Control of Gene Expression

Question 1

housekeeping proteins

Answer 1

-genes that are expressed in all cell types

Question 2

chromatin

Answer 2

• large amounts of DNA that are wrapped around histone complexes.
• chromatin make up chromosomes

Question 3

non-accessible DNA with regards to transcription and DNAse accessibility

Answer 3

-this is DNa that is wrapped tightly around histones and is not accessible to enzymes such ate RNA pol of DNAse1

Question 4

heterochromatin

euchromatin

Answer 4

heterochromatin: tightly wrapped, non actively transcribed DNA (condensed)
euchromatin: loose DNA that can be actively transcribed

Question 5

hypersensitive sites

-location

Answer 5

• very accessible site for enzymes such as DNAse1

- found in upstream control regions

Question 6

locus control region (LCR)

Answer 6

-regulates the expression of families of genes over long distances by regulating chromatin organization

Question 7

nucleosome remodeling

Answer 7

-regulates gene expression by increasing the mobility of nucleosomes throughout the genome thereby altering the chromatin structure

Question 8

histone acetylation

• function
• mechanism
• enzyme and type
• converse

Answer 8

• allows DNA to be transcribed by acetylating histones.
• this process dulls the positive charge on histones which is causing the binding to DNA, allowing the DNA to become more loosely affiliated with the histone therefore allowing the DNa to be transcribed
• many activators and co-activators possess histone acetyltransferase activity
• conversely, histone deacetylases are repressors

Question 9

DNA methylation

• function
• enzyme and where it acts on the nucleotide
• pattern of methylation
• tissue type
• housekeeping genes

Answer 9

• methylation of certain cytosine residues may play a key role in gene inactivation
• this process is carried out by DNA methyltransferase which methylates cytosine residues at the 5’ C, typically next to guanine residues
• it has been found that tissues that do not express a certain gene show that gene to be methylated within its genome
• housekeeping genes are not found to be methylated

Question 10

CpG islands

Answer 10

• long CpG rich stretches of DNa that almost always lack methylation
• typically found within the promoters of housekeeping genes

Question 11

Simple overview of the steps involved in establishing transcriptional competence

Answer 11

• activation of the locus control region
• chromatin remodeling by acetylation of histone
• chromatin remodeling by removing methyl groups from cytosine residues

Question 12

activators

• role in transcription
• necessity
• communication with basal transcription factors

Answer 12

• class of transcription factors which bind to regulatory regions known as enhancers
• these must be present for the gene to be transcribed at a measurable rate
• communicate with the basal transcription factors through co-activators

Question 13

coactivtors

Answer 13

• linked tightly to the TATA binding protein
• interaction with the activator proteins allows the basal factors to position the RNA pol 2 at the start of the coding region and being transcribing

Question 14

silencers and repressors

Answer 14

-silencers bind proteins called repressors which interfere with the function of activators and block the initiation of transcription

Question 15

multifunctional character of transcription factors with regards to p53

• multiple regions of p53
• transactivation domain of p53

Answer 15

• transcritption factors typically play many key roles in transcription simultaneously such as (DNA binding, dimerization, activation of transcription)
• p53 has multiple regions conserved across all species and mutations at any of these regions can cause tumor formation.
• p53 has a transactivation domain which is likely involved in protein-protein interactions that stimulate RNA pol2 transcription

Question 16

Covalent modification of proteins

-RNA pol 2

Answer 16

• many TFs have enzymatic activity which allow them to modify other proteins involved in transcription by phosphorylation or activation etc.
• RNA pol2 is extensively phosphorylated in early transcription

Question 17

heat shock

• what happens
• protein involved in the regulation and its role

Answer 17

• at elevated temperature, transcription and translation are suspended
• however, in a certain group of proteins, called heat shock proteins which help with cell survival at higher temperatures, transcription is promoted
• specifically a protein called heat shock factor is activated by the increased temp and it binds to a certain DNA site upstream of certain genes (which is free of nucleosomes in standard condition) resulting in increased transcription

Question 18

steroid hormones and intracellular steroid receptors
response element concentration and activity
-steroid-receptor complex role in chromatin restructuring

Answer 18

• substances derived from cholesterol which are soluble in lipid membranes and can diffuse into the cell
• once inside the cell they bind to intracellular steroid receptors which are site-specific DNa binding molecules
• the receptor-hormone complex is responsible for the displacement of nucleosomes from promoter regions
• response elements (enhancers) are the binding sites on DNa for these steroid-receptor complexes. these response elements are specific to the hormone involved
• response elements are present at different concentration in different cell types and have a transient effect (are not turned constitutively on)

Question 19

DNA Microarray

Answer 19

• a poly-l-lysine coated glass slide (positive charged) is spotted with DNA of varying length
• the DNA is then denatured into a single strand form allowing to base pair when introduced to a compliment
• RNA is extracted from two samples of interest and converted to cDNA in the presence of a fluorescent dye
• this cDNA is then introduced to the microarray slide where it can bind to its complimentary strand if present
• if each sample (red and green) bind at the same spot, it will show yellow, meaning both samples were expressing that gene
• intensity of the color can also be measured to determine the relative expression level of a gene
• this can be used to determine the difference in expression of diseased and non diseased cells as well as cells that have been given a pharmaceutical vs those that have not

Question 20

RNA seq

Answer 20

• used to determine the composition and quantity of RNA in a cell at a given time
• this requires the previous creation of a cDNA library
• applications include identifying alterations in cellular pathways during infection and changes in gene expression during cancer

Question 21

ANtisense therapy

-stabilizing the antisense RNA strand

Answer 21

-theory that one could eliminate or terminate the transcription of a given mRNA by introducing its complimentary strand into the cell and therefore by base pairing the mRNA, block the ribosome from translating it
in order to inhibit the degradation of the antisense RNA, sulfur atoms are substituted for oxygen on the phosphate links between the nucleotides
-this hasn’t shown a ton of promise as these particles must enter and be retained by the cell

Question 22

RNAi

• description
• mechanism
• application for what genetic class of disease

Answer 22

• sequence specific, post-transcriptional gene silencing initiated by dsRNA homologous to the gene attempting to be silenced.
• this is carried out by a protein called RISC which binds the dsRNA and chaperons it to its compliment
• this is being used to treat disease that act via dominant mutant alleles such as cancer and neurodegenerative disease as well as combat viral infection