Gene regulation Flashcards
Cis-regulatory sequences
DNA sequences flanking a gene in non-coding regions that are bound by trans-acting regulatory molecules and influence expression of gene on same chromosome
Trans-acting factors
Transcription factors who are regulatory molecules themselves, able to diffuse through cell to get to target. Synthesized from genes that are different from the genes targeted for regulation. Bind to DNA using structural motifs.
General transcription factors
Minimal requirement of recognition by promoter, required by all mRNA genes. Transcription can occur alone with these factors.
Specific transcription factors
Required for maximal level of transcription or for induction.
Operon
Group of genes with related function which are localized on the DNA and regulated together by single promoter and operator. Can be inducible or repressible.
Lac operon
Inducible system in prokaryotes. Regulation depends on the presence of lactose and glucose. Glucose is preferred. Lac Z, Lac Y, and Lac A required to metabolize lactose and are transcribed together into 1 RNA that make 3 proteins.
Lac Z
Makes beta-galactosidase which increases and decreases with presence of lactose. If glucose present the expression still goes up a little but not as much as if only lactose. Breaks lactose into glucose and galactose.
Lac Y
Makes lactose-permease which allows lactose to move across membrane
Lac A
Makes thiogalactotransacetylase
Lac P
Promoter region where RNA polymerase with sigma factor binds (then moves through operator region). CAP protein either on or off–if on then enhances transcription.
Lac O
Operator region where RNA polymerase must go through to transcribe
Lac I
Makes the repressor protein which is able to bind Lac O and prevents RNA polymerase from transcribing when lactose absent (negative control because binding inhibits gene expression) or binds lactose if lactose is present
CAP protein
Binds to cAMP which allows binding to promoter region and helps enhance transcription. CAP is off in high levels of glucose and CAP is on in low levels of glucose.
Adenylate cyclase
Enzyme which catalyzes reaction of ATP to cAMP which is inhibited in the presence of glucose.
cAMP in Lac operon
Trans-acting factor. If glucose levels low then cAMP levels high. Binds to CAP protein when glucose present (whether or not lactose is present)
Enhancers
Cis-acting DNA sequences which increase rate of trascription
Activators
Proteins bound by transcription factors to regulate assembly of initiation transcription complex
Repressors
Bind to promoter or regulatory sequence to prevent transcription. Repressor genes are near the operon.
If glucose present and lactose absent
Lac operon off
If glucose absent and lactose present
Lac operon on
If glucose present and lactose present
Lac operon off
Tryptophan operon of E.Coli
Encodes for enzymes needed to synthesize Trp and regulated by Trp.
Steps if Trp is present (4)
- Trp (corepressor) binds to repressor protein 2. Undergoes conformational change 3. Binds to operator and blocks transcription 4. Operon repressed
Steps if Trp is absent (2)
- Repressor protein will not bind operator 2. Transcription of mRNA occurs
Transcriptional attenuation in Trp operon
2nd mechanism of control. Transcription initiated but terminated before completion due to hairpin formation in mRNA. Results in non-functional peptide which is degraded.
E.Coli rRNA operons
7 operons that synthesize rRNA for ribosome assembly
Stringent response
Regulation of each operon in response to amino acid starvation. Selective inhibition of rRNA and tRNA. Transcription for genes encoding enzymes needed for AA biosynthesis not inhibited.
ppGpp
Produced when uncharged tRNA binds to A site of ribosome. Synthesis mediated by stringent factor ReIA.
ReIA
Mediates synthesis of ppGpp. Elevated levels inhibit rRNA synthesis until amino acids available again.
Inducible system
Repressor binds to operator unless it’s already bound by an inducer (LAC operon)
Inducer
Molecule at the start of metabolic pathway goverened by enzymes encoded by operon genes (like lactose in LAC operon)
Repressible system
Repressor only binds to operator if it binds to a co-repressor (Trp in TRP operon) which is the end product of the metabolic pathway goverened by enzymes encoded by the operon genes
Transcriptional attenuation
Transcription initiated but terminated well before completion due to formation of hairpin structure
Translational control in prokaryotes
When excess of ribosomal proteins, bind to Shine-Dalgarno sequence on their own polycistronic mRNA, preventing ribosomes from binding
Regulation of r-protein operons
Self-regulated: operons for r-proteins inhibited by excess of their own protein products. R-proteins bind rRNA with higher affinity than mRNA. If low concentration of rRNA r-protein binds its’ own mRNA and inhibits translation.
3 common DNA binding motifs
- Helix-turn-helix 2. Leucine zipper 3. Zinc finger
Helix-turn-helix
2 alpha helices joined by short strand of AA which binds to DNA
Homeodomain
Helix-turn-helix made of 2 alpha helices
Leucine zipper
Dimerizes and generates adhesion forces in parallel alpha helices. Leu residue at every 7th position.
c-fos and c-jun
Leucine zippers important in regulating normal development
Zinc finger
Small and may coordinate one or more Zinc ions. Protrusions make contact with their target
Cys2His2
Zinc finger made of 2 ligands forming knuckle and 2 more forming C-terminus of a helix
Hormones
Regulate transcription by binding of the hormone-receptor hormone complex itself to the DNA or through binding of a protein activated in response to 2nd messenger
apo B in intestine
Full length version in the liver. In intestine, deamination causing Gln to change to stop codon. Shorter protein produced and incorporated into chymicrons (plasma lipoprotein particle which transports lipids from intestine to tissues).
elF-2
Phosphorylation (inhibition) regulates at the translational level in eukaryotes. Catalyzed by kinases in response to environment.
Intracellular receptors
Alter DNA-binding activity of transcriptional factors
Glutocorticoid receptor regulation
- Binding of cortisol (steroid hormone) to GR (its receptor) causes conformational change and becomes dimer uncovering zinc finger DNA binding domain 2. Steroid-receptor complex interacts with GRE (regulatory DNA sequences) 3. Hormone-receptor complex with coactivator proteins controls transcription
cAMP response element binding protein (CREB)
When phosphorylated it can bind to CRE and activate transcription
Phospho-(P)-CREB
Binds via leucine-zipper CRE resulting in transcription of target genes with CRE in their promoters
cAMP/CRE/CREB
Upregulates key enzymes of gluconeogenesis
Tamoxifen
Drug used to treat breast cancer by competitively inhibiting the estrogen receptor which reduces transcription of genes regulated by ER and reduces cancer cell growth
Estrogen
Activates the ER and increases proliferation rate
Regulation of transferrin receptor (TfR)
TfRs on cell surface bound to Tf are internalized and provide target cells with iron
Iron regulatory proteins (IRPs)
If low iron, IRPs bind to iron responsive elements (IREs) and stabilize mRNA for TfR synthesis. If high iron IRPs bind iron instead of IREs and mRNA for TfR degraded.
RNAi process
Mediated by microRNA. 1. Dicer endonuclease cleaves cytosolic trigger dsRNA 2. Guide strand of dsRNA associates with RISC and hybridizes with target mRNA 3. Slicer/Argonaute/Ago of RISC cleaves target mRNA
RISC
Either represses translation of target mRNA or cleaves target mRNA
Histone modifications
Covalently modified at NH2 terminal end by acetylation or phosphorylation
DNA hypermethylation
Silences gene expression
Transposase
Mediates movement of transposons and encoded by transposone itself
2 ways transposons work
- Direct: Cut out and inserted into new site 2. Replicative: Copied and the copy is inserted elsewhere while original remains in place
Retrotransposon
RNA intermedite for replicative transposition
