Gene Expression (I and II) Flashcards

Question

Describe a gel retardation experiment and what it shows us.

Answer 1

Used to examine protein-DNA or protein-RNA interactions The basic idea is that DNA with proteins complexed onto it will move slower than those without proteins bound in a gel electrophoresis experiment. Size and charge of the proteins will impact how the complex moves through the gel

Answer 2

DNA in living cells has regulatory proteins bound to the gene regulatory elements These proteins are cross-linked to the DNA with formaldehyde Cells are lysed and the DNA is broken into small fragments Antibodies for a specific regulatory protein (that is now cross-linked to its DNA fragment) are used to precipitate out the DNA of interest The only DNA left following precipitation will be the DNA that the regulatory protein was bound to Crosslinks can be removed (with acid) and the DNA can be amplified for further analysis

Answer 3

Reporter genes are used to study the role that enhancers play in gene regulation. An enhancer of interest is inserted into a bacterial plasmid This enhancer is used to enhance the activity of a reporter gene that is easy to assay (example: luciferase, beta-galactosidase) If the reporter gene shows high expression, then the transcription factor was active in promoting the transcription of the gene of interest

Answer 4

Multiple different regulatory proteins can bind to an identical regulatory element in a gene. The combination of proteins that bind to an element depends on the cell type or physiological state of the cell Some combinations will activate and some will repress gene expression

Answer 5

Max exists as a homodimer Max-Max Max can also heterodimerize to form Myc-Max and Mad-Max

Answer 6

These dimers bind to E-box elements of genes required for cell division and determine whether a cell will proliferate or differentiate Max-Max binds the E-box and silences transcription (this is the normal state) Myc is produced when cells want to divide, so Myc-Max dimers bind and upregulate the genes for cell division causing transcription. Mad is produced when a cell wants to differentiate, so the Mad-Max dimers bind and repress the transcription of differentiation genes.

Answer 7

Helix-loop-helix

Answer 8

Myc is expresed in the G1 to S transition of the cell cycle. When cells want to divide.

Answer 9

An extracellular signal (mitogen) activates a kinase. This kinase then activates (terminal phosphate from ATP transferred onto the serine of a protein) another, which activates another ... and so on. The final kinase in the cascade is usually a nuclear kinase (MAPK) which is found on the nuclear membrane. When phosphorylated, the MAPK enters the nucleus and activates the transcription factor by phosphorylation

Answer 10

Fos is phosphorylated by ERK (a MAPK protein) and Jun is phosphorylated by JNK (a MAPK protein)

Answer 11

Dosage compensation: if no silencing occured, then expression of the genes found on the X-chromosome would be twice as high as that seen in males, which would be toxic

Answer 12

In the early embryo, each cell contains an active paternal and maternal X-chromosome One of the X-chromosomes is randomly condensed and inactivated All progeny cells from here will have the same x-chromosome inactivated as the parent cells This leads to a mosaic in which patches of cells express each x-chromosome (Calico cat example)

Answer 13

Different regulatory control proteins bind and induce opening of the globin gene at different positions depending on the stage of life. This causes the different hemoglobin subunit types between conception, birth, and early childhood

Answer 14

FALSE: epigenetics Modification of DNA and regulatory proteins can lead to different inheritable genetic information from identical nucleotide sequences

Answer 15

1) Positive feedback transcription factor loops (self-activation) 2) DNA methylation 3) Acetylation and deacetylation of histones (interconvert between euchromatin and heterochromatin) 4) Histone phosphorylation and histone methylation

Answer 16

Protein A is not made because it is required for its own transcription A transient signal turns on expression of protein A, which then promotes the synthesis of more protein A When the cell divides, protein A will be present, so A will be produced in the progeny as well.

Answer 17

In successive cell divisions, different regulatory proteins will exist in each daughter cell. The presence of different combinations of transcription factors leads to cell differentiation. After 2 divisions with 5 transcription factors, 8 cell types can form With 25 regulator proteins, 10,000 cell types can form

Answer 18

CpG sequences These are palindromic

Answer 19

Methylation usually inhibits expression of the gene

Answer 20

True The NH2, H and carbonyl O of the cytosine are all still available to participate in hydrogen bonding

Answer 21

Maintenance methylases recognize hemi-methylated CpG's following DNA replication and produces dimethylated CpG's to match the parent DNA

Answer 22

If gene regulatory proteins are lost from the DNA, the gene is off but leaky (expressed at a basal rate) The exposed DNA can be methylated, which prevents RNA polymerase from binding properly Proteins recognize the methylated DNA and recruit enzyme remodeling complexes and histone deacetylases which condense the gene and turn it completely off

Answer 23

CG islands are found at the 5' end of many housekeeping genes They have repetitive CG sequences close together that actually protect the DNA from methylation rather than induce methylation like CpG bases found elsewhere

Answer 24

They act to acetylate histone proteins of nucleosomes that are hemi-acetylated in newly formed progeny cells. Preserves the acetylation patern of the parental cells

Answer 25

Certain genes are expressed in a parent-of-origin manner rather than following Mendelian genetic rules A particular gene retains its methylation in either the sperm or the egg, but not both Most genes lose their methylation during meiosis, but a small percentage do not