Micro Ch 9

Front 1

What is the central dogma?

Back 1

DNA gets trascribed into RNA which gets translated into proteins

Front 2

gene expression

Back 2

transcription of a gene into mRNA and translations of mRNA into protein

Front 3

What do most proteins do?

Back 3

carry out biochemical reactions essential for cell growth

Front 4

What do you call proteins that are needed at the same level all the time?

Back 4

constitutive proteins

Front 5

what are the two major levels of regulation in the cell?

Back 5

-control of preexisting enzymes
-control of amount of an enzyme

Front 6

Name 2 characteristics of controlling the activity of preexisting enzymes.

Back 6

-post translational regulation
-rapid process

Front 7

Name 3 characteristics of controlling the amount of an enzyme.

Back 7

-regulate level of transcription
-regulate translation
-slower process

Front 8

Control of enzyme activity results in what

Back 8

no product

Front 9

translational control results in what?

Back 9

no protein synthesis

Front 10

transcriptional control results in what?

Back 10

no mRNA synthesis

Front 11

Why do mRNA have short half-lives?

Back 11

prevent production of unneeded proteins

Front 12

Regulation of transcription requires proteins that can bind to ___

Back 12

DNA

Front 13

How do most DNA-binding proteins interact with DNA?

Back 13

sequence specific manner

Front 14

how do DNA-binding proteins guarantee specificity?

Back 14

interactions between amino acid side chains and chemical groups on the DNA backbone

Front 15

What is the main site of protein binding?

Back 15

major groove of DNA

Front 16

What part of the regulatory protein interacts with inverted repeats?

Back 16

protein dimers (polypeptide binds to inverted repeat)

Front 17

Define homodimeric proteins

Back 17

proteins composed of two identical polypeptides

Front 18

What holds a protein dimer together?

Back 18

protein-protein contacts

Front 19

Describe the structure of helix-turn-helix DNA binding domain of protein. Give two E. coli examples of proteins that have helix-turn-helix domains

Back 19

Helix 1 = recognition helix
Helix 2 = stablizing helix
lac and trp

Front 20

Name 3 classes of protein domains

Back 20

helix-turn-helix
zinc finger
leucine zipper

Front 21

Name 2 characteristics of the zinc finger protein domain

Back 21

-protein structure that binds to a zinc ion
-2-3 zinc fingers on a protein that uses them to bind to DNA

Front 22

Name 2 characteristics of a leucine zipper

Back 22

-leucine residues spaced every 7 aa
-does not interact directly with DNA

Front 23

What are 3 possible outcomes after DNA binding?

Back 23

1. protein may catalyze a specific reaction on the DNA molecule (transcription via RNAp)
2. block transcription (negative regulation)
3. activate transcription (positive regulation)

Front 24

Name 3 mechanisms for controlling gene expression in bacteria

Back 24

-environment
-presence/absence of specific small molecules
-interaction between small molecules and DNA bind protein results in control of transcription or translation

Front 25

Define a negative control of transcription

Back 25

regulatory mechanism that stops transcription

Front 26

Name 2 types of negative control of transcription

Back 26

repression and induction

Front 27

Define repression. What type of enzymes are affected by this type of control?

Back 27

preventing the synthesis of an enzyme in response to a signal. Anabolic.

Front 28

Give an example of anabolic repression

Back 28

aa Arginine present in environment binds/represses synthesis of proteins that create enzymes to make Arg.
absence of argnine allows these genes to turn on

Front 29

Define induction

Back 29

production of an enzyme in response to a signal

Front 30

why is induction considered negative?

Back 30

starts "off" until necessary

Front 31

Give an example of catabolic induction

Back 31

Lac operon

Front 32

What do you call a substance that induces enzyme synthesis

Back 32

inducer

Front 33

What do you call a substance that represses enzyme synthesis

Back 33

corepressor

Front 34

what's the collective term for inducers and repressors

Back 34

effectors

Front 35

how do effectors affect transcription

Back 35

indirectly affect transcription by binding to specific DNA binding proteins

Front 36

What kind of protein do repressor molecules bind to?

Back 36

allosteric repressor proteins

Front 37

Explain how allosteric repressors work.

Back 37

allosteric repressor becomes active and binds to a region of DNA (operator) near the promoter

Front 38

Define operon

Back 38

cluster of genes arranged in a linear fashion whose expression is under control of a single operator

Front 39

How is transcription blocked when a repressor binds to the operator

Back 39

the repressor physically blocks transcription

Front 40

is the operator located downstream or upstream from the promoter

Back 40

downstream

Front 41

how can enzyme induction be controlled by a repressor

Back 41

inducer inactivates the repressor and transcription can proceed

Front 42

define positive control

Back 42

regulator protein activates the binding of RNAp to DNA

Front 43

what's an example of positive control

Back 43

maltose catabolism in E. coli:
maltose binds to maltose protein, enabling it to bind to DNA

Front 44

what do you call the DNA sequence that activators bind to?

