Chapter 10 - Prokaryotic Genome Organization & Regulation Flashcards
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).
Singluar
The DNA in prokaryotic chromosomes is __________________, a consequence of the action of a class of enzymes called DNA __________________.
Supercoiled
Gyrases (topoisomerases)
The chromosome is organized into about 50 discrete ______________.
Domains
What are domains?
Domains are regions of the genome where supercoiling can be eliminated by nicking DNA and allowing DNA to rotate
Most of the prokaryotic genome is noncoding. True or false?
False; most of the prokaryotic genome is coding
Most of the prokaryotic genome encodes for proteins or ______________ molecules.
RNA
Do prokaryotes have many nucleotides between genes?
No; they typically have relatively few nucleotides between genes
Prokaryotic chromosomes contain multiple ____________________, genetic sequences that can change their location on a DNA molecule.
Transposons
Transposable elements are flanked by ____________ repeats.
Inverted
What enzyme catalyzes the movement of transposons?
Transposase
There are two basic types of transposition. What are they?
Replicative
Nonreplicative
In __________________ transposition, one copy of the transposon remains at its original site while a second copy is inerted elsewhere.
Replicative
In ___________________ transposition, the transposon is physically removed from its original site and reintegrated into the new site.
Nonreplicative
Do transposons transpose often?
No; transposons normally transpose only rarely
The simplest transposons are called ____________________ __________________.
Insertion sequences
Other transposons are called _________________ _________________.
Composite transposons
_____________________ are usually circular molecules of supercoiled DNA that encode dispensable functions.
Plasmids
What are three ways in which plasmids differ from chromosomes?
- Plasmids are usually much smaller
- Plasmids are present in some members of a species but not in others
- Plasmids encode no functions that are essential to the cell under all conditions of growth
F plasmids are __________________ plasmids while R plasmids are _________________ plasmids.
Conjugative plasmids
Resistance plasmids
What is a gene?
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
Prokaryotic genes are often organized into _____________________.
Operons
Multiple genes are commonly grouped together into a single transcriptional unit under the control of a single promoter in what is known as an __________________.
Operon
A ______________________ _________ is a stretch of DNA transcribed into a molecule of RNA.
Transcriptional unit
Prokaryotic ribosomes bind to particular sequences called __________ ___________ ______________________ on mRNA to initiate translation.
Shine-Dalgarno sequences
Transcriptional units tend to be oritened so that they are transcribed in the ______________ direction as the chromosome is replicated.
Same
The E. coli core polymerase is a large unit composed of two ___ units, two ___ units, and a ___ unit.
Alpha units
Beta units
Omega unit
What unit do bacteria have that associates with the enzyme before promoter binding but can dissociate after transcription is initiated?
The sigma factor
What is the role of the sigma factor?
Recognition of promoters and DNA melting
What is the name given to the complex formed when the sigma factor and RNA polymerase bind?
Holoenzyme
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.
Housekeeping
Heat-shock
Promoter recognition by RNA polymerase is different in bacteria than in archaea and eukarya. What is the primary difference?
RNA polymerases in archaea and eukarya lack the sigma factor; thus, they are unable to recognize promoters and require transcription factors to assist
Specific proteins called __________________ __________ recognize and bind to sites adjacent to promoters in archaea and eukarya.
Transcription factors
The __________________ ______________ is one at which the RNA polymerase holoenzyme recognizes easily and will efficiently initiate transcription.
Consesus sequence
Promoters may be ____________ or ___________.
Weak
Strong
When a consensus sequence is easily recognized and efficiently initiates transcription, what is the promoter called?
Strong promoter
Many promoters have significant differences from the consensus sequence, and these _________ __________ are recognized less effectively by RNA polymerase.
Weak promoters
There are two principal strategies for optimizing promoter strength for each transcriptional unit. What are they?
- 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)
- 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
There are two types of bacterial transcription termination. What are they?
Rho-dependent termination
Rho-independent termination
What happens in rho-dependent transcription termination?
- Rho binds to a “rut” in mRNA rich in C residues
- Rho slides along mRNA in a 5’ to 3’ direction
- RNA polymerase is paused at a G-C rich site with secondary structure
- Rho catches up to RNA polymerase and pulls the transcript free of the polymerase and template, releasing it
____________ is a protein that binds to C-rich sequences in RNA that are not translated and eventually terminates transcription.
Rho
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.
Rho-independent
Intrinsic termination
Why does RNA polymase release DNA in Rho-independent transcription termination?
The A-U base pairs are weak, and after a few seconds, the mRNA dissociates
_________________ is a section of DNA or RNA that codes for a product.
Cistron
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.
Regulatory sites
Gene expression can be regulated at many levels. What are they?
Transcriptional
Post-transcriptional
Translational
Post-translational
Transcription initiation is controlled by _____________ proteins known as transcription factors (repressors or activators).
Allosteric
Allosteric proteins that bind to DNA and turn off transcription are called ______________, and this mode of control is termed _____________ control.
Repressors
Negative control
Allosteric proteins that bind to DNA and turn transcription on are called __________________, and this mode of control is termed ___________ control.
Activators (or transcription factors)
Positive control
An operon is called _________________ if the presence of a small molecule known as an ________________ turns the system on.
Inducible
Inducer
In negative inducible control, when is the repressor active?
When it is bound to DNA but unbound to inducer
In negative inducible control, when an inducer binds to a repressor, what happens?
The repressor is inactivated and transcription can proceed
In positive inducible control, when is the activator active?
When bound to the DNA and its activator
____________________ operons are turned off by the presence of a _________________.
Repressible operons
Co-repressor
In negative repressible control, when is the repressor active?
When bound to its co-repressor
In negative repressible control, when is transcription blocked?
When the corepressor binds the repressor, which can then bind DNA and halt transcription
In positive repressible control, when is repressor active?
When it is not bound to a co-repressor
In positive repressible control, when is transcription blocked?
When the corepressor is not bound to the repressor; when not bound to its co-repressor, the repressor binds DNA and inhibits transcription
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 ________________.
Inhibits
Activator
Induction
Repression
Corepressor
