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Chapter 11: Gene Control
Terms in this set (76)
An endangered species in Indonesia
Where did scientists get skin tissue?
The frozen zoo in San Diego, CA where samples of rare or endangered species are stored
What did the scientists do with the tissue?
Inserted nuclei from frozen skin cells into nucleus- free eggs from domestic beef cattle
The resulting embryos were implanted into surrogate domestic cows and 2 bantengs were born
What does the banteng show?
Since the banteng had died, animals that have been dead can be cloned by using closely related animals as surrogates
Hope this will help with endangered species
The development of different types of cells must depend on the turning on and off of different genes
What must be present for this to work?
The starting cell must contain a complete set of genes capable of directing the production of all the cell types in an organism
The turning on and off of genes can help organisms respond to environmental changes
What do genes determine?
The nucleotide sequence of specific mRNA which then determines the sequence of amino acids in a protein
What is happening to a gene that is turned on?
It is being transcribed into mRNA and its message is being translated into a protein
The process by which genetic information flows from genes to proteins (genotype to phenotype)
Control of this allows cells to produce specific kinds of proteins when they need to
Easliest study was of E. coli
Has a great ability to change its metabolic activities in response to changes in the environment and it can produce enzymes needed to metabolize a specific nutrient only when the nutrient is available
Can make lactose by using 3 enzymes that are regulated as a single unit
Which bacterial cells have an advantage?
Those that can conserve resources and energy
short sections of DNA that help control gene expression (In E Coli there are 2 across from the group of lactose enzyme genes)
Site where RNA polymerase attaches and initiates transcription
Between the promoter and enzyme genes
Acts as a switch
Determines whether RNA polymerase can attach to the promoter and start transcribing genes
A cluster of genes with related functions along with the control sequences, typically only exists in prokaryotes
This is an advantage because a single "on- off" switch controls the whole cluster
When E coli is involved with lactose the operon is called this
When lactose is encountered, all the enzymes needed for metabolism are made at once (bc single switch)
Lac operon is off when there is no lactose
inducible operon- usually turned off but can be turned on
How is transcription turned off when the lac operon is off?
A protein called a repressor binds to the operator and physically blocks the attachment of RNA polymerase to the promoter
A gene located outside the operon that codes for the repressor.
Always expressed so the cell always has a small supply of repressor molecules
How is the lac operon induced?
There is always a little bit of repressor molecules
Lactose binds to the repressor and changes its shape so that it can not bind to the operator and the switch remains on
What happens when the "operator switch" is on?
RNA polymerase can bind to the promoter (since it isn't blocked anymore) and can transcribe the genes of the operon
What does the resulting mRNA carry?
Coding sequences for all 3 enzymes needed for lactose metabolism
Why can the cell translate the single mRNA message into 3 polypeptides?
The mRNA has multiple codons signaling the start and stop of translation
How efficient is the lac operon?
So efficient that the addition of lactose to an environment multiplies lactose utilization enzymes by thousands
What happens when lactose is no longer present?
The mRNA and proteins are broken down
Usually turned off but can be induced/ turned on by the presence of a certain molecule
Usually operate as part of the pathway that breaks down a nutrient into simpler molecules
By producing these enzymes only when the nutrient is there avoids wasting resources
An operon that is normally turned on but can be inhibited/ repressed when a specific molecule is present in abundance
Ex. Trp- E Coli makes this unless it is in the environment
Proteins that turn operons on by binding to DNA and stimulating gene transcription.
Make it easier for RNA polymerase to bind to the promoter rather than blocking it like repressors
During repeated cell divisions that lead from a zygote to an adult cells become specialized in structure and function
How do cells maintain a specialized role?
Each cell must maintain a specific program of gene expression in which some genes are expressed and others are not
All cells in an organism have an identical genome, it is the gene expression that makes each cell unique to its function
Each adult cell expresses a small fraction of its total genes at a time
Cells can change gene expression over time in response to env changes or signals
What causes the difference between cell types?
Not due to different genes present, but selective gene expression
Proteins that account for half the mass of eukaryotic chromosomes that are essential for DNA packing (prok do not have the degree of packing as euks)
DNA histone complex- level one
At the first level- histones attach to DNA double helix and look like beads on a string
Each bead is a nucleosome- made of DNA wound around 8 histone molecules
Short stretches of DNA called linkers join the nucleosomes
DNA histone complex- level two
The beaded string is wrapped into a tight helical fiber of 30 nm. The fiber coils further until it has a diameter of 300 nm.
