1. VII. DNA and Genome Structure

2. VII. DNA and Genome Structure
A. Search for the Genetic Information

3. VII. DNA and Genome Structure
A. Search for the Genetic Information
1. Early Work
a. Miescher – 1868 – isolated nuclein from the nucleus of cells. An acidic, nitrogen rich material.

4. VII. DNA and Genome Structure
A. Search for the Genetic Information
1. Early Work
a. Miescher – 1868 – isolated nuclein from the nucleus of cells. An acidic, nitrogen rich material.
b. Levene – Chromosomes consist of DNA and proteins. DNA was very simple (4 nucleotides) whereas proteins were very complex (21 amino acids).

5. VII. DNA and Genome Structure
A. Search for the Genetic Information
1. Early Work
a. Miescher – 1868 – isolated nuclein from the nucleus of cells. An acidic, nitrogen rich material.
b. Levene – Chromosomes consist of DNA and proteins. DNA was very simple (4 nucleotides) whereas proteins were very complex (21 amino acids).
Levene found that these nucleotides were in approximately an even ratio, and he hypothesized a very simple “tetranucleotide” structure that was similar over it’s length.

6. VII. DNA and Genome Structure
A. Search for the Genetic Information
1. Early Work
a. Miescher – 1868 – isolated nuclein from the nucleus of cells. An acidic, nitrogen rich material.
b. Levene – Chromosomes consist of DNA and proteins. DNA was very simple (4 nucleotides) whereas proteins were very complex (21 amino acids).
Levene found that these nucleotides were in approximately an even ratio, and he hypothesized a very simple “tetranucleotide” structure that was similar over it’s length.
Given that the genetic system must encode the diversity of life, it seemed likely that the more complex molecule (proteins) was responsible.

7. VII. DNA and Genome Structure
A. Search for the Genetic Information
1. Early Work
a. Miescher – 1868 – isolated nuclein from the nucleus of cells. An acidic, nitrogen rich material.
b. Levene – Chromosomes consist of DNA and proteins. DNA was very simple (4 nucleotides) whereas proteins were very complex (21 amino acids).
Levene found that these nucleotides were in approximately an even ratio, and he hypothesized a very simple “tetranucleotide” structure that was similar over it’s length.
Given that the genetic system must encode the diversity of life, it seemed likely that the more complex molecule (proteins) was responsible.
c. Chargaff – 1940’s – [A] = [T], [C] = [G]; disproving Levene’s model.

8. VII. DNA and Genome Structure
A. Search for the Genetic Information
1. Early Work
2. Major Experiments

9. VII. DNA and Genome Structure
A. Search for the Genetic Information
1. Early Work
2. Major Experiments
a. Griffiths – 1927
Streptococcus pneumoniae
causes pneumonia, meningitis, sepsis
Virulent strain has a polysaccharide capsule that protects the cell from being engulfed by white blood cells… and it makes them appear smooth (IIIS).

10. VII. DNA and Genome Structure
A. Search for the Genetic Information
1. Early Work
2. Major Experiments
a. Griffiths – 1927
Streptococcus pneumoniae
causes pneumonia, meningitis, sepsis
Non-virulent strain has no capsule and are killed by the immune system; they are ‘rough’ (IIR).

11. VII. DNA and Genome Structure
A. Search for the Genetic Information
1. Early Work
2. Major Experiments
a. Griffiths – 1927
Streptococcus pneumoniae
causes pneumonia, meningitis, sepsis
If virulent IIIS are killed by heat, they can be injected without causing disease.

12. VII. DNA and Genome Structure
A. Search for the Genetic Information
1. Early Work
2. Major Experiments
a. Griffiths – 1927
Streptococcus pneumoniae
causes pneumonia, meningitis, sepsis
If virulent IIIS are killed by heat, they can be injected without causing disease.
Griffith found that a combination of LIVE IIR and DEAD IIIS, both non-virulent independently, would kill the mouse.

