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Molecular and genetic
mechanisms of evolution
529 - Development
Study of evolution on molecular level
Study of mutations in DNA and RNA
and changes in amino acids sequences.
Comparison of genomes, comparison of
chromosomal segments and structural parts of
DNA or proteins between species.
Study and comparisons of genome‘s sizes
RNA as the first NA molecule
The first molecules formed abiotically.
Some RNA are able to replicate autonomously.
Some have catalytic properties
Errors in replication form different sequences, differentiation of RNA
molecules, origin of family with closely related RNA molecules.
Ribosyms
• have auto-replication activity
• ribosome, spliceosome have enzymatic properties
Coenzyms
are non-protein parts of some enzymes. Some are derived from
nucleotides.
Genetic code
is nearly universal with small exceptions. Codons have the
same sense in all living organisms, from viruses to humans.
The most important exception is in mitochondria of mammals, yeast and
other species:
4 different codons (stop codons), further 60 codons in mammalian
mitochondria have the same meaning as in the nuclear mRNA.
Comparison of genes, genomes
The most conserved sequences:
genes for rRNA
genes for tRNA
genes of histons
genes for globins
genes pro cytochromes
(gene repetition)
TATA box
70-75% genes of mice have equivalents in humans. 96% to 98% of
genome is identical between human and chimpanzee.
Comparison of protein sequences
Many different types of organisms used the same proteins with small
changes in amino acids sequences.
Many proteins in human and chimp are similar, 99% percent of their
amino acids are identical.
Two strongly preserved proteins are cytochrome C and
proteins of homeobox, histons, globins.
CYTOCHROME C - Cytochrome C occur in all eukaryotes.
20 of 104 amino acids in the molecule of protein occupy the
identical positions.
Proteins of Homeobox
occur in all multicellular species.
Sequence of 60 amino acids = homeodomain is highly
preserved part of proteins that are encoded by homeobox
genes. They are mostly genes for transcription factors.
Mechanisms of evolutional changes of genome:
1. Intragenic combinations
2. Duplication
3. Structural chromosomal aberrations
4. Horizontal transfer – parasexual mechanisms
5. Recombination
6. Mutations
1. Intragene combination
- exons, introns combination
- Insertion of transposons – mobile DNA elements in the
genome. They can cause reconstructions, breaks, mutations
„jumping genes“
Types: 1. "cut and paste" transposons
2. transposons replicative
3. retrotransposons - similar to retroviruses, mobility based on
reverse transcriptase.
LTR retrotransposons consist of central coding region for enzymes,
bounded by long terminal repeats - LTRs
NON-LTR retrotransposons:
human LINE, SINE
LINE "long interspersed nuclear element
about 1kb long, original transposons, encode enzymes, proliferate and
migrate
SINE "short interspersed nuclear element"
less than 400 bp long – inactive, no code for protein
44-45% od human genome derived from the trans. elements
Heterochromatin, repetitive DNA is a cemetery of inactive transposons.
2. Gene duplication
Caused by unequal crossing-over
Duplication of chromosome parts leads to:
• degradation of gene, origin of pseudogene
• new function
• same or similar function - become a member of gene
family
Consequences of duplication
Strachan and Read: Human genetics ,2. edition
Types of sequential duplicates:
Partial gene duplication internal duplication
Exons duplication and exon shuffling
Complete gene duplication - gene families
Partial or complete duplication of chromosomes - very rare
Polyploidy - duplication of entire genome - general
mechanism in plants, animals (beetles, fish, amphibian)
Gene families
occur is Eukaryotic genomes.
They have similar nucleotide sequence and encode very similar proteins -
isoforms with the same or overlapping functions.
They could occur in one chromosome or scattered over the genome.
Pseudogenes - a secondary non-active product of evolution.
Superfamily
-
immunoglobulin gene family, HLA (MHC) genes, TCR genes
on chromosomes 2, 14, 22, 6, 7
- genes for LDL receptor
- alpha, beta-globin family on chromosomes 16, 11
evolution of
globin family
Globin family on
11 a 16 chromosome
Density of coding genes
Density of coding genes relates to the number of duplicated
genes. Eukaryotic genomes have a lower density of
coding genes as these genomes contain a considerable
amount of repetitive DNA.
