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Copy of AP Bio- Molecular Genetics 3: Regulation of Gene Expression

3 of 6 of my molecular genetics unit. Image Credits: Biology (Campbell) 9th edition, copyright Pearson 2011, & The Internet. Provided under the terms of a Creative Commons Attribution-NonCommercial-ShareAlike 3.0 Unported License. By David Knuffke.

Paul Saia

on 18 January 2013

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Transcript of Copy of AP Bio- Molecular Genetics 3: Regulation of Gene Expression

Regulation of Gene Expression Prokaryotes Eukaryotes In prokaryotes, transcription and translation happen simultaneously (they are "coupled")

Prokaryotes regulate gene expression (and therefore their metabolism) almost entirely by regulating transcription.

The lack of a nucleus makes this very efficient. Eukaryotes regulate gene expression (and therefore their metabolism) at every step of protein synthesis from pre-transcription to post-translation Refer to organized clusters of genes that all contribute to a particular metabolic task.

Prokaryotes only!!!

2 main types: Inducible and Repressible Operons: Inducible: Repressible: "Up Regulation": Precursor Enzyme 1 Enzyme 2 Enzyme 3 - - Gene 1 Gene 2 Gene 3 Gene 4 Gene 5 Product Inhibition of
enzyme activity Inhibition of
transcription Francois Jacob & Jacques Monod
Nobel Prize: 1965 For metabolic pathways that are usually "off".

Ex: The Lac Operon (digests lactose) For metabolic pathways that are usually "on".

Ex: The Trp Operon (synthesizes tryptophan) When Lactose is absent:
The repressor protein (made by the LacI gene) is able to attach to the operator (a region of the promoter)
RNA polymerase cannot transcribe the structural genes (LacZ, LacY and LacA) that the cell needs to be able to digest lactose, since it can not attach to the promoter.
This is how things remain in the cell as long as there is no lactose present. When Lactose is present:
The inducer molecule (allolactose, a form of lactose) binds to the repressor protein.
This changes the shape of the repressor protein so that it can not attach to the promoter.
RNA polymerase is then able to transcribe the structural genes that the cell needs to be able to digest lactose.
This is how things remain in the cell until lactose is digested When tryptophan is absent:
The repressor protein (made by the TrpR gene) is unable to attach to the operator
RNA polymerase can transcribe the structural genes (TrpE, TrpD, TrpC, TrpB, & TrpA) that the cell needs to be able to synthesize tryptophan.
This is how things remain in the cell as long as there is no tryptophan present. When Tryptohan is present:
The corepressor molecule (tryptophan) binds to the repressor protein.
This changes the shape of the repressor protein so that it can attach to the promoter.
RNA polymerase can not transcribe the structural genes that the cell uses to synthesize tryptophan.
This is how things remain in the cell until tryptophan is no longer present. A way to increase the rate of transcription of an operon

Ex: The CAP/cAMP System When Lactose is present and glucose is low:
Low glucose means the amount of cyclic AMP (cAMP) is high
cAMP binds to the Catabolite Activator Protein (CAP), activating it
The Activated cAMP/CAP complex increases the rate of transcription of the lac operon (and ~100 other catabolic operons), boosting the rate of transcription several fold, by increasing the affinity of RNA polymerase for the promoter When Glucose and Lactose are both present:
Normal glucose level means the amount of cyclic AMP (cAMP) is low
cAMP is not bound to CAP
CAP is inactive.
Very little lac structural gene transcription occurs. Levels of Control 1.DNA Access 2.Pre-Transcription 3.Post-Transcription A very small percentage of an organisms genome is protein coding DNA(only 1.5% in humans)

A small fraction of non protein coding DNA consists of genes for ribosomal and transfer RNA

Recent research has uncovered many forms of "non-coding" RNA (ncRNA) molecules in cells.

We'll look at one example, active in regulation of gene expression post-transcription and pre-translation 4.Pre-Translation 5.Post-Translation The
decoupling of


allows for
more control
points Only keep necessary genes accessible. In eukaryotes, DNA is "wound" around histone proteins.

The addition of acetyl groups (-CH2CH3) to histones causes them to become less tightly packed, allowing for access to the DNA.

Heterochromatin: more tightly packed DNA, unavailable for transcription.

Euchromatin: less tightly packed DNA, available for transcription. Recent research shows that even in interphase, the "loose" chromosomes occupy distinct nuclear regions.

"Transcription factories": Areas of the nucleus where active regions of different chromosomes interface. May be associated with common functions

Thousands of transcription factories in any nucleus Everything must be in place for transcription to begin. Eukaryotic genes interact with many "upstream" regulatory elements. These are DNA sequences that preceede a transcription unit that need to have specific proteins present for RNA polymerase to begin transcription. The proteins that mediate RNA Polymerase are known as "Transcription Factors": Control of transcription factor availability is one of the major ways that cells of a multicellular organism accomplish "differential gene expression", which in turn allows cells to "differentiate" to serve different functions in the organism. So many options lead to so many outcomes. Following transcription, 5' capping and 3' poly-adenylation are necessary for eukaryotic mRNA to remain functional and be transported to the cytoplasm for translation. "Alternative splicing" of exons allows for multiple functional (or non-functional) gene products to be made from a single primary transcript.

