Lecture 5 - Elements of Protein Structure Flashcards
Amino acids are joined by?
Peptide bonds
How are the amino acid residues in a polypeptide chain numbered?
Starting from the amino terminus to the carboxyl terminus (N-terminus to C-terminus)
What is each protein made of?
At least one protein (or polypeptide) chain
How many chains may proteins have?
Anywhere from one to several
What is the most common variety of proteins?
Proteins with one chain
Proteins are mostly…
Globular so the main chain has to double back and form a more compact shape
What is the structure of proteins primarily composed of?
Alpha helix, beta structure and turns
What are the levels of protein structures?
Primary, Secondary, Tertiary, Quaternary
Primary:
amino acid sequence of a protein
Secondary:
Local 3D arrangement of a protein chain over a short stretch of adjacent amino acid residue
Tertiary:
3D structure of a complete protein chain
Quaternary:
Interchain packing and structure for a protein that contains multiple protein chains
What do the protein main chain and side chain atoms have?
Bonds which can rotate and are somewhat flexible
What are the main chain atoms in a protein?
Nitrogen, alpha carbon and carbonyl carbon
How are the main chain atoms in a protein connected?
By single covalent bonds
What is the bond between N and alpha carbon called?
Phi
What is the bond between alpha carbon and carbonyl carbon called?
Psi
What is the range of values for phi and psi?
0 +/- 180 degrees
What is the bond angle between the carbonyl carbon and N (peptide bond) called?
Omega
What is the angle value of omega usually?
very close to 180 degrees or 0
What is one way a 3D structure can be described?
By listing the rotation angles found around the bonds of each residue of the protein chain
What bonds can twist
Phi and Psi
What bond cannot twist
Omega
Why do phi and psi angles have restrictions in their values?
Due to steric hindrance
What can phi rotation lead to?
O-O collision
What can psi rotation lead to?
NH-NH collisions
What may their be steric hinderance between?
The hydrogen on the amide nitrogen and the carbonyl oxygen
What are most peptide bonds?
Trans
What does omega equal for a trans peptide bond?
About 180 degrees
Where are the alpha carbon atoms found in a trans peptide bond?
On opposite sides of the peptide bond
What does omega equal for a cis peptide bond?
About 0 degrees
Where are the alpha carbon atoms found in a cis peptide bond?
On the same side of the peptide bond
When is steric hinderance increased?
For cis peptide bonds
which bond is shorter:
C-N bond or Ca - N bond.
C-N bond.
What does the combination of all the rotations and twists around all the bonds in a protein lead to?
Its overall 3D structure
What does a proteins 3D structure lead to?
The arrangement of all the side chains in the protein
What does the arrangement of all the side chains in the protein lead to?
Its function
What is secondary protein structure dominated by?
Two structures - alpha helices and beta strands/sheets
What does the main chain do in an alpha helix?
Spirals around the central axis like a spiral axis - right handed spiral
What type of interaction is there in alpha helices?
A non-covalent interaction called a hydrogen bond between the carbonyl oxygen which is partially negatively charged and the hydrogen attached to the N which is slightly positively charged
What symbol is the carbonyl oxygen given?
n
What symbol is the nitrogen with hydrogen attached given?
n+4
What is the O-N distance?
approximately 2.9 A
What do hydrogen bonds do in alpha helices?
Help stabilise the structure, (adding 3-7 cal/mol or 12-28kJ/mol of stability)
How many residues/turn in alpha helices?
3.6
What is the rise/turn in alpha helices?
5.4 A
What is the d of one amino acid residue?
1.5 A / residue
Where are the side chains in alpha helices?
They point outwards to help stabilise the alpha helix
What is phi in an alpha helix?
about -57 degrees
What is psi in an alpha helix?
About - 47 degrees
Which amino acid residues break the alpha helix pattern?
Glycine and proline
What exists in the alpha helix?
A helix dipole, positive at the N terminus
What is the beta structure comprised of?
Peptide chains with a more extended structure than the alpha helix. Each is called a beta strand (not stable on own)
What occurs between adjacent beta strands?
Hydrogen Bonding
What can adjacent beta strands form?
A beta sheet (with two or more strands)
How many beta strands per beta Sheet?
typically 2-10
What is the average beta strand length?
About 6 amino acid residues which is typically shorter than alpha helices
How many amino acid residues may each strand have?
Up to 15
What are the two types of hydrogen bonding interactions between beta sheets?
Parallel and antiparallel
Describe parallel strutcure?
The two strands run in the same direction but the hydrogen bonds aren’t parallel
Describe antiparallel strutcure?
The two strands run in the opposite direction and the hydrogen bonds are parallel
How is a beta sheet described?
Extended and pleated, not planar with right handed twist
Where are the side chains in beta sheets?
Above and below
What will commonly form a beta strand?
Any NP-P-NP-P stretch of amino acid residues
What is the model beta sequence in silk?
Gly-Ser-Gly-Ala-Gly-Ala
What do the Ala side chains do in silk?
Interlock with the Ala side chain from another sheet
Is beta sheets in silk parallel or antiparallel?
Antiparallel
What are turns needed for?
To form globules
What are turns often like?
Short, hairpin like, involving 3 or 4 residues
What amino acids are in high amounts in turns?
Gly (flexibility) and Pro (rigidity)
What portion of residues are involved in turns?
Almost 30%
What is common across turns?
Hydrogen Bonding
How many types of turns are there?
More than 16, which are given Roman numeral names
What are the common types of turn?
Type I and Type II
Where is the oxygen in Type I turns?
Up
Where is the oxygen in Type II turns?
Down
How are helices shown in the consensus protein structural display?
As spirals (or cylinders)
How are strands shown in the consensus protein structural display?
Arrows pointing from N terminus to C terminus
How are turns and random coils shown in the consensus protein structural display?
As loops or rope-like structures
What is a random coil?
A section of protein structure that does not fit into any of the standard groups
