Genomes & Genome evolution

1. Genomes & Genome evolution

2. Genomes and Genome Evolution - BIOL 4301/6301What to expect and some suggestions. • I like think of myself as fair but reasonably tough • I want people to do well but I’m not willing to compromise on the material or ethical guidelines to make it happen. • There is no extra credit. This is non-negotiable. • Study for the exams and do well on them. • Ask questions IN CLASS • Makes things more interesting for me • Others probably have the same question • You’re paying, get your money’s worth • Interactions with other humans tends to wake people up • Office hours!!!!!!!!!! I have them. Take advantage. • I am an evolutionary biologist. This class is taught from an evolutionary perspective.

3. Genomes and Genome Evolution - BIOL 4301/6301What to expect and some suggestions. • Absorb and critique anything related to the subject. This includes but is not restricted to: • Popular news articles, TV shows (CSI, Bones, etc.), textbooks, wikipedia, etc. Genomics is everywhere. • Bring in what you find for discussion. • Website - http://www.myweb.ttu.edu/daray/Teaching.htm • Username & password • Again, ask questions during class • Ask questions DURING CLASS • Did I mention that you should ask questions during class? • You WILL see pictures of my adorable children. This is also non-negotiable.

5. Course Objectives and Assumptions • Objectives: By the end of this course you should… • have a working knowledge of genome structure and function in prokaryotes, eukaryotes, and viruses • be able to explain the basics of how genomes are investigated using modern tools • describe the ways in which genomes can change and have changed over time

6. Course Objectives and Assumptions • Assumptions: I am assuming that you… • have a working knowledge of Mendelian genetics • have a working knowledge of DNA, RNA and proteins • understand the basic differences between eukaryotes and prokaryotes • have a basic understanding of the concept of a gene • have a working knowledge of the ‘central dogma’ of Biology • give a rat’s behind about learning this stuff • while not required, it would be a good idea to take Caleb Philips’ course concurrently

7. “No course should ever be taught the first time”

8. Fundamental Concepts UNIT 1

9. The biggest failure of science education is… • Most people can’t discriminate between what is scientific and what is not scientific. • This is due, in part, to the fact that definitions of science tend to be fairly nebulous. • Moreover, any moron can get a Ph.D.

10. Science • A method for discovering how the world around us works • Assumes that all things can be explained by natural processes • Does not allow supernatural explanations • Why? • Rooted in hypothesis formation, observation, testing, and constant re-examination of evidence • Hypotheses MUST be abandoned if they are not supported by evidence • The scientific community is intensely critical of its own ideas and the ideas of others. The advantage of this isn’t that mistakes aren’t made, its that this method pretty much guarantees that mistakes are caught quickly.

11. Science • Step 1. Propose as many ideas as you can think of to explain a phenomenon then pick one or several. • Step 2. Try to disprove it/them. • Step 3. Allow others to try and disprove it/them. • Basic philosophy - Ideas that survive this process are more likely to reflect the real world than ideas that don’t.

12. Other belief systems Religion • A way of “knowing” that is not rooted in scientific principles, but rather is based upon alternate philosophies, mythologies, etc. Most religions have some supernatural aspects. Many religions are opposed to critical inquiry of the beliefs professed. Pseudoscience • Any non-scientific belief system that uses scientific jargon in an attempt to give it scientific credence. Again, criticism of the concepts is often discouraged.

13. Ways of thinking • Of these ways of thinking, science is the “new kid on the block” • Science is a relatively new invention (arguably only a few hundred years old, if that) • But think of all the progress that’s been made in those few hundred years because of scientific thinking

14. Fundamental Biological Concepts UNIT 1

15. Genome • Definition depends upon organism, organelle, or virus one is talking about • Generic definition: Minimum DNA complement that define an organism/organelle/virus • Organelles are not, in and of themselves, living creatures. Thus something can have a genome and not be “alive.” • Viruses may or may not be alive, depending upon how one defines life • The dead have genomes too.

16. Things with genomes • Prokaryotes • Monera (bacteria) • Archaea • Mitochondria • Chloroplasts • Viruses • Eukaryotes • Animals • Plants • Fungi • Protists

17. Things without genomes • Dirt • Rocks • Water • Air • Fire • But even these things may be contaminated with genomic DNA (…well, maybe not fire)

18. What genomes can and can’t do • A genome constrains but does not dictate the features of an organism • Environmental impacts • Toxins, exercise, exposure to disease • Epigenetic impacts • If someone were to clone Hitler…?

