Peptides Flashcards
Where does a peptide bond form?
Between two amino acids
Middle of a dipeptide
How does a peptide bond form?
Condensation reaction between two amino acids which results in the loss of h2o
What are some characteristics of the peptide bond?
Rigid
Planar
Partial double bond character
Nearly always trans
Which type are pure single bonds?
Between α-carbon and carbonyl carbon
Between α-carbon and peptide nitrogen
What do the single peptide bonds allow for?
Free rotation
What type of chains do small peptides form?
Flexible
What type of structure does α-helix have?
Rod-like structure
Side chain extend our from the rod
What stabilises the alpha helix structure?
Hydrogen bonds between every main C=O and the N-H group four residues ahead in the sequence
What is the pitch of the alpha helix?
1.5Å
What is the diameter of an alpha helix?
5.4Å
What types of turns can alpha helixes have? Which is in proteins?
Right or left
Right in proteins
What is a β sheet made from?
Almost fully extended peptide chains called β-strands
How is the β sheet stabilised?
Hydrogen bonds between strands
Which directions can strands run in?
Same direction (parallel) Opposite direction (antiparallel)
What is the most common amount of strands per sheet?
2-5
What are most proteins made of?
Mixture of alpha helixes and beta sheets
What is a β-turn?
Regular structure allowing a reverse of direction
What is a β-turn made up of?
four residues
What do β-turns often connect?
The strands of antiparallel β-sheets
In β-turns, what does the C=O of residue n H-bond to?
the N-H of residue n+3
What do peptide bonds form?
The backbone of the protein
Where are disulfide bonds formed?
Between two cysteine residues
What do disulfide bonds form?
Crosslinks within the peptide backbone or peptide chains
How do you sequence large proteins?
They need to be broken down into smaller peptide fragments before the sequence is read
What is an example of chemical cleavage?
Cyanide bromide
Cleaves the carboxyl side of methoinine resides
What is an example of an enzymic cleavage?
Cleaves the carboxy side of lysine and arginine residues
What does the Edman degradation determine?
The primary sequence peptides up to 50 amino acids
How does Edman sequencing work?
The N terminal amino acid residue reacts with phenyl isothiocyanate, treatment with two different amino acids produces a phenyl thiohydantoin
What does analysis of the thiohydantoin show?
Do it by hplc
Shows the amino acids at this position
How do you reconstruct a protein sequence?
The cyanogen bromide peptides and trypsin peptides are overlapped to complete the primary structure of the protein
What is a primary structure?
Amino acid sequence
What is a secondary structure?
α-helixes, β-sheets, β-turns
What is a tertiary structure?
overall 3D structure of molecule
