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

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








c. Supercoiling

d. Folding to condensed chromosome






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’






2. Bacterial Chromosomes







- ds-DNA with a few associated proteins similar to histones of eukaryotes.








- typically a circular chromosome








- typically a circular chromosome

- tends to be concentrated around the periphery of a cell - nucleoid







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.







3. Mt-DNA and Cp-DNA

4. Viral Chromosomes

ss or ds DNA or RNAsmall





D. Genome Structure





D. Genome Structure

1. viruses





D. Genome Structure

1. viruses (103 – 106)

Base pairs Genes NotesPhi-X 174 5,386 10 virus of E. coliEpstein-Barr virus (EBV) 172,282 80 causes mononucleosis

Rickettsia prowazekii 1,111,523 834 bacterium that causes epidemic typhus

Mimivirus 1,181,404 1,262A 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.

http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/E/Eubacteria.html







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.

D. Genome Structure

1. viruses 2. Eubacteria/Archaea (105 – 106)

Base pairs Genes NotesPhi-X 174 5,386 10 virus of E. coliEpstein-Barr virus (EBV) 172,282 80 causes mononucleosis

Nanoarchaeum equitans 490,885 552This parasitic member of the Archaea has the smallest genome of a true organism yet found.

Mycoplasma genitalium 580,073 485three of the smallest true organismsUreaplasma urealyticum 751,719 652

Mycoplasma pneumoniae 816,394 680

Chlamydia trachomatis 1,042,519 936most 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 1,262A virus (of an amoeba) with a genome larger than the six cellular organisms above

Pelagibacter ubique 1,308,759 1,354smallest 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]





http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/A/Archaea.html

http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/A/Archaea.html




http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/E/Esch.coli.html

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 genesare so different from those of either bacteria or eukaryotes that they areclassified in a third kingdom: Archaea.

Methanococcus jannaschii 1,664,970 1,783Aeropyrum pernix 1,669,695 1,885Pyrococcus horikoshii 1,738,505 1,994

Methanobacteriumthermoautotrophicum 1,751,377 2,008

Vibrio cholerae 4,033,460 3,890 in 2 chromosomes; causes choleraMycobacterium tuberculosis 4,411,532 3,959 causes tuberculosisMycobacterium 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 5,416strain 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 5,570Increasingly common cause of opportunistic infections in humans.



http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/E/Endosymbiosis.html

http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/E/Endosymbiosis.html

http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/P/Protists.html


http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/N/NitrogenFixation.html




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

D. Genome Structure

1. viruses 2. Eubacteria/Archaea3. Eukaryotes (107 – 1011)

Base pairs Genes NotesHuman 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 4,929Fission 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.

http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/C/Caen.elegans.html

http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/A/Arabidopsis.html

http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/A/Angiosperm.html

http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/D/Drosophila.html

http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/I/Invertebrates.html

http://users.rcn.com/jkimball.ma.ultranet/BiologyPages/H/HGP.html

D. Genome Structure

1. viruses 2. Eubacteria/Archaea3. Eukaryotes


Thalassiosira pseudonana 34.5 x 106 11,242A 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 37,544Sea urchin 8.14 x 108 ~23,300Dogs 2.4 x 109 19,300Humans 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??

D. Genome Structure



Thalassiosira pseudonana 34.5 x 106 11,242A 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 37,544Sea urchin 8.14 x 108 ~23,300Dogs 2.4 x 109 19,300Humans 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)

D. Genome Structure


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!!

Repetitive DNA:

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

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.

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.

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.

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!

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!!

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.

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