BIOL 241 Exam 3 Purdue Actual study
Questions and correct/verified Answers
GAL genes in yeast - ANSW-inducible by the presence of galactose, but only if the concentration of
glucose is low; subject to catabolite repression; not operon; GAL1 and GAL10 genes controlled by UAS
UASg - ANSW-central control region of yeast gal genes that contains four binding sites for the GAL4
protein; the chromatin structure is constitutively open/DNase hypersensitive
Eukaryotic promoter - ANSW-contains several elements, including TATA box, CAAT box, and the GC box;
TATA box is where general/basal transcription factors bind; the CAAT box and GC box are elements that
bind regulatory transcription factors
Mutational analysis - ANSW-used to identify cells or DNA that have genotype and allele frequency
differences from the normal genome
enhancers - ANSW-differ from elements in the regulatory promoter region- the position is not fixed and
can be upstream, downstream, or within the gene; its orientation can be inverted w/o significant effect;
if it is experimentally moved to another location in the genome, the transcription of the adjacent gene is
enhanced
examples of enhancers - ANSW-within the gene- an enhancer in the intron of the immunoglobulin heavy
chain gene and is only active in cells expressing Ig genes. Downstream- human beta globin gene.
Upstream- UAS upstream activation in yeast
Structural motifs of transcription factors - ANSW-helix-turn-helix (HTH)
zinc finger
leucine zipper (Fos/Jun dimers)
helix-loop-helix (HLH) (Myc and partner proteins)
helix-turn-helix motif - ANSW-A major structural protein motif that is common in proteins that regulate
gene expression by binding DNA. It is composed of two alpha helices joined by a short strand of amino
acids.
helix-loop-helix motif - ANSW-a short alpha helix is connected to a longer alpha helix by a loop
zinc finger motif - ANSW-A protein structural motif involved in DNA recognition by some DNA-binding
proteins; characterized by a single atom of zinc coordinated to four Cys residues or to two His and two
Cys residues.
leucine finger motif - ANSW-consists of periodic repetition of a leucine residue at every seventh position
and forms an alpha helical conformation, which facilitates dimerisation
transcriptional activation via TFIID - ANSW-The activator/coactivator complex recruits TFIID to the core
promoter and/or activates its function. Transcription will be enhanced.
, Transcriptional repression via TFIID - ANSW-The repressor protein inhibits the binding of TFIID to the
core promoter or inhibits its function. Transcription is silenced.
change in chromatin structure - ANSW-eukaryotic chromosomal DNA is complexed with histones to form
chromatin, nucleosomes in the chromatin can inhibit transcription, and chromatin remodeling is
required for transcription
this can occur through the SWI/SNF remodeling complex or the histone modification
Examples of histone modifications - ANSW-phosphorylation, acetylation, methylation
SWI/SNF complex - ANSW-chromatin remodeling complex that can be directed to specific DNA sites by
transcription factors, by acetylation of histones or by binding to methylated DNA
ATP-dependent chromatin remodeling - ANSW-histone eviction creates a gap with no nucleosomes;
variant histones affect transcription
DNA methylation and gene regulation - ANSW-high level of DNA methylation is associated with low level
of gene expression
methylation state of a gene can be determined by restriction enzyme analysis with HpaII and MspI
inverse relationship exists between the degree of methylation and the degree of gene expression
DNA methylation - ANSW-The addition of methyl groups to bases of DNA after DNA synthesis; may serve
as a long-term control of gene expression; methylation of cytosine- down by DNA methyltransferase
Molecular model for inheritance of DNA methylation - ANSW-De novo methylation is an infrequent and
highly regulated event
mechanisms of transcriptional silencing by DNA methylation - ANSW-methylation inhibits the binding of
an activator protein; methyl-CpG-binding protein recruits other proteins that change the chromatin to a
closed conformation
insulators - ANSW-barrier to change in chromatin structure; blocks the effects of neighboring enhancer
Posttranscriptional regulation of gene expression - ANSW-although transcriptional control is the major
type of regulation in eukaryotes, posttranscriptional regulation also occurs in many organisms;
alternative splicing and RNA-mediated gene silencing
alternative splicing - ANSW-can generate many different proteins from one gene because it can generate
different forms of mRNA from a pre-mRNA; the number of proteins that a cell can make is not directly
related to the number of genes in the genome
MicroRNAs - ANSW-mediate RNA silencing by binding to the 3' untranslated regions of mature mRNAs to
block translation.
