Genome Organization

Genome Organization and
Gene Structure
Ni Nyoman Ayu Dewi

Dept. of Biochemistry
Faculty of Medicine Udayana University
Genome: total genetic information carried by a cell or an
organism
Gene: physical and functional unit of heredity, which
carries information from one generation to the next
Chromosome: structural unit of genetic material consisting
of a single, linear double-stranded DNA molecule and
associated proteins
Chromatin: complex of DNA, histone and nonhistone
proteins from which eukaryotic chromosomes are formed
The human genome consists of all the DNA present in
the cell.
Humans contain in their cells two distinct genomes, the
nuclear genome (about 3200 Mbp) that resides is a
cells nucleus and the mitochondrial genome (16.6 kb) in
the mitochondrion
The nuclear genome contains almost all (99.5%) of the
DNA of a cell in its linear DNA molecules, the
chromosomes, while the remainder of a cells DNA is
contained in the mitochondria in a cells cytoplasm. The
DNA of the nuclear genome is linear and arranged into
23 pairs of chromosomes, while the DNA contained in
mitochondria are circular molecules.
Genes
Probably about 30,000 genes
Most genes (90-95% probably) code for
proteins. However, there are a significant
number of RNA-only genes, and recent work has
shown that RNA genes are far more important
than previously thought.
RNA Genes
Protein-coding genes are
transcribed by RNA polymerase 2
(pol2), while RNA genes are
transcribed by pol1 or pol3.
The best known RNA genes are
ribosomal RNA and transfer RNA
genes.
Ribosomal RNA: 3 of the 4 rRNAs
are transcribed from a single
transcription unit. The other
ribosomal RNA, 5S RNA, is
transcribed from large clusters
elsewhere in the genome.
Transfer RNA genes are

dispersed throughout the genome,
usually in small clusters. There
are 49 families of tRNA genes
Other RNA Genes
Catalytic RNA molecules (ribozymes) are involved with RNA splicing

and RNA base modification. The genes for these are small nuclear
RNA (snRNA) and small nucleolar RNA (snoRNA) genes.
MicroRNAs (miRNA) and small interfering RNAs (siRNA) regulate

translation of specific mRNAs by binding to the mRNA: they are
antisense RNAs, complementary to the sense strand of the mRNA.
miRNA seems to have a role in development. This is a very hot
area of research at the moment.
siRNA is a basis for a popular technique called RNA interference,
which allows specific genes to be inactivated.
Protein-coding Genes
Genes vary greatly in size and intron/exon organization.
Some genes dont have any introns. Most common
example is the histone genes.
Some genes are quite huge: dystrophin (associated with
Duchenne muscular dystrophy) is 2.4 Mbp and takes 16
hours to transcribe. More than 99% of this gene is intron
(total of 79 introns).
However, highly expressed genes usually have short introns
Most exons are short: 200 bp on average. Intron size
varies widely, from tens to millions of base pairs.
Packaging of DNA into Chromosomes
Challenges of Packaging DNA

How to get 2 meters of DNA into nucleus of 6 m
Packaging accomplished with help of proteins
Must be compacted in manner that still allows for it to be
accessed by enzymes that govern replication,
transcription, and repair
Packaging of DNA into
Chromosomes
Eukaryotic DNA is packaged into a
set of chromosomes
DNA divided into set of chromosomes

Chromosome= single DNA molecule and
proteins associated with it
Each human cell contains 46
chromosomes
22 homologous chromosomes
2 sex chromosomes
Packaging of DNA into Chromosomes
Chromatin= nuclear DNA plus all the proteins bound to it
Two classes of proteins bind to DNA to form chromosome

1. histones
2. nonhistone
Histone Proteins
Responsible for packaging DNA into nucleosomes
4 different types: H2A, H2B, H3, H4
Highly conserved, 102-135 aa (147 aa)
Rich in Lys and Arg
Mitochondrial DNA
Mitochondria have some of their own
DNA, ribosomes, and can make many of
their own proteins.
The DNA is circular and lies in the matrix
Mitochondria also have their own
ribosomes and tRNA
Human
genome
Gene and Extragenic

gene-related DNA
sequences
Repetitive Unique and

Coding Non-coding
DNA low copy
DNA DNA
number
Pseudogenes Gene Introns, Tandemly Interspersed

fragments leaders repeated genome wide
repeats
Satellite Microsatellite LTR SINEs

elements
Minisatellite LINEs transposons

Genome Organization

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What are the two distinct genomes present in human cells?

How is DNA packaged into chromosomes in eukaryotic cells?

Genome Organization and

Ni Nyoman Ayu Dewi

Transfer RNA genes are

Catalytic RNA molecules (ribozymes) are involved with RNA splicing

MicroRNAs (miRNA) and small interfering RNAs (siRNA) regulate

Challenges of Packaging DNA

DNA divided into set of chromosomes

Chromatin= nuclear DNA plus all the proteins bound to it

Two classes of proteins bind to DNA to form chromosome

Gene and Extragenic

Repetitive Unique and

Pseudogenes Gene Introns, Tandemly Interspersed

Satellite Microsatellite LTR SINEs

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