1. VII. DNA and Genome Structure A. Search for the Genetic Information B. Determining DNA Structure C. Chromosome Structure

2. VII. DNA and Genome Structure A. Search for the Genetic Information B. Determining DNA Structure C. Chromosome Structure 1. Eukaryotic Chromosomes

3. VII. DNA and Genome Structure A. Search for the Genetic Information B. Determining DNA Structure C. Chromosome Structure 1. Eukaryotic Chromosomes a. DNA wrapped around 8 histone proteins = “nucleosome”… form ‘beads on a string’

4. VII. DNA and Genome Structure A. Search for the Genetic Information B. Determining DNA Structure C. Chromosome Structure 1. Eukaryotic Chromosomes a. DNA wrapped around 8 histone proteins = “nucleosome”… form ‘beads on a string’ b. 6 nucleosomes are coiled into a ‘solenoid’

5. VII. DNA and Genome Structure A. Search for the Genetic Information B. Determining DNA Structure C. Chromosome Structure 1. Eukaryotic Chromosomes a. DNA wrapped around 8 histone proteins = “nucleosome”… form ‘beads on a string’ b. 6 nucleosomes are coiled into a ‘solenoid’ c. Supercoiling

6. VII. DNA and Genome Structure A. Search for the Genetic Information B. Determining DNA Structure C. Chromosome Structure 1. Eukaryotic Chromosomes a. DNA wrapped around 8 histone proteins = “nucleosome”… form ‘beads on a string’ b. 6 nucleosomes are coiled into a ‘solenoid’ c. Supercoiling d. Folding to condensed chromosome

7. VII. DNA and Genome Structure A. Search for the Genetic Information B. Determining DNA Structure C. Chromosome Structure 1. Eukaryotic Chromosomes e. Tightly coiled regions stain dark heterochromatin that often lacks genes. Lightly staining areas are euchromatin and have a higher density of coding sequences. These can be seen in a ‘polytene chromosome’

8. VII. DNA and Genome Structure A. Search for the Genetic Information B. Determining DNA Structure C. Chromosome Structure 1. Eukaryotic Chromosomes 2. Bacterial Chromosomes

9. VII. DNA and Genome Structure A. Search for the Genetic Information B. Determining DNA Structure C. Chromosome Structure 1. Eukaryotic Chromosomes 2. Bacterial Chromosomes - ds-DNA with a few associated proteins similar to histones of eukaryotes.

10. VII. DNA and Genome Structure A. Search for the Genetic Information B. Determining DNA Structure C. Chromosome Structure 1. Eukaryotic Chromosomes 2. Bacterial Chromosomes - ds-DNA with a few associated proteins similar to histones of eukaryotes. - typically a circular chromosome

11. VII. DNA and Genome Structure A. Search for the Genetic Information B. Determining DNA Structure C. Chromosome Structure 1. Eukaryotic Chromosomes 2. Bacterial Chromosomes - ds-DNA with a few associated proteins similar to histones of eukaryotes. - typically a circular chromosome - tends to be concentrated around the periphery of a cell - nucleoid

12. VII. DNA and Genome Structure A. Search for the Genetic Information B. Determining DNA Structure C. Chromosome Structure 1. Eukaryotic Chromosomes 2. Bacterial Chromosomes 3. Mt-DNA and Cp-DNA - Mitochondria and chloroplasts have their own DNA that is very similar to bacteria DNA in structure (circular with few proteins) and sequence (no introns, repeats). Mt-DNA from a frog cell mitochondrion.

13. VII. DNA and Genome Structure A. Search for the Genetic Information B. Determining DNA Structure C. Chromosome Structure 1. Eukaryotic Chromosomes 2. Bacterial Chromosomes 3. Mt-DNA and Cp-DNA 4. Viral Chromosomes ss or ds DNA or RNA small

14. VII. DNA and Genome Structure A. Search for the Genetic Information B. Determining DNA Structure C. Chromosome Structure D. Genome Structure

15. VII. DNA and Genome Structure A. Search for the Genetic Information B. Determining DNA Structure C. Chromosome Structure D. Genome Structure 1. viruses

16. VII. DNA and Genome Structure A. Search for the Genetic Information B. Determining DNA Structure C. Chromosome Structure D. Genome Structure 1. viruses (10 3 – 10 6 ) Base pairsGenesNotes Phi-X 1745,38610virus of E. coli Epstein-Barr virus (EBV)172,28280causes mononucleosis Rickettsia prowazekii1,111,523834 bacterium that causes epidemic typhus Mimivirus1,181,4041,262 A virus (of an amoeba) with a genome larger than some cellular organisms Small genomes because viruses (typically) rely on the metabolism of their host cell; they are cellular/genetic parasites.

