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Peptides "sense of direction"
An amino end and a carboxyl end, from n to c terminus
Primary structure for polypeptide
The sequence of amino acids: covalent peptide bonds join each amino acid to the next, every protein or polypeptide has a unique sequence
A single component within a polymer. The chemical formula of a residue is that of the corresponding monomer minus the elements of water
Peptide bonds planar and rigid
The electrons are somewhat delocalized generating two resonance forms, exhibiting partial double-bond characteristics
General formula for Amino acid
- The chemical groups found in peptide binds are highly polar
- Carbonyl groups are hydrogen bond acceptors, NH groups are hydrogen bond donors
Four major levels of protein structure
- Primary (AA order)
- Secondard (alpha helix, beta helix and irregular)
- Tertiary (arrangement of all atoms in a single polypeptide) (arrangement of 2nd structures, positions of AA sidechains, prosthetic groups (heme, FAD))
- Quarternary (protiens composed of more than one polypeptide chain)
Carbony oxygen of each AA residue forms a hydrogen bond with the amide hydrogen of the 4th residue further toward the C-terminus
extended polypeptide chains stabilized by hydrogen bonds between the carbonyl oxygen of one peptide bond and the amide hydrogen of another on the same or an adjacent polypeptide chain. The hydrogen bonds are nearly perpendicular to the extended polypeptide chains, which may be parrellel or anti-parrallel.
Regular versus inrregular
- Alpha helix and beta sheets are regular secondary strucuters. The peptide backbone has the same configuration regardless of the AA composition.
- These are linked together by polypeptide loops of various sizes ranging from simple hairpins to longer loops (irregular)
Secondary struture stabilised by:
- Arrangement of all atoms in a single polypeptide
- Arrangement of 2nd structures in relation to one another
- Positions of AA sidechains
- Prosthetic groups (heme, FAD, etc)
- Can be classified into 2 general morphologies: fibrous or globular
- Stabilized mainly by hydophobic interactions between side chains, h-bonding and ion-pairs
- Proteins composed of more than one polypeptde chain (each polypeptide chain is called a subunit)
- Stabilized by hydrophobic interactions and h-bonds, ion pairs "fine-tune"
Surface and core regions of soluble proteins
- core - nonpolar
- surface - polar
- An electrostatic interaction between ionic groups of opposite charge within the interior of a macromolecule such as a globula protein
- These help to "fine tune" and stabilize 30 structures
- "Fine tune" quartinary
- A weak electrostatic interacion that formed when a hydrogen atom bonded covalently to a strongly electronegative atom is partially shared by interacting with electron pair of another electronegative atom
- Help "fine tune" and stailize 20, and 30 structures
- Help "fine tune" quarternary
- A covalent linkage formed by oxidation of the sulfhydryl groups of two cysteine residues. Important is stabilizing the 3-dimensional structures of some proteins
- Help "fine tune" and stabilize 30 structures
- A coenzyme that is tightly bound to an enzyme. A prosthetic group, unlike a cosubstrate, remains bound to a specific site of the enzyme throughout the catalytic cycle of the enzyme.
- A non-protein component that is permanently incorporated into a protein. These provide structure and reactive groups
Structure of myoglobin and hemoglobin
- 1 pp chain with 8 alpha helixes, and 1 heme Mb binds 1 O2
- 4 pp chains, 2 alpha chains, 2 beta chains; each pp chain has 8 alpha helices and 1 heme. Hb binds 4 O2
Physiological functions of myoglobin and hemoglobin
- Myoglobin binds O2 in the muscle, facilitate O2 diffusion through muscle tissue, act as local reserve of O2 during intense exercise, store O2 in aquatic animals
- Hemeglobin binds O2 in the lungs and releases it in the tissues
A biological catalyst, almost always a protein. Some enzymes may require additional cofactors for activity. Virtually all biochemical reactions are catalyzed by specific enzymes
A reactant in a chemical reaction. In enzymatic reactions, substrates are specifically acted upon by enzymes, which catalyze the conversion of substrates to products
The portion of an enzyme that contains the substrate-binding site and the amino-acid residues involved in catalyzing the conversion of substrate(s) to product(s). Active sites are usually located in clefts between domains or subunits of proteins or in indentations of the protein surface.
Activation of an enzyme by a substrate-initiated conformational change
An inorganic ion or organic molecule required by an apoenzyme to convert it to a holoenzyme. There are two types of cofactors; essential ions and coenzymes.
A coenzyme that is a substrate in an enzyme-catalyzed reaction. A cosubstrate is altered during the course of the reactio and dissociates from the active site of the enzyme. The original form of the cosubstrate can be regenerated in a subsequent enzyme-catalyzed reaction