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Lecture 2 (exam notes).docx

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Department
Biopharmaceutical sciences
Course
BPS3101
Professor
Linda Bonen
Semester
Fall

Description
Lecture 2 DNA structure  DNA is double helix, with purines and pyramidine rings  Purines are double rings- guanine and adenine  Pyramidine are single rings- cytosine and thiamine  Furthermore, there are 3 H-bonds between C-G and 2 H-bonds between A-T  DNA strands are anti-parallel  And A,T,C,G are bases and there is H-bonding between them  How to define a gene?- sequence of DNA essential for specific function  Codes for protein OR structural RNA  DNA is transcribed to RNA   UTR (untranscribed regions) are the red parts- they flank the coding sequence in the mRNA (UTRs are therefore in transcribed regions)  Where is the translation initiation site? Where the AUG is (the beginning of the black area  Where is the transcription inititation site? At the beginning of the UTR the beginning of the red part  Where is the promotor? The promotor is upstream of the transcription site  This gene is a protein coding gene because of the start and stop codons  NOTE: always 5’ is upstream and 3’ is downstream  Eukaryotic genes often contain introns, and introns are NOT as common in prokaryotic genes  Introns- non coding sequences removed from pre-RNA (by splicing)  Exon- sequences that remain in mature RNA (mostly coding)  The “nomenclature problem” 1. Textbooks and papers often show only coding sequences as exons but first exon includes the 5’UTR and last exon includes the 3’ UTR 2. Dilemma because often the positions of RNA ends are not known/ or tissue specific differences 3. Introns can also occur within UTR regions 1. UTR regions (which is non coding for protein) is within the first exon and the 3’ UTR is also within the last exon 2. Some introns are removed in some tissue and in other they remain 3. If the intron is within the UTR (because the UTR comes before intron 1) what is that intron called?  Example: the human pax6 gene UTR   What does the bent arrow mean?- the transcription initiator site, the promotor would be upstream of this arrow st  Where would the initiation and stop codons be?- ATG would be located at the 1 large bar after the bent arrow and the TAA stop codon would occur after the last tall bar (red star)  Intron* and intron** are 2 introns which are within the 5’ UTR regions (before the first tall bar) this is because the first tall bar is the first coding exon therefore that where the start codon is located  Long 3;UTR occurs after the stop codon (last exon) and might contain cis regulation (discussed in the last part of this lecture)  Human genes: o Intron length ~200nt to>10kb o Number/ gene; several to dozens o Exon length 100-200nt o Extreme example- dystrophin gene (~2400kb and ~78 introns)  Plant genes: o Intron density similar to animals but shorter length (100-300nt)  Yeast genes o <5% have introns (vs mammals where >95% genes have introns) o Mostly tRNA genes and intron length 20-30nt o And in ribosomal protein genes (intron length 100-500nt)  Genes within genes- other genes are sometimes located within long introns, in same/opposite orientation  Intron density= how many introns/gene  Structure of NF2 gene in various animals (neurofibromatosis type II)   What are the differences in genes in the above? o Humans and mice have long introns and short exons (property of mammals) o D.melano h
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