Genetics Chapter 15: Gene Regulation in Eukaryotes

binding of regulatory transcription factors to TFIID

TFIID is a general transcription factor that binds to the TATA box and is needed to recruit RNA polymerase to the core promoter. activators (coactivators) and repressors bind to TFIID

alpha helix

a protein secondary structure that is frequently found in transcription factors that is the proper width to bind to the major groove of DNA double helix

repressor

a regulatory TF that prevents transcription from occurring; binds to silencers

cAMP response element-binding protein

a regulatory transcription factor that becomes activated in response to cell-signaling molecules that cause an increase in the cytoplasmic concentrations of cAMP

regulatory TFs bind to mediators

activators bind and enhance the mediators ability to switch from initiation to elongation, repressors have the opposite effect.

DNA methyltransferase

an enzyme that attaches a methyl group to the number 5 position of the cytosine base, forming 5-methyltransferase (DNA methylation)

methyl-CpG binding proteins

bind methylated sequences and inhibit transcription

3 possible effects of chromatin remodelers

change in location of nucleosomes, eviction of histones from DNA, replace histones with histone variants

chromatin remodeling

dynamic changes in the structure of chromatin that occur during the life of a cell

zinc finger motif

each zinc finger is composed of one alpha helix and two antiparallel beta sheets. A zinc ion holds a zinc finger motif together

histone variants

encoded by genes that have accumulated mutation that change the amino acid sequence of histone proteins. play a role in regulating the structure of chromatin, proper segregation of chromosomes, and influence transcription

histone acetyltransferases

enzymes that acetylate positively charged lysines within the core histones. The attachment of the acetyl group (-COCH3) eliminated the positive charge on the lysine side chain, thereby disrupting the elctrostatic interaction between the histone and the negatively charged DNA backbone

full methylation vs hemimethylation

full: methylation of cytosine in both strands hemi: methylation of only one strand

tissue specific genes

genes that are highly regulated and only expressed in certain parts of a cell

housekeeping genes

genes that encode proteins required in most cells of a multicellular organism

glucocorticoid receptors

glucocorticoid hormones enter the cell by diffusing through the plasma membrane. Once inside, the hormone specifically binds to these receptors. Hormone shock protein is released, exposing a nuclear location signal that directs a protein to the nucleus. Two glu receptors form a homodimer and enter the nucleus

CpG islands

occur near mane promoters of genes in vertebrates and plants. unmethylated in housekeeping genes, methylated in many tissue-specific genes

transcription factor

proteins that influence the ability of RNA polymerase to transcribe a given gene

domains

regions on transcription factor proteins that have specific functions

general transcription factors

required for the binding of RNA polymerase to the core promoter and it's progression to the elongation stage; necessary for basal transcription

enhancer

sequence that an activator binds to to enhance the rate of transcription

control/regulatory elements

sequences of DNA that are analogous to the operator sites found near promoters

regulatory transcription factors

serve to regulate the rate of transcription of target genes

silencers

sites that repressor proteins bind to to stop transcription from happening

ATP dependent chromatin remodeling

the energy of ATP hydrolysis is used to drive change in the locations and/or compositions of nucleosomes, thereby making DNA more or less amenable to transcription. Important for activation and repression of transcription

leucine zipper motif

the leucine zipper promotes the dimerization of two TF proteins. Two alpha helices are intertwined via the leucines

helix-turn-helix motif

two alpha helices connected by a turn. The a helices lie in the major groove of DNA

heterodimer

two different TF proteins

homodimer

two identical transcription factor proteins

chromatin immunoprecipitation sequencing (ChIP-Seq)

used to determine where in the genome particular proteins such as histones are located within the genome

three ways that regulatory transcription factors can be modulated

1) binding of a small effector molecule 2) protein-protein interactions 3) covalent modifications

DNA translocases

a catalytic ATPase subunit that is similar to other motor proteins; move along the DNA

combinatorial control

a combination of factors determines the expression of any given gene; most multicellular species use this mechanism

motif

a domain or portion of a domain that has a similar structure in many different proteins

activator

a regulatory transcription factor that enhances the rate of transcription. Binds to an enhancer

steroid receptor

a regulatory transcription factor; the steroid hormone binds directly to this protein to affect transcription

insulator

a segment of DNA that acts as a boundary between two genes

helix loop helix motif

a short alpha helix is connected to a longer alpha helix by a loop; longer helix binds to DNA

nucleosome free region (NFR)

a site that is missing histones; core promoter is located here in genes that can be activated

DNA Methylation

a way to modify DNA structure; the covalent attachment of methyl groups

maintenance methylation

hemimethylated DNA is efficiently recognized by DNA methyltransferase which makes it fully methylated; preserves the methylated condition in future cells

de novo methylation

the methylation of DNA that was previously unmethylated

histone code hypothesis

the pattern of histone modification acts much like a language or code in specifying alterations in chromatin structure