Genome structure and regulation Flashcards
Gene structure
- Structure of a gene
- Regulation of gene expression
- Regulation of transcription
- Regulation of translation
- Regulation of protein degradation
- Differential expression in space (sub-cellular localisation,
different cells, different tissues) and tim
How can we regulate transcription
- Number of transcribed copies
- Localisation of transcripts
- Timing of transcription
- Chromatin structure and histones modification
- DNA methylation
- Initiation of transcription: promoters and σ factors
- Transcription factors, activators, repressors, etc.
- Post-transcriptional regulation
Histones
How can they be modified, give to examples of this and what happens to the DNA
DNA is wrapped around histones.
They are positive
there are 4 main histones
H2A H2B H3 and H4 they make an octamer (8 different proteins)
H1 usually present on linker DNA between two different histones
there are different levels of organisation
Thye are proteins they can be modified such as adding
methyl group
acetyl group
phosphate
ubiquitin
When there is an acetyl group, the DNA around seems to be expressed.
When there is methyl group this “shuts down” the gene (wrapped more tightly)
Regulation at the promoter’s level
Different promoters (as well as mutations in the promoter)
affect gene expression
Regulation by σ factors in bacterial cells
The σ factors provides specificity:
* the specificity of the binding the RNA Pol to the promoter is
controlled by the σ factors
* bacterial cells have different σ factors
* genes with similar/related functions have similar promoter
* => gene transcription can be regulated by promoter sequence
and therefore σ factors
* => gene regulation (up-regulation or down-regulation)
Give examples of sigma (σ) factors in bacteria, which play a key role in regulating gene expression by directing RNA polymerase to specific promoters in bacterial cells
σ70: Housekeeping genes; primary sigma factor for exponential growth
σ32: Heat-shock gene transcription
σ38: Stationary phase gene expression
σ54: Expression of genes for nitrogen metabolism
What influences sigma 70 activity?
Why is it important?
Regulatory mechanisms involving (p)ppGpp, DksA, and other factors that influence the activity of the σ^70 sigma factor in response to stress and nutrient starvation in E. coli.
This modulation of sigma factor activity is crucial for the adaptive transcriptional response of the bacteria under changing environmental conditions.
What do eukaryotic cells do for regulation of transcription?
Promoters and Transcription Factors:
DNA sequences at gene promoters bind transcription factors, activating or repressing transcription.
Enhancers and Silencers:
Enhancers boost, and silencers suppress, gene expression by interacting with transcription factors.
Epigenetic Modifications:
DNA methylation and histone modifications alter chromatin structure, affecting gene accessibility.
Chromatin Remodeling:
Complexes rearrange nucleosomes, influencing gene accessibility for transcription.
RNA Interference (RNAi):
Small RNAs regulate gene expression post-transcriptionally by degrading or inhibiting mRNA.
Alternative Splicing:
Pre-mRNA splicing generates diverse mRNA isoforms, influencing protein variants.
Nuclear Pore Regulation:
mRNA export factors control the movement of mRNA from the nucleus to the cytoplasm.
RNA Polymerase Regulation:
Phosphorylation of RNA polymerase II CTD affects transcription initiation, elongation, and termination.
Cell Signaling Pathways:
Extracellular signals activate pathways influencing transcription factors and co-regulators.
Feedback Mechanisms:
Gene products regulate their own expression through feedback loops.
Further regulation: transcription factors, activators, repressors give an example
Different genes have different activator proteins bound to its regulatory region, but these bound proteins are not sufficient on their own to fully activate transcription. One additional gene regulatory protein (glucocorticoid receptor, complexed with glucocorticoid hormone) binds
to the regulatory region of each gene => max initiation of
transcription => the genes are switched on as a set.
2 activators might be needed for transcription
An example of a transcript factor to de-differentiate
and re-differentiate cells
Some genes can regulate many other genes in a “cascade”
* e.g. MyoD for cellular differentiation
“(A) Fibroblasts from the skin of a chick embryo have been converted to muscle cells by the experimentally induced expression of the myoD gene. The fibroblasts that have been induced to express the myoD gene have fused to form elongated multinucleated muscle-like cells, which are stained green with an antibody that detects a muscle-specific protein. Fibroblasts that do not express
the myoD gene are barely visible in the background.”
Signals on UTRs can affect mRNA localisation
How can a zygote differentiate in the many different cells in an organism?
During early development, the zygote undergoes asymmetrical divisions influenced by cytoplasmic determinants. The localization of these determinants is guided by signals in the UTRs of mRNA molecules. Swapping UTRs between genes can alter the localization of mRNA and, consequently, gene expression, leading to changes in the development of specific body regions in organisms like Drosophila melanogaster.
Regulation at/after translation
- Availability of charged tRNA (attached to amino acid)
- Eukaryotic elongation factors (e.g. eEF)
- Post-translational modification (phosphorylation, acetylation, glycosylation).
Another way to regulate gene expression.
Protein localisation
Destination of Newly-Produced Proteins:
Intracellular:
Proteins can be targeted to organelles (nucleus, mitochondria, peroxisomes) or the cytosol.
Some proteins are produced on free ribosomes and translocated/modified after translation (post-translational translocation).
Extracellular:
Proteins destined for extracellular spaces or plasma membranes (transmembrane).
Some proteins are produced on endoplasmic reticulum (ER)-bound ribosomes and translocated during translation (co-translational translocation) into the lumen of the rough ER (RER) and Golgi apparatus.
Further processing occurs, and proteins may be packaged into lysosomes for exocytosis.
Key Point:
The type of protein produced depends on where it is needed in the cell or organism, whether inside organelles, in the cytosol, on the cell membrane, or for secretion/excretion.
Example of post-translational translocation
- Translation Location: Proteins destined for mitochondria are translated on free ribosomes in the cytosol.
- Signal Peptide: The presence of a signal peptide in the nascent polypeptide chain marks it for mitochondrial transport.
- Recognition and Translocation: Receptor proteins on the mitochondria recognize the signal peptide and facilitate the translocation of the protein into the mitochondrial compartments.
4.Signal Peptide Removal: After successful translocation, the signal peptide is cleaved and removed by a signal peptidase.
In summary, the signal peptide acts as a guiding signal, ensuring that the protein is directed to the correct destination within the cell, in this case, the mitochondria.
What is TOM and TIM
translocase of the outer mitochondrial membrane
translocase of the inner mitochondrial membrane
