Genome structure Flashcards
How do we know the difference between a deoxyribose and a ribose?
Ribose sugar has a Hydroxyl group on the 2’ carbon. This is absent in deoxyribose. (Both have OH group on 3- carbon)
How many bp does the human genome contain, and how many genes?
Human genome is 3 x 10^9 base pairs – 3Gbp.
It contains ~20,000 genes
What is the basis of the ‘Packing problem’?
In a nucleated cell there is around 2m of DNA. There is an estimate of >37 trillion cells in your body, which would be 7.44x10^13 metres of DNA. However, the avg cell is 50um in length. Thus, there is a huge packing problem- fitting 2m of DNA in a 50um cell.
What is the solution to the packing problem?
Histones. They are basic (positively charged – perfect as DNA is negatively charged hence they can strongly associate) proteins that bind DNA.
What is the structure of a histone?
Eight histones 2x (H2A+H2B+H3+H4), hence a histone octamer forms the nucleosome. (DNA wraps around a histone octamer twice to make a nucleosome). Histone 1 binds the linker DNA. Nucleosomes referred to as ‘beads on a string’
What is the order of DNA packing? Smallest to largest.
Starts off with DNA double helix, which winds around histones to form nucleosomes. This is then wound further to form chromatin fibre. This is further wound to form extended section of chromosome. Which are from Loops of chromatin fibre, that of which forms part of the metaphase chromosome – the densest form of packaged DNA.
What are the three types of chromosome structures?
- Metacentric. Short arm and long arm equal in length
- Submetacentric. Contains a short, short arm and long, long arm (unequal in length)
- Acrocentric. Does not contain short arm. Instead, has satellites.
What is the primary DNA sequence?
The primary DNA sequence encodes all the gene products necessary for a human. It also includes a large number of regulatory signals (non-coding)
What is the exome?
The exome is made up of gene sequences. Some definitions use all of the coding sequences only (~36Mbp – 1.2% of genome). Other definitions use all of the gene sequences (i.e., the whole gene) (~60Mbp – 2% of genome)
What is a gene?
All of the DNA that is transcribed into RNA plus all of the cis-linked (meaning these regions are physically close to the exons On the DNA strand compared to trans regulatory regions that can be on different chromosomes) local controlled regions that are required to ensure quantitatively appropriate tissue-specific expression of the final protein. The gene promoter is usually the source of most of these signals. It typically influences/controls where, when and how much the genes are expressed.
A gene is NOT just the coding sequence (the bits that encode the final protein). This is why regulation of the gene is very important. Gene needs to have all the regulatory signals that allow it to be properly expressed.
What are intergenic regions?
Between genes, there are big gaps which are known as the intergenic reason (~98% of the genome). Intergenic regions contain sequences of no known function, such as repetitive DNA, endogenous retroviruses, pseudogenes, as well as many regulatory elements.
What is the structure of a gene?
Genes are often very different in size. They often cluster in families -e.g. globin clusters. This allows for co-ordinated gene regulation. A single gene is broken up into two parts:
Promoter and transcription unit (both containing exons).
The transcription unit is transcribed into RNA. The exons contain coding sequences. Between exons, are Introns. They don’t code, they are initially transcribed but aren’t in the final mRNA. For every n exons you have, you have n-1 Introns e.g 4 exons, 3 introns.
What is the structure of a gene (from beginning to end)?
5’ end, Promoter (Basal promoter sequences -CAAT Box , TATA Box – which are transcription factor binding sites), 5’UTR within the first exon (transcription initiation, followed by translation initiation at ATG) , introns and exons, translation termination within last exon, followed by transcription termination, 3’UTR (within last exon)
What is within the promoter region?
Regulatory element 5’..GGGAAATTCC..3’ ( 3’..CCCTTTAAGG..5’) – Needed to regulate recruitment of RNA polymerase
TATA box 5’..ATATAAATA..3’ (3’..TATATTTAT..5’) – Needed to recruit general transcription factors and RNA polymerase.
Everything after this (Starting with 5’UTR and ending at 3’UTR) is the transcription unit.
What is the promoter?
Promoters recruit RNA polymerase to a DNA template. RNA polymerase binds asymmetrically and can only move 5’ to 3’. Regulation occurs via transcription factors.
