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GENETICS - CLUTCH
CH.13 GENE REGULATION IN EUKARYOTES
CONCEPT: REVIEW OF EUKARYOTIC GENE REGULATION
● Gene expression is regulated at every __________________ from transcription to translation □ Transcription initiation is controlled via several factors
- Enhancers, activators, and silencers all control transcription
- Transcription factors both specialized and generalized which activate transcription
□ Transcription regulatory factors have specific DNA binding ____________________
- Helix-turn-helix: Two alpha helices separated by a turn
- Zinc-Finger: Structure that binds zinc and folds into a finger like structure
- Leucine Zipper: A dimer structure that “zips” together multiple leucines
- Helix-loop-helix: Two alpha helices connected by a loop
EXAMPLE:
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CH.13 GENE REGULATION IN EUKARYOTES
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● Gene expression is also ___________________________ through RNA processing, stability and translation □ RNA interference uses small noncoding RNAs (miRNA or siRNAs) to degrade certain transcripts
□ RNA processing events like splicing help regulate gene expression
- Alternative splicing creates many different protein isoforms which result in different phenotypes
□ Drosophila sex determination is controlled through alternative splicing
- Ratio of X chromosomes to Autosomal chromosomes (x:a ratio)
- If the ratio = 1 this activates sxl gene, which regulates splicing of tra gene
- Splicing of tra stimulates female-specific splicing of dsx
- If ratio = 0.5 this inactivates the sxl gene, and therefore tra is nonfunctional
- Without tra, the male-specific form of dsk is produced
□ mRNA degradation is often gene specific and helps to regulate protein production
EXAMPLE:
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PRACTICE:
1. Which of the following is NOT a DNA binding motif? a. Helix-Turn-Helix b. Zinc-Finger c. Helix-Finger d. Luecine Zipper
2. Drosophilia sex determination is controlled through which of the following mechanisms? a. Alternative splicing of the dsx gene b. Alternative splicing of sxl gene c. Inactivation of dsx gene d. Ratio of X chromosomes to Y chromosomes
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3. True or False: Gene regulation in eukaryotes only occurs during the transcription stage of gene expression. a. True b. False
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CONCEPT: GAL REGULATION
● The GAL gene system produces genes that transport and ______________________ galactose sugar in yeast cells □ This system is inducible because it is regulated by the presence or absence of galactose
- Absense of galactose = no transcription of GAL genes
- Prescense of galactose = transcription of GAL genes (positive control)
□ Transcription of the GAL genes is controlled by the UAS region
- The Gal4 protein can bind to the UAS region at four sites
- Gal80p negatively regulates GAL4 gene (makes Gal4 protein)
- Absence of galactose: Gal80p binds to Gal4p and prevents transcription activation
- Presence of galactose: galactose interacts with Gal3p which binds to UAS/Gal4p promoting transcription
EXAMPLE:
UAS GAL Genes
Gal4
Gal80Inactive
UAS GAL Genes
Gal4Active
+ Galactose+ Gal3
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PRACTICE:
1. Which of the following is the purpose of the GAL gene system? a. To synthesize galactose b. To break down galactose c. To synthesize glucose d. To break down glucose
2. The GAL gene system is activated in which of the following conditions? a. Absence of galactose b. Presence of galactose c. Absence of glucose d. Presence of glucose
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3. True or False: When the GAL gene system is activated, galactose binds to the UAS regulatory region. a. True b. False
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CONCEPT: EPIGENETICS, CHROMATIN MODIFICATIONS, AND REGULATION
● Eukaryotic DNA packaging can __________________________ gene expression □ There are two forms of chromatin (DNA and Proteins)
- Euchromatin is loosely packaged DNA, which contains genes being expressed
- Heterochromatin is tightly packaged DNA, which contains non-expressed DNA
EXAMPLE:
● There are ________________- types of chromatin modifications that affect gene expression 1. Chromatin re-modeling is the process of moving nucleosomes to new DNA sequences
- Promoters wrapped in a nucleosome will be less accessible for transcription initiation
- SWI-SNF complex is a protein complex that repositions nucleosomes
EXAMPLE:
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Histone protein modifications
2. Histone protein modifications can affect how __________________ DNA is packaged in chromatin
- Histone proteins have protein tails with lysines and arginines
- These amino acids can be modified through methyl or acetyl groups
□ Acetylation is the process of adding acetyl groups onto the histone tails
- Addition of acetyl group results in open chromatin that promotes transcription
- Acetylation is reversible, and histone deacetylase (HDAC) removes acetyl groups
□ Methylation is the process of adding methyl groups onto the histone tails
- Methyl groups often cause closed chromatin, but can occasionally support open chromatin
- Methylation creates binding sites for additional proteins with activate/suppress transcription
□ The histone code is the combination of histone modifications that affect gene ___________________
- There are 150+ histone modifications, and the pattern of activation/suppression is not understood
□ CpG islands are regions of unmethylated CG dinucleotides
- Most CG dinucleotides are methylated
- Unmethylated CpG islands are often found in promoter regions
EXAMPLE:
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3. Histone variants are slightly altered histone proteins which can effect gene expression
- Histone variants are rare, but often found in unique chromosomal regions
- Centromeres contain their own histone H3 protein variant
Other Chromatin Regulatory Mechanisms ● Eukaryotic DNA packaging can cause entire ________________________________ effects □ X-inactivation is the process of creating an entirely inactivated X chromosome (barr body)
- X-inactivation is created via heterochromatin
□ Genetic imprinting is when one copy (either paternal or maternal) of a chromosome is inherited as inactive
- Genes are expressed as if there is only one allele (from the other parent)
EXAMPLE:
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PRACTICE:
1. Chromosomal regions that form heterochromatin contain: a. Highly expressed genes b. Associations with the nucleolus c. Few genes d. Lots of open chromatin
2. Which of the following are examples of epigenetic marks? a. Acetylated guanines in DNA b. Methylated nucleotides in histone tails c. Methylated amino acids in histone tails d. All of the above
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3. CpG islands are defined as which of the following? a. Highly methlayed CG dinucleotides b. Groups of unmethylated CG dinucleotides c. Methylated CG dinucleotides found in gene coding regions d. CG nucleotides that become methylated to activate the gene
4. Which of the following terms is associated with closed chromatin? a. CpG islands b. Heterochromatin c. Methylation d. Euchromatin
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CONCEPT: POSTTRANSLATIONAL REGULATORS
● Polypeptide chains, and proteins can be modified by small molecules, which can change their structure or function □ These _________________________________________ include:
- Protein folding: Chaperone proteins correctly fold polypeptide chains into functional conformations
- Phosphorylation: is the addition of phosphates, which can change the activity of the protein
- Kinases add phosphates and phosphatases remove phosphates
- Ubiquitination: is the addition of an ubiquitin protein, which marks the protein for degradation
- Signal sequences are short sequences that direct proteins to certain cellular locations
- These are generally removed once the protein arrives at the correct organelle
- Ex: Nuclear localization signal (NLS) targets proteins to the nucleus
- Cleavage occurs when a section of the protein is removed
EXAMPLE:
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PRACTICE:
1. Which of the following posttranslational modifications is defined by the addition of phosphates to a protein? a. Phosphorylation b. Ubiquitination c. Signal Sequences d. Protein Cleavage
2. Which of the following posttranslational modifications are removed once a protein arrives at its final destination? a. Phosphorylation b. Ubiquitination c. Signal Sequences d. Protein Cleavage
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3. Which of the following posttranslational modifications marks a protein for degradation? a. Phosphorylation b. Ubiquitination c. Signal Sequences d. Protein Cleavage
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