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Molecular Biology Sabah Linjawi ١
Lecture 2
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Molecular Biology Sabah Linjawi ٢
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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Molecular Biology Sabah Linjawi ٤
Primary Structure
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Molecular Biology Sabah Linjawi ٥
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
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Molecular Biology Sabah Linjawi ٦
Planar amide group (1)
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Molecular Biology Sabah Linjawi ٧
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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Molecular Biology Sabah Linjawi ٨
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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Molecular Biology Sabah Linjawi ١٠
β -Sheet
Ball and Stick Representation of a β-Sheet
Ribbon Depiction of β-Sheet
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Molecular Biology Sabah Linjawi ١١
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
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Molecular Biology Sabah Linjawi ١٢
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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Molecular Biology Sabah Linjawi ١٦
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.
