True or False. All the cells in your body have the same genes.
True
What is considered the most important level of regulation?
Initiation of Transcription
Regulation of Transcription Initiation is divided into what two levels?
Basal Level Transcription
Regulated Expression
What is Basal Level Transcription?
It is driven by the interaction of:
Core Promoter Elements
General Transcription Factors
RNA Polymerase II
What is Regulated Expression?
It is driven by the interaction of:
Promoter Proximal Elements
Enhancers
Activators & Repressors
(Things that modify Basal Level)
In tightly packaged chromatin, the basal level of transcription is what?
Zero
Eukaryotes have how many RNA Polymerases?
3
What does Polymerase I transcribe?
5.8S, 18S, and 28S rRNA genes
What does Polymerase III transcribe?
5S rRNA
tRNA
several other small genes
What does Polymerase II transcribe?
Protein Coding Genes
Eukaryotic mRNAs encode how many polypeptide each?
One polypeptide
Eukaryotic mRNAs are generally LESS or MORE stable than Prokaryotic mRNAs?
MORE stable.
The default state for most Prokaryotic genes is what?
On
The default state for most Eukaryotic genes is what?
Off
What is the major form of gene regulation?
Transcription Initiation
Name three Eukaryotic cis-elements.
Enhancers
Promoter Proximal Elements
Core Promoter
Where are Enhancers often located?
Thousands of BPs upstream or downstream of a gene, even within the transcription unit it regulates.
What type structure do Transcription Regulatory Proteins of Eukaryotes have?
Modular Structure
Regulatory Transcription Factors have some combination of what kinds of Functional Domains?
DNA Binding Domain
Domain that interacts Basal Level
Domain that binds with other Specific Transcription Regulatory Proteins
Domain that alters Chromatin condensation
Domain that senses a physiological state
Coregulators do what?
Help alter Chromatin condensation
Coregulators are recruited by what?
Transcription Factors
What is a Transcription Factor?
A sequence of specific DNA binding protein that somehow alters the rate of transcription at a gene.
What are Coregulators?
They are recruited to genes by Transcription Factors but do not bind directly to DNA. They indirectly regulate the rate of transcription.
What bind to Promotor Proximal Elements and Enhancers and change the rate of Transcription?
Activators & Repressors
Specific Transcription Factors act in what ways?
They can bind & help recruit GTFs or the Polymerase to the Promoter.
They can bind & help recruit Chromatin Remodeling Complexes to the region.
They can bind & help recruit Histone Modifying Enzymes to the region.
They can bind to other TFs & alter their activities.
What is a model of Eukaryotic gene regulation?
GAL system in Budding Yeast
What genes are used by Saccharomyces cerevisiae to enconde enzymes to convert galactose to glucose?
GAL1
GAL2
GAL7
GAL10
In S. cerevisiae, each of these are controlled by a SINGLE or SEPARATE regulatory sequences?
Separate.
Does S. cerevisiae have Operons?
No.
What are the Regulatory Proteins for the expression of the GAL1, GAL2, GAL7, and GAL10 genes?
GAL3
GAL4
GAL80
What is the equivalent of enhancers in yeast?
Upstream Activator Sequence (UAS)
What binds to UAS elements associated with GAL genes?
GAL4 Transcriptional Activator Protein
GAL4 transcription activator protein has what kind of structure?
Modular
GAL4 Protein contains what?
Structurally and functionally separable DNA binding and transcription activation domains
What happens in S. cerevisiae in the absence of glucose?
Gal80 protein binds and blocks the function of the Gal4 activation domain
What happens in S. cerevisiae in the presence of glucose?
Gal3 protein facilitates the release of Gal80, exposing the Gal4 activation domain.
What does the Gal4 activation domain do?
Recruits RNA pol II
How does Gal4 activation domain recruit RNA pol II?
By binding to TFIID & Mediator
What is a Mediator?
A coactivator complex
In Eukaryotic chromosomal DNA, what can inhibit transcription initiaton?
Nucleosomes in Chromatin
What is required for Transcriptin Eukaryotes regarding Chromatin?
Chromatin Remodeling
Histone Modification
Each nucleosome contains two copies of the core histones. What are the core histones?
H2A
H2B
H3
H4
Are Core Histones Highly Basic, Neutral, or Highly Acidic?
Highly Basic (+)
Histone H1 does what?
Binds to the Linker DNA between Histones
Chromatin Remodeling requires what kind of energy source?
ATP
Chromatin Remodeling does what?
Repositions nucleosomes or
Alters the interaction of histones and DNA within a nucleosome
What is an example of a Histone Remodeling Complex?
SWI/SNF
SWI/SNF can be recruited to specific sites by what?
Transcription Factors or
Acetylated Histones
What is an example of a TF that recruits SWI/SNF?
Gal4
What is the best studied form of Histone Modification?
Acetylation of Histone Tails by Histone Acetyltransferase (HAT)
What does Acelyation of Lysine Residues do within the histone tails?
It lessens the attraction between histones and DNA and provides binding sites for several proteins involved in transcription.
What can Histone Acetylation be reversed by?
Histone Deactylases (HDACs)
How does the presence of Glucose repress expression of the GAL genes?
Mig1 protein binds a DNA sequence found between the UAS and the GAL1 promoter. Mig1 then recruits the HDAC containg corepressor complex Tup1 to the gen, resulting in a more condensed chromatin structure.
Enhancers contain what?
Binding sites for multiple specific transcription factors.
What is an Enhanceosome?
A large complex created by TFs bind to the Enhancer
Enhanceosomes help recruit Transcriptional Machinery by bind what?
Coactivator Complexes
How can Enhancers act at a distance from the promoter?
They can loop out the intervening DNA and interact with proteins in the promoter region.
What prevents Enhancer Activation?
Enhancer-Blocking Insulators
How do Enhancer-Blocking Insulators work?
Insulators segregates regulatory sequences into separate loops of chromatin preventing them from interactin with each other.
In maternal impriting, the copy of the gene inherited from WHICH parent is inactive?
the Mother
In paternal impriting, the copy of the gene inherited from WHICH parent is inactive?
the Father
An imprinted gene will be expressed as if there were how many copies present in the genome?
One
What is the most common DNA modification in higher eukaryotes?
The modification of cytosine to form 5-methylcytosine
About how many of the C's are methylated?
5%
The methyl group on the methylated C does not alter base pairing, but it can alter the ability of a DNA binding protein to recognize a sequence HOW?
Because it protrudes into the Major Groove
What kind of relationship (proportional or inverse) exists between the degree of Methylation an the degree of Gene Expression?
Inverse
Genomic imprinting was discovered how?
Because of the unusual inheritance of imprinted genes.
What are two examples Epigenetic Information?
DNA Methylation
Covalent Modification of Histones
How can epigenetic information be inherited?
Through Mitosis or from Parent to Offspring
For Epigenetic Information to be Inherited, where must the information be preserved?
In the daughter molecules each time DNA replication occurs.