13. VII. DNA and Genome Structure
A. Search for the Genetic Information
1. Early Work
2. Major Experiments
a. Griffiths – 1927
Streptococcus pneumoniae
causes pneumonia, meningitis, sepsis
If virulent IIIS are killed by heat, they can be injected without causing disease.
Griffith found that a combination of LIVE IIR and DEAD IIIS, both non-virulent independently, would kill the mouse.
Concluded that the IIR received a HERITABLE ‘transforming factor’ from dead IIIS cells, and turned into live IIIS cells.

14. VII. DNA and Genome Structure
A. Search for the Genetic Information
1. Early Work
2. Major Experiments
a. Griffiths – 1927
Streptococcus pneumoniae
causes pneumonia, meningitis, sepsis
Thought it was a chemical that induced capsule formation.

15. VII. DNA and Genome Structure
A. Search for the Genetic Information
1. Early Work
2. Major Experiments
a. Griffiths – 1927
b. Dawson – 1931
Transformation in vitro (test tube)

16. VII. DNA and Genome Structure
A. Search for the Genetic Information
1. Early Work
2. Major Experiments
a. Griffiths – 1927
b. Dawson – 1931
Transformation in vitro (test tube)
c. Alloway – 1933
Transformation with an extract from hk-IIIS – don’t even need the intact cells to cause a HERITABLE change in the live IIRIIIS
What causes this heritable change: DNA, RNA, or protein?

17. 2. Major Experiments
d. Avery, McCarty, and MacLeod
Took hk-IIIS extract and added live IIR – got transformation (control).

18. 2. Major Experiments
d. Avery, McCarty, and MacLeod
Took hk-IIIS extract and added live IIR – got transformation (control).
Took hk-IIIS and added proteases that destroy proteins – got transformation; Transforming factor is NOT a PROTEIN

19. 2. Major Experiments
d. Avery, McCarty, and MacLeod
Took hk-IIIS extract and added live IIR – got transformation (control).
Took hk-IIIS and added proteases that destroy proteins – got transformation; Transforming factor is NOT a PROTEIN
Took this solution, added RNAases – got transformation; Transforming factor is NOT an RNA

20. 2. Major Experiments
d. Avery, McCarty, and MacLeod
Took hk-IIIS extract and added live IIR – got transformation (control).
Took hk-IIIS and added proteases that destroy proteins – got transformation; Transforming factor is NOT a PROTEIN
Took this solution, added RNAases – got transformation; Transforming factor is NOT an RNA
Added DNAases – NO TRANSFORMATION; transforming factor is DNA.

21. 2. Major Experiments
d. Hershey and Chase
Viruses replicate within a bacterium… requiring the replication of the genetic information.

22. 2. Major Experiments
d. Hershey and Chase
Viruses replicate within a bacterium… requiring the replication of the genetic information.
Viruses are about 50% DNA and 50% protein. Which goes inside the cell to cause change?

23. 2. Major Experiments
d. Hershey and Chase
Viruses replicate within a bacterium… requiring the replication of the genetic information.
Viruses are about 50% DNA and 50% protein. Which goes inside the cell?
Labelled proteins with radioactive sulfur and DNA with radioactive phosphorus by growing virus on labelled bacteria for one generation.

24. 2. Major Experiments
d. Hershey and Chase
4) Then, they exposed normal bacteria to these differentially labelled viruses.

25. 2. Major Experiments
d. Hershey and Chase
4) Then, they exposed normal bacteria to these differentially labelled viruses.
5) Then they shook the solutions, separating the viral component from the bacterial component.

26. 2. Major Experiments
d. Hershey and Chase
4) Then, they exposed normal bacteria to these differentially labelled viruses.
Then they shook the solutions, separating the viral component from the bacterial component.
Both replicates confirmed that only DNA, and not protein, entered the cell and must be responsible for orchestrating viral reproduction. DNA is the genetic information.

27. VII. DNA and Genome Structure
A. Search for the Genetic Information
1. Early Work
2. Major Experiments
3. Other Evidence

28. VII. DNA and Genome Structure
A. Search for the Genetic Information
1. Early Work
2. Major Experiments
3. Other Evidence
a. Mutagenesis
The wavelengths of radiation that cause damage to the genetic information are the wavelengths absorbed by DNA, not proteins.

