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