19. Genomics • Study of genomes? • Research in which robotics, automated sequencing, and advanced computational methods are utilized to rapidly and efficiently characterize genomes and their components

20. Graduate discussion section will meet in ESB 201.

21. The Central Dogma • DNA  RNA  Protein • Generally unidirectional

22. Nucleic Acids • Ribonucleic acid (RNA) and deoxyribonucleic acid (DNA) • Composed of chains of nucleotides (ribonucleotides for RNA, deoxyribonucleotides for DNA)

23. Nucleic Acids • Deoxyribonucleic acid • A polymer of nucleotides linked by phosphodiester bonds

24. Nucleic Acids • Purine vs. pyrimidine • Carbon positions

25. Nucleic Acids • Deoxyribonucleic acid • Antiparallel strands held together by hydrogen bonds • Strands are complementary

26. Scanning-tunneling electron micrograph DNA in 3D Pretty uncanny resemblance, don’t you think?

27. Nucleic Acids • Deoxyribonucleic acid can denature, renature & hybridize • Denaturation – separation of the double helix by the addition of heat or chemicals • Renaturation – the reformation of double stranded DNA from denatured DNA • The rate at which a particular sequence will reassociate is proportional to the number of times it is found in the genome • Given enough time, nearly all of the DNA in a heat denatured DNA sample will renature.

28. Nucleic Acids • Ribonucleic acid • Ribose vs. deoxyribose • Thymine = 5 methyl-uracil • Usually single stranded

29. Nucleic Acids • Intramolecular base-pairing • Enhanced base-pairing capacity due to G:U bonding • Hairpins • Bulges • Loops • Stem-loop structures • Pseudoknots

30. Nucleic Acids • Complex tertiary structures • Much more flexible than DNA • Capable of triple bonds and base-backbone interactions • Often ‘molded’ by proteins and snoRNPs • Leads to complex 3° structures with catalytic capability - ribozymes

31. Nucleic Acids OH OH NB NB NB NB DNA RNA OH O OH OH P O C OH O P P P O O O C C C O OH OH

32. RNA World • RNAs can have complex 3D structures • They can store genetic information • Some RNAs known as ribozymes can catalyze reactions • Thus it has been hypothesized that life may have arisen first through RNA with protein and DNA being integrated later

33. Replication • DNA is replicated in a semi-conservative fashion, i.e., each daughter molecule is composed of one strand of the original molecule and one newly synthesized strand. • DNA polymerase is the enzyme that catalyzes synthesis of new strands out of dNTPs.

34. Replication: Key points • DNA polymerase cannot generate a new strand without a 3’ OH on which to add a nucleotide. Primers are required. • New strands generated from 5’ to 3’. • Replication is bidirectional. Replication forks proceed from an initiation site in both directions. • Multiple sites of initiation are found along a chromosome. Initiation sites are often AT rich as AT base pairs are less stable and thus come apart more easily. • Okazaki fragments are generated along lagging strand. • http://www.johnkyrk.com/DNAreplication.html • http://www.dnalc.org/resources/3d/04-mechanism-of-replication-advanced.html

35. RNA • Normally single-stranded • Generated from NTPs by RNA polymerase using DNA as a template (transcription) • As with DNA replication, new strand assembled in 5’ to 3’ direction by phosphodiester bond formation • RNA is inherently less stable than DNA

36. Major types of RNA • Messenger RNA (mRNA) – carries genetic instructions (coded in DNA) from the nucleus into the cytoplasm. mRNA molecules are often called transcripts. • Ribosomal RNA (rRNA) – a structural component of ribosomes (the complexes that are involved in assembling proteins based upon information in mRNA templates) • Transfer RNA (tRNA) – acts as carrier of amino acids during protein assembly • Regulatory RNAs – Many groups; miRNAs, siRNAs, CRISPR RNAs, antisense RNAs, long non-coding RNAs

37. Transcription • Generation of an RNA strand from a DNA template • Much of the control over cell development comes at the transcriptional level – All somatic cells have same DNA but can differ tremendously in morphology and function • Differential gene expression