29. VII. DNA and Genome Structure
A. Search for the Genetic Information
1. Early Work
2. Major Experiments
3. Other Evidence
a. Mutagenesis
b. Recombinant DNA Technology
1986 – gene for luciferase (from fireflies) was transferred to plant embryos. When they grew, and then were injected with luciferin (the enzymes substrate), the action of the enzyme (oxidation of luciferin) releases light.

30. VII. DNA and Genome Structure
A. Search for the Genetic Information
1. Early Work
2. Major Experiments
3. Other Evidence
a. Mutagenesis
b. Recombinant DNA Technology
c. RNA is the genetic information in some viruses
RNA injected by virus can act directly (TMV), or can be copied into DNA (retroviruses) and inserted into the hosts genome and inherited during host cell replication (HIV).

31. VII. DNA and Genome Structure
A. Search for the Genetic Information
B. Determining DNA Structure

32. VII. DNA and Genome Structure
A. Search for the Genetic Information
B. Determining DNA Structure
1. Background Work:
- Chargaff’s ratios

33. VII. DNA and Genome Structure
A. Search for the Genetic Information
B. Determining DNA Structure
1. Background Work:
- Chargaff’s ratios
- Astbury’s 3.4A periodicity

34. VII. DNA and Genome Structure
A. Search for the Genetic Information
B. Determining DNA Structure
1. Background Work:
2. Race for the Prize:
a. Linus Pauling (CalTech) – Nobelist for describing helical structure of proteins, turned his attention to DNA.

35. VII. DNA and Genome Structure
A. Search for the Genetic Information
B. Determining DNA Structure
1. Background Work:
2. Race for the Prize:
a. Linus Pauling (CalTech) – Nobelist for describing helical structure of proteins, turned his attention to DNA. He used X-Ray crystallography, and with impure samples of DNA, suggested DNA was a triple-helix…

36. VII. DNA and Genome Structure
A. Search for the Genetic Information
B. Determining DNA Structure
1. Background Work:
2. Race for the Prize:
a. Linus Pauling
b. Maurice Wilkins and Rosalind Franklin
- The King College Lab, Univ. of London.
- They had a more purified sample of DNA, but lab tensions made their supervisor assign Wilkins the ‘B’ form and Franklin the ‘A’ form. Wilkins concluded that the B form was helical; Franklin did not agree.

37. VII. DNA and Genome Structure
A. Search for the Genetic Information
B. Determining DNA Structure
1. Background Work:
2. Race for the Prize:
a. Linus Pauling
b. Maurice Wilkins and Rosalind Franklin
- However, her subsequent work and beautiful x-rays ultimately convinced her of a double-helical structure… submitted to journals in March 1953 but without describing a specific model.
Critical contributions were confirming Astbury’s 3.4A periodicity, and finding a larger periodicity at 34.0A.

38. VII. DNA and Genome Structure
A. Search for the Genetic Information
B. Determining DNA Structure
1. Background Work:
2. Race for the Prize:
a. Linus Pauling
b. Maurice Wilkins and Rosalind Franklin
c. Francis Crick and James Watson
- Cavendish Lab, Cambridge University.

39. VII. DNA and Genome Structure
A. Search for the Genetic Information
B. Determining DNA Structure
1. Background Work:
2. Race for the Prize:
a. Linus Pauling
b. Maurice Wilkins and Rosalind Franklin
c. Francis Crick and James Watson
- Cavendish Lab, Cambridge University.
- Crick was the crystallographer and a modeller.
- Were working on helical structures with the ‘backbone’ on the inside. On seeing Franklin’s picture 51 in January 1953, they changed direction and ultimately produced a model of DNA that explained Franklin’s regularities and Chargaff’s Ratios.

