Genome structure and chromatin (8) Flashcards
Minor and major groove
The major groove occurs where the sugar-phosphate backbones are far apart, the minor groove occurs where they are close together.
Structure of the DNA molecule
The DNA molecule consists of 2 polynucleotide chains forming a double helix. The repeating unit is a nucleotide, consisting of a phosphate group, a sugar (2´ deoxyribose), and a nitrogen base (purines adenine, guanine and pyramidines thymine and cytosine). There´s always a purine interacting with a pyrimidine, with either 2 or 3 hydrogen bonds. Nucleotides are joined together in polypeptide chains, with so-called phosphodiester linkages.
The two stands are complementary, with one strand in 3´-5´direction and the oter in 5´-3´direction. The molecule is negatively charged because of the negative phosphate group.
Differences in genome organization between prokaryotes and eukaryotes (origin of replication, telomeres, centromeres)
Prokaryotic cells have their circular chromosome organized in the nucleoid (as well as plasmids), whereas eukaryotic have their linear chromosomes organized within the cell nucleus.
Both have origins of replication, but while prokaryotic cells one have a single origin, eukaryotic cells have several (each 30-40 kb throughout) -> enables effective replication
Prokaryotes don´t need telomeres because of their circular chromosomes, while eukaryotes have it to maintain the ends of their linear chromosomes. Consists of tandem repeats and act as specialized origins of replication.
Only eukaryotes have centromeres. Consist of tandem repeats and direct the formation of kinetochores.
How do you determine complexity of an organism? Genome size, number of genes, gene density? How do you calculate gene density?
Genome size generally increases with the complexity of the organism, but we can’t only look at genome size to describe the complexity. The same goes for number of genes. Gene density (number of genes/Mb) is the best way to determine complexity, as it decreases with the complexity -> Complex organisms like humans have low gene density. This is because complexity isn´t determined by the number of genes, but rather by their regulation from intergenic sequences.
What % of the human genome is classified as pure genes?
1.5%
Of human genes, approx. how many % are made up of introns? What’s the average number of introns per human gene?
95%, average is 6 introns per gene
Gene fragment
A former function gene has been truncated due to mutations, leaving only a small part of the gene. This gene fragment is no longer functional.
Pseudogene
Originates from reverse-transcribed mRNAs. When a gene is transcribes into an mRNA strand, this strand might be reversely transcribed back into DNA and reincorporated in the gene. The result is a pseudogene that can no longer produce a protein, but might play a role in the regulation of their parent genes.
Types of repetitive intergenic sequences in the human genome
Microsatellites: Short repeated sequences (< 13 bp), approx. 3% of the genome. Can be either tandemly repeated (same repeat over and over) or interspersed throughout the genome.
Genome wide repeats: Repeats originating from transposable elements (100 to > 1000 bp), approx. 45% of the genome. Interspersed, caused by transposable elements “jumping” throughout the genome and leaving copies behind. Rare event, but accumulates over time.
Nucleosome
The fundamental unit of the chromatin, consisting of two copies of each of the core histones (H2A, H2B, H3 and H4) and approximately 147 basepairs (bp) of DNA. Protein-DNA complex, first level of compaction (6-fold). Nucleosomes are connected by linker DNA (length varies between and within species)
Histone octamer
Consists of 2 times the 4 core histone proteins H2A, H2B, H3 and H4 - equal amounts of the histones. The DNA is wrapped around the histone core to form the nucleosome.
Histone-fold domain
All the core histones consists of a histone-fold domains, which is generated by 3 alpha-helixes. This domain is conserved between species, and aids the histones with nucleosome assembly.
Histone tails
The N-terminals (amino-terminal) of the histone proteins, protruding out of the nucleosome through the minor groove channels. These tails can be covalently modified.
Assembly of a nucleosome
With the help of the histone-fold domain, a tetramer of H3 and H4 and two dimers of H2A and H2B assembles into a histone core. The DNA strand first associates with the H3-H4 tetramer before two H2A-H2B dimers associate. All together there are 8 histone proteins in the core of an assembled nucleosome, with the DNA strand wrapped around the core 1.7 times.
DNA nucleosome interactions
The central 60 bp of DNA interacts with H3-H4 at the top half of the nucleosome, whereas the H2A and H2B associates with about 30 bp on the sides of the central. These interactions are around equal in strength. The interaction within the nucleosome are completely sequence-independent, meaning that there’s so sequence specificity and it doesn’t matter which nitrogen base takes part in the interaction (gene and repeat is equally treated).
There are 14 distinct sites of contacts, and they are all to the minor groove of the DNA molecule. Between histones and the DNA there are about 40 hydrogen bonds, mostly between the oxygen of the histone and the phosphodiester in the DNA backbone.
Such interactions facilitates the bending of DNA; DNA is generally negatively charged, and without basic (positive) histones it would not be able to bend because the two negative strands would repel each other.
Histone H1
(not core) Histone which facilitates the formation into more complex structures after the first level of compaction (the nucleosome). Binds to linker DNA between nucleosomes and the central helix, which facilitates compaction of DNA into the structure called 30 nm fiber, which is a 40-fold compaction. A consequence of this is the DNA being less accessible to many DNA binding proteins. H1 is 50% as abundant as core histones.
The 30nm chromatin fiber
40-fold compaction structure facilitated by H1-binding of nucleosomes. Histone tails are also required for formation of the 30 nm fiber, as the positively charged tails most likely stabilizes the fiber through interaction with the negative DNA on adjacent nucleosomes.
2 models of structures (configurations) of the chromatin fiber
Solenoid: The DNA forms a superhelix with (approx.) 6 nucleosomes in a “circle”, where the linker DNA is buried within the circle. As a consequence, the entry/exit is not accessible.
Zigzag: Requires linker DNA to pass through the centre axis, meaning that there are DNA strands throughout the entire structure. This configuration is favored by longer linker DNA.
A higher-order structure of chromatin after 30 nm chromatin fiber involves a nuclear scaffold . What is this, and which proteins are involved?
A popular model propose that the 30 nm chromatin fiber forms loops around a protein scaffold, which leads to a higher level of compaction. The proteins involved in this scaffold is topoisomerase II (which can cut both DNA strand simultaneously, thereby manage DNA tangles and supercoils) and SMC proteins (structural maintenance of chromosomes) like cohesin and condensin.
Euchromatin
A low compaction of chromatin (lightly stained) where the DNA strand is open and easier to accessed, although not all genes are expressed even though they are located in euchromatin areas.
Heterochromatin
A high compaction of chromatin (densely stained) where the DNA strand is more closed off and difficult to access, although there can still be some degree of gene expression in heterochromatin areas (not 9%).
What are the 2 types of chromosome organization during the cell cycle? What are the key differences between the two?
Interphase chromosomes and metaphase chromosomes
