genome organization protein synthesis and processing in plants l.
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Genome Organization & Protein Synthesis and Processing in Plants. Viral genomes. Viral genomes: ssRNA, dsRNA, ssDNA, dsDNA, linear or ciruclar Viruses with RNA genomes: Almost all plant viruses and some bacterial and animal viruses Genomes are rather small (a few thousand nucleotides)

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viral genomes
Viral genomes
  • Viral genomes: ssRNA, dsRNA, ssDNA, dsDNA, linear or ciruclar
  • Viruses with RNA genomes:
  • Almost all plant viruses and some bacterial and animal viruses
  • Genomes are rather small (a few thousand nucleotides)
  • Viruses with DNA genomes (e.g.lambda = 48,502 bp):
  • Often a circular genome.
  • Replicative form of viral genomes
  • all ssRNA viruses produce dsRNA molecules
  • many linear DNA molecules become circular
  • Molecular weight and contour length:
  • duplex length per nucleotide = 3.4 Å
  • Mol. Weight per base pair = ~ 660
procaryotic genomes
Procaryotic genomes
  • Generally 1 circular chromosome (dsDNA)
  • Usually without introns
  • Relatively high gene density (~2500 genes per mm of E. coli DNA)
  • Contour length of E.coli genome: 1.7 mm
  • Often indigenous plasmids are present




Extra chromosomal circular DNAs

  • Found in bacteria, yeast and other fungi
  • Size varies form ~ 3,000 bp to 100,000 bp.
  • Replicate autonomously (origin of replication)
  • May contain resistance genes
  • May be transferred from one bacterium to another
  • May be transferred across kingdoms
  • Multicopy plasmids (~ up to 400 plasmids/per cell)
  • Low copy plasmids (1 –2 copies per cell)
  • Plasmids may be incompatible with each other
  • Are used as vectors that could carry a foreign gene of interest (e.g. insulin)

foreign gene

eukaryotic genome
Eukaryotic genome
  • Moderately repetitive
    • Functional (protein coding, tRNA coding)
    • Unknown function
      • SINEs (short interspersed elements)
        • 200-300 bp
        • 100,000 copies
      • LINEs (long interspersed elements)
        • 1-5 kb
        • 10-10,000 copies
eukaryotic genome6
Eukaryotic genome
  • Highly repetitive
    • Minisatellites
      • Repeats of 14-500 bp
      • 1-5 kb long
      • Scattered throughout genome
    • Microsatellites
      • Repeats up to 13 bp
      • 100s of kb long, 106 copies
      • Around centromere
    • Telomeres
      • Short repeats (6 bp)
      • 250-1,000 at ends of chromosomes
eucaryotic genomes
Eucaryotic genomes
  • Located on several chromosomes
  • Relatively low gene density (50 genes per mm of DNA in humans)
  • Contour length of DNA from a single human cell = 2 meters
  • Approximately 1011 cells = total length 2 x 1011 km
  • Distance between sun and earth (1.5 x 108 km)
  • Human chromosomes vary in length over a 25 fold range
  • Carry organelles genome as well
mitochondrial genome mtdna
Mitochondrial genome (mtDNA)
  • Multiple identical circular chromosomes
  • Size ~15 Kb in animals
  • Size ~ 200 kb to 2,500 kb in plants
  • Over 95% of mitochondrial proteins are encoded in the nuclear genome.
  • Often A+T rich genomes.
  • Mt DNA is replicated before or during mitosis
chloroplast genome cpdna
Chloroplast genome (cpDNA)
  • Multiple circular molecules
  • Size ranges from 120 kb to 160 kb
  • Similar to mtDNA
  • Many chloroplast proteins are encoded in the nucleus (separate signal sequence)
cellular genomes
“Cellular” Genomes







Viral genome




(Nuclear genome)





Genome: all of an organism’s genes plus intergenicDNA

Intergenic DNA = DNA between genes

estimated genome sizes
Estimated genome sizes




bacteria (>100)

mitochondria (~ 100)

viruses (1024)