40. VII. DNA and Genome Structure
A. Search for the Genetic Information
B. Determining DNA Structure
1. Background Work:
2. Race for the Prize:
a. Linus Pauling
b. Maurice Wilkins and Rosalind Franklin
c. Francis Crick and James Watson
- Cavendish Lab, Cambridge University.
- Crick was the crystallographer and a modeller.
- Were working on helical structures with the ‘backbone’ on the inside. On seeing Franklin’s picture 51 in January 1953, they changed direction and ultimately produced a model of DNA that explained Franklin’s regularities and Chargaff’s Ratios.
d – Franklin dies of ovarian cancer; probably related to her x-ray work.

41. VII. DNA and Genome Structure
A. Search for the Genetic Information
B. Determining DNA Structure
1. Background Work:
2. Race for the Prize:
a. Linus Pauling
b. Maurice Wilkins and Rosalind Franklin
c. Francis Crick and James Watson
- Cavendish Lab, Cambridge University.
- Crick was the crystallographer and a modeller.
- Were working on helical structures with the ‘backbone’ on the inside. On seeing Franklin’s picture 51 in January 1953, they changed direction and ultimately produced a model of DNA that explained Franklin’s regularities and Chargaff’s Ratios.
d – Franklin dies of ovarian cancer; probably related to her x-ray work.
e – Nobel Prizes for Crick, Watson, and Wilkins

42. VII. DNA and Genome Structure
A. Search for the Genetic Information
B. Determining DNA Structure
1. Background Work:
2. Race for the Prize:
3. The Structure of DNA

43. 3. The Structure of DNA (and RNA)
- basic unit is a “nucleotide”, that has three parts:
i. pentose sugar:

44. 3. The Structure of DNA (and RNA)
- basic unit is a “nucleotide”, that has three parts:
i. pentose sugar:
ii. Nitrogenous base:

45. 3. The Structure of DNA (and RNA)
- basic unit is a “nucleotide”, that has three parts:
i. pentose sugar:
ii. Nitrogenous base:

46. 3. The Structure of DNA (and RNA)
- basic unit is a “nucleotide”, that has three parts:
i. pentose sugar:
ii. Nitrogenous base:
iii. Phosphate group:

47. 3. The Structure of DNA (and RNA)
- basic unit is a “nucleotide”, that has three parts:
i. pentose sugar:
ii. Nitrogenous base:
iii. Phosphate group:
- nucleotide diphosphates and triphosphates can also occur, and two of these (ATP and GTP) are energetically important, too.

48. 3. The Structure of DNA (and RNA)
- basic unit is a “nucleotide”, that has three parts:
- nucleotides are linked by phosphodiester bonds to form a helix:

49. 3. The Structure of DNA (and RNA)
- basic unit is a “nucleotide”, that has three parts:
- nucleotides are linked by phosphodiester bonds to form a helix:
- typically, synthesis occurs by adding new bases to the 3’ hydroxyl group…

50. 3’ 3. The Structure of DNA (and RNA)
- basic unit is a “nucleotide”, that has three parts:
- nucleotides are linked by phosphodiester bonds to form a helix:
- typically, synthesis occurs by adding new bases to the 3’ hydroxyl group…
- the helix has a 5’ to 3’ “polarity” 3’

51. 3. The Structure of DNA (and RNA)
- basic unit is a “nucleotide”, that has three parts:
- nucleotides are linked by phosphodiester bonds to form a helix:
- DNA double-helices have helices that are ‘complementary’ (base pair pairing)
A purine (A or G) always binds with a pyrimidine (T or C)
In fact, A with T (2 h-bonds)
And G with C (3 h-bonds)

52. 3. The Structure of DNA (and RNA)
- basic unit is a “nucleotide”, that has three parts:
- nucleotides are linked by phosphodiester bonds to form a helix:
- DNA double-helices have helices that are ‘complementary’ (base pair pairing)
and ‘antiparallel’ (polarity is in opposite directions).

53. 3. The Structure of DNA (and RNA)
- basic unit is a “nucleotide”, that has three parts:
- nucleotides are linked by phosphodiester bonds to form a helix:
- DNA double-helices have helices that are ‘complementary’ (base pair pairing)
and ‘antiparallel’ (polarity is in opposite directions).

