Genome structure Flashcards
In its 3D structure why does DNA have a major and a minor groove?
Because the glycosidic bonds that bond the base pairs to the sugar phosphate backbone aren’t directly opposite each other
Describe the process of DNA supercoiling
- It occurs when the DNA double helix is wound around 8 histone proteins (an octamer of histones)
- The octamer of histones includes 2 molecules each of the 4 different types of histone protein: Histone 2A, 2B, 3 and 4.
- This coiling of DNA around the histone proteins forms a nucleosome
Describe the role of histone 1 in DNA supercoiling once the nucleosome has been formed
Histone 1 binds to the outside of the nucleosome and then to the linker DNA. This binding neutralises the negative charge on the linker DNA allowing it to link nucleosomes together.
Formation of the nucleosome is the first level of DNA packaging. Describe the the steps involved in the other levels of DNA packaing which result in the formation of the chromosome.
- Nucleosomes bound together via histone 1 and which causes the formation of the 30nm fibre (Solenoid fibre)
- Solenoid fibre coiled and looped further via addition of scaffold proteins to form 80-100nm fibre
- Further scaffold proteins added to 80-100nm fibers causing them to be packaged further into a chromosomal-like structure
- Chromosomal-like structure is condensed even further to form loops of chromatin
- Loops of chromatin can be condensed to form chromosomes
What form is DNA usually present in within the nucleus of a cell?
DNA normally seen as a structure that resembles the loops of chromatin.
When is DNA in the nucleus present in the form of chromosomes?
When a cell undergoes mitosis/meiosis
What are the 3 types of chromosome structure?
- Metacentric - Centromere is in the middle of the chromosome
- Submetacentric - Centromere positioned closer to one end of the chromosome
- Acrocentric - Chromosome has no short arms
What is genome size and is it correlated to organism complexity? E.g. A more complex organism will have a larger genome size than a less complex one
- Genome size is defined as the total amount of DNA contained within one copy of a single complete genome.
- Genome size is not really related to organism complexity as the human genome size is 3 x 109 base pairs – 3Gbp. There are less complex organisms that have a larger genome size e.g. marbled lungfish has a genome size of 130Gbp
Is gene number more closely correlated to organism complexity than genome size is?
Yes gene number is more closely correlated to organism complexity as the trend tends to be the simplier organisms have fewer genes. E.g. humans have around 20,000 genes while bacteria only have around 1,000 genes.
What are the 2 different definitions of the exome?
- Exome is only the coding sequence
Exome is the whole gene sequence (includes regulatory signals and parts of gene sequence with no function)
What is the definition of a gene?
All of the DNA that is transcribed into RNA plus all of the local control regions that are required to quantitatively regulate tissue-specific expression of the gene
Within the genome why is it that genes tend to cluster into families?
- Allows for coordinated gene regulation - Cluster of genes may make up part of macromolecule so ideal for them to be close together and be regulated by the same signals
- May just reflect evolutionary history of those genes
The regions between genes are called intergenic regions. What structures are thought to be found within these intergenic regions?
- Repetitive DNA
- Endogenous retroviruses (no longer functional)
- Pseudogenes (genes that have lost at least some functionality).
- May also contain many regulatory elements.
What are the major strcutures found within a gene?
- Promoter region - controls the expression of the gene by allowing RNA polymerase to bind
- Exons (situated within the transcription unit) - the part of the DNA that is transcribed into RNA
- Introns (Between the exons) - These get removed from the pre-mRNA to form mature mRNA
What other important structures do you find within a gene?
- DNA sequences that promote gene expression e.g. TATA box - found within the promoter region
- Transcription initiation site
- Translation initiation site
- Translation termination site
- Transcription termination site
What is a promoter region and what is its primary function?
- The sequence immediately 5’ to the region to be transcribed is called a “promoter”
- Promoters recruit RNA polymerase to a DNA template
Explain the process of capping
- Shortly after beginning transcription, a guanine nucleotide is added to the 5’ end of the mRNA as well as a 5’-5’ triphosphate bridge.
- The guanine nucleotide that was added to the 5’ end of the mRNA is then methylated at position 7 by the enzyme methyltransferase to give rise to the 7 methylguanine cap.
Explain the process of polyadenylation?
- After the stop codon there is a sequence called polyadenylation signal or termination signal (AAUAAA).
- This sequence is recognised by the CPSF (cleavage and polyadenylation specificity factor) which then cleaves the DNA after the polyadenylation signal.
- Polyadenylate polymerase then adds 250 adenosine monophosphates to the 3’ end of pre-mRNA to produce the poly A tail.
Explain the process of splicing
- snRNPs (small nuclear ribonucleoproteins) bind to the introns of the pre-mRNA that contain GU at the 5’ splice site (5’ SS and AG at the 3’ SS.
- Spliceosome then cleaves the GU at the 5’ SS of intron
- GU sequence then loops around and joins with the branch point (A or adenine) to form lariat – like intermediate
- Spliceosome then cleaves the AG at the 3’ SS of the intron
- Ligase then joins the 2 exons together
Explain the idea of alternative splicing
Alternative splicing is the idea that not all the exons present within a gene are needed to produce mature mRNA which means that exons can be removed or even added to pre-mRNA to produce variations of a protein (called isoforms) from the same gene.
