LBC03 Flashcards
When is DNA most tightly packed/condensed?
During cell division when chromatin condenses to form visible chromosomes
What is an origin of replication?
- Regions of DNA that initiates replication bubbles
2. Often have sequence-specific activation cues
Origins of replication found in mammalian cells direct DNA replication based on their specific nucleotides ONLY.
True/False?
FALSE.
The isolated origins of replications found in mammals have been found to be highly variable and suggests that 3D structure of DNA is also involved in gene regulation.
What is a replication unit?
- It is a cluster of origins of replication, usually found in groups of 20-80
- Each origin is separated from another origin within each replication unit with a spacing of 30-300kb
- Replication units are active only in S phase
Chromatin refers to…
DNA complexed with protein
DNA-binding proteins package DNA into a compact and less-fragile form.
TRUE/FALSE?
True
Histones are the major protein component of chromatin. TRUE/FALSE?
True
The structure of chromatin is dependent on DNA sequence. TRUE/FALSE? Why?
False. DNA sequence is highly variable. Chromatin structure is determined by other factors that all the bases share in common such as their phosphate backbone that allows for interaction with histone proteins that ultimately determine chromatin structure.
Histones are negatively charged which allows it to form H-bonds with the DNA backbone.
TRUE/FALSE?
False. Histones are positively charged due to their amino acid composition.
What are the components of the octameric histone core?
One pair of each: H2A H2B H3 H4
Which segment of a histone is variable?
N-terminal tail
What are the structures found in the conserved region of histones?
Alpha helices which loop into histone folds and allow for heterodimerisation. Heterodimer = two different histone come together to form a dimer
Describe the assembly of histones
- Alpha helices which loop into histone folds and allow for heterodimerisation
- Heterodimers form tetramers
- Tetramers assemble into functional octamer histone
H1 Histone is found in the core histone. TRUE/FALSE?
FALSE.
What is the function of H1 Histones?
They package nucleosomes into tighter arrays by guiding DNA entry and exit from the nucleosomal complex and neutralizes DNA charges to facilitate closer packing.
How does the variable N-terminal tail of histones contribute to DNA compaction?
The variable region of histones allows for different histones to have histone-histone interaction between different nucleosomes, allowing the nucleosomes to be packed even closer.
The histone H3 appears to have a highly conserved N-terminal domain when compared across multiple species. Briefly suggest why.
It is likely that these H3 histones are orthologs which have a function that is critical for survival and is thus highly conserved.
What are the 4 histone tail modifications?
MeAcUP
Methylation Acetylation Ubiquitination Phosphorylation
Methylation of histone tail is associated with gene silencing. TRUE/FALSE?
TRUE
Acetylation of histone tail is associated with gene expression. TRUE/FALSE?
TRUE
Phosphorylation of histone tail is associated with gene silencing. TRUE/FALSE?
FALSE. Phosphorylation has the same effect as acetylation because it imparts negative charge to histone core so DNA can be dissociated for allowing access to transcription machinery.
What are the two characterized types of chromosome structures we see in interphase?
- Polytene chromosome
2. Lampbrush chromosome
What are chromomeres?
Chromomeres are regions of highly condensed chromatin which contains genes that are turned off.
The loops found in lampbrush chromosomes are active in gene expression and contains only one gene per loop. TRUE/FALSE?
False. Yes the loops are transcriptionally active but they can encode more than one gene per loop.
What are lampbrush chromosomes?
- Lampbrush chromosomes are giant chromosomes found in prophase 1 of meiosis after DNA replication.
- The structure of a lampbrush chromosome consists of two intertwined DNA strand which are sister chromatids.
- The characteristic structure of lampbrush chromosomes are the many loops and chromomeres; the many loops are necessary to allow transcription of many genes necessary for cell division to proceed.
- The lampbrush chromosome represents a very transcriptionally active form of chromosomes.
What are polytene chromosomes?
- Polytene chromosomes are giant chromosome structures formed when cells have multiple cycles of DNA synthesis but do not undergo cell division.
- As a result, the new sister chromatid strains are all fused together side-by-side to form one thick gigantic chromosome.
- Polytene chromosomes have regions of dark bands formed by highly compacted DNA. The space in between the bands are called interband regions and are less compact. As such, the interband regions are more likely to contain genes.
- When genes are expressed, the polytene chromosome puffs up at the sites containing the genes to allow for transcription.
Polytene chromosomes only contains genes in the interband region. TRUE/FALSE?
FALSE.
Genes are found also in the darker banded regions but they are less actively expressed.
