Download proteins

Basic concepts
of molecular biology
Gabriella Trucco
Email: gabriella.trucco@unimi.it
Life
 The main actors in the chemistry of life are molecules called
 proteins
 nucleic acids
 Proteins:
 many different kinds: Structural proteins, enzymes, …
 Two kinds of nucleic acids: ribonucleic acid, abbreviated by RNA, and
deoxyribonucleic acid, or DNA
Proteins
 chain of simpler molecules called amino acids
 Aminoacid





one central carbon atom
hydrogen atom
amino group (NH2)
carboxy group (COOH)
side chain
Proteins
There are 20 common amino acids (aa’s); two systems of abbreviations are used:
3-letter-code and 1-letter-code. We usually use the 1-letter-code.
 alanine Ala A
 arginine Arg R
 asparagine Asn N
 aspartic acid Asp D
 cysteine Cys C
 glutamine Gln Q
 glutamic acid Glu E
 glycine Gly G
 histidine His H
 isoleucine Ile I
 leucine Leu L
 lysine Lys K
 methionine Met M
 phenylalanine Phe F
 proline Pro P
 serine Ser S
 threonine Thr T
 tryptophan Trp W
 tyrosine Tyr Y
 valine Val V
Proteins
 Peptide bonds
 Backbone
 Primary, secondary, tertiary, and quaternary structures of proteins
DNA: nucleotides
 Double chain
 Simple chain: strand
 Basic unit
(nucleotide):
 Sugar
 Phosphate group
 Nitrogenous base
 4 bases: A C G T:
adenine, cytosine,
guanine, thymine
(bases, nucleotides)
DNA: nucleotides
5’ ...AACAGTACCATGCTAGGTCAATCGA...3’
3’ ...TTGTCATGGTACGATCCAGTTAGCT...5’
 orientation (read from 5’ to 3’ end)
 length measured in bp (base pairs)
 double stranded, the two strands are antiparallel
 A - T and C - G complementary (Watson-Crick pairs)
 DNA as string of letters, each letter representing a base.
 "string-view" of DNA: one of the strings on top of the other
 reverse complementation: (ACCTG)rc = CAGGT
RNA: nucleotides
Like DNA, except:
 4 characters: A C U G: adenine, cytosine, uracil, guanine (U instead of
T)
Genes
 Certain contiguous stretches along DNA encode information for
building proteins, but others do not
 This stretch is known as a gene
 Protein: chain of amino acids
 Triplets of nucleotides specify each amino acid
 Each nucleotide triplet is called a codon
 Genetic code: table that gives the correspondence between each
possible triplet and each amino acid
The genetic code
Degeneracy of the
genetic code: 64
codons but only 20
aa’s plus stop codon
Silent mutations: if
third position
mutates, this often
does not alter the aa
The central dogma of molecular biology
 How the information in the
DNA results in proteins
 Promoter – AUG
 Transcription: copy of the
gene made on an RNA
molecule (messenger RNA, or
mRNA ).
 This resulting RNA will have
exactly the same sequence as
one of the strands of the gene
but substituting U for T
 The strand identical to the
mRNA is called coding strand
 The other strand (the one
which is used for the
transcription) is called template
strand
The central dogma of molecular biology
 Protein synthesis inside cellular
structures called ribosomes
 tRNA: transfer RNA
 Translation: tRNA make the
connection between a codon
and the specific amino acid this
codon codes for.
 Each tRNA molecule has, on one
side, a conformation that has
high affinity for a specific codon
and, on the other side, a
conformation that binds easily to
the corresponding amino acid.
 As the messenger RNA passes
through the ribosome, a tRNA
matching the current codon
binds to it, bringing the
corresponding amino acid
 When a STOP codon appears, no
tRNA associates with it, and the
synthesis ends
Strings in molecular biology
 Many other problems in molecular biology can be modelled by strings (e.g.
gene order, haplotypes, . . . )
 Strings are finite sequences over an alphabet S (also called sequences)
 DNA (characters: nucleotides) S = {A,C,G,T}
 RNA (characters: nucleotides) S = {A,C,G,U}
 Proteins (characters: peptides) S = {A,C,D,E,F,. . . ,W,Y}
Reading frames
 Reading frame: one of the three possible ways of grouping bases to form
codons in a DNA or RNA sequence
 3 different reading frames for translation: The DNA sequence
5’ ...TATTCGAATCGGC...3’
can be translated in 3 different ways, leading to different aa sequences
Exercise
Translate this DNA sequence according to the 3 different reading
frames:
5’ ...TATTCGAATCGGC...3’