3_4 Genetic Regulation

What are (a)barr bodies? (b) How are they examples of heterochromatin & chromatin structure regulation?

(a) an extra X chromosome that becomes an inactive mass in males and females. (b)the genes contained within barr bodies do not get expressed because the chromatin is highly condensed.

(a) The trp Operon is what kind of operon? (b)Explain how it works

(a) repressible operon; (b) If tryptophan is not present, structural genes are transcribed and the enzymes needed to synthesize tryptophan are produced. When tryptophan becomes present in abundance, these enzymes are no longer needed by the cell. This is the moment when the trp Operon is activated. tryptophan binds to an inactive repressor protein, thus activating it. The now active repressor bind to the operator and prevents transcription of structural genes. [Caveat...it should be noted that the regulator gene synthesizes inactive repressor protein whether tryptophan is absent or present. However when tryptophan[the corepressor] is present, it binds to the repressor, thus activating said repressor, and allowing it to perform its inhibitory function.]

How does posttranscriptional control work?

Post transcriptional control works in one of two ways: (1) The pre-mRNA strand can be modified during processing; (2) The speed at which mRNA leaves the nucleus is altered. The first control mechanism[mRNA modification] is enacted via alternative RNA splicing. In alternative RNA splicing, multiple proteins are produced from the same mRNA strand. A spliceosome selectively cuts up a pre-mRNA strand by selecting to remove specific exons with introns. If an exon between introns also gets removed, the same sequence of mRNA will code for different proteins. Example of alternative splicing include the differences in hypothalamic and thyroid produced calcitonin. More examples include differences in neurotransmitters, muscle regulatory proteins & antibodies in other cells. As for the second posttranscriptional control mechanism [mRNA exit speed], not much is known about it. However, we do have evidence that indicates mRNA exits the nucleus at different speeds.

positive control [gene regulation]

control that involves the use of an activator protein to turn transcription[or operon possibly on]

translational control

one of five eukaryotic mechanisms for controlling genetic expression[in the cytoplasm] that controls when translation begins and how long it continues; Any changes to the 5' G cap or the 3' poly A tail can affect the length of translation; It has recently been discovered that introns[using microRNA] may also be involved in affecting the life span of mRNA; translational control is one of two processes that occurs in the cytoplasm;

DNA unpacking

the process where the chromatin remodeling complex pushes aside the histone portion of a nucleosome so that DNA polymerase can attach to the DNA promoter and transcription can begin.

What is the difference between the histones of heterochromatin & euchromatin?

Heterochromatin nucleosomes have histones with methyl groups on their tails; Euchromatin nucleosomes have acetyl (-COCH3 ) groups on their tails.

In what situation is CAP control of the lac Operon used?

If both glucose and lactose are present, bacteria prefers to breakdown glucose. When glucose is absent CAP turns on transcription of the lac Operon's structural genes.

What happens when euchromatin genetically activates?

In a process commonly referred to as unpacking, a structure called "chromatin remodeling complex" pushes aside the histone portion of a nucleosome so DNA can be transcribed. Chromatin remodeling complex also functions in changing heterochromatin into euchromatin.

Name & classify the (a)5 mechanisms of eukaryotic gene regulation. (b) Which is most critical?

(a) [1] chromatin structure [2] transcriptional control [3] post-transcriptional control [4] translational control [5]post-translational control; first 3 control gene activity in the nucleus & the last two control mechanism occur in the cytoplasm; (b)The most critical control mechanism is transcriptional control.

(a) The lac Operon is what type of operon? (b)Explain how it works...

