Module 12 - Gene Regulation Flashcards
Differentiate Constitutive and Regulated gene expression.
Constitutive gene expression is when a gene is transcribed at a relatively constant level under all conditions and cell types.
Regulated gene expression is when a gene is transcribed only under certain cellular or environmental conditions, or in certain cell types.
Differentiate Activators and Repressors
Activators are positive regulatory factors of gene expression/transcription that increases gene activity, Repressor has the opposite function.
Describe the ligand regulation of transcription factor binding.
The binding of a ligand of a transcrition factor (activator or repressor) can change its conformation and affect its binding capability to the DNA. Hence, the addition/removal of ligand from activators/repressors may prevent/allow the binding of the factor which switches on/off the gene.
Describe the mechanism of activators in regards to its effects on transcription machinery and chromatin (eukaryote).
Prokaryotes:
- Activators bind near promoter and help recruit RNA Pol. which initiates transcription
Eukaryotes:
- Activator can bind to enhancer sites (can be a long way from the promoter)
- DNA loops and can bring the activator into contact with the initiation complex and initiates transcription by activating the trancription machinery
In eukaryotes, activators can recruit Histone Acetylase (HAT), which looses the bond betwee the histones and DNA making the TATA box and promoter region more accesible.
What is the prokaryotic promoter structure and how it relates to the sigma factor.
Prokaryotic promoter contains highly conserved regions of DNA sequences (-35 and -10 region) seperated by 16-18 bp. These regions are conserved because they are binding sites of the sigma-factor, which recruits the core enzyme in prokaryotic transcription
Mention the three lac operon genes and what do they encode.
- lacZ encodes a ß-galactosidase enzyme
- lacY encodes a lactose transporter (permease)
- lacA encodes a thiogalactoside transacetylase (removing toxic thiogalactosides that is transported in by permease)
Mention the role of ß-galactosidase and permease in lactose utilisation as a carbon source.
Lactose needs permease (a lactose transporter protein) to get it into the cell. ß-galactosidase can cleave the ß-galactoside linkage in lactose releasing glucose and galactose.
Mention the role of LacI repressor and lactose ligand
The lacI gene encodes the lac repressor protein (LacI) which binds to the operator and inhibits transcription of lac operon. In the presence of lactose, it will bind and induce a conformational change of the LacI, causing it to dissociate and allowing RNA Pol. to function.
Mention the role of CAP and cAMP in response to glucose.
The crp gene encodes for CAP (catabolite activator protein). In the presence of cAMP it will help the CAP protein to bind to the CAP binding site and activate the transcription machinery. Glucose and cAMP levels are inversely related, as glucose represses the activity of the enzyme adenylate cyclase which converts ATP to cAMP.
Mention the levels of gene regulation.
Transcriptional, Post-transcriptional, Post-translational
Describe the mechanism of repressors in regards to its effects on transcription machinery and chromatin.
Repressor can inhibit transcription machienry process by three methods;
- Preventing activator form binding (competitive inhibition)
- Binding to activator (inhibit function)
- Direct interaction with GTFs and interfer with transcriptional machinery.
It can also recruit chromatin modelling complex (CMC), which condenses the chromatin state making TATA box inaccesible.
Define operons, cistron, and polycistron.
Operons are groups of adjacent genes that are transcribed *as a single mRNA molecule* which encodes several different polypeptide.They are controlled only by a promoter.
Cistron is a section of DNA encoding a single polypeptide which functions as a hereditary unit (individual gene units in a prokaryotic operon).
Polycistron: mRNA that encodes several different polypeptide
What are operators?
In prokaryotes, it is a DNA region (a part of the promoter) that controls the transcription of an adjacent gene. It is also a binding site for a Repressor.
What are cis-acting elements and trans-acting factors?
Cis-acting elements are DNA sequences that are near to the structural portion of a gene that are required for gene expression. Exp. operators, promoters
Trans-acting factors are usually proteins that bind to the cis-acting sequence to control gene expression. Exp. Transcription factors
Describe spatiotemporal regulation of gene expression.
Spatiotemporal gene expression refers to the control of where and when a gene is expressed.
What is Twist? Explain its affect on gene expression and cell behaviour during development and cancer.
Twist is an transcriptional activator found in Drosophila. It is expressed in mesodermal cells of the early fly embryo, which causes these cell to undergo a cell type change (stationary epithelial cell -> dissociates/migratory cell). In addition to that, inappropriate expression of activators like Twist can induce metastastic tumour/cancer (migratory and invasive).
Explain the concept of gene regulatory networks using an example.
The Twist factor activates the genes snail and rhomboid. However, snail itself is a repressor to rhomboid expression hence the expression patterns of rhomboid is not similar to those of twist and snail.
Describe the layout of alpha and beta globin clusters on the chromosome.
The alpha globin cluster is located on chromosome 16, while a cluster of beta globins is located on chromosome 11. Each cluster contains embryo gene, adult genes, and pseudogenes. For beta globin cluster, there are laso fetal genes.
How is globin gene expression regulated during development? Explain in regard to foetal oxygen requirement.
During embryonic stage, ε (beta embryonic globin) and ζ (alpha embryonic globin) are predominant but quickly diminish by week 7. After that, adult alpha globin and γ globin (foetal beta globin) became predomiannt for the rest of prenatal age. This combination of α and γ globins lead to a foetal haemoglobin structure that has a higher affinity for oxygen compared to adult heamoglobin. Since foetus gets its blood supply from its mother, a higher affintiy would allow the mother’s Hb to release O2 to the foetus’ Hb. Quickly after birth, the γ globin diminish replaced by beta globins leading to a normal adult haemoglobin structure,
Explain the concept of an enhancer and the role of insulators and barriers in limiting their influence.
Enhancers are regulatory DNA sequence to which regulatory factors (trans-acting factors) bind, increasing the rate of transcription of a gene. Since enhancers act by DNA “looping”, it is able to influence genes from a distance. Therefore, mechanisms, such as insulators and barriers, need to present to confine their influence to correct genes. Insulators create loops in which the enhancer and the correct gene are confined. Barrier sequence prevents the spread of heterochromaticity to functional genes.
Explain the molecular basis for ß-thalassaemmia.
Mutations fall into two classes:
- B0 - no beta globin produced
- B+ - reduced beta globin levels (severity vary)
