Unit 1 Random facts Flashcards
In humans, _______ protects the single-stranded DNA during replication. In prokaryotes it is called SSB (Single Stranded Binding protein).
RPA
*Sliding clamps enhance the processivity of DNA polymerase.
_______ is the sliding clamp for eukaryotic DNA Pol D.
B-subunit is the sliding clamp of prokaryotic DNA Pol III
Clamp is loaded to DNA by clamp loader proteins.
PCNA
Maturation of okazaki fragments in eukaryotes
![](https://s3.amazonaws.com/brainscape-prod/system/cm/226/048/150/a_image_thumb.png?1511751410)
Cellular levels of some DNA replication proteins such as________ can be sentitive biomarkers for early detection and prognosis of many common cancers.
MCM5 (which is a helicase)
Describe the Direct reversal of damaged bases repair
This mechanism of DNA repair takes care of simple issues. For example:
- Reversal of a specific type of single-stranded DNA break by DNA ligase. In other words, ligation of a break in the phosphodiester backbone of the DNA by DNA ligase.
- Reversal of UV-caused base damage (T-T T-C dimers) by photolyase.
- Reversal of base alkylation by O6-meG methyltransferase (MGMT).
Explain Nucleotide excision repair (NER):
This repair removes DNA lesions that distort the DNA structure and block RNA or DNA polymerase movement on the DNA. Examples of these types of lesions are thymine dimers resulted from exposure to UV and bulky DNA adducts caused by exposure to carcinogens.
Steps of NER
- Recognition and binding of the damaged site by a multi-protein complex (two different ways depending on local transcription activity).
- Local unwinding of the DNA duplex by helicases (parts of the TFIIH protein complex) to form a bubble of ~25 bases.
- Double incision of the damaged strand by two endonucleases and removal of a ~30 base oligonucleotide containing the
lesion.
- Filling in the gap by a DNA polymerase.
- Rejoining the two ends by a DNA ligase.
Over 30 different proteins are needed for NER in humans. The lesions are recognized by two different pathways: Global genome NER recognizes distorting DNA lesions in any region of the genome; Transcription-coupled NER recognizes distorting DNA lesions in regions that are actively transcribed. Following recognition of the distorting DNA lesion by proteins unique to each of the two pathways (they only differ in their 1st step), the remainder of the NER occurs in the same manner.
* Defects in the global genome NER —> Xeroderma pigmentosum (Sun hypersensitivity, Skin cancers, neurologic & cognitive dysfunction).
* Defect in the Transcription-coupled NER—> Cockayne’s Syndrome (Sun hypersensitivity, Premature aging (progeria), Impaired development, Neurological degeneration).
Describe Base Excision Repair mechanism (BER):
This repair mechanism removes DNA lesions that are missed by the NER process, but do not necessarily block polymerase function or distort the DNA structure.
- BER requires a family of enzymes called *glycosylases, each recognizing a specific type of altered base. For example, uracil glycosylase recognizes uracils in DNA that result from cytosine deamination, and 5- methylcytosine-DNA glycosylase recognizes 5-methylcytosine to initiate DNA demethylation.
- See photo for steps.
![](https://s3.amazonaws.com/brainscape-prod/system/cm/226/054/439/a_image_thumb.png?1511760025)
Explain Mismatch Repair (MMR):
This repair mechanism fixes errors in nucleotide incorporation made by DNA polymerase during DNA replication. The mismatched base pair is recognized shortly after DNA synthesis by the MutS and MutL proteins in bacteria; their mammalian counterparts are *MSH (MutS Homolog) and MLH (MutL Homolog) proteins.
In bacteria, the newly synthesized strand of DNA is identified by the MMR machinery because it is not yet methylated. An endonuclease cleaves the phosphodiester backbone of the new strand of DNA. An exonuclease chews away the new DNA strand including the mismatch nucleotide while a helicase assists with the unwinding of the double helix. DNA polymerase repairs the resulting single strand gap by incorporating complimentary base pairs, and DNA ligase seals the phosphodiester backbone.
It is critical in mismatch repair to remove the wrongly inserted base (on the newly synthesized daughter DNA strand) rather than its mismatching partner (on the parental DNA strand), and that is why mismatch repair is geared to remove ONLY the portion of the newly replicated DNA that contains the wrongly incorporated base.
How does MMR know which strand is new?
1- Bacteria recognize the newly synthesized strand because, in contrast to the parental strand, it has not yet been methylated.
2- The recognition mechanism used in eukaryotes MMR appears to require DNA nicks that are more abundant on the newly replicated strand.
What disease is caused by mutations in the MMR system?
Hereditary non-polyposis colorectal cancer (HNPCC)
-in most cases (60%) MSH2 is mutated and MLH1 in some cases (30%).
Explain Lesion Bypass:
If a cell encounters so much DNA damage of the type that normally blocks DNA replication (such as UV-induced thymidine dimers) that the excision repair systems cannot fix it all, cells resort to a pathway called lesion bypass or translesion synthesis. Lesion bypass allows cells to continue replicating and dividing in the face of immense damage. However, it is highly mutagenic because alternate DNA polymerases that lack 3’ to 5’ proofreading exonuclease activity are used to replicate past the DNA lesion. The result is an error rate 100-10,000 higher than normal DNA replication.
See image for details of the mechanism.
![](https://s3.amazonaws.com/brainscape-prod/system/cm/226/055/337/a_image_thumb.png?1511760815)
What mechanism is activated by a single-strand break and adds poly (ADP-Ribose) chains to proteins?
PARP: Poly(ADP-Ribose) Polymerase
What is the purpose of PARP?
It is a reversible poly(ADP-ribosylation) of proteins near a single-strand break sites, facilitates DNA repair by amplification of the damage signal**, **focal enrichments of repair proteins**, and **change in local structure of chromatin*.
The RNA pol II large subunit has a unique C-terminal domain, CTD, composed of heptad repeats (YSPTSPS) which are reversibly phosphorylated. The CTD binds to proteins that regulate __________ and processing of the RNA transcript.
How? The serine residues at 2 and 5 positions are phosphorylated to start the elongation process.
elongation
____________ from the death cap mushroom Amanita phalloides is a non-competitive inhibitor of RNA pol II. It binds the bridge helix and blocks RNA chain elongation by preventing translocation
alpha-amanatin
Binding of TATA box binding protein to the TATA box in the ___________ helps direct assembly of the pre-initiation complex at the promoter.
minor groove
![](https://s3.amazonaws.com/brainscape-prod/system/cm/226/216/355/a_image_thumb.png?1511935564)
Transcription factor II H (TFIIH) is a important for transcription and DNA repair.
Mutations in the XPB, XPD and p44 subunits of TFIIH cause:
Xeroderma pigmentosum
Cockaynes syndrome
Trichothiodystrophy
-________ helicase opens DNA at the promoter to permit initiation
of transcription.
XPB
What are the three steps of 5-cap of mRNA?
![](https://s3.amazonaws.com/brainscape-prod/system/cm/226/217/168/a_image_thumb.png?1511936198)
What are the functions of the 5’cap?
Cap binding complex (CBC) in the nucleus is replaced by eIF4E in the cytoplasmm, which promotes initiation of translation in ribosomes.
![](https://s3.amazonaws.com/brainscape-prod/system/cm/226/217/210/a_image_thumb.png?1511936331)