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Last Class. 1. Transcription 2. RNA Modification and Splicing 3. RNA transportation 4. Translation . Quality control of translation in bacteria Rescue the incomplete mRNA process and add labels for proteases. Folding of the proteins Is required before functional.

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Presentation Transcript
slide1
Last Class
  • 1. Transcription
  • 2. RNA Modification and Splicing
  • 3. RNA transportation
  • 4. Translation
slide2
Quality control of translation in bacteria

Rescue the incomplete mRNA process and add labels for proteases

slide4
Folding of the proteins

Is required before functional

slide6
Protein Folding Pathway

Molecular Chaperone

slide7
An example of molecular chaperone functions

Hsp70, early binding to proteins after synthesis

summary
Summary
  • RNA translation (Protein synthesis), tRNA, ribosome, start codon, stop codon
  • Protein folding, molecular chaperones
  • Proteasomes, ubiquitin, ubiqutin ligase
slide16
Control of Gene Expression
  • 1. DNA-Protein Interaction
  • 2. Transcription Regulation
  • 3. Post-transcriptional Regulation
slide17
Neuron and lymphocyte

Different morphology, same genome

slide19
Regulation at DNA levels

Double helix Structure

slide20
The outer surface difference of base pairs without opening the double helix

Hydrogen bond donor: blue

Hydrogen bond acceptor: red

Hydrogen bond: pink

Methyl group: yellow

slide22
One typical contact of Protein and DNA interface

In general, many of them will form between a protein and a DNA

slide23
DNA-Protein Interaction
  • Different protein motifs binding to DNA: Helix-turn-Helix motif; the homeodomain; leucine zipper; helix-loop-helix; zinc finger
  • Dimerization approach
  • Biotechnology to identify protein and DNA sequence interacting each other.
slide24
Helix-turn-Helix

C-terminal binds to major groove, N-terminal helps to position the complex, discovered in Bacteria

slide26
Zinc Finger Motifs

Utilizing a zinc in the center

An alpha helix and two beta sheet

slide29
A dimer of the zinc finger domain of the glucocorticoid receptor (belonging to intracellular receptor family) bound to its specific DNA sequence

Zinc atoms stabilizing DNA-binding Helix and dimerization interface

slide30
Beta sheets can also recognize DNA sequence

(bacterial met repressor binding to s-adenosyl methionine)

slide31
Leucine Zipper Dimer

Same motif mediating both DNA binding and Protein dimerization

(yeast Gcn4 protein)

slide38
Gel-mobility shift assay

Can identify the sizes of proteins associated with the desired DNA fragment

slide40
DNA affinity Chromatography

After obtain the protein, run mass spec, identify aa sequence, check genome, find gene sequence

slide42
Chromatin Immunoprecipitation

In vivo genes bound to a known protein

summary43
Summary
  • Helix-turn-Helix, homeodomain, leucine zipper, helix-loop-helix, zinc-finger motif
  • Homodimer and heterodimer
  • Techniques to identify gene sequences bound to a known protein (DNA affinity chromatography) or proteins bound to known sequences (gel mobility shift)
slide45
Tryptophan Gene Regulation (Negative control)

Operon: genes adjacent to each other and are transcribed from a single promoter

slide49
Combinatory Regulation of Lac Operon

CAP: catabolite activator protein; breakdown of lactose when glucose is low and lactose is present

slide50
The difference of Regulatory system in eucaryotes and bacteria
  • Enhancers from far distance over promoter regions
  • Transcription factors
  • Chromatin structure
slide52
Regulation of an eucaryotic gene

TFs are similar, gene regulatory proteins could be very different for different gene regulations

slide53
Functional Domain of gene activation protein

1. Activation domain and 2. DNA binding domain

slide55
Gene engineering revealed the function of gene activation protein

Directly fuse the mediator protein to enhancer binding domain, omitting activator domain, similar enhancement is observed

slide56
Gene regulatory proteins help the recruitment and assembly of transcription machinery

(General model)

slide57
Gene activator proteins recruit

Chromatin modulation proteins to induce transcription

slide58
Two mechanisms of histone acetylation in gene regulation
  • Histone acetylation further attract activator proteins
  • Histone acetylation directly attract TFs
slide59
Synergistic Regulation

Transcription synergy

slide66
Gene regulatory proteins can affect transcription process at different steps

The order of process may be different for different genes

summary67

Summary

Gene activation or repression proteins

DNA as a spacer and distant regulation

Chromatin modulation, TF assembly, polymerase recruitment

combinatory regulations

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