Teodoro Lectures Flashcards
What is the end replication problem?
The end replication problem arises during DNA replication, particularly affecting linear DNA.
It occurs because DNA polymerases cannot fully replicate the ends of linear chromosomes.
Without mechanisms to help with this problem, DNA strands would shorten with every replication, leading to potential loss of essential genetic information.
What is the mechanism of DNA replication?
1) Leading strand: it is synthesized continuously. The DNA polymerase moves processively along the template strand until it reaches the end, completing replication without leaving gaps. (no issue)
2) Lagging strand: it is synthesized discontinously, RNA primers initiate synthesis of short fragments (okazaki fragments), after RNA primer removal, gaps remain where the primer was located, leading to incomplete replication of the chromosome end, this results in progressively short DNA strands after each replication cycle (issue ** end replication problem**)
What are coping mechanisms in organisms for the end replication problem?
1) Circular Genomes:
- bacteria and viruses, circular genomes do not have ends, so this completely avoids the end replication issue.
2) Linear Genomes:
- Telomeres:
-> found at the ends of linear chromosomes in eukaryotes, composed of repetitive non-coding sequences (telomeric repeats), these sequences are added by the enzyme telomerase, which helps maintain chromosome length during replication.
How do Small DNA viruses deal with the end replication problem?
- many small viruses (some causing cervical cancer) have circular genomes, allowing them to avoid to issue.
How does Large DNA viruse: Pox Virus, deal with the end replication problem?
1) Pox virus:
- structure: membrane-bound core containing a long linear genome (around 200,000 base pairs)
- mechanism: the virus employs unique enzymes that covalently seal the ends of the DNA to stabilize it.
- Terminal Groups: Seal the ends of the DNA, preventing degradation.
- Tandem Repeats: Allow for complementarity at the ends, enhancing stability.
- AT-Rich Regions: Designed with mismatches that create weak base pairing, facilitating melting during replication.
- self-priming mechanism: the terminal repeats can fold back and anneal, allowing virus to utilize leading strand synthesis, enabling the viral polymerase to replicate the DNA effectively.
How does Large DNA viruse: Adeno Virus, deal with the end replication problem?
- Structure: linear double-stranded genome (40,000 base pairs, containing a terminal protein (TT protein) covalently attached to the 5’ end of the DNA.
- Replication mechanism:
Inverted Terminal Repeats (ITR): Present at both ends of the adenoviral genome, comprising 100 nucleotide repeats. This terminal protein facilitates the priming of DNA replication right at the ends. - the terminal protein recruits’ viral DNA polymerase, ensuring precise positioning for replication. Other proteins, such as single-stranded DNA binding proteins, assist in stabilizing displaced strands during the replication process.
- newly synthesized viral genome and displaced viral genome can fold back to form a panhandle structure, enabling efficient replication.
Telomerase In Eukaryotes/mammalian cells
- enzyme that adds repetitive nucleotide sequences to the 3’ ends of linear chromosomes.
- this extension compensates for the inability of DNA polymerase to fully replicate the ends of linear DNA.
How do insects (e.g., Drosophila) deal with the end replication problem?
- do not encode telomeras enzyme
- utilize retrotransposons to maintain the ends of their chromosomes
What are the types of transposons? What is the mechanism that takes place?
1) Healing transposon
2) Telomere-associated transposon 3)Het-A related transposons
- Drosophila has HTT arrays (HeT-A, TART, Telo-Associated Retrotransposons) at the end of their chromosomes.
-> the reigions containing HTT arrays are transcribed into mRNA, the mRNA is polyadenylated and transported to the cytoplasm, mRNA forms with a ribonucleoprotein complex with reverse transcriptase, this returns to the nucleus and uses the mRNA as a template to synthesize DNA.
-> this process involves target-primed reverse transcription: RNA serves as a template for synthesizing additional telomeric DNA copies, adds more telomeric sequences to the ends of the chromosomes, compensating for any potential loss during replication.
Why do we need Telomeres?
1) End Replication Problem
2) dsDNA breaks happen
- chromosome ends must be distinguishable from sporadic DNA breaks
- Extensive exposed dsDNA breaks lead to cell death by apoptosis
-X-Ray Irradiation causes double stranded breaks.
What are the characteristics of Telomeres at the end of our DNA?
- Non-coding sequence
- 10-15 kbp in humans
- 3’ end overhang of ssDNA
- 150-200 bases
- Hexametric repeats of (TTAGGG)
- allows us to learn a lot about cancer, how we age, etc.
The Telomerase Holoenzyme Complex (RNA-dependent DNA Polymerase)
- Has an RNA and DNA component (both essential)
- TERC (abundant)
- TERT (limiting)
- In different organisms, telomerase varies in size, composition, and sequence, but certain features are conserved: all telomerase complexes contain TERC (the RNA component) and TERT (the reverse transcriptase), with TERC providing a template for telomere repeats (e.g., TTAGGG in humans, though with slight sequence variations in other organisms like yeast). In humans, telomerase also includes accessory proteins that help extend and maintain telomere ends.
- binds to DNA, positions it properly so that the end can be extended, added with the reverse transcriptase.
