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5 Proteins

5 Proteins

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Published by Ameerah Ali

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Published by: Ameerah Ali on Oct 02, 2011
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AML 2008
Proteins - Lecture 1
There are four levels of protein structurePrimary structure describes the linear sequence of amino acid residues in the protein molecule (writtenfrom N to C terminal left to right). The three-dimensional structure of a protein is described by threeadditional levels namely, secondary, tertiary and quaternary.Secondary Structure refers to regularities in local conformation maintained by hydrogen bonding betweenamide hydrogens and carbonyl oxygens of the peptide backbone. The major secondary structures are
 helices and
strands (including
sheets). Tertiary structure describes the completely folded andcompacted protein and quaternary structure describes the association of two or more polypeptide chain inoligomeric proteins.The
HelixIn this structure the polypeptide backbone is tightly wound around an imaginary axis drawn longitudinallythrough the middle of the helix and the R groups of the amino acid residues protruding outward from thehelix. The repeating unit is a single turn of the helix which extends about 5.4 Å along the long axis (3.6residues).The structure is stabilized by a hydrogen bond between the hydrogen atom attached to the electronegativenitrogen atom of a peptide bond and the carbonyl oxygen atom of the 4
amino acid on the amino-terminalside of the peptide bond. Interactions between amino acid side chains can stabilize or destabilize thestructure.The
sheet has the polypeptide chain extended into a zigzag conformation. These arrangements can bearranged side by side to form a structure resembling a series of pleats. It is this arrangement that is termedthe
sheet. Hydrogen bonds are formed between adjacent segments of the polypeptide chain. The R groupsof the adjacent amino acid residues protrude from the sheet in opposite directions. The adjacent polypeptidechains in a
sheet can be either parallel amino to carboxyl or antiparellel.Tertiary StructureTertiary structure results from the folding of a poly peptide into a closely packed three-dimensionalstructure. Whereas secondary structure is stabilized by hydrogen bonding between amide hydrogens andcarbonyl oxygens of the polypeptide backbone, tertiary structure is stabilized primarily by noncovalentinteractions between the side chains of amino acid residues. Disulphide bonds though covalent are alsoelements of tertiary structure.A. Super-secondary structureSuper-secondary structure or motifs are recognizable combinations of 
strands and loops thatappear in a number of different proteins. Sometimes motifs are associated with a particular function,although structurally similar motifs may have different functions in different proteins. These includestructures such as the helix-loop-helix, the coiled coil, the helix bundle, the
unit, the hairpin, the
 meander, the Greek key and the
sandwich.B. Domains
AML 2008Many proteins are composed of several discrete, independently folded, compact units called domains.Domains may consist of combinations of motifs. The size of a domain can range from 25-30 amino acidresidues to about 300. Domains are usually connected by loops, but they are also bound to each otherthrough weak interactions formed by amino acid side chains on the surface of each domain.Protein domains can be classified by their structures. One commonly used classification scheme groupeddomains into four categories. The all
-category contains domains that consist of entirely
helices andloops. All
domains contain only
sheets and non repetitive structures that link the
strands. The othertwo categories contain domains that have a mixture of 
helices and
strands. Domains in the
classhave supersecondary structures such as the
motif and others, in which regions of 
helix and
strandalternate in the polypeptide chain. In the
category the domains consist of local clusters of 
sheet where each type of secondary structure arises from separate contiguous regions of thepolypeptide chain.Within each of the four main structural categories, protein domains can be further classified by the presenceof characteristic folds. A fold is a combination of secondary structures that form the core of the domain.Some domains have easily recognizable folds such as the
meander, or helix bundles. Other folds are morecomplex e.g. the parallel twisted sheet, the
barrel, the
barrel and the
helix.Quaternary StructureQuaternary structure refers to the organization and arrangement of subunits in a protein with multiplesubunits. Each subunit is a separate polypeptide chain. A multisubunit protein is referred to as an oligomeror a complex.The subunits of oligomeric proteins are usually held together by weak non covalent interactions.Hydrophobic interactions are the principle forces involved, although electrostatic forces may contribute tothe proper alignment of the subunits. Because intersubunit interactions are weak the subunits can be oftenseparated in the laboratory. In vivo however the subunits usually remain tightly associated.
AML 2008
Proteins are the most complex and most diverse group of biological compounds. Theyhave an astonishing range of different functions, as this list shows.structure e.g. collagen (bone, cartilage, tendon), keratin (hair), actin (muscle)enzymes e.g. amylase, pepsin, catalase, etc (>10,000 others)transport e.g. haemoglobin (oxygen), transferrin (iron)pumps e.g. Na
pump in cell membranesmotors e.g. myosin (muscle), kinesin (cilia)hormones e.g. insulin, glucagonreceptors e.g. rhodopsin (light receptor in retina)antibodies e.g. immunoglobulinsstorage e.g. albumins in eggs and blood, caesin in milkblood clotting e.g. thrombin, fibrinlubrication e.g. glycoproteins in synovial fluidtoxins e.g. diphtheria toxinantifreeze e.g. glycoproteins in arctic fleaand many more!Proteins are made of amino acids. Aminoacids are made of the five elements C H ON S. The general structure of an aminoacid molecule is shown on the right.There is a central carbon atom (called the"alpha carbon"), with four differentchemical groups attached to it:
a hydrogen atom
a basic amino group
an acidic carboxyl group
a variable "R" group (or sidechain)Amino acids are so-called because they have both amino groups and acid groups, whichhave opposite charges. At neutral pH (found in most living organisms), the groups are

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