WHAT ARE PROTEINS?
a simple sequence of amino acids linked together by peptide bonds
PEPTIDE BONDS
amide bonds that link alpha amino acids from C1 of one amino acid to N of another along the protein chain. each amino acid linked with another by condensation reaction gives polypeptide directionality which means both the ends are different
one amino acid has a free amino terminal (N-ter) while the other has a free carboxyl group (C-ter)
depending on these bondings proteins attain different conformations
1. primary structure:
a simple sequence of an amino acid (polymer of amino acid) linked together by a peptide bond. it can attain
linear form: both N-terminal and C-terminal free.
number of peptide bonds formed= a number of amino acids
circular form: N-ter and C-ter will not be free
number of peptide bonds formed= number of amino acids-1
2. secondary structure
it refers to local folded structures that form within a polypeptide due to interactions between the atoms of the backbone. (main chain)
TYPES OF SECONDARY STRUCTURE
HELIX
( most common) : 310 helices, 3.613 helices (alpha helix) an alpha-helical conformation was proposed in 1950 by Linus Pauling and Robert Corey. this results from the coiling of the protein such that peptide bonds make up the backbone of protein from the hydrogen bonds between each other. the hydrogen bonds are directed along the axis of the helix. alpha helices have 3.6 amino acid residues per turn i.e. a helix 36 amino acids long would form 10 turns.
PROPERTIES OF ALPHA HELIX
phi and psi =-60 degree
hydrogen bonds between C=O of residue n, and NH of residue n+4.
3.6 residue/turn
1.5 angstrom/ residue turn
100 degree/ residue turn
the alpha helix is stabilized by hydrogen bonds from the carbonyl group of one amino acid to the amino group of the fourth amino acid. the amino acids connected by each hydrogen bond are four apart in primary sequence. hence these main chain hydrogen bonds are from n to n+4. this hydrogen bonding is intrachain and directional.
almost all amino acids of the particular alpha helix are involved in hydrogen bonding.
helix former amino acid: Glu, Gln, Leu, Arg, Ala
helix deformer amino acids: Gly and Pro
these are deformer because glycine does not have any side chain due to which rotation around the bond is unconstrained.
proline does not contain NH from any of its side chains
axial length of alpha helix is 5.4 angstrom. in extended form axial length is 12.6 Angstrom.
the average molecular weight of amino acid= 128
the average molecular weight of amino acid residue= 110
molecular weight= (number of amino acid x molecular weight of single amino acid) - ( number of water x18)
for alpha helix, there are 3.6 aa/turns
number of turns= given number of amino acids/ number of amino acids in one turn
axial length = number of turns x pitch of the alpha helix
number of residue = pitch/ number of turns
beta pleated sheets
beta-strand is a helical arrangement although an extremely elongated form with two residues per turn. the side chains are oriented alternating up and down. if the pitch of anti-parallel and parallel beta-strands are (6.84 angstroms per turn) and (6.4 angstroms per turn). this leads to a pitch or repeats distance
of ~0.7 nm in a regular beta-strand.
PARALLEL VS ANTIPARALLEL BETA SHEET
TURNS
beta turn
they are known as well as reverse turns, hairpin bends or omega loops. they allow the polypeptide to turn abruptly and go in the opposite direction. this allows the protein to attain a more globular compact shape. proline and glycine are frequently found in beta turns, proline because its cyclic structure is ideally suited for the beta-turn and glycine because, with the smallest side chain of all the amino acids, it is most sterically flexible.
LOOPS
loops, which connect two adjacent antiparallel beta strands called hairpin loops. 2 residues long hairpin loops are often called reverse turns, beta turns or simply turns.
loops and turns connect alpha helices and beta strands. loops have hydrophilic residues and they are found on the surface of the protein. loops are made up of more than 10 amino acids. loops that have only 4 or 5 amino acids. they have internal hydrogen bonds. reverse turns are a form of tight turn where the polypeptide chain makes a 180-degree change in direction.
reverse turns are also called beta turns because they usually connect adjacent beta strands in a beta-sheet.
loops involve 4 amino acid residues. may or may not be stabilized by intratum hydrogen bond which is formed between CO (i) and backbone NH(i+3). it is most commonly characterized as turns.
both alpha helix and beta sheets are held in shape by hydrogen bonds which are formed by the carbonyl "O" of one amino acid and amino H of another (peptide bond).
3. SUPER SECONDARY STRUCTURE
it involves the association of secondary structures in a particular geometric arrangement. if we think of each secondary structure as a unit then a super secondary structure would be comprised of at least two units of secondary structure. some of these super secondary structures are known to have a specific biological or structural role but for others their role is unknown.
HELIX SUPER SECONDARY STRUCTURE
helix-turn-helix
helix-loop-helix
helix-hairpin-helix
helix corner
SHEET SUPER SECONDARY STRUCTURE
beta hairpins
beta corner
greek key motif
MIX SUPER SECONDARY STRUCTURE
beta -alpha- beta
Rossmann fold
4. TERTIARY STRUCTURE
tertiary structure is the three-dimensional conformation of a polypeptide. the common features of protein tertiary structure reveal much about the biological functions of the protein and their evolutionary origins. the function of a protein depends on its tertiary structure. if this is disturbed protein loses its functions
bonds involved:
COVALENT BONDS: peptide bonds
disulphide bonds
NON COVALENT BONDS
hydrogen bonds
van der Waal bonds
ionic bonds
hydrophobic force
DOMAINS
polypeptide chains containing more than 200 residues usually fold into two or more globular clusters known as domains. fundamental functional and 3-dimensional structure of the protein. domains often have a specific function such as the binding of a small molecule. many domains are structurally independent units that have the characteristics of small globular proteins
4. QUATERNARY STRUCTURE
the biological function of some molecules is determined by multiple polypeptide chains- multimeric proteins. arrangement of polypeptide subunit is called quaternary structure. subunits are held together by non-covalent interactions
for eg. haemoglobin has the subunit composition a2b2
it can attain fibrous form or globular form
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