17. Smallest genome – Porcine circovirus (PCV) – 1768 bp… 4 genes! 1 accagcgcac ttcggcagcg gcagcacctc ggcagcacct cagcagcaac atgcccagca 61 agaagaatgg aagaagcgga ccccaaccac ataaaaggtg ggtgttcacg ctgaataatc 121 cttccgaaga cgagcgcaag aaaatacggg agctcccaat ctccctattt gattatttta 181 ttgttggcga ggagggtaat gaggaaggac gaacacctca cctccagggg ttcgctaatt 241 ttgtgaagaa gcaaactttt aataaagtga agtggtattt gggtgcccgc tgccacatcg 301 agaaagccaa aggaactgat cagcagaata aagaatattg cagtaaagaa ggcaacttac 361 ttattgaatg tggagctcct cgatctcaag gacaacggag tgacctgtct actgctgtga 421 gtaccttgtt ggagagcggg agtctggtga ccgttgcaga gcagcaccct gtaacgtttg 481 tcagaaattt ccgcgggctg gctgaacttt tgaaagtgag cgggaaaatg cagaagcgtg 541 attggaagac caatgtacac gtcattgtgg ggccacctgg gtgtggtaaa agcaaatggg 601 ctgctaattt tgcagacccg gaaaccacat actggaaacc acctagaaac aagtggtggg 661 atggttacca tggtgaagaa gtggttgtta ttgatgactt ttatggctgg ctgccgtggg 721 atgatctact gagactgtgt gatcgatatc cattgactgt agagactaaa ggtggaactg 781 tacctttttt ggcccgcagt attctgatta ccagcaatca gaccccgttg gaatggtact 841 cctcaactgc tgtcccagct gtagaagctc tctatcggag gattacttcc ttggtatttt 901 ggaagaatgc tacagaacaa tccacggagg aagggggcca gttcgtcacc ctttcccccc 961 catgccctga atttccatat gaaataaatt actgagtctt ttttatcact tcgtaatggt 1021 ttttattttt catttagggg ttaagtgggg ggtctttaag attaaattct ctgaattgta 1081 catacatggt tacacggata ttgtagtcct ggtcgtattt actgttttcg aacgcagtgc 1141 cgaggcctac gtggtccaca tttctagagg tttgtagcct cagccaaagc tgattccttt 1201 tgttatttgg ttggaagtaa tcaatagtgg agtcaagaac aggtttgggt gtgaagtaac 1261 gggagtggta ggagaagggt tgggggattg tatggcggga ggagtagttt acatatgggt 1321 cataggttag ggcattggcc tttggtacaa agttatcatc tagaataaca gcagtggagc 1381 ccactcccct atcaccctgg gtgatggggg agcagggcca gaattcaacc ttaacttttc 1441 ttattctgta gtattcaaag ggtatagaga ttttgttggt cccccctccc gggggaacaa 1501 agtcgtcaag cttaaatctc atcatgtcca ccgcccagga gggcgttgtg actgtggtac 1561 gcttgacagt atatccgaag gtgcgggaga ggcgggtgtt gaagatgcca tttttccttc 1621 tccaacggta gcggtggcgg gggtggacga gccaggggcg gcggcggagg atctggccaa 1681 gatggctgcg ggggcggtgt cttcttctgc ggtaacgcct ccttggatac gtcatagctg 1741 aaaacgaaag aagtgcgctg taagtatt Circular ss-DNA, in a protein capsid that is 17nm wide (that’s nanometers!!) Codes for 2 replication enzymes, the protein, and a fourth protein required for replication.

18. VII. DNA and Genome Structure A. Search for the Genetic Information B. Determining DNA Structure C. Chromosome Structure D. Genome Structure 1. viruses (10 3 – 10 6 ) Small genomes because viruses rely on the metabolism of their host cell; they are cellular/genetic parasites. Many viruses have introns – intervening sequences in their genes that are spliced out after transcription. They have been spliced from eukaryotic genomes. They are often transposons, too. High mutation rates – one point mutation per genome replication!!

19. Viruses and the Evolution of Life - Viruses Late: Since viruses use host cells to metabolize, it would seem that cellular life must have evolved first. Are they degenerate cells that have lost capacity to replicate (and are now genetic parasites), or are they “rogue genes” that have escaped from genomes and evolved the capacity to replicate in other cells?

20. Pithovirus, 1.5 um long! 500 genes, replicates in Ameoba without integrating into nucleus…rather independent Pandoravirus, about 1um long, 2.4 gigabase genome! About 2500 genes. Linear ds-DNA - Viruses Early - Genes with no relationships to the rest of life - Viral genetic diversity exceeds diversity in the rest of life - reverse transcriptase, which is required to make DNA in “RNA world”, is of retroviral origin.

