Section 4 Flashcards
What does the primary structure of a protein refer to? How is this sequence read?
The linear sequence of AA. It is read from the amino (N) terminus to the carboxyl (C) terminus.
A ___________ reaction occurs to form a peptide bond, linking the _________ group to the _________ group of the next amino acid.
condensation reaction in order to form a peptide bond linking the carboxyl group to the amino group of the next amino acid
The alpha-helix arises due twisting of a section of the primary structure into a ______-handed screw.
a) Right
b) Left
a) right-handed screw
What is one major difference between the alpha-helix and the DNA helix?
R groups project outwards and perpendicular in the alpha-helix. It is also one stranded.
The DNA double helix has it’s R groups projecting inwards.
What are some bonds in the alpha helix?
Imino groups (NH) of each AA residue forms H-bonds to the carbonyl (CO) of another amino acid in the adjacent turn of the helix
Are hydrogen bonds further apart in a-helices or b-sheets?
In b-sheets they are a lot further apart than a-helices. This is because instead of forming a coiled structure, the backbone of the polypeptide is expanded outward.
Describe the difference in the orientation of H-bonds in antiparallel vs parallel beta-sheets.
Antiparallel Beta-Sheet:
- Adjacent beta strands run in opposite directions, and the hydrogen bonding occurs between the oxygen from carbonyl group of one amino acid and the H from the amide in the neighboring strand.
- The atoms involved in the hydrogen bond are approximately in a straight line, allowing for STRONGER hydrogen bonding interactions.
Parallel Beta-Sheet:
- Adjacent beta strands run in the same direction, and the hydrogen bonding also occurs between the carbonyl oxygen of one amino acid residue and the amide hydrogen of a residue in the neighboring strand.
- The atoms involved in the hydrogen bond are not in line; they are at an angle to each other, which results in WEAKER hydrogen bonding interactions.
How are secondary structures linked?
By reverse turns in order to reverse direction and fold into tertiary structures.
Beta-turns are small, precise reverse turns, stabilized by H-bonds between the imino (NH) group and carbonyl (CO) of nearby amino acids that form the turn
Which one is more favourable in linking secondary structures:
a) beta-turns
b) gamma-turns
a)
Why are secondary structures like alpha helices and beta sheets not always stable?
Secondary structures can transiently form and break apart until sufficient stabilizing interactions (e.g., hydrogen bonds, van der Waals forces) are established.
What happens in that location when amino acids within a protein resist or hinder the formation of preferred secondary structures?
Amino acids within a protein may not always encourage the formation of preferred secondary structures, potentially resisting or hindering these structures. this is where we can find a turn in the alpha helices.
What are “turns” in the context of alpha helices, and what role do they play?
“Turns” or “bends” in alpha helices represent regions where the helical structure changes direction. They are essential for flexibility but can disrupt the helical pattern when excessive.
What can happen when deviations from the ideal secondary structure accumulate in a protein?
Accumulation of deviations can lead to the formation of non-functional or misfolded proteins, which may have the correct shape but lack proper functionality.
True or false: There is no partial double bond character in a peptide bond.
False. There is a sharing of electrons between the carboxyl oxygen and the amide nitrogen, creating partial double bond character.
True or false: the N-C(alpha) and the C(alpha)-C bons are free to rotate.
True. But the angles between these bonds are constrained. These angles are called torsion angles (or dihedral angles).
Match the torsion angles with the bonds.
Phi for ______________
Psi for ______________
Phi for the N-C(alpha) bond
Psi for the C(alpha)-C bond
Why are psi and phi angles limited?
Due to “steric clash”between an amino acid side chain and neighbouring atoms. The size of the bulky side chain may prevent a close approach to nearby atoms in the polypeptide chain.
What is a ramachandran plot?
A way to graphically represent the allowed values of psi and phi for each amino acid.
Darker areas are easily allowed conformations. Lighter areas represent conformations that are allowed if some flexibility is permitted in the torsion angles. Unshaded regions indicated conformations that are not allowed or are ‘disfavoured’.
True or false: A typical protein contains about one-third alpha-helix and 1/3 b-sheet
True.
In the alpha helix do the R groups protrude outward or inward?
Outward
Is the alpha helix a left or right handed helix?
Right-handed helix
What is one helical turn of an alpha helix?
The hydrogen on the amide nitrogen forms a hydrogen bond with the carbonyl oxygen of the fourth residue toward the N-terminus, which makes about one helical turn.
Can carbonyl (CO) and imino groups (NH) on the same peptide chain hydrogen bond?
Yes. Favourable psi and phi angles accommodate regular pattern of hydrogen bonding between carbonyl and imino groups on the same peptide chain (strand).
What is the most and second most stable arrangement of the polypeptide backbone?
Alpha helix is #1
Beta sheet is #2
How is the beta-sheet formed?
By hydrogen bonds between the backbone amide and carbonyl groups
Forms from multiple beta-strands forming hydrogen bonds together
How are interactions of R groups of adjacent residues prevented in beta-sheets?
The R groups of adjacent amino acid residues in a beta-strand lie on opposite sides of the sheet, and this alternating geometry prevents the interaction of R groups of adjacent residues.
This makes a zigzag pattern with pleats involving 4-6 strands, therefore the beta-sheet is referred to as a “Beta-pleated sheet”
What is a parallel vs antiparallel beta sheet?
ANTIPARALLEL: When beta-strands are oriented in the opposite N- to C-terminal directions
PARALLEL: When they run in the same direction
The sheets can also be composed of a mixture of both
True or false: the beta-sheet can readily accommodate large aromatic residues.
True, such as Tyr, Trp and Phe residues
Which one is proline unfavoured in:
a) alpha-helix
b) beta-sheets
a) alpha-helix
It is often found in beta-sheets, especially in the “edge” strands
Can a Ramachandran plot identify the types of secondary structure within a specific protein?
Ye
what are the small and precise turns of secondary structures of polypeptide chains called?
beta-turns
How does a beta turn work?
- Complete Reversal of Direction: A beta turn is a structural motif within a protein where the polypeptide chain changes direction. In other words, it makes a U-turn or a complete reversal of its path.
- Four Residues: This structural feature involves four consecutive amino acid residues in the protein’s primary sequence.
- Hydrogen Bond Formation: hydrogen bonds between specific atoms in these four residues. Specifically, the backbone carbonyl oxygen of the first residue forms a hydrogen bond with the amide hydrogen of the fourth residue
- Lack of Inter-Residue Hydrogen Bonds: In contrast to the strong hydrogen bond between residues 1 and 4, the second (position 2) and third (position 3) residues do not typically form hydrogen bonds with each other or with other residues in the beta turn.
Location on the Protein Surface: Beta turns are often found on the surface of proteins because the structure of the beta turn allows the backbone atoms to be exposed to the surrounding water molecules. This exposure makes it possible for the backbone atoms to form hydrogen bonds with water, which helps stabilize the protein’s overall structure.
Common Amino Acid Residues: It’s common to find a Proline (abbreviated as Pro) residue at position 2 and a Glycine (abbreviated as Gly) residue at position 3.Proline’s unique structure allows it to fit well in the tight turns (due to the imino nitrogen readily assuming a cis configuration) of the beta turn, and glycine’s small side chain helps accommodate the bend in the protein chain.
What is the gamma turn?
- less common reverse turn
- consists of only three amino acids
- backbone carbonyl and amide groups of the first and third amino acid residues form a hydrogen bond, and the second (middle) amino acid is not involved in inter-residue hydrogen bonding
what are globular proteins? provide an example
- water soluble
- spherical in shape
- often found in aqueous environments of cells
- ex. hemoglobin
