1. Function and Dysfunction in Genomic Regulation Flashcards
What base does Adenine pair with? How many double bonds does it form?
Thymine bonds with Adenine
Two double bonds
What base does Cytosine pair with? How many bonds does it form?
Guanine bonds with Cytosine
Three double bonds (G and C both rhyme with 3)
How many autosomes do Humans have?
How many sex chromosomes?
Usually 22 autosomes
Usually 2 sex chromosomes
In DNA packaging, 142 hydrogen bonds are formed between DNA and what? What packaging unit is formed from DNA and this protien?
The Histone Octamer
Nucleosomes
What two amino acids make up an unusually high percentage of Histone protiens? What is the reasoning behind the density of these amino acids?
Lysine and Arginine They contain positive charges that attract the DNA’s (phosphates) negative charges for wrapping.
Where might Post Translational Modifications (PTMs) occur, specifically?
Lysine residues in the histone protiens
A Nucleosome is complex of what proteins?
How many make up one Nucleosome?
Histones
8 Histones make up one Nucleosome
What is Chromatin?
Protien + Nuclear DNA is defined as Chromatin
What is the difference between Euchromatin and Heterochromatin?
Euchromatin
- is thought to be genetically active,
- it’s lightly packed so its easy to get to,
- and stains lightly.
- 92% of human DNA is euchromatin
Heterochromatin
- Tightly packed
- hard to get to
- genetically inactive
Where might we expect to find more Heterochromatin?
Centromeres and Telemeres
What happens to an active gene even just being NEAR to heterochromatin?
What is the name of this effect?
It gets silenced!
Position effect
How much of the human genome (in percentage) exists in exons? (Coding regions)
1.5%
What test is used to detect genomic differences / abnormalities?
CGH Arrays
What is RNA Interference (RNAi)?
What kind of RNA does this?
A process for RNA molecules to inhibit gene expression / translation.
Micro RNA (miRNA)
Where do Long Terminal Repeats come from?
Where are they found?
Retroviral DNA
On either side of a retrotransposon. (Proviral DNA)
How might the same 5 exons code for multiple different protiens?
Alternative RNA Splicing
What base sequence do you expect to find at the beginning of an intron? What base sequence do you expect to see at the end?
Begins with (something)GT
aaaaand GeT intron
Ends with AG(something)
- intron All Gone*
- The variables are on the far sides!*
What enzyme is responsible for deacetylation of histones?
Histone Deacetylase (HDAC)
What enzyme is responsible for acetylation of histones?
Histone Acetyl Transferase (HAT)
Acetyl Groups are Histone’s HAT
Does acetylation turn histones on or off?
What changes to turn them on / off?
Acetylation turns histones on.
The Acetyl group makes them less compactly bound so they can interact with their enzymes.
Histones never go anywhere without their HAT. It helps them loosen up.
Why might Histone protein tails be important to genetic regulation?
They are important targets of post-translational modifications.
What does methylation do to a DNA segment?
It represses transcription by binding to the gene promoter.
What two nucleobases are typically directly affected by methylation?
Cytosine and Adenine
In which direction does DNA Polymerase synthesize DNA?
5’ to 3’
What does DNA Polymerase require to begin DNA replication (besides DNA)?
A primer with a free 3’ OH group!
What do you call the sporadic “fragments” of the lagging strand in DNA replication?
Okazaki fragments
What is the basic function of DNA Helicase?
How does it move?
Unwinds DNA for DNA replication.
Conformational changes make it spin around the DNA, which propels it forward like a rotary engine.
What does Single Stranded DNA Binding Protein (SSBP) do?
Binds to a DNA strand to prevent it from sticking to itself (forming hairpins).
Note: The bases remain expased.
What does topoisomerase do?
Relieves supercoils
How many base pairs constitute one turn in a DNA helix?
10 Base Pairs
Pharmacologically speaking, what is the significance of DNA Topoisomerase I and II?
They are targets for anti cancer agents.
What is the given example of a Topoisomerase I inhibitor?
Irinotecan
I, for the roman numeral 1
What are the TWO given examples of Topoisomerase II inhibitors?
Etoposi_s_de
and
What enzyme is responsible for proofreading itself during DNA replication?
DNA Plymerase
About how many mistakes are made each time a full strand of DNA is replicated?