(a)inducible operon. (b) If lactose is not present in a bacterial cell, there is no need to express genes that code enzymes that catabolize it. But when glucose is not available and lactose is, structural genes are transcribed and the enzymes needed to catabolize lactose are produced. The regulator gene of the lac Operon codes for an active repressor. This repressor protein is ordinarily bound to the operator site and prevents transcription. [NOTE: you should note one difference between the lac & trp operons is that the trp Operon's regulator gene codes for an inactive repressor while the lac Operon's codes for an active repressor.] When lactose [or more specifically allolactose.] is present in the cell, it binds to the repressor thus deactivating it. The deactivation of the repressor now allows RNA polymerase to bind to the promoter,carry out transcription and, subsequently, synthesize the catabolic lactose enzymes. Lactose is called an inducer because it brings about the expression of the gene.

operon model

A model used to explain gene regulation in prokaryotes;

repressor

A protein that binds to an operator to prevent the transcription of DNA; also called repressor protein;

Transcription factors, activators and repressors are always present in the nucleus but they most likely have to be activated in some way before they bind to DNA. We don't know exactly how they are activated but what is the current prevailing thought?

A signaling/regulatory pathway that may use kinases[enzymes that phosphorylate] or phosphatases[enzymes that remove phosphate groups] to activate.

inducible operon

An operon that initially is off [does not undergo transcription] but then gets turned on when the repressor protein is removed[deactivated] by the binding of an inducer. The lac Operon is an example of an inducible operon; inducible operons are usually involved in catabolic processes.

Explain CAP control of the lac operon....

CAP control involves the use of a molecule called cyclic AMP(cAMP). [1]When glucose is absent, cAMP accumulates in the cell. [2] A molecule of cAMP then binds to CAP, thus activating CAP to bind to DNA at the CAP binding site, adjacent to the lac promoter site. [3] When CAP binds to DNA, DNA bends exposing its promoter site to RNA polymerase. Only then does transcription occur. Now lets consider what happens when glucose is present. If present, only a small amount of cAMP is found in the cell. The CAP protein remains inactive and the lactose operon does not function maximally.

How does chromatin structure affect gene expression?

Chromatin exists in one of two genetic states. It can occur as genetically active euchromatin or genetically inactive heterochromatin. Euchromatin appears as a loosely coiled, diffuse and lightly colored "string of beads." Because it is loosely coiled RNA polymerase and other factors needed for transcription can access the genes contained on DNA. Heterochromatin is a highly compacted, darkly stained "string of beads". It is considered genetically inactive because the DNA is so highly compacted that RNA polymerase cannot find or attach to DNA to transcribe genes. While one may infer that chromatin exist in one form or the other, the truth is that most cells exhibit both levels of compaction simultaneously. It just depends on which portion of the DNA strand is used more often.

transcription factors

DNA binding proteins that control transcription; groupings of transcription factors locate and bind to a single promoter [just adjacent to a gene]. They then attract and bind RNA polymerase. Transcription still may not occur until an activator or repressor binds initiating their own specific transcriptional effect.

transcription activators

DNA binding proteins the speed up transcription;

transposons

DNA sequences that move between chromosomes & shut down genes;

Briefly describe why E. coli needs the trp operon...

E. Coli uses the trp operon to turn off the anabolic pathway that synthesizes tryptophan. If tryptophan is already present in E. coli, there is no reason to continue synthesizing more. E. coli uses trp operon to stop tryptophan production.

What are the functions of the chromatin remodeling complex?

In euchromatin it pushes aside the histones so DNA can be transcribed. This process is called DNA unpacking. The complex also affects gene expression by adding acetyl or methyl groups to histone tails.

What regulates whether a specific segment of chromatin is in its genetically active form [euchromatin] or genetically inactive form [heterochromatin]?

The proteins that complex with DNA, histones, have amino acid "tails" on them. In heterochromatin these tails have methyl groups. In euchromatin the tails have acetyl groups. A structure called the "chromatin remodeling complex" puts acetyl groups on heterochromatin, changing it to euchromatin.

How does translational control work?

