Proteins Translation

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ProteinsTranslation
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Amino acids
Amino acids are the basic structural units of
proteins. All proteins in all organisms are
constructed from 20 primary amino acids.
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Amino acids
The side chains of the amino acids (R) vary in
size, shape, charge, bonding, composition, and
reactivity.
Amino acids are distinguished from one another by
their side chains.
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There are 20 primary amino acids.
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Amino acids
With the exception of glycine (R H), all amino
acids can form mirror-image enantiomers around
the ? carbon levorotatory (L) and dextrorotatory
(D). In proteins synthesized via translation of
mRNA, only L-amino acids are used.
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• The smallest amino acid is Gly (molecular weight
  75).
• The largest amino acid is Trp (molecular weight
  204).
• Pro is an an imino acid.
• Three amino acids (Phe, Tyr, Trp) have aromatic
  side chains.
• Cys contains a sulfur atom.
• Lys and Arg are positively charged at neutral pH.
• Asp and Glu are negatively charged at neutral pH.
• At pH 6.0, 50 percent of His are positively
  charged at pH 7.0, 10 percent have a positive
  charge.
• Gln and Asn are uncharged derivatives of glu and
  asp, respectively.

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Venn diagram showing the division of the 20
primary amino acids into overlapping categories
according to size, polarity, charge, and
hydrophobicity. Note that C appears in two
distinct places, as reduced cysteine (CH) and as
cystine (CS-S).
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Proteins Four levels of structural organization
Primary structure Secondary structure Tertiary
structure Quaternary structure
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Primary structure the linear amino acid sequence
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Secondary structure spatial arrangement of
amino-acid residues that are adjacent in the
primary structure
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a helix A helical structure, whose chain coils
tightly as a right-handed screw with all the side
chains sticking outward in a helical array. The
tight structure of the a helix is stabilized by
same-strand hydrogen bonds between -NH groups and
-CO groups spaced at four amino-acid residue
intervals.
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The b-pleated sheet is made of loosely coiled b
strands are stabilized by hydrogen bonds between
-NH and -CO groups from adjacent strands.
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An antiparallel ß sheet. Adjacent ß strands run
in opposite directions. Hydrogen bonds between NH
and CO groups connect each amino acid to a single
amino acid on an adjacent strand, stabilizing the
structure.
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A parallel ß sheet. Adjacent ß strands run in the
same direction. Hydrogen bonds connect each amino
acid on one strand with two different amino acids
on the adjacent strand.
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Silk fibroin
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Tertiary structure three-dimensional structure
of protein
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The tertiary structure is formed by the folding
of secondary structures by covalent and
non-covalent forces, such as hydrogen bonds,
hydrophobic interactions, salt bridges between
positively and negatively charged residues, as
well as disulfide bonds between pairs of
cysteines.
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Quaternary structure spatial arrangement of
subunits and their contacts.
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Holoproteins Apoproteins
Prosthetic group
Holoprotein
Apoprotein
Holoprotein
Prosthetic group
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Apohemoglobin 2a 2b
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Prosthetic group
Heme
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Hemoglobin Apohemoglobin 4Heme
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Christian B. Anfinsen 1916-1995
Sela M, White FH, Anfinsen CB. 1959. The
reductive cleavage of disulfide bonds and its
application to problems of protein structure.
Biochim. Biophys. Acta. 31417-426.
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The denaturation and renaturation of proteins
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Reducing agents Ammonium thioglycolate
(alkaline) pH 9.0-10 Glycerylmonothioglycolate
(acid) pH 6.5-8.2
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Oxidant
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A defective protein-coding gene may either
produce a protein that does not work properly or
may not produce a protein at all.
X
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A protein that does not work properly or is not
produced may have phenotypic consequences.
Tyrosinase deficiency ? Albinism
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Translation
RNA ? Protein
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translation decoding
Conversion of information from one language into
another.
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George Gamow The Diamond Code (1956)
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translation decoding
Conversion of information from a language with a
4-letter alphabet (RNA) into one with a 20-letter
alphabet (protein). What should the conversion
minimal size (codon) be?
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Marshall Nirenberg (right) and Heinrich Matthaei
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Rules of Translation The Universal Genetic Code
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Nonoverlapping Code
AAAAACGAA lys lys
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Comaless Code
AAAAACGAA lys thr
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Degenerate Code
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Unambiguous Code
CTACTCCTG leu leu leu
gly tyr ser
Exceptions that involve termination codons
readthrough. Example in Escherichia coli, the
termination codon UGA can direct the
incorporation of the unusual amino acid
selenocysteine.
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six
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Rules of Translation The Universal Genetic Code
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The Vertebrate Mitochondrial Genetic Code
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Updated to April 7, 2008
17 genetic codes
http//www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintg
c.cgi
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In some organisms, some codons may never appear
in protein-coding genes. These are called absent
codons.
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In some organisms, some codons may not have
appropriate tRNA to pair with. These codons are
called unassigned codons. Examples Codons
AGA and AUA are unassigned in Micrococcus luteus.
Codon CGG is unassigned in Mycoplasma
capricolum.
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Unassigned codons differ from stop codons by not
being recognized by release factors. Thus, upon
encountering an unassigned codon, translation
stalls, and the polypeptide remains attached to
the ribosome.
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Loading the amino acid onto the tRNA.
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initiation AUG
mostly
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initiation
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glycylalanine ? alanylglycine
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Flow of information
transcription
translation
DNA
RNA
Protein
replication
The Central Dogma
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Flow of information
DNA
RNA
Protein