Lecture 1 - DNA, RNA, Chromosomes Review PDF

MOLECULAR ANATOMY: DNA & RNA – REVIEW OF STRUCTURE LOs A. Relate concepts from BIOL 1000 to those in BIOL 2040. C. Describe the molecular anatomy of genes and genomes (how DNA is organized) and how genetic information is duplicated. Differentiate between...

MOLECULAR ANATOMY: DNA & RNA – REVIEW OF STRUCTURE LOs A. Relate concepts from BIOL 1000 to those in BIOL 2040. C. Describe the molecular anatomy of genes and genomes (how DNA is organized) and how genetic information is duplicated. Differentiate between the structure of DNA and RNA and the properties that characterize each molecule, explaining how the physical properties of DNA enable it to function as heritable genetic information. NOT FOR SALE OR DISTRIBUTION PROPERTY OF YORK UNIVERSITY A molecule must exhibit certain characteristics for it to be considered genetic material. 1. Information storage carry variable inforamtion of all the traits of an organisms pass on information with 2. Replication accuracy mechanisms to express 3. Expression of information itself into RNA, proteins provides raw material 4. Variation by mutation for evolution LO: Explain how the physical properties of DNA enable it to function as heritable genetic information. NOT FOR SALE OR DISTRIBUTION PROPERTY OF YORK UNIVERSITY Figures: R. Redfield, UBC  Nucleic acids (i.e., DNA & RNA) are composed of nucleotides, which can be categorized according to the base involved. pyrimidines one ring purines two rings NOT FOR SALE OR DISTRIBUTION PROPERTY OF YORK UNIVERSITY The type of sugar molecule in a nucleotide determines whether the nucleic acid is RNA or DNA Consequences in terms of the releative stabilities of the two molecules RNA DNA Lacks an oygen NOT FOR SALE OR DISTRIBUTION PROPERTY OF YORK UNIVERSITY  Nucleotides have a base, sugar, & a phosphate group; nucleosides lack a phosphate group. NucleoSide NucleoTide lacks phosphate group NOT FOR SALE OR DISTRIBUTION PROPERTY OF YORK UNIVERSITY Multiple nucleotides join together to form polynucleotide chains Polynucleotide vs. oligonucleotide? 20-30 nucleotides many few NOT FOR SALE OR DISTRIBUTION PROPERTY OF YORK UNIVERSITY https://en.wikipedia.org/wiki/Nucleic_acid_structure  Within a nucleic acid, nucleotides are joined by covalent phosphodiester bonds NOT FOR SALE OR DISTRIBUTION PROPERTY OF YORK UNIVERSITY http://www.chemguide.co.uk/organicprops/aminoacids/dna1.html 3' carbon of one This bond formation nucleotide is bonded to difference between the 3' and 5' end of a pattern gives each the 5' phosphateof the nucleotide plays a role in the replication of strand polarity/ next nucleotide directionality DNA and translation of RNA Multiple nucleotides join together to form polynucleotide chains that have directionality https://en.wikipedia.org/wiki/Nucleic_acid_structure NOT FOR SALE OR DISTRIBUTION PROPERTY OF YORK UNIVERSITY  Nucleic acids have a sugar-phosphate backbone phosphates carry a negative charge long chain = carry a lot of genetic information NOT FOR SALE OR DISTRIBUTION PROPERTY OF YORK UNIVERSITY https://en.wikipedia.org/wiki/Nucleic_acid_structure Secondary structure of DNA is the double helix, 2 antiparallel DNA strands hydrogen bonds hold the strands together 1 molecule dsDNA NOT FOR Pearson SALE Education, 2013. OR DISTRIBUTION PROPERTY OF YORK UNIVERSITY  Purines pair with pyrimidines – i.e., there is specificity to base pairing in nucleic acids pair through 3 pair through 2 hydrogen bonds hyfrogen bonds the nature of the hydrogen bonds limit what bases Pearson Education, 2013. can pair thymine adenine cytosine guanine Based on what you know, predict how many H bonds uracil would have. NOT FOR SALE OR DISTRIBUTION PROPERTY OF YORK UNIVERSITY Chargaff’s Rules: can use the complementary nature of DNA to tell us about base composition of the molecule of DNA Chargaff’s Rules %A=%T %G=%C if your given the amout of one nucleotide in a DNA sample, you can figure out the frequency of the other three nucleotides NOT FOR SALE OR DISTRIBUTION PROPERTY OF YORK UNIVERSITY  Practice Questions (try first without looking up answers!) 