54. VII. DNA and Genome Structure
A. Search for the Genetic Information
B. Determining DNA Structure
1. Background Work:
2. Race for the Prize:
3. The Structure of DNA
4. Function of DNA and RNA overview

55. 4. Function of DNA and RNA overview
i. DNA is a template for RNA production (transcription)
GENE
DNA
RNA

56. 4. Function of DNA and RNA overview
i. DNA is a template for RNA production (transcription)
ii. RNA may be functional, or may itself be a template for protein formation (translation). DNA coding for RNA coding for proteins is called the “central dogma” of genetics.
PROTEIN GENE
RNA GENE
DNA
RNA
M-RNA: Protein-gene transcript
Functional RNA
(r-RNA, t-RNA)
Protein

57. 4. Function of DNA and RNA overview
i. DNA is a template for RNA production (transcription)
ii. RNA may be functional, or may itself be a template for protein formation (translation). DNA coding for RNA coding for proteins is called the “central dogma” of genetics.
iii. Introns are sequences in a gene (and the RNA transcript) that are ‘cut out’ of the RNA and are not translated into protein sequence. Exons are the coding sequences.
PROTEIN GENE
RNA GENE
DNA
exon
Initial RNA
(same process)
Transcript splicing
Functional RNA
(r-RNA, t-RNA)
m-RNA
Protein
Post-translational processing

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

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

60. 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’

61. 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’

62. 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

63. 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

64. 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’

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

66. 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.

67. 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

68. 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

69. 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.

70. 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

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

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

73. VII. DNA and Genome Structure A. Search for the Genetic Information
B. Determining DNA Structure
C. Chromosome Structure
D. Genome Structure
1. viruses
(103 – 106)
Base pairs
Genes
Notes
Phi-X 174
5,386 10
virus of E. coli
Epstein-Barr virus (EBV)
172,282 80
causes mononucleosis
Rickettsia prowazekii
1,111,523
834
bacterium that causes epidemic typhus
Mimivirus
1,181,404
1,262
A virus (of an amoeba) with a genome larger than some cellular organisms
Small genomes because viruses rely on the metabolism of their host cell; they are cellular/genetic parasites.

74. VII. DNA and Genome Structure
A. Search for the Genetic Information
B. Determining DNA Structure
C. Chromosome Structure
D. Genome Structure
1. viruses
(103 – 106)
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!!

75. 2. Eubacteria/Archaea (105 – 106)
D. Genome Structure
1. viruses
2. Eubacteria/Archaea (105 – 106)
Base pairs
Genes
Notes
Phi-X 174
5,386 10
virus of E. coli
Epstein-Barr virus (EBV)
172,282 80
causes mononucleosis
Nanoarchaeum equitans
490,885
552
This parasitic member of the Archaea has the smallest genome of a true organism yet found.
Mycoplasma genitalium
580,073
485
three of the smallest true organisms
Ureaplasma urealyticum
751,719
652
Mycoplasma pneumoniae
816,394
680
Chlamydia trachomatis
1,042,519
936
most common sexually-transmitted disease (STD) bacterium in the U.S.
Rickettsia prowazekii
1,111,523
834
bacterium that causes epidemic typhus
Treponema pallidum
1,138,011
1,039
bacterium that causes syphilis
Mimivirus
1,181,404
1,262
A virus (of an amoeba) with a genome larger than the six cellular organisms above
Pelagibacter ubique
1,308,759
1,354
smallest genome yet found in a free-living organism (marine α-proteobacterium)
Borrelia burgdorferi
1.44 x 106
1,738
bacterium that causes Lyme disease [Note]

