Chapter 10

Question 1

Regulatory proteins

Answer 1

• sense changes and alter gene expression

- activity may be changed by the binding of a small ligand molecule or by covalent modification such as phosphorylation

Question 2

Repressors

Answer 2

bind to regulatory sequences in the DNA and prevent transcription

Question 3

Activators

Answer 3

bind to regulatory sequences in the DNA and stimulate transcription

Question 4

Two-component signal transduction systems sense the external environment

Answer 4

(1) Sensor kinase in the cell membrane
- Binds to environmental signal, which causes autophosphorylation

(2) Response regulator in the cytoplasm
- Transcription factor that binds DNA and regulates genes
- Takes phosphate from sensor to turn target gene(s) either on or off depending on the specific regulator

Question 5

Microbes control gene expression at several levels

Answer 5

• Alterations of DNA sequence
• Control of transcription
• Control of mRNA stability
• Translational control
• Posttranslational control of protein function or stability

Question 6

the Lactose Operon

Answer 6

• in Escherichia coli, enzymes used to metabolize lactose were inducible, while those for glucose were constitutive
• Lactose Induces Expression of the lacZYA Operon

Question 7

lacZYA operon

Answer 7

• LacI binds to the operator region.
• It represses the lac operon by preventing transcription by RNA polymerase.
• b-galactosidase (LacZ), when at low levels, cleaves and rearranges lactose to make the inducer allolactose.
• Allolactose binds to LacI, reducing its affinity to the operator and thus allowing induction of the operon

Question 8

lacO

Answer 8

-operator sequence at the beginning of the operon where transcription factors can bind

Question 9

Activation of Transcription by cAMP-CRP

Answer 9

• Maximum expression of the lac operon requires cAMP (cyclic AMP)
• increases only in the absence of glucose, and cAMP receptor protein (CRP).
• CRP is a transcription activator
• cAMP-CRP complex binds to the promoter, and interacts with RNA pol to increase the rate of transcription initiation

Question 10

Glucose and the lac Operon

Answer 10

• Glucose Represses the lac Operon
• E. coli utilizes glucose first
• as glucose goes up, cAMP and lacZ go down
• as glucose goes down, cAMP and lacZ go up

Question 11

catabolite repression

Answer 11

-an operon enabling the catabolism of one nutrient is inhibited by the presence of a more favorable nutrient (commonly glucose)

Question 12

diauxic growth

Answer 12

-biphasic curve of a culture growing on two carbon sources

Question 13

repressing anabolic pathways

Answer 13

• down-regulate if the end product is available

- Don’t make something you don’t need more of

Question 14

aporepressor

Answer 14

• transcription factor protein alone is an inactive

- The end product molecule acts as a corepressor

Question 15

holorepressor

Answer 15

• complex can bind to the operator sequence upstream of the target gene or operon
• Blocks RNA polymerase, and transcription is off

Question 16

trp operon

Answer 16

• biosynthetic operon encoding enzymes that make the amino acid tryptophan
• internal tryptophan levels exceed cellular needs, the excess tryptophan (the corepressor) will bind to an inactive aporepressor, TrpR

The holorepressor then binds to an operator DNA sequence upstream of the trp operon.

• Represses expression of the structural genes by blocking RNA polymerase
• Repression lowers expression about 100-fold

Question 17

regulon

Answer 17

• a set of genes and operons scattered around the chromosome with related functions
• coordinately controlled by a common repressor and/or activator protein
• Example: the heat-shock response of E. coli is regulated by sigma factor RpoH (Rpo = RNA polymerase, gene H)

Question 18

Regulatory RNAs

Answer 18

• typically affect gene expression posttranscriptionally
• binding to complementary sequences of target mRNA transcripts in ways that either stimulate or prevent translation
• interacting with proteins to change their activity

Question 19

Quorum sensing

Answer 19

• allows bacterial cells to determine their density
• pathogens use quorum sensing to control virulence genes
• pathogen wants to make sure it has a high population density before expressing genes that will prompt a response from the host
• some microbial species use quorum sensing to communicate with other species.
• coordinate multispecies interactions such as complex biofilms

Question 20

autoinducer

Answer 20

• accumulation of a secreted small molecule
• causes induction of a quorum-sensing gene system
• can diffuse across membranes

Question 21

transcriptome and proteome

Answer 21

• constitute all of a cell’s mRNA molecules and proteins
• provide information on gene expression for the entire genome in a specific condition
• like during interaction of a pathogen with a host
• Can follow changes in expression of all genes in response to a changing environment

Question 22

DNA microarrays

Answer 22

• contain tiny dots of DNA for each gene in the genome
• They are “hybridized” with labeled RNA samples
• The intensity of the label for each dot (gene) provides quantitation of the amount of RNA for that gene

Question 23

RNA-seq

Answer 23

determines the sequence of every RNA molecule in a sample from cells. The more RNA from a gene, the more sequences are read

Question 24

Two-Dimensional Gel Electrophoresis

Answer 24

is used to view and capture fluctuations in the proteome

Question 25

Mass Spectrometry

Answer 25

• mass of each peptide and its amino acids can identify which gene encoded it
• Tells you which genes are expressed under different environmental and growth conditions
• Provides information on the functions of genes and their proteins