Chapter 17: Control of Gene Expression in Eukaryotes Flashcards
differences between eukaryotic gene regulation and bacterial gene regulation
- many bacterial and archaeal genes are organized into operon and are transcribed into a single molecule; most eukaryotic genes have their own promoters that are transcribed separately
- chromatin structure affects gene expression in eukaryotic cells; DNA must unwind from the histone proteins before transcription can take place
- the presence of the nuclear membrane is eukaryotic cells separates transcription and translation in time and space
transcription and translation location in eukaryotes
transcription - the nucleus
translation - the cytoplasm
transcription and translation location in prokaryotes
simultaneously occur in the cytoplasm
modification of chromatin structure
chromatin structure must change before transcription so that DNA becomes more accessible to transcription machinery
- chromatin is tightly coiled around the octamers, making it difficult for proteins to bind to it
DNase I hypersensitive sites
regions around genes become highly sensitive to the action of DNase I
- frequently develop 1000 nucleotides upstream of the transcription start site
three processes that affect gene regulation by altering chromatin structure
- chromatin remodeling
- modification of histone proteins
- DNA methylation
chromatin-remodeling complexes
protiens that alter chromatin structure without altering the chemical structure of the histones directly
- bind to particular sites on DNA and reposition the nucleosome, allowing other transcription factors and RNA polymerase to bind to promoters and initiate transcription
two domains of histones in the octamer core
- a globular domain that associates with other histones and the DNA
- a positively charged tail domain that interacts with the negatively charged phosphate groups on the DNA
histone code
tails of histone proteins are modified by the addition or removal of phosphate groups, methyl groups, or acetyl groups
- encode information that affects how genes are expressed
methylation of histones
- the addition of CH3 to the tails of histone proteins
- can bring about the activation or repression of transcription
histone methyltransferases
add methyl groups to specific amino acids of histones
histone demethylases
remove methyl groups from histones
acetylation of histones
addition of acetyl groups (CH3CO) to histones
- usually stimulates transcription
- destabilizes chromatin structure, allowing transcription to take place
acetyltransferase enzymes
enzymes that add acetyl groups to histone proteins
deacetylase enzymes
enzymes that strip acetyl groups from histones and restore chromatin structure, repressing transcription
DNA methylation
- methylation of cytosine bases
- most common on cytosine bases adjacent to guanine nucleotides
- associated with the repression of transcription
transcription factors
proteins that bind to specific DNA sequences and regulate transcription
cofactors
proteins recruited by transcription factors that stimulate or repress transcription
general transcription factors
transcription factors that bind to the core promoter and are part of the basal transcription apparatus
- required for the initiation of transcription
basal transcription apparatus
the complex of RNA polymerase, transcription factors, and other proteins that assemble to carry out transcription
- binds to a core promoter and is capable of minimal levels of transcription
enhancer
DNA sequence stimulating transcription a distance away from the promoter
- abundant in eukaryotes
insulator
DNA sequence that blocks or insulates the effect of enhancers in a position dependent manner
- if one lies between an enhancer and promoter, it blocks the action of the enhancer
mediator
complex of proteins that interacts with RNA polymerase
- component of the basal transcription apparatus
super-enhancer
number of enhancers clustered together
- able to stimulate levels of transcription higher than regular enhancers are
silencers
sequences that have an inhibitory effect on the transcription of distant genes
heat-shock proteins
proteins that help prevent damage by stressors like extreme hear
response elements
regulatory sequences that typically contain the same consensus sequence at varying distances from the gene being regulated
- binding sites for transcription factors, which bind to the response elements and elevate transcription
exonic/intronic splicing enhancers and splicing silencers
additional sequences that promote or repress the use of particular splice sites during the process of RNA splicing, resulting in alternative splicing outcomes
- proteins or ribonucleoprotien particles bind to these sites
SR proteins
group of proteins involved in splice-site selection that has two protein domains:
1. an RNA binding region
2. alternating serine and arginine amino acids
SR proteins bind to splicing enhancers on the pre-mRNA and stimulate the attachment of small nuclear ribonucleoprotiens (snRNPs) , which then commit the site to splicing
ribonucleases
enzymes that specifically break down RNA
poly(A) binding proteins (PABPs)
bind to the poly(A) tail and contribute to its stability enhancing effect
RNA silencing
RNA interference; small RNA molecules are diced and produce a silencing complex
post translational protein modification
- selective cleavage and trimming of amino acids from the ends
- acetylation
- addition of phosphate groups, methyl groups, carboxyl groups, carbohydrates, or ubiquitin
