Genomic Regulation

Question 1

What does the nucleus do and what is the total volume of it in a cell?

Answer 1

Cell regulation, proliferation, DNA trasncription, 6% total volume of cell

Question 2

Central dogma of genetics?

Answer 2

DNA (replication) -> RNA by transcription -> Protein by translation. RNA can go to DNA by virus

Question 3

How many bonds do AT and GC make

Answer 3

AT makes 2 and GC makes 3

Question 4

What is important about DNA?

Answer 4

Double stranded, antiparallel, nucleotides connected by phosphodiester bonds, and complementary base pair by hydrogen bonds. Has a sugar phosphate backbone. Has major and minor groove

Question 5

Why are mitotic chromosomes condensed 500 times when compared with interphase chromosomes?

Answer 5

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

Question 6

Characteristics of Histone proteins?

Answer 6

1. 20% are either lysine or aginine (many +++ charges)
2. Attracted to - - - charged DNA backbone
3. Lysine in histone proteins are target of post-translation modifications (PMT)

Question 7

What are nucleosomes and what do they consist of?

Answer 7

Basic unit of chromosome packing, consist of 8 histone proteins and non histone chromosomal proteins… Chromatin = histone + DNA

Question 8

What is euchromatin?

Answer 8

Lightly packed form of chromatin, often under active trasncription, 92% of human genome. Not tightly packed so very active

Question 9

What is heterochromatin?

Answer 9

Very condensed chromatin found at the centromeres and telomeres of chromosome. Packed very tight so not active at all. 8% of human genome

Question 10

What is the postition effect?

Answer 10

Activity a gene depends on relative to the position on the chromosome: activly expressed genes will be silenced if near heterochromatin

Question 11

What percentage of human genome is responsible for coding (in exons)?

Answer 11

1.5%

Question 12

What test is used to detect genomic differences / abnormalities?

Answer 12

Comparative genome hybridization arrays (CGH arrays)

Question 13

What is RNAi? and what does it do?

Answer 13

Interference RNA: a process in which RNA molecules inhibit gene expression or translation by neutralizing target mRNA molecules

Question 14

What are and where are long terminal repeats LTRs found?

Answer 14

repeat same sequences thousands of times, found in retro transposons, formed by retroviral RNA

Question 15

What does microRNA (miRNA) do?

Answer 15

It attaches to protein complexes and degreades mRNA or blocks translation

Question 16

How do 5 of the same exons code for different proteins?

Answer 16

Alternative RNA splicing, 26000 genes encode 100000 proteins, much variability

Question 17

Introns in RNA splicing….

Answer 17

always (99% of the time) start with GT and end with AG

Question 18

What percent of mutations affect RNA splicing?

Answer 18

15%

Question 19

What do Histone deactylase (HDAC) do to histones?

Answer 19

they deacetylate lysine residues, which allows the chromatin to be compact and transcriptionally repressed (OFF)

Question 20

What do Histone acetylation transferase (HAT) do to histones?

Answer 20

They acetylate lysine residues, which opens chromatin and makes it transcriptionally active (ON) – unwinds

Question 21

What are the purpose for H3 and H4 (core of H2A and H2B can be modified as well) long tails on histones?

Answer 21

For post-translational modification (PTM), including mehtylation, acetylation, phosphorylation, etc which target K/R residues.

Question 22

Why is PMT methylation to cytosine and adenine needed?

Answer 22

Done by methyl transferase enzymes, it changes the activity of a DNA segment without changing the sequence… represses gene transcription at gene promoter

Question 23

Why is methylation important to cancer?

Answer 23

1. if too methylated at CpG (promoter) causes transcriptional silencing (inherited by daughter cells)
   can also silence oncogene suppressors which will not inhibit cancer growth

Question 24

What is hypo and hypermethylation?

Answer 24

Hypo: under-methylation, causes instability and loss of imprinting
Hyper: excess methylation, causes silencing of gene promoters

Question 25

What is the difference between the lagging and leading stand in DNA replication?

Answer 25

Leading strand is synthesized continuously, lagging strand is synthesized in segments, known as okazaki fragments.

Question 26

What is DNA helicase and what does it do?

Answer 26

It unwinds DNA for replication. Has 6 subunits, binds a hydrolyzes ATP, 1000bp/sec

Question 27

What is single-stranded DNA - binding protein (SSBP) and what does it do?

Answer 27

it binds cooperatively to exposed ssDNA (singlestranded). helps stabilize the unwound DNA, prevents hairpins

Question 28

What does topoisomerase do in DNA replication?

