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Flashcards in BC 20 Control of Gene Expression Deck (22):

how can we control gene expression

1. Transcriptional
2. RNA processing
3. RNA transport control
4. translational control
5. mRNA degradation control
6. protein activity control

refer to first few slides for any you cant define


Transcription Regulation

Cis Elements: DNA sequences where the transcription factors bind.

Trans acting elements gene regulatory proteins that recognize cis elements

Upsteam promoter elements: the promoter region os where the RNA pol binds to and beings its RNA synth. tata in human or -10 -35 in bac



functional unit under the control of a single promoter

includes regulatory (promoter/operator) and structural genes

Bac: polycistronic-group of proteins in same frame required for same metabolic fxn, one message, multiple ORFs- SAME biochemical pathway


lac operon

Bacterial operon

glucose used for energy, lactose provides enery source broken down by B-galactosidase to glucose and galactose

-lac operon drives group of proteins involved in this pathway.

inducible system: always off unless lactose (inducer) present


lac operon positive control

low/no exogenous glucose

1. adenylatecyclase is activated at low glucose
2. cAMP concentration increases
3. cAMP binds to catabolite activator protein (CAP)
4. complex binds at CAP site
5. CAP interacts with RNA pol, makes promoter more accessible
6. bends DNA to enhance RNA pol binding

-high levels of exogenous glucose will repress gene expression by lowering the cAMP levels, preventing cap fro binding


lac operon negative control

-transcription of the operon is controlled by o (a regulatory sequence)

-lac repressor is encoded by I gene

-I gene is constitutively expressed

in ABSENCE of lactose
-lac repressor binds to operator preventing transcription from lac operon
-no transcription, neg control

in PRESENCE of lactose (inducer)
-lactose binds repressor and removes repressor from binding to the operator.

for lac operon to express must not only block repressor but also positive effect (CAP)


Euk Gene transcriptional regulation

3 RNA pols.
-RNApol I for RNA's
-RNApol II for protein coding genes
-RNApol III for tRNA, rRNA, snRNA

-all multiunit complexes and regulated by a variety of GTF



upstream promoter element for RNApolII to bind



Cis acting elements to enhance expression
-activators bind to enhancers and regulate GE
-can only act on CIS linked promoters. (on same chromosome)

1. upstream or downstream
2. can be KB away
4. distance and position independent


DNA looping

enhancer function

activators bind to enhancer sequences and DNA loops for activator to complex with various TF's


Tissue specific

DNA biding protiens only work in specific tissues. IG heavy chain enhancer, NINE different reg proteins.
-sum effect between these, not all bound at once necessarity



trans acting elements

two domains, binding (sequence specific) and activating domain

Four binding domains


Zinc Finger Binding domain

zinc ions fold loops that bind DNA

zinc binds cysteine, cysteine, histidine, histidine

steroid hormone receptors function int this way.
-regulate GE in response to hormones such as est and test
-cis element =hormons response element


Leucine Zipper and Helix Loop Helix

both have dna binding domain formed by dimerization of the PP chains

-CREB -cyclic AMP response element binding protein

HLH: myc TF- Ebox

Different members of each family can dimerize with another- heterodimerizatio, increases possible number of recognition sequences


Helix Tun Helix

one helix makes most of contact with DNA other helix lays across it to stabilize it.

HOX proteins
-embryonic dev
-cis element :homeobox
-fused fingers
-arms out of eyes drosophila


Pit-1 clinical note

GH is produced by pituitary gland and is needed for normal growth and development. 1/5000-1/10000 newborns deficient in GH leading to pituitary dwarfs

-mutation in Pit 1, which encodes a homeodomain containing trans factor.
-Pit 1 is TF required for transcription of GH and prolactin genes and pituitary dev. can be treated with GH injections


Activation Domains

allow TF's to
-bind to other rans factors
-interact with RNA pol to stabilize initiation complex
-interact with coactivators to modify chromatin structure

-synergistically stimulate transcription


Chromatin Remodeling

making DNA more or less accessible

-global regulation
-trans elong and term
-DNA repair/recomb/repl
-trans active and repre


Transcriptional Repressors

bind to specific DNA sequences and inhibit transcription
-share same DNA binding as activators
-allow for tissue specific activity

4 ways:
1. compete with activators for same DNA reg sequence
2. inhibit transcription by protein protein interaction after binding DNA
3. Direct repression
4. indirect repression


Genomic Imprinting

two copies of alleles present.

-oneo f the alleles should be turned off
-imprinting is when they are turned off

-improper imprinting or chromosomal segregation can result in two active alleles, sever developmental abnormalities and cancer

Angelman syndrome



Regulation of translation

silence expression of target genes

natural phenomenon

targets to make dsRNA
-causes cleavage and degredation of site
-blocks translation

short about 20bp

1. long dsRNA hairpin,
2. DICER cutes into short miRNA
3. RISC complex binds to target mRNA
4. RISC binds TARGET RNA with RNAi

siRNA-wet aged macular degeneration AMD
-siRNA against VEGF administered directly to eye to stop blood vessel growth, improves vision



overall translation regulation, not just one gene
-response to cell stress

eIF2 can be phosphorylated by kinases, blocks exchange of GDP for GTP, inhibits initiation

-seen in reticulocytes for synthesis of hemoglobin

-if heme is available, then the exchange fo bound GDP for GTP is able to proceed and translation occurs