Term
| What does 'spatial control' mean? |
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Definition
| only a specific subset of the genome is expressed in each specific organ, tissue, cell type etc. |
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Term
| What does 'temporal' control mean? |
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Definition
| different genes are switched on/off at different stages of development & cellular processes |
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Term
| Give an example of induction of gene expression |
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Definition
Biolgical factors: steroid hormones, peptide hormones
Environment: heat shock |
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Term
| What is a hormone response element? |
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Definition
| short sequence of DNA in a promoter, which can bind to a specific receptor to regulate transcription |
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Term
| Describe gene expression regulation by steroid hormones |
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Definition
1. steroid hormone enters receptor cell, combines with receptor protein to form a complex
2. complex binds to hormone response element
3. HRE stimulates transcription
4. pre-mRNA transcript is processed
5. mRNA is transported to cytoplasm
6. mRNA translated into proteins |
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Term
| Describe gene expression regulation by peptide hormones |
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Definition
1. Hormone binds to receptor protein in MEMBRANE of target cell to form a complex
2. Complex activates cytoplasmic protein
3. Protein transduces a signal to the nucleus
4. Signal induces a transcription factor to bind to DNA
5. Transcription factor binding stimulates transcription
6. mRNA is transported to cytoplasm
7. mRNA translated into proteins |
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Term
| Describe gene expression regulation by heat shock |
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Definition
| -heat shock transcription factor binds to heat shock response elements to activate transcription |
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Term
| When a heat-shock response element is not bound to an HSTF, is transcription active or no? |
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Definition
| no transcription is taking place |
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Term
| What is the most important step of gene regulation? |
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Definition
| transcriptional regulation |
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Term
| What are the DNA components that regulate transcription? |
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Definition
|
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Term
| What are the protein components that regulate transcription? |
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Definition
basal transcription factors
&
special transcription factors |
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Term
| Where are enhancers typically found relative to the promoter? |
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Definition
| anywhere, they are not necessarily in close proximity to the promoter |
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Term
| What do basal transcription elements do? |
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Definition
| Regulate basal promoter strength |
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Term
| Where do special transcription factors bind? |
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Definition
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Term
True or False
Promoters are not essential for transcription |
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Definition
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Term
| Where do RNA polymerase & transcription factors bind? |
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Definition
|
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Term
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Definition
-control where transcription starts
-determine the basal level of transcription |
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Term
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Definition
-facilitate the assembly of the transcription activation complex
-increase rate of transcription
-regulate inducible & tissue-specific gene expression |
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Term
True or False
You can often move enhancers within the gene without any negative effects |
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Definition
| True, location of enhancers doesn't usually matter |
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Term
True or False
Cells within an organism have different genomes & enhancers depending on what tissue they are forming |
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Definition
False
All cells will have the same genome & enhancers, it's the proteins in the environment that activate/inactivate different enhancers |
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Term
| Describe the characteristics of promoters |
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Definition
| -function within a few hundred b.p. from intiation site -upstream from the initiation site -position depending (moving = loss of function) -orientation dependent (drive transcription in one direction only) |
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Term
| Why are promoters position-dependent? |
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Definition
| This is where RNA polymerase binds, if you move the promoter then you are changing where transcription occurs |
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Term
| Describe the characteristics of enhancers |
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Definition
-can function over a long distance
-can be up/down stream, or within the introns
-position independent
-orientation independent |
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Term
What should the opposing strand be in order to create a palindrome?
5' - GGACATCTCC - 3' |
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Definition
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Term
| Why is deletion mapping only used to determine the sequence & location of enhancers? |
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Definition
| We already know that promoters are within 200 base pairs from the initiation site, but enhancers could be anywhere |
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Term
| Describe deletion mapping |
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Definition
-delete segments of a genetic sequence until the reporter gene stops being expressed
-used to determine the location of an enhancer |
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Term
| Describe DNA footprinting |
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Definition
-label a segment of DNA with an isotope
-allow a protein(s) to bind to the segment of DNA
-allow DNAse I to digest the DNA
-the DNAse I will cut at various positions except where the proteins were bound
-compare the image generated to that of a digested DNA that was not protected by proteins
-the 'blank' spot is the footprint, show where the protein(s) were bound |
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Term
| What is the term for a pattern in a protein structure? |
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Definition
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Term
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Definition
| blocks/segements of independently functioning proteins in a polypeptide |
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Term
| What two domains are typically found in transcription factors, and are essential in complexes? |
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Definition
-DNA binding domain (t oattach to DNA promoter/enhancer/response element)
-transcriptional activation domain (for binding other proteins) |
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Term
| What are the characteristics of transcription factors? |
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Definition
-DNA binding domain
-transcriptional activation domain
-may contain ligand-binding domain for external signals |
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Term
| What are the 4 kinds of structural motifs for transcription factors? |
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Definition
zinc fingers
helix-turn-helix
leucine zipper
helix-loop-helix |
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Term
| What are the two DNA-binding motifs? |
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Definition
zinc fingers
helix-turn-helix |
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Term
| What are the characteristics of zinc fingers? |
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Definition
