BOTC Chapter 8
House keeping proteins
-common to ALL cells -expressed in all genes - Rna polymerase, DNA repair enzymes, ribosomal proteins, other enzymes
A cluster of genes with related function controlled by a single promoter in bacterial genomes.
Operon
regulatory RNAs
RNA molecule that plays a role in controlling gene expression
Differentiated cells:
contain all the genetic instructions needed to direct the formation of a complete organism.
Regulation step 2
controlling how an RNA transcript is spliced or otherwise processed
Regulation: step 1
controlling when and how often a given gene is transcribed
What does a eukaryotic repressor do?
decrease transcription by preventing the mediator (protein complex) to form
The DNA sites to which eukaryotic gene activators bind
enhancers
How do eukaryotic cells coordinate the expression of multiple genes?
even though control of gene expression is combinatorial, the effect of a single transcription regulator can still be decisive in switching any particular gene on or off
When genes are used to make protein.
expression (The term gene expression refers to the formation of a functional protein by using the information contained in a gene).
True or false. Repressor proteins turn genes on and activator proteins turn genes off
false
Non-coding regions of DNA sometimes have this role to play.
gene regulation
the operon is highly expressed only when two conditions are met:
glucose is absent and lactose is present
The lac operon encodes proteins to do what?
import and digest the disaccharide lactose
It is estimated that approximately 1000 transcription regulators are sufficient to control the 24,000 genes that give rise to an individual hum
just know this
RNA interference (RNAi)
keeps the potentially destructive elements in check
A master transcription regulator, if expressed in the appropriate precursor cell, can trigger the formation of a specialized cell type or even an entire organ.
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A typical eukaryotic cell expresses only a fraction of its genes, and the distinct types of cells in multicellular organisms arise because different sets of genes are expressed as cells differentiate.
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Cells can regulate gene expression by controlling events that occur after transcription has begun. Many of these post-transcriptional mechanisms rely on RNA molecules that can influence their own stability or translation
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Cells have a defense mechanism for destroying "foreign" doublestranded RNAs, many of which are produced by viruses. It makes use of small interfering RNAs (siRNAs) that are produced from the foreign RNAs in a process called RNA interference (RNAi)
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Cells in multicellular organisms have mechanisms that enable their progeny to "remember" what type of cell they should be. A prominent mechanism for propagating cell memory relies on transcription regulators that perpetuate transcription of their own gene—a form of positive feedback
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Eukaryotic transcription regulators act in two main ways: (1) they can directly affect the assembly process that requires RNA polymerase and the general transcription factors at the promoter, and (2) they can locally modify the chromatin structure of promoter regions
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In bacteria, transcription regulators usually bind to regulatory DNA sequences close to where RNA polymerase binds. This binding can either activate or repress transcription of the gene. In eukaryotes, regulatory DNA sequences are often separated from the promoter by many thousands of nucleotide pairs.
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In eukaryotes, the expression of a gene is generally controlled by a combination of different transcription regulators
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In multicellular plants and animals, the production of different transcription regulators in different cell types ensures the expression of only those genes appropriate to the particular type of cell.
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In principle, gene expression can be controlled at any of the steps between a gene and its ultimate functional product. For the majority of genes, however, the initiation of transcription is the most important point of control.
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MicroRNAs (miRNAs) control gene expression by base-pairing with specific mRNAs and inhibiting their stability and translation.
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One differentiated cell type can be converted to another by artificially expressing an appropriate set of transcription regulators. A differentiated cell can also be reprogrammed into a stem cell by artificially expressing a different, specific set of such regulators
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The pattern of DNA methylation can be transmitted from one cell generation to the next, producing a form of epigenetic inheritance that helps a cell remember the state of gene expression in its parent cell. There is also evidence for a form of epigenetic inheritance based on transmitted chromatin structures.
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The recent discovery of thousands of long noncoding RNAs in mammals has revealed new roles for RNAs in assembling protein complexes and regulating gene expression.
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The transcription of individual genes is switched on and off in cells by transcription regulators, proteins that bind to short stretches of DNA called regulatory DNA sequences
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the Lac repressor shuts off the operon in the absence of
lactose
What are transcription regulators?
proteins that bind to specific DNA sequences and control gene transcription.
transcription regulators
proteins that determine whether and how frequently a gene will be transcribed into messenger RNA
Why do the vast majority of gene include regulatory DNA sequences?
that are used to switch the gene on or off
When lactose is present AND glucose is absent
the cell executes the appropriate program
RNA-induced silencing complex (RISC)
the complex that mediates RNA interference
regulatory DNA sequences
used to switch the gene on or off. Some regulatory DNA sequences are as short as 10 nucleotide pairs and act as simple switches that respond to a single signal; such simple regulatory switches predominate in bacteria.
A positive feedback loop ensures
cell memory in daughter cells
cell differentiation occurs when
cells express different genes
terminally differentiated cells
cells that are considered to be permanently committed to a specific function
A protein made by bacteria that assists RNA polymerase to bind the promoter; not sigma factor.