Back 44

activator binding site

Front 45

true or false: promoters of positively controlled operons only weakly bind RNA polymerase

Back 45

true

Front 46

how do activator proteins help RNA polymerase

Back 46

help RNAP recognize the promoter by changing DNA structure or interacting directly with RNAP

Front 47

true false: activator binding site is always close to the promoter

Back 47

false

Front 48

define a regulon

Back 48

multiple operons controlled by the same regulatory protein

Front 49

true/false: Genes for maltose are spread out over the chromosome in several operons

Back 49

true

Front 50

does each operon of maltose have its own activator binding site?

Back 50

yes

Front 51

T/F regulons exist for only positively controlled systems

Back 51

false

Front 52

t/f prokaryotes regulate cellular metabolism in response to environmental fluctuations

Back 52

true

Front 53

in two component regulatory systems, is the external signal always transmitted directly to the regulation target?

Back 53

no

Front 54

In signal transduction the signal can be detected by a ______ and transmitted to the ______ _________

Back 54

sensor; regulatory machinery

Front 55

are most signal transduction systems two-component?

Back 55

yes

Front 56

what are the two components of the two component system?

Back 56

1. sensor kinase- (cytoplasmic membrane) detects environmental signal and autophosphorylates
2. Response regulator - (cytoplasm) DNA binding protein that regulates transcription

Front 57

two component regulatory systems are absent in bacteria that...

Back 57

live as parasites of higher organisms

Front 58

how can prokaryotes respond to the presence of other cells of the same species?

Back 58

quorum sensing

Front 59

define quorum sensing

Back 59

mechanism by which bacteria assess their population density

Front 60

what's the advantage of quorum sensing?

Back 60

ensures a sufficient number of cells are present before initiating a response that requires a certain cell density to have an effect

Front 61

Give an example of a bacteria that use quorum sensing

Back 61

-Erwinia carrotova, a plant pathogen
-Pneumoniae aeruginosa (free living --> biofilm)
-virulence factor of S. aureus

Front 62

how does quorum sensing work in a bacterium?

Back 62

-bacteria produces a species-specific autoinducer molecule which diffuses across membranes and works as a concentratin gradient (more bacteria, more AI).
-autoinducer binds to activator protein and triggers transcription of specific genes

Front 63

what was the first autoinducer to be identified?

Back 63

acyl homoserine lactone

Front 64

quorum sensing was first discovered as a mechanism for regulating light production in what bacteria?

Back 64

V. fischeri

Front 65

Does quorum sensing exist in eukaryotes? archaea?

Back 65

some eukaryotes; probably archaea

Front 66

describe what the two-component chemotaxis system does.

Back 66

-sense temporal changes in attractants/repellents
-regulate flagellar rotation

Front 67

what are the 3 main steps of chemotaxis?

Back 67

1. response to signal
2. controlling flagellar rotation
3. adaptation

Front 68

Describe Step 1 of chemotaxis

Back 68

sensory proteins in the cytoplasmic membrane, such as Methyl-accepting chemotaxis proteins (MCPs) bind to attractant/repellent and initiate interactions that eventually affect flagellar rotation

Front 69

Describe Step 2 of chemotaxis

Back 69

controlled by CheY protein
-CheY = CCW = run
-CheY-P = CW = tumble

Front 70

Describe Step 3 of chemotaxis

Back 70

-adaptation = feedback loop
-allows the system to reset itself and continue to sense presence of signal
-involves modification of MCPs

Front 71

In chemotaxis, attractants decrease/increase the rate of autophosphorylation.

Back 71

decrease; prevents CheY-P from forming so it can't bind to the motor and change direction of flagellum

Front 72

in chemotaxis, repellents decrease/increase the rate of autophosphorylation

Back 72

increase; inducing the formation of CheY-P, allowing it to bind to the motor and change flagellar direction to CW (tumble)

Front 73

in chemotaxis, what is the sensor kinase protein called?

Back 73

CheA

Front 74

Why is CheY a key protein in the chemotaxis system?

Back 74

because CheY controlls the direction of rotation of the flagellum

Front 75

How can the chemotaxis system sense changes in the concentration of the attractant or repellent with time?

Back 75

adaptation; fully methylated MCPs no longer respond to attractants...

Front 76

What do Archaea use to control transcription?

Back 76

DNA-binding Proteins

Front 77

Do Archaea mostly resemble eukarya or bacteria?

Back 77

bacteria

Front 78

When Nitrogen levels are low, describe what happens in Archaea

Back 78

alpha ketoglutarate binds to NrpR, derepresses the motor

Front 79

If levels of nitrogen are high, then what happens in archaea

Back 79

nothing; NrpR represses operators, no transcription

Front 80

define global control systems

Back 80

regulate expression of many different genes simultaneously

Front 81

Give an example of global control

Back 81

catabolite repression

Front 82

what are 3 characteristics of catabolite repression?

Back 82

-synthesis of unrelated catabolic enzymes is repressed if glucose is present in growth medium
-lac operon is under control of catabolite repression
-ensures best carbon and energy source is used first

Front 83

define diauxic growth

Back 83

two exponential growth phases

Front 84

T/F Catabolite repression only affects the lac operon

Back 84

false

Front 85

Are flagellar genes controlled by catabolite repression?

Back 85

yes, so there's no need to swim in search of nutrients