| -have Cys-N-Cys-N-His-N-His-N repeats |
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Term
| What is another term for the helix-turn-helix motif |
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Definition
|
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Term
| What are the two protein dimerization motifs? |
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Definition
leucine zipper
helix-loop-helix |
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Term
| What are the characteristics of leucine zippers? |
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Definition
| 2 proteins joined together, leucine in every 7th position (every 2 turns in the alpha-helix) |
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Term
| What are the characteristics of the helix-loop-helix? |
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Definition
| 2 proteins joined with a half-loop between each alpha helix |
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Term
| How can a single gene code for multiple proteins? |
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Definition
alternative splicing
-depending on where the mRNA is spliced (cut) you will get different sequences of codons, and therefore different proteins |
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Term
| How can gene expression be controlled post-transcriptionally? |
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Definition
-differences in the poly(A)tail and 3' untranslated region
-RNA interference (RNAi) |
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Term
| Are siRNAs exogenous or internal? |
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Definition
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Term
| Are miRNAs exogenous or internal? |
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Definition
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Term
| Do small RNA regulators need to have perfect base pairing to stop translation? |
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Definition
no, if they are imperfectly complementary they are often still capable of silencing translation
-a loop will often be formed to 'skip' the nucleotides that don't pair perfectly |
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Term
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Definition
RNA-Induced Silencing Complex
-incorporates a strand of siRNA or miRNA, complex binds to complementary strand, cleaves the RNA or halts translation |
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Term
| Describe the formation of a RISC complex |
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Definition
-double stranded RNA molecule is diced into small double stranded RNAs
-small interfering RNA + proteins = ribonucleoprotein particle
-small interfering RNA in the particle unwinds to produce RISC |
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Term
| Describe the action of RISC on mRNA |
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Definition
-RISC targets a sequence on mRNA complementary to the interfering RNA
-interfering RNA in RISC base pairs with the target
-imperfect base pairing = translation stops, polypeptide synthesis is repressed
-perfect base pairing = mRNA is cleaved and degraded |
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Term
| Describe the characteristics of miRNA |
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Definition
-originates from single stranded RNA
-endogenous (from miRNA genes)
-often not 100% complementary to target
-results in translational repression |
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Term
| Describe the characteristics of siRNA |
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Definition
-originates from dsDNA
-exogenous (from viruses, transposons, transgenes)
-often 100% complementary to target
-results in cleavage of target mRNA |
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Term
| What are some examples of posttranslational control? |
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Definition
protein modification
protein subcellular localization (targeting)
proteasome degradation of excess of misfolded proteins |
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Term
| Give an example of protein modification? |
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Definition
phosphorylation
glycosylation |
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Term
What kind of postranslational control is this?
Luman (transcription factor) is normally tethered to the ER membrane. Under stress it is cleaved, the N-terminal region translocates to the nucleus and the target genes are activated. |
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Definition
protein subcellular localization
(protein targeting) |
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Term
| This is a heritable state that is determined by DNA modification/chromatin organization, not by genetic sequence. |
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Definition
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Term
| What causes clonal inheritance? |
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Definition
| genes are passed on from parent to daughter cells during mitosis |
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Term
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Definition
| -highly repetitive, condensed DNA sequences, usually found around centromered & telosphere |
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Term
| Where are more eukaryotic genes located? |
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Definition
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Term
True or False
DNA in heterochromatin is readily accessible by transcription machinery |
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Definition
False
It is not easily accessed by transcription machinery. |
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Term
| What is position-effect variegation? |
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Definition
| abnormal gene expression that results from moving a gene from a euchromatic to heterochromatic region |
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Term
| What is chromatin remodeling? |
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Definition
| alteration of nucleosomes in preparation for transcription |
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Term
| What are the two main chromatin remodeling complexes? |
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Definition
HATs (histone acetyltransferases)
SWI/SNF |
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Term
True or False
HAT & SWI/SNF are gene-specific chromatin remodeling complexes |
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Definition
False
They are not specific to any genes |
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Term
|
Definition
| transfer acetyl groups to lysine residues of histones, which loosens the DNA-histone association and 'opens' the chromatin |
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Term
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Definition
shift nucleosomes along the DNA by sliding or transferring the histone octamers in nucleosomes
-exposes the DNA so it can be accessed by transcription proteins |
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Term
| What is a CpG island and where is it usually located? |
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Definition
a sequence rich in CG, usually methylated
-near the transcription initiation site |
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Term
| Does methylation of DNA repress or induce transcription? |
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Definition
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Term
| If a gene is imprinted, will it be expressed or repressed? |
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Definition
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Term
| Are imprinted genes methylated in both sexes or just one? |
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Definition
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Term
| When is imprinting re-established in each generation? |
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Definition
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Term
| What is responsible for imprinting methylation? |
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Definition
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Term
| What is dosage compensation of x-linked genes? |
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Definition
Inactivation, hyperactivation or hypoactivation of the X chromosome to make up for 'extra' or lacking genetic information
e.g. male Drosophila have only 1 X chromosome, which is hyperactivated |
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Term
| Are all genes on an inactivated X chromosome silent? |
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Definition
No
e.g. some genes encode for RNA that play a key role in chromosome inactivation will be active |
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