Protein Structure Flashcards
What are the three important features regarding the peptide bond?
1) It is a partial double bond, which makes the peptide bond rigid and planar. However, adjacent bonds do rotate with angles of rotation (phi & psy
2) The R-groups are in Trans configuration, ie they are on opposite sides of the backboner.
3) The peptide bond is an uncharged polar bond. The C=O and N-H groups of the polar bond participate in H-bond formation (for alpha-helixes)
What is the difference between a polypeptide and a protein?
If a polypeptide chain has a function, it is a protein
In what convention is the sequence of amino acids in peptides and proteins written?
From the amino (N-terminis) to the Carboxy (C-terminus)
Primary structure
The linear structure of amino acids forms the primary structure of proteins, and is specified by the genetic code. Evolution has conserved those amino acids that are important to protein structure and function across species.
Secondary structure
the local folding of a polypeptide backbone of amino acids into regular, repeating geometric patterns constitutes the secondary structure of proteins. It is stabilized by H-bonds between the C=O and N-H groups in the peptide bond itself, rather than side chains!
What bonds stabilize secondary structure?
It is stabilized by H-bonds between the C=O and N-H groups in the peptide bond itself, rather than side chains!
What are the three types of secondary structure?
a-helix, b-sheet and loops
a-helix
a spiral of 3.6 amino acids/turn, stabilized between the C=O bond of one peptide bond (n) and the N-H group of a peptide bond 4 Residues Away (n+4) in the polypeptide. Groups that form the peptide bond stay parallel to the axis of the helix, while the R-groups are directed towards the outside of the coil. The center of the helix is not open, but is a very tightly packed structure so that R groups will not fit, they extend outwards from a-helix.
Is the a-helix composed of polar or non-polar amino acids?
The a-helix is a very versatile structure. Depending on the location of the a-helix within a protein, it may be composed of non-polar amino acids (membrane-spanning regions) or polar amino acids (cytoplasmic region).
What is a coiled-coil?
Two alpha-helices can combine to form this supersecondary structure (motif). The a-helix may have hydrophobic residues would lie with one sid oriented toward the center of the protein and the opposite side interacting with the aqueous environment (example: a-Keratin)
Beta-sheet
an extended region of polypeptide chains that lie next to one another (regions are called strands). They are stabilized by inter-strands H-bonds between the C=O and N-H in adjacent strands or chains. The groups forming the H-bonds might be located hundreds of residues apart. It contains the groups forming the peptide bond in a zig-zag while the R-groups are directed above and below the plane. Strands have directionality and can lie parallel or antiparallel to each other. Beta-sheets are often found in the core of a protein and display a twist.
Loops
this is the part of the sequence not in regular folding (a-helix or b-sheet) which serves as connecting region. a/b secondary structures maintain characteristic phi and psy angles, loops are not repetitive but variable depending on the needs of the structure. These guys are stabilized by covalent and noncovalent interactions. They contain at least four residues in order to connect adjacent regions of secondary structure.
What are turns?
Loops containing only a few (4 or 5) residues are referred to as turns if they cause an abrupt change in the direction of a polypeptide chain. The most common types of tight turns are called B-turns, which involve 4 residues in which the first residue is forming a H-bond with the fourth residue, resulting in a tight 180-degree turn. It usually contains Gly and Pro, and is usually connecting antiparallel B-strands.
Supersecondary structures or motifs
a recognizable folding pattern involving two or more elements of secondary structure and the connections between them. First the protein must adopt various secondary structures, then adjacent regions with secondary structural elements often combine to form a “supersecondary” strucure or “motif”. Motifs have a function, but only when they are part of the entire protein structure, not if they are by themselves (isolated out of a the protein).
Tertiary structure
The folding and packing together of the secondary structure makes the tertiary structure. It is the final folded conformation of a protein, and it is the first level of folding where protein function can be observed. The formation of the hydrophobic core is the driving force behind the folding of globular proteins. Other interactions also stabilize the structure (covalent and noncovalent). Tertiary structure is the final arrangement of the domains within in a protein.
