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Lecture

Lecture 1

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Department
Biology (Sci)
Course
BIOL 300
Professor
Siegfried Hekimi
Semester
Fall

Description
th BIOL 300 September 5 2012 Lecture 1 Dr. Hekimi As we all know, DNA stores all genetic information in the cell.  The DNA sequence is transcribed into RNA (transcription) and particularly in eukaryotes  Then, mRNA processing occurs (poly A tail, 5’ cap, etc.) followed by RNA export into the cytoplasm, and then translation into polypeptides In molecular terms a gene is the entire DNA sequence necessary for production of a functional protein or RNA including: exons, introns, non- coding transcription-control regions The genome is defined as the total heritable genetic information carried by a cell or organism (i.e. not only nuclear DNA, but plasmid DNA as well) All cellular organisms (prokaryotic and eukaryotic) have DNA genomes  RNA viruses such as HIV which have an RNA genome, are the exception The DNA sequences of the extra-chromosomal plasmids of bacteria and certain lower eukaryotes (e.g. yeast) are typically included in the genomes of these organisms.  Plasmid: circular extrachromosomal DNA molecules capable of autonomous replicate For higher eukaryotes (sexually-reproducing species) the term genome is taken to refer to the complete DNA sequence of chromosomes present in somatic cells of a diploid individual (Autosomes plus X and Y chromosome  DNA from organelles (mitochondrial and chloroplast) are not considered as a part of genome as convention (in contrast to prokaryotes) Nucleotides are the common building block of DNA and RNA  The different sugar molecules differentiate DNA from RNA (deoxyribose with an OH vs. ribose with an H)  The base (purine or pyrimidines) will differentiate the type of nucleotide (A, C, T in DNA, G, U in RNA) Nucleic acids are negatively charged because of the phosphate group (without the PO4 it’s called a nucleoside which is relatively neutral) 1 th BIOL 300 September 5 2012 Lecture 1 Dr. Hekimi DNA & RNA are linear polymers of nucleotide monomers  The chemical linkage between adjacent nucleotides is termed a phosphodiester bond which links carbon 5 of the sugar with the phosphate group of the adjacent nucleotide, creating a biased structure with a 5’ and a 3’ end  By convention a polynucleotide sequence is normally written in the 5’ to 3’ direction. (e.g. CAG for the sequence to the right)  The linear sequence of nucleotides constitutes the primary structure of nucleic acids RNA molecules are quite reactive because of the OH group on the sugar making it unstable and not a good choice for storing the genetic code because it interacts with the phosphate group. DNA, on the other hand, has an H and is quite unreactive DNA exists as a double stranded helix which is anti-parallel (one is 5;  3’while the other is 3’  5’) which is held together via Watson and Crick base pairing (hydrogen bonds)  The sugar phosphate backbone is on the outside while the bases are on the inside creating major and minor grooves  The most common DNA shape in living cells is the B type DNA, which is water soluble, right handed, and 10.5bp/turn. o B type DNA is for DNA/DNA complexes  The A type is also right handed, and happens when B type DNA dries up; it’s more compact and has 11bp/turn. o A type DNA can be used in RNA/DNA helices as well as double stranded RNA helices  A rarer type of DNA helix is the Z type, which is rarely found in living cells but can be made in vitro. o It is made of a left handed helix and is mainly found in places with alternating base pairs between purines and pyrimidines (e.g. GCGCGCG…) DNA replication and transcription of DNA the strands of the double helix must separate.  In the cell, this is done by enzymes and transcription factors. This can be simulated in the test tube by raising the temperature. 2 th BIOL 300 September 5 2012 Lecture 1 Dr. Hekimi  The temperature at which half the bases in the DNA have separated is termed the Tm (melting temperature).  Separation is monitored by an increase in absorption of light at 260 nm wavelength (ultraviolet) o Double stranded DNA absorbs a lot less light than single stranded DNA because they are more compact and sometimes create a ring structure o As the temperature increases, H bonding will break up and the DNA strands will separate and light absorbance will increase o The temperature at which the DNA reaches half its maximal absorption is Tm, which is used commonly to design probes for PCR and other techniques o Tm is dependent on GC content in the DNA because there are 3 H bonds in a GD linkage making it the strongest of the base pairings Separation of strands does not happen randomly in the cell; there are specific enzymes and proteins which carry out these functions at specific sites  The bases of DNA helices are accessible in the major and the minor grooves, which are determines by the different shapes of the different base pairings; different proteins will recognize different groove patterns o E.g. the TATA box binding protein binds the minor groove and bends the DNA to recruit RNA polymerase as well as transcription factors Torsional stress and supercoiling of DNA occurs through localized unwinding of DNA during replication and transcription  Torsional stress caused by the unwinding leads to supercoiling in circular DNAs (e.g. mtDNA or chloroplast DNA, certain prokaryotic and eukaryotic chromosomes)  This can also happen locally in linear eukaryotic DNA loops in which supercoiling can create tangled circul
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