Tuesday, November 29, 2011
Blog 12 due 12/04 at 10:00 pm
Compare and contrast eukaryotic and prokaryotic controls for transcritpion. Which one primarily uses negative control? Positive control? Be specific and make sure to include transcriptional control, post transcriptional control, translational control, and post translational control. (250 word minimum)
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The controls that act on gene expression are much more complex in eukaryotes than in prokaryotes. A major difference is the presence in eukaryotes of a nuclear membrane, which prevents the simultaneous transcription and translation that occurs in prokaryotes. Whereas, in prokaryotes, control of transcriptional initiation is the major point of regulation, in eukaryotes the regulation of gene expression is controlled equivalently from many different points.
ReplyDeleteIn bacteria, genes are clustered into operons: gene clusters that encode the proteins necessary to perform coordinated function, including the operator, promoter, and the genes they control. RNA that is transcribed from prokaryotic operon are a multiple proteins that are encoded in a single transcript.
In bacteria, control of the rate of transcriptional initiation is the predominant site for control of gene expression. As with the majority of prokaryotic genes, initiation is controlled by two DNA sequence elements These 2 sequence elements are termed promoter sequences, because they promote recognition of transcriptional start sites by RNA polymerase. These promoter sequences are recognized and contacted by RNA polymerase.
Gene expression in prokaryotes is negative feedback, while gene expression in eukaryotes is positive feedback.
The activity of RNA polymerase at a given promoter is in turn regulated by interaction with accessory proteins, which affect its ability to recognize start sites. These regulatory proteins can act both positively (activators) and negatively (repressors). The accessibility of promoter regions of prokaryotic DNA is in many cases regulated by the interaction of proteins with sequences termed operators. The operator region is adjacent to the promoter elements in most operons and in most cases the sequences of the operator bind a repressor protein.
In eukaryotic cells, the ability to express biologically active proteins comes under regulation at several points. Chromatin Structure: The physical structure of the DNA, as it exists compacted into chromatin, can affect the ability of transcriptional regulatory proteins (termed transcription factors) and RNA polymerases to find access to specific genes and to activate transcription from them. Epigenetic Control: Epigenesis refers to changes in the pattern of gene expression that are not due to changes in the nucleotide composition of the genome. Transcriptional Initiation: This is the most important mode for control of eukaryotic gene expression. Specific factors that exert control include the strength of promoter elements within the DNA sequences of a given gene, the presence or absence of enhancer sequences (which enhance the activity of RNA polymerase at a given promoter by binding specific transcription factors), and the interaction between multiple activator proteins and inhibitor proteins. Transcript Processing and Modification: Eukaryotic mRNAs must be capped and polyadenylated, and the introns must be accurately removed.Several genes have been identified that undergo tissue-specific patterns of alternative splicing, which generate biologically different proteins from the same gene. RNA Transport: A fully processed mRNA must leave the nucleus in order to be translated into protein. Transcript Stability: Unlike prokaryotic mRNAs, eukaryotic mRNAs can vary greatly in their stability. Certain unstable transcripts have sequences that are signals for rapid degradation. Translational Initiation: Since many mRNAs have multiple methionine codons, the ability of ribosomes to recognize and initiate synthesis from the correct AUG codon can affect the expression of a gene product. Several examples have emerged demonstrating that some eukaryotic proteins initiate at non-AUG codons. Small RNAs and Control of Transcript Levels: Within the past several years a new model of gene regulation has emerged that involves control exerted by small non-coding RNAs. This small RNA-mediated control can be exerted either at the level of the translatability of the mRNA, the stability of the mRNA or by changes in chromatin structure. Post-Translational Modification: Common modifications include glycosylation, acetylation, disulfide bond formations. Protein Transport: In order for proteins to be biologically active following translation and processing, they must be transported to their site of action. Control of Protein Stability: Many proteins are rapidly degraded, whereas others are highly stable. Specific amino acid sequences in some proteins have been shown to bring rapid degradation. Post-translational control can be defined as the mechanisms by which protein structure can be altered after translation. Proteins are polymers of amino acids, and there are twenty different amino acids. Both the order and identity of these amino acids are important for the role that the protein plays in the cell. In some cases, the chemical identity of these amino acids is changed after translation. Alternatively, the sequence or number of the amino acids in a protein can be altered. These changes can alter the structure or function of the protein and also cause its destruction.
