Functions and Dysfunctions of Genomic Regulation

Question 1

snRNA

Answer 1

Small nuclear RNA

Packaged with protein to form small nuclear riboproteins (snRNPs) that are part of the spliceosome.

Involved with splicing precursor mRNA and export of mature mRNA

Question 2

scRNA

Answer 2

Small cytoplasmic RNA

Associated with small cytoplasmic ribonucloproteins (scRNPs) involved in protein processing and secretion.

Question 3

RNase P

Answer 3

Ribozyme that cleaves and removes extra RNA sequences in the 5’-leader sequence of precursor tRNA molec.

In Euks, RNase P assists RNA pol III in transcribing noncoding RNAs.

Question 4

siRNA

Answer 4

Short interfering RNA

Short antisense transcript derived from transposons and complementary to certain mRNAs.

siRNA inhibit the translation of target mRNA and enhance their degradation in RNA-inducing silencing complexes.

Question 5

miRNA

Answer 5

Micro RNA involved in posttranscriptional regulation of gene expression

Question 6

Long Terminal Repeats (LTRs)

Answer 6

Identical sequences of DNA
Repeats hundreds/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 genome

Question 7

Chromatin

Answer 7

Protein + nuclear DNA

Question 8

Heterochromatin

Answer 8

Condensed chromatin
Genetically inactive
Highly concentrated at centromeres and telomeres
Contains few genes
Gene will be silences if relocated near heterochromatin

Question 9

Euchromatin

Answer 9

Less condensed chromatin

Genetically active

Question 10

Histone positive charge comes from what 2 aa?

Answer 10

Lys & Arg

Question 11

Histone acetylation

Answer 11

Keep histone interaction loose (removes (+) charge)

–> More transcription

Question 12

Histone methylation

Answer 12

Keep histone interaction loose (due to physical interference)

–> More transcription

Question 13

DNA Methylation

Answer 13

Physical interference that usually silences transcription and marks certain regions of DNA

Question 14

HAT

Answer 14

Histone acetyltransferase

Acetylates core histones to neutralize (+) lysines to promote chromatin decondensation (make histone with DNA interaction more loose)

Question 15

HDAC

Answer 15

Histone deactylases

Remove acetyl groups from lysines on core histone proteins (restores (+) on lysine so histone can bind to DNA more tightly)

Cancer cells are sensitive to inhibitors of lysine deacetylases

Question 16

Helicase

Answer 16

Unwinds DNA helix

Protein at the replication fork

Question 17

Topisomerase

Answer 17

Relieves overwound supercoils
DNA gyrase in bacteria

Every 10bp replicated corresponds to 1 turn
Topoisomerase, breaks a phosphodiester bond to change superhelicity

Inhibitors:
Etoposide (Euk); Flouroquinolones (Prok)

Question 18

Telomerase

Answer 18

Fills in telomere gap with hexameric repeats (TTAGGG)

Telomeres shorten after each cell division until eventually cell division stops
Cancer cells have active telomerase activity

Question 19

Spontaneous DNA Damage

Answer 19

Lead to either a deletion or a bp substitution in the daughter strand

Depurination- spontaneous rxn –> loss of purine
Spontaneous deamination- C –> U

Question 20

DNA Damage: UV Radiation

Answer 20

Forms covalent linkage b/w 2 adjacent pyrimidines
(T-T or C-T)
*Thymine Dimers

Question 21

Methylated Cytosines = Problem, Why?

Answer 21

Occurs at Cytosine-phosphate-Guanine (CpG sequences)

Methylation of CpG islands stably silences genes (Cancer/DNA repair genes)

Deamination of methyl-C produces T mismatched with G.
DNA glycosylase recognizes & removes the T
*Repair is relatively ineffective
Only 3% of C nucleotides in human genome are methylated but they account for 1/3 of all point mutations associated with inherited human diseases.

Question 22

Benzopyrenes

Answer 22

Adduct formed b/w guanine & BPDE

Question 23

Intercalating agents

Answer 23

Ethidium bromide

Thalidomide

Question 24

Base Excision Repair

Answer 24

Enzyme involved: DNA glycosylases

Damaged repaired: Single base mismatches (ex. Depurination)

Question 25

Direct repair (enzymatic repair)

Answer 25

Damage repaired: Pyrimidine dimer damage, O6-methylguanine Enzymes involved: DNA photolyase Methylguanine methyltransferase

Question 26

Nucleotide excision repair

Answer 26

Damage repaired: Chemical adducts that distort DNA (ex. pyrimidine dimers, BPDE-guanine adducts, cisplatin adducts) Enzymes involved: NER protein complex, DNA pol, DNA ligase Xeroderma pigmentosum

Question 27

Mismatched excision repair

Answer 27

Damage repaired: Mismatched base in daughter strand Enzymes involved: MER complex, helicase/endonuclease, DNA pol delta, DNA ligase Hereditary nonpolyposis colorectal cancers

Question 28

Recombination repair: Non-homologous end joining

Answer 28

Damage repaired: Double strand breaks, interstrand cross-linking Mech: Damaged ends filled in and joined; some bases may be missing. Multiple proteins and enzymes including DNA ligase

Question 29

Recombination repair: Homologous recombination

Answer 29

Damage repaired: Double-strand breaks, interstrand cross-linking Mech: Exonucleases, DNA pol, MER system. Damaged duplex repair using info on undamaged homologous duplex. BRCA1/2 Breast cancer

Question 30

Transcription-coupled repair

Answer 30

Damaged repaired: Stalled RNA pol during transcription (not replication) Cockayne syndrome

Question 31

Translesion synthesis (bypass synthesis)

Answer 31

Damaged repaired: Unrepaired thymine dimers or apurini AP sites Mech: DNA pol (reduced-fidelity polymerases)

Question 32

Single stranded DNA binding protein

Answer 32

Binds the ssDNA that has been separated

Question 33

DNA polymerase alpha

Answer 33

Synthesizes RNA-DNA primer

Question 34

DNA polymerase delta and epsilon

Answer 34

Synthesize new DNA chain in the 5'-->3' direction (DNA Pol III in prok)

Question 35

Flap endonuclease 1 (FEN1)

Answer 35

Removes RNA primers (DNA Pol I in proks)

Question 36

DNA Pol delta

Answer 36

Fills in gaps (DNA Pol I in proks)

Question 37

DNA Ligase

Answer 37

Seals nicks

Question 38

Cross-linking and Intercalating

Answer 38

Damage by chemical agents; Benzopyrenes Adduct formed b/w guanine & BPDE (epoxide) Cross-linking agents: Nitrogen mustard, cisplastin, mitomycin C, carmustine Alkylating agents: Dimethyl sulfate (DMS), Methyl methansulfonate (MMS) Intercalating agents: Ethidium bromide, Thalidomide, Doxorubicin, Daunomycin