Biochemistry Online: An Approach Based on Chemical Logic

Biochemistry Online

CHAPTER 5 - BINDING

D:  BINDING AND THE
CONTROL OF GENE TRANSCRIPTION

BIOCHEMISTRY - DR. JAKUBOWSKI

Last Updated: 03/30/16

Learning Goals/Objectives for Chapter 5D:  After class and this reading, students will be able to

  • describe general mechanisms of how a gene for a given protein might be negatively and positively regulated at the level of gene transcription;
  • describe the structure/function/role of promoters, response elements, RNA polymerase, transcription factors, nucleosomes, histone proteins, epigenetic modifications of DNA in gene transcription;
  • explain the differences (structural, Kds) between specific and nonspecific binding of a ligand to a macromolecule, at the structural level;
  • describe the structural features of both proteins and DNA that result in specific and nonspecific binding;
  • describe and give examples of how post-translational modifications of proteins and epigenetic modifications of DNA can alter gene expression;
  • explain how the apparent Kd for a protein binding to DNA can be altered by the presence of another protein bound to DNA at a proximal site
  • describe the basis of RNA interference in gene expression

D1. Introduction to Transcription

D2.  Control of Transcription in Prokaryotes

D3.  Control of Gene Transcription in Eukaryotes

D4.  DNA Binding Sites

D5.  DNA Binding Proteins

D6.  Studying the Interactome

D7.  Phosphorylation and Control of Gene Expression

D8.  Classification of Transcription Factors

D9.  Cooperative Binding of Proteins to DNA

D10.  Epigenetic Control of DNA - Methylation

D11.  Chromatin Remodeling and Gene Expression

D12.  Acetylation and Methylation of Histones

D13.  Control of Gene Expression by RNA

D14.  Recognition of viral  and bacterial DNA by the immune system

D15.  ENCODE:  Encyclopedia of DNA Elements

D16.  Eukaryotic Species Complexity

D17.  Gene Expression Differences Between Humans and Chimpanzees

D18.  Links and References

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