Control of gene expression in Eukaryotes - week 8 Flashcards
in a human eukaryotic cell, how much of the DNA is encoding for protein/ polypeptide
A single human cell, a eukaryotic cell, contains enough DNA (6 billion bp) to encode several million different polypeptides.
but most of this DNA does not actually code for proteins, mammalian genomes contain ~35,000 protein-coding genes but a typical mammalian cell may only make ~5000 different polypeptides at any given time. Most DNA doesn’t code for proteins because they are housing genes.
which cells are expressed all the time and not always, with example
- Some genes are expressed in all cells all the time (housekeeping genes)
Some genes are always expressed in particular cell types but not in others. For example, a plasma cell continuously expresses the gene for the antibody it synthesizes - Some are expressed only as conditions around and in the cell change. For example, a hormone’s arrival may turn on/off certain genes in that cell.
where does regulation of gene expression occur in eukaryotes and what does each step regulate
regulation of gene expression in eukaryotes can occur at any of the steps in the process (the process that produces a functional protein) of gene expression.
Gene expression can occur at
-the DNA (genome),
-Transcription,
>Transcriptional Control is turning on and off, of mRNA formation.
-RNA processing,
>Regulation of the processing of a pre-mRNA into a mature mRNA
-Translation
>Regulation of the rate of Initiation
-Post-translation (after translation when the protein is already completed)
>Regulation of the modification of an immature or inactive protein to form an active protein
What is chromatin remodelling
In eukaryotes, DNA is associated with proteins to form a structure which is called chromatin.
The first potential point of the control of gene expression is chromatin remodelling.
Chromatin Remodelling is the region of the chromosome that must be opened up for enzymes and transcription factors to access the gene.
what are the 2 forms of chromatin
Chromatin exists in 2 forms:
* Euchromatin
* Heterochromatin
Euchromatin is less condensed, Euchromatin is the open conformation form, and Euchromatin is associated with the activation of the transcription.
Heterochromatin is highly condensed, and it is usually associated with the inhibition of transcription.
what is nucleosome and how does it affect transcription
Chromatin looks like beads on a string, each bead is called a nucleosome. Each nucleosome is made up of DNA wrapped around histone proteins.
chemical modifications to histones and DNA can affect the conversion between Heterochromatin and Euchromatin. Essentially, chemical modifications to histones and DNA of the nucleosome can affect transcription.
what domain of histone is subject to chemical modifications and what do these modifications affect
A particular protein domain, that is the main terminal domain of histones is the N-terminal domain of the histones, this is usually subject to chemical modifications.
These potential modifications are:
* Acetylation
* Methylation
* Ubiquitination
* Sumohylation
* Phosphorylation
These chemical modifications that can affect the amino acid of the amino ‘tail’ domain, which is usually Lysine’s, can directly affect the interaction between DNA and the histone proteins.
what is acetylation and what does it affect
Acetylation is the covalent attachment of the acetyl group to the Lysine but acetylation of the Lysine eliminates the positive charge of the Lysine.
The acetylation affects the electrostatic interaction between the DNA and the histone protein and because of this interference affects the transcription.
what is methylation
Lysine methylation retains the positive charge whether mono-, di-, or trimethylated. The addition of methyl groups can condense chromatin. It is associated with reduced transcription.
What is the HAT enzyme and how does it activate transcription
HAT are enzymes that can attach an acetyl group to the histone.
The activity of enzymes that are called Histone Acetyl Transferases (HAT) results in the decondensation of the chromatin. As the decondensed (loosened) chromatin is associated with the activation of the transcription thus histone acetyl transferases (HAT) enzymes are activators of the transcription.
how does HDCA enzyme inhibit transcription
Histone deacetylases (HDCA) enzymes condense the chromatin, so they are associated with the inhibition of transcription.
what enzymes are examples of how gene expression is regulated
HAT enzymes activate transcription whereas HDCA inhibits transcription.
There is an example of how eukaryotes can regulate the expression of a given gene by affecting the DNA, and the modification of the chromatin.
where the core promoter and control elements found
A typical eukaryote gene is organised in a eukaryotic cell. In eukaryotes, proteins-encoding genes have a core promoter and control elements (regulatory elements)
what is a core promotor and what does it consist of
The core promoter is the binding site of the general transcription factors and RNA polymerase. The core promoter has a sequence that is common to most genes of eukaryotes.