38. Transcription: Key points • Transcription starts at the promoter, a site along the DNA molecule where RNA polymerase binds. • RNA polymerase is recruited to the promoter by transcription factors. • New strand generated from 5’ to 3’. • Only one of the two DNA strands serves as a template(antisense strand). The other strand (sense strand) has the same sequence as the mRNA molecule except dTMPs have been substituted with UMPs. • Which stand is used as a template differs between genes. • After transcription, mRNA undergoes post-transcriptional modifications. Generally, a methyl-guanosine cap is added to the 5’ end and a tail of adenosine nucleotides (poly-A tail) is added to the 3’ end. • In eukaryotes, the mRNA undergoes post-transcriptional splicing – introns are removed and exons are spliced together.

39. Transcription models • http://www.johnkyrk.com/DNAtranscription.html • http://www.dnalc.org/resources/3d/13-transcription-advanced.html

40. A few definitions • Precursor mRNA (pre-mRNA) or heterogeneous nuclear RNA (hnRNA): mRNA immediately after transcription and before post-transcriptional modification • Mature mRNA (or simply mRNA): Transcript after post-transcriptional modifications. • cDNA (complementary DNA): A DNA molecule generated in a reaction catalyzed by reverse transcriptase using mature mRNA as the template.

41. rRNA • Associated with proteins to form ribosomes • Several different rRNAs • Genes that code for rRNA are typically referred to as rDNA sequences • rDNA sequences found in more or less tandem repeats in genome

42. tRNA • tRNA molecules deliver amino acids to ribosomes during protein synthesis (translation) • tRNAs have considerable secondary structure due to base pairing • Clover leaf 2D structure • L-shaped 3D structure • There are more than 20 tRNAs (i.e., there is some redundancy) • tRNA structure is highly conserved (e.g., human tRNAs can function in yeast) • http://www.myweb.ttu.edu/daray/Genomes/ribosome/ribosome/ribosome_jmol_play.html

43. Amino acids • Proteins are made of chains of amino acids • There are 20 amino acids utilized by biological systems • Each codon in mRNA represents an amino acid or a start/stop signal • Amino acids can be acidic (net negative charge), basic (positive charge), uncharged polar (ends have different net charges), and non-polar. • Uncharged polar, acidic, and basic amino acids tend to be hydrophilic and thus are often found on the outside of proteins. • Non-polar amino acids tend to be hydrophobic and thus are clustered in the middle of proteins.

44. Genetic code

45. Formation of a peptide bond • At physiological pH (7.0), both the amino and carboxyl groups are ionized. • The peptidyltransferase ribozyme catalyzes the formation of peptide bonds with the concomitant release of a water molecule.

46. Translation • Construction of an amino acid chain (protein) by a ribosome based upon the nucleotide sequence of a mRNA molecule • While there are minor differences between eukaryotic and prokaryotic translation processes, most steps in translation are well conserved. http://www.johnkyrk.com/DNAtranslation.html

47. Spatial separation of transcription and translation is seen in eukaryotes, not prokaryotes

48. What is a gene? • How do we identify a gene? • A priori methods – • recognize sequence patterns within expressed genes and the regions flanking them • Distinctive patterns of codon statistics (most obviously, a reduced frequency of stop codons) • Proximity of start codon and known promoter sites • GT/AG pairs in exons • Codon usage statistics can be ‘typical’ of genes in an organism • Use a set of known genes to identify regions with similar codon usage stats • ‘Been there, seen that’ methods – • Recognize regions corresponding to previously characterized genes. • The changing definition of a ‘gene’

49. Genes vs. alleles vs. loci • Gene: “Region of DNA that controls a discrete hereditary characteristic, often (but not always) corresponding to a single protein or RNA. This definition includes the entire functional unit, encompassing coding DNA sequences, non-coding regulatory DNA sequences, and introns.” • Allele: “One of a set of alternative forms of a gene.” • Locus: “The position of a gene on a chromosome. Different alleles of the same gene all occupy the same locus.” • Definitions from Alberts et al. (1994)

50. Recombination • Protein-mediated (1) exchange of a DNA region between two different DNA molecules OR (2) replacement of a DNA region in one molecule by DNA from another • Almost always requires at least some homology between sequences involved