Final Exam Prep Flashcards
Transcription Initiation (Level of prokaryotic Gene Control)
Control if and how much housekeeping genes will be transcribed or not
- includes regulators
Types of Transcriptional Factors for Prokaryotes (Regulators)
Activators: increase expression (turn on or up genes) and increase the amount of transcription happening in these genes- These bind to
activator binding sites
Repressors: decrease expression (turn off or down genes);
decrease the amount of transcription happening in those genes and
binds to repressor binding sites
Positive Control
–> The gene is always off or little to no activity in the gene - Unless activator is there to help RNA polymerase bind to the promoter region
–> RNA polymerase has less affinity for the activator binding site, which is why the activator binds to RNA polymerase thus initiating transcription more often
–> Trans-acting factor must bind to cis-acting site in order for RNA polymerase to initiate transcription at the promoter
Negative Control
–> Gene is always on unless repressor is there to prevent RNA polymerase from binding to the promoter
–> Trans-acting repressor binds to cis-acting operator site to turn off transcription
Induction
–> Interaction of inducer molecule with the gene’s regulatory protein to enhance/turn on transcription
–> Negative control = Inducer changes the shape of the repressor so that it is no longer able to block RNA polymerase thus it can resume transcription
–> Positive control = The presence of the inducer turns an inactive activator to be active so that it can bind to RNA polymerase to help start transcription
Repression
–> Negative control = another molecule turns the inactive repressor to become an active repressor thus the gene is turned OFF
–> Positive control = another molecule turns an inactive activator to become activated and thus the gene is turned ON
Bacteria vs Eukaryote Regulator sites
- Eukaryotes do not contain many repressors but rather activators
- Bacteria have activator and repressor binding sites
- If the sites are close to the gene = easier interaction
- if there are far from the gene = DNA loops so regulators can interact with RNA polymerase
(common in eukaryotes and called enhancers - DNA bends so that activation can still occur)
Architectural Regulators
- Regions that bend between the activator and promoter sites which create contact between them and initiate transcription
- Help with DNA looping and common in eukaryotes
Why do Regulators use co-activators or co-repressors?
- coactivator helps bind the activator and RNA polymerase so that they can directly interact
- corepressor blocks activator from interacting with the RNA polymerase and prevents transcription
Both are very specific for particular genes
Insulators
Promoters are adjacently situated on a gene as transcriptions would occur upstream or downstream and so if genes are close together, insulators may be between them to prevent regulators from acting on the wrong promoter regions
Combinatorial Control of Regulators
- Use of specific combinations of regulatory proteins to control gene expression
- some regulators are shared for different regulatory binding sites since some genes need to be turned on at the same time
- Some are unique to the binding site because you might need these genes less than others
- Combinations help to turn on genes fully
Post-transcriptional process (level of gene expression control)
Includes:
- mRNA splicing: preRNA needs to have sections spliced before it can be used for translation
-modification of RNA: capping and poly A tail and RNA editing
(e.g., attenuation which is mRNA stopped before it is finished being transcribed)
Post transcriptional Stability (Level of gene expression control)
- If preRNA is made but not needed yet, then it can be silenced
-miRNAs are made temporarily and form duplexes with the target RNA - used in developmental timing, repressing transposons and destroying invading RNA viruses
-If preRNA is made but not needed yet, then interference to remove
-dicer cuts miRNAs into siRNAs which can be used to bind to mRNA to stop it from being used so that the function of the gene can be studied without making a mutant organism
-process called RNAi (RNA interference)
-DNA eventually destroyed
How do Regulator Molecules Interact with DNA in Prokaryotes?
- Through structural motifs (sequences)
- regulatory proteins often appear as dimers with short, inverted repeats as their structural motif
Helix-turn-helix motif
- often used by bacterial regulators
-the recognition helix inserts into the major groove of DNA
-INTRINSICALLY UNSTABLE AND PART OF A LARGER MOLECULE - Seen in lactose repressor
Homeodomain motif
-conserved 60 amino acid sequence motif
-repeats in many proteins
- 3 alpha helices that interact with minor groove
-dimers come in from both sides of DNA and hold it together
Leucine zipper motifs
● Interaction between 2 proteins
such as transcriptional factors -
leucine in every 7th position
● Part of dimer interacts w/ DNA
● Other part of dimer has leucine at
every 7th position
- Leucine interacts w/ other
leucines on the other part
of the protein dimer and
holds it together (leucine
acts as a zipper region)
- Allows DNA to open and
close flexibly
Viral Replication Strategies for Viruses
Lytic:
- Viruses that enter the cell, replicates, then leaves the cell
Lysogenic:
- Viruses that incorporate themselves into chromosomes of the cell, cell
division occurs, viral genetic material gets replicated and stays in the
cell, then it can choose to become lytic
Lytic Cycle
- Takes place by producing phage genomes and protein particles that are assembled into progeny phages (class 1 = 5 genes with RNA polymerase and host interference, class 2 = 7 genes with DNA synthesis and lysozyme and class 3 = 12 genes with heads and tails and DNA maturation)
-Phage lytic development
proceeds by a regulatory cascade where a gene product at each stage is needed for expression of the genes at the next stage
Stages of Lytic Cycle
Early: Phage genes are transcribed by host RNA polymerase (regulator gene products: RNA POLYMERASE, sigma factor or antitermination factor needed)
Middle: Early product causes transcription of middle genes (regulator gene products: sigma factor or antitermination factor; structural genes products: replication enzymes)
Late: Middle product causes transcription of late genes (structural gene products: phage components)
Lysogenic Phage
- Lysogeny is where they recombine their genetic material into the chromosome
-when they recombine they are called prophage (dormant/ static for an undetermined period of viral replication stages until an environmental stage that induces lytic cycle)
How can Viruses switch from one pathway to another?
- Low nutrient levels and high MOI → makes viruses stay in their lysogenic stage
- Prophage is incorporated into host cell chromosome
- Prophage leaves when host cell is under stress and goes back to the lytic cycle
Lambda
-A bacteriophage
- bacteriophage chromosome is circular when not integrated into host
- lambda Can integrate into E.coli chromosome at specific locations via recombination at att site- linear form
- E.coli has Gene for galactose and biotin → once lambda integrates there, its chromosome becomes linear
Pre (lambda)
- promoter used for repressor establishment in lambda
- Transcribes to the left
- Makes mRNA that eventually becomes a repressor