1. Describe two differences between DNA and RNA. 2. What’s a nucleic acid? (Be specific.) 3. In your own words explain to someone (who hasn’t taken BIOL 1000) how DNA functions as our hereditary material. 4. What base does uracil pair with? How many H bonds does it share with that base? 5. The diagram to the right is from the video. a. Label the 5’ and 3’ ends of this nucleic acid. b. To what does the 5’ and 3’ refer? c. Is this DNA or RNA? How can you tell? NOT FOR SALE OR DISTRIBUTION PROPERTY OF YORK UNIVERSITY 1. DNA uses T, RNA uses U DNA is double stranded, RNA is single stranded  Review Video MOLECULAR ANATOMY: REVIEW OF DNA REPLICATION LOs A. Relate concepts from BIOL 1000 to those in BIOL 2040. C. Describe the molecular anatomy of genes and genomes (how DNA is organized) and how genetic information is duplicated. Describe DNA replication using appropriate terminology and referencing appropriate components, relating DNA replication to the formation of sister chromatids. Apply knowledge of DNA replication (both in vivo & in vitro) to molecular techniques used to study genetics. NOT FOR SALE OR DISTRIBUTION PROPERTY OF YORK UNIVERSITY There are a variety of ways to represent DNA visually The most realistic representation is rarely the most helpful. DNA is made 5’ up of two |||||||||||||||||||||||||||||5’ strands Figures: R. Redfield, UBC NOT FOR SALE OR DISTRIBUTION PROPERTY OF YORK UNIVERSITY  The secondary structure of DNA is the double helix, 2 antiparallel DNA strands One strand runs in the 5' to 3' dirention and the Pearson Education, 2013. other strand runs in the 3' to 5' direction 1 molecule DNA NOT FOR SALE OR DISTRIBUTION PROPERTY OF YORK UNIVERSITY DNA structure facilitates replication, which occurs semi-conservatively each parent strand acts as a template for the sythesis of a new DNA strand Old strand Daughter DNA Modified from Hartwell et New strand al. 2009 (McGraw-Hill, 2009) NOT FOR SALE OR DISTRIBUTION PROPERTY OF YORK UNIVERSITY Sister chromatid Sister chromatid the pairing of a parent strand and a daughter strand results in a sister chromatid Several experiments provided evidence that DNA replicates semi- conservatively After 1 round of replication Dispersive Semiconservative NOT FOR SALE OR Conservative DISTRIBUTION PROPERTY OF Pearson Education, 2013. YORK UNIVERSITY two parent strands seperate and act as a template, but then they seperate and the parent strands pair up and the new DNA strands pair up Several experiments (e.g., Meselson-Stahl) provided evidence that DNA replicates semi-conservatively used two nitrogen isotopes pyrimidines purines 14N 15N Pearson Education, 2013. NOT FOR SALE OR DISTRIBUTION naturally naturally PROPERTY OF YORK UNIVERSITY occuring occuring in smaller amounts and heavier (stable)  The Meselson-Stahl experiment was one experiment that provided evidence that DNA replicates semi-conservatively shows that DNA replicates semi- conservatively Pearson Education, 2013. NOT FOR SALE OR DISTRIBUTION PROPERTY OF YORK UNIVERSITY for production of a new complementary strand of DNA DNA undergoes localized unwinding of the double helix so that DNA synthesis can begin Pearson Education, 2013. replication fork moves in multiple origins of replication each strands both directions to make the process more serves as a efficient template for a new strand NOT FOR SALE OR DISTRIBUTION PROPERTY OF YORK UNIVERSITY  DNA replication requires a primer to provide a free 3’-OH group Template DNA DNA polymerase cant start synthesis on a bare template - RNA polymerase (primase) creates a short strech of nucleotides that DNA polymerase can begin adding new nucleotides to NOT FOR SALE OR DISTRIBUTION PROPERTY OF YORK