Answer 28

Relieves overwound supercoilds (called DNA gyrase in bact.)

Question 29

Why do topoisomerase inhibitors act as anti-cancer agents?

Answer 29

1. They block the cell cycle because they are not able to keep the DNA unwound. 2. They generate single/double stranded breaks 3. Harms integ of genome 4. Leads to apoptosis and cancer cell death

Question 30

Why are there so little errors during DNA replication (1 mistake in every 10^9 bp, 3 every human genome)?

Answer 30

Because DNA polymerase can proofread! if not caught, will be fixed by repair mechanisms

Question 31

Topoisomerase I and II inhibitors?

Answer 31

Irinotecan (colorectal cancer) | Etoposisde, Anthracyclines (Doxo/Daunorubocin) for leaukemia and cardiotoxicity

Question 32

What DNA damage occurs by UV radiation?

Answer 32

Production of a covalent linkage between 2 adjacent pyrimidines (T-T C-T) called pyrimidine dimers

Question 33

What DNA damage occurs by ionizing radiation?

Answer 33

Double stranded breaks

Question 34

What DNA damage occurs by non-ionizing radiation?

Answer 34

Adjacent thymine dimers form

Question 35

What DNA damage occurs spotaneously? and what other products can be formed?

Answer 35

Depurination (loss of A/G) 5000 lost a day Deamination C changed to U, 100 a day Deamination products: (A) Hypoxanthine, (G) Xanthine, (C) Uracil

Question 36

What is the risk of eating well done meat compared to not well done?

Answer 36

Well done is a carcinogen (BPDE a epoxide) which was originally a pre-carcinogen (benzo[a]pyrene)

Question 37

What are cross-linking agents (can cause DNA damage)?

Answer 37

Nitrogen Mustard Cisplatin Mitomycin C Carmustine

Question 38

What are alkylating agents (can cause DNA damage)?

Answer 38

``` dimethyl sulfate (DMS) methyl methanesulfonate (MMS) ```

Question 39

What is an important intercalating agent (in between DNA bases)?

Answer 39

Thalidomide! cause birth defects in babies when mother took for morning sickness

Question 40

Both outcomes of DNA damage?

Answer 40

1. Repaired = normal function | 2. Deleted sequences= impaired fucntion, cell death, mutations/genetic instability (CANCER)

Question 41

3 types of genetic defects in DNA repair pathways?

Answer 41

Ataxia telangiectasia (AT) BRCA2 Fanconi anemia groups A-G

Question 42

What type of DNA damage is repaired by direct repair, and how?

Answer 42

Pyrimidine dimers, by using DNA photolyase (photoreactivation)

Question 43

What type of DNA damage is repaired by base excision repair and how?

Answer 43

single base mismatches, using glycolases to remove mismatch, AP endonuclease, lyases to remove sugar backbone, DNA polymerase and ligase adds new tide and seals

Question 44

What type of DNA damage is repaired by nucleotide excision repair and how?

Answer 44

chemical aducts like pyrimdine dimers, using NER complex (recognizes) nuclease cuts backbone, DNA helicase takes out cut piece, DNA polymerase makes new 12 according to other strand, ligase seals together

Question 45

What type of DNA damage is repaired by mismatch repair, and how?

Answer 45

mismatched bases in daughter strands, MER complex binds at mismatch, endonuclease cuts daughter strand, helicase removes seg, poly sigma fills in gap and ligase seals

Question 46

What are the two types of Recombination Repair enzymes, and what is their general job?

Answer 46

Damage: double strand breaks. Non-Homolologous End Joining (NHEJ) rejoin portions of DNA that have "double strand breaks," where the entire helix is cut like a string. They join the ends back together. Homologous Recombination check a newly created helix of DNA that has been cut against the old helix, and reintroduces any missing nucleotides at the point of the break.

Question 47

What is affect by these factors and process... Development, environmental chemicals, drugs, aging, diet?

Answer 47

Epigenetics (mechanisms)

Question 48

What are HDAC inhibitors?

Answer 48

vorinostat, entinostat

Question 49

What do trasncription factors do?

Answer 49

They talk to eachother, do not work alone!

Question 50

What are the relevance of CpG islands around a start codon?

Answer 50

1/10 are CpG. 70% of promoters contain these, this is to let the DNA know that Start is happening soon! if there is hypermethylation, will most likely silence start

Question 51

Methylation of CpG islands do what?

Answer 51

occurs at 5 position of cytosine residues, forming 5-methylcytosines, Stably silence genes