Lecture 2

Molecular Biology ٣٢٥ Sabah Linjawi ١

 The Structure of Proteins

„ Proteins are synthesised primarily during a

process called translation
„ The building blocks of the proteins are amino
acids
„ Proteins are made of a long chain of amino
acids
„ sometimes modified by the addition of heme,
sugars, or phosphates

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 Primary Structure

„ This is the sequence of amino acids, which

form a chain connected by peptide bonds
„ The amino acid sequence of a protein
determines the higher levels of structure of
the molecule.
„ If there are some cysteines in the amino-acid
sequence, they often react two by two to form
disulphide bridges.
„ Disulphide bridges are part of the primary
structure
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 Primary Structure

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 Primary Structure
„ Association properties of peptide (C-N) that the six atoms in the
linkage must be located in one level so do not get rotation which
is known as Planar amide group
„ The turnover on the links that connect the carbon atom in the
acid part with the nitrogen atom in the base part can get.
„ The size and shape of the elements that are in the chain its
important for the rotation
„ The distance between atoms of limited rotation
„ so its not close a lot from each other and this means that the
chain can bend or bow down to a certain extent

Molecular Biology ٣٢٥ Sabah Linjawi ٥

 Planar amide group (1)

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 Secondary Structure

„ The secondary structure is the way a small part,

near in the linear sequence of a protein folds up
into:
„ α-helix: is a common secondary structure encountered
in proteins of the globular class
„ The formation of the α-helix is spontaneous
„ and is stabilized by H-bonding between amide
nitrogens and carbonyl carbons of peptide bonds.
„ This orientation of H-bonding produces a helical
coiling of the peptide backbone
„ such that the R-groups lie on the exterior of the
helix

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 Alpha-Helix

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 β-Sheets
„ β-sheets are composed of 2 or more different regions of stretches of at
least 5-10 amino acids.
„ The folding of stretches of the polypeptide backbone aside one another
to form β-sheets
„ is stabilized by H-bonding between amide nitrogens and carbonyl
carbons.
„ β-sheets are said to be pleated. This is due to positioning of the α-
carbons of the peptide bond which alternates above and below the
plane of the sheet.
„ β-sheets are either parallel or antiparallel
„ In parallel sheets adjacent peptide chains proceed in the same direction
(i.e. the direction of N-terminal to C-terminal ends is the same)
„ whereas, in antiparallel sheets adjacent chains are aligned in opposite
directions.
„ β-sheets can be depicted in ball and stick format or as ribbons in certain
protein formats.

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 β-Sheet

„ Ball and Stick Representation of a β-Sheet

„ Ribbon Depiction of β-Sheet

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 Tertiary Structure of Proteins

„ The tertiary structure of a protein is a description of

the way the whole chain (including the secondary
structures) folds itself into its final 3-dimensional
shape.
„ This is often simplified into models like the following
one for the enzyme dihydrofolate reductase.
„ Enzymes are, of course, based on proteins.
„ The tertiary structure of a protein is held together by
interactions between the side chains - the "R"
groups. There are several ways this can happen.
„ Ionic interactions -Hydrogen bonds- van der Waals
dispersion forces

Molecular Biology ٣٢٥ Sabah Linjawi ١١

 Tertiary Structure of Proteins

„ The model shows the

alpha-helices in the
secondary structure as coils
of "ribbon".
„ The beta-pleated sheets are
shown as flat bits of ribbon
ending in an arrow head.
„ The bits of the protein chain
which are just random coils
and loops are shown as bits
of "string".

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 The tertiary structure interactions

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 Quaternary Structure
„ Many proteins contain 2 or more different polypeptide chains that
are held in association by the same non-covalent forces that
stabilize the tertiary structures of proteins.
„ Proteins with multiple polypetide chains are oligomeric proteins.
„ The structure formed by monomer-monomer interaction in an
oligomeric protein is known as quaternary structure.
„ Oligomeric proteins can be composed of multiple identical
polypeptide chains or multiple distinct polypeptide chains.
„ Proteins with identical subunits are termed homo-oligomers.
„ Proteins containing several distinct polypeptide chains are
termed hetero-oligomers.

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 Quaternary Structure

„ Hemoglobin, the
oxygen carrying protein
of the blood
„ contains two α and two
β subunits arranged
with a quaternary
structure
„ in the form, α2β2.
Hemoglobin
„ is, Therefore, a hetero-
oligomeric protein.

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 References
„ www.vivo.colostate.edu/hbooks/genetics/.../prostruct.html
„ en.wikipedia.org/wiki/Protein_structure
„ www.chemguide.co.uk/organicprops/.../proteinstruct.html
„ www.rothamsted.ac.uk/notebook/courses/guide/prot.htm
„ www.friedli.com/herbs/phytochem/proteins.html
„ themedicalbiochemistrypage.org/protein-structure.html
„ Molecular Biology. P.C. Turner, A.G. Mclennan, A.D. Bates &
M.R.H. White.School of Biological Sciences, University of Liverpool,
Liverpool, UK. Second edition. BIOS Scientific Publishers, 2000.

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