Amino Acid Theory Flashcards
What is the primary structure of a protein?
The linear sequence of amino acids in a polypeptide chain joined by peptide bonds.
What is a peptide bond?
Peptide bonds line amino acids and are formed by condensation of the α-carboxyl group of Anne amino acid with the α-amino group of another amino acid
Define the term torsion angle.
- sometimes called dihedral angles
- a measure of rotation about a bond typically taken to lie between -180 and +180 degrees
What is the phi φ angle?
The angle of rotation about the bond between the nitrogen and the α-carbon atom.
What is the psi (ψ) angle?
The angle of rotation about the bond between the α-carbon and the carbonyl carbon atoms.
What is the meaning of the φ and ψ angles?
They determine the path of the polypeptide chain.
What does the Ramachandran plot show?
The 2-D plot shows the allowed combinations of φ and ψ angles when steric clashes between the atoms are absent or minimised.
What is the secondary structure of a protein?
Regions of regularly repeating conformations of the peptide chains I.e. α-helices and β-sheets.
What is the screw sense?
The direction in which a helical structure rotates with respect to its axis.
- if viewed down the axis of a helix, the chain turns in a clockwise direction - right handed screw sense
- if the turning is anticlockwise the screw sense is left-handed
What is the secondary structure of a protein?
The regular folding of regions of the polypeptide
- formed by a regular pattern of hydrogen bonds between the peptide N-H and C=O groups of amino acids near one another in a linear sequence
- common types are: α-helix, β-pleated sheets, turns and loops
Describe the α-helix.
- rod-like coiled structure stabilised by interchain hydrogen bonds
- a tightly coiled backbone forms inner rod.
- R groups extend outward, helically
- each of the residues are related by a translation of 1.5 Å - this results in 3.6 amino acids per turn
How is the α-helix schematically represented?
As twisted ribbons or rods.
Which amino acid residues are unlikely to be utilised in α-helix and why?
- valine, threonine, isoleucine- destabilise α-helices because of steric clashes
- serine, aspartate, asparagine- tend to disrupt α-helices because their R groups contain H-bond donors or acceptors in close proximity
- proline- α-helix breaker because it lacks NH group and because it’s ring structure prevents it from assuming the φ value that fits the helix
Describe the β-sheets.
- stabilised by hydrogen bonding between polypeptide strands
- β-pleated sheet consists of two or more polypeptide chains-β-strands
- the distance between adjacent aas along a β-strand is 3.5 Å
- chains can run parallel or antiparallel
- the R groups project alternately above and below the plane of the strands
What are β-strands?
Polypeptide chains that are almost fully extended.
What are β-sheets?
Multiple β strands arranged side-by-side.
How are β strands stabilised?
By hydrogen bonds between C=O and -NH on adjacent strands.
What are parallel β sheets?
Strands that run in the same N- to C- terminal direction.
Describe the antiparallel β sheet?
- strands run in opposite N- to C- terminal directions
- the H-bonds are nearly perpendicular to the chains
- they are more stable than parallel chains with distorted H-bonds
What roles do loops and turns play in protein structure?
They connect α-helices and β-strands and allow a peptide chain to fold back on itself to make a compact structure.
What are loops?
Containing hydrophilic residues I.e. Methionine
-found on the protein surfaces.
What are turns?
These are loops containing 5 residues or less
-often containing Gly
How are β-strands schematically represented?
-broad arrows pointing in the direction of the carbonyl-terminal end to indicate the type of β-sheet formed- i.e. Parallel or antiparallel
What is a motif?
Recurring protein structure that crop up in different proteins
What are some of the Supersecondary structure motifs?
- helix-loop-helix: two helices connected by a turn
- Coiled-coil: two amphipatic α-helices that interact parallely via their hydrophobic edges
- βαβ unit: two parallel β strands connected to an intervening α-helix by two loops
What is a hairpin motif?
Two adjacent antiparallel β strands connected by a β turn
What is a β meander?
An antiparallel composed of sequential β strands connected by loops or turns
What is a Greek key motif?
4 antiparallel strands -strands 1,2 in the middle, 3 and 4 on the outer edges
What is a β sandwich motif?
Stacked β strands or sheets
What is the tertiary structure of proteins?
Results from the folding of a polypeptide chain into a closely packed 3 dimensional structure.
-i.e. Myoglobin
Describe globular proteins?
- usually water soluble, compact, roughly spherical
- hydrophobic interior, hydrophilic surface
- they include enzymes, carrier and regulatory protein
What are the three molecular representations of Ribonuclease A?
- space-filling model- bound substrate analog black
- cartoon ribbon model- shows secondary structure
- substrate binding site view
Describe fibrous proteins.
- proteins that provide structural support for cells and tissues
i. e. α-keratin and collagen
Describe α-keratin.
- primary competent of wool, hair, nails,
- forms coiled coils
- consists of two right-handed α helices intertwined
- the two helices are cross-linked by weak interactions i.e. van der Waals forces and ionic interactions
Describe Collagen.
- major component of skin, bones, tendon, cartilage and teeth
- an extracellular protein, rod-shaped molecule
- contains 3 helical polypeptide chains each nearly 1000 residues
- glycine appears at every third residue in the amino acid sequence
What is a fold?
- a combination of secondary structures that form the core of a domain
- simple domains have simple folds, others have more complex folds
- domains can be classified by characteristic folds
What are domains?
- independently folded, compact units in proteins
- domain size: ~25 to ~300 amino acid residues
- domains are connected to other domains by loops
- they illustrate the evolutionary conversation of protein structure
