Lecture 12 Flashcards
What is the charge of Lysine at pH 7?
It is positively charged because of the amino group in the side chain
What does the side chain of Lysine contain?
A positively charged side chain
What kind of H bonds is the side chain of Lysine capable of forming?
It is an H-bond donor through its amino group at neutral pH’s
What is the Polarity of Lysine?
It is very polar
What is the pKa of the amino group in the R group of Lysine?
It has a pKa of 10
What charge does Lysine have at pH 7?
A positive charge
Why does Lysine have a positive charge at pH 7?
Because it has an NH3 group
Why is Lysine know as a basic amino acid?
Because it exists as a base at neutral pH through it amino group
What is the charge of Arginine at pH 7?
It is positively charged
What is a Guanido group?
The end part of the R group of arginine
What is the pKa of the NH2 of Arginine?
12.5
Why is it difficult to deprotonate the functional group of Arginine?
Because it is very stable due to resonance
Why can Arginine be described as a basic amino acid?
Because the side chain is neutral when it is in the base form
What is the polarity of arginine?
It is very polar
What is the H-bond capability of Arginine?
It is an H-bond donor
What are the exceptions for the amino acid abbreviation rules?
- Asparagine (Asn)
- Glutamine (Gln)
- Isoleucine (Ile)
- Tryptophan (Trp)
Where are Polar side chains usually found?
In proteins on the surface where they can interact with water
Where are non-polar side chains usually found?
Buried in the protein core to minimize interaction with water
Which parts of the amino acid is a peptide bond between?
The carboxyl of one amino acid and the amino group of another amino acid
What is removed in the formation of a peptide bond?
Two H’s from the amino group and one O from the carboxyl group to form a water
What is the symmetry of the bond that connects amino acids together?
It is asymmetrical
What does the N-terminal describe?
The presence of a free amino group
What does the C-terminal describe?
The presence of a C terminal on one end
What is a Dipeptide, Tripeptide, Tetrapeptide, Pentapeptide?
Two amino acids, three amino acids, four amino acids, five amino acids
What is an Oligopeptide?
The general term for a larger number of amino acids, often refers to synthetic. peptides
What is a Polypeptide?
A long chain of amino acids, usually produced naturally
What is a Protein?
A large polypeptide a with a biological function
What retains their charge in a peptide?
- Terminal amino group (+1)
- Carboxylate group (-1)
- Side chains (if they have one)
How are the number of connected amino acids related to the peptide bond?
There will always be one less peptide bond than amino acids
What is the Primary Structure?
The sequence of amino acids in a polypeptide
What joins each amino acid to the next?
A covalent peptide bond
From which terminus do we read polypeptide chains?
From N-terminus to C-terminus
Where is no rotation permitted in peptide bonds?
Rotation is not permitted around the C-N bond because of the double bond character
In a peptide bond, which atoms are found in the same plane?
- Two Alpha carbons
- Carbonyl carbon
- Oxygen
- Nitrogen
- Hydrogen on the nitrogen
What are the three kinds of bonds in a peptide bond?
- N - Calpha
- Calpha - carbonyl carbon
- Carbonyl carbon - nitrogen
Which bonds in a peptide bond allow for rotation?
N - Calpha and C-alpha to Carbon of the carbonyl
What does the Primary structure determine?
The 3D structure
Why is the folding conformations of polypeptides limited?
Due to steric hindrance
What is the hydrogen bonding potential of a peptide bond?
The carbonyl and N-H can hydrogen bond with each other