ReplyDeleteEukaryotes
ReplyDeleteIn eukaryotic cells, the ability to express biologically active proteins comes under regulation at several points:
Chromatin Structure: The physical structure of the DNA, as it exists compacted into chromatin, can affect the ability of transcriptional regulatory proteins (termed transcription factors) and RNA polymerases to find access to specific genes and to activate transcription from them. The presence modifications of the histones and of CpG methylation most affect accessibility of the chromatin to RNA polymerases and transcription factors.
Epigenetic Control: Epigenesis refers to changes in the pattern of gene expression that are not due to changes in the nucleotide composition of the genome. Literally "epi" means "on" thus, epigenetics means "on" the gene as opposed to "by" the gene.
Transcriptional Initiation: This is the most important mode for control of eukaryotic gene expression (see below for more details). Specific factors that exert control include the strength of promoter elements within the DNA sequences of a given gene, the presence or absence of enhancer sequences (which enhance the activity of RNA polymerase at a given promoter by binding specific transcription factors), and the interaction between multiple activator proteins and inhibitor proteins.
Transcript Processing and Modification: Eukaryotic mRNAs must be capped and polyadenylated, and the introns must be accurately removed (see RNA Synthesis Page). Several genes have been identified that undergo tissue-specific patterns of alternative splicing, which generate biologically different proteins from the same gene.
RNA Transport: A fully processed mRNA must leave the nucleus in order to be translated into protein.
Transcript Stability: Unlike prokaryotic mRNAs, whose half-lives are all in the range of 1 to 5 minutes, eukaryotic mRNAs can vary greatly in their stability. Certain unstable transcripts have sequences (predominately, but not exclusively, in the 3'-non-translated regions) that are signals for rapid degradation.
Translational Initiation: Since many mRNAs have multiple methionine codons, the ability of ribosomes to recognize and initiate synthesis from the correct AUG codon can affect the expression of a gene product. Several examples have emerged demonstrating that some eukaryotic proteins initiate at non-AUG codons. This phenomenon has been known to occur in E. coli for quite some time, but only recently has it been observed in eukaryotic mRNAs.
Small RNAs and Control of Transcript Levels: Within the past several years a new model of gene regulation has emerged that involves control exerted by small non-coding RNAs. This small RNA-mediated control can be exerted either at the level of the translatability of the mRNA, the stability of the mRNA or via changes in chromatin structure.
Post-Translational Modification: Common modifications include glycosylation, acetylation, fatty acylation, disulfide bond formations, etc.
Protein Transport: In order for proteins to be biologically active following translation and processing, they must be transported to their site of action.
Control of Protein Stability: Many proteins are rapidly degraded, whereas others are highly stable. Specific amino acid sequences in some proteins have been shown to bring about rapid degradation.
Prokaryotes:
ReplyDeleteIn bacteria, genes are clustered into operons: gene clusters that encode the proteins necessary to perform coordinated function, such as biosynthesis of a given amino acid. RNA that is transcribed from prokaryotic operons is polycistronic a term implying that multiple proteins are encoded in a single transcript.
In bacteria, control of the rate of transcriptional initiation is the predominant site for control of gene expression. As with the majority of prokaryotic genes, initiation is controlled by two DNA sequence elements that are approximately 35 bases and 10 bases, respectively, upstream of the site of transcriptional initiation and as such are identified as the -35 and -10 positions. These 2 sequence elements are termed promoter sequences, because they promote recognition of transcriptional start sites by RNA polymerase. The consensus sequence for the -35 position is TTGACA, and for the -10 position, TATAAT. (The -10 position is also known as the Pribnow-box.) These promoter sequences are recognized and contacted by RNA polymerase.