There are three different mechanisms for translational control. These mechanisms also affect the mRNA strand, but unlike posttranscriptional control they occur in the cytoplasm. Specifically, sometime after the mRNA has reached the cytoplasm but before the protein is synthesized. [1]The first mechanism involves cytoplasmic activities that remove the 5' G cap. If the cap is removed translation may not happen &/or the mRNA may be destroyed. If the G cap is left alone, translation occurs. [2] In the next mechanism, cytoplasmic activities that remove or affect the length of the 3' poly-A tail also function to regulate gene expression. If the poly-A tail is shortened the mRNA strand time in the cytoplasm is also shortened. This results in differential protein expression because the ribosome will synthesize a smaller than expected protein. If the poly-A tail is left alone a longer protein is produced. However If the poly-A tail is completely removed, the mRNA may be destroyed and no protein produced. [3] The third mechanism involves the use of microRNA (miRNA). microRNA regulate genetic translation by binding to mRNA[which forms a double-stranded RNA complex] & either inhibiting or destroying it. This also results in no protein synthesis.

How does transcriptional control work?

Transcriptional control is achieved when the mechanism utilizes transcription factors and either an activator or a repressor. The control mechanisms works in the following way: [i] a group of transcription factors bind to a promoter just adjacent to a gene. [ii] It then attracts and helps RNA polymerase bind. [iii]transcription activators bind to DNA at a region called an enhancer. [iv] a hairpin loop forms in DNA to bring the activator attached enhancer into contact with the promoter. Mediator proteins act as a bridge between transcription factor & activator which then causes transcription to occur quickly; This same process happens when transcription is turned off with the exception that repressors bind to silencers instead of activators to enhancers.

What three enzymes are synthesized by the lac Operon to catabolize/breakdown] lactose?

[1] beta-galacatosidase: enzyme that catabolizes lactose into monomers glucose and galactose; [2] permease: enzyme that allows lactose to enter the cell; [3] transacetylase: enzyme with accessory function in lactose metabolism;

*cyclins

a family of internal signaling proteins produced during phases of the cell cycle; the amount of cyclin present in the cell will either increase or decrease as the cell cycle continues; specific cyclin must be present for the cell to proceed from G1 to S and from G2 to M.

operon

a functional unit of genomic DNA containing a cluster of genes under the control of a single regulatory signal[or gene]. An operon typically includes a promoter, operator, structural genes & the regulatory signal.

regulator gene:

a gene located outside of the operon that will code for a protein[repressor protein] that controls whether the operon is active or inactivce.

Explain how lampbrush chromosomes in vertebrate euchromatin is genetically active?

a lampbrush chromosome is genetically active because it has had its histone pushed aside by the chromatin remodeling complex so that its DNA is unwound into large loops that can easily be accesed by RNA polymerase.

enhancer

a region of DNA, that transcription activators bind to in order to speed up transcription. Enhancers often are far away from the promoter site;

operator

a short segment of DNA that is the location where an active repressor binds to prevent RNA polymerase from attaching to the promoter. This action prevents transcription.

**promoter

a short segment of DNA, usually occurring upstream from a gene's coding region, where RNA polymerase first attaches when a gene is to be transcribed. the promoter acts as a control site in the expression of the gene.

corepressor

a substance that activates a repressor protein by causing it to bind to the operator and stop transcription. In the trp Operon, tryptophan is the corepressor;

microRNA

abbreviated miRNA: microRNA are small processed pieces of introns that combine with protein to form a complex called the RNA-induced silencing complex[RISC] This complex targets specific mRNA molecules, complementary base pairs with them[ forming a double-stranded RNA complex] and then destroys or inhibits it from being translated by the ribosomes.

repressible operon

an active operon that gets turned off when a repressor protein binds to its operator. Said another way, repressible operons are operons that go from on to off. They are usually involved in anabolic pathways.

inducer

any substance that binds to a repressor protein[deactivating it] thus causing the repressor to be removed from the operator. Removal of the repressor allows RNA polymerase to bind to the promoter and transcribe the gene.