Yeast ........... 30% of duplicated genes
Cenorhabditis ..... 10% of medium repetetive DNA
Mammalian DNA genomes .. 45% of medium repetetive DNA
sequences - most derived from transposons
3. Structural chromosomal aberration
Translocation, inversion, duplication, fusion
Synteny - co-localization of genetic loci within individuals or
species, based on preservation, conservation of segments
and blocks of genes. There wasn‘t recombination in time,
also because of incomplete gene linkage.
Comparison of chromosomes:
human chromosome 17, bovine chromosome 19, pig chromosome 12.
Large chromosome segments - chromosome 2
Combination of chromosome segments - chromosome 3, 21
Karyotype of human (left)
and karyotype of chimpanzee
(right)
Differences: fusion
between chromosomes 15
and 17 with origin of
chromosome 2, also
inversions and
duplications.
http://www.riverapes.com/Me/Work/HumanHybridisationTheory.htm
High
resolution
chromosome
banding
Human chromosome banding patterns compared to the great apes
(From Strachan & Dean 1998 p 344)
Notes H, C, G, O for Human, Chimpanzee, Gorilla and Orang-utan respectively.
Chromosomes 2, 5 & 6 shown only.
Gonosomes
Sexual chromosomes developed from a pair of
homologous autosomes by mutation, deletions,
translocation and unequal crossing over.
Lower vertebrates (fish, amphibians, reptiles) - is no morphological
differentiation from gonosomes
Higher vertebrates – shape of chromosome Y is different only a small part are homologous = pseudoautosomal
area
4. Horizontal transfers of NA between species
provide recombination of genomes predominantly of prokaryotic organisms;
bacteria could developed in time, adapt to new environment and become
resistant to changes and to new conditions.
endosymbiosis
somatic hybridization – fusion of cells
parasexual processes:
transformation – free income of DNA
conjugation - direct transfer of DNA
transduction - transfer of DNA by virus
transfer of plasmids
Bacterial transformation
= free intake of DNA into bacterial cells. Only
competent bacteria with relevant enzymes are
capable of transformation (not Escherichia coli)
Proof that DNA carries genetic information:
Griffith (1928) 1. Experiment with S. pneumoniae
Avery, McLeod, McCarthy (1944) - the same effect with an isolated DNA
Exchange,
recombination of
homologous parts
after transfer
Bacterial conjugation
= direct transfer of DNA
The F+ plasmid of donor cell is transferred to the
acceptor F- by conjugation bridge
F pilli on the surface of F+ bacteria
(encoded by F plasmid)
Hfr strain „High frequency of recombination“
is strain with the F plasmid integrated
into genomic DNA (episom)
Conjugation F+ into F- bacteria
Conjugation Hfr into
F- bacteria
Transduction
= when bacteriophages spontaneously transmit bacterial
genes
It comes to pass for all bacteria.
Specialized = incorrect cut out of the genome of
bacteriophage from the bacterial genome during the
transition from lysogenic to lytic cycle
General = into small number of phage particles are
packaged molecules of bacterial DNA instead of phage‘s
DNA molecules
Application in history - mapping of DNA: How often the
genes are transmitted together in the general
transduction, more about that are localized closer.
General transduction
5. Recombination – sexual reproduction
evolutionary significance of diploidy - masking of recessive
alleles
evolutionary significance of sexual reproduction – origin of
new combinations and genetic variants due to combination of parental
genomes in offspring and alternation of haploid and diploid phase of their
cells
Variability is done by
• a combination of genomes in zygotes
• a combination of chromosomes in the gametes
• crossing-over in meiosis
6. Mutation - origin of alleles
Mutations are sources of new genetic variations. More
variants of one locus is called polymorphism.
Polymorphism of standard alleles – caused by neutral
mutations
pathologic alleles – caused by negative mutations
Mutations positive - advantageous
negative - disadvantageous, losing
neutral
Selection, genetic drift, migration, non-random mating
Genetika, D P. Snustad
M.J. Simmons, 5. edition, 2009
Human genetics, Ricki Lewis, 5. vydání, 2003
Thank you for your attention