Gene Expression I Test Two Flashcards
How can an epidermal cell be different from a liver cell when they have the same genes?
They are different because they express their proteins differently
What are house keeping genes?
Genes that are present in all cells such as actin glucose, DNA replication transcription translation enzymes…
What two things does gene regulation require?
Short stretches of DNA sequences called recognition sites and Regulatory proteins
What is a LOGOS
demonstrates the flexibility of DNA binding proteins and what bases they can bind too. It is shown in a graph and the larger the letter represents the higher affinity.
Where are DNA recognition sequences located in regards to the first exon?
They can being either proximal or distal to the exon.
Where do most DNA binding proteins/motifs bind on DNA?
To the major groove (must be complementary). Usually make contact with the DNA in multiple places, the individual hydrogen bonds are weak but together they are strong.
What are the different domains found on a DNA motif?
Binding domain, dimer domain, activation domain, regulatory domain
Which two domains are not absolutely necessary?
Dimer and regulatory domains
Describe the experiment that proved a reporter and promoter gene exist? (Transcription Factors are modular).
DNA was put into a mouse and wild type DNA Beta galactose was produced. In the mutant type the first 50 AA were clipped off so no binding occurred. Another mutant strand had the C terminus cut away so even though the protein could bind there was no production of Beta Galactose (Activation).
What DNA Motif is connected by a short turn of amino acids to a short alpha helix and a long alpha helix, can be a dimer, and has a long alpha helix that recognizes the sequences on the major groove?
Helix Turn Helix
What is a Zinc Finger DNA Motif?
Zn atom in the center of two alpha helices, it is typically found in clusters, and each “finger” binds to the major groove of DNA.
Describe a Leucine Zipper.
2 Alpha helices interacting (Dimer, hetero or homo), similar to a clothespin when it binds DNA major groove, activation domain overlaps dimer domain, held together by hydrophobic interactions. between amino side chains (leu)
What DNA motif looks similar to a clothespin, has a short alpha helix connected with a loop of amino acids to another alpha helix. Also flexible, the helices can bend over one another and can be a hetero or homo dimer .
Helix Loop Helix
What is the most common and simplest DNA binding motif?
Helix turn helix
What separates dimers in a helix turn helix?
One turn
What domains are found in a Helix Loop Helix domain?
DNA binding, Dimerization and activation domains are found
Describe Hereditary Spherocytosis?
Mutation in the Zn finger Motif leading to a type of hemolytic anemia with round RBC’s. Caused from a mutation in a gene that codes for the EMS in RBC’s.
What is an example of a mutated zn finger protein that causes HS?
KLF1 zn finger protein binds to promoters of all genes in the EMS to turn them on. There are three exons involved, when a mutation occurs in this gene transcription does not occur and therefore not enough RNA is made so no protein is made.
What is the single nucleotide mutation in Hereditary Spherocytosis?
GAA to GAT changing Glu to Asp within exon three zn finger domain two. This will bind different and no transcription will occur.
What makes up the Erythrocyte Membrane Skeleton?
Spectrin, anchorin, and alpha and beta subunits forming dimers and tetramers.
What is EMSA? (Gel Mobility Shift Assay)
Electrophoresis on a protein gel using DNA mixed with protein. The DNA that binds to protein won’t travel far and can be found near the insertion site, while free DNA will move to the base.
Affinity Chromatography?
Used to isolate DNA binding proteins. Purify the sequence specific binding proteins through salt baths. Start broad by having column with random DNA sequences add proteins. Then get specific using the particular sequence you are looking for.
CHIP?
Chromatin Immuno-precipitation. Allows for hte identification of the sequence that a known protein binds too. Done in living cells and uses PCR to ID sequence at the end.
What transcribes all protein coding genes?
RNA Polymerase II