The activity of RNA polymerase at a given promoter is in turn regulated by interaction with accessory proteins, which affect its ability to recognize start sites. These regulatory proteins can act both positively (activators) and negatively (repressors). The accessibility of promoter regions of prokaryotic DNA is in many cases regulated by the interaction of proteins with sequences termed operators. The operator region is adjacent to the promoter elements in most operons and in most cases the sequences of the operator bind a repressor protein. However, there are several operons in E. coli that contain overlapping sequence elements, one that binds a repressor and one that binds an activator.
As indicated above, prokaryotic genes that encode the proteins necessary to perform coordinated function are clustered into operons. Two major modes of transcriptional regulation function in bacteria (E. coli) to control the expression of operons. Both mechanisms involve repressor proteins. One mode of regulation is exerted upon operons that produce gene products necessary for the utilization of energy; these are catabolite-regulated operons. The other mode regulates operons that produce gene products necessary for the synthesis of small biomolecules such as amino acids. Expression from the latter class of operons is attenuated by sequences within the transcribed RNA.
A classic example of a catabolite-regulated operon is the lac operon, responsible for obtaining energy from β-galactosides such as lactose. A classic example of an attenuated operon is the trp operon, responsible for the biosynthesis of tryptophan.
Prokaryotes:
ReplyDeleteprokaryotes primarily use negative control (unlike the eukaryotic cells). This enables the bacteria to express only the genes whos products are needed by the cell, which allows them to conserve energy and resources. Bacteria often respond to environmental change by regulating transcription. The basic mechanism for the control of gene expression in bacteria is described as the operon model (discovered by Franqois Jacob.
During transcription, the trpRepressor can turn off an operon by attaching to its operator and as a result not allowing the RNA polymerase to bind to it. For example, after transcrition occurs, and there is a lot of tryptophan, it binds to the repressor, thus making it bind to the operator and shutting it down temporarily. There also is a inducible operon. For Example if lactose is in the surrounding area of the cell, then the inducer allactose bind to the otherwise active lac repressor and deactivvating it, thus creating more lactose. For positive control, cAMP binds to the inactive CAP, makes it active and causes it tobind to the promoter region of the operon. This, in turn causes the RNA polymerase to be more likely to bing to the operon and beegin transcrition.
Eukaryotes:
Chromatin modifying enzymes provide initial control of gene expression by making a region of the DNA more or less able to bind the transcription machinery. As in bacteria redulation of transcription initiation in eukaryotes involves proteins that bind to DNA the either facilitate or inhibit the binding of RNA polymerase. but the process is more complpicated with eukaryotes, which includes distal and proximial control element. activators and general transcription factors bind to the DNA. And unlike prokaryotes, eukaryotes have post-transcriptional regulation. This includes RNA processing and mRNA degradation.
During translation, the translation of some mRNA's can be blocked by some regulatory proteins that bind to the specific sequences or structures of the mRNA preventing the binding of ribosomes. After translation the protein may be degraded by the binding of Ubiquitin and Proteasomes.
Transcriptional in Eukaryotes: The addition of acetyl groups to the histone tails of DNA reduces the condensation, promoting transcription. When methyl groups are added, condensation is promoted, thereby slowing or inhibiting transcription. These examples are of positive control because transcription is either accelerated or slowed. Furthermore, transcription factors such as enhancers, which could be located several map units away from the promoter, are needed for transcription to go forward. Activators bind to the enhancers, and are required to bind to the promoter region. If this is inhibited, transcription will be controlled.
ReplyDeletePosttranscriptional in Eukaryotes: In alternative RNA splicing, different introns could be removed, changing which proteins are made and which genes are expressed.
Translational in Eukaryotes: Certain proteins could bind to the promoter region of the mRNA, preventing the binding of the ribosome.
Posttranslational in Eukaryotes: If the proteins produced by translation are misfolded, ubiquitin attaches to it and the protein is degraded by a proteasome.
