Chapter 1 : Genome
Rekayasa Biomolekuler
Mochamad Untung Kurnia Agung, S.Kel., M.Si. Marine Molecular Biotechnologist
Genome • The genome is all the DNA in a cell. – All the DNA on all the chromosomes – Includes genes, intergenic sequences, repeats
• Specifically, it is all the DNA in an organelle. • Eukaryotes can have 2-3 genomes – Nuclear genome – Mitochondrial genome – Plastid genome
• If not specified, “genome” usually refers to the nuclear genome.
Genome • The genome is all the DNA in a cell. – All the DNA on all the chromosomes – Includes genes, intergenic sequences, repeats
• Specifically, it is all the DNA in an organelle. • Eukaryotes can have 2-3 genomes – Nuclear genome – Mitochondrial genome – Plastid genome
• If not specified, “genome” usually refers to the nuclear genome.
Genomics is the study of genomes, • G e n o m i c s is including large chromosomal segments containing many genes. • The initial phase of genomics aims to map and sequence an initial set of entire genomes. • Functional genomics aims to deduce information about the function of DNA sequences. – Should continue long after the initial genome
Nuclear Genome
Genome, Chromosome, Gene, and DNA
Genome Map Features
Human genome • 22 autosome pairs + 2 sex chromosomes • 3 billion base pairs in the haploid genome • Where and what are the 30,000 to 40,000 genes? • Is there anything else interesting/important?
From NCBI web site, photo from T. Ried, Natl Human Genome Research Institute, NIH
Components of the human Genome • Human genome has 3.2 billion base pairs of DNA • About 1-3% codes for proteins • About 40-50% is repetitive, made by (retro)transposition • What is the function of the remaining 50%?
Proportion of Protein Encoding Genes in Human Genome
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Human haploid genome contains 22 autosomes plus the X and Y chromosomes, and the chromosomes range from 45 to 279 Mb DNA The total haploid genome size is 3286 Mb (~3.3 x 10 9 bp) The chromatin comprises majority of genome, ~2.9 x 10 9 bp) Although about 25% of the human genome are for protein coding genes, the actual exons are only 1%
The Structure of Average Human Gene
Much DNA in large genomes is non-coding • Complex genomes have roughly 10x to 30x more DNA than is required to encode all the RNAs or proteins in the organism. • Contributors to the non-coding DNA include: – Introns in genes – Regulatory elements of genes – Multiple copies of genes, including pseudogenes – Intergenic sequences – Interspersed repeats
Distinct components in complex genomes • Highly repeated DNA – R (repetition frequency) >100,000 – Almost no information, low complexity
• Moderately repeated DNA – 10
• “Single copy” DNA – R=1 or 2 – Much information, high complexity
Sequence complexity is not the same as length • Complexity is the number of base pairs of unique, i.e. nonrepeating, DNA. • E.g. consider 1000 bp DNA. • 500 bp is sequence a, present in a single copy. • 500 bp is sequence b (100 bp) repeated 5X a
b
b
b
b
b
|___________|__|__|__|__|__| L = length = 1000 bp = a + 5b N = complexity = 600 bp = a + b
Genome Size and Gene Numbers in Various Organisms
The number of genes in bacterial and archael genomes is proportional to the genome size
Molecular Definition of a Gene
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Definitation of a “Gene” : The entire nucleic acid sequence that is necessary for the synthesis of a functional gene product (polypeptide or RNA)
• A gene includes:
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Nucleic acid sequence not only encoding the amino acid sequence of the protein (coding region) It is also required for the synthesis of an RNA transcript It also contains the transcription-control region (i.e., enhancer or silencer) Sequences that specifies 3’ cleavage and polyadenylation [poly(A)] sites, and splice sites
Most genes are transcribed into mRNAs, but some are transcribed into RNA molecules such as tRNA, rRNA and shRNA
Gene Expression in Prokaryotes and Eukaryotes Prokaryotes
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Gene expression in prokaryotes takes place in a single compartment, but gene expression in eukaryotes takes place in multiple compartments in multiple stages
Eukaryotes
Gene inside Genome
Sizes of Genes in Various Organisms
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Yeast genes are short
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Genes in flies and mammals have a dispersed bimodal distribution extending to very long sizes
Simple Eukaryotic Transcription Unit
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In eukaryotes, some DNA encodes a single protein while the others encode more than one protein It means that some genes have simple transcription unites while others have complex transcription units. This slide shows a simple transcription unit
Complex Eukaryotic Transcription Unit
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Three different ways to process the primary transcription product of a gene to give rise to different mRNAs : Using different splice sites to produce different mRNA species Using alternative poly(A) sites to produce mRNAs with different 3’ exons Using alternative promoters to produce mRNA with different 5’exons and same 3’ exons Differential splicing of an precursor mRNA leads to production of isoforms of gene products
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The Use of Genomic Study DNA Fingerprinting Minisatellite DNA: 14 to 100 bp repeat in a region of 1 to 5 kb region which makes up of 20-50 repeat units. A slight difference in the total length of the repeats can be detected by PCR analysis. This forms the basis of DNA fingerprinting This technique can be used in population studies, paternal or maternal identity test and criminal identification
The Use of Genomic Study DNA Microarray
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This slide shows results of DNA microarray analysis to determine expression of 12 genes in 59 individual breast tumor tissues of breastfed and breast-unfed women Genes highly expressed are shown “red”, lower expression in “blue”, equal expression in “grey”
The Use of Genomic Study DNA Mutation
The Use of Genomic Study Ancestrality