21. D. Genome Structure 1. viruses 2. Eubacteria/Archaea (10 5 – 10 6 ) Base pairsGenesNotes Nanoarchaeum equitans490,885552 This parasitic member of the Archaea has the smallest genome of a true organism yet found. Archaea Mycoplasma genitalium580,073485 three of the smallest true organisms Ureaplasma urealyticum751,719652 Mycoplasma pneumoniae816,394680 Chlamydia trachomatis1,042,519936 most common sexually- transmitted disease (STD) bacterium in the U.S. Rickettsia prowazekii1,111,523834 bacterium that causes epidemic typhus Treponema pallidum1,138,0111,039bacterium that causes syphilis Mimivirus1,181,4041,262 A virus (of an amoeba) with a genome larger than the six cellular organisms above Pelagibacter ubique1,308,7591,354 smallest genome yet found in a free-living organism (marine α- proteobacterium)α- proteobacterium Borrelia burgdorferi1.44 x 10 6 1,738 bacterium that causes Lyme disease [Note]Note

22. D. Genome Structure 1. viruses 2. Eubacteria/Archaea Base pairsGenesNotes Borrelia burgdorferi1.44 x 10 6 1,738 bacterium that causes Lyme disease [Note]Note Thermoplasma acidophilum1,564,9051,509 These unicellular microbes look like typical bacteria but their genes are so different from those of either bacteria or eukaryotes that they are classified in a third kingdom: Archaea. Archaea Methanococcus jannaschii1,664,9701,783 Aeropyrum pernix1,669,6951,885 Pyrococcus horikoshii1,738,5051,994 Methanobacterium thermoautotrophicum 1,751,3772,008 Vibrio cholerae4,033,4603,890in 2 chromosomes; causes cholera Mycobacterium tuberculosis4,411,5323,959causes tuberculosis Mycobacterium leprae3,268,2031,604causes leprosy E. coliE. coli K-124,639,2214,377 4,290 of these genes encode proteins; the rest RNAs E. coli O157:H75.44 x 10 6 5,416 strain that is pathogenic for humans; has 1,346 genes not found in E. coli K-12 Salmonella enterica var Typhi4,809,0374,395 + 2 plasmids with 372 active genes; causes typhoid fever Pseudomonas aeruginosa6.3 x 10 6 5,570 Increasingly common cause of opportunistic infections in humans.

23. D. Genome Structure 1. viruses 2. Eubacteria/Archaea (10 5 – 10 6 ) - again, parasitic forms are generally the smallest - protein genes do not have introns (non-coding sequence in genes) - only t-RNA and r-RNA genes have introns (Archaea); not protein-encoding genes

24. D. Genome Structure 1. viruses 2. Eubacteria/Archaea 3. Eukaryotes (10 7 – 10 11 ) Base pairsGenesNotes Human mitochondrionmitochondrion16,56937 nucleomorph of Guillardia theta551,264511 all that remains of the nuclear genome of a red alga (eukaryote) engulfed long ago by another eukaryotered alga Schizosaccharomyces pombe12,462,6374,929 Fission yeast. A eukaryote with fewer genes than the two bacteria below. Streptomyces coelicolor6,667,5077,842 An actinomycete whose relatives provide us with many antibioticsactinomycete Sinorhizobium meliloti6,691,6946,204 The rhizobial symbiont of alfalfa. Genome consists of one chromosome and 2 large plasmids.rhizobial symbiont Saccharomyces cerevisiae12,495,6825,770Budding yeast. A eukaryote. Cyanidioschyzon merolae16,520,3055,331A unicellular red alga.red alga Plasmodium falciparum22,853,7645,268 Plus 53 RNA genes. Causes the most dangerous form of malaria. Again, organelles and other obligate symbionts have very reduced genomes because they rely on their host’s metabolism.

25. D. Genome Structure 1. viruses 2. Eubacteria/Archaea 3. Eukaryotes Base pairsGenesNotes Thalassiosira pseudonana34.5 x 10 6 11,242 A diatom. Plus 144 chloroplast and 40 mitochondrial genes encoding proteinsdiatom Caenorhabditis elegans100,258,17119,427 The first multicellular eukaryote to be sequenced. Arabidopsis thaliana115,409,949~28,000 a flowering plant (angiosperm) See note.angiospermSee note. Drosophila melanogaster122,653,97713,379the "fruit fly" Anopheles gambiae278,244,06313,683Mosquito vector of malaria. Rice3.9 x 10 8 37,544 Sea urchin8.14 x 10 8 ~23,300 Dogs2.4 x 10 9 19,300 Humans3.3 x 10 9 ~20,500[Link to more details.]Link to more details. Amphibians10 9 –10 11 ? Psilotum nudum2.5 x 10 11 ?Note The amount of DNA DOES NOT correlate with the complexity of the organism… this is called the c-value paradox. Why? What does the EXTRA DNA in some simple organisms do??