Prokaryotes: DNA of prokaryotes have operons, which are groups of genes that function to produce proteins needed by the cell. Prokaryotes generally use negative feedback inhibition. In the case of the tryp operon, tryptophan is produced when it is not present in the environment. Therefore, tryptophan acts as a corepressor because production is stopped when it is available. The tryp operon is considered a repressible operon because it is active until the corepressor binds to the repressor, inactivating it. There is also the lac operon, which is an inducible operon because it is only activated when the corepressor, lactose, is present and the repressor is removed. When lactose is present in E Coli, it is digested. However, the reaction is repressed when lactose is not present because it does not need to be digested.
Gene expression is much more complex in eukaryotes than in prokaryotes because of the presence of a nuclear membrane, which separates translation and transcription into two independently-occurring processes. Prokaryotic bacterial genes are typically clustered into operons. These clustered genes normally encode proteins. Prokaryotic gene transcription is controlled at the promoter regions of the gene. Thus, transcriptional initiation is the dominant control mechanism of prokaryotic gene regulation. Prokaryotes display negative feedback during gene regulation, while eukaryotes embrace positive feedback. Like prokaryotes, transcriptional initiation is the dominant control site of gene regulation. However, eukaryotes fashion many different, more complex methods of gene regulation, including chromatin structure, epigenetic control, RNA Transport, transcript processing and modification, RNA and protein degradation, translational initiation, miRNAs and other small non-coding RNAs, and Post-Translational Modification. Chromatin structure can affect regulation through the loosening or condensing of chromatin due to acetylation of histones, methylation, or phosphorylation . Acetylation loosens chromatin structure, increasing transcription of the particular gene or genes. Methylation has an opposite effect: it condenses the chromatin by adding methyl groups to the RNA nucleotide bases, slowing transcription. Epigenetic control does not change individual nucleotides but it also may affect the chromatin structure through DNA methylation and phosphorylation, the addition of phosphate groups to transcription proteins that decrease the affinity of these proteins to bind to the gene and block transcription. Epigenetic control and protein structure are closely tied. Alternate RNA splicing allows one gene to code for different proteins. Before translation, unstable and incorrect sequences of mRNA may be degraded into small molecules, which will be reused to assemble the correct sequence. Some genes have multiple start codons, and ribosomes’ ability to initiate translation is also a form of gene regulation. Small RNAs can affect gene regulation at the transcriptional and translational level, as well as during RNA degradation. In addition, eukaryotic gene regulation displays positive feedback while prokaryotic genes almost only fashion negative feedback mechanisms of gene regulation.
ReplyDeleteProkaryotes-
ReplyDeleteprokaryotes use negative control, opposite eukaryotic cells. By using negative control prokaryotes express the genes that are needed by the cell, which enables prokaryotes to conserve energy. Prokaryotes have two levels of gene control. Transcriptional mechanisms control the synthesis of mRNA and translational mechanisms control the synthesis of protein after mRNA has been produced. Operons are groups of genes that function to produce proteins needed by the cell. There are two different kinds of genes in operons: structural genes and regulatory genes. Lactose is a sugar found in milk. If lactose is present, E. coli (the common intestinal bacterium) needs to produce the necessary enzymes to digest it. Three different enzymes are needed. genes A, B, and C represent the genes whose products are necessary to digest lactose. In the normal condition, the genes do not function because a repressor protein is active and bound to the DNA preventing transcription. When the repressor protein is bound to the DNA, RNA polymerase cannot bind to the DNA. The protein must be removed before the genes can be transcribed.The repressor protein is produced by a regulator gene. The region of DNA where the repressor protein binds is the operator site. The promoter site is a region of DNA where RNA polymerase can bind. The entire unit (promoter, operator, and genes) is an operon.
The operator acts like a switch that can turn several genes on or off at the same time. The lac operon is an example of an inducible operon because the structural genes are normally inactive. They are activated when lactose is present. Repressible operons are the opposite of inducible operons. Transcription occurs continuously and the repressor protein must be activated to stop transcription. Tryptophan is an amino acid needed by E. coli and the genes that code for proteins that produce tryptophan are continuously transcribed. If tryptophan is present in the environment, however, E. coli does not need to synthesize it and the tryptophan-synthesizing genes should be turned off. This occurs when tryptophan binds with the repressor protein, activating it. Unlike the repressor discussed with the lac operon, this repressor will not bind to the DNA unless it is activated by binding with tryptophan.. Tryptophan is therefore a corepressor. The trp operon is an example of a repressible operon because the structural genes are active and are inactivated when tryptophan is present.
