Module 10 - DNA Replication Repair Flashcards
What are nucleosomes and histones?
Nucleosomes:
- the basic unit of DNA packaging in eukaryotes
- consist of a DNA segement wound in a sequence around eight histone protein cores
Histones:
- octamer of histones in each nucleosome, with a pair of each type
- H4, H3, H2a, H2b
- positively-charged to bind strongly with the the negatively charged DNA
- > 20% R and K amino acids
What are chromatins? Differentiate between heterochromatin & euchromatin.
Chromatin:
- a complex of DNA/RNA and protein found in eukaryotic cells
- packaging long DNA/RNA molecules into a more compact and denser shape
- has two conformations:
- Euchromatin: open and accessible to other molecules
- Heterochromatin: highly compacted and not transcribed
What are histone tail modifications and what is their importance?
Chemical modifications to the residues in histone tails can regulate chromatin, which includes acetylation, phosphorylation, methylation, ubiquitylation. It can alter the properties of the histones (e.g. acetylation reduces +ve charge) and can provide new binding sites for proteins that regulate chromatin state.
What are the 3 main chromosomal structural elements and how do they relate to the cell cycle?
Origin of Replication: regions where DNA replication is initiated
Telomeres: protective cap on the ends of linear chromosomes
Centrosomes: points of attachment of microtubules during mitosis
What is unique regarding the structure of replication origins and their relationship to the origin recognition complex in regards to the replication initiation?
Origo is the location on a chromosome where DNA replication is initiated. Features include:
- AT-rich: easier to separate due to only two H-bonds
- Histone H4 methylated; enriched for H4K20me2 (binding site for ORC)
The initiation process of DNA replication involves the following steps:
- The ORC binds to the origin (detecting H4K20me2)
- DNA helicase then binds along with the ORC, forming the preeplicative complex.
- S-Cdk (Cyclin-dependent kinase) phosphorylates both the DNA helicase (activated) and ORC (deactivated).
- Helicase then opens up the strand for DNA polymerase to bind and do its function.
What is the structure of centromeres and their function?
Centromere is the heterochromatic region of a chromosome, which joins sister chromatids during mitosis. It is the region to which microtubules attach via the kinetochor. It has the following featres:
- Pericentric regions (rich in LINEs and SINEs)
-
Centric region: consist of tandem repeat called the alpha-satellite repeat which contains this histone modifications
- Dimethylated histone (H3K4me2)
- Histone H3 variant called CENP-A: binds to the kinetochore
What is the structure and function of a telomere?
Telomeres is a protective structure at both ends of a linear chromosome with the following features:
- consist of a tandem repeat of 5’-GGGTTA-3’ (Telomere repeats)
- Variant repeat region
- Subtelomeric region (rich in pseudogenes and transposable elements)
Telomeres protect the chromosome ends from loss of functional base pairs by allowing itself to degrade. Chromosomes lacking telomeres are unstable and may be susceptible to chromosomal rearrangement.
What is the structure of telomerase?
Telomerase is a ribonucleoprotein that elongates telomere sequences with the following features:
- The RNA portion: of telomerase has the sequence 5’-CUAACCCUAAC-3’ which is complementary to the telomere tandem repeat (5‘-TTAGGG-3’)n.
- TERT: protein component which has Reverse Transcriptase activity.
What are examples of chromosomal aberrations/translocations?
- Gain/loss of chromosomes
- Duplication/deletion of parts of chromosome
- Chromosomal fusion
- Reciprocal translocation
- Robertsonian translocation
What types of DNA damage can occur and what are the repair mechanisms?
What’s the business of both helicase and ORC being phosphorylated by the S-Cdk?
First, helicase is activated by the phosphorylation, while ORC is deactivated. Activation of helicase is to ensure the entire DNA strans is open for transcription by DNA polymerase. Then, ORC is deactivated to prevent further recruitment of helicase that will disrupt process of transcription.
Mention the problem regarding to DNA replication.
DNA replication on the lagging strand is incomplete due to the space left by the final RNA-primer is not sufficient for DNA polymerase to function. Hence, exonucleases will remove the overhang leading to a loss of base pairs (shorten chromosome)
Describe how telomerase functions.
Telomerase extends the 3’ end of the overhanging strand (leading strand) due to it only being able to recognize the hydroxyl group on the 3’ end. It does this by:
- Binding to the 3’ end of the telomere (complementary to the telomerase RNA)
- TERT (part of telomerase) with its reverse transcription activity elongates the hanging strand.
- Telomerase relocates and process repeats
- DNA Polymerase then complements the overhang.
How can chromosomal abberations arise?
- Non-disjunction - failure for microtubules to attach to the the centromere
- No centromeres - random segregation
- Multiple centromeres - chromosome breakage
What are acrocentric chromosomes?
Acrocentric chromosomes are chromsoomes in which the centromere is located close to the end of the chromosome.
Desricbe the mechanism of Robertsonian translocation. Explain how it can lead to Down Syndrome (trisomy 21)
Robertsonian translocation usually occur with acroncentric chromosomes (13, 14, 15, 21, 22). The short arms of the chromosomes does not contain any essential genes; hence when two of these chromosomes are translocated (leading to centromeric fusion) all necessary genes are still expressed.
When chromosomes 14 and 21 undergo Robertsonian translocation, and later on meiosis, one gamete possibility will have two copies of chromosome 21. When combined with a normal gamete, it may arise to trisomy 21.
Describe the process of depurination and deamination and their effects to the DNA sequence.
Depurination means the hydrolytic attack to the N-C1 bind, leading to the loss of the purine residue. Deamination is the lost of the amine group from cytosine (C) due to hydrolytic attack as well, forming uracil (U) in the end.
After DNA replication, depurination (A or G) can cause a 1 bp deletion in the mutated strand. While deamination of C -> U, will lead to a G converted to an A in the mutated strand.