Activator (These are proteins made by bacteria that activate transcription. Activators assist RNA polymerase to bind to the promoter to activate the process of transcription).
reporter gene
A genetic marker included in recombinant DNA to indicate the presence of the recombinant DNA in a host cell.
In frog egg experiment, what happened?
A skin cell is taken, put into a new frog egg, and the same type of cells are produced. This further proved that all cells have the same DNA, even with specialization. Same effect for other experiments.
Master transcription regulators
A transcription regulator is specifically required for the formation of a particular cell type.
A quality of proteins that have multiple binding sites.
Allosteric (An allosteric protein has multiple ligand binding sites, such that binding of ligand to one site may affect ligand binding at another. This is also known as cooperative binding).
How many protein coding cells does a typical differentiating human cell express?
About 19,000 total
Control over the expression of a gene by many transcription regulators.
Combinatorial (The expression of genes are controlled by several different transcription regulators, which require specific combination to turn 'on' a gene. This is called combinatorial regulation).
combinatorial control
Describes the way in which groups of transcription regulators work together to regulate the expression of a single gene.
When cells become specialized into tissues.
Differentiation (The process by which cells, tissue, organs acquire specilized features is called differentiation).
Two proteins that bind/work together.
Dimer (two proteins that bind or work together are called dimer to increase their functional cooperativity).
DNA sequences recognized by activator proteins in eukaryotes; sequence may be far from the gene it's activating.
Enhancer (DNA sequences recognized by activator proteins in eukaryotes and may be far from the gene its activating).
True or false. Only Eukaryotic cells use gene expression/use genes selectively.
False
True or false.Do the various cell types of an organism differ because they contain different genes?
False they express them differently.
True or false. A single transcription regulator can only initiate the formation of once cell type.
False. A single transcription regulator can form an entire organ.
epigenetic inheritance
Inheritance of traits transmitted by mechanisms not directly involving the nucleotide sequence.
cell memory
The ability of differentiated cells and their descendants to maintain their identity.
The most important complex of proteins that serves as an adapter to close the loop of DNA between the enhancer and the protein
Mediator
Mass Spectroscopy
This technique is much more sensitive than electrophoresis and it enables the detection of proteins that are produced even in minor quantities.
Protein is the fundamental form of this; your outward appearance
Phenotype (the observable morphological appearance and is determined by different combination of alleles. Proteins is the fundamental form of this).
True or false. A transcription regulator interacts with the DNA double helix.
true
A protein made by bacteria that physically restricts the binding of RNA polymerase.
Repressor (It is a protein synthesized by regulator gene and is meant for blocking the operator gene so that the structural gene is unable to form mRNA.).
What two transcription regulators that control Lac Operon
The LAC repressor and the CAP
True or false. Many transcription regulators bind to DNA as dimers.
true
gene expression
The process by which information encoded in DNA directs the synthesis of proteins or, in some cases, RNAs that are not translated into proteins and instead function as RNAs.
What happens to a liver cell that receives cortisol/hormone signals?
The protein production increases
small interfering RNAs (siRNAs)
The resulting double-stranded RNA fragments
True or false. A single transcription regulator can coordinate the expression of many different genes
True
True or false. All cell types contain the same DNA (i.e. skin cells, plant cells, bacteria)
True
True or false. Can a cell change the Expression of Its Genes in Response to External Signals?
True
True or false. Regulatory DNA sequences, in eukaryotes especially, have very long nucleotides. Some as long as 100,000 pairs.
True
The TATA box is...
a DNA recognition sequence for the first general transcription factor that binds to the promoter
DNA methylation patterns can be faithfully inherited when
a cell divides
long noncoding RNAs
a class of RNA molecules that are defined as being more than 200 nucleotides in length
positive feedback loop
a master transcription regulator activates transcription of its own gene, in addition to that of other cell-type-specific genes.
dimer
a molecule or a molecular complex consisting of two identical molecules linked together.
DNA methylation
adding a methyl group to DNA
histone acetyltransferases
an enzyme that attaches acetyl groups to the amino terminal tails of histone proteins
Where are regulators and chromatin-modifying proteins assembled?
at the promoter (by the mediator)
Transcription: promoter
binds to RNA polymerase
When glucose is not present, the bacterium makes...
cAMP, which allows the CAP to switch on genes that allow the cell to use alternative types of carbon such as lactose
Hemoglobin
red blood cells
miRNA
regulate gene expression
post-transcriptional controls
regulate gene expression after transcription initiation
Regulation step 4
regulating how quickly certain mRNA molecules are degraded
histone deacetylases
remove acetyl groups
Regulation step 3
selecting which mRNAs are exported from the nucleus to the cytosol
Regulation step 5
selecting which mRNAs are translated into protein by ribosomes
induced pluripotent stem (iPS) cells
somatic cells reprogrammed to differentiate into any of several cell types
embryonic stem (ES) cells
stem cells from early embryos that can develop into any cell type
Pluripotency
the potential of a cell to develop into more than one type of mature cell depending on the environment
What is cell differentiation?
the process by which unspecialized cells develop into their mature forms and functions
As long as different genes contain regulatory DNA sequences that are recognized by the same transcription regulator...
they can be switched on or off together as a coordinated unit.
Regulations step 6
they have been made
