Functions & Dysfunctions of Genomic Regulation

Question 1

Mitotic chromosome are condensed 500 x when compared with interphase chromosomes why?

Answer 1

To prevent physical damage to DNA as chromosomes are separated and passed on to daughter cells

Question 2

Heirachial organization of DNA

Answer 2

Chromatin= de-condensed nucleosome
Nucleosome= histone octomer + DNA

Question 3

Euchromatin vs Heterochromatin location on chromosome

Position Effect

Answer 3

Euchromatin on 92% of human genome
   -  in middle regions of chromosome
Heterochromatin on 8% of human genome
   - on centrosome and telomeres
Position Effect: gene activity depends on position on chromosome ( gene activity will be silenced when closer to heterochromatin)

Question 4

Information found in Chromosomes (2)

Answer 4

1) Genes ( encoding proteins and RNA molecules)

2) Interspersed DNA that don’t contain genes ( regulatory information or junk DNA)

Question 5

Important Years of DNA

Answer 5

1909- Wilhelm Johannsen coined “gene”
1953- Watson & Crick described DNA double helix
1966- Nirenberg, Khorana, and Holley determine genetic code
1990- Human Genome Project launched
2001- 90% of human genome
2003/2004- human genome finished

Question 6

Percentage of DNA sequence in exons

Answer 6

1.5%

Question 7

CGH Arrays ( Comparative Genome Hybridization)

Answer 7

Scan a person’s DNA along with a normal “reference” DNA

- to detect deletions of genes or copy number variation

Question 8

RNAi , Long Terminal Repeats (LTRs)

Answer 8

RNAi: miRNA will inhibit gene expression
- hairpin DNA: folded on itself
- Dicer degrades RNA to miRNA
-miRNA bind with protein complex
-miRNA bind to target mRNA and degrade or block translation
LTRs: identical sequences of DNA repeated hundreds of times
- found on proviral DNA (end of retrotransposons)
-formed by reverse transcription of retroviral RNA

Question 9

ALL introns begins and ends with ?

Answer 9

Begins with […GT]

Ends with [AG…]

Question 10

Methylation added to which DNA molecule

Answer 10

Cytosine and adenine

- REPRESSES GENE TRANSCRIPTION

Question 11

(3 Characteristic) Gene Promoter CpG islands

Answer 11

1) acquire abnormal hypermethylation
2) transcriptional silencing
* *3) can be inherited by daughter cells following cell division

Question 12

DNA polymerase requires primer with ______ to begin processing?

Answer 12

free 3’ OH

Question 13

SSBP

Answer 13

Single-stranded DNA Binding Protein

• prevent single strand DNA after helicase from binding to itself
• stabilize the unwound DNA

Question 14

Types of Spontaneous DNA Damage

Answer 14

1) Depurination ( AG)
- cut the adenosine/ guanine off -> base deletion
2) Deamination ( C to U Change, but still bp to G) -> base substitution

Question 15

Carcinogen effects (well-done steak)

Answer 15

Procarcinogen-> BPDE (carcinogen) EPOXIDE

Metabolism can produce carcinogens -> cause intercalating agents

Question 16

Types of DNA Repair

Answer 16

1) Polymerase proofreading- check during DNA replication
- mutation 1/ 10^9 or 3, 3 every cellular division
2) direct repair (use light to repair back to normal- photlolyase)
- thymidine dimer
3) base excision repair (takes out only one base)
- one bp mismatch
- depurination
- glycolase, endonuclease, phosphodiesterase, polymerase, ligase
4) nucleotide excision repair (takes out a strand of nucleotides)
- distort shape of DNA
- pyrimidine dimer
- NER complex (nick & endonuclease), HELICASE (unwind strand) polymerase, ligase
5) mismatch repair ( goes on DURING DNA replication in daughter strand)
* *mut S binds
* *Mut L- scans for nicks and degraded the error strand
6) recombination (ONLY DOUBLE STRANDED break)
- ionizing radiation, replication error, oxidizing agent
1. non-homologous end joing- will just degrade regoing that broke and ligase
2. homologous recombination- remove region of messed up nucleotide-> use sister chromatid to look and copy and repair region

Question 17

Which disease/ disorder to which repair

Answer 17

• Xeroderma pigmentosa= nucleotide excision repair
• Cockayne Syndrome- Transcription Coupled Repair/ NER
• BRCA- Recombination Repair
• Hereditary nonpolysis Colorectal cancer- Mismatch excision Repair

Question 18

Epigenetics

Answer 18

regulating gene activity independent of DNA sequence that turns genes on or off (depends on development, environmental, aging, diet)