What is the effect of high levels of packing?
Tends to prevent gene expression by preventing RNA polymerase and other transcription proteins from contacting the DNA.
Can inactivate genes for the long term
Genes within chromatin as seen in mitotic chromosomes such as duplicated chromosomes and in interphase some chromosomes are not expressed at all
How does addition of methyl groups to amino acids in histone proteins affect gene expression?
Adding acetyl groups?
Can cause chromosomes to become compact, leading to reduced transcription
Adding acetyl groups opens up the chromatin structure, promoting transcription
Individual genes are more heavily methylated in cells they aren't expressed in, removing this methyl can turn these genes on
Methylation is essential for turning genes off
Insufficient DNA methylation can lead to abnormal embryonic development in many species
Once methylated, genes stay that way through many divisions and pass on modifications of DNA and histones
Inheritance of traits transmitted by mechanisms not directly involving the nucleotide sequence
Ex. One twin could have schizophrenia bc of different methylation patterns or chromatin structure even though they have identical genomes
DNA mutations are permanent while modifications of chromatin can be changed
Enzymes that modify chromatin are essential to eukaryotic cell's way of regulating transcription
In females, one X chromosome in each somatic cell is highly compacted and modified so that it is basically inactivated
This involved modification of the DNA and histone proteins
A gene on the X chromosome makes sure only 1 will be inactivated
When does X inactivation occur?
Early in embryonic development when one of the 2 X chromosomes in each cell is inactivated at random
The cells of females and males have the same effective dose of these genes
Inactive X in each cell condenses into this
Once an X chromosome is inactivated, all descendant cells have the same copy turned off
X inactivation expression
Females have active X derived from father and active X derived from mother
If a female is heterozygous for a gene on the X chromosome, half the cells will express one allele and half will express another
How does the process of packing and unpacking DNA have an effect?
Provides a coarse adjustment for eukaryotic gene expression by making a region of DNA either more or less available for transcription- the synthesis of RNA
How does this start?
Begins with the initiation of transcription
In all organisms this is the most important stage for regulating gene expression
All organisms use these activators and repressors that bind to specific segments of DNA and either promote or block the binding of RNA polymerase (turning transcription of genes on or off)
Most euk genes have individual promotors and other control sequences and are not clustered together like in operons (common in proks)
Regulator proteins interact with DNA and one another to turn genes on or off
Activator proteins in eukaryotes
Activator proteins seem to be more important than repressors
What is the default state in animals and plant cells?
Animals only need to turn on (transcribe) a small amount of genes that are required for the cell's structure and function
So the default state seems to be off
Exception to default state?
Some things that are continually active in virtually all cells such as glycolysis which is on by default
What does eukaryotic RNA polymerase require?
Assistance of proteins called transcription factors to function
What is the first step in initiating gene transcription?
The binding of activator proteins to DNA control sequences called enhancers
Located far away on the chromosome from the gene they help regulate (in euks) Then a DNA bending protein brings the bound activators closer to the promoter
What happens after DNA is bent?
Bound activators interact with other transcription factor proteins which then bind as a complex at the gene's promoter
This large assembly of proteins helps facilitate the correct attachment of RNA polymerase to the promoter and the initiation of transcription
What happens after the complete complex of proteins has assembled?
The polymerase can begin to move along the gene, producing an RNA strand
Multiple activators and enhancers can be involved in turning on a single gene
Where are genes coding for the enzymes of a metabolic pathway located?
Scattered across different chromosomes
How can a eukaryotic cell still turn on or off all functionally related genes at the same time?
The key is the association of a specific combination of control sequences with every gene of a particular metabolic pathway
Copies of the activators that recognize these control sequences bind to them all at once (bc they are identical), promoting simultaneous transcription of genes no matter where they are in the genome
What is the most important step in gene regulation?
Regulation of transcription
Transcription alone does not equal gene expression
Several points along the path from DNA to a protein can be regulated
ex. RNA transcripts are processed into mRNA before moving to the cytoplasm for translation by ribosomes
What does RNA processing include?
The addition of a cap and tail as well as the removal of any introns (noncoding DNA) and splicing together of exons
How can the splicing process help the flow of mRNA?