UNIVERSITY DNA polymerase catalyzes the addition of new nucleotides to the 3’ end of the growing strand DNA ploymerase add new nucleotides DNA can only be built in a 5' to 3' direction NOT FOR SALE OR DISTRIBUTION PROPERTY OF YORK UNIVERSITY  replication form moving to the right During DNA replication there is a leading (continuous synthesis) & a okazaki fragments lagging (discontinuous synthesis) strand each okazaki fragement require a primer - primers are later cut out by DNA polymerase - fragements are joined by DNA ligase NOT FOR SALE OR DISTRIBUTION PROPERTY OF YORK UNIVERSITY DNA structure facilitates replication & error correction https://en.wikipedia.org/wiki/D NA_replication#/media/File:D NOT FOR SALE OR DISTRIBUTION PROPERTY OF YORK UNIVERSITY NA_polymerase.svg DNA synthesis (replication) occurs at a specific time during the cell cycle DNA replication NOT FOR SALE OR DISTRIBUTION PROPERTY OF YORK UNIVERSITY Practice Questions (try first without looking up answers!) 1. Where does DNA replication take place? 2. If DNA polymerase can add nucleotides only in the 5’ à 3’ direction, what direction is the DNA template read? 3. We know that DNA replication occurs semiconservatively, but what would the results of the Meselson-Stahl experiment look like if it happened conservatively? 4. Aside from S phase, when else might DNA replication occur? 5. The diagram to the right is from the video. a. Label a – f with the following terms: Lagging strand, RNA primer, replication fork, leading strand template strands, Okazaki fragments b. Where on the diagram would DNA ligase function? NOT FOR SALE OR DISTRIBUTION PROPERTY OF YORK UNIVERSITY  Review video MOLECULAR ANATOMY: REVIEW OF RNA LOs A. Relate concepts from BIOL 1000 to those in BIOL 2040. C. Describe the molecular anatomy of genes and genomes (how DNA is organized) and how genetic information is duplicated. Describe the structure of RNA and the properties that characterize it NOT FOR SALE OR DISTRIBUTION PROPERTY OF YORK UNIVERSITY Information stored in DNA is expressed DNA is not Information transferred from "converted" it is one DNA molecule to another (replication) read and copied Information transferred from DNA to RNA molecule Information transferred from RNA to a protein through a code that specifies the amino acid sequence NOT FOR SALE OR DISTRIBUTION PROPERTY OF YORK UNIVERSITY  Information stored in DNA is expressed Information transferred from one DNA molecule to another (replication) RNA can also Information can be be reversed transferred from copied back to RNA to DNA DNA Some viruses can use RNA Information not DNA as transferred from hereditery RNA to a protein through a code that material specifies the amino acid sequence NOT FOR SALE OR DISTRIBUTION PROPERTY OF YORK UNIVERSITY RNA is chemically similar, but not identical, to DNA Extra hydroxyl group Uracil replaces thymine RNA is single stranded NOT FOR SALE OR DISTRIBUTION PROPERTY OF YORK UNIVERSITY Pearson Education, 2013.  RNA – more than the usual suspects All originate as complementary copies of one of the two DNA strands (i.e., by transcription) Informational Functional Functional tRNA – transfer RNAs RNAs do not rRNA – ribosomal RNAs code for protein (like snRNA – small nuclear RNAs mRNA does) miRNA – micro RNAs they do things siRNA – small interfering RNAs - noncoding lncRNA –long noncoding RNAs RNA NOT PearsonFOR SALE Education, 2013. OR DISTRIBUTION PROPERTY OF YORK UNIVERSITY Different types of RNA have different structures & roles mRNA tRNA rRNA NOT FOR SALE OR DISTRIBUTION PROPERTY OF YORK UNIVERSITY Pearson Education, 2013.  Translation produces proteins by reading the genetic code The genetic code is read from RNA not DNA NOT FOR SALE OR DISTRIBUTION PROPERTY OF YORK UNIVERSITY replication for cells to transcription and divide for copies of translation to produce genetic information for products that help a cell to new cells survive Practice Questions (try first without looking up answers!) 