Chapter 14 learning outcomes

Describe the organization of an operon and its advantage in bacteria and how this contrasts with eukaryotic gene organization.

An operon is a set of two or more genes in bacteria that are under the transcriptional control of a single promotor. The two or more genes that are being transcribed by a single promotor are grouped together which allows for the bacteria to coordinately regulate a group of genes that encode proteins whose functions are used in a common pathway. For eukaryotic cells, genes are organized on chromosomes. There are not one transcriptional control for multiple genes, each gene is transcribed independently. Although more than one gene can be transcribed at the same time there is not one transcribing factor.

Identify where gene regulation can occur in the pathway of gene expression for bacteria and eukaryotes

Bacteria: most commonly occurs at the level of transcription (how much mRNA is made from genes). It is efficient because cells avoid wasting energy when the product is not needed. Gene regulation also occurs at translation and post translation. Eukaryotes: Gene regulation takes place during transcription, RNA modification, translation, and post-translation.

Explain how an open (accessible) or closed (inaccessible) chromosomal conformation affects gene expression

Closed conformation is chromatin that cannot be transcribed into RNA. An example of this is Methylation of DNA. It occurs at regions of CpGs where DNA becomes more tightly wrapped. This makes it NOT available for RNA polymerase to bind Open conformation is chromatin that can be transcribed into RNA. Histone modifications aka "Histone Code". DNA becomes more loosely wrapped and is available for RNA polymerase to bind

Outline the process of alternative splicing and how it increases protein diversity

Different mRNA molecules are produced from the same primary transcript, depending on which RNA segments are treated as exons and which as introns. Sometimes have multiple introns. One cell will splice the mRNA one way and another cell may splice the mRNA a different way. This gives rise to different proteins

Compare and contrast how activators, repressors, and mediator play a role in gene regulation using response elements including silencers and enhancers

Enhancer regions are binding sequences, or sites, for transcription factors. When a DNA-bending protein binds to an enhancer, the shape of the DNA changes. This shape change allows the interaction between the activators bound to the enhancers and the transcription factors bound to the promoter region and the RNA polymerase to occur. Transcriptional repressors can bind to promoter or enhancer regions and block transcription. Like the transcriptional activators, repressors respond to external stimuli to prevent the binding of activating transcription factors. The main function of mediator complexes is to transmit signals from the transcription factors to the polymerase.

Explain the conditions under which operons are inducible or repressible.

For the lac operon, it is inducible when lactose is present and is repressed when lactose is absent. The Trp operon is repressed when there are high levels of the amino acid tryptophan.

Discuss the various ways that organisms benefit from gene regulation.

It conserves energy, ensures that genes are expressed in the appropriate cell types and at the correct stage of development, cell differentiation,

Be able to identify the lac or top operon as examples of negative and positive control.

Lac operon: High lactose, high glucose: negative control (low transcription) High lactose, low glucose: positive control (high transcription) Low lactose, high glucose: negative control (transcription inhibited) Low lactose, low glucose: negative control (transcription inhibited) Trp operon: Low tryptophan: positive control (transcription occurs) High tryptophan: negative control (transcription is inhibited)

Describe how RNA polymerase and general transcription factors initiate transcription at the core promoter.

RNA polymerase can attach to the promoter only with the help of proteins called basal (general) transcription factors. They are part of the cell's core transcription toolkit, needed for the transcription of any gene. A typical transcription factor binds to DNA at a certain target sequence. Once it's bound, the transcription factor makes it either harder or easier for RNA polymerase to bind to the promoter of the gene. Some transcription factors activate transcription. Other transcription factors repress transcription.

Explain how regulatory transcription factors (activators and repressors) and small effector molecules are involved in the regulation of transcription

Regulatory transcription factors, a protein that binds to DNA, usually in the vicinity of a promotor and affects the rate of transcription of one or more nearby genes. A repressor is a transcription factor that binds to DNA to inhibit transcription (negative control), where an activator is a transcription factor that binds to DNA to increase the rate of transcription (positive control). A small effector molecule is a molecule that affects gene transcription by binding to a regulatory transcription factor, causing a conformation change in the protein. This change in the protein determines if it can bind to the DNA. If the small effector molecule is not present in the cytoplasm, the repressor can bind to DNA and inhibit transcription. If the small effector molecule is present it will bind to the repressor and inhibit the ability of the protein to bind to DNA, allowing transcription to occur.

Identify the core components of eukaryotic gene promoter.

TATA box: a 5'-TATAAA-3' sequence, is usually about 25 base pairs upstream from the transcriptional start site, it indicates where a genetic sequence can be read and decoded. Transcriptional start site: the place where DNA transcription actually begins

Explain the concept of combinatorial control

the phenomenon whereby combination of many factors determines the expression of any given gene