1. Chapter 9 Organization of the Human Genome
General organization of the human genome:
Nuclear genome:
Mb, ~ 30,000 genes, 4.5% highly conserved including 1.5% coding DNA and 3% of conserved untranslated & regulatory sequences. 90%-95% of the coding DNA is protein coding while the remaining (5-10%) is untranslated (RNA genes).
- The coding sequence is present in families of related sequences generated by gene duplication which resulted in pseudogenes and gene fragments.
- The 95.5% non-coding DNA of the human genome is made up of tandem repeats (head to tail) or dispered repeats resulting from retrotransposition of RNA transcripts.

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3. Mitochondrial genome: 16,569 bp, 37 genes, 44% (G+C), Heavy strand (rich in G), Light strand (rich in C) , and a small section of the genome (7S DNA) is triple stranded (due to repetitive synthesis).
Human cells vary in the number of mt DNA molecules (typically thousands of copies/cell).
Sperms do not contribute mtDNA to the zygote (strictly maternal). During mitosis, mitochondria are passed on to daughter cells by random assortment.

4. Mt DNA contains 37 genes, 28 use H strand (rich in G) as their sense strand and 9 use L strand (rich in C).
Of the 37 mt genes: 22 are tRNA genes; 2 rRNA (23S rRNA and 16S rRNA); 13 are polypeptide coding (oxidative phosphorylation).
Because mt DNA encodes 13 proteins only, its genetic code has drifted from the universal genetic code.
93% of mt DNA is coding, all genes lack introns, for some coding sequences are overlapping, some lack stop codons (added post-transcriptionally), replication of H strand starts at the D loop unidirectionally and 2/3 into the mtDNA replication shifts to using the L strand from a new origin of replication and it proceeds in the opposite direction.

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7. - content: DNA, RNA, histones, non- histones.
Human genome consists of 24 different DNA molecules making 24 chromosomes.
- content: DNA, RNA, histones, non- histones.
- divided to euchromatic portion (3000Mb) which was used in the Human Genome Project and constitutive heterochromatin (200Mb) which is inactive transcriptionally (found at centromeres, long arm of Y, short arm of acrocentric chromosomes 13, 14, 15, 21, & 22, and secondary constriction of long arm of 1, 19, & 16.
- Base composition:
average GC = 41%, variable by chromosome.
Giemsa bands (dark bands, low GC, 37%; light bands, hi GC 45%).
CpG dinucleotides, why are they depleted from vertebrate DNA?

8. Human gene number:
- 30,000 – 35,000
- 14,000 genes/chromosome
- most are polypeptide-coding but 5%-10% encode RNA that is untranslated.
- C. elegans (1 mm long worm) has 959 somatic cells, genome is 1/30 that of humans, contains 19,099 protein-coding genes & >1000 RNA-coding genes.
Therefore, genome complexity is not parallel to biological complexity.
Human gene distribution:
- Done by hybridizing CpG islands to metaphase chromosomes. The results showed that gene density in subtelomeric regions & that some chromosomes (19 & 22) are gene rich while others are gene poor (X & 18).

9. 2. Organization, distribution & function of human RNA genes
Nuclear genome: 3000 RNA (non-coding) genes)
mt genome: 24 out of 37 genes are RNA coding
- Types of RNA genes (Fig. 9.4 & Table 9.3)
rRNA & tRNA: involved in translation
Other types are involved in RNA maturation (cleavage & base-specific modification of other RNA molecules such as mRNA, tRNA, and rRNA.

10. rRNA: 700-800 rRNA genes, tandem repeat clusters and many related pseudogenes.
16S & 23 S rRNA in mitochondria.
4 type of cytoplasmic rRNA, 3 of which associated with large subunit (18S, 5.8S & 5S rRNA) & one with small subunit (18S rRNA).
18S, 5.8S & 5S rRNA are encoded by a single transcription unit organized in 5 clusters, each with tandem repeats located on short arms of chromosomes 13, 14, 15, 21, and 22.
About S rRNA genes (others are pseudogenes) in tandem arrays
tRNA:
nuclear: 497 cytoplasmic tRNA & 324 tRNA pseudogenes.
mt: 22 tRNA.

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