Chapter 16: Control of Gene Expression in Bacteria

Question 1

structural genes

Answer 1

encode proteins that are used in metabolism or biosynthesis or that play a structural role in the cell

Question 2

regulatory genes

Answer 2

RNA or proteins that interact with other DNA sequences and affect the transcription or translation of those sequences

Question 3

constitutive genes

Answer 3

structural genes that encode essential cellular functions; expressed continually and are not regulated

Question 4

regulatory elements

Answer 4

DNA sequences that are not transcribed; affect the expression of DNA sequences to which they are physically linked

Question 5

levels of gene regulation

Answer 5

1. alteration of DNA or chromatin structure
2. transcriptional level
3. mRNA processing
4. mRNA stability
5. translational level
6. post-translational modification

Question 6

alteration of DNA or chromatin structure

Answer 6

can change which sequences are available for transcription and the rate at which sequences are transcribed
- DNA methylation

Question 7

domains

Answer 7

discrete functional part of regulatory proteins that are responsible for binding to DNA

Question 8

domain binding process

Answer 8

• only a few AAs of the domain will make contact with the DNA (lysine, asparagine, glutamine, glycine)
• AAs form hydrogen bonds to DNA bases or the sugar phosphate backbone
• many proteins have multiple domains that can bind to other molecules such as other regulatory proteins

Question 9

dynamic DNA-binding proteins

Answer 9

DNA-binding proteins are never permanently attached; they bind and unbind DNA and other regulatory molecules
- other molecules can compete w DNA binding proteins for regulatory sites on the DNA

Question 10

motifs

Answer 10

simple structures that can fit into the major groove of the DNA double helix

Question 11

helix-turn-helix

Answer 11

two alpha helices; found in bacterial regulatory proteins

Question 12

zinc finger

Answer 12

loop of amino acids with zinc at the base; found in eukaryotic regulatory and other proteins

Question 13

steroid receptor

Answer 13

two perpendicular alpha helices with zinc surrounded by four cysteines; found in eukaryotic proteins; binds to the DNA backbone as well as the major groove

Question 14

leucine zipper

Answer 14

helix of leucine and a basic arm; two leucines interdigitate; found in eukaryotic proteins; binds to the two adjacent major grooves

Question 15

helix-loop-helix

Answer 15

two alpha helices separated by a loop of amino acids

Question 16

homeodomain

Answer 16

three alpha helices; found in eukaryotic regulatory proteins

Question 17

operon

Answer 17

a group of bacterial structural genes that are transcribed together along with their promoter and additional sequences that control their transcription

Question 18

controlling transcription

Answer 18

most important level of gene regulation in bacteria

Question 19

operon structure

Answer 19

• one end has structural genes that are transcribed into a single mRNA
• transcription is under control of a single promoter which lies upstream of the first structural gene
• RNA polymerase binds to the promoter then moves downstream to transcribe

Question 20

regulator gene

Answer 20

• helps control the expression of the structural genes of the operon by increasing or decreasing their transcription
• not considered part of the operon
• has its own promoter and is transcribed into a short mRNA, which is translated into a short protein

Question 21

regulator protein

Answer 21

small protein transcribed by the regulator gene that binds to a region of the operon called the operator and affected whether transcription can take place

Question 22

operator

Answer 22

DNA sequence in an operon to which a regulator protein binds; this binding affects the rate of transcription of the structural genes
- overlaps the 3’ end of the promoter and sometimes the 5’ end of the first structural gene

Question 23

negative control

Answer 23

transcriptional control where the regulatory protein is a repressor, binding to DNA and inhibiting transcription

Question 24

positive control

Answer 24

transcriptional control where the regulatory protein is an activator, stimulating transcription

Question 25

inducible operons

Answer 25

operons in which transcription is normally off ; something happens to induce transcription or turn it on

Question 26

repressible operons

Answer 26

operons in which transcription is normally on; something happens to turn it off or repress transcription

Question 27

negative inducible operons

Answer 27

• encodes an active repressor protein that readily binds to the operator
• the binding of the repressor protein physically blocks the binding of RNA polymerase to the promoter
• for transcription to take place, something must happen to prevent the binding of the repressor to the operator
• transcription is turned on by an inducer binding to the repressor proteins

Question 28

inducer

Answer 28

small molecule that binds to the repressor, altering its shape and preventing it from binding to DNA, allowing transcription to take place

Question 29

allosteric proteins

Answer 29

proteins that change shape upon binding to another molecule

Question 30

negative repressible operons

Answer 30

• always on, needs something to turn it off
• regulator protein is a repressor but it can’t bind to the operator without a corepressor
• typically control proteins that carry out the biosynthesis of molecules needed in the cell

Question 31

activator

Answer 31

regulatory protein that binds to the DNA (at a site other than the operator) and stimulates transcription

Question 32

catabolite activator protein (CAP)

Answer 32

site that is about 22 nucleotides long that is located within or slightly upstream of the promoter of lac genes

Question 33

coordinate induction

Answer 33

simultaneous synthesis of several proteins stimulated by a specific molecule, the inducer

Question 34

attenuation

Answer 34

transcription begins at the transcription start site, but termination takes place prematurely, before the RNA polymerase even reaches the structural genes

Question 35

attenuator

Answer 35

secondary structure that forms in the 5’ untranslated region of some operons and causes the premature termination of transcription
- one hairpin produced by the base pairing of regions 1 and 2 and another hairpin produced by the base pairing of regions 3 and 4
- hairpins are followed by a string of uracil nucleotides that stop transcription

Question 36

antiterminator

Answer 36

protein or DNA sequence that prevents the termination of transcription
- hairpin is formed but there is no string of uracil nucleotides to stop transcription

Question 37

bacterial enhancers

Answer 37

increase the rate of transcription at genes that are distant from the enhancer
- contain binding sites for proteins
- causes the DNA between the promoter and the enhancer to loop out, so that the transcription activator that is bound to the enhancer can directly interact with the RNA polymerase that is bound to the promoter

Question 38

antisense RNA

Answer 38

RNA molecules that are complementary to particular sequences on mRNAs
- control gene expression by binding to sequences on mRNA and inhibiting translation
- blocks the ribosome binding site

Question 39

riboswitches

Answer 39

regulatory sequence in an RNA molecule
- when an inducer binds, this changes the configuration of the RNA molecule and alters the expression of RNA, usually by affecting the termination of transcription or by affecting translation

Question 40

structural gene mutations

Answer 40

alter amino acid sequence of protein encoded by gene in which mutation occurs

Question 40

regulator gene mutations

Answer 40

affect transcription of structural genes

Question 41

operator mutations

Answer 41

affect transcription of structural genes

Question 42

promoter mutations

Answer 42

affect transcription of structural genes