CAP

catabolite activator protein: a protein that activates transcription of a catabolic operon's structural genes when glucose is not available for catabolism. CAP does this by binding to DNA and exposing the promoter site to RNA polymerase;

negative control [gene regulation]

control of gene regulation that involves the use of a repressor that turns that either activates or deactivates the operon.

genomic imprinting

gene expression that depends on whether the chromosome carrying the gene is inherited from the mother or the father; Methylation of DNA accounts for genomic imprinting because an inherited gene that has been methylated does not get expressed. Only the gene coming from the parent without methylation is expressed for a specific trait.

structural genes

gene or genes in the operon that code for the enzymes needed in a specific metabolic pathway.

proteasomes

giant protein complexes that degrade or destroy proteins so they are no longer active;

*histones

highly alkaline proteins found in eukaryotic cells that package and order DNA into structural units called nucleosomes; they do so by acting as a spool around which DNA winds; histones also provide the chromosome with structural support; there are 5 different types of histones;

posttranslational control

one of five eukaryotic mechanisms for controlling genetic expression[in the cytoplasm] that involves additional changes to the synthesized protein before it becomes biologically functional.

posttranscriptional control

one of five eukaryotic mechanisms for controlling genetic expression[in the nucleus] that involves changes in mRNA processing or mRNA exit speed. In other words, post transcriptional control involves differential mRNA processing or changes in the speed at which a mature [processed] mRNA leaves the nucleus.

transcriptional control

one of five eukaryotic mechanisms for controlling genetic expression[in the nucleus] that stimulates or stifles transcription.Of the five mechanism for gene regulation, this one is most critical. Transcription factors, activators, repressors, & transposons are the "instruments" of transcriptional control.

chromatin structure [genetic regulation]

one of five eukaryotic mechanisms for controlling genetic expression[in the nucleus]. Mechanism uses variations in chromatin structure to control when transcription occurs. If genes are not accessible to RNA polymerase, they cannot be transcribed. Highly condensed chromatin cannot be transcribed because RNA polymerase cannot attach to DNA. However, loosely condensed chromatin can be transcribed because RNA polymerase attaches easily.

How does posttranslational control work?

posttranslational control is the last chance a cell has to control genetic expression. It happens after a protein has been synthesized & before or after it has been activated. There are two main mechanisms for posttranslational control. [1] The first means of control includes cleaving or folding of the protein to activate or deactivate it. For example, bovine insulin is activated when a 30 amino acid sequence is removed (cleaved). [2] The second mechanism involves destroying [or degrading] the protein after it has been activated to prevent it from continuing to be expressed (in other words, to stop the protein from continuing to perform its function). For example, proteasomes are used to destroy [degrade] cyclins to stop them from functioning in the cell cycle.

epigenetic inheritance

term used to describe inheritance patterns that do not depend on the genes themselves. Said another way, epigenetic inheritance are changes in genetic expression [or phenotype] that are caused by mechanisms not found in the DNA genes. For example, a structure called "chromatin remodeling complex" has the ability to add methyl or acetyl groups to histones. If when adding a methyl group to a histone, it also adds one to DNA, the DNA becomes inactive. This is a specific example of epigenetic inheritance called genomic imprinting;

An Interesting fact about red blood cells

the main function of red blood cells is to transport oxygen through-out the body. Red blood cells use the protein hemoglobin to carry oxygen. The interesting fact about red blood cells is that they eject their nucleus, along with its DNA. How are red blood cells able to replenish its supply of hemoglobin if it no longer contain hemoglobin's genetic code? The poly-A tail on the hemoglobin mRNA strand is very long which allows it to remain in the cytoplasm for a long period of time before it is degraded. In fact hemoglobin, can be synthesized for several months in red blood cells. This happens to coincide with how long a red blood cells lives. Once this time has passed, the cell is no longer functional and is then replaced by new red bloods cells.

*chromatin

threadlike material made up of DNA, and protein; chromatin is the uncondensed & uncoiled version of chromosomes; under a microscope chromatin appears threadlike or grainy; chromatin is located in the nucleoplasm of the nucleus