Unit 12

12.1 Overview of Gene Regulation

• Gene regulation conserves energy

Bacteria regulate genes in response to charges in environment

• E.coli carries genes that code for proteins that enables metabolization of lactose

  • B-galactosidase metabolizes lactose when E.coli is placed in an environment with lactose

  • Permease allows lactase to enter cell

Cell Differentiation

• Cell differentiation is an example of gene regulation

• Process by which cells become specialized into particular types with distinctive structure and functions

• Gene regulation is responsible for producing different cell types

Gene regulation in developmental stages

• Certain genes are expressed throughout developmental stages

  • different hormones are released during embryo stage, fetus stage, and from birth to adult

Gene Regulation occurs at different points

• Bacterial gene regulation

  • Transcription: most common during transcription, regulates amount of mRNA made from genes

    • transcriptional regulation is an efficient way to regulate genes

  • Translation: can control ability of mRNA translated into protein

  • Post translation: protein amount or function may be regulated

• Eukaryotic Gene expression

  • Transcription: common during transcription

  • RNA Modification: Eukaryotes modify mRNA transcripts differently than bacteria

  • Translation: another fairly common way of gene expression

12.2 Regulation of Transcription in Bacteria

• Regulation of transcription involves regulatory transcription factors

  • proteins that bind to regulatory sequences rate of transcription

• Repressors

  • binds to DNA and decrease the rate of transcription, known as negative control

• Activators

  • increase rate of transcription, known as positive control

• Operon

  • arrangement of 2 or more genes under a single promoter

    • lac operon in E.coli

• Gene is an operon results in production of polycistronic RNA

  • mRNA that codes more than one polypeptide

12.3 Regulation of Transcription in Eukaryotes: Rules of Transcription Factor

• Transcription regulation in eukaryotes have characteristics seen in bacteria

• Combinatorial Control

  • many factors control expression of any given gene

• Four steps

  • Activators stimulate ability of RNA polymerase to initiate transcription

  • repressors inhibit ability of transcriptions

  • Function of activators/repressors may be motivated in several ways

  • Activators are necessary to alter chromatin structure in region where gene is regulated

  • DNA methylation usually inhibits transcription

Eukaryotic Protein coding genes have a core promoter and regulatory elements

• Core Product: TATA box and transcriptional start site form the core promoter

  • Transcriptional start site is the place in the DNA and where transcription actually begins

  • TATA box determines precise starting point for transcription

    • results in lowest level transcription known as basal transcription

• Regulatory Elements: DNA segments that regulate eukaryotic genes

  • comes in two general steps

    • enhancers: play a role in RNA polymerase transcription

      • enhances rate of transcription

    • Silencers: prevents transcription of a given gene when expression isn’t needed

RNA polymerase II

• There are three forms of RNA polymerase (I,II, and III)

  • Requires 5 different proteins to initiate transcription

    • known as general transcription factors (GTFs)

• Preinitiation box: completed assembly of RNA polymerase II and GTFs at the TATA box

Activators and Repressors May Influence the functions of GTFs

• Three steps to start of eukaryotic translation

  • activators bind to an enhancer

    1. activator also interacts with coactivator

  • activator/coactivator complex improves ability of GTF

  • Function of TFIID is to promote the assembly of other GTFs

12.4 Regulation of Transcription in Eukaryotes

• region of chromatin containing a gene may be in closed formation

  • makes transcription difficult to impossible

• Open conformation is accessible to GTFs and RNA polymerase I

Transcription controlled by changes in chromatin structure

• Chromatin remodeling complex: complexes of proteins that alter chromatin structure

  • uses ATP to drive a change

• 3 effects possible

  • It may bind to chromatin changing locations of nucleosomes

  • May evict histone octamer from DNA, creating gaps where nucleosomes aren’t found

  • May remove histone and replace it with variant histone

Histone Modifications Affect Gene Transcription

• Histone acetyl transferase: an example of amino terminal tail undergoing modifications

• Effects of covalent modifications of histones

  • may influence interactions between DNA and histone proteins

  • Provides binding sites that are recognized by other proteins

    • histone code hypothesis

Eukaryotic Genes are flanked by nucleosome free regions

• Core promoter is found within nucleosome free region

• Recruiting appears to be critical

  • activator binds to an enhancer in the NFR

  • activator then recruits chromatin-remodeling complexes and histone modifying complexes in the region

  • Actions of chromatin-remodeling complexes histone-modification

  • Histones are evicted, partially displaced, or destabilized so that RNA polymerase II can pass

DNA Methylation Inhibits Gene Transcription

• DNA structure can be modified by covalent attachment of methyl groups

  • done via enzyme DNA methyltransferase

• DNA methylation inhibits transcription in two ways

  • may prevent activator from binding to an enhancer

  • altering chromatin structure

Facultative Heterochromatin is a way to silence genes

• Facultative heterochromatin: differs among different cells of body

  • thought to play a big role in silencing genes in a tissue specific manner

12.5 Regulation of RNA splicing and translation in eukaryotes

• Alternative splicing: a form of regulation that allows an organism to use the same gene to make different proteins

• This process is regulated

  • each cell type produces a unique set of splicing factors

Prevention of Ion Toxicity

• Iron Regulatory Protein: RNA binding protein that controls mRNA that codes ferritin

  • Low Iron: IRP binds to regulatory element known as Iron regulatory element

  • High Iron: When ferritin is needed, Iron binds to IRP, causing a conformational change to IRE, causing ferritin to be released