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Eukaryotic Gene Expression (Bacterial Gene Regulation (How is gene…
Eukaryotic Gene Expression
Gene expression can be regulated at many stages
Gene expression involves many steps and almost all of them can be regulated.
Chromatin accessibility - The structure of chromatin (DNA and its organizing proteins) can be regulated. More open or "relaxed" chromatin makes a gene more available for transcription.
Transcription - a key regulatory point for many genes. Sets of transcription factor proteins bind to specific DNA sequences in or near a gene and promote or repress its transcription into an RNA
RNA Processing - Splicing, capping and addition of a poly-A tail to an RNA molecule can be regulated, and so can exit from the nucleus. Different mRNAs may be made from the same pre-mRNA by alternative splicing.
RNA Stability - The lifetime of an mRNA molecule in the cytosol affects how many proteins can be made from it. Small regulatory RNAs called miRNAs can bind to target mRNAs and cause them to be chopped up.
Translation - \translation of an mRNA may be increased or inhibited by regulators. For instance, miRNAs sometimes block translation of their target mRNAs (rather than causing them to be chopped up)
Protein activity - Proteins can undergo a variety of modifications, such as being chopped up or tagged with chemical groups. These modifications can be regulated and may affect the activity or behavior of the protein.
Although all stages of gene expression can be regulated, the main control point for many genes is transcription. Later stages of regulation often refine the gene expression patterns that are "roughed out" during transcription.
Gene regulation differentiates cells
GR is how a cell controls which of its many genes, within its genome are "turned on" (expressed).
Due to GR each cell type within the body has a different set of active genes.
Despite the fact that almost all the cells in your body contain the exact same DNA. These different patterns of gene expression cause your various cell types to have different sets of proteins, making each cell uniquely specialized to do it's job.
For example, one of the jobs of the live is to remove toxic substances like alcohol from the bloodstream. To do this, liver cells express genes encoding subunits of an enzyme called alcohol dehydrogenase. This enzyme breaks alcohol down into a non-toxic molecule. The neurons in a person's brain don't remove toxins from the body, so they keep these genes unexpressed.
Similarly the cells of the liver don't send signals using neurotransmitters, so they keep their neurotransmitter genes unexpressed.
There are many other genes that are expressed differently between liver cells and neurons
How do cells "decide" which genes to turn on/turn off?
Many factors that can affect which genes a cell expresses.
Different cell types express different sets of genes. However, two different cells of the same type may also have different gene expression patterns depending on their environment and internal state.
A cell's gene expression pattern is determined by information from both inside and outside the cell.
Examples of information inside the cell: the proteins it inherited from its mother cell, whether its DNA is damaged, and how much ATP it has.
Examples of information outside the cell: chemical signals from other cells, mechanical signals from the extracellular matrix, and nutrient levels.
Cells have molecular pathways that convert information - such as the binding of a chemical signal to its receptor - into a change in gene expression.
A growth factor is a chemical signal from a neighboring cell that instructs a target cell to grow and divide. The cell "notices" the growth factor and "decides" to divide.
The cell detects the growth factor through physical binding of the growth factor to a receptor protein on the cell surface.
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Key Points
GR- the process of controlling which genes in a cell's DNA are expressed.
Used to make a functional product; such as a protein
Different cells in multicellular organisms may express very different sets of genes, even though they contain the same DNA
The set of genes expressed in a cell determines the set of proteins and functional RNAs it contains.
cause for its unique properties
In eukaryotes, like humans, gene expression involves many steps, and gene regulation can occur at any of these steps.
Many genes are regulated primarily at the level of transcription.
Bacterial Gene Regulation
Bacterial genes are often found in operon. Genes in an operon are transcribed as a group and have a single promoter.
Each operon contains regulatory DNA sequences, which act as binding sites for regulatory proteins that promote or inhibit transcription.
Regulatory proteins often bind to small molecules, which can make the protein active or inactive by changing its ability to bind to DNA.