1. What are two differences between RNA and DNA? Which is more stable? Why might that be? 2. Head back to the first slide and identify—for each of the processes of replication, transcription, and translation: a. Where each process takes place within the cell; b. When within the cell cycle each process takes place. NOT FOR SALE OR DISTRIBUTION PROPERTY OF YORK UNIVERSITY  Review video MOLECULAR ANATOMY: CHROMOSOMES! LOs A. Relate concepts from BIOL 1000 to those in BIOL 2040. C. Describe the molecular anatomy of genes and genomes (how DNA is organized) and how genetic information is duplicated. Discuss how DNA is packaged into chromosomes (in terms of histones, nucleosomes, & chromatin). Describe characteristics of homologous chromosomes, including how the relative positions of individual genes on a given chromosome are related to their positions on the homologue of that chromosome (i.e., the relative positions of a gene on homologous chromosomes). Explain the meaning of ploidy (e.g., haploid, diploid), & how it relates to the number of homologues of each chromosome. Recognize/use appropriate representations of chromosomes, identifying cytological anatomy of eukaryotic chromosomes (e.g., p & q arms, relative centromere positions, gene maps, karyotyping) NOT FOR SALE OR DISTRIBUTION PROPERTY OF YORK UNIVERSITY Similarities & differences in structural organization of DNA Eukaryotic cell Bacterial cell Bacterial cell Bacterial cell Intergenic sequences NOT FOR2012SALE OR DISTRIBUTION PROPERTY OF YORK UNIVERSITY WH Freeman,  DNA is associated with proteins that help it pack into a smaller space DNA is wrapped around proteins to compact it Cells hold a total of 2m DNA (it’s not all 1 long strand!), but nuclei ~ 10um! NOT FOR SALE OR DISTRIBUTION PROPERTY OF YORK UNIVERSITY Compaction & condensation are different processes Condensation of chromosomes (during prophase) Compacted chromatin (throughout cell cycle) (including cell division) NOT FOR SALE OR vs. DISTRIBUTION http://www.ashg.org/education/gena/AdventuresInKaryotyping_L2.pdf PROPERTY OF YORK UNIVERSITY During interphase, G1, S, G2, DNA is not condensed  Ploidy refers to the # of complete sets of chromosomes (each set has all unique/different chromsomes) Haploid (n): Diploid (2n): e.g., Dogs 2n = 72 Fruit fly 2n = 4 Chimpanzee 2n = 48 Human 2n = 46 The number of chromosomes in a set is not linked to an organism’s complexity. NOT FOR SALE OR DISTRIBUTION PROPERTY OF YORK UNIVERSITY For each chromosome in a set, diploid organisms carry two homologues Diploid = 2 coipes of each Chr 1a chromosome Chr 1m Chr Chr 1b 1p From Parent 1 Chr Chr 2m2a From mom From From dad 2 Parent From From mom 1 Parent Homologuous pairs of chromosomes are: ChrChr 2p 2b Parent 2 - identical in size Fromdad From - centromere in the same location - carry the same genes Since they are from differnt parents, they may carry different alleles NOT FOR SALE OR DISTRIBUTION Modified from McGraw-Hill, 2009. PROPERTY OF YORK UNIVERSITY  We can identify chromosomes based on where their centromere is located centromere = metacentric area of highly p = short arm condensed DNA sub-metacentric centromere acrocentric q = long arm NOT FOR SALE OR telocentric DISTRIBUTION PROPERTY OF YORK UNIVERSITY Pearson Education, 2013 Can distinguish chromosomes based on their banding patterns C-banding Differences in staining X chromosome patterns b/w different pairs (e.g., Chr 3 & Chr 17) indicate differences in DNA sequence. G-banding NOT FOR SALE OR DISTRIBUTION PROPERTY OF YORK UNIVERSITY  Can use bands to show location of genes on chromosome bands can show the location of a - chromosome 12 particular gene on a - p arm chromosome - band 11.1 mapping genes and relating them to band position is only useful if chromosomes are similar NOT FOR SALE OR DISTRIBUTION PROPERTY OF YORK