Key Concepts & Study Questions for BIOL 303 (F2013) Lecture Set 2
Key Concepts (you should be able to describe or define these):
• genome equivalence & differential gene expression
• enhancers, reporter genes, & reporter constructs
• transcription factors
• genomic imprinting
• alternative (or differential) RNA splicing
• microRNA (miRNA)
1. What is the ultimate test for genomic equivalence?
The ultimate test for genomic equivalence is to have the nucleus of a
differentiated cell to generate every other type of differentiated cell in the
body. If each cell’s nucleus is identical to the zygote nucleus then each cell’s
nucleus should also be capable of directing the entire development of the
organism when transplanted into an activated enucleated egg. In 1997, Ian
Wilmut produced a mature fertile sheep cloned from a somatic nucleus.
2. Histones are commonly subjected to what types of modifications? What general effects
are associated with these modifications?
Histones are commonly subjected to:
acetylation by histone acetyltransferases, which activates transcription –
addition onto lysine () residues neutralizes the basic charge
methylation by histone methyltransferases can either repress or activate
transcription – depending on which lysine residue is being methylated
and other nearby methylation or acetylation (methylation at 4, 38, 79
promotes gene activation, methylation at 9 and 27 repress gene
expression, histone H3 Nterm)
3. Why do you think enhancer elements are so important during development?
Enhancer elements are so important during development because they
control the efficiency and rate of transcription from a specific promoter. This is important because an organism needs a different amount of a certain
protein at different periods of its life. One gene can have more than one
enhancer element, and different genes can be expressed in different tissues.
For example: during puberty a certain gene may be expressed at a higher
rate compared to earlier on in the organisms life.
4. If you were examining the sequence of an unknown protein, how might you be able to
determine whether or not it functions as a transcription factor?
I would be able to determine if it functions as a transcription factor because
transcription factors have a DNA binding domain (recognizes and binds to
particular DNA sequences within the enhancer) and transactivating domain
(activates or suppresses transcription of the associated gene by interacting
with proteins that in turn bind to RNA polymerase. Some transcription
factors also have proteinprotein interaction domains (allow the transcription
factor to be modulated by transcription associated factors).
5. Name and describe a technique that would allow you to define the DNA sequence to
which a given transcription factor binds. What are the prerequisites for being able to use
Chroatin Immunoprecipitaton sequencing would allow you to define the
DNA sequence to which a given transcription factor binds. The chromatin is
isolated chemically crosslinked. The DNA is then fragmented into ~500 bp
pieces, which are incubated which an antibody specific for a particular
binding protein. Antibodies are precipitated (immunoprecipitation) and the
DNA from the immunoprecipitate