1e1 1e2 1e3 1e4 1e5 1e6 1e7 1e8 1e9 1e10 1e11 1e12

Size in nucleotides. Number in ( ) = completely sequenced genomes

chromosome organization
Chromosome organization

Eucaryotic chromosome






  • Centromere:
  • DNA sequence that serve as an attachment for protein during mitosis.
  • In yeast these sequences (~ 130 nts) are very A+T rich.
  • In higher eucaryotes centromers are much longer and contain
  • “satellite DNA”
  • Telomeres:
  • At the end of chromosomes; help stabilize the chromosome
  • In yeast telomeres are ~ 100 bp long (imperfect repeats)
  • Repeats are added by a specific telomerase

5’ – (TxGy)n

3’ – (AxCy)n

x and y = 1 - 4

n = 20 to 100; (1500 in mammals)

gene classification
Gene classification





coding genes



Messenger RNA

Structural RNA








Structural proteins


what is a gene
What is a gene ?
  • Definitions
    • Classical definition: Portion of a DNA that determines a single character (phenotype)
    • One gene – one enzyme (Beadle & Tatum 1940): “Every gene encodes the information for one enzyme”
    • One gene – one protein: “One gene contains information for one protein (structural proteins included) one gene – one polypeptide
    • Current definition: A piece of DNA (or in some cases RNA) that contains the primary sequence to produce a functional biological gene product (RNA, protein).
coding region
Coding region

Nucleotides (open reading frame) encoding the amino acid sequence of a protein

The molecular definition of gene includes more than just the coding region

noncoding regions
Noncoding regions
  • Regulatory regions
    • RNA polymerase binding site
    • Transcription factor binding sites
  • Introns
  • Polyadenylation [poly(A)] sites

Molecular definition:

Entire nucleic acid sequence necessary for the synthesis of a functional polypeptide (protein chain) or functional RNA

anatomy of a gene
Anatomy of a gene
  • ORF. From start (ATG) to stop (TGA, TAA, TAG)
  • Upstream region with binding site. (e.g. TATA box).
  • Poly-a ‘tail’
  • Splices. Bounded by AG and GT splice signals.
bacterial genes
Bacterial genes
  • Most do not have introns
  • Many are organized in operons: contiguous genes, transcribed as a single polycistronic mRNA, that encode proteins with related functions

Polycistronic mRNA encodes several proteins

bacterial operon
Bacterial operon

What would be the effect of a mutation in the control region (a) compared to a mutation in a structural gene (b)?

eucaryotic genes
Eucaryotic genes

Hemoglobin beta subunit gene

Exon 1

90 bp

Intron A

131 bp

Exon 2

222 bp

Intron B

851 bp

Exon 3

126 bp


Introns: intervening sequences within a gene that are not translated

into a protein sequence. Collagen has 50 introns.

Exons: sequences within a gene that encode protein sequences

Splicing: Removal of introns from the mRNA molecule.

regulatory mechanisms
Regulatory mechanisms
  • ‘organize expression of genes’ (function calls)
  • Promoter region (binding site), usually near coding region
  • Binding can block (inhibit) expression
  • Computational challenges
    • Identify binding sites
    • Correlate sequence to expression
eukaryotic genes
Eukaryotic genes
  • Most have introns
  • Produce monocistronic mRNA: only one encoded protein
  • Large
alternative splicing
Alternative splicing
  • Splicing is the removal of introns
  • mRNA from some genes can be spliced into two or more different mRNAs
nonfunctional dna
“Nonfunctional” DNA
  • Higher eukaryotes have a lot of noncoding DNA
  • Some has no known structural or regulatory function (no genes)

80 kb

duplicated genes
Duplicated genes
  • Encode closely related (homologous) proteins
  • Clustered together in genome
  • Formed by duplication of an ancestral gene followed by mutation