Some operons are inducible, meaning they can be turned on by the presence of a particular small molecule. Others are repressible, meaning that they are on by default but can be turned off by a small molecule.
The bacteria in your gut or between your teeth have genomes that contain thousands of different genes. Most of these genes encode proteins, each with its own role in a process such as fuelling metabolism, maintenance of cell structure, and defense against viruses.
Some of these proteins are needed routinely, while others are needed only under certain circumstances. Thus, cells don't express all the genes in their genome all the time.
The genome acts like a cookbook with many recipes inside of it. The cell will only use those recipes (specific genes) when necessary.
How is gene expression regulated?
There are various forms of gene regulation, that is, mechanisms for controlling which genes get expressed and at what levels. However, a lot of gene regulation occurs at the level of transcription.
Bacteria have specific regulatory molecules that control whether a particular gene will be transcribed into mRNA.
Often, these molecules act by binding to DNA near the gene and helping or blocking the transcription enzyme, RNA polymerase.
In bacteria. genes are found in Operons.
Related genes are often found in a cluster on the chromosome where the are transcribed from one promoter (RNA Polymerase binding site) as a single unit. Such a cluster of genes is under control of a single promoter known as an operon.
Operons are common in bacteria, but they are rare in eukaryotes, such as humans.
an operon will contain genes that function in the same process.
For example, a well studied operon called the lac operon contains genes that encode proteins involved in uptake and metabolism of a particular sugar, lactose..
Operons allow the cell to efficiently express sets of genes whose products are needed at the same time.
Anatomy of an Operon
Operons are just made up of the coding sequences of genes and contain regulatory DNA sequences that control transcription of the operon. Typically, these sequences are binding sites for regulatory proteins, which control how much the operon ins transcribed.
The promoter, or the site where RNA polymerase binds, is one example of a regulatory DNA sequence.
Most operons have other regulatory DNA sequences in addition to the promoter. These sequences are binding sites for regulatory proteins that turn expression of the operon "up" or "down".
Some regulatory proteins are called repressors that bind to pieces of DNA called operators. When bound to its operator, a repressor reduces transcription (e.g by blocking RNA polymerase from moving forward on the DNA)
Some regulatory proteins are activators. When an activator is bound to a DNA binding site, it increases transcription of the operon (e.g by helping RNA polymerase bind to the promoter).
Regulatory proteins are produced within an organism, they are encoded by genes in the bacterium's genome. The genes that encode regulatory proteins are sometimes called regulatory genes
Many regulatory proteins can themselves be turned "on" or "off" by specific small molecules. The small molecule binds tot he protein, changing its shape and altering its ability to bind to DNA. For instance, an activator may only become active (able to bind to DNA) when it's attached to a certain small molecule.
Operons may be inducible or repressible.
Some operons are usually "off", but can be turned "on" by a small molecule. The molecule is called an inducer, and the operon is said to be inducible.
For example, the lac operon is an inducible operon that encodes enzymes for the metabolism of lactose. It only turns on when the sugar is present. The inducer, in this case, is allolactose, a modified form of lactose.
Some operons are usually "on", but can be turned "off" by a small molecule. The molecule is called a corepressor, and the operon is said to be repressible.
For example, the trp operon is a repressible operon that encodes enzymes for the synthesis of the amino acid tryptophan. This operon is expressed by default but can be repressed when high levels of the amino acid tryptophan are present. The corepressor, in this case, is tryptophan
Gene Regulation between species
Differences in gene regulation makes the different cell types in a multicellular organism unique in structure and function.
Gene regulation can also help us explain some of the with differences in form and function between different species relatively similar gene sequences.
Human and chimpanzees have genomes that are about 98% identical at the DNA level. Thee protein-coding sequences are different between human and chimpanzees, contributing to the differences between the species.
However, researchers also think that changes in gene regulation play a major role in making humans and chimps different from one another. For instance, some DNA regions are present in the chimpanzee genome but missing in the human genome, contain known gene regulatory sequences that control when, where or how strongly a gene is expressed.