76. D. Genome Structure 1. viruses 2. Eubacteria/Archaea Base pairs Genes
Notes
Borrelia burgdorferi
1.44 x 106
1,738
bacterium that causes Lyme disease [Note]
Thermoplasma acidophilum
1,564,905
1,509
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.
Methanococcus jannaschii
1,664,970
1,783
Aeropyrum pernix
1,669,695
1,885
Pyrococcus horikoshii
1,738,505
1,994
Methanobacterium thermoautotrophicum
1,751,377
2,008
Vibrio cholerae
4,033,460
3,890
in 2 chromosomes; causes cholera
Mycobacterium tuberculosis
4,411,532
3,959
causes tuberculosis
Mycobacterium leprae
3,268,203
1,604
causes leprosy
E. coli K-12
4,639,221
4,377
4,290 of these genes encode proteins; the rest RNAs
E. coli O157:H7
5.44 x 106
5,416
strain that is pathogenic for humans; has 1,346 genes not found in E. coli K-12
Salmonella enterica var Typhi
4,809,037
4,395
+ 2 plasmids with 372 active genes; causes typhoid fever
Pseudomonas aeruginosa
6.3 x 106
5,570
Increasingly common cause of opportunistic infections in humans.

77. D. Genome Structure
1. viruses
2. Eubacteria/Archaea (105 – 106)
- 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

78. D. Genome Structure 1. viruses 2. Eubacteria/Archaea
3. Eukaryotes (107 – 1011)
Base pairs
Genes
Notes
Human mitochondrion
16,569 37
nucleomorph of Guillardia theta
551,264
511
all that remains of the nuclear genome of a red alga (eukaryote) engulfed long ago by another eukaryote
Schizosaccharomyces pombe
12,462,637
4,929
Fission yeast. A eukaryote with fewer genes than the five bacteria below.
Streptomyces coelicolor
6,667,507
7,842
An actinomycete whose relatives provide us with many antibiotics
Sinorhizobium meliloti
6,691,694
6,204
The rhizobial symbiont of alfalfa. Genome consists of one chromosome and 2 large plasmids.
Saccharomyces cerevisiae
12,495,682
5,770
Budding yeast. A eukaryote.
Cyanidioschyzon merolae
16,520,305
5,331
A unicellular red alga.
Plasmodium falciparum
22,853,764
5,268
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.

79. D. Genome Structure 1. viruses 2. Eubacteria/Archaea 3. Eukaryotes
Base pairs
Genes
Notes
Thalassiosira pseudonana
34.5 x 106
11,242
A diatom. Plus 144 chloroplast and 40 mitochondrial genes encoding proteins
Caenorhabditis elegans
100,258,171
19,427
The first multicellular eukaryote to be sequenced.
Arabidopsis thaliana
115,409,949
~28,000
a flowering plant (angiosperm) See note.
Drosophila melanogaster
122,653,977
13,379
the "fruit fly"
Anopheles gambiae
278,244,063
13,683
Mosquito vector of malaria.
Rice
3.9 x 108
37,544
Sea urchin
8.14 x 108
~23,300
Dogs
2.4 x 109
19,300
Humans
3.3 x 109
~20,500
[Link to more details.]
Amphibians
109–1011 ?
Psilotum nudum
2.5 x 1011
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??

80. D. Genome Structure 1. viruses 2. Eubacteria/Archaea 3. Eukaryotes
Base pairs
Genes
Notes
Thalassiosira pseudonana
34.5 x 106
11,242
A diatom. Plus 144 chloroplast and 40 mitochondrial genes encoding proteins
Caenorhabditis elegans
100,258,171
19,427
The first multicellular eukaryote to be sequenced.
Arabidopsis thaliana
115,409,949
~28,000
a flowering plant (angiosperm) See note.
Drosophila melanogaster
122,653,977
13,379
the "fruit fly"
Anopheles gambiae
278,244,063
13,683
Mosquito vector of malaria.
Rice
3.9 x 108
37,544
Sea urchin
8.14 x 108
~23,300
Dogs
2.4 x 109
19,300
Humans
3.3 x 109
~20,500
[Link to more details.]
Amphibians
109–1011 ?
Psilotum nudum
2.5 x 1011
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)

81. 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; most serves no know function!!

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

83. 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.

84. 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 bp long.

85. 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 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.

86. 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!

87. 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):
bp, present millions of times. Alu sequence in humans comprises 5% of the genome – more than coding sequence!!

88. 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):
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.