Download Genom

Genes, genomes
Seminar of molecular and cell biology
Mgr. M. Jelínek
[email protected]
Plan of seminary:
• The contain of the lesson
• Some views into world of genes
• Tasks and then my questions
1) Chemical principles of genes
2) Genes in a cell
3) Genes as a fundamental resourse of
informations
4) Genomic as a science
http://www.biologyj
unction.com/nucleo
tide_model_preap.
htm
1) Chemical principles of genes
Fosfoester
bound
• The elementary unit of
DNA is nucleotide
• Nucleotide consists of
phosphate and
nucleoside
• Nucleoside consists of
nitrogen-containing base
and sugar – ribose or
deoxyribose
N - Glycosidic
bond
Thymidine nucleoside
Bases and sugars
Purins
Carbon 5...to
phosphate
Carbon 7
Pyrimidins
Carbon 1...to
base
Carbon 3...to
phosphate
Carbon 1
The other functions of nucleotides
Energy carriers, chemical groups carriers
Specific regulators
http://academic.brookl
yn.cuny.edu/biology/b
io4fv/page/molecular
%20biology/dnastructure.html
Connection of nucleotides
• DNA chain is made of
nucleotides connected
to each other
Nucleid acid are polymers of nucleotids. Double-stranded DNA containing
deoxyribose can have several conformations
A - DNA
BDNA
Z - DNA
RNA can contain various
modificated bases
Uracil (Why not in DNA ???)
Dihydrouridin
Pseudouridin
RNA :
can have (3D) conformation: the intramolecular
base-pairing (one nucleotide can bind two other
nucleotides by hydrogen bounds) is a reason for
that (A-U, G-C)
10
Modifications of DNA
• The methylation of cytosin
• GpC islands, in promotores, in non-coding
regions
• They are involved in the gene imprinting and
condenzation of X chromozom
Genetic vs epigenetic information
and heredity
12
2) Genes in cell - DNA
• DNA is mostly situated in nucleus
• DNA is in mitochondia, chloroplasts and
other semiautonomic organeles
• Plasmid DNA
• Some external DNA
The elementary structural unit of
DNA is nucleosome
Histons: H2A, H2B, H3,
H4 are present in
nucleosome core (each
twice). This protein octamer - scaffold and
DNA altogether form
nucleosome
The lenght of DNA from
one nucleosome to
another is 200 bp
cca 150 bases pairs is
wounded around
nucleosome
Composition of
nucleosome
Histons are very conservative proteins
containing so call histon fold and long N-ends.
Octamer of histons composes from tetramers
H3/H4 and two dimers H2A/B
15
Nucleosome is dynamic structure
Dynamic of nucleosome condensing
and releasing is regulated by other
proteins
Other various types of
histones can be found in
some specific
nucleosomes and
sequences
Higher level of chromatin
organisation – „solenoid“
Nucleosomes are bound
together by H1 activity
and activity of N- ends,
e.g. H4 free ends
Nucleosome
beads on DNA
wire
Very important step in condensation to 30 nm fiber - solenoid
This DNA is not
expressed
10 000 fold condensated DNA form mitotic...
...chromosome
Stick structure is in next step
condensated by group of proteins
- condensins
Important sequences in
chromosome
Telomere
Centromere
Origin of
replication
Condensation of chromosome
is tighly associated to its
function
Modification of chromatin
Chromatin remodeling complexes
Modification of histons: acetylation, methylation, fosphorylation
21
Histon code
Modificated histons are bound to other
types proteins - system readers and
writers
Histon code is second level of genome
information realization, genetic code is
the first level
Pozition effect: genes placed to the
heterochromatin region become
silent – they are not expressed
Modification of DNA and histones
are associated in epi-genetic
regulation of gene expression
If the genetic or epi-genetic
information is changed, it can lead
to cancer transformation (mutation
in somatic cell) or to transmiting of
genetic disease ( mutation in germ
cell)
Histone modifications can be
transimited to next generations of
cells as well as across the genome
3) Genes are basic source of
informations
• There are nearly all information that is cell realized by
• It is carried through generation
• It must be changeable but not too much
• Rest of informations is in the histones (histones
modification and histone code)
• Genom is complete set of DNA (and thus information )
Genofore: it carries gene information
Genes
• Sequences in nucleid acid
• Eukaryotic and prokaryotic genes differs in many
features (monocistrony, introns)
• Regulation genes - promotors, enhancers
• Repetitive sequences: are used for identification
• Mobil elementes (transposons): spread in genom
• Pseudogenes
Gene locus
Seqences in DNA:
• Coding aminoacids – proteins (mRNA)
• Coding RNA as a final product
Sekvences in DNA II: Mobile
elementes
They do not spread in genome
absolutly free, they can damage
genome if divide too intensively. Useful
genes can be multipled and transfered
by transposones.
Genetical code
tripletive, universal, redundant
Three bases code one amino acid = triplet = codon
20 coded amino acids
Some aminoacids
can be encoded by
one codon
(methionine,
tryptophan) some by
six codons (leucine,
serine, arginine).
4 bases (A, G, C, T) → 64 (43) combination of triplets
(codons)
initiation codon is codone for methionin too
3 triplets function as stop codons
3 possibilities of reading of the sequence of triplets: reading
frames
29
Genomic
Task 1
Tyrosine - Y
Tryptofan - W
Glutamine - Q
Arginine - R
Asparagine - N
Lysine - K
Aspartic acid - D
Glutamic acid - E
AGUGAAAUGAUUAAUGCAAGGUGAGGGGAGAACGAGUGAUAA
Task 2
To find nucleotide sequence on web sites
A) What is the sequence?
B) Which sequences are relative to it?