UNIVERSITY http://ghr.nlm.nih.gov/chromosome/13 How does DNA replication fit into all this? both sister chromatids should have the same alleles NOT FOR SALE OR DISTRIBUTION PROPERTY OF Each becomes a sister chromatid YORK UNIVERSITY Replication increases the amount of DNA in a cell - it does not Keep yer’ terms straight! Vocabulary matters! change the Use the right terms to identify chromosomes number of chromosomes Chr 1m Chr 1p Chr 2m Chr 2p These chromosomes are shown after DNA replication NOT FOR SALE OR DISTRIBUTION PROPERTY OF YORK UNIVERSITY McGraw-Hill, 2009 Practice Questions (try first without looking up answers!) 1. Explain how to identify if two chromosomes are homologous? 2. What is the difference between sister chromatids and non-sister chromatids? Do they all carry the same genes? The same alleles? 3. Why is a replicated chromosome considered one chromosome even though it has twice the amount of DNA as an unreplicated chromosome. 4. If an organisms cells have 3 complete sets of chromsomes how would you describe its ploidy? NOT FOR SALE OR DISTRIBUTION PROPERTY OF YORK UNIVERSITY  8/17/22 DNA is associated with proteins that help it pack into a smaller space positively charged histones bind electrostatically to the negative phosphate backbone of DNA Cells hold a total of 2m of nuclear DNA (it’s not all 1 long strand!) & it all fits in nuclei ~ 10um in diameter! https://www.travelwanderlust.co/articles/ranger-roll-clothes-for-packing/ https://www.genome.gov/genetics-glossary/Nucleosome 16 DNA is compacted throughout the cell cycle & then condenses https://www.genome.gov/genetics-glossary/Nucleosome during prophase COMPACTED chromatin Double helix (throughout cell cycle) (including cell division) “beads on a string” = DNA Nucleosome wound on chromosomes Chromatin fibre CONDENSATION of chromosomes (during prophase) chromosome https://www.genome.gov/genetics- glossary/Nucleosome https://www.youtube.com/watch?v=K6DklbzBN4gc 17 For most of the cell During prophase, cycle, chromatin is condensation occurs where in a diffuse and the chromatin is further condensed state condensed - DNA no longer 1 diffuse  8/17/22 DNA replication occurs BEFORE mitosis or meiosis Chromosomes are condensed Cell is growing Fig. 17-3 Molecular Biology of the Cell, 4th Ed DNA is doubled 2009. Nature Education 22 Same cycle but with chromosomes the way we normally picture them. Fig. 17-3 Molecular Biology of the Cell, 4th Ed sister chromatids are pulled apart so each goes into a daughter cell 2009. Nature Education 24 1  8/17/22 A more “realistic” depiction of DNA throughout the cell cycle… Fig. 17-3 Molecular Biology of the Cell, 4th Ed 2009. Nature Education 25 2  8/18/22 Many molecular techniques exploit the structure of DNA & its replication NOT FOR SALE OR DISTRIBUTION PROPERTY OF YORK UNIVERSITY 61 Can structures that resemble nucleotides be incorporated into DNA or RNA? Hypoxanthine = base analog = molecules that base analogs can be naturally hae similar stures to formed by muting a noraml bases and can be base, others are synthetic incorporated into DNA and RNA NOT FOR SALE OR DISTRIBUTION PROPERTY OF YORK UNIVERSITY 62 1  an antibody that 8/18/22 cells need to be activley dividing recognizes BrdU will give to pick up a BrdU and place it off fluoresecense once it where tymine would normally go binds to the BrdU Base analogs get incorporated due to their structural similarity to specific bases BrdU is a synthetic e.g., BrdU analog of tymine BrdU Thymidine When does the label get incorporated? NOT FOR SALE OR DISTRIBUTION PROPERTY OF YORK UNIVERSITY https://en.wikipedia.org/wiki/Nucleic_acid_structure 63 We can label DNA using various base analogs & isotopes 15N 32P 5-azacytidine cytidine can stop the 3H-thymidine rapid replication BrdU tumour cells NOT FOR SALE OR DISTRIBUTION https://en.wikipedia.org/wiki/Nucleic_acid_structure PROPERTY OF YORK UNIVERSITY 64 2