Bio 111 online Ch. 13

Describe how Eukaryotic genes are flanked by nucleosome free region and how nucleosomes are altered during gene transcription

ATP dependent chromatin remodeling complexes which are a group of proteins that alert chromatin structure. Such complex use energy from ATP hydrolysis to drive a change in the locations and / or compositions of nucleosomes of, thereby making the DNA more or less amenable to transcription. Therefore chromatin remodeling is important for both activation and repression for transcription. This may involve a shift of the relative positions of a few nucleosomes or a change in the relative spacing of nucleosomes or a long stretch of DNA. A second effect is that remodeling complexes may evict histone octamers from the DNA, thereby creating gaps where nucleosomes are not found.

Explain how regulatory transcription factors and small effector molecules fare involved in the regulation of transcription.

regulation of the transcription involves the action of regulatory transcription factors in binding to regulatory sequences in the DNA in the vicinity of a promoter and affect the rate of transcription of one or more nearby genes. Repressors are called negative control and Activators are called positive control. Small effector molecules often play a critical role in transcriptional regulation. A small effector molecule exerts its effects by binding to a regulatory transcription factor.

Compare and contrast how activators , coactivators, repressors, TFIID and mediator play a role in gene regulation

Activator and repressors commonly regulate the function of RNA polymerase II bind to GTFs or mediator. The function of TFIID is to recognize the TATA box and begin the assembly process An activator may recruit TFIID a to the TATA box, thereby promoting the assembly of GTFs and RNA polymerase II into the preinitiation. A second way that regulatory transcription factors control RNA polymerase II is via mediator. An activator also interacts with a coactivator which does not directly bind to the DNA itself. the activator co activator complex stimulates the funcrtoin fo mediator , thereby causing RNA polymersase II to precoeeed to the elongation phase of tanscirpint more quickly

Discuss the various ways that organism benefit from gene regulation

Bacteria Regulate genes to respond to changes in their environment.Eukaryotic Gene Regulation produces different cell types in a single organism.Eukaryotic Gene Regulation enables multicellular organism to proceed through developmental stages.Gene Regulation occurs at different points in the process from DNA to Protein.

Explain how DNA methylation affects transcription

DNA structure can be modified by the covalent attachment of methyl groups by an enzyme called DNA metylase. this modification termed DNA methylation is common in some eukaryotic species but not all. For example, yeast and Drophsophilia have little or no detectable methylation of the DNA whereas DNA methylation in vertebrates and plants is relatively abundant. Methylation is also associated with an inheritance pattern called epigenetic in which gene expression is altered in a way that is fixed during an induvidual's lifetime.

inducible operon

Is the lac operon

Analyze the results of the experiments of Jacob, Monod, and Pardee

Lacl gene encodes an enzyme that degrades an internal inducer of the lac operon Lacl mutation made it unnecessary for cells to be exposed to lactose for induction. Their experiments defined cis-acting element. The lac operator is the example of a cis acting element. A trans effect to form of gene regulation that can occur even though two DNA segments are no physically adjacent. The reaction of the lac repressor the lac operon is a trans effect. A cis-effect is mediate by a cis acting element that binds regulatory proteins.

Explain the concept fo combinatorial control

Msot eukaryotinc genes, parilfuclary thos found in multicellular species are regulated by many factors. Combinal control is the combination of many factors determining the expression fo any given gene. At eh elvel of transciptoin, ocommon factor that onctroibute to combinatorial control.

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

RNA polymerase II transcribe structural genes that encode proteins. Researchers have identified three types of proteins that play a role in initiation transcription at the the core promoter of structural genes. RNA polymerase II and GTFs must come together a the TATA box of the core promoter so transcription can be initiated A series of interaction occurs between these proteins so RNA polymerase II can bind to the DNA. The completed assembly of RNA polymerase II and GTFs a the TATA box is known as the preinitiation complex.

Cell differentiation

The process by which cells become specialized into particular types.

Discuss where gene expression and gene regulation meet

The regulation of gene expression can occur at any of the steps that are needed to produces a functional protein. Gene regulation most commonly occurs at the level of transcription, which means that bacteria regulate how much mRNA is made form genes.

corepressor

Tryptophan acts as a small molecule bind to the trp repressor protein

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

When a pre mRNA has multiple introns and exons, splicing may occur in more than one-way resulting the production of two or more different polypeptides. Alternative splicing is a form of gene regulation that allows an organism to sue the same gene to make different proteins at different stages of development, in different cells types and /or in response to a change in the environmental conditons. An advantage is that two or more poly peptides can be derived form a single gene thereby increasing the size of the proteomes while minimizing the sized of the genome.

Describe how the trp operon is under negative control

Which encodes enzyme s that are reuire to make the amino acid tryptophan a building block of cellular proteins. TRPe, TRPd, TRPc, TRPb AND TRP genes encode enzyme s that are involved in pathways that leads tryptophan synthesis. The trp operon is regulated by a repressor protein that I encoded by the trp R gene. The binding of the trp operator site inhibits transcription.

cis- acting element

a DNA segment that must be adjacent to the genes that it regulates

trans-effect

a form of gene regulation that can occur even though two DNA segments are not physically adjacent.

operator

a regulatory sequence in the DNA. The sequences of bases at the lacOs site provides a binds for a repressor protein.

CAP site

a regulatory sequence recognized by an activator protein.

Inducer

a small effector molecule that increases the rate of transcription.

Describe the organization of the lac operon and how it is under the negative and positive control

allolactose is important in the regulation of the lac opereon.it contains a promoter, lacP that is used to transcribe three structural genes:lacZ, lacY, and lacA. LacZ encodes-galactosidase which is an enzyme that breaks down lactose. Lac promoter are two regulatory sequences designated the operator and the CASP site. The operator is a regulatory sequence in the DNA. The lac repressor is a negetive control.

Mediator

composed of many proteins that bind to each other to form an elliptically shaped complex that partially wraps. around RNA polymerase II and the GTFs.

cis effect

mediated by a cis-acting element that binds regulatory proteins., whereas a trans-effects is mediated by gene that encodes diffusible regulatory proteins

Small effector molecule

often play a critical orle in trasniptoinal regulation . It exerts its effects by binding to a regulatory transciptoin factor and causing a conformational chagnege in the protein.

operon

structural genes are sometimes clustered together and under the transcriptional control of a single promoter.

lac operon

that contains the genes for the proteins that allow it to metabolize lactose. The genome of E Coli carries this

proteomes

the collection of proteins

Lac repressor

the repressor proteins is important in the regulation of lac operon

polycistronic mRNA

the transcription of genes occurs as a single unit and results in its production.

genome

they carry genes the same set of genes.

repressible operon

trp operon is considered because its small effector molecule, namely tryptophan, represses transcription.