The core promoter contains the TATA box, which is the binding site of RNA polymerase, and it contains the transcriptional start site, the nucleotide is the start site, where the transcription begins.
what are control elements
The core promoter has a sequence that is common to most genes of eukaryotes. But in contrast, control elements (also called regulatory elements) are regions within the DNA located upstream of the core promoter, and they have a sequence that is unique to a specific gene.
what are the 2 types of control elements and what is their function
Most eukaryotic control elements can be divided into 2 types:
1) Proximal control elements – regulate the frequency of transcription by interacting with regulatory transcription factors. its structure and associated TFs (transcription factors) differ from gene to gene.
2) Distal control elements – enhancers or silencers, can be far away from the core promoter Enhancers and silencers are the binding sites of the regulatory transcription factors.
what are activators and repressors and how do they affect transcription
activators are regulatory transcription factors that when bind to the enhancer increase the rate of the transcription of a particular gene.
In contrast, repressors are regulatory transcription factors that bind to silencers and thus decrease the rate of transcription of a particular gene.
how does an activator protein initiate transcription
- An activator protein binds to the enhancer elements forming an enhanceosome.
- The binding (the formation of this complex enhancer-activator) causes a bend in the DNA. The bending of the DNA brings the enhanceosome (the activator) closer to the core promoter.
- The DNA-bound activators interact with specific coactivators.
- The other general transcription factors, mediator proteins and RNA polymerase join the complex, and transcription is initiated.
This is an example of how regulatory transcription factors affect the ability of general transcription factors and RNA polymerase to promote transcription.
what do transcription factors interact with and what are the 2 different types
Transcription factors interact with the cis-acting elements (regions within the DNA that are adjacent to the promoters). There are 2 groups of transcription factors:
* General TFs (transcription factors)
* Regulatory Tfs
what do general transcription factors do and what are the different types
General TFs bind at core promoter sites in association with RNA polymerase. they are necessary for transcription to occur.
Examples of general factors are TFIIA, TFIIB, TFIID (TBP &TAFs), TFIIE, TFIIF, and TFIIH.
what do regulatory transcription factors do
Regulatory TFs bind to various regulatory sites of specific genes; they either stimulate (transcriptional activators) or inhibit (transcriptional repressors) transcription of adjacent genes. These transcription factors are critical to making sure that genes are expressed in the right cell at the right time.
How do eukaryotes regulate the expression of genes at either the level of RNA modification (RNA processing) or at the level of the translation
At the level of RNA
- RNA processing (splicing and other events) and stability.
- Example - Alternative RNA splicing, Alternative RNA splicing is an example of a mechanism of gene regulation at the level of RNA.
At the level of translation –
- use of RNA-binding proteins
- use of non-coding RNAs
These regulatory mechanisms allow eukaryotes to regulate, to fine-tune. the expression of genes rapidly in response to environmental changes at a particular developmental stage.
what is immature RNA and what 3 modifications does it undergo to then be exported to the cytosol
In eukaryotes, the outcome of the transcription is the formation of a primary RNA transcript/ immature RNA transcript.
This immature RNA transcript is then subject to modifications, specifically to 3 modifications:
1. Capping (the synthesis of the CAP)
The synthesis of CAP is the addition of guanosine 3-phosphate at the 5’-end and the addition of the polyA tail at the 3’-end.
2. Removal of introns from the primary RNA transcript and the formation of the mRNA containing only exons that are the coding sequences of the mRNA.
3. Synthesis of the poly(A) tail - When transcription is complete, the transcript is cut at a site and the poly(A) tail is attached to the exposed 3’ end.
mRNA molecule is now ready for export to the cytosol.
mRNA that is formed after RNA modification contains 2 untranslated(UTR) sequences, where are the 2 sequences found and for what are they important for
The mRNA that is formed after the RNA processing/ RNA modifications contains 2 sequences that are not translated. One at the 5’-end, this is an untranslated region and the other untranslated region at the 3’-end. This means that this region is present in the mRNA but will not be present in the polypeptide that will be formed from the mRNA.
The 2 untranslated (UTR) sequences are important for the regulation of the expression of mRNA.
