Chapter 10 - Prokaryotic Genome Organization & Regulation

Question 1

Most prokaryotes have a _________________ circular chromosome; however, exceptions exist - some have two or three circular chromosomes and others have linear ones (or a combination thereof).

Answer 1

Singluar

Question 2

The DNA in prokaryotic chromosomes is __________________, a consequence of the action of a class of enzymes called DNA __________________.

Answer 2

Supercoiled

Gyrases (topoisomerases)

Question 3

The chromosome is organized into about 50 discrete ______________.

Answer 3

Domains

Question 4

What are domains?

Answer 4

Domains are regions of the genome where supercoiling can be eliminated by nicking DNA and allowing DNA to rotate

Question 5

Most of the prokaryotic genome is noncoding. True or false?

Answer 5

False; most of the prokaryotic genome is coding

Question 6

Most of the prokaryotic genome encodes for proteins or ______________ molecules.

Answer 6

RNA

Question 7

Do prokaryotes have many nucleotides between genes?

Answer 7

No; they typically have relatively few nucleotides between genes

Question 8

Prokaryotic chromosomes contain multiple ____________________, genetic sequences that can change their location on a DNA molecule.

Answer 8

Transposons

Question 9

Transposable elements are flanked by ____________ repeats.

Answer 9

Inverted

Question 10

What enzyme catalyzes the movement of transposons?

Answer 10

Transposase

Question 11

There are two basic types of transposition. What are they?

Answer 11

Replicative

Nonreplicative

Question 12

In __________________ transposition, one copy of the transposon remains at its original site while a second copy is inerted elsewhere.

Answer 12

Replicative

Question 13

In ___________________ transposition, the transposon is physically removed from its original site and reintegrated into the new site.

Answer 13

Nonreplicative

Question 14

Do transposons transpose often?

Answer 14

No; transposons normally transpose only rarely

Question 15

The simplest transposons are called ____________________ __________________.

Answer 15

Insertion sequences

Question 16

Other transposons are called _________________ _________________.

Answer 16

Composite transposons

Question 17

_____________________ are usually circular molecules of supercoiled DNA that encode dispensable functions.

Answer 17

Plasmids

Question 18

What are three ways in which plasmids differ from chromosomes?

Answer 18

1. Plasmids are usually much smaller
2. Plasmids are present in some members of a species but not in others
3. Plasmids encode no functions that are essential to the cell under all conditions of growth

Question 19

F plasmids are __________________ plasmids while R plasmids are _________________ plasmids.

Answer 19

Conjugative plasmids

Resistance plasmids

Question 20

What is a gene?

Answer 20

A unit of heredity that determines a trait; a sequence of nucleotides where the order determines the order of monomers in a nucleic acid and/or polypeptide product

Question 21

Prokaryotic genes are often organized into _____________________.

Answer 21

Operons

Question 22

Multiple genes are commonly grouped together into a single transcriptional unit under the control of a single promoter in what is known as an __________________.

Answer 22

Operon

Question 23

A ______________________ _________ is a stretch of DNA transcribed into a molecule of RNA.

Answer 23

Transcriptional unit

Question 24

Prokaryotic ribosomes bind to particular sequences called __________ ___________ ______________________ on mRNA to initiate translation.

Answer 24

Shine-Dalgarno sequences

Question 25

Transcriptional units tend to be oritened so that they are transcribed in the ______________ direction as the chromosome is replicated.

Answer 25

Same

Question 26

The *E. coli* core polymerase is a large unit composed of two ___ units, two ___ units, and a ___ unit.

Answer 26

Alpha units Beta units Omega unit

Question 27

What unit do bacteria have that associates with the enzyme before promoter binding but can dissociate after transcription is initiated?

Answer 27

The sigma factor

Question 28

What is the role of the sigma factor?

Answer 28

Recognition of promoters and DNA melting

Question 29

What is the name given to the complex formed when the sigma factor and RNA polymerase bind?

Answer 29

Holoenzyme

Question 30

Different categories of genes can be turned on by simply using a different sigma factor. For example, sigma-70 recognizes ________________ genes, and sigma-32 recognizes _______________ genes.

Answer 30

Housekeeping Heat-shock

Question 31

Promoter recognition by RNA polymerase is different in bacteria than in archaea and eukarya. What is the primary difference?

Answer 31

RNA polymerases in archaea and eukarya lack the sigma factor; thus, they are unable to recognize promoters and require transcription factors to assist

Question 32

Specific proteins called __________________ \_\_\_\_\_\_\_\_\_\_ recognize and bind to sites adjacent to promoters in archaea and eukarya.

