Chapter 1 : Genome

Rekayasa Biomolekuler

Mochamad Untung Kurnia Agung, S.Kel., M.Si.
Marine Molecular Biotechnologist

• 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,
including large chromosomal segments
containing many genes.
• The initial phase of genomics aims to map
and sequence an initial set of entire
• Functional genomics aims to deduce
information about the function of DNA
– Should continue long after the initial genome
sequences have been completed.

Nuclear Genome .

Chromosome.Genome. and DNA . Gene.

Genome Map Features .

Natl Human Genome Research Institute. NIH interesting/important? .000 genes? • Is there anything else From NCBI web site.000 to 40.Human genome • 22 autosome pairs + 2 sex chromosomes • 3 billion base pairs in the haploid genome • Where and what are the 30. Ried. photo from T.

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%? .Components of the human Genome • Human genome has 3.

and the chromosomes range from 45 to 279 Mb DNA The total haploid genome size is 3286 Mb (~3. the actual exons are only 1% The Structure of Average Human Gene .3 x 109 bp) The chromatin comprises majority of genome.9 x 109 bp) Although about 25% of the human genome are for protein coding genes. ~2.Proportion of Protein Encoding Genes in Human Genome • • • • Human haploid genome contains 22 autosomes plus the X and Y chromosomes.

including pseudogenes – Intergenic sequences – Interspersed repeats . • Contributors to the non-coding DNA include: – Introns in genes – Regulatory elements of genes – Multiple copies of genes.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.


low complexity • Moderately repeated DNA – 10<R<10.000 – Almost no information.000 – Little information. moderate complexity • “Single copy” DNA – R=1 or 2 – Much information. high complexity .Distinct components in complex genomes • Highly repeated DNA – R (repetition frequency) >100.

• 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 . present in a single copy. i.e. nonrepeating.g. • 500 bp is sequence a. consider 1000 bp DNA. DNA.Sequence complexity is not the same as length • Complexity is the number of base pairs of unique. • E.

Genome Size and Gene Numbers in Various Organisms .

The number of genes in bacterial and archael genomes is proportional to the genome size .

enhancer or silencer)  Sequences that specifies 3’ cleavage and polyadenylation [poly(A)] sites.e. and splice sites Most genes are transcribed into mRNAs.. but some are transcribed into RNA molecules such as tRNA.Molecular Definition of a Gene • • • 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:  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. rRNA and shRNA .

Gene Expression in Prokaryotes and Eukaryotes Prokaryotes • 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 • • Yeast genes are short Genes in flies and mammals have a dispersed bimodal distribution extending to very long sizes .

Simple Eukaryotic Transcription Unit • • In eukaryotes. This slide shows a simple transcription unit . 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.

• • Complex Eukaryotic Transcription Unit 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 .

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. paternal or maternal identity test and criminal identification . This forms the basis of DNA fingerprinting This technique can be used in population studies.

The Use of Genomic Study DNA Microarray • • 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 .





Next Chapter 2 : DNA Recombination .

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