Transcript Aminoacids

Structure of Proteins
Quick review
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DNA -> RNA -> AA
Many AA = peptide
Lots of AA = protein
3 nucleotides specify a AA
– Nucleotide sequence is 3 X longer than protein
sequence.
• If you know the nucleotide sequence you can
determine the protein sequence
• If you know the protein sequence you cannot
completely define the nucleotide sequence that it
came from.
• Sequence != function or structure
Amino acids
• Characteristics of amino acids that help to
determine structure.
– 1.Charge +/• Asp/Glu have typically one negative charge
• Lsy/Arg have typically one positive charge
• These charges attract each other form an ion pair or
salt bridge
• There is also the net charge of the protein
• Polarity the ability to participate in
hydrogen bonding
– No electrons are exchanged as in charge effect
but electrons are shared creating an attraction
– Some amino acids can participate in multiple
reactions acting as both donors and acceptors
• Hydrophobicity
– Containing no polar side chains
– Interact less favorably with water
– Mainly found in the proteins interior
Aromicity
If the protein has an aromatic side chain
Have a tendency to be stacked rather than
participate in hydrogen bonds
Size
Unusually small or large amino acids
Prolyne The most rigid of the amino acids because of
the covalent linkage between the side chain and the
main chain nitrogen
Glycine Lacks much of a side chain frequently found
where the protein makes a sharp bend
Special
Cycteines
Can form a disulfide bridge a Sulfur to sulfur linkage,
responsible for the structure of tough proteins such
as hair and keratin
Classes of amino acids
• Non-polar/alaphatic - usually found on the
interior of a protein
– Ala Val Leu Ile
• Hydrophobic/aromatic - usually found on
the interior of a protein
– Tyr Trp, mostly non polar Phe non-polar
• Neutral/polar
– Ser, Thr, Cys, Met,Asn,Gln
• Acidic
– Asp,Glu
• Basic
– His,Arg,Lys
• Conformation ally important
– Gly,Pro
Letter codes for amino acids
• There are twenty amino acids
– Each one has both a three letter code as well as
a single letter code. Some frequent substitutions
also have a single letter code.
• It is useful to know these
Basic structure of a protein
How proteins are formed
from amino acids peptide bonds
– Two ends of the amino
acid the amino terminal
end and the carboxy
terminal end.
Abbreviated N and C
Same idea with the
peptide
Types of structure
• Alpha helix - one type
of helical structure. Has
allowed conformational
angles and favorable
hydrogen bonding
between the amino
acids
• B sheets - anti parallel
the most common
configuration
– 2-15 strands are
common
• Subunits
Looking at protein structures
• Installing NCBI’s free
viewer Cn3D
• NCBI viewer
• www.ncbi.nlm.nih.gov/
Structure/CN3D/cn3d.s
html
Finding motifs
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Blocks
Interpro
ProDom
Others
All have similar strategies look though databases
of conserved elements from other proteins that
have been shown to be important and try and find
those elements in your sequence.
• www.blocks.fhcrc.org
Prep for the bioperl section
go to bio.perl.org
•get the bioperl-0.7.1.tar.gz file
tar -xzvf bioperl-0.7.1.tar.gz
rm bioperl-0.7.1.tar.gz
cd bioperl-0.7.1/
perl Makefile.PL PREFIX=/home/guest/Perl_Modules
make
make test
make install
Go to www.ncbi.nlm.nih.gov/BLAST
follow the links to the blast db
get swissprot.Z
gunzip swissprot
formatdb -i swissprot