What are the 3 chromatin domains typically found?
- Heterochromatin - highly condensed chromatin and normally does not contain genes and are transcriptionally inactive. They are mostly found in centromeres and telomeres.
- Active euchromatin - least condensed chromatin, transcriptionally active chromatin.
- Inactive euchromatin - intermediate compaction form and is transcriptionally inactive
Suggest how heterochromatin may protect genetic integrity from transposable elements.
Heterochromatin contains DNA that do not encode genes. Heterochromatin lowers the probability of transposable elements from inserting itself into euchromatin regions. As such, it lowers the risk of transposable elements inserting itself into essential genes and disrupting these genes.
Why are interphase chromatins bound to a protein chromosome scaffold that contains a lot of topoisomerase?
DNA topoisomerase relieves supercoiling of interphase chromatin when the chromatin undergoes DNA replication or transcription.
What is variegation?
Variegation is the diversifying of phenotype in genetically identical cells due to the dynamics of heterochromatin packaging.
Explain how heterochromatin can silence genes.
- Heterochromatin consists of highly condensed DNA which is inaccessible to transcription machinery
- Heterochromatin can spread to encompass even more parts of DNA, causing genes in those regions to be silenced
What is position effect variegation?
Position effect variegation is caused when genes originally located in euchromatin region gets translocated to regions of the genome that contain heterochromatin. The closer a gene is to the heterochromatin region, the lower the likelihood of the gene being expressed.
Position effect variegation
Centromeres contain heterochromatin. TRUE/FALSE?
TRUE
What is alpha satellite DNA? Where are they found?
- Alpha satellite DNA are AT-rich short tandem repeats with slight sequence variation among themselves. They are flanked by heterochromatin made of non-satellite repeats.
- They are found in the centromere.
Where are telomeres found?
At the end of chromosomes.
What are sir proteins used for in the yeast telomere model?
- Sir proteins are NAD+ dependent histone deacetylases
- They facilitate heterochromatin formation by removing acetyl groups on the nucleosomal histones and allows for close packing of the DNA.
- They bind to nucleosomes that contain histones that are deacetylated and forms a scaffold that allows chromatin to wrap around it at telomeric ends (before t-loop)
State 2 functions of telomeres.
- Prevents the end replication problem by protecting chromosomal content
- Telomeres may serve as cellular clocks; shorter telomere = older age
What are orthologous genes?
Orthologous genes are genes that descended from one ancestral copy and diversified to be found in two separate species.
For example, hemoglobin in mice and hemoglobin in homo sapiens are orthologs.
What are paralogous genes?
Paralogous genes arise from duplications of an ancestral gene which then eventually diversifies to form two closely related but different gene in a later organism.
For example, globin gene duplicated and diversified to form myoglobin and hemoglobin.
What are LINEs?
Long interspered nuclear elements
What do LINEs encode?
Endonuclease/reverse transcriptase complex
What do LINEs do?
They are transposable elements that are able to code for a RNA copy of themselves that gets translated to produce endonuclease and reverse transcriptase. This allows it to insert itself into other sites of the genome.
LINEs are located near AT-rich regions. Suggest why?
LINEs already contain poly-A tail. It is possible that this poly-A tail leads to a bias in inserting itself into regions that are AT-rich by complementary base-pairing.
Explain how retropseudogenes are found in the human genome?
Retropseudo genes are sequences that look like genetic sequences, even containing a poly-A tail but yet are not transcribed.
It is possible that the reverse transcriptase/endonuclease produced by LINEs might have accidentally inserted a mature mRNA sequence into the host genome, leading to a pseudogene to be found in the genome.
Describe how LINEs (L1 element) propagate.
- L1 elements gets transcribed to produce L1 RNA
- L1 RNA translated to produce endonuclease/reverse transcriptase protein complex
- Host DNA is nicked and L1 RNA is reverse transcribed into the nicked strand
- RNAse H removes RNA
- The other host strand is nicked and DNA polymerase fills it up to complete insertion of L1 RNA into new site
Most LINEs and SINEs are non-functional. True/False?
TRUE
SINEs are propagated utilising the same RT/endonuclease complex as LINEs. TRUE/FALSE?
TRUE
SINEs are biased towards A-T rich regions despite using the same RT/Endonuclease complex as LINEs. TRUE/FALSE?
FALSE. They are biased towards GC-rich regions.
Mitochrondrial DNA contains histones. TRUE/FALSE?
False. But they contain nucleoids that have other proteins which have the same function as histones, suggesting a necessity in protein complexing for DNA compaction.
