Lecture 19 Flashcards
(36 cards)
1
Q
control of alteration of structure
A
chromatin structure must be altered to make accessible to machinery
2
Q
hypersensitive sites
A
- regions around the genes that become highly sensitive to DNase I
- suggests that chromatin is adopting a more open configuration during transcription
- correspond to known binding sites for regulatory proteins
3
Q
two processes that affect gene regulation by altering chromatin structure
A
- chromosome remodeling
- histone modification
4
Q
chromatin remodeling complexes
A
- bind to particular sites on the DNA and reposition the nucleosomes, allowing transcription factors and RNA polymerase to bind to promotors
- makes a sequence more or less accessible to transcription
- targeted to specific DNA sequences by transcriptional activators or repressors that attach to a remodeling complex and then bind to the promotors of specific genes.
5
Q
nucleosome
A
- core particle consisting of DNA wrapped around an octomer of eight histone proteins
6
Q
two domains of histones in the octomer
A
- globular domain that associates with other histones
- positively charged tail domain that possibly interacts with negatively charged phosphate groups on the backbone of the DNA
7
Q
histone code
A
- the modified of the tails of histones by the addition or removal of phosphate groups, methyl groups, or acetyl groups.
- encode information on how genes are expressed.
8
Q
methylation of histones
A
- methyl groups may be added to the histone tails, resulting in activation or repression of transcription depending on which amino acid is modified.
9
Q
acetylation of histones
A
- the addition of acetyl groups to histone proteins usually STIMULATES TRANSCRIPTION by destabilizing chromatin structure (nucleosome) which makes the DNA accessible.
10
Q
acetyl groups added to histones by
A
acetyltransferase enzymes
11
Q
deacetylation of histones
A
- strip acetyl groups from nucleosomes and restore chromatin structure (making more stabilized)
- DNA inaccessible
- inhibits transcription
12
Q
epigenetics
A
- alterations to DNA and chromatin structure that affect traits and are passed on to cells or generations but are not caused by changes in the DNA base sequence.
13
Q
Flower development in Arabidopsis
A
- flowering locus C controls flowering. Encodes a regulator protein that represses the activity of other genes that affect flowering
- FLC active, flowering suppressed.
- FLC activity controlled by flowering locus D
- FLD stimulates flowering by repressing action of FLC.
- FLD encodes deacetylase enzyme that removes acetyl groups and inhibits transcription of FLC repressor gene
- flowering can now begin.
14
Q
Chromatin Immunoprecipitation definition
A
- technique that allows researchers to identify the specific locations in the genome where proteins interact with DNA
15
Q
Chromatin immunoprecipitation technique
A
- crosslinked ChIP (xChIP), formaldehyde, or UV light is used to crosslink protein and associated DNA (sticks together)
- cells lysed and chromatin broken into pieces
- antibodies specific for a particular protein are applied. Antibodies attach to the protein-DNA complexes and cause them to precipitate
- Protein removed using enzyme that digests protein and not DNA
- remaining DNA fragments can be sequenced for info about location of binding site
16
Q
DNA methylation
A
- methylation of cytosine bases associated with repression of transcription.
17
Q
CpG islands
A
- cytosine bases immediately adjacent to guanine nucleotides
- CpG methylation also associated with most common long-term gene repression.
18
Q
evidence for association between DNA methylation and deacetylation of histones
A
- methylation appears to attract deacetylases, which remove acetyl groups from the histone tails, stabilizing the nucleosome structure and repressing transcription.
19
Q
transcriptional activators
A
- bind to DNA at a specific base sequence, usually a consensus sequence in a regulatory promotor or enhancer
- interact with other components of the transcriptional apparatus and influence the rate of transcription
- transcriptional activator proteins bound to DNA make contact with the mediator complex to affect the rate of transcription initiation.
20
Q
GAL4 regulation
A
- GAL4 is an activator protein that controls the transcription of yeast genes involved in galactose metabolism
- GAL4 binds an enhancer region and activates genes needed for galactose metabolism
- in the absence of galactose, GAL80 blocks GAL4 from activating transcription
- When galactose is present, it binds to GAL3 and brings about a conformational change of GAL80
- GAL4 can now interact with basal transcription apparatus and stimulate transcription.
21
Q
silencers
A
- silence transcription by binding to eukaryotic repressors
- may also bind to inhibit transcription by binding to elements in the regulatory promotor
22
Q
enhancers
A
- capable of affecting transcription at distant promoters and most are capable of stimulating any promotor in their vicinity (trans)
- may enhance more than one gene’s transcription
- cis elements bound by trans acting factors
23
Q
insulators
A
- block or insulate the effect of enhancers from activating genes they should not activate
- both cis elements
24
Q
coordinated gene regulation
A
- accomplished through the use of short regulatory sequences in common with their promotors or enhancers
- a single gene may be regulated by several difference response elements
25
response elements
- common regulatory elements upstream of the start sites of a collective group of genes that respond to a common environmental stimulus.
- short sequences that typically contain consensus sequences at varying distances from the genes being regulated.
- binding sites for transcriptional activators.
26
Alternative splicing
- allows pre-mRNA to be spliced in multiple ways, generating different proteins in different tissues or at different times in development
27
RNA interference
- gene silencing
- mechanism used for regulation of many eukaryotic genes
- triggered by miRNAs and siRNAs
28
RNA cleavage
- dsRNA cleaved by Dicer to produce siRNAs
- siRNAs combine with RISC and pair with complementary sequences on mRNA
- complex cleaves the mRNA
- after cleavage the RNA is degraded
29
inhibition of translation
- ds regions of RNA molecules are cleaved by dicer to produce miRNAs
- some miRNAs combine with RISC and pair imperfectly with an mRNA which leads to inhibition of translation
30
regulation of transcription
can be mediated through DNA accessibility or RNA polymerase binding
31
regulation by RNA processing
modifications determine the stability of the mRNA, whether it can be translated and the amino acid sequence of the protein through alternative splicing
32
Regulation by RNA stability
the amount of protein produced depends not only on the amount of mRNA synthesized but the rate at which it is degraded
33
Translational control
affects how well the mRNA is translated into protein
34
Posttranslational Regulation
includes modifications that determine whether the protein products become active or where they are localized within the cell
35
cis elements
- DNA elements
- sequence in DNA. not produce proteins
- promotors, enhancers, and silencers
36
trans factors
- diffusable proteins or RNA
| - RNA polymerase, basal transcription factors, cell-specific transcription factors (activators or repressors)