Telomerase Reaction Cycle
- cycle is very short.
- at the core, has a primer (from the RNA component).
- the domain is the primer anchoring site, the primer is the single stranded end of our DNA, it binds and positions in the active site, so that the RT activity can extend it by 5 or 6 nucleotides. 1 repeat of telomere is added before it stops and cinches up, then it releases and can bind again and repeat the cycle, eventually it just falls off.
Telomere Loop (T-Loop)
The Telomere Loop (T-loop) is a structure formed at the end of telomeres to protect chromosome ends. The single-stranded 3’ end of the telomere invades the double-stranded region, creating a closed loop. This invasion displaces a segment of DNA, forming a D-loop (displacement loop), which stabilizes the T-loop. The G-rich strand (G-strand) and C-rich strand (C-strand) in this region are also covered by protective proteins, helping to shield telomeres from degradation and improper repair.
How could you determine Telomere length?
- By the Terminal Restriction Fragment Protocol (Assay)
-Isolate genomic DNA from a cell, digest with restriction enzyme, cut most DNA around it but not the telomeres. This is over population doubling, so you don’t have telomerase activity. Start to see this smearing going downward and can see the size of the telomeres at any given time.
How could you measure Telomerase activity?
- Telomere Repeat Amplification Protocol (TRAP) Assay.
- Take nuclear extract, add oligonucleotide called TS. This corresponds to telomeric repeat and binds to primer, and telomerase will add to the repeats. Let the reaction happen, allow to be extended. Add reverse primer, to assess how many repeats have been added (done by PCR), this is SCX reverse primer, and then you run on gel to see if there is activity, if there is a ladder that increases, then you see there is telomerase activity.
What do the G-strands form?
- Quadraplexes
- At ends, G-rich, thought to be important to protect the ends of the telomers, and forms the G-strand quadruplexes. Very stable hydrogen bonding that forms these complexes.
-There are antibodies that will detect these quadraplex structures.
The Shelterin Complex
- It is a protein complex that binds to the ends of telomeres to protect them from being recognized as DNA damage.
- It maintains telomere integrity and stability, preventing chromosomal fusion and degradation.
- made up of 6 different proteins that interact with telomeres:
Core proteins: - TRF1 and TRF2 (form dimers that bind telomeric repeats, nucleate the binding of other Shelterin components)
- Tin2: acts as a bridge between TRF1 and TRF2, facilitating their interaction.
-RAP1: binds to TRF2, playing a role in telomere protecting and length regulation.
-POT1 (protector of telomeres): binds to a single-stranded regions of telomeres, within the D-loop.
* if does not function properly, telomeres can be misidentified as sites of DNA damage, leading to inappropriate DNA repair responses*
Why do Shelterin complex proteins exhibit features like transcription factors? give a few examples.
- due to their ancient DNA-binding domains
1) Myb domain: needed for their DNA-binding capability.
2) POT1: contains an OB (oligonucleotide/oligosaccharide-binding) domain, which is conserved across many species.
3) CDC13: yeast protein like POT1, featuring two OB domains and functioning similarly to protect telomeric DNA.
Summarize the Roles of the Shelterin Complex
- Protects telomeres from degradation and recognition as DNA damage.
- Maintains the structure of telomeres, preventing chromosomal fusion.
- Essential for the proper functioning of telomeres during DNA replication.
- the shorter the telomerase gets, the more accessible it is, as it gets longer, it is less accessible. A bunch of different factors control accessibility.
Telomere Regulation by POT1
- The formation of a T-loop at the telomere end affects its accessibility for maintenance and repair.
- When telomeres are too short, the T-loop unfolds, making the telomere end accessible.
- If the OB domain (which binds single-stranded DNA) in POT1 is deleted, POT1 can still attach to the Shelterin complex but cannot bind the D-loop. This lack of stabilization leads to excessive telomere lengthening in the mutant. Conversely, with a stabilized D-loop, the 3’ end remains inaccessible, preventing uncontrolled telomere extension.
Telomere Repeat Non-Coding RNA (TERRA)
Long Telomeres:
TERRA levels are low.
TERRA is degraded by an enzyme called RNAseH2, which helps control its levels.
Short Telomeres:
TERRA levels are higher.
TERRA forms structures called R-loops (RNA-DNA hybrids), which cause replication stress. This stress is a signal for the cell to repair and lengthen the telomeres.
The cell uses a process called Homology-Directed Repair (HDR), which helps fix the damaged telomeres and extends their length.
- associated with telomeres, crucial for telomere maintenance and regulation.
What is an extra telomeric function?
is that it can bind to intergenic regions and regulate nearby gene expression.
How are telomeres related to cancer?
- In humans, Telomerase is expressed at very high levels during embryonic development, but then down-regulated a few weeks after birth in most tissues.
- In humans, normal differentiated cells do not expressed Telomerase (hTERT), only cells with replicative capacity express telomerase including stem cells, skin keratinocytes, germ cells and some immune cells.
- Lack of Telomerase expression in most somatic cells is an important tumour supressor mechanism.
- Telomerase is an extremely potent oncogene (immortality enzyme - all by increasing telomere length)