Eukaryotes-
ReplyDeleteGene expression in eukaryotes is controlled by a variety of mechanisms that range from those that prevent transcription to those that prevent expression after the protein has been produced. Transcriptional - These mechanisms prevent transcription. Post-transcriptional, these mechanisms control or regulate mRNA after it has been produced. Translational, these mechanisms prevent translation. They often involve protein factors needed for translation. Post-translational, these mechanisms act after the protein has been produced. Heterochromatin is tightly wound DNA and visible during interphase. It is inactive because DNA cannot be transcribed while it is tightly wound. Euchromatin is not tightly wound. It is active. Condensation of DNA involves coiling around proteins called histones. Acetylation is when acetyl groups (-COCH3) are attached to lysine's in the histone tails. This reduces condensation and promotes transcription because the transcription machinery has better access to the DNA. Translational Control, these mechanisms prevent the synthesis of protein. They often involve protein factors needed for translation. Preventing ribosomes from attaching, proteins that bind to specific sequences in the mRNA and prevent ribosomes from attaching can prevent translation of certain mRNA molecules. Initiation factors are proteins that enable ribosomes to attach to mRNA. These factors can be produced when certain proteins are needed. For example, the eggs of many organisms contain mRNA that is not needed until after fertilization. At this time, an initiation factor is activated.
Post-translational control, these mechanisms act after the protein has been produced. Protein Activation, some proteins are not active when they are first formed. They must undergo modification such as folding, enzymatic cleavage, or bond formation. Many proteins are activated by adding phosphate groups. They can be inactivated by removing phosphate groups. For example, kinases activate by adding phosphate groups and phosphodiesterase inactivates by removing the phosphate groups. Some enzymes in a metabolic pathway may be negatively inhibited by products of the pathway, using feedback control.
Gene expression is much more complex in eukaryotes than in prokaryotes. Starting with the fact that eukaryotes have a nuclear membrane that separates translation and transcription. In prokaryotes the genes are compacted into operons, where gene expression takes place.
ReplyDeleteProkaryotes- Gene regulation is expressed through negative feedback (on until turned off, or off until turned on.)Gene transcription is controlled by the prometer.An operator region is adjacent to the prometer. If the RNA polymerase is stopped by a repressor infront of the prometer, then the RNA cannot be transcribed. Transcriptional initiation is the control mechanism of the prokaryotic gene regulation.
Eukaryotes- Eukaryotes display Postive feedback during gene regulation, and the transcriptional iniation is the control mechanism of gene regulation for Eukaryotes as well. However the process of gene regulation is much more complex in eukaryotes. Chromatin structure- in eukaryotic gene regulation the structure of the chromatin can affect the ability of the transcriptional regulatory proteins and RNA polymerase. Transcriptional Initiation- it is the control mechanism for both eukaryotic and prokaryotic gene expression. Many factors can contribute to the initiation of gene expression: strength of the prometer, enhancers, repressors, and inhibitor protein are all control by this control mechanism. Transcript processing and modification- in order for RNA/DNAs to go through geneexpression they first need to be capped by a poly-A tail and a cap. Translational Initiation- Since many mRNAs have multiple methionine codons, the ability of ribosomes to recognize and initiate synthesis from the correct AUG codon can affect the expression of a gene product. miRNAs and transcript levels- new research has shown that there is gene regulation that is exerted by small- non coding RNAs. Post Translational Modification- includes acetylation and methylation( that can affect the future of a growing zygite).RNA degradation- Many RNA are degraded rapidly, but some have longer tails that protect the telomere which defines protein stability.
