Lecture 5 Fundamentals DNA 2024 PDF

DNA! Darrin Hulsey 22 October 2024 Halloween DNA questions Who was the killer?! Halloween DNA questions Who was the killer?! Am I not the father?! Halloween DNA questions Who was the killer?! Am I not the father?! The monster is clearly half-human. But is he also half-wolf?! DNA Deoxy...

DNA! Darrin Hulsey 22 October 2024 Halloween DNA questions Who was the killer?! Halloween DNA questions Who was the killer?! Am I not the father?! Halloween DNA questions Who was the killer?! Am I not the father?! The monster is clearly half-human. But is he also half-wolf?! DNA DeoxyriboNucleicAcid Made of nucleotides – building blocks of DNA Average human gene contains 10-15k nucleotides DNA very long, so needs to be coiled and folded to fit into the nucleus of the cell Proteins called histones hold DNA in this folded state  DNA is amazing! It is amazing enough that DNA can encode the information required to build the cells Baby at Play, by Thomas Eakins, 1876 and tissues in an entire organism.  DNA is amazing! It is amazing enough that DNA can encode the information required to build the cells Baby at Play, by Thomas Eakins, 1876 and tissues in an entire organism. But perhaps equally amazing is the ability cells have to replicate all that information with almost perfect precision. https://www.prosofteng.com/blog/warning-signs-and- symptoms-of-hard-drive-failure  DNA is amazing! It is amazing enough that DNA can encode the information required to build the cells Baby at Play, by Thomas Eakins, 1876 and tissues in an entire organism. But perhaps equally amazing is the ability cells have to replicate all that information with almost perfect precision. 3 billion bases in haploid form are passed on almost perfectly to offspring https://www.prosofteng.com/blog/warning-signs-and- symptoms-of-hard-drive-failure  DNA is amazing! It is amazing enough that DNA can encode the information required to build the cells Baby at Play, by Thomas Eakins, 1876 and tissues in an entire organism. But perhaps equally amazing is the ability cells have to replicate all that information with almost perfect precision. 3 billion bases in haploid form are passed on almost perfectly to offspring 3 billion base pairs are passed on almost perfectly every time a cell divides https://www.prosofteng.com/blog/warning-signs-and- symptoms-of-hard-drive-failure DNA Structure and replication https://www.youtube.com/watch?v=8kK2zwjRV0M Human Genome 22 autosome pairs + 2 sex chromosomes ~3 billion bases in the haploid genome. Paired in the diploid genome  President Bill Clinton on June 26th 2000 the announcement of the sequencing of the human genome Today, we are learning the language in which God created life. Today's announcement represents more than just an epic-making triumph of science and reason. After all, when Galileo discovered he could use the tools of mathematics and mechanics to understand the motion of celestial bodies, he felt, in the words of one eminent researcher, "that he had learned the language in which God created the universe." But today's historic achievement is only a starting point. There is much hard work yet to be done. http://www.genome.gov/10001356 The cost of sequencing genomes has dropped exponentially and is currently somewhere ~200 to 100 Euros C value paradox: the amount of DNA in a haploid genome (the 1C value) does not seem to correspond strongly to the complexity of an organism C-value paradox 22 Are the ‘directions’ to make a whole animal encoded in all animal cells? Are the ‘directions’ to make a whole animal encoded in all animal cells? Are the ‘directions’ to make a whole animal encoded in all animal cells? The directions to make a whole plant are encoded in virtually all cells 27 The directions to make a whole plant are encoded in virtually all cells Pluripotent: capable of giving rise to several different cell types. Totipotent: capable of giving rise to any cell types or a complete organism Cells are Genomically Totipotent Hypothesis that the nucleus of a specialized cell contains the complete genome. In 1962, Gurdon transferred the nucleus from an intestinal cell of a tadpole into an unfertilized frog’s egg. The egg with the replaced nucleus matured into a complete tadpole. Cloning was born! Cloning Creation of viable whole organisms from insertion of nuclei from differentiated cells Modern Whole Genome Sequencing Sequencing of whole genomes is now done every day with various non-essential tissues/cells in a wide diversity of organisms. Modern-day test repeated millions of times of the hypothesis that the entire genome is present in every cell ***Animal cellular differentiation is generally not accomplished by deletion of part of the genome in particular cell lines*** Despite having split ~7 million years ago, 96% of the genome between chimpanzees and humans is similar. So, what is different? Feuk et al. 2005 Most of the genome is NOT protein coding Where is the variation? Genetic markers are an identifiable peace of DNA sequence that can be used to tell apart individuals, populations or species! Examples: SNP – Single Nucleotide Polymorphism, SSR: Simple Sequence/Tandem Repeat or Microsatellite SNP SSR Individual I Individual 2 Individual 3 Where is the variation? Variation between two humans: 1. SNPs (~3,5 million) 2. Microsatellites (~10,000) most of this variation is biologically insignificant! But, they provide ample markers to blanket the genome and tease apart the genetic basis of traits What are microsatellites? Microsatellites are simple sequence repeats (SSRs). The repeat units are generally di-, tri- tetra- or pentanucleotides. For example, a common repeat motif in an organism is ACn, where the two nucleotides A and C are repeated in bead-like fashion a variable number of times (n could range from 8 to 50) SNP SSR Individual I Individual 2 Individual 3 What are microsatellites? SSR DNA can repeat a few times. How many times these parts repeat varies from person to person. That makes them useful markers for telling people apart! What are microsatellites? SSR DNA can repeat a few times. How many times these parts repeat varies from person to person. That makes them useful markers for telling people apart! What are microsatellites? In a child, a certain SSR repeats 9 times on one copy of his DNA, and 11 times on the other. We can look at his parents and see that his mom gave him the 9-repeat version, and his dad gave him the 11-repeat version. What are microsatellites? If you think about this example, there are probably lots of men that have an 11 repeat as one of their copies of that marker. This means that we need to test several markers to be sure of paternity. What are microsatellites? Say if we had a 24-marker paternity test, if the man being tested was the father, we’d expect that each marker would play out like the example above. That means that all 24 markers should match up.  What are microsatellites? ??? If some of the 24 different markers do not match up, 5 , 12 6,7 then not the father. Who is your Daddy Luke? 6 , 10  What are microsatellites? Father! ??? If several of the 24 Locus 1 3 , 11 different markers do Locus 2 2, 10 5 , 12 6,7 not match up, then not the father. But, if all 24 do match, then it is very, very likely they are the father! 6 , 10  Halloween DNA questions We can now determine if you are half-human half-wolf! If you are the daddy! Or if you were the killer! Question 1 Which of the following force or type of chemical bond keeps the oxygen and carbon together in a carbon dioxide (CO2) molecule? A Van der Waals force B Ionic bond C Metal bond D Covalent bond E Hydrogen bond Which of the following force or type of chemical bond keeps the oxygen and carbon together in a carbon dioxide (CO2) molecule? A Van der Waals force B Ionic bond C Metal bond D Covalent bond E Hydrogen bond Question 2 Of the following, which is the most abundant and diverse vertebrate group? A Amphibians B Birds C Ray-finned fishes D Lizards E Mammals Of the following, which is the most abundant and diverse vertebrate group? A Amphibians B Birds C Ray-finned fishes D Lizards E Mammals Question 3 Which ONE of these is NOT a characteristic of all forms of life? A Nutrition B Organisation C Excretion D Reproduction E Photosynthesis Which ONE of these is NOT a characteristic of all forms of life? A Nutrition B Organisation C Excretion D Reproduction E Photosynthesis