Five functional genes and two pseudogenes

  • Nonfunctional copies of genes
  • Formed by duplication of ancestral gene, or reverse transcription (and integration)
  • Not expressed due to mutations that produce a stop codon (nonsense or frameshift) or prevent mRNA processing, or due to lack of regulatory sequences
repetitive dna
Repetitive DNA
  • Moderately repeated DNA
    • Tandemly repeated rRNA, tRNA and histone genes (gene products needed in high amounts)
    • Large duplicated gene families
    • Mobile DNA
  • Simple-sequence DNA
    • Tandemly repeated short sequences
    • Found in centromeres and telomeres (and others)
    • Used in DNA fingerprinting to identify individuals
types of dna repeats
Types of DNA repeats

Perfect repeats vs degenerate repeats

Tandem repeats (e.g. satellite DNA)



Inverted repeats (e.g. in transposons)





  • Form stem-loop structures
  • Palindroms = adjacent inverted repeats
  • (e.g. restriction sites)
  • Form hairpin structures


repetitive sequences
Repetitive sequences

Satellite DNA

Chromosomal DNA

Caesium chloride

density gradient

Repeats in the mouse genome

dna repeats and forensics
DNA repeats and forensics


  • Gender determination
  • Standard technique: PCR amplification of the amelogenin locus
    • (Males = XY => 103 + 109 bp)
  • AluSTXa Alu insertion on X
  • AluSTYa Alu insertion on Y

M F Suspect

878 bp

556 bp


X-Y homologous regions


M F Suspect


528 bp

199 bp


Alu sequence

mobile dna
Mobile DNA
  • Move within genomes
  • Most of moderately repeated DNA sequences found throughout higher eukaryotic genomes
    • L1 LINE is ~5% of human DNA (~50,000 copies)
    • Alu is ~5% of human DNA (>500,000 copies)
  • Some encode enzymes that catalyze movement
  • Movement of mobile DNA
  • Involves copying of mobile DNA element and insertion into new site in genome
  • Molecular parasite: “selfish DNA”
  • Probably have significant effect on evolution by facilitating gene duplication, which provides the fuel for evolution, and exon shuffling
rna or dna intermediate
RNA or DNA intermediate
  • Transposon moves using DNA intermediate
  • Retrotransposon moves using RNA intermediate
ltr long terminal repeat
LTR (long terminal repeat)
  • Flank viral retrotransposons and retroviruses
  • Contain regulatory sequences

Transcription start site and poly (A) site

lines and sines
  • Non-viral retro-transposons
    • RNA intermediate
    • Lack LTR
  • LINES (long interspersed elements)
    • ~6000 to 7000 base pairs
    • L1 LINE (~5% of human DNA)
    • Encode enzymes that catalyze movement
  • SINES (short interspersed elements)
    • ~300 base pairs
    • Alu (~5% of human DNA)
  • Most protein sequences (today) are inferred
  • What’s wrong with this?
  • Proteins (and nucleic acids) are modified
  • ‘mature’ Rna
  • Computational challenges
    • Identify (possible) aspects of molecular life cycle
    • Identify protein-protein and protein-nucleic acid interactions
genetic variation
Genetic variation
  • Variable number tandem repeats (minisatellites). 10-100 bp. Forensic applications.
  • Short tandem repeat polymorphisms (microsatellites). 2-5 bp, 10-30 consecutive copies.
  • Single nucleotide polymorphisms
single nucleotide polymorphisms
Single nucleotide polymorphisms
  • 1/2000 bp.
  • Types
    • Silent
    • Truncating
    • Shifting
  • Significance: much of individual variation.
  • Challenge: correlation to disease
yeast genome
Yeast genome
  • 4.6 x 106 bp. One chromosome. Published 1997.
  • 4,285 protein-coding genes
  • 122 structural RNA genes
  • Repeats. Regulatory elements. Transposons.
  • Lateral transfers.