Lecture 6 bacterial Genome and Replication expression, and regulation 2 Flashcards Preview

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Flashcards in Lecture 6 bacterial Genome and Replication expression, and regulation 2 Deck (84):
1

Transcription regulation

- nucleoid-associated proteins can either increase or decrease transcription
- genetic regulatory proteins can bind to the DNA and control whether or not transcription begins
- Attenuation: transcription can terminate very early after it has begun due to the formation of a transcriptional terminator
-binding of a metabolite to a riboswitch in mRNA can cause premature termination of transcription

2

Regulation of Translation

- Secondary structure in 3' end of mRNA prevents degradation of mRNA
- Translational repressor proteins can the mRNA and prevent translation from starting
- Antisense RNA can bind to mRNA and control whether or not translation begins
- Binding of a metabolite to a riboswitch in mRNA can block translation

3

Posttranslational regulation

- small molecules can bind (noncovalently) to a protein and affect its function. An example is feedback inhibition, in which the product of a metabolic pathway inhibits the first enzyme in the pathway
- The structure and function of a protein can be altered by covalent changes to the protein. These can be reversible (phosphorylation/dephosphorylation) or irreversible (removal of amino acid residues) these are called post translational modifications

4

Constitutive genes

housekeeping genes that are expressed continuously

5

inducible enzymes

levels of the enzymes rise in presence of a small effector molecule called an inducer (ex. Beta-galactosidase)

6

Repressible enzymes

- enzymes that are responsible for repressing formation
- usually present in biosynthetic pathways

7

what kind of regulation is Trp operon

negative transcriptional control of repressor genes

8

Characteristics of regulatory proteins

- have DNA binding domains
- either inhibit transcription (negative control) or promote transcription (negative control)
- Can also have allosteric regulatory site

9

The lac repressor binds to the ___ and inhibits transcription

lac repressor (LacO)

10

The binding of ____ to the lac repressor prevents it from binding to the operator (LacO) site

Allolactose

11

what is the positive control of the lac operon

Regulated by catabolite activator protein (CAP)

12

Catabolite activator protein regulates in response to

presence or absence of glucose
thus allows for preferential use of glucose

13

what is the negative control of the lac operon

Lac repressor

14

What are the 3 structural genes of the lac operon

Lac Z: encodes for beta-galactosidase, lacY: endcodes for lactose permease, LacA encodes galactoside transacetylase

15

The catabolite activator protein (CAP) is also called

cyclic AMP receptor protein (CRP)

16

CAP exists in what to forms

- active form when 3',5'- cycle adenosine monophosphate (cAMP) is bound
- inactive form when free of cAMP

17

what happens to the lac operon in the presence of lactose and glucose

transcription is inhibited by lack of CAP

18

What happens to lac operon in presence of lactose but absence of glucose

binding of RNA polymerase to promotor is enhanced by CAP and repressor is inactive

19

what happens to lac operon in absence of both lactose and glucose

CAP is activated but transcription is blocked due to activated repressor

20

What happens to the lac operon when glucose is present but there is no lactose

transcription is inhibited by lack of CAP and presence of repressor

21

CAP activity is modulated by ____

cAMP

22

Levels of cAMP are controlled by

-adenyl cyclase (converts ATP to cAMP and PPi) by PEP
- adenyl cyclase is active only when little or no glucose is present
- in absence of glucose, CAP is active and promotes transcription of operons used for catabolism of other sugars

23

Explain the regulation of cAMP

when glucose is available, the phosphate of PEP is transferred to EIIA by way of EI and HPr. EIIA then transfers the phosphate to EIIB, which in turn transfers it to the incoming glucose. When glucose is not available, the phosphate cannot be transferred to EIIB and instead remains on EIIA. EIIA-P activates adenyl cyclase and cAMP is made.

24

What kind of regulation is the tryptophan operon

negative control of repressible genes

25

what kind of regulation is the Arabinose (ara) Operon

Transcriptional Control by a protein that acts both positively and negatively
- when arabinose is absent then the operon is closed
- when arabinose is present it can bind to the AraC protein and actually open up the operon increasing transcription

26

what is the difference between riboswitches in gram positive and gram negative bacteria

in gram positive bacteria they function by transcriptional termination, whereas the riboswitches discovered in Gram-negative bacteria regulate the translation of mRNA (note that effector biding elements at 5' end alters mRNA leader folding pattern)

27

Translation is usually regulated by

blocking its initiation

28

functions of sRNAs and noncoding (ncRNAs)

some have been implicated in the regulation of DNA replication and transcription, while many others regulate at the level of translation (may inhibit or enhance)

29

What are antisense RNAs

RNAs that are complementary to mRNA and function by base pairing (these are ncRNAs or sRNAs that can inhibit or enhance translation)

30

regulatory systems that affect many genes and pathways simultaneously

global regulatory systems

31

Genes or operons controlled by a common regulatory protein

Regulon

32

Operon network under control of a common global regulatory protein but individual operons are controlled separately by their own regulators

Modulon

33

what is an example of a Modulon

Catabolite repression

34

Global regulatory systems often use many types of regulation such as

- two component signal transduction systems
- Phosphorelay system
- regulatory proteins
- alternative sigma factors

35

Many genes and operons are turned on or off in response to enviromental conditions. What are the two types of regulatory system that function this way

Two-component regulatory systems, and phosphorelay systems

36

The _____ proteins involved are part of a two-component signal system which links external events to regulation of gene expression

Regulatory proteins

37

Is the two component regulatory system in all three domains

yes

38

what are the two proteins that govern the two component regulatory system

- Sensory Kinase
- Response-regulator protein

39

What is the sensor kinase

- one of the proteins that govern the two component regulatory system
- extracellular receptor for metabolite
- intracellular communication pathway

