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Flashcards in Gene Regulation Deck (32):
1

Cellular protein levels can be altered by:

1. transcription: (no mRNA no protein), need a 5' cap, tail, intron splicing, etc to give us diff stability of transcript which gets transported to cytoplasm to get translated. How long its there before it gets degraded det how many copioes of it get translated to proteins.
2. mRNA stability
3. Translation

2

chromatin =

DNA and all of its protein.

3

2 major modifications that happen:

1. DNA methylation on methyl cytosine
2. Histone modification

4

Most eukaryotic genes are ____. Subset varies dependent on tissues.

silenced.

5

what are the two types of chromatin

1. Heterochromatin: not transcribed (silent); DNA is hypermethylated at CpG dinucleotides. Histones are deacetylated. (inactivates DNA).
2. Euchromatin: transcribed. DNA is hypomethylated. Histones are acetylated.

6

What are some changes that the transcribed regions of genomes undergo?

1. histones become modified
2. Chromatin relaxes, resulting in hypersensitivity to DNase treatment ("CpG islands")

7

_____ unwind DNA to promote transcription. _______ reverse the process and form nucleosomes.

Histone acetyl transferases (HATs); Histone deacetylases (HDACs)

8

Which enzymes are responsible for histone modification?

1. PCAF: histone acetyltransferases; acetylates residues in H3 & H4
2. NuA4: Acetylates H2A & H4

9

Which enzymes are responsible for histone movement?

1. SWI/SNF: nucleosome movement; transcriptional activation
2. ISWI family: nucleosome movement; transcriptional repression.

10

____refers to changes in phenotype without changes in genotype.

Epigenetic

11

DNA methylation = _____
Histone acetylation = ______

1. gene silencing
2. gene activation

12

What are the activating marks in epigenetic modifications?

1. Histone acetylation: H3 and H4.
2. Unmethylated CpG

13

What are the silencing marks in epigenetic modifications?

1. Histone deacetylation: H3 and H4.
2. methylated CpG

14

____ are considered to be "hotspots" for genetic mutation. Deamination of 5 methylcytosine converts to _____

CpG; bc. closely associated with genes.

Thymine

15

the 2 major DNA methylases are ____ which maintain methylase and _____ which de novo methylation.

1. DNMT1
2. DNMT3

16

Whenever we have____ ____ and ____ of DNA we block transcription

chromatin condensation and methylation

17

how do methylcytosines turn off a gene?

They attract repressor proteins to gene region.
1. Methylations directly block trnscription factor bindng
2. they will recruit other proteins to methylated site,
3. or recruit histone deacytelates to block transcription or chromatin modifiers.
4. Some methylation sites are found internally which causes truncation of transcription.

18

when does methylation/demethylation occur?

Development. There are huge changes. Silent until we start dev into gametes (adolescence). Gametes sit there for a long time for women. During dev everything is methylated until fertilization occurs.

19

what is X inactivation? What is the gene that causes this?

Occurs in females (at diff time points). There is a transcript called the Xist which doesn't have an ORF (no protein product) which remains as an RNA transcript and sssociates with X chromosome randomly and inactivates it.

20

What is the importance of genomic imprinting in DNA methylation patterns?

Dna methylation patterns differ in male and female chromosomes for the purpose of dosage compensation gene silencing. If we have extra chromosome we can't live. All extra genes being transcribed. They are differentially methylated...1 chromsome will do it, the other wont so you get 1 dose of those partic set of genes. This differential methylation affects the expression of certain disease phenotypes.

21

What are the two diseases that could occur to due genomic imprinting of differential DNA methylation?

1. Prader Willi Syndrome
2. Angelman Syndrome

No gender diff in these diseases!

22

PWS and Angelman Syndrome was first identified as a ____ in region 15q11-13. If mutant chromosome 15 is inherited from father, only maternal genes from that region are expressed and vice versa. If there is a mutant maternal chromosome on 15, then only paternal genes expressed = ____ Syndrome. If mutant paternal chromosome on 15 then only maternal genes expressed = ___ syndrome

deletion.
Angelman
Prader- Willi

23

What are side effects of Prader Willi Syndrome

Only maternal genes expressed:
1. mental retardation
2. obesity
3. hyogonadism
4. small hands & feet
5. itchy skin
6. voracious apetite

24

What are side effects of Angelman syndrome

Only paternal genes expressed:
1. mental retardation
2. hyotonia
3. absence of speech
4. large mandible
5. tongue thrusting
6. epilepsy

25

DNA methyltransferases uses ___ as the methyl donor

SAM

26

Cigarette smoke causes global epigenetic changes in multiple tissues:

1. Hypomethylation of oncogenes: inc production of genes that push proliferation
2. Hypermethylation of tumor suppressor genes

27

what are two basic classes of genes

1. Constitutive: essential for cell survival. turned on all the time. "unregulated" gene expression.
-genes for glycolysis
-TCA cycle
-respiratory chain

2. Inducible/repressible: highly regulated . respond to cell signals
-hormone responsive proteins
-inflammatory proteins

28

what does transcription regulation require

DNA-protein interactions:
1. Proteins: DNA binding proteins, chromatin modifiers
2. DNA: core promoter seq's, enhancer/repressor DNA sequences.

29

What are transcription factors

DNA binding proteins that regulate transcription initiation:
1. serve as "recruiters" for the basal transcriptional machinery such as RNA polymerase
2. Enhance the speed & efficiency of RNA polymerase binding and initiation of transcription
3. Binding of TF can inc the transcription rate of a gene many thousand fold.

30

What are classes of transcription factors

1. Basal factors: position RNA pol on the core promoter: TFIID, A, B, E, F & H
2. Activators: (NFkB and steriod binding sites) bind to enchancer elements and inc the rate of assembly of transcriptional machinery.
3. Mediator: Adaptor molecules that connect activators to basal factors
4. Repressors: bind to silencer elements; interfere with activators to slow transcription or induce heterochromatin formation.
5. chromatin modifiers: HATs. HDACs, HMG proteins

31

What are some euk. gene regulatory sequences?

1. TATA box: core promoter at -25-30
2. Inr: where RNA pol begins transcription (+1 site on DNA).
3. Enhancer elements: help recruit RNA pol and chromatin modiefiers to that region.
-CCAAT box
-GC box
-Hormone response elements
4. Silencers

32

What are HMG proteins?

Stabilize open conformation of DNA