Chapter 8: Manipulating Genes and Cells
ANSWERS are on the next page!
1. What are the primary purposes of gene control?
2. What is the primary means of gene regulation?
3. Where can you find control elements in reference to the gene of interest?
4. How many types of polymerases in eukaryotes? Which subunits are homologous with
bacterial beta’ , beta, alpha and omega subunits?
5. What do the three polymerases of eukaryotes synthesize?
6. What is the function of carboxy terminal domain (CTD), and where is it located?
7. Where does Polymerase II start transcription?
8. Be able to list three types of promoters.
9. Do transcription factors bind to polymerase II randomly or in a sequential manner?
10. What are the functions of NELF and DSIF with respect to their association with
polymerase II?
11. What is the primary function of PAF and SPT6 elongation factors?
12. Please remember that regulation sites can be next to the promoter or thousands of
bases away.
13. And by the way… what is the function of a promoter?
14. Are promoter regions, enhancers and other regulatory sites the same in all tissues?
15. What are the most common DNA binding motifs (structures)?
16. Can transcription factors display cooperativity in their functions? (if you haven’t had
biochem, cooperativity is when a multi subunit or multiple proteins bind sequentially to a
substrate with increasing binding affinity)
17. The term enhanceosome is a relatively new term. What does it mean?
, 1. What are the primary purposes of gene control?
Gene control is essential for cellular function, differentiation, and adaptation. The main purposes
include:
• Cellular Differentiation: Ensures that different cell types express specific genes (e.g.,
neurons vs. muscle cells).
• Response to Environmental Signals: Allows cells to adapt to changes (e.g., stress,
nutrients, hormones).
• Conservation of Energy & Resources: Prevents unnecessary protein synthesis,
optimizing cellular energy use.
• Temporal Regulation: Ensures genes are activated at the right time (e.g., during
development, cell cycle, or response to stimuli).
• Spatial Regulation: Ensures genes are expressed in the correct cell types and tissues.
• Prevention of Disease: Dysregulation of gene expression can lead to diseases like
cancer or metabolic disorders.
2. What is the primary means of gene regulation?
The most crucial level of gene regulation in eukaryotic cells is transcriptional control—
regulating the initiation of transcription. This is primarily achieved through:
• Promoters & Enhancers: DNA sequences that interact with transcription factors.
• Transcription Factors (TFs): Proteins that either activate or repress transcription by
binding to regulatory elements.
• Epigenetic Modifications: DNA methylation and histone modifications that alter
chromatin accessibility.
• Chromatin Remodeling: ATP-dependent remodeling complexes that open or close
chromatin.
• RNA Polymerase Recruitment: Controlled by general and specific transcription factors.
Although transcriptional control is primary, gene expression can also be regulated at post-
transcriptional (RNA splicing, stability), translational (ribosome binding, mRNA degradation),
and post-translational (protein modifications, degradation) levels.
3. Where can you find control elements in reference to the gene of interest?
Control elements are specific DNA sequences that regulate gene transcription. They can be
found:
• Promoter (proximal control elements): Located immediately upstream of the gene
(~ -50 to -200 bp from transcription start site).
• Enhancers/Silencers: Can be upstream, downstream, or even within introns, and
can function thousands of base pairs away from the gene.
ANSWERS are on the next page!
1. What are the primary purposes of gene control?
2. What is the primary means of gene regulation?
3. Where can you find control elements in reference to the gene of interest?
4. How many types of polymerases in eukaryotes? Which subunits are homologous with
bacterial beta’ , beta, alpha and omega subunits?
5. What do the three polymerases of eukaryotes synthesize?
6. What is the function of carboxy terminal domain (CTD), and where is it located?
7. Where does Polymerase II start transcription?
8. Be able to list three types of promoters.
9. Do transcription factors bind to polymerase II randomly or in a sequential manner?
10. What are the functions of NELF and DSIF with respect to their association with
polymerase II?
11. What is the primary function of PAF and SPT6 elongation factors?
12. Please remember that regulation sites can be next to the promoter or thousands of
bases away.
13. And by the way… what is the function of a promoter?
14. Are promoter regions, enhancers and other regulatory sites the same in all tissues?
15. What are the most common DNA binding motifs (structures)?
16. Can transcription factors display cooperativity in their functions? (if you haven’t had
biochem, cooperativity is when a multi subunit or multiple proteins bind sequentially to a
substrate with increasing binding affinity)
17. The term enhanceosome is a relatively new term. What does it mean?
, 1. What are the primary purposes of gene control?
Gene control is essential for cellular function, differentiation, and adaptation. The main purposes
include:
• Cellular Differentiation: Ensures that different cell types express specific genes (e.g.,
neurons vs. muscle cells).
• Response to Environmental Signals: Allows cells to adapt to changes (e.g., stress,
nutrients, hormones).
• Conservation of Energy & Resources: Prevents unnecessary protein synthesis,
optimizing cellular energy use.
• Temporal Regulation: Ensures genes are activated at the right time (e.g., during
development, cell cycle, or response to stimuli).
• Spatial Regulation: Ensures genes are expressed in the correct cell types and tissues.
• Prevention of Disease: Dysregulation of gene expression can lead to diseases like
cancer or metabolic disorders.
2. What is the primary means of gene regulation?
The most crucial level of gene regulation in eukaryotic cells is transcriptional control—
regulating the initiation of transcription. This is primarily achieved through:
• Promoters & Enhancers: DNA sequences that interact with transcription factors.
• Transcription Factors (TFs): Proteins that either activate or repress transcription by
binding to regulatory elements.
• Epigenetic Modifications: DNA methylation and histone modifications that alter
chromatin accessibility.
• Chromatin Remodeling: ATP-dependent remodeling complexes that open or close
chromatin.
• RNA Polymerase Recruitment: Controlled by general and specific transcription factors.
Although transcriptional control is primary, gene expression can also be regulated at post-
transcriptional (RNA splicing, stability), translational (ribosome binding, mRNA degradation),
and post-translational (protein modifications, degradation) levels.
3. Where can you find control elements in reference to the gene of interest?
Control elements are specific DNA sequences that regulate gene transcription. They can be
found:
• Promoter (proximal control elements): Located immediately upstream of the gene
(~ -50 to -200 bp from transcription start site).
• Enhancers/Silencers: Can be upstream, downstream, or even within introns, and
can function thousands of base pairs away from the gene.
