CHEM 53.10 - Levels of Protein Structure 01

Primary

Level of structure: sequence of amino acid residues

Secondary

Level of structure: Localized conformation of the polypeptide backbone

Tertiary

Level of structure: 3-D structure of an entire polypeptide including all the side chains

Quaternary

Level of structure: Describes the spatial arrangement of poly-peptide chains in a protein with multiple subunits

True

T or F: Sequence of the primary structure of a polypeptide cannot give you a clear shape of what the general shape of a protein is

False

T or F: Shape and function of a protein arises from the secondary structure

Covalent

The primary structure of a protein is the ___ structure of a polypeptide

True

T or F: If the sequence of a polypeptide is known, then all the other atoms covalently linked will also be known

N, C

The naming of polypeptides follows the ___ → ___ orientation

Similar

A sequence can be compared with other known sequences to locate regions of significant ***. For example, if a new protein has a ___ (similar/dissimilar) sequence to myglobin’s oxygen binding cavity, then it may also indicate an oxygen-binding property.

Constant

The random rate of mutation of protein sequences is ___.

True

T or F: Sequence similarities can provide evolutionary relationships between organisms

Alpha-helix

Secondary structure that are right-handed helices

Beta-helix

Secondary structure that looks like flat-sheets

Steric

Rotation around the bonds is restricted due to ___ hindrances

3.6

Number of residues for each turn of an alpha helix

1.5

Vertical distance between residues of an alpha helix

5.4

Length or helical pitch of an alpha helix

Positive

The N-terminus of the alpha helix is partially ___

Negative

The C-terminus of the alpha helix is partially ___

N-terminus

A negatively charged molecule, like phosphate, would bind to what terminus?

Intrachain hydrogen bond

Alpha helix is stabilized by what kind of bonding or interaction

Carbonyl O, amino hydrogen 4

What are the atoms found in the intrachain hydrogen bonding of the alpha helix structure

12

Most alpha helices are ____ residues long

Upwards, downwards

Carbonyl O’s would be pointing ___ and amino H’s would be pointing ___ in an alpha helix

Nitrogen atom

What atom in a helix would mark the beginning of a new residue?

100

Side chains are projected outward from the helical axis at ___ degree intervals

False

T or F: The center of the alpha helix is hollow

18

The pattern of an alpha helix repeats every ___ residues per turn

20

Residue 2 will be at the same place as residue ___ for each turn

Neighboring strands

In beta strands, hydrogen bonding is between ____

True

T or F: Beta sheets may be parallel or antiparallel

Amino acid residues from separate strands

H-bonding in antiparallel beta sheets is between ____

NH group, CO group

H-bonding in parallel beta sheets is between ___

Tetrahedral C atom

The pleated appearance of Beta sheets are due to ____

6

Average number of residues in a beta sheet

2, 12

A single beta sheet can contain from ___ to ___

Reverse turns

Refers to the turns that reverse the direction of the polypeptide backbone

Reverse turns

Beta strands or alpha helices are found to be connected by ____

False

T or F: Two parallel beta strands connected have a shorter loop

4

A beta or B turn has ___ residues

Carbonyl oxygen, amide proton, stable

In a B-turn, a tight loop is formed through the ____ atom hydrogen bonded to the ____ atom which makes the the B-turn a ___ (stable/unstable) structure

Proline, Glycine

Two amino acids frequently found in the B-turns

Proline

Presence of ____ amino acid makes the formation of a B-turn more favorable

Lack of amino hydrogen

Reason why proline cannot participate in H-bonding requirements of alpha helices and beta sheets

Coils

Secondary structures that do not have a regular or characteristic geometric property

True

T or F: There is more conformational flexibility in coil strands

True

T or F: lack of inter- and intra-strand non-covalent interactions allow stretches to interact with water, ligands, or other proteins