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Flashcards in Gene regulation Deck (61):
1

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

2

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.

3

General transcription factors

Minimal requirement of recognition by promoter, required by all mRNA genes. Transcription can occur alone with these factors.

4

Specific transcription factors

Required for maximal level of transcription or for induction.

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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.

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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.

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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.

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Lac Y

Makes lactose-permease which allows lactose to move across membrane

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Lac A

Makes thiogalactotransacetylase

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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.

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Lac O

Operator region where RNA polymerase must go through to transcribe

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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

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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.

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Adenylate cyclase

Enzyme which catalyzes reaction of ATP to cAMP which is inhibited in the presence of glucose.

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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)

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Enhancers

Cis-acting DNA sequences which increase rate of trascription

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Activators

Proteins bound by transcription factors to regulate assembly of initiation transcription complex

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Repressors

Bind to promoter or regulatory sequence to prevent transcription. Repressor genes are near the operon.

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If glucose present and lactose absent

Lac operon off

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If glucose absent and lactose present

Lac operon on

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If glucose present and lactose present

Lac operon off

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Tryptophan operon of E.Coli

Encodes for enzymes needed to synthesize Trp and regulated by Trp.

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Steps if Trp is present (4)

1. Trp (corepressor) binds to repressor protein 2. Undergoes conformational change 3. Binds to operator and blocks transcription 4. Operon repressed

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Steps if Trp is absent (2)

1. Repressor protein will not bind operator 2. Transcription of mRNA occurs

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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.

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E.Coli rRNA operons

7 operons that synthesize rRNA for ribosome assembly

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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.

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ppGpp

Produced when uncharged tRNA binds to A site of ribosome. Synthesis mediated by stringent factor ReIA.

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ReIA

Mediates synthesis of ppGpp. Elevated levels inhibit rRNA synthesis until amino acids available again.

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Inducible system

Repressor binds to operator unless it's already bound by an inducer (LAC operon)

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Inducer

Molecule at the start of metabolic pathway goverened by enzymes encoded by operon genes (like lactose in LAC operon)

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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

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Transcriptional attenuation

Transcription initiated but terminated well before completion due to formation of hairpin structure

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Translational control in prokaryotes

When excess of ribosomal proteins, bind to Shine-Dalgarno sequence on their own polycistronic mRNA, preventing ribosomes from binding

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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.

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3 common DNA binding motifs

1. Helix-turn-helix 2. Leucine zipper 3. Zinc finger

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Helix-turn-helix

2 alpha helices joined by short strand of AA which binds to DNA

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Homeodomain

Helix-turn-helix made of 2 alpha helices

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Leucine zipper

Dimerizes and generates adhesion forces in parallel alpha helices. Leu residue at every 7th position.

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c-fos and c-jun

Leucine zippers important in regulating normal development

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Zinc finger

Small and may coordinate one or more Zinc ions. Protrusions make contact with their target

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Cys2His2

Zinc finger made of 2 ligands forming knuckle and 2 more forming C-terminus of a helix

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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

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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).

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elF-2

Phosphorylation (inhibition) regulates at the translational level in eukaryotes. Catalyzed by kinases in response to environment.

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Intracellular receptors

Alter DNA-binding activity of transcriptional factors

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Glutocorticoid receptor regulation

1. 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

48

cAMP response element binding protein (CREB)

When phosphorylated it can bind to CRE and activate transcription

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Phospho-(P)-CREB

Binds via leucine-zipper CRE resulting in transcription of target genes with CRE in their promoters

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cAMP/CRE/CREB

Upregulates key enzymes of gluconeogenesis

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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

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Estrogen

Activates the ER and increases proliferation rate

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Regulation of transferrin receptor (TfR)

TfRs on cell surface bound to Tf are internalized and provide target cells with iron

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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.

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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

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RISC

Either represses translation of target mRNA or cleaves target mRNA

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Histone modifications

Covalently modified at NH2 terminal end by acetylation or phosphorylation

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DNA hypermethylation

Silences gene expression

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Transposase

Mediates movement of transposons and encoded by transposone itself

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2 ways transposons work

1. Direct: Cut out and inserted into new site 2. Replicative: Copied and the copy is inserted elsewhere while original remains in place

61

Retrotransposon

RNA intermedite for replicative transposition