gene expression and control Flashcards
define transciption factors
proteins that bind to cis acting elements of a gene
general vs cell/tissue specific TFs
general: minimum TF required for transcription
cell/tissue specific: regulate transcription of unique sets of genes in those cells/tissues
why do all cells of the individual have the same DNA
DNA from zygote is replicated many times with high fidelity
what genes are expressed in nearly all cells
housekeeping genes such as RNA/DNA pol coding genes, ribosome coding genes etc
define differentiation and what it is marked and preceded by
expression of appropriate subset of genes to carry out specialised functions
marked by a change in cell morphology, preceded by rapid proliferation
levels of gene expression regulation
- chromatin accessibility
(modify histones, chromatin remodelling, DNA methylation) - transcription regulation
- mRNA processing
- mRNA transport, localisation, stability
- translation
- post-translational modification
how does acetylation increase accessibility
negative acetyl group neutralises positively charged lysine and arginine, DNA less tightly bound, more accessible
what enzymes adds and removes acetyl group to histones
acetyl transferase, histone deacetylase
define histone code, how its maintained
distinct set of modifications to histone tails
preserved during DNA replication because its copied by proteins from parental histones to newly synthesised histones during chromosome replication
why is histone code important
proper gene expression, DNA repair, differentiation, prevents cancers and disorders
how are transcriptional activators and suppressors triggered
cell signalling due to cellular/environmental cues so body can adapt to changing conditions
what is SWI/SNF and what does it do
it is an ATP dependent chromatin remodelling protein complex
- pushes DNA around nucleosomes
- ejects histomes/octamers to expose TATA box
- remains bound in decondensed region for continuous gene expression
DNA methylation and CpG islands
CpG islands are regions with many C-G pairs
methyl groups are added to Cs in CpG islands, decrease accessibility and expression
fragile X syndrome and methylation
syndrome that results in in-vitro breaks on X chromosome
due to excessive (CGG)n repeats in UTR of X chromosome
causes methylation even when its not supposed to
number of repeats influences amount of methylation which influences severity of disease
how do general and specific TFs control transcription
general: control and are needed for initiation of transcription
specific: controls rate of initiation of transcription
specific TF bind their alpha helixes to the specific cis acting element in the DNA
transcriptional activators and supressors function
both are TFs
activators/suppressors bind to enhancer or promotor or repressor regions of the gene, increase/decrease recruitment of TFs and RNA pol to gene, increase/decrease gene expression
how do general TFs, transcriptional activators and architectural proteins work together
- TBP binds to TATA box etc
- transcription activators (type of TF) binds to enhancers
- architectural proteins bend the DNA
- DNA and TF complex at enhancer loops to interact with TATA factors and architectural proteins, which increase rate of transcription initiation
what is cooperative binding
when many different types of TFs bind and interact together, conformational changes occur, gene control options have increased
(e.g. 2 during transcription initiation, after TBP binds, other TFs can bind on because TBP serves as a base)
what is combinatorial control of gene expression and what does it depend on
control of transcription rate due to combinations of TFs binding to promotors and enhancers
- DNA sequences present
- TFs present
- interactions between these TFs (eg through cooperative binding)
functional domains function
- part of TFs that recognise and bind to DNA promotor/enhancer
- interacts with initiation complex
- influences chromatin remodelling
- sensor for internal/external cellular conditions
3 ways that RNA processing contribute to gene expression
need 5’ cap and 3’ tail or else RNA pol will not recognise mRNA and gene will not be translated and expressed
secondary structure of mRNA must be removed by RNA processing for RNA pol to bind
alternative splicing means many proteins can be translated and hence expressed from 1 gene
what must happen before RNA is exported
all RNA processing is finished and left over or damaged RNA has been degraded by exonucleases
3 mechanisms for mRNA localisation
- direct transport on cytoskeleton
- random diffusion and trapping
- generalised degradation and local protection
anchor proteins function
bind to mRNA and make sure mRNA stays localised during translation
