D2.2 Gene expression Flashcards
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phenotype vs genotype
genotype: combination of alleles inherited by an organism
phenotype: observable traits of an organism, resulting from its genotype and environmental factors
differences btwn protein synthesis and gene expression
Protein synthesis:
- genetic material translated from mRNA to a polypeptide chain
- polypeptide chain folds and is modified, becoming a functional protein
Gene expression:
- the ENTIRE process by which genetic material is expressed to synthesise a functional gene product, typically a protein
- usually involves transcription, RNA processing, translation, and post-translational modifications
- also involves regulatory mechanisms that control when and how much of the gene product is made
How is transcription regulated? (4)
Transcription factors:
- REGULATORY proteins that bind to promoter regions to regulate the transcription of DNA e.g. to encourage RNA polymerase to attach to DNA and start transcription
- also bind to enhancer regions to interact with the promoter region
Promoter region:
- a sequence of non-coding DNA found upstream that serves as the binding point for RNA polymerase
- the length varies btwn genes, where longer promoter regions are able to bind to more transcription factors = more complicated control mechanisms to regulate transciption. Hence shorter promoter regions have less fine control over transcription as less transcription factors bind to them
Enhancers and silencer region:
- Transcription factors bind to ENHANCER region (“on” switch) of DNA (found upstream) to encourage transciption
- Transcripton factors bind to SILENCER region (“off” switch) of DNA to prevent transcription.
Intracellular receptors (e.g. steroid hormone receptors):
- When activated by their specific molecule, the receptor undergoes a structural change that allows it to bind to the specific DNA sequences to promote transcription of a certain gene
Why and how is the degradation of mRNA controlled?
To regulate transcription by rendering a mRNA molecule useless before it can be used to produce a protein (e.g. if a cell needs to stop producing a specific protein, it will not only stop producing new mRNA molecules but destroy the old mRNA molecules circulating inside the cell)
- special enzymes caled exonucleases have the ability to “chop up” RNA by removing nucleotides one by one from their extremities, and there are two types:
1. exonuclease decapping complex - group of enzymes that remove the guanine cap at the 5’ end
2. exonuclease deadenyelase complex - removes adenine nucleotides from the polyA tail at the 3’ end
How is mRNA stabalised/protecting against degredation by exonucleases?
- Chemical modifications, such as the addition of the guanine cap to the 5’ end of the molecule and the polyA tail to the 3’ end of the molecule = increase stability of mRNA
- (presence of) stabalizing proteins which intefere with exonucleases, blocking their active sites = preventing them from binding to and degrading mRNA
- stabalizing protines also encourage the binding of protective proteins to mRNA = alters the structure of mRNA making it less accessible to exonucleases
What happens during epigenesis?
Epigensis is the process that results in the formation of organs and specalised tissue from a single undiffentiated cell and is dependent on NON-GENETIC factors (e.g. environmental stressors) for the expression of genes
- DOES NOT AFFECT DNA base sequences, so PHENOTYPE is affected but NOT GENOTYPE
- this is as epigenesis only modifies which part of the geneome is expressed or not
Difference btwn genome, proteome, and transcriptome
Genome:
- includes: all the genetic information of an organism (INCLUDING chromosal, mitochondrial, chloroplast DNA)
- no cell expresses all of its genes in the genome = instead they specialise and only express the genes needed for their function
Proteome:
- includes: the complete set of proteins present in an organism at a specific time
- each diffenentiated cell has a different proteome
Transcriptome:
- includes: all RNA molecules transcribed at a specific time within an organism, representing ACTIVE GENES AND THEIR EXPRESSION within an organism
Examples of epigenetic tags (3)
methyl groups (CH3) and acetyl groups (CH3COO-) can act as epigenetic tags
Methylation of cytosine in DNA of the promoter:
- methyl (CH3) groups attach to cytosine in the PROMOTER region = suppress the activity of the promoter = gene prevented from being transcibed, silenced
Methylation of amino acids (lysine) in histones
- If Lysine found near the tip of the histone tail (lyseine 4) is methyalted, DNA loops are loosened to separate the histones from one another to make DNA avaliable for transcription = gene is expressed
- If Lysine found along the tail (lysine 9/27) is methylated, DNA loops are tightned around histones such that they are compressed arnd each other making DNA unaccessible = gene is silenced
Acetylation of histones
- Acetyl group (CH3COO-) to histone decerases OVERALL CHARGE of histone protein = reduced ELECTROSTATIC attraction btwn histone and DNA
- DNA is less tightly wrapped around histone = easier for RNA polymerase and other molecules to bind to DNA = gene expression promoted
- removal of acetyl (CH3COO-) group reverses this process
Describe the properties of epigenetic inheritance
- epigenetic tags often remain in place during mitosis and meiosis = daughter cells inherit phenotypic changes from parent cells W/O a change to the DNA sequence
- However most epigenetic tags are erased at fertilisation, some are passed on to the next generation. This process is called REPROGRAMMING
What is an epigenome
All epigenetic tags on DNA and histone proteins in an organism
Example of environment affecting epigenome (1)
Due to air pollution (e.g. diesel fumes) can add/remove methyl (CH3) epigentic tags from the epigenome, changing which genes are expressed
Example of the consequence of some, but not all epigenetic tags removed at fertilisation (1)
Lion (f) and Tiger (m) = tigon
Lion (m) and Tiger (f) = liger
Genomic imprinting is the process by which only ONE of TWO inherited genes for a trait is expressed, as the other inherited genes are silenced by epigenetic tags during fertilisation
As a result, Ligers are able to grow to enormous size as the genes inherited from the father are switched on
Whereas Tigons do not grow to such large size
= it matters which genes come from the mother and father, because zygote tend to activate genes from one parent and silence the other (GENOMIC IMPRINTING)
Difference btwn heterozygotic and monozygotic twins
Heterozygotic twins form when 2 separate eggs fertilised at the same time by different sperm cells
Monozygotic twins form from the SAME zygote, have the SAME genome and VERY SIMILAR epigenomes.
- But phenotype will differ as it is based on environmetal factors = throughout life, the epigenomes of the monozygotic twins become increasingly different resulting in differing gene expression.
Examples of external factors affecting the pattern of gene expression (2)
Gene expression of E.coli bacteria impacted by the presence/absence of lactose:
- E.coli regulate the production of enzymes involved in lactose metabolism
- the LAC OPERON consists of:
- promoter region (RNA polymerase binds to it)
- repressor region (repressor proteins bind to the region when no lactose is present, blocking RNA polymerase from transcibing the genes to mRNA which become proteins involved in lactose metabolism. When lactose is present, it binds to the repressor protein, deactivating it and allowing RNA polymerase to transcibe the genetic code)
- a sequence of 3 genes, LacZ, LacY, LacA
Testeserone regulates gene expression:
- testesrone diffuses through the cell membrane, binding to a hormone receptor, forming a hormone-receptor complex
- the complex moves into the nucleus where it interacts with androgen response elements (DNA sequences) which are found in the regulatory sections of the target genes
- the complex may enhance/repress the transcription of target genes
