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Lesson 3: Peptide Bonds and 3D structure
Terms in this set (28)
leucine zipper motif
A structural motif found in a number of proteins (some of the DNA-binding regulatory proteins) in which certain amino acid residues align along one edge of the helix can bond by hydrophobic interactions with a similar structure on another protein molecule.
folded secondary structure between secondary and tertiary in protein folding complexity. The same folded structure is found in a variety of other molecules.
Two alpha-helices which are joined by a short sequence of amino acids that make the turn. Commonly found in proteins that bind to nucleic acids.
structural motif in proteins in which alpha helices are twisted together like the strands of a rope (dimers and trimers are the most common types).
An amino acid with a dipole moment
linear organic polymer consisting of a large nuyber of amino-acid residues joined by peptide bonds.
cyclic (ring-shaped), planar (flat) molecule with a ring of resonance bonds.
covalent bond derived from two thiol groups. The most common way of creating this bond in proteins is by the oxidation of sulfhydryl groups on cysteine amino acids. Also called an S-S bond, or disulfide bridge.
AA conserved part of a given protein sequence and (tertiary) structure that can evolve, function, and exist independently of the rest of the protein chain.
An enzyme that catalyzes the transfer of the gamma phosphate group from ATP to a specified molecule.
amino acid R-group (side chain)
The chemical group unique to each type of amino acid. The chemical group is attached to the alpha carbon.
test of the hypothesis that "protein amino acid sequence determines the final shape a protein assumed in a water solution."
protein quaternary structure
The final specific geometric shape that a protein assumes. This final shape is determined by a variety of bonding interactions between the "side chains" on the amino acids. These bonding interactions may be stronger than the hydrogen bonds between amide groups holding the helical structure. As a result, bonding interactions between "side chains" may cause a number of folds, bends, and loops in the protein chain. Different fragments of the same chain may become bonded together. There are four types of bonding interactions between "side chains" including. hydrogen bonding, salt bridges, disulfide bonds, and non-polar hydrophobic interactions.
protein tertiary structure
The final geometric shape of two or more polypeptides (proteins). The polypeptides may or may not be the same. Each of the proteins is called a subunit. This structure of multiple proteins itself is called a protein - a protein with subunits. A variety of bonding interactions including hydrogen bonding, salt bridges, and disulfide bonds hold the various chains (polypeptides) into a particular geometry.
protein secondary structure
The specific geometric shape caused by intramolecular and intermolecular hydrogen bonding of amide groups in local segments of proteins. The two most common secondary structural elements are alpha helices and beta sheets. Secondary structure elements typically spontaneously form as an intermediate before the protein folds into its three dimensional tertiary structure.
protein primary structure
The linear order of amino acids from the amino end to the carboxyl end of a polypeptide (protein). Each individual amino acid also is called a "residue" and is numbered from the amino end starting with amino acid or residue 1 at the amino terminal end. The use of the word residue is a holdover from a chemical hydrolysis method developed to determine the order of amino acids in a protein.
common motif in the secondary structure of proteins and is a righthand-coiled or spiral conformation (helix) in which every backbone N-H group donates a hydrogen bond to the backbone C-0 group of the amino acid located three or four residues earlier along the protein sequence.
An alpha helix with opposing polar and nonpolar faces oriented along the long axis of the helix.
In peptides, the angle of the bond between the alpha carbon and the amine group.
In peptides, the angle of the bond between the alpha carbon and the carboxyl group.
numeric scale used to specify the acidity or basicity of an aqueous solution. It is the negative of the logarithm to base 10 of the activity of the hydrogen ion Solutions with a value less than 7 are acidic and solutions with a value greater than 7 are basic.
biochemical process that involves the addition of phosphate to an organic compound. It is carried out through the action of enzymes known as phosphotransferases or kinases.
polypeptide amino (N or NH2) terminus (also known as the amino-terminus, NH2- terminus, N-terminal end or amine-terminus)
The start of a protein or polypeptide terminated by an amino acid with a free amine group (-NH2).
polypeptide carboxyl (C or COH) terminus (also known as carboxyl-terminus, carboxy-terminus, C-terminal tail, C-terminal end, or COOH-terminus.)
The end of an amino acid chain (protein or polypeptide), terminated by a free carboxyl group. The convention for writing peptide sequences is to put the this COOH group on the right.
molecule that assists protein folding. The potential energy to assist in protein folding is supplied by structural changes imposed by adenosine triphosphate (ATP) binding and/or hydrolysis.
A chemical bond formed between two amino acids when the carboxyl group of one molecule reacts with the amino group of the other molecule, releasing a molecule of water. This is a dehydration synthesis reaction (also known as a condensation reaction).
The loss of quaternary structure, tertiary structse and secondary structure in a protein or nucleic acid.
An oligomer consisting of two monomers joined by bonds that can be either strong or weak, covalent or intermolecular.
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