Proteins, Muscles, Antibodies COPY Flashcards
What value describes the conformation of a polypeptide backbone?
Torsion angles
What are the two torsion angles of a polypeptide backbone?
⍦ - C-C bond
∅ - C-N bond
-amide bond has little rotation because it is planar and has some double bond character
What is a Romachandran diagram?
- indicates allowed conformations for a polypeptide (due to side chains only certain are allowed)
- ⍦ vs ∅ plotted
What are the two exceptions to the romachandran diagram?
Proline and glycine
Describe proline’s torsion angles.
- ∅ values are restricted to -60
- restricted to one side of the plot, can only rotate on the side that has the H, not on the side with the R-group
- more restrained motion
Describe glycine’s torsion angles.
- less steric hinderance, allowed angles are greater
- no R group, just 2 Hs
Describe the structure of a typical alpha helix.
(handed, residues, pitch, bonds, side chains)
- right handed helix
- 3.6 amino acids/residues per turn
- pitch (distance covered per turn) = 5.4Ă
- carbonyl (C=O) of Nth residue is hydrogen bonded to the N-H of the N+4th residues
- side chains point outward and downward
How are beta sheets stabilized?
- held together by H-bonds
- H-bonds are between neighboring polypeptide chains
What are the two types of beta sheets?
parallel and antiparallel
Describe parallel beta sheets.
- polypeptides run in the same direction (N-C) and (N-C)
- H-bonds between the strands are angled
- the crossover connection between strands is longer and goes out of the plane
Describe antiparallel beta sheets.
- polypeptides run in opposite directions (N-C) and (C-N)
- H-bonds between the strands are parallel
- the crossover connection between strands is shorter and on the same plane
What are the two classes of proteins?
- fibrous and globular
Describe fibrous proteins.
- have repeating second degree structures
- are structural proteins: hair, nails, muscle tendons
- keratin and collagen are examples
How are disulfide bonds formed?
cysteine residues have thiol groups that form disulfide bonds under oxidizing conditions
Describe globular proteins.
have non-repetitive second degree structures
What is the tertiary structure of a protein?
- the folding of second degree structural elements
- positions of each atom in a protein, including side chains
- Where is every atom located in 3D space?
Describe the quaternary structure of proteins.
- more than one polypeptide chain
- eg. dimer, trimer
- geometry of association of multiple polypeptides
- non-covalent associations
What is the hydropathy scale?
- (-4.5) - (4.5)
- number rating how hydrophobic each amino acid is
- larger = more hydrophobic
What are two examples of chaotropic agents?
urea, guanidinium
What are intrinsically disordered proteins?
- unfolded
- fold when in contact with their binding partner
When proteins fold, they go from _______ to _______
- high energy, high entropy
- low energy, low entropy
Describe the process of protein folding.
- Secondary structural elements and local segments of second degree structure form (Rapid process)
- Tertiary structure forms, second degree elements collapse to form tertiary structure (Slow process)
What chart illustrates protein folding?
- folding funnel
- energy x entropy
- local energy minima are the dips
- the lowest point is the most stable native structure
What do chaperone proteins do?
- assist with protein folding when stuck in minima
- eg. heat shock proteins (Hsp70/90)
- many of these are ATPases that catalyze the hydrolysis of a phosphate to allow a reaction that would not otherwise occur happen
