PROTEINS

FOLDED POLYPEPTIDES

© 2007 Paul Billiet ODWS

PRIMARY STRUCTURE
The sequence of amino acids

MIL1 sequence:
>gi|7662506|ref|NP_056182.1| MIL1 protein [Homo sapiens]
MEDCLAHLGEKVSQELKEPLHKALQMLLSQPVTYQAFRECTLETTVHASGWNKILVPLVLLRQMLL
ELTRLGQEPLSALLQFGVTYLEDYSAEYIIQQGGWGTVFSLESEEEEYPGITAEDSNDIYILPSDN
SGQVSPPESPTVTTSWQSESLPVSLSASQSWHTESLPVSLGPESWQQIAMDPEEVKSLDSNGAGEK
SENNSSNSDIVHVEKEEVPEGMEEAAVASVVLPARELQEALPEAPAPLLPHITATSLLGTREPDTE
VITVEKSSPATSLFVELDEEEVKAATTEPTEVEEVVPALEPTETLLSEKEINAREESLVEELSPAS
EKKPVPPSEGKSRLSPAGEMKPMPLSEGKSILLFGGAAAVAILAVAIGVALALRKK

length: 386amino acids © Anne-Marie Ternes

PRIMARY STRUCTURE
 The numbers of amino acids vary
(e.g. insulin 51, lysozyme 129, haemoglobin
574, gamma globulin 1250)
 The primary structure determines the folding of
the polypeptide to give a functional protein
 Polar amino acids (acidic, basic and neutral)
are hydrophilic and tend to be placed on the
outside of the protein.
 Non-polar (hydrophobic) amino acids tend to be
placed on the inside of the protein

© 2007 Paul Billiet ODWS

Infinite variety
 The number of possible sequences is
infinite
An average protein has 300 amino acids,
At each position there could be one of 20
different amino acids
= 10390 possible combinations
 Most are useless
Natural selection picks out the best

© 2007 Paul Billiet ODWS

SECONDARY STRUCTURE
The folding of the N-C-
C backbone of the
polypeptide chain
using weak hydrogen
bonds

© Text 2007 Paul Billiet ODWS

© Science Student
 SECONDARY STRUCTURE
 This produces the alpha helix and beta pleating
 The length of the helix or pleat is determined by certain amino acids that will not
participate in these structures
(e.g. proline)

© Text2007 Paul Billiet ODWS

© Dr Gary Kaiser
TERTIARY STRUCTURE
The folding of the polypeptide into
domains whose chemical properties are
determined by the amino acids in the
chain

MIL1 protein

© 2007 Paul Billiet ODWS

© Anne-Marie Ternes
TERTIARY STRUCTURE
 This folding is sometimes held together by
strong covalent bonds
(e.g. cysteine-cysteine disulphide bridge)
 Bending of the chain takes place at certain
amino acids
(e.g. proline)
 Hydrophobic amino acids tend to arrange
themselves inside the molecule
 Hydrophilic amino acids arrange themselves
on the outside

© 2007 Paul Billiet ODWS

 © Max Planck Institute for Molecular Genetics
Chain B of Protein Kinase C
QUATERNARY STRUCTURE
Some proteins are
made of several
polypeptide subunits
(e.g. haemoglobin has
four)

Protein Kinase C

© Max Planck Institute for Molecular Genetics

© Text 2007 Paul Billiet ODWS

QUATERNARY STRUCTURE
 These subunits fit together to form the
functional protein
 Therefore, the sequence of the amino
acids in the primary structure will influence
the protein's structure at two, three or
more levels

© 2007 Paul Billiet ODWS

Result
Protein structure depends upon the
amino acid sequence
This, in turn, depends upon the sequence
of bases in the gene

© 2007 Paul Billiet ODWS

PROTEIN FUNCTIONS
 Protein structure determines protein
function
 Denaturation or inhibition which may
change protein structure will change its
function
 Coenzymes and cofactors in general may
enhance the protein's structure

© 2007 Paul Billiet ODWS

Fibrous proteins
 Involved in structure: tendons ligaments
blood clots
(e.g. collagen and keratin)
 Contractile proteins in movement: muscle,
microtubules
(cytoskelton, mitotic spindle, cilia, flagella)

© 2007 Paul Billiet ODWS

Globular proteins
 most proteins which move around (e.g.
albumen, casein in milk)
 Proteins with binding sites:
enzymes, haemoglobin, immunoglobulins,
membrane receptor sites

© 2007 Paul Billiet ODWS

Proteins classified by function
 CATALYTIC: enzymes
 STORAGE: ovalbumen (in eggs), casein (in milk), zein
(in maize)
 TRANSPORT: haemoglobin
 COMMUNICATION: hormones (eg insulin) and
neurotransmitters
 CONTRACTILE: actin, myosin, dynein (in microtubules)
 PROTECTIVE: Immunoglobulin, fibrinogen, blood
clotting factors
 TOXINS: snake venom
 STRUCTURAL: cell membrane proteins, keratin (hair),
collagen
© 2007 Paul Billiet ODWS