2.3 micro

Question 1

DNA-binding proteins act as

Answer 1

transcription factors to regulate transcription by turning it ON or OFF

Question 2

Activator proteins turn transcription ON when

Answer 2

bound to activator binding sites upstream of the promoter

Question 3

What do activator proteins help recruit?

Answer 3

RNA polymerase to the promoter

Question 4

Repressor proteins

Answer 4

Turn transcription OFF when bound to operator sites downstream of the promoter

Question 5

What do repressor proteins form a physical block around?

Answer 5

RNA polymerase advancements down the operon

Question 7

The ability of activator and repressor proteins to bind DNA is controlled by small molecules called

Answer 7

effectors

Question 8

Inducers

Answer 8

are effectors that result in turning transcription ON. When bound to activator proteins, they
facilitate the activator’s binding to the activator binding site. When bound to repressor proteins, they
prevent the repressor’s binding to the operator.

Question 9

Corepressors

Answer 9

are effectors that result in turning transcription OFF. When bound to activator proteins,
they prevent the activator’s binding to the activator binding site. When bound to repressor proteins,
they facilitate the repressor’s binding to the operator.

Question 10

The lac operon controls

Answer 10

lactose catabolism through the expression of lacZYA genes

Question 11

What is the lac operon a classic example of?

Answer 11

negative regulation of transcription initiation

Question 12

components of the lac operon

Answer 12

▪ LacI: repressor protein
▪ Allolactose: inducer of LacI
▪ CRP: activator protein
▪ cAMP: inducer of CRP

Question 13

what is a better energy source, glucose or lactose?

Answer 13

glucose

Question 14

catabolite repression

Answer 14

since glucose is a better energy source than lactose, when glucose is present, the operon needs to be repressed so energy is not wasted producing genes to get energy from lactose

Question 15

When glucose is present…

Answer 15

The activity of adenylate cyclase (the enzyme that produces cAMP) is inhibited; thus, CRP induction does not occur.

Question 16

When glucose is absent,

Answer 16

Adenylate cyclase is activated, leading to the production of cAMP, allowing CRP to bind and recruit RNAP.

Question 17

When lactose is present,

Answer 17

It is readily converted to
allolactose, which induces the LacI repressor, allowing
RNAP to proceed with transcription

Question 18

When lactose is absent,

Answer 18

LacI is not induced and
Therefore remains bound to the operator, preventing
RNAP.

Question 19

major operator

Answer 19

O1

Question 20

Monomeric LacI

Answer 20

Monomeric LacI can bind O1 and sterically inhibit RNAP

Question 21

tetrameric LacI

Answer 21

can bind O1 in conjunction with either O2 or O3, forming a secondary structure that makes the promoter inaccessible to RNAP.

Question 22

ara operon

Answer 22

controls arabinose catabolism through the expression of araBAD genes

Question 23

The ara operon is a classic example of

Answer 23

positive regulation of transcription initiation.

Question 24

Components of the ara operon include:

Answer 24

AraC: regulator protein that can act
as either an activator or a repressor
▪ CRP: activator protein
▪ cAMP: inducer of CRP
▪ Arabinose: inducer of AraC

Question 25

The operon contains

Answer 25

two operators (O1 and O2), and an activator region containing a CRP-binding site and two other regulatory sites (I1 and I2).

Question 26

Attenuation

Answer 26

is a form of transcriptional control in Bacteria and Archaea that functions by prematurely terminating mRNA synthesis

Question 27

Attenuation is most common in

Answer 27

in controlling amino acid biosynthesis.

Question 28

In attenuation, the first part of the mRNA to be made

Answer 28

called the leader sequence,

Question 29

leader sequence

Answer 29

can fold into two alternative secondary structures.

Question 30

One mRNA secondary structure allows

Answer 30

continued synthesis of the mRNA, whereas the other secondary structure causes premature termination.

Question 31

Secondary structure formation depends either on

Answer 31

events at the ribosome or on the activity of regulatory proteins.

