Biochem Chapter 4
Terms
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- denaturation
- partial or complete unfolding of the specific native conformation of a polypeptide chain, protein, or nucleic acid
- protomer
- a general term describing any repeated unit of one or more stably associated protein subunits within a larger protein structure. If a protomer has multiple subunits, the subunits may be identical or different
- oligomer
- a short polymer, usually of amino acids, sugars, or nucleotides; usually less than 50 subunits
- domain
- a distinct structural unit of a polypeptide; domains may have separate functions and may fold as independent, compact units
- fold
- a distinct folding pattern for elements of secondary structure, observed in one or more proteins; also called a motif or supersecondary structure
- motif
- a distinct folding pattern for elements of secondary structure, observed in one ore more proteins; also called a fold or supersecondary structure
- supersecondary structure
- a distinct folding pattern for elements of secondary structure, observed in one or more proteins; also called a motif or fold
- globular proteins
- soluble proteins with a globular (somewhat rounded) shape
- fibrous proteins
- insoluble proteins that serve in a protective or structural role; contain polypeptide chains that generally share a common secondary structure
- quaternary structure
- the 3-D structure of a multisubunit protein; particularly the manner in which the subunits fit together
- tertiary structure
- the 3-D conformation of a polymer in its native folded state
- β turn
- a type of secondary structure in polypeptides consisting of four amino acid residues arranged in a tight turn so that the polypeptide turns back on itself
- β conformation
- an extended, zigzag arrangement of a polypeptide chain; a common secondary structure in proteins
- α helix
- a helical conformation of a polypeptide chain, usually right-handed, with maximal intrachain hydrogen bonding; one of the most common secondary structures in proteins
- secondary structure
- the residue-by-residue conformation of the backbone of a polymer
- peptide group
- two or more amino acids covalently joined by peptide bonds
- native conformation
- the biologically active conformation of a macromolecule
- conformation
- the spatial arrangement of substituent groups that are free to assume different positions in space, without breaking any bonds, because of the freedom of bond rotation
- solvation layer
-
When water surrounds
a hydrophobic molecule, the optimal arrangement of hydrogen bonds results in a highly structured shell, or solvation layer of water - β sheet
-
The zigzag polypeptide
chains can be arranged side by side to form a structure
resembling a series of pleats. Can be either antiparallel or parallel - α-keratin
-
The α-keratin helix is a right-handed α helix, which has evolved for strength.
Found in mammals, these proteins constitute almost
the entire dry weight of hair, wool, nails, claws, quills, horns, hooves, and much of the outer layer of skin. - collagen
-
Like the α-keratins, collagen has also evolved to provide strength. It is found in connective tissue such as tendons, cartilage, the organic matrix of bone, and
the cornea of the eye. The collagen helix is a unique
secondary structure quite distinct from the α helix. It
is left-handed and has three amino acid residues per
turn. It has high tensile strength, without stretch - silk fibroin
-
Fibroin, the protein of silk, is produced by insects and spiders. Its polypeptide chains are predominantly
in the β conformation. Fibroin is rich in Ala and
Gly residues, permitting a close packing of β sheets and
an interlocking arrangement of R groups - protein family
-
Proteins with significant primary sequence similarity,
and/or with demonstrably similar structure and function are of the same protein family - multimer
- A multisubunit protein is also referred to as a multimer. Multimeric proteins can have from two to hundreds of subunits.
- molten globule
- a spontaneous collapse of the polypeptide into a compact state, mediated by hydrophobic interactions among nonpolar residues. The state resulting from this “hydrophobic collapse†may have a high content of secondary structure, but many amino acid side chains are not entirely fixed.
- Molecular chaperones
-
proteins that interact with partially folded or improperly folded polypeptides, facilitating correct folding pathways or providing microenvironments in
which folding can occur. - Two classes of molecular chaperones
-
-Hsp70
and
-chaperonins - Hsp70
- generally have a molecular weight near 70,000 and are more abundant in cells stressed by elevated temperatures. Hsp70 proteins bind to regions of unfolded polypeptides that are rich in hydrophobic residues, preventing inappropriate aggregation. (Protects proteins)
- chaperonin
- elaborate protein complexes required for the folding of a number of cellular proteins that do not fold spontaneously (i.e. E. coli)