The regulation of gene expression is much more complex in eukaryotes than in prokaryotes because of the specialization and unique functional properties of each individual cell. Prokaryotes mostly display negative feedback during gene regulation, while eukaryotes show both positive feedback as well as negative feedback. Prokaryotes use repressible and inducible operons to display negative feedback, while eukaryotes show positive feedback with the use of CAPs and enhancers that increase the rate of transcription. Also, eukaryotes have different, more complex methods of gene regulation, including post transcriptional control, translation control, and post translational control. They can even regulate transcription at the chromatin level by either methylation or phosphorilation of histone tails that condense or loosens the chromatins, allowing for transcription to take place. There is also epigenic control where cytoplasmic determinants dictate the cells’ function. Before and during transcription, many transcription factors and mediators attach to the DNA with RNA polymerase II to begin transcription. Enhancers increase protein-specific gene transcription allowing for the production of specific functional proteins like actin and myosin in muscle cells. Also, CAPs that are activated from the binding of cAMP binds to DNA and attracts RNA polymerase II to bind with it, thus increasing the rate of transcription. In post-trancriptional control, the RNA formed must be spliced to rmove all introns and exon shuffling occurs to create different functioning proteins. A poly-A tail and Guanine cap must attach to the RNA in order for it to be translated, and to prevent degredation. During translation, certain proteins can bind to the beginning of the mRNA to prevent translation, also miRNA s can bind to it to either block translation, or to even degrade it to prevent it from being translated. In post-translation control, the protein can go through modification by either cleavage, folding, or other chemical changes. Any misfolded or irregular proteins are tagged and then degraded by giant protein complexes called proteosomes. Prokaryotes on the other hand, have much more simpler ways of gene expression. They have repressible operons where genes are consistently transcribed until they are turned off by active repressors created from specific regulatory genes. These operons are usually associated with anabolic pathways. Inducible operons are always turned off until the repressor that prevents transcription becomes inactive by an inducer. Inducible operons are associated with catabolic pathways. These operons display negative feedback because they either inhibit the production of substrate when there are many present, or they begin to break down substrate when there is too much, thus having an opposite reaction to the environment. Also, the RNA produced have very short lives and degrade quickly which allows for prokaryotes to quickly adapt to the changing environment.
ReplyDeleteprokaryotes - mostly display negative feedback during gene regulation
ReplyDeleteuse repressible and inducible operons to display negative feedback
have much more simpler ways of gene expression
they have repressible operons where genes are consistently transcribed until they are turned off by active repressors created from specific regulatory genes. yhese operons are usually associated with anabolic pathways
inducible operons are always turned off until the repressor that prevents transcription becomes inactive by an inducer and are associated with catabolic pathways
these operons display negative feedback because they either inhibit the production of substrate when there are many present, or they begin to break down substrate when there is too much, thus having an opposite reaction to the environment
the RNA produced have very short lives and degrade quickly which allows for prokaryotes to quickly adapt to the changing environment
eukaryotes - show both positive feedback as well as negative
show positive feedback with the use of CAPs and enhancers that increase the rate of transcription
have more complex methods of gene regulation, including post transcriptional control, translation control, and post translational control
regulate transcription at the chromatin level by either methylation or phosphorilation of histone tails that condense or loosens the chromatins, allowing for transcription to take place there is also epigenic control where cytoplasmic determinants dictate the cells’ function
before and during transcription, many transcription factors and mediators attach to the DNA with RNA polymerase II to begin transcription
enhancers increase protein-specific gene transcription allowing for the production of specific functional proteins like actin and myosin in muscle cells
CAPs that are activated from the binding of cAMP binds to DNA and attracts RNA polymerase II to bind with it, thus increasing the rate of transcription
in post-trancriptional control, the RNA formed must be spliced to rmove all introns and exon shuffling occurs to create different functioning proteins, a poly-A tail and Guanine cap must attach to the RNA in order for it to be translated, and to prevent degredation
during translation, certain proteins can bind to the beginning of the mRNA to prevent translation, also miRNA s can bind to it to either block translation, or to even degrade it to prevent it from being translated
in post-translation control, the protein can go through modification by either cleavage, folding, or other chemical changes. any misfolded or irregular proteins are tagged and then degraded by giant protein complexes called proteosomes