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Developmental Biology > Ch. 3 pt 1 > Flashcards

Ch. 3 pt 1 Flashcards

1
Q

What is the central idea to Development biology?

A

differential gene expression

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2
Q

What are the 3 major ideas of differential gene expression?

A

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

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3
Q

What are the 4 levels of regulating gene expression?

A

1) differential gene transcription
2) mRNA splicing
3) selective mRNA translation
4) differential protein modification

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4
Q

What is an example of genomic equivalence?

A

Dolly the sheep

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5
Q

When was dolly the sheep cloned?

A

1997

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6
Q

What cells were removed from the two sheep in the dolly cloning experiment?

A

1) enucleated oocyte
2) mammary gland cell in G1

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7
Q

In the cloning experiment, the oocytes were prepared and maintained while in _______

A

meiosis metaphase II

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8
Q

_______: DNA and protein mixture that makes up our chromosomal DNA

A

chromatin

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9
Q

What are the 2 types of chromatin?

A

1) heterochromatin: regions that are tightly packed
2) euchromatin: regions that are loosely packed

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10
Q

_______: major protein component of chromatin

A

histones
- about half the weight

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11
Q

_______: basic unit of chromosome structure made of 8 histones
What is it made up of?

A

nucleosome
- made up of H2A, H2B, H3, H4

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12
Q

How many times does DNA wrap around a histone?

A

2 (140 bp)

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13
Q

60 bp “linker” between nucleosomes bound by _______ stabilizes solenoid structure of chromatin in chromosomes

A

Histone H1

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14
Q

_______ add methyl groups to tails of H3. Can either allow or prevent transcription

A

histone methyltransferases
- H3K4, K48, K79 activate
- H3K9, K27 repress

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15
Q

What two proteins aid to the addition and subtraction of acetyl groups to H3 and H4 histones

A

1) histone acetyltransferase
- addition
2) histone deacetylases
- subtraction

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16
Q

Histone _______ destabilize nucleosomes, allowing transcription

A

acetyltransferases

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17
Q

Histone _______ stabilize nucleosomes, preventing transcription

A

deacetylases

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18
Q

RNA Pol II binds to _______ to initiate transcription, which is rich in cytosine and guanine (_______)

A

promotor
CpG islands

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19
Q

TATA-binding protein (TBP), and other _______ are attracted to CpG-rich sites creating a “saddle” that can recruit RNA pol II

A

basal transcription factors

20
Q

Enhancers and silencers (can be upstream or downstream) bind to ________ and can only affect ____-linked promotors

A

Transcription Factors
cis

21
Q

What are the 2 ways that transcription factors activate gene transcription?

A

1) bind cofactors (such as acetyltransferases etc.)
2) form bridges (loops)

22
Q

A bridging structure is found in any genes that involves a large (30+) protein complex called the _______

A

mediator

23
Q

following chromatin remodeling and basal transcription factor binding, the mediator binds along with _______, _______, and _______ to form the pre-initiation complex

A

basal TF, cohesin, and RNA pol II

24
Q

What are the two possible outcomes from bridge formation of preinitiation complex in transcription

A

1) transcription elongation
2) transcription pause

25
Q

transcription elongation stimulated by _______, with coincident 5’ capping and phosphorylation and phosphorylation of RNA Pol II

A

transcription elongation complex (TEC)

26
Q

Transcription pause caused by _______ preventing TEC association

A

NELF (repressive transcription factor)

27
Q

Enhancer sequences are the same in all cells, however the combination of _______ available for binding differs between cell types

A

transcription factors

28
Q

What are the 5 categories of transcription factors?

A

1) Homeodomain
2) helix-loop-helix
3) basic leucine zipper (bZip)
4) Zinc-finger
5) Sry-Sox

29
Q

_______: can penetrate repressed chromatin and bind to enhancers

A

pioneer transcription factors

30
Q

an example of a pioneer transcription factor is _______, which recruits MyoD/E12 to help transcribe genes for muscle development

A

PBX

31
Q

_______: a series of successive “switches” must be executed in order to complete the differential of a given cell type

A

gene regulatory network
- first input is egg cytoplasm

32
Q

Recent advances in _______ has suggested that variations in promoters can be grouped into two main classes

A

ChIP-seq

33
Q

What does ChIP-seq stand for?

A

chromatin immunoprecipitation sequencing

34
Q

_______ regulate synthesis of transcription factors and other regulator proteins used in constructing the organism

A

High CpG-content promotors

35
Q

The default state for High CpG-content promotors is (on/off)

A

on

36
Q

HCP’s must be actively repressed by _______

A

histone methylation

37
Q

_______ regulate genes typical of mature organs/cells

A

Low CpG-content promotors

38
Q

The default state for Low CpG-content promotors is (on/off)

A

off

39
Q

LCP’s must be activated by _______ and _______

A

TF binding and switching methylation

40
Q

Promotors of inactive genes become methylated on cytosine residues producing _______. These stabilize nucleosomes structure and prevents transcription factors from binding

A

5-methylcytosine

41
Q

What are the two ways that DNA methylation can inhibit transcription?

A

1) blocks transcription factors from binding
2) bind MeCP2 which recruits deacetylases or methyltransferases

42
Q

Methylated cytosines can bind _______, which then recruits histone deacetylases and histone methyltransferases

A

MeCP2

43
Q

Methylated cytosines of DNA affect chromatin structure in a way that can be transmitted through cell cycles and even from _______ to _______

A

parent to child

44
Q

_______ methylates previously un-methylated surrounding DNA

A

DNA methyltransferase 3 (Dnmt3)

45
Q

_______ recognizes methyl-cytosines on one strand of newly synthesized DNA and methylates the newly formed strand opposite it

A

DNA methyltransferase 1 (Dnmt1)

46
Q

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

A

DNA methylation

47
Q

DMR stands for?

A

differentially methylated region

Developmental Biology (5 decks)

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