Functions and Dysfunctions of Genomic Regulation Flashcards Preview

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Flashcards in Functions and Dysfunctions of Genomic Regulation Deck (55)
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1

How does histone protein bind to DNA?

Hydrophobic Interactions and Salt Linkages

~20% of histone protein amino acid residues are Lysine (Lys) or Arginine (Arg).

Positive charges bind to negative backbone of DNA

2

Proteins that bind to DNA are divided into what two classes?

Histone Proteins

Non-histone chromosomal proteins (Transcription Factors)

3

How many histone proteins per nucleosome core particle?

Eight

4

_____ is protein in which DNA is wound.

What are the protein and DNA together referred to as?

Histone octamer

Protein + DNA = Chromatin

5

The lightly packed form of chromatin, highly enriched in genes and often under active transcription.

 

What percentage of the human genome is this type?

Chromatin

92%

6

What is very condensed chromatin, containing very few active genes?
 

Where is this found?

Heterochromatin (thought to be late replicating and genetically inactive)


Found at the centromeres and telemeres

7

What is the position effect?

Activity a gene depends on relative position on chromosome

 

Actively expressed genes will be silenced if relocated near heterochromatin
 

8

Why are mice great genetic models? What accounts for their differences?

90% amount of mouse genome is the same

99% of mouse genes have human analogues

Major proteomic differences

A lot of alternative splicing

9

What percentage of the genome is exons?

1.5%

10

What is comparative genome hybridization?

Detection of Copy Number Variations (1000 differences)

 

CGH is done through probing Human Genome CHIP with DNA from one person and comparing it to normal reference.

 

Being used clinically now and can detect copy number variation.

11

What are long terminal repeats and how do Virus's utilize them?

Identical sequences of DNA repeat hundreds or thousands of times


Found at either end of retrotransposons (proviral DNA)

Formed by reverse transcription of retroviral RNA

Used by viruses to insert their genetic material into the
host genomes
 

12

How are ~100,000 proteins encoded by only 26,000 genes

Alternative splicing

15% of mutations affect this

13

What do 99% of introns begin and end with?

...GT.......AG...

14

How are histones activated?

How are they deactivated?

Acetylation - Histone Acetyl Transferases (HATS)

Deacetylation - Histone Deacetylase (HDAC)

15

How do HDACs and HATs directly regulate gene expression?

A ligand binds to a receptor and recruits a coactivator (HATs) after displacing a corepressor (HDACs).

 

This upregulates transcription factor associated proteins that acetylate the DNA

16

What on histones stands out for Post Translational Modification

Histone protein tails

17

How does DNA Methylation occur and on what DNA bases?

Methyl groups added to cytosine and adenine by methyltransferase enzymes

 

Represses Gene when at gene promoter.

18

What does DNA topoisomerase do?

Reversible enzyme
Breaks a phosphodiester bond
Changes superhelicity
Relieves supercoiling
 

19

Why are gene promoter CpG islands considered in carcinogenesis?

Acquire abnormal hypermethylation

Transcriptional silencing

Can be inherited by daughter cells following cell division

20

Methylation resulting in chromosomal instability and loss of imprinting.

Hypomethylation

21

What happens with Hypermethylation?

Associated with gene promoters

Can arise secondary to an oncogene suppressor promotor resulting in its suppression

 

Can be a epigenetic target for therapy

22

DNA polymerase requires ______ to begin processing.

a primer with a free 3’ -OH

23

What is DNA Helicase do?

Binds and hydrolyzes ATP

Pries apart DNA at 1000bp/sec

24

What do SSBP do?

Helps stabilize the unwound DNA

Prevents the formation of hairpins

 

25

What are the type one topoisomerase inhibitors and what do they do?

Inhibit topoisomerase I during the S phase

Irinotecan/Folfori- used in colorectal cancer

26

Type II Inhibitors of topoisomerase do what?

Etoposide, anthracyclines, doxorubicin, and daunorubocin

Etoposide causes secondary leukemias (dose dependent)

Anthracyclines cause cardiotoxicity (dose dependent)

27

What is a pyrimidine dimer and how is it formed?

UV radiation, produces covalent linkage between two adjacent pyrimidines (T-T or C-T)

28

What kind of damage can Ionization radiation cause?

Double-stranded breaks

29

What is Depuration and how often does it occur?

5000 purines lost per day

A purine is lost to an OH group.

 

Can lead to base deletion

30

What is deamination and how often does it occur?

A change from C to U, 100 Bases a day

 

Can lead to point mutations