound to operator

level of lacZ, lacY, and lacA transcription: high

lactose metabolized: yes

32
Q

operon status?
level of lacZ, lacY, lacA transcription?
is lactose metabolized?

glucose conc: low
lactose conc: low
cAMP conc: high

A

operon status:
- cAMP (coactivator) bound to CRP (activator) bound to activator binding of promoter
- NO allolactose (inducer) bound to LacI (repressor); repressor STILL bound to operator

level of lacZ, lacY, and lacA transcription: low

lactose metabolized: no

33
Q

operon status?
level of lacZ, lacY, lacA transcription?
is lactose metabolized?

glucose conc: high
lactose conc: low
cAMP conc: low

A

operon status:
- NO cAMP (coactivator) bound to CRP (activator), NOT bound to activator binding of promoter
- NO allolactose (inducer) bound to LacI (repressor), repressor STILL bound to operator

level of lacZ, lacY, and lacA transcription: low

lactose metabolized: no

34
Q

operon status?
level of lacZ, lacY, lacA transcription?
is lactose metabolized?

glucose conc: high
lactose conc: high
cAMP conc: low

A

operon status:
- NO cAMP (coactivator) bound to CRP (activator), NOT bound to activator binding of promoter
- allolactose (inducer) bound to LacI (repressor), not bound to operator

level of lacZ, lacY, and lacA transcription: low

lactose metabolized: no

35
Q

does digesting lactose increase cell’s detection of glucose levels?

A

lactose makes glucose + allolactose
- however, happens inside cell
- glucose detection happens when it enters
- NO does not increase detected glucose lvl

36
Q

negative control (common for anabolic operons)

A
  • effector molecules can inhibit transcription by binding to repressor protein and enhancing its ability to bind to operator (repression)
    ex. tryptophan amino acid synthesis operon
37
Q

attenuation

A

(quenching of signal)
- interruption of transcription after initiation but before termination
- control of transcription by mRNA secondary structure (terminator loop or lack of)

  • interaction between translation and transcription
    – if ribosome quickly follows RNA pol, rho-independent terminator hairpin RNA loops are formed in the leader seq and pol detaches
    – “stalling out” of ribosome in mRNA leader seq (i.e., not enough of that AA loaded in tRNA) allows transcription to CONTINUE
38
Q

does attenuation happen in euk?
reason?

A

no; bacteria and archaea perform transcription and translation simultaneously in same space

39
Q

E.coli tryptophan attenuation example

A

high levels of trp -> terminator loop forms, stops transcription of structural genes
- if region 2 is avail, it would bind to 3 or 4; ribosome stops at region 2 and blocks it
- regions 3 and 4 (if made) make a terminator loop for Rho-independent transcription STOP if high lvl of trp

low levels of trp -> terminator loop does not form, transcription continues
- region is not blocked, binds to region 3 (terminator loop NOT FORMED)

40
Q

Quorum sensing

A

quorum - members of a group (numbers) that MUST be present in order to conduct business
- a chemical signaling system that allows microbes to communicate with each other
- regulation of gene exp based on pop density

  • cells release autoinducer molecules into env as pop density increases!!
41
Q

regulation of gene exp based on pop density (quorum sensing)

A
  • positive feedback
  • rapid induction (quick changes to env conditions)
  • links behaviour to pop density
  • coordinates expensive, additive processes
  • roles in interactions w euk
42
Q

bioluminescence of Aliivibrio fischeri: example of ____? details, enzyme

A

quorum-sensing

  • Lux is a prototypical quorum-sensing system in A. fischeri
  • A. fischeri lives freely or symbiotically with Hawaii bobtail squid
    – 95% flushed out, then division allows squid to use again at night during hunting for camouflage
    – cells only emit light (via enzyme LUCIFERASE) when in light organ of squid
43
Q

Aliivibrio fischeri details
(AHL, LuxI, LuxR, lux box, luciferase)

A
  • cells only emit light via enzyme luciferase when in squid’s light organ
  • when grown to high density, cells produce lots of N-acyl-homoserine lactose (AHL - coactivator, autoinducer), which stimulates luminescence
  • LuxI protein catalyzes AHL synthesis
  • LuxR (activator) = a regulator transcriptional activator, interacts with AHL when it reaches high enough conc
    – binds “lux box” DNA regulatory site (activator binding site)
  • leads to transcription of luciferase protein genes and luxI, which creates positive feedback loop, making more AHL
44
Q

mechanisms controlled by quorum sensing (general) (4)
____ may play a role in _____

A
  • motility
  • conjugation
  • biofilm formation
  • pathogenesis

autoinducers may play a role in competition
- interruption or inhibiting a control pathway in other organisms in the env

45
Q

two-component regulatory systems

A
  • can use one protein as a sensor, another to control transcription
  • allows for response to changes in env
  • signal transduction (chemical communication between proteins) induced inside cell alters it to respond appropriately
46
Q

two-component regulatory systems often involve:

