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UKCD Biochem Lec 2

terms from Biochem lecture 2

1) The key element that determines the functional properties of a protein is its structure 1) Primary (1o) Structure: Sequence 2) Secondary (2o) Structure: Helices, Sheets, Loops, and Turns 3) Tertiary (3o) Structure: Folding 4) Quaternary (4o) Structure: Subunit Composition
2) N- and C-Terminus Polypeptide chains have polarity due to amino group and carboxyl group at ends. amino end is beginning (N-terminus) and carboxyl end is end (C-terminus). direction polypeptide sequence read.
3) Disulfide Bond polypeptide chain backbone has a repeating series of peptide bonds, rich in hydrogen bonding potential. In some proteins, the linear polypeptide chain can be cross-linked to form a disulfide bond.
4) Daltons / Kilodaltons (kDa) A peptide or polypeptide has a weight in Daltons (1 Dalton
5) Helices, Strands, Loops and Turns Alpha helix- is shown here in several different demodel, a ribbon model, and a cylinder model. alpha helix is a periodic structure (note the limited range of torsion angles for Phi and Psi in the Ramachandran plot). The C
Beta strand side chains alternate above and below the plane of the strand. Unlike the coiled alpha helix, the beta strand is almost fully extended. The side chains of a beta strand alternate above and below the plane of the strand.
Beat Turns and omega loops In helices and strands the polypeptide chain travels in one direction so to change direction requires these structures. often well-defined structures. ex, in one beta turn, C=O of one amino acid forms a hydrogen bond with the NH group 3 residues ahead.
6) Ramachandran Plot A tool can be used to map all of the possible angle combos. illustrates most possible conformations are disallowed b/c steric clashes. limitation on combs of Phi/Psi lead to significant restrictions on possible configurations
7) Domains additional features created by 3D folding aka motifs, or supersecondary structure. can be associated with a specific function, usually shared within a family of protein,
8) Hydroxyproline Proline with an OH substituted for an H at one position. EX. Vitamin C is a required co-factor for an enzyme (prolyl hydroxylase) that is responsible for the conversion of the amino acid proline to hydroxyproline through the addition of an –OH group.
9) Subunit The packing together of these chains makes up the protein’s quaternary structure. Each individual chain is called a subunit. The polypeptide subunits that make up the quaternary structure of a protein can be either identical, or different
10) Denatured Unfolded proteins are devoid of structure and activity - they are referred to as random coils, a state which is also referred to as denatured.
11) Holoprotein fully matured protein
12) Scurvy weakness in collagen structure are responsible for some of the symptoms including severe periodontal disease. caused by a dietary deficiency of vitamin C
13) Chiral With four different groups attached, the carbon is chiral, leading to two mirror image forms called the L- and D-isomers.
14) Stereoisomers are isomeric molecules w/same molecular formula and sequence of bonded atoms differ only in 3D orientations of atoms in space,
15) Zwitterions that is, they have a positive charge at one end, and a negative charge on the other.
16) Polypeptide Linear polymers of amino acids are formed by linking the carboxyl group of one amino acid to the amino group of another, forming a peptide or amide bond. A series of amino acids bonded this way is called a polypeptide and each amino acid in the chain is c
17) Residue each amino acid in the chain is called a residue
18)PHI- Psi torsion Unlike the peptide bond, the backbone bonds on either side of each alpha carbon are free to rotate. These two forms of rotation are called Phi (the rotation between the alpha carbon and the adjacent nitrogen in the peptide bond on one side) and Ps
19) Coiled-Coil Domain which are composed of two or more intertwined helices. These structures are held together by regions of imperfect repeats that associate through a combination of van der Waals and ionic interactions.
20) Superhelical Cable from from 3 strands that wind around each other that isstabilized by hydrogen bonds between strands) In context-Collagen consists of three strands of polypeptide chain coiled around one another in a left-handed polyproline II helical conformation
21) Collagen case of unusual secondary structure, most abundant, important, structural protein in mammals, as major structural component of CT, has ability to hydrogen bond
22)Amphipathic They have a buried hydrophobic side and an exposed polar side
23) Random Coil Unfolded proteins are devoid of structure and activity - they are referred to as random coils, a state which is also referred to as denatured.
24) Cooperative Transition process of denaturation is relatively sudden suggests only folded/unfolded states present ex unfolding of one part of the molecule can lead to the entire protein “unraveling”.
25) Amyloid and Prions highly insoluble, rich in beta sheet content, insoluble fibrous protein aggregates sharing specific structural traits, alter proper configuration such erroneously interact forming insoluble fibrils
Prions is an infectious agent composed of protein in a misfolded form
26) Prolyl Hydroxylase In context- As it turns out, vitamin C is a required co-factor for an enzyme (prolyl hydroxylase) that is responsible for the conversion of the amino acid proline to hydroxyproline through the addition of an –OH group.
Disulfide Bonds (sometimes called disulfide bridges) are very important for stabilizing a variety of proteins. Note that two cysteine residues connected by a disulfide bridge are referred to as a cystine (the “e” is dropped).
Structural Isomers share the same molecular formula, but the bond connections and/or their order differ(s) between different atoms/groups.
Stereoisomers order and bond connections of the constituent atoms remain the same, but their orientation in space differs.
Created by: wiechartm