3
(Human genome = 3x109 Base Pairs, one in every 109 is messed up)
What DNA damage can sun exposure cause?
Pyrimidine dimers
What happens in Depurination?
A purine is spontaniously hydrolyzed from the sugar phosphate.
Purines think they’re too pure and special to be in DNA, so they leave.
What two bases are exchanged during pyrimidine deamination of DNA?
Cytosine spontaneously becomes Uracil.
What bases are exchanged during purine deamination of DNA?
Adenine becomes Hypoxanthine
AH, I see depurination has occured
Guanine becomes Xanthine
What base is produced in the deamination of methyl-cytosine,
and where might this be a particular issue?
Thymine
it’s a particular issue in CpG islands, where methyl-cytosine is an important gene silencer. The thymine ends up paired to a guanine, and DNA Glycosylase removes the Thiamine.
What chemical agents can cause cross-linking in DNA?
Nitrogen Mustard
Cisplatin
Mitomycin C
Carmustine
I’m cross, because I got Mustard on the _plat_e, and my oven _mit_ts are _must_y.
Benzo(a)pyrene and Aflatoxin B1 aren’t toxic by themselves, but they are toxic in vivo. Why is this?
The liver (through the cyctochrome P450 system) converts them into BPDE and Aflatoxin B1 Epoxide ( respectively), which can cause DNA damage.
Where might one find Benzo(a)pyrine in everyday life?
In (over) cooked meat.
Well done steak - subjectively overcooked.
What two agents mentioned are capable of damaging DNA through Alkylation?
Dimethyl Sulfate (DMS) and Methyl Methanesulfonate (MMS)
Dj’s DMS and MMS are dropping the base into your DNA!
What once-common medication is capable of intercalating into DNA?
Thalidomide
What important DNA direct repair enzyme uses light to fix pyrimidine dimers?
DNA Photolyase
What do Base Excision Repair enzymes do?
What fills the hole that they leave?
Single base mismatch repair and nondistorting alterations. They scan through DNA and cut out basis that don’t match.
What do Nucleotide Excision Repair (NER) enzymes do?\
What fixes the holes that they leave?
Detect distortions in the shape of DNA that would require the removal of several nucleotides to correct. It then makes a nick on either side of a 29 nucleotide long space and removes it.
NDA Polymerase ε fills in the gap using the undamaged strand as a template.
What disease is associated with a disfunction in Nucleotide Excision Repair?
What are the basic symptoms?
Xeroderma Pigmentosum
Sensitivity to sunlight due to an inability to repair Cyclobutane Thymine Dimers (which are common due to sunlight)
What do Mismatch Excision Repair (MER) enzymes specialize in?
What two important protiens do they use?
Removing and replacing mismatched bases in a newly synthesized daughter strand of DNA.
Essentially cleans up after a mistake in DNA Polymerase
MutS and MutL
What are the two types of Recombination Repair enzymes, and what is their general job?
Non-Homolologous End Joining (NHEJ)
These 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
These enzymes 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.
(These Recombination Repair enzymes are like the trauma surgeons of the DNA repair world.)
What is the issue with using non-homologous end joining enzymes to repair a double stranded break?
Why is this an acceptable issue?
Some nucleotides are lost at the site of the break.
Most of human DNA is non-coding, so it is more beneficial to lose some of what is probably non-coding DNA, to repair the integrity of the whole strand.
A defect in Mismatch Excision Repair can cause individuals to be more susceptable to what disease?
What is the pattern of inheritance?
Hereditary nonpolyposis colorectal cancer
Autosomal Dominant!
BRCA is a gene that is associated with a defect in what kind of DNA repair enzyme?
What does the defect cause?
Homologous Repair
Significant (5 fold) increase in the incidence of breast cancer in both women and men, as well as increased risk for a bunch of other kinds of cancers.
What is the main function of Transcription-Coupled repair enzymes?
These keep watch while transcription is happening, and if anything stalls RNA synthesis, they step in and perform Nucleotide Excision Repair.
Cockayne syndrome is associated with a mutation in the genes for what type of DNA repair?
Transcription-Coupled Repair
RNA Polymerase is working away when it comes across a rooster. Due to a crippling fear of roosters, it permanantly stalls
What do Translesion** Synthesis** enzymes do?
They add Adenine bases opposite Thymine Dimers.
Do Post translational modifications talk to each other?
Yes.
