1.15 alpha helices and beta sheets are the architectural elements of protein structure

alpha helices, beta sheets

There is a major problem that the protein chain must overcome in order to form a hydrophobic core. This problem is solved in a very elegant way by the formation of two kinds of structural elements that accommodate the hydrogen-bonding requirements of the backbone, _____ _____ and ________ ____.

donor, acceptor

To bring the sidechains into the core, the protein backbone must also fold into the interior. The backbone is highly polar and therefore hydrophilic, with one hydrogen-bond _____ (NH) and one hydrogen-bond ____ (C=O) for each peptide unit. These groups form hydrogen bonds with water when the protein is unfolded, and their hydrogen-bonding needs must be satisfied as the protein chain crosses through hydrophobic regions.

right, C=0, NH, four

Th e α helix, illustrated in Figure 1.36, is a _____-handed helical structure adopted by the protein backbone, which is enforced by the formation of hydrogen bonds between the ___ group of one residue and the ___ group of another residue __ positions ahead of it in the chain

three, three

Thus, all NH and C=O groups are joined with hydrogen bonds, except the first ____ NH groups and the last ____ C=O groups at the ends of the α helix.

interior

Because backbone hydrogen bonds are satisfied, an α helix that bears hydrophobic sidechains can pass through the _____ of the protein without an energetic penalty

length

α helices vary considerably in _____, ranging from four or five to over 40 amino acid residues in globular proteins. The average length is around 10 residues, corresponding to three helical turns.

3.6

Alpha-helices have __ amino acid residues per turn

5.4

If you were to mesure, the rise of a full turn is ___ Angstroms (Â). Alpha helices are nearly all right-handed.

beta strands

The second major structural element found in globular proteins is the β sheet, which is formed by two or more _______ _____.

beta strand

A ____ ___ is a stretch of peptide consisting of amino acids with a repeating hydrophobic (H), hydrophilic (P) residue pattern (HPHPHP…) with the backbone in an almost fully extended conformation.

noncontiguous, contiguous

The β sheet is formed through interactions between _____ (distant/diff chains) amino acids in the polypeptide chain, in contrast to the α helix, which is formed from one ____ (nearby/continousous chain) segment of the chain.

10

β strands are usually from five to __ residues long and are in an almost fully extended conformation

adjacent

To satisfy their hydrogen-bonding capacity, they form sheets in which β strands are aligned _____ to each other (Figure 1.37 and Figure 1.38) such that hydrogen bonds can form between C=O groups and NH groups across the strands

alpha carbon

Th e β sheets that are formed from several such β strands are “pleated”, with _____ ____ atoms alternately a little above and below the plane of the β sheet.

sidechains

The _____ follow this pattern, pointing alternately above and below the β sheet.

Antiparallel

________ β sheets have narrowly spaced hydrogen bonds that alternate with widely spaced ones.

Parallel

_______ sheets have evenly spaced hydrogen bonds that bridge the β strands at an angle

two

Within both types of β sheets, all possible backbone hydrogen bonds are formed, except in the ___ outside strands of β sheet, which have only one neighboring β strand each, but are exposed and so can form hydrogen bonds with water

twisted, right

Finally, the plane of almost all β sheets is itself ______, is always ______-handed, as shown in Figure 1.39.

loop regions

Most protein structures, such as the one shown in Figure 1.39, contain specific arrangements of α helices and β sheets that are connected by ________ _____ of various lengths and irregular shapes.

surface

The loop regions are typically at the _______ of the molecule.

water

The backbone C=O and NH groups of these loop regions, which in general do not form hydrogen bonds to each other, are exposed to the solvent and can form hydrogen bonds to ______ molecules.

hand

The right-handed twist of the beta sheet can be appreciated by comparing it to a right ___. If the thumb of the hand is aligned along one of the strands, then the other strands are seen to curl in the directions of the fingers of the right hand