Anywhere from 75 - 100 percent of human genes with multiple exons probably undergo alternative splicing.

Shown here: the Troponin T gene produces 2 different mRNA sequences to produce 2 different gene products.

Not shown: A Drosophila gene that has enough exons to produce 19,000 different transcripts. Lots still left to learn RNA Interference (RNAi): Mediated by a group of tiny RNA molecules ("Micro RNA" or miRNA).

The miRNAs are produced from longer RNA's that fold back on themselves(forming "hairpins")

An enzyme cuts the hairpin from the primary miRNA transcript and then cleaves them into miRNA fragments by a an enzyme called "dicer"

The miRNAs complex with proteins.

Any mRNA with a sequence complementary to an miRNA is "tagged" with the miRNA/protein complex.

Tagged miRNA molecules are not translated, they are either degrade or translation is blocked

2006 Nobel Prize to Andrew Z. Fire and Craig C. Mello Don't let unnecessary proteins hang around. Ubiquitin (a protein so plentiful in all eukaryotic cells it is "ubiquitous"), will tag unnecessary proteins for transport to a proteasome. Inside the proteasome, the protein is broken down.

Nobel Prize: 2004 Aaron Ciechanover, Avram Hershko, Irwin Rose Proteasomes are abundant in eukaryotic cells (why?) Big Question Make sure you can: Polyribosomes demonstrating the coupling of transcription and translation in prokaryotes: Prokaryotic control of metabolism through control of transcription: How is gene expression controlled? Explain the structure and function of all expression control systems described in this presentation.

Compare and contrast the expression control systems utilized in prokaryotic and eukaryotic cells.

Relate prokaryotic expression control systems to prokaryotic cellular organization and feedback mechanisms.

Relate eukaryotic expression control systems to eukaryotic cellular organization and the decoupling of transcription and translation. RNAi Developmental Genetics Differentiation Pattern Formation Developmental Regulators How do cells with the same genetic information acquire different structures and functions? Cytoplasmic Determinants Maternal substances present in the cytoplasm of the egg cell that are unevenly distributed

These determinants direct different gene expression in subsequent generations of cells.

Important in early development Induction Chemicals are released by surrounding early embryonic cells that signal nearby cells to change their gene expression

Important in later development. Determination The regulatory events in a cell's genome lead to differentiation of structure and function.

Once a cell commits to a particular fate, it can not uncommit.

Determination preceeds differentiation. Cytoplasmic determinants and inductive signals both contribute to spatial organization of tissues and organs Positional Information The molecular cues that control pattern formation that tell a cell its location relative to body axes and adjacent cells.

Much of the work on genetic development was done in Drosophila. Lots of work, done over a long period of time.

We'll look at one specific example. Homeotic Genes Bicoid: An Example Bicoid is a protein that is present in a differential gradient in the unfertilized egg.

Cells that develop in a high concentration of bicoid become the anterior (head) of the organism.

Bicoid controls head development directly, so it is referred to as a "morphogen". Control pattern formation in the late embryo, larva and adult. First discovered in Drosophila by Edward B. Lewis, for which he won the Nobel Prize in 1995

Have since been discovered in all animal lineages.

Homeotic genes include a characteristic "box" of bases called a "homeobox", which is a sequence of DNA, coded to express a protein that will bind to other DNA and regulate the way it is expressed Clearly, something pretty important has to happen to get from (a) to (b) Simplified diagram of determination leading to differentiation in a muscle cell Morphological differences between normal (top) and bicoid mutant (bottom) fruit fly larvae Distribution of bicoid in normal fruit fly egg and early-stage embryo Antennapedia mutants have legs in the wrong places mutants have vestigial eyes in odd places It quickly becomes clear why these experiments are done in fruit flies Differences in homeobox expression patterns account for the different body plans of brine shrimp(above)and the grasshopper and lead directly to differences in segmentation Flourescence image showing 7 different homeobox expression patterns in a fruit fly embryo. Each color marks where a specific gene is expressed as mRNA Make Sure You Can: Development:
Explain the role of cytoplasmic determinants and induction in contributing to development.
Describe the relationship between determination and differentiation in a cell.
Explain how positional information is conveyed to the cells in a developing organism.
Explain the role of homeotic genes in contributing to the development of an animal. Big Questions How do genetics contribute to the development of an organism? Regulatin' Genes While vertebrates have more Homeotic genes than invertebrates, the sequences are highly conserved, which means there are very little changes in the gene in its millions of years; one change in the nucleotide sequence can mess up everything else
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