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 .

Gene. and DNA .Genome. Chromosome.

Genome Map Features .

000 to 40. Natl Human Genome Research Institute. photo from T. Ried.Human genome • 22 autosome pairs + 2 sex chromosomes • 3 billion base pairs in the haploid genome • Where and what are the 30.000 genes? • Is there anything else From NCBI web site. NIH interesting/important? .

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.

Proportion of Protein Encoding Genes in Human Genome • • • • Human haploid genome contains 22 autosomes plus the X and Y chromosomes.3 x 109 bp) The chromatin comprises majority of genome. the actual exons are only 1% The Structure of Average Human Gene . ~2. and the chromosomes range from 45 to 279 Mb DNA The total haploid genome size is 3286 Mb (~3.9 x 109 bp) Although about 25% of the human genome are for protein coding genes.

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


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

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

Genome Size and Gene Numbers in Various Organisms .

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

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

but gene expression in eukaryotes takes place in multiple compartments in multiple stages Eukaryotes .Gene Expression in Prokaryotes and Eukaryotes Prokaryotes • Gene expression in prokaryotes takes place in a single compartment.

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 .

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

• • 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 .

This forms the basis of DNA fingerprinting This technique can be used in population studies. A slight difference in the total length of the repeats can be detected by PCR analysis. paternal or maternal identity test and criminal identification .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.

lower expression in “blue”.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”. equal expression in “grey” .

The Use of Genomic Study DNA Mutation .

The Use of Genomic Study Ancestrality .





Next Chapter 2 : DNA Recombination .