A
  • a sensor kinase (e.g., HPK): detects env stimulus (component 1)
  • a response regulator (RR): regulates transcription (component 2)
  • kinases add phosphate group to typically histidine residues (called histidine protein kinases (HPK)
  • response regulators dephosphorylate (short-lived, temporary response)
47
Q

two-component regulatory system general steps

A
  • external signaling molecule binds input domain of component 1 (sensor)
  • transmitter domain of component 1 becomes phosphorylated using ATP
  • sensor transfers phosphate group to component 2 (response regulator)
  • phosphorylated response regulator interacts w DNA of target gene + RNA pol to control transcription (+/-)
48
Q

virulence of A. tumefaciens (what genes, what type of control)

A
  • vir genes found on Ti plasmid only expressed under conditions similar to a plant wound site (crown gall tumours)
  • virA/virG required for expression of the other virulence genes
  • positive control
  • two-component regulatory system senses sugars and phenolic compounds in low pH
49
Q

chemotaxis (general)

A
  • complex bacterial behaviour modulated by shifts in protein activity
  • chemotactic bacteria sense changes in chemical gradients over time
  • changes induce altered directions and duration of flagella rotation, leading to directed movement over time
50
Q

how to isolate mutants using chemotaxis

A
  • isolated using a capillary tube filled w/ nutrients
  • motile wild-type microbes w/ normal chemotaxis will move into tube
  • those w/ mutated chemotactic proteins will remain outside tube
51
Q

regulation of chemotaxis general steps (3)

A

step 1: response to signal
step 2: control of flagella rotation
step 3: adaptation

52
Q

chemotaxis:
step 1: response to signal

A

MCPs sense specific attractants and repellents
- MCP = methyl-accepting chemotaxis proteins (in all bacteria)
- initiates signal transduction (or not)
- lower sensitivity when closer to attractants/repellents
- higher sensitivity when farther away

  • CheA = sensor protein
53
Q

chemotaxis:
step 2: controlling flagella rotation

A

CheY protein
- phosphorylated by CheA-P when attracts = low
- CheY-P intiates flagellar reversal: tumbling

54
Q

“Che” in CheY/CheA =?

A

chemotaxis

55
Q

chemotaxis:
step 3: adaptation

A

feedback loop
- allows system to reset
- allows temporal detection of signal conc
- requires modification of MCPs by methylation

methylation alters “sensitivity” to binding chemicals
- phosphorylation (from repellent binding) -> affects CheA, CheZ, CheB (no flagellar change if no phosphorylation)
- methyl groups added to MCPs (when approaching attractants) = fully methylation -> low sensitivity

56
Q

Che proteins: a two-component regulatory system

A
  • CheA = sensor kinase, becomes phosphorylated
  • CheA then phosphorylates CheY (RR)
  • CheY binds to flagellar motor, changing activity
57
Q

by interacting with CheW proteins, ____ of CheA is _____; meaning?

A

by interacting with CheW, autophosphorylation of CheA is modulated;

  • attractants decrease phosphorylation
  • repellents increase phosphorylation
58
Q

if MCP is bound by an attractant, does CheA phosphorylate? How is CheY affected?

A

No
CheY is also not phosphorylated, so direction does not change

59
Q

meaning of adaptation in chemotaxis

A

methylation of MCPs also regulates attraction during periods of very high attractant levels in a process - adaptation
- highly methylated MCPs will only respond to very high lvls of attractant
- if very high lvl aren’t maintained, phosphorylation of CheA/CheB will lead to eventual demethylation of MCP
- results in greater sensitivity to attractant, helping system reset and avoid saturation over time

60
Q

regulons (meaning, 2 situations)

A

set of genes that are coordinated together, responding to the same regulatory systems
- catabolite repression: shutdown of several systems that use various nutrients when GLUCOSE = present
- SOS response: multigene system for wide-scale DNA repair in response to serious DNA dmg

61
Q

two most important regulatory proteins for SOS response regulon are:

A

recA lexA

62
Q

SOS response general steps (RecA/LexA)

A

DNA is damaged:
- RecA binds ssDNA and becomes active
- LexA is destroyed
- SOS genes expressed

RecA cleaves LexA repressor; SOS genes are induced

DNA is repaired:
- ssDNA not present
- RecA is inactive
- LexA represses SOS genes

low level of LexA production keeps SOS regulon genes repressed

63
Q

alternative sigma factors

A

in bacteria, use of diff sigma factors directs RNA pols to certain genes
- most E. coli promoters are recognized sigma-70

64
Q

sigma-54 / sigma-32 / sigma-38

A

sigma-54: nitrogen utilization genes regulator
sigma-32: heat shock protein gene regulator
sigma-38: general stress response gene regulator

BIOL 240 Microbiology (10 decks)

Brainscape helps you reach your goals faster, through stronger study habits.
© 2024 Bold Learning Solutions. Terms and Conditions