Questions and correct/verified Answers
GAL genes in yeast - ANSW-inducible by the presence of galactose, but only if the concentration of
glucose is low; subject to catabolite repression; not operon; GAL1 and GAL10 genes controlled by UAS
UASg - ANSW-central control region of yeast gal genes that contains four binding sites for the GAL4
protein; the chromatin structure is constitutively open/DNase hypersensitive
Eukaryotic promoter - ANSW-contains several elements, including TATA box, CAAT box, and the GC box;
TATA box is where general/basal transcription factors bind; the CAAT box and GC box are elements that
bind regulatory transcription factors
Mutational analysis - ANSW-used to identify cells or DNA that have genotype and allele frequency
differences from the normal genome
enhancers - ANSW-differ from elements in the regulatory promoter region- the position is not fixed and
can be upstream, downstream, or within the gene; its orientation can be inverted w/o significant effect;
if it is experimentally moved to another location in the genome, the transcription of the adjacent gene is
enhanced
examples of enhancers - ANSW-within the gene- an enhancer in the intron of the immunoglobulin heavy
chain gene and is only active in cells expressing Ig genes. Downstream- human beta globin gene.
Upstream- UAS upstream activation in yeast
Structural motifs of transcription factors - ANSW-helix-turn-helix (HTH)
zinc finger
leucine zipper (Fos/Jun dimers)
helix-loop-helix (HLH) (Myc and partner proteins)
helix-turn-helix motif - ANSW-A major structural protein motif that is common in proteins that regulate
gene expression by binding DNA. It is composed of two alpha helices joined by a short strand of amino
acids.
helix-loop-helix motif - ANSW-a short alpha helix is connected to a longer alpha helix by a loop
zinc finger motif - ANSW-A protein structural motif involved in DNA recognition by some DNA-binding
proteins; characterized by a single atom of zinc coordinated to four Cys residues or to two His and two
Cys residues.
leucine finger motif - ANSW-consists of periodic repetition of a leucine residue at every seventh position
and forms an alpha helical conformation, which facilitates dimerisation
transcriptional activation via TFIID - ANSW-The activator/coactivator complex recruits TFIID to the core
promoter and/or activates its function. Transcription will be enhanced.
, Transcriptional repression via TFIID - ANSW-The repressor protein inhibits the binding of TFIID to the
core promoter or inhibits its function. Transcription is silenced.
change in chromatin structure - ANSW-eukaryotic chromosomal DNA is complexed with histones to form
chromatin, nucleosomes in the chromatin can inhibit transcription, and chromatin remodeling is
required for transcription
this can occur through the SWI/SNF remodeling complex or the histone modification
Examples of histone modifications - ANSW-phosphorylation, acetylation, methylation
SWI/SNF complex - ANSW-chromatin remodeling complex that can be directed to specific DNA sites by
transcription factors, by acetylation of histones or by binding to methylated DNA
ATP-dependent chromatin remodeling - ANSW-histone eviction creates a gap with no nucleosomes;
variant histones affect transcription
DNA methylation and gene regulation - ANSW-high level of DNA methylation is associated with low level
of gene expression
methylation state of a gene can be determined by restriction enzyme analysis with HpaII and MspI
inverse relationship exists between the degree of methylation and the degree of gene expression
DNA methylation - ANSW-The addition of methyl groups to bases of DNA after DNA synthesis; may serve
as a long-term control of gene expression; methylation of cytosine- down by DNA methyltransferase
Molecular model for inheritance of DNA methylation - ANSW-De novo methylation is an infrequent and
highly regulated event
mechanisms of transcriptional silencing by DNA methylation - ANSW-methylation inhibits the binding of
an activator protein; methyl-CpG-binding protein recruits other proteins that change the chromatin to a
closed conformation
insulators - ANSW-barrier to change in chromatin structure; blocks the effects of neighboring enhancer
Posttranscriptional regulation of gene expression - ANSW-although transcriptional control is the major
type of regulation in eukaryotes, posttranscriptional regulation also occurs in many organisms;
alternative splicing and RNA-mediated gene silencing
alternative splicing - ANSW-can generate many different proteins from one gene because it can generate
different forms of mRNA from a pre-mRNA; the number of proteins that a cell can make is not directly
related to the number of genes in the genome
MicroRNAs - ANSW-mediate RNA silencing by binding to the 3' untranslated regions of mature mRNAs to
block translation.
