Principles of Gene Expression Flashcards
What is the concentration of a protein determined by? (7 processes)
-synthesis of the primary RNA transcript
-post-transcriptional modification of mRNA
-mRNA degradation
-protein synthesis (translation)
-post-translational modification
-protein targeting and transport
-protein degradation
Transcription :
Translation :
-DNA -> mRNA
-mRNA -> Protein
What is a transcription factor?
-must bind DNA
-bind other proteins (pol II, other regulatory proteins)
-have common structural motifs:
Primarily involved in DNA binding:
helix-turn-helix and zinc fingers
Involved in DNA binding and protein dimerization:
leucine zippers, basic helix-loop-helix
Eukaryotic DNA:
-DNA packaged into chromosomes (23 pairs in humans)
-DNA complexed with histones, this complex is called chromatin
How is transcription regulated in eukaryotes? General
-access of promoters is restricted by the structure of chromatin
-eukaryotic cells have more complex, multimeric regulatory proteins
-postive regulatory mechanisms predominate
-transcription separated from translation in time and space
Explain Covalent modification of histones
-important in regulation of transcription
-alters accessibility of DNA
-methylation of lysine and arginine (SAM)
-phosphorylation of serines and threonines
-acteylation of lysines (HATs, HDACs)
How is transcription regulated by regulatory proteins?
can be regulated by multiple factors in different combinations
How can transcription be regulated by extracellular signals?
-steroid hormone receptors
-bind to hormone response elements on DNA
-steroid hormone receptors are transcription factors as they bind to DNA and have 8 steps
More on phosphorylation regulating transcription factors: cAMP
-cAMP response element (CRE)
-cAMP activated PKA
-catalytic subunit migrates to nucleus and phosphorylated CRE-binding protein (CREB)
-CREB binds to CREs and regulates transcription
Explain CREB activation
-“classic activator” is cAMP
-can be activated by other pathways: growth factors and CA2+ ions
What is the nuclear factor-kB (NF-kB)?
-identified as nuclear protein in B-cells that binds to k-lg light-chain enhancer
-complex of two subunits- p50 and p65
-widely expressed
-activates different genes in different tissues and cell types
-a central mediator of the inflammatory response
How can genes be silenced?
RNA interference
What is RNA interference?
-involved in regulation of ~30% of mammalian genes
-eukaryotes only
-mediated by micro-RNAs (miRNAs)
-thousands, double stranded RNA precursors, cleaved by endonuclease drosha and dicer
What are dsRNAs?
-introns, specific genes
-cleaved by dicer to form miRNA
-forms RNA-induced silencing complex (RISC) which prevents transcription or induces degradation
What are the practical applications of RNAi?
-can design small interfering RNA (siRNA) to silence almost any gene
-limitations: off-target effects, delivery