26. D. Genome Structure 1. viruses 2. Eubacteria/Archaea 3. Eukaryotes Base pairsGenesNotes Thalassiosira pseudonana34.5 x 10 6 11,242 A diatom. Plus 144 chloroplast and 40 mitochondrial genes encoding proteinsdiatom Caenorhabditis elegans100,258,17119,427 The first multicellular eukaryote to be sequenced. Arabidopsis thaliana115,409,949~28,000 a flowering plant (angiosperm) See note.angiospermSee note. Drosophila melanogaster122,653,97713,379the "fruit fly" Anopheles gambiae278,244,06313,683Mosquito vector of malaria. Rice3.9 x 10 8 37,544 Sea urchin8.14 x 10 8 ~23,300 Dogs2.4 x 10 9 19,300 Humans3.3 x 10 9 ~20,500[Link to more details.]Link to more details. Amphibians10 9 –10 11 ? Psilotum nudum2.5 x 10 11 ?Note The amount of DNA DOES NOT correlate with the complexity of the organism… this is called the c-value paradox. Why? What does the EXTRA DNA in some simple organisms do?? Actually, it may do nothing – it may be highly repetitive DNA (transposons)

27. D. Genome Structure 1. viruses 2. Eubacteria/Archaea 3. Eukaryotes Types of DNA: - single copy sequences: functional genes and pseudogenes (vestigial genes) - repetitive DNA ONLY 1-10% of a eukaryotic genome codes for protein

28. Repetitive DNA: - Highly Repetitive DNA – typically concentrated in heterochromatic regions such as the centromere and telomere.

29. Repetitive DNA: - Highly Repetitive DNA – typically concentrated in heterochromatic regions such as the centromere and telomere. There are repeated sequences consisting of 2 bases (‘tandem’ repeats) like GGATGGAT that may occur 1000’s of times in a row in these areas.

30. Repetitive DNA: - Highly Repetitive DNA – typically concentrated in heterochromatic regions such as the centromere and telomere. Tandem repeated sequences are repeated as immediate neighbors like GGATGGAT that may occur 1000’s of times in a row in these areas. - Moderately Repetitive DNA: There are Variable Number Tandem Repeats (VNTR’s) that are within (intronic) and between genes and are 10-100 bp long.

31. Repetitive DNA: - Highly Repetitive DNA – typically concentrated in heterochromatic regions such as the centromere and telomere. Tandem repeated sequences are repeated as immediate neighbors like GGATGGAT that may occur 1000’s of times in a row in these areas. - Moderately Repetitive DNA: There are Variable Number Tandem Repeats (VNTR’s) that are within (intronic) and between genes and are 10-100 bp long. Short Tandem Repeats (STR’s) are 25 bp long, and have 5-50 repeats. The number of repeats in VNTR’s and STR’s varies among individuals, and is the basis of DNA fingerprinting.

32. Repetitive DNA: - Highly Repetitive DNA - Moderately Repetitive DNA - Transposons: Short sequences that have millions of copies throughout the genome (not repeated in sequence). Also, they COPY THEMSELVES and insert their copies elsewhere in the genome!

33. Repetitive DNA: - Highly Repetitive DNA - Moderately Repetitive DNA - Transposons: Short sequences that have millions of copies throughout the genome (not repeated in sequence). Also, they COPY THEMSELVES and insert their copies elsewhere in the genome! i. Short Interspersed Elements (SINE): 100-500 bp, present millions of times. Alu sequence in humans comprises 5% of the genome – more than coding sequence!!

34. Repetitive DNA: - Highly Repetitive DNA - Moderately Repetitive DNA - Transposons: Short sequences that have millions of copies throughout the genome (not repeated in sequence). Also, the COPY THEMSELVES and insert their copies elsewhere in the genome! i. Short Interspersed Elements (SINE): 100-500 bp, present millions of times. Alu sequence in humans comprises 5% of the genome – more than coding sequence!! ii. Long Interspersed Elements (LINE): 6kb long, present 100,000 times. L1 in humans codes for a reverse transcriptase that makes a DNA copy that is inserted elsewhere. Also called retrotransposons. = 49% of human genome; 8% are ERV (endogenous retroviruses that lost capacity to make capsid 99% are no longer capable of mobilization