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.

Genomics
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
genomes.
Functional genomics aims to deduce
information about the function of DNA
sequences.
Should continue long after the initial genome
sequences have been completed.

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 From NCBI web site, photo from T. Ried,
Natl Human Genome Research Institute, NIH
interesting/important?

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

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 109 bp)
The chromatin comprises majority of
genome, ~2.9 x 109 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<R<10,000
Little information, moderate complexity

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

|___________|__|__|__|__|__|
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

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., 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

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, 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
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
5exons 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.
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

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