Question 32

Stem loops can form between...

Answer 32

2:3 and 3:4.

Question 33

which is the more energetically favorable stem loop?

Answer 33

The 2:3 stem loop is more energetically favorable so if all regions 2-4 are accessible than the 2:3 loop will form

Question 34

2:3 stem loop

Answer 34

anti-attenuator loop that allows RNAP to transcribe the trp operon.

Question 35

3:4 stem loop

Answer 35

an attenuator loop that prevents RNAP from transcribing the trp operon.

Question 36

The leader sequence (region 1) of the trp operon encodes

Answer 36

a peptide rich in tryptophan amino acids.

Question 37

When tryptophan levels are high,

Answer 37

the ribosome can translate through the leader sequence to region 2. With the ribosome blocking region 2, the attenuator loop (i.e., the 3:4 stem loop) can form and RNAP is disengaged, preventing biosynthesis of more tryptophan.

Question 38

With the ribosome blocking region 2,

Answer 38

the attenuator loop (i.e., the 3:4 stem loop) can form and RNAP is disengaged, preventing biosynthesis of more tryptophan.

Question 39

When tryptophan levels are low,

Answer 39

the ribosome cannot translate through the leader sequence, leaving region 2 available for binding to form the anti- attenuator loop (i.e., the 2:3 stem loop), allowing transcription to proceed to enable tryptophan biosynthetic genes to be expressed.

Question 40

What signals the formation of the transcriptional terminator in the trp operon during attenuation? a. Binding of tryptophan to the repressor b. Interaction between the ribosome and mRNA c. Binding of RNA polymerase to the promoter

Answer 40

b. Interaction between the ribosome and mRNA

Question 41

What are riboswitches?

Answer 41

Riboswitches are RNA molecules (often in the 5′-UTR) that bind small metabolites and regulate gene expression, similar to repressors or activators

Question 42

Where are riboswitches usually located in relation to coding sequences?

Answer 42

Upstream of coding regions in the 5′-UTR

Question 43

What is the name of the riboswitch region that binds the ligand?

Answer 43

The aptamer region — it folds into specific 3D structures to recognize the ligand.

Question 44

How many structural forms can a riboswitch aptamer adopt?

Answer 44

Two — one ligand-bound and one unbound, each leading to different downstream effects.

Question 45

What determines whether the riboswitch folds into its ligand-bound or unbound structure?

Answer 45

The presence or absence of the ligand (small molecule).

Question 46

What is the expression platform in a riboswitch?

Answer 46

The downstream RNA region whose secondary structure is controlled by the aptamer and determines whether transcription continues or stops.

Question 47

How does ligand binding to the aptamer affect transcription?

Answer 47

It influences the formation of either a terminator loop or an anti-terminator loop in the expression platform.

Question 48

What happens if a terminator loop forms?

Answer 48

Transcription is terminated before the expression platform is transcribed.

Question 49

What happens if an anti-terminator loop forms?

Answer 49

Transcription proceeds, allowing expression of the downstream genes.

Question 50

What is the overall role of riboswitches in bacteria?

Answer 50

They act as direct sensors of metabolites, controlling transcription (and sometimes translation) without proteins.

Question 51

How do riboswitches regulate gene expression at the translational level?

Answer 51

By controlling the accessibility of the ribosome binding site (RBS) through structural changes in the RNA.

Question 52

What happens if ligand binding causes the RBS to become occluded?

Answer 52

The expression platform is unavailable, and translation is blocked.

Question 53

What happens if ligand binding causes the RBS to become exposed?

Answer 53

The expression platform is open, allowing the ribosome to bind, and translation proceeds.

Question 54

What region of the riboswitch binds the ligand to trigger these structural changes?

Answer 54

The aptamer region.

Question 55

What determines whether the RBS is exposed or occluded?

Answer 55

The presence or absence of the ligand influences the RNA secondary structure.