DNA And RNA Review Lecture 2020 PDF

Lecture 2020 - 1.3 Review of DNA and RNA Figure BB2.3: James Watson and Francis Crick discover the structure of DNA. ( a) Watson (on left) and Crick examine a model of DNA in 1953. (b) Watson and Crick in 1993....

Lecture 2020 - 1.3 Review of DNA and RNA Figure BB2.3: James Watson and Francis Crick discover the structure of DNA. ( a) Watson (on left) and Crick examine a model of DNA in 1953. (b) Watson and Crick in 1993. HHMI video on the discovery of DNA structure (17.08 mins.) https://www.youtube.com/watch?v=1vm3 od_UmFg James Watson TED talk in 2005 (20 min.) https://www.ted.com/talks/james_watson_ how_we_discovered_dna?language=en Fig. BB2-3, p. 96 Structure of DNA and RNA - review Composition: Nucleotide: Bond: DNA: double stranded RNA: single stranded, always? Building blocks for DNA and RNA Bases DNA Is a Double Helix DNA is a double helix consisting of two polynucleotide chains that run ______________ The double helix maintains a constant width because purines always face pyrimidines in the complementary A-T and G-C base pairs.  3’ 5’ Figure BB2.8: Nucleotide Chains in a DNA Molecule. The two chains run in opposite directions; a G in one chain pairs with a C in the opposite chain, and A pairs with T. The dotted lines between the bases represent Simple video ofthe weak chemical DNA structure https:// bonds that hold the chains www.youtube.com/watch?v=qy8dk5iS1f0 together. 3’ 5’ Fig. BB2-8, p. 98 Right-handed DNA Major groove Minor groove One turn is 34 angstroms Hydrogen bonds hold strands together  Dimensions of DNA molecule The width of a single DNA molecule is approximately 20 Angstroms or 2 nm. The length of one repeating nucleotide chain link (phosphate, sugar, base) is about 3.4 Angstroms. Around 10.4 nucleotide units are required to complete one full twist of the DNA helix which is 34 Angstroms. Excellent video of DNA structure from MITx Biology (5.58 mins.) https://www.youtube.com/watch?v=o_-6JXLYS-k Three forms of DNA - B-DNA - - A-DNA – - Z-DNA – Coiling of DNA What is it’s function? Space saver Affects expression Supercoiling Affects the Structure of DNA Closed DNA is either circular DNA or linear DNA in which the ends are anchored so that they are not free to rotate. A closed DNA molecule has a linking number (L), which is the sum of twist (T) and writhe (W). Twist - the number of helical turns in the DNA Writhe - the number of times the double helix crosses over on itself (supercoils) Extra helical twists are positive and lead to positive supercoiling; subtractive twisting causes negative supercoiling The linking number can be changed only by Supercoiling Affects the Structure of DNA Supercoiling occurs only in “closed” DNA with no free ends. supercoiling – Photo courtesy of Nirupam Roy Choudhury, International Centre for Genetic Engineering and Biotechnology (ICGEB) Figure 1.10: A supercoiled DNA has a twisted and condensed form.  DNA, the genome and chromosomes The blueprint of the cell is the DNA genome which is contained in the nucleus. The genome is arranged into 23 pairs of chromosomes, each carrying genes in a specific order and in a specific location or locus on the chromosome. Video showing packaging of DNA in chromatin (1.46 mins) https://www.youtube.com/watch?v=gbSIBhFwQ4s Chromatin and DNA Kinetochore Chromosome Chromatin Centromere Histone Chromatid proteins DNA (a) (b) Figure from Seeley’s A and P 10th Ed. b: © Dr. Donald Fawcett, A. Olins/Visuals Unlimited  Supercoiling with additional proteins b) Protein structures that assemble on DNA: i) ii) Additional proteins that associate with ________ (can be moved easier than __________)  X Inactivation - In humans and other organisms, there is random X inactivation in every cell to form a highly condensed Barr body caused by an RNA called ______. - Leads to chimeric individuals where one section may express a different allele of a gene than another section. - Defects on the X chromosome have variable defects depending on which allele is expressed in a particular cell. - One example of random X inactivation are ___________ which are normally ____________. Video explaining random X inactivation and epigenetics (6.22 mins.) https://www.youtube.com/watch?v=Y9vXhmI5FXM Example of heterochromatin - inactivated of X chromosome XX individuals – one X chromosome is inactivated in each cell, however not necessarily the same X chromosome This ensures that both XX and XY individuals have only one functional copy of the genes on the X chromosome in each Another example of PEV (position effect variation) - _______________ happens at the ends of chromosomes (telomeres) but it can spread into the ______________ area and cause genes in that area not to be expressed - Ex: eye colour in fruit flies - Ex: yeast mating types DNA Replication The Meselson–Stahl experiment. Used radioactive/________ N to label parental DNA molecules and proposed what they would see in each of the scenarios Base pairing provides the mechanism for replicating DNA. The Meselson-Stahl Experiment The Meselson-Stahl Experiment – the results The Meselson-Stahl Experiment – the results DNA Replication Is Semiconservative Semiconservative replication – DNA replication accomplished by separation of the strands of a parental duplex, each strand then acting as a template for synthesis of a complementary strand.. © Photodisc Figure 1.14: The two strands of DNA form a double helix. Polymerases Act on Separated DNA Strands at the Replication Fork Replication fork – the point at which the parental strands are separated. DNA polymerases – the enzymes that synthesize DNA. The replication fork. Other enzymes Nucleases are enzymes that degrade nucleic acids; they include DNases and RNases and can be categorized as endonucleases or exonucleases. An ______________ cleaves a An ________________ removes bond within a nucleic acid. This bases one at a time by example shows an enzyme cleaving the last bond in a that attacks one strand of a polynucleotide chain. DNA duplex. Genetic Information Can Be Provided by DNA or RNA Cellular genes are DNA, but viruses may have genomes of RNA. DNA is converted into RNA by _______________ RNA may be converted into DNA by ___________________ RNA polymerase – An enzyme that synthesizes _____ using a _______________ (formally described as DNA-dependent RNA polymerases). Genetic Information Can Be Provided by DNA or RNA central dogma – Information cannot be transferred from protein to protein or protein to nucleic acid, but can be transferred between nucleic acids and from nucleic acid to protein. The Information in nucleic acid can be perpetuated or transferred, but the transfer of information into a polypeptide is irreversible. DNA can be unzipped and then re-zipped ___________ – In DNA, this involves the separation of the two strands due to breaking of hydrogen bonds between bases. ___________ – The re-association of denatured complementary single strands of a DNA double helix.  Nucleic Acids Hybridize by Base Pairing Heating causes the two strands of a DNA duplex to separate. The melting temperature (Tm) is the midpoint of the temperature range for denaturation – Complementary single strands can renature or anneal when the temperature is reduced. Denatured single strands of DNA can renature to give the duplex form.  Nucleic Acids Hybridize by Base Pairing The melting temperature (Tm) is the midpoint of the temperature range for denaturation.  Nucleic Acids Hybridize by Base Pairing Denaturation and renaturation/hybridization can occur with Hybridization can be intermolecular or intramolecular. Base pairing occurs in duplex DNA and also in intra- and intermolecular interactions in single- stranded RNA (or DNA).  Nucleic Acids Hybridize by Base Pairing The ability of two single- stranded nucleic acids to hybridize is a measure of their complementarity. Filter hybridization. Trivia note: Does a lot of DNA make you smart? C-Value Paradox The observation that more complex organisms will not always need more genes than simple organisms is called the C-value paradox Explanation 1: Less complex organisms have more DNA that does not code for genes. Explanation 2: