Chem 40 Reviewer

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  • Topic: Ribosome, DNA, RNA
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  • Published : January 13, 2013
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11.5 Transcription Regulation in Eukaryotes

Basal level
-Low level of transcription

Activators
-Gene specific transcription factors

Enhancers
-Regulatory sequences that augment transcription

Silencers
-Regulatory sequences that diminish transcription

Initiator
-RNA polymerase II
-Promoter, together with TATA (TFIID)

*Looping enhances transcription

Transcription-coupled Repair (TCR)
-DNA repair mechanism

Response Elements
-Enhancers that respond to metabolic factors
-Ex. Heat-shock element (HSE), glucocorticoid-response element (GRE), metal-response element (MRE), and cyclic-AMP-response element (CRE)

Heat-shock Response Element
-Elevated temperatures lead to the production of heat-shock transcription factors that activate the associated gene -Physiological signal: heat-shock
-Consensus Sequence: CNNGAANNTCCNNG, where N stands for any nucleotide -Transcription Factor: HSTF
-Size: 93 kDa

Glucocorticoid-Response Elements
-Glucocorticoid hormone binds to a steroid receptor, this becomes a transcription factor that will bind to GRE -Physiological Signal: Presence of glucocorticoids
-Consensus Sequence: TGGTACAAATGTTCT
-Transcription Factor: Glucocorticoid receptor
-Size: 94

Cyclic-AMP-Response Element
-Physiological Signal: cAMP-dependent activation of protein kinase A -Consensus Sequence: TGACGTCA
-Transcription Factors: CREB, CREM, ATF1
-Size: 43

Metal-Response Element
-Physiological Signal: Presence of Cadmium
-Consensus Sequence: CGNCCCGGNCNC

cAMP
-Involved in the control of prokaryotic operons via CAP proteins -When levels of cAMP rise, activity of cAMP-dependent protein kinase (Protein Kinase A) is stimulated

Cyclic-AMP
-Produced as a second messenger from several hormones (e.g. epinephrine and glucagon)

Protein Kinase A
-Phosphorylates many other proteins and enzymes inside the cell -Usually associated with switching cell to a catabolic mode -Phosphorylates protein called cyclic-AMP-response-element building protein (CREB) which binds to CR

Cyclic-AMP-Response-Element Building Protein
-Does not directly contact basal transcription machinery
-Activation requires another protein, CREB binding protein (CBP)

CREB-Binding Protein
-Binds to CREB
-Called a mediator or co-activator
-Major bridge to several different hormone signals

Genetic Anticipation
-Disease becoming worse in successive generations

11.6 Non-Coding RNAs

NcRNAs
-Linked to many processes, such as regular transcription, gene silencing, replication, RNA processing, RNA modification, translation, protein stabilization, and protein translocation -Ex. Micro RNAs and Small Interfering RNA

Micro RNAs (miRNA)
-About 22 nucleotides long
-Cut from longer hairpin shaped RNA by the enzyme Dicer
-Binds imperfectly to specific mRNAs and blocks their transcription -Ex. Lin-4 and let-7
-Plays a role in response to stress

Small Interfering RNAs (siRNA)
-Formed similarly as miRNAs
-RNA interference (RNAi) – the cut nucleotides, about 22-25 long, by the dicer binds to mRNA

RNA interference
-mRNA molecules bind to small pieces of nucleotides, targeting them for destruction -Molecular process that is the backbone of a protective mechanism called RNA Silencing

miRNA vs. siRNA
-miRNA prevents translation of mRNA
-siRNA causes destruction of mRNA

RNA Silencing
-Evolutionary conserved process that is analogous to the protection of our genomes by an immune system

11.7 Structural Motifs in DNA-Binding Proteins
*Most proteins that activate or inhibit transcription by RNA polymerase II have two functional domains: DNA-binding domain and transcription-activation domain

DNA-Binding Domains
-DNA binding proteins have domains that fall into three categories: helix-turn-helix (HTH), zinc fingers, and basic-region leucine zipper (bZIP)

Helix-Turn-Helix Motifs
-Common feature seen in proteins that bind to DNA is...
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