Ch. 3 pt 1 Flashcards
What is the central idea to Development biology?
differential gene expression
What are the 3 major ideas of differential gene expression?
1) every cell contains a complete genome (genomic equivalence)
2) only some of the genome is expressed in a given cell type (differential gene expression)
3) unused genes are retained within a cell
What are the 4 levels of regulating gene expression?
1) differential gene transcription
2) mRNA splicing
3) selective mRNA translation
4) differential protein modification
What is an example of genomic equivalence?
Dolly the sheep
When was dolly the sheep cloned?
1997
What cells were removed from the two sheep in the dolly cloning experiment?
1) enucleated oocyte
2) mammary gland cell in G1
In the cloning experiment, the oocytes were prepared and maintained while in _______
meiosis metaphase II
_______: DNA and protein mixture that makes up our chromosomal DNA
chromatin
What are the 2 types of chromatin?
1) heterochromatin: regions that are tightly packed
2) euchromatin: regions that are loosely packed
_______: major protein component of chromatin
histones
- about half the weight
_______: basic unit of chromosome structure made of 8 histones
What is it made up of?
nucleosome
- made up of H2A, H2B, H3, H4
How many times does DNA wrap around a histone?
2 (140 bp)
60 bp “linker” between nucleosomes bound by _______ stabilizes solenoid structure of chromatin in chromosomes
Histone H1
_______ add methyl groups to tails of H3. Can either allow or prevent transcription
histone methyltransferases
- H3K4, K48, K79 activate
- H3K9, K27 repress
What two proteins aid to the addition and subtraction of acetyl groups to H3 and H4 histones
1) histone acetyltransferase
- addition
2) histone deacetylases
- subtraction
Histone _______ destabilize nucleosomes, allowing transcription
acetyltransferases
Histone _______ stabilize nucleosomes, preventing transcription
deacetylases
RNA Pol II binds to _______ to initiate transcription, which is rich in cytosine and guanine (_______)
promotor
CpG islands
TATA-binding protein (TBP), and other _______ are attracted to CpG-rich sites creating a “saddle” that can recruit RNA pol II
basal transcription factors
Enhancers and silencers (can be upstream or downstream) bind to ________ and can only affect ____-linked promotors
Transcription Factors
cis
What are the 2 ways that transcription factors activate gene transcription?
1) bind cofactors (such as acetyltransferases etc.)
2) form bridges (loops)
A bridging structure is found in any genes that involves a large (30+) protein complex called the _______
mediator
following chromatin remodeling and basal transcription factor binding, the mediator binds along with _______, _______, and _______ to form the pre-initiation complex
basal TF, cohesin, and RNA pol II
What are the two possible outcomes from bridge formation of preinitiation complex in transcription
1) transcription elongation
2) transcription pause
transcription elongation stimulated by _______, with coincident 5’ capping and phosphorylation and phosphorylation of RNA Pol II
transcription elongation complex (TEC)
Transcription pause caused by _______ preventing TEC association
NELF (repressive transcription factor)
Enhancer sequences are the same in all cells, however the combination of _______ available for binding differs between cell types
transcription factors
What are the 5 categories of transcription factors?
1) Homeodomain
2) helix-loop-helix
3) basic leucine zipper (bZip)
4) Zinc-finger
5) Sry-Sox
_______: can penetrate repressed chromatin and bind to enhancers
pioneer transcription factors
an example of a pioneer transcription factor is _______, which recruits MyoD/E12 to help transcribe genes for muscle development
PBX
_______: a series of successive “switches” must be executed in order to complete the differential of a given cell type
gene regulatory network
- first input is egg cytoplasm
Recent advances in _______ has suggested that variations in promoters can be grouped into two main classes
ChIP-seq
What does ChIP-seq stand for?
chromatin immunoprecipitation sequencing
_______ regulate synthesis of transcription factors and other regulator proteins used in constructing the organism
High CpG-content promotors
The default state for High CpG-content promotors is (on/off)
on
HCP’s must be actively repressed by _______
histone methylation
_______ regulate genes typical of mature organs/cells
Low CpG-content promotors
The default state for Low CpG-content promotors is (on/off)
off
LCP’s must be activated by _______ and _______
TF binding and switching methylation
Promotors of inactive genes become methylated on cytosine residues producing _______. These stabilize nucleosomes structure and prevents transcription factors from binding
5-methylcytosine
What are the two ways that DNA methylation can inhibit transcription?
1) blocks transcription factors from binding
2) bind MeCP2 which recruits deacetylases or methyltransferases
Methylated cytosines can bind _______, which then recruits histone deacetylases and histone methyltransferases
MeCP2
Methylated cytosines of DNA affect chromatin structure in a way that can be transmitted through cell cycles and even from _______ to _______
parent to child
_______ methylates previously un-methylated surrounding DNA
DNA methyltransferase 3 (Dnmt3)
_______ recognizes methyl-cytosines on one strand of newly synthesized DNA and methylates the newly formed strand opposite it
DNA methyltransferase 1 (Dnmt1)
In some of the genes the sex of the parent does matter. _______ patterns are not identical resulting in different patterns of gene activation/inactivation in each genome
DNA methylation
DMR stands for?
differentially methylated region