Splicing may help the flow of mRNA from nucleus to cytoplasm because until splicing is complete, the RNA is attached to the molecules of the splicing machinery and cannot pass through the nuclear pores
Alternative RNA splicing
Sometimes, a cell can carry out splicing in more than one way, generating different mRNA molecules from the same RNA transcript
This causes an organism to produce more than one type of polypeptide from a single gene
In humans, more than 90% of protein coding genes seem to undergo alternate splicing
How much of the human genome codes for proteins?
Another small fraction of DNA consists of genes for rRNA and tRNA
Most of the remaining RNA was thought to be untranscribed and lacking genetic info, however lots of the genome is transcribed into functioning, non- protein- coding RNA's
Bind to complementary sequences on mRNA molecules
Each miRNA has 22 nucleotides and forms a complex with one or more proteins
The miRNA protein complex can bind to any mRNA molecules with 7 or 8 nucleotides
Then the complex either degrades the target mRNA or blocks its translation
MiRNA may regulate the expression of at least all human genes and can be used to artificially control gene expression
What regulations occur after a eukaryotic mRNA is fully processed and transported to the cytoplasm
mRNA breakdown, initiation of translation, protein activation, protein breakdown
Breakdown of mRNA
Enzymes in cytoplasm break down mRNA
Long lived mRNA can be translated into more protein molecules than short lived ones
(prok mRNA have a short life span// one reason why bacteria can change protein production fast)
Long lived mRNAs are found in vertebrate blood cells that produce lots of hemoglobin
Mammals are an exception- when red blood cells mature they lose ribosomes and stop making hemoglobin
What molecules are involved in translation?
Proteins that control the start of polypeptide synthesis
Red blood cells
Have an inhibitory protein that prevents translation of hemoglobin mRNA unless the cell has a supply of heme, the iron containing chemical group essential for hemoglobin function
After translation, some polypeptides require alterations before they can become functional
Post translational control mechanisms in euks often include the cutting of a polypeptide to yield a smaller final product that is an active protein that can carry out a specific function
Ex. When a long polypeptide (insulin) is made it has no activity, only after it starts being folded does it work
The final control mechanism is the breakdown of proteins
Regulation allows a cell to adjust the kinds and amounts of its proteins in response to env changes
What causes cellular differentiation in euks?
The selective turning on and off of genes
This is most important during the development of an embryo from a zygote
Ex. in fruit flys one had legs where the antennas should be this is a cause of cellular differentiation
Master control gene that regulates the "batteries" of other genes that determine the anatomy of body parts and where they will develop
A mutation of the homeotic genes caused the leg to be where the antennas should have been
A glass or plastic surface with tiny amounts of thousands of different kinds of single stranded DNA fragments attached to a microscope wells in a tightly spaced array or grid
Carries DNA from thousands of genes bc each fixed DNA fragment is from a particular gene
How are microarrays used?
1. A researcher collects all of the mRNA transcribed from genes in a particular type of cell at a given moment
2. This collection of of mRNA's is mixed with reverse transcriptase to produce a mixture of single stranded DNA.
Called cDNAs because each one is complementary to one of the mRNAs
3. A small amount of fluorescently labeled cDNAs is added to each of the pieces in the microarray. If the molecule is complementary to a DNA fragment the cDNA will bind to it
4. The patterned glowing spots of bound cDNA and DNA fragments allows researchers to determine which genes are transcribed in starting cells
Different cancers can be identified with a DNA microarray can be used to choose chemotherapy
Can also reveal general profiles of gene expression over the lifetime of an organism
How do cells communicate?
Cells must be able to communicate messages that will coordinate gene expression by signaling via proteins from signaling cells to receiving (target) cells
A signaling molecule binds to a receptor protein in the plasma membrane and initating a signal transduction pathway in the target cell
Signal Transduction Pathway
A series of molecular changes that converts a signal on a target cell's surface to a specific response inside the cell
Signal Transduction Process
1. The cell sending a message secretes a signaling molecule
2. This molecule binds to a specific receptor protein embedded in the target cell's plasma membrane
3. The binding activates a series of relay proteins within the cell
4. The last relay molecule in the series activates a transcription factor that triggers the transcription of a specific gene and translation of the mRNA produces a protein that performs the function originally called for by the signal
This process is CRUCIAL
Cells of yeast and other microbes identify their mates this way
The 2 mating factors cause the cells to grow toward each other and bring about other cellular changes
Result is mating of 2 cells of opposite types
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