Answer 32

Transcription factors

Question 33

The __________________ \_\_\_\_\_\_\_\_\_\_\_\_\_\_ is one at which the RNA polymerase holoenzyme recognizes easily and will efficiently initiate transcription.

Answer 33

Consesus sequence

Question 34

Promoters may be ____________ or \_\_\_\_\_\_\_\_\_\_\_.

Answer 34

Weak Strong

Question 35

When a consensus sequence is easily recognized and efficiently initiates transcription, what is the promoter called?

Answer 35

Strong promoter

Question 36

Many promoters have significant differences from the consensus sequence, and these _________ \_\_\_\_\_\_\_\_\_\_ are recognized less effectively by RNA polymerase.

Answer 36

Weak promoters

Question 37

There are two principal strategies for optimizing promoter strength for each transcriptional unit. What are they?

Answer 37

1. The promoter strength is matched to the maximum amount of gene product the cell needs (i.e., the more the cell needs a product, the stronger the promoter will be, and vice versa) 2. The promoter strength is weakened when products of genes are needed at high amounts and the use of transcription factors is used to facilitate activation and repression of gene expression

Question 38

There are two types of bacterial transcription termination. What are they?

Answer 38

Rho-dependent termination Rho-independent termination

Question 39

What happens in rho-dependent transcription termination?

Answer 39

1. Rho binds to a "rut" in mRNA rich in C residues 2. Rho slides along mRNA in a 5' to 3' direction 3. RNA polymerase is paused at a G-C rich site with secondary structure 4. Rho catches up to RNA polymerase and pulls the transcript free of the polymerase and template, releasing it

Question 40

\_\_\_\_\_\_\_\_\_\_\_\_ is a protein that binds to C-rich sequences in RNA that are not translated and eventually terminates transcription.

Answer 40

Rho

Question 41

In \_\_\_-\_\_\_\_\_\_\_\_\_\_\_\_\_ termination, the RNA polymerase falls off the template when it is paused at a series of A-U pairs, which is caused by a stem-loop structure in the RNA immediately behind the polymerase. This type of termination is also known as _______________ termination.

Answer 41

Rho-independent Intrinsic termination

Question 42

Why does RNA polymase release DNA in Rho-independent transcription termination?

Answer 42

The A-U base pairs are weak, and after a few seconds, the mRNA dissociates

Question 43

\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_ is a section of DNA or RNA that codes for a product.

Answer 43

Cistron

Question 44

In addition to control sequences (e.g., promoter), most transcriptional units have one or more _____________ \_\_\_\_\_\_\_\_ that allow the rate of transcription and/or the rate of translation to be controlled.

Answer 44

Regulatory sites

Question 45

Gene expression can be regulated at many levels. What are they?

Answer 45

Transcriptional Post-transcriptional Translational Post-translational

Question 46

Transcription initiation is controlled by _____________ proteins known as transcription factors (repressors or activators).

Answer 46

Allosteric

Question 47

Allosteric proteins that bind to DNA and turn off transcription are called \_\_\_\_\_\_\_\_\_\_\_\_\_\_, and this mode of control is termed _____________ control.

Answer 47

Repressors Negative control

Question 48

Allosteric proteins that bind to DNA and turn transcription on are called \_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_, and this mode of control is termed ___________ control.

Answer 48

Activators (or transcription factors) Positive control

Question 49

An operon is called _________________ if the presence of a small molecule known as an ________________ turns the system on.

Answer 49

Inducible Inducer

Question 50

In negative inducible control, when is the repressor active?

Answer 50

When it is bound to DNA but unbound to inducer

Question 51

In negative inducible control, when an inducer binds to a repressor, what happens?

Answer 51

The repressor is inactivated and transcription can proceed

Question 52

In positive inducible control, when is the activator active?

Answer 52

When bound to the DNA and its activator

Question 53

\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_ operons are turned off by the presence of a \_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_.

Answer 53

Repressible operons Co-repressor

Question 54

In negative repressible control, when is the repressor active?

Answer 54

When bound to its co-repressor

Question 55

In negative repressible control, when is transcription blocked?

Answer 55

When the corepressor binds the repressor, which can then bind DNA and halt transcription

Question 56

In positive repressible control, when is repressor active?

Answer 56

When it is not bound to a co-repressor

Question 57

In positive repressible control, when is transcription blocked?

Answer 57

When the corepressor is not bound to the repressor; when not bound to its co-repressor, the repressor binds DNA and inhibits transcription

Question 58

Positive or negative control tells me about the effect of protein binding: a repressor _______________ transcription while a ________________ activates transcription. ______________ or ________________ tells me that the ability of these protein to bind can be prevented or activated via a \_\_\_\_\_\_\_\_\_\_\_\_\_\_\_\_.

Answer 58

Inhibits Activator Induction Repression Corepressor