40

what is the response-regulator protein

- one of the two proteins that govern the two component regulatory system
- Activated by sensor kinase
- DNA binding protein
- activator- enhances transcription needed
- repressor- inhibits transcription unless needed

41

what is an example of sensor kinase in E. coli

EnvZ

42

What is an example of a response regulator in E. coli

OmpR

43

What is the function of EnvZ (sensor kinase) in E. coli

Autophosphorylates in high osmolarity

44

What is the function of OmpR (response regulator) in E. coli

phosphorylated and regulates transcription

45

The EnvZ and OmpR is a soluble, cytoplasmic protein that controls the expression of porin proteins ___ and ____ depending on ___-

ompF, ompC, osmolarity

46

Which is the smaller porin protein OmpC or OmpF

OmpC

47

When is porin protein ompC dominant

When E. coli is in high osmolarity intestinal tract

48

What is the function of OmpC

lower levels of diffusion

49

When is the porin protein OmpF dominant

dominant when E. coli is in dilute environment

50

What is the function of porin protein OmpF

allows more diffusion of solutes

51

Regulatory enzymes control chemotaxis proteins by

-phosphorelay system and covalent modification

52

what is irreversible covalent modification

proteolysis

53

What is reversible covalent modification

- methylation/demethylation
- phosphorylation/dephosphorylation

54

methyl-accepting chemotaxis proteins (MCPs) are chemoreceptors in membrane that bind _______ and initiates

binds environmental chemicals and initiates a series of interactions with cytoplasmic proteins that affects flagellar rotation

55

MCPs acitvates ______ (with help of ___) which autophosphorylates

sensor kinase CheA (with help of CheW) which autophosphorylates

56

CheA phosphorylates the response regulator ___

CheY

57

CheY governs ____

roation of the flagella

58

what is the default (unphosphorylated) state of MCPs

CCW rotation (run)

59

when attractant concentration is high MCP is ____ and what occurs

methylated (CheR) then CheA autphosphorylates with the help of CheW an passes this phosphorylation onto CheY. CheY diffuses to flagellar motor and switches to clockwise (CW) rotation thus causing a tumble. Concentration of attractant is measured every few seconds (receptors reset)

60

When attractant concentration decreases MCP is ______ and what occurs

not methylated (CheB) this means that CheA is inactive (not phosphorylated) thus it can not activate CheY and flagellar rotation continues in its default CCW rotation thus a run occurs

61

cell-to-cell communication mediated by small signaling molecules such as N-acyl-homoserine lactone (AHL)

Quorum sensing

62

quorum sensing couples cells ____ and ______ to transcription regulation

density and intercellular communication

63

Quorum sensing in V. fischeri and many other Gram-negative bacteria uses an _____________ signal

N-acylhomoserine lactone (AHL)

64

Explain Quorum sensing in V. fischeri

- High concentrations of AHL produced by increased density of cells diffuse back into the cell, bind to the transcriptional regulator LuxR and activate transcription.
- LuxR stimulates transcription of the genes for AHL synthase (Luxl) and proteins needed for light production

65

V. harveyi responds to how many autoinducers and for what purpose

- 3
- maximizes expression of bioluminescence

66

What happens when the three autoinducers of V. harveyi are in low cell density

LuxR is not made and there is no bioluminescence

67

What happens when any combination of the V. harvey autoinducers are in high cell density

LuxR is made, bioluminescence occurs

68

The ____ response occurs when bacterial cells are starved for amino acids and is regulated by the second messenger guanosine tetraphosphate (ppGpp)

Stringent response

69

What does cyclic dimeric GMP (c-di-GMP) regulate

- virulence genes
- regulates transition from motile to nonmotile lifestly in biofilm formation

70

What is the stringent response

- when cells are starved for amino acids
- protein synthesis cannot proceed
- Cell decreases production of tRNA and rRNA to conserve energy (protein RelA downregulates synthesis through production of ppGpp, ppGpp and DksA destabilizes transition initiation open complexes)
- cell increases biosynthesis of needed amino acids

71

in sporulation of bacillus subtilis starvation signal induces produciton fo

alternative sigma factors

72

Explain sporulation

KinA and Kin B autophosphorylate due to starvation signals and phosphorylate Spo0F-P this passes the phosphate to Spo0B and then to Spo0A, which activates sigma F for early sporulation gene transcription, sigma f activates sigma g for late sporulation gene transcription

73

Mutations can be _____ or ____

spontaneous or induced

74

Spontaneous mutations arise without

exposure to external agents

75

Spontaneous mutations may result from

errors in DNA replication and action of mobile genetic elements such as transposons

76

What is the most prevalent form of a gene

the wild type

77

What is a forward mutation

wild type to mutant form

78

what is a reversion mutation

mutant phenotype to wild type phenotype

79

what is a suppressor mutation

is a type of reversion mutation in which the second mutation is at a different site than the original mutation

80

what are conditional mutations

mutations expressed only under certain environmental conditions

81

What are auxotrophic mutant

unable to make an essential macromolecule such an amino acid or nucleotide (has a conditional phenotype, wild-type strain from which it arose is called a prototroph)

82

conditional lac operon mutants

-many of these mutations map in the operator site and produce altered operator sequences not recognized by repressor
- Operon is always transcribed and beta-galactosidase is always synthesized

83

Is protein synthesis disrupted when their are mutations in tRNA and rRNA genes

yes

84

mutations are generally rare about 1 per ____ cells

1 per 10^7 to 10^11 cells