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The first protein to be seen in detail is __, the oxygen carrier in muscle. It is a single polypeptide chain of __amino acids with a capacity to bind oxygen depending on the presence of __
, a nonpolypeptide __
consisting of __and a central iron atom
It is very compact; about __ of the main chain is folded into __, and much of the rest of the chain forms turns and loops between helices
- prosthetic (helper) group
- protoporphyrin IX
- 8 alpha helices
In tertiary structure, the interior consists almost entirely of __ like __(4)__. Charged residues are __, except for the only __, which bind __ and __.
The exterior has the __ and __
- nonpolar residues like leucine, valine, methionine, and phenylalanine
- two polar residues inside, which are two histidine residues
- iron and oxygen
- polar and nonpolar residues
This architecture reveals that, in an aqueous environment, protein folding is driven by what?
The polypeptide chain, as a result, folds so that its __ are __ and its __ are __
Because many alpha helices and beta strands are __, the __is interior and the __ is exterior
- the strong tendency of hydrophobic residues to be excluded from water
- hydrophobic side chains
- polar, charged chains
- on the surface
- hydrophobic face
- polar face
The fate of the __ accompanying the hydrophobic side chains is important, too.
An unpaired peptide NH or CO group prefers __to a nonpolar milieu; and so, to bury a segment of main chain in a hydrophobic environment, what must be done?
__between tightly packed hydrocarbon side chains also helps __the proteins
- main chain
- pair all the NH and CO groups by H bonds, which is accomplished by an alpha helix or B sheet
- Van der Walls interactions
Some proteins that span membranes are “exceptions that prove the rule” because they have the __ (ex: porins, which contain a center of polar molecules and are considered inside out in hydrophobic environments
reverse distribution of hydrophobic and hydrophilic amino acids
can exist when certain combos of secondary structure are present in proteins (ex: alpha helix separated from alpha helix by a turn (helix-turn-helix
unit is found in many proteins that bind DNA)
Supersecondary structures (motifs)
Some polypeptide chains fold into __ that may be connected by a flexible segment of polypeptide chain, rather like pearls on a string
These compact globular units, called __
, range in size from about 30-400 amino acid residues
- two or more compact regions
The difference between secondary and tertiary structure is what?
that secondary is the spatial arrangement of amino acid residues that are nearby in the sequence, while tertiary refers to the spatial arrangement of amino acid residues that are far apart in the sequence and to the pattern of disulfide bonds
Each polypeptide chain is a __; and, quaternary structure refers to the __
§ Simplest: __(two identical subunits)
Viruses use the same kind of subunit repetitively, like __, which has 60 copies of each of four subunits to form a spherical shell that encloses the viral genome
- spatial arrangement of subunits (can be identical or diverse) and the nature of their interactions