Section 2 Flashcards
Name the 20 amino acids
Look at chart online
What are the five groups that side chains can be assorted into according to their polarity and charge?
Nonpolar: Aliphatic or Aromatic
Polar: Uncharged, Negatively charged, Positively charged
What are the non-polar, aliphatic amino acids?
Glycine (Gly, G)
Alanine (Ala, A)
Valine (Val, V)
Leucine (Leu, L)
Isoleucine (Ile, I)
Methionine (Met, M)
Proline (Pro, P)
What are the non-polar, aromatic amino acids?
Phenylalanine (Phe, F)
Tyrosine (Tyr, Y)
Tryptophan (Trp, W)
What are the polar, uncharged amino acids?
Cysteine (Cys, C)
Asparagine (Asn, N)
Glutamine (Gln, Q)
Serine (Ser, S)
Threonine (Thr, T)
What are the polar, negatively charged amino acids?
Aspartate (Asp, D)
Glutamate (Glu, E)
What are the polar, positively charged amino acids?
Lysine (Lys, K)
Arginine (Arg, R)
Histidine (His, H)
What does nonpolar, aliphatic side chain mean for an amino acid?
- composed of hydrocarbon chains (–CH2—) which are nonpolar and quite hydrophobic
- this causes these AAs to interact with other hydrophobic AAs, usually in the interior of proteins, to minimize their contact with water
- this is a major driving force behind PROTEIN FOLDING
Which amino acid has the smallest side chain out of the 20 amino acids?
Glycine (only a single H atom as its side chain)
________ is nonpolar, but since it has only a single H atom as its side chain, it contributes little to hydrophobic effects.
Glycine
In which amino acid does the side chain connect to its own amino acid? What does this result in?
Proline. The resulting 5-membered ring causes proline to be very rigid and thus limits its possible conformations.
Which one out of the nonpolar, aromatic amino acids is the most hydrophobic, and why?
a) F
b) Y
c) W
a) F (phenylalanine)
The tyrosine (Y) hydroxyl group and the tryptophan (W) nitrogen can form hydrogen bonds, and thus impart some polarity to these residues.
Note: All of them can participate in hydrophobic interactions
How can we tell the concentration of Phe, Tyr, and Trp in a protein?
Since the aromatic rings absorb ultraviolet light.
Note: tryptophan and tyrosine are able to absorb much more UV light than phenylalanine
_______, _________ side chains can interact extensively with water, or with atoms in other side chains, through hydrogen bonds.
Polar, uncharged
What is special about cysteine?
- contains a sulfhydryl group
- two cysteines that are in close proximity to each other can be oxidized to form a disulfide bond (a covalent bond between the two sulfhydryl groups)
- this bond can enhance protein stability
- cysteine residues are also important for the catalytic functions of many enzymes, as the deprotonated -SH is a good nucleophile (e- pair donor)
What are features of Asn and Gln side chains?
They contain an amide group that can act as a donor or acceptor of electrons.
They also contain a carbonyl group (C=O) that can participate in hydrogen bonding and dipole-dipole interactions.
What is the amide group important for in N and Q side chains?
It can act as a donor or acceptor of electrons
What is the carbonyl group, and what is it important for in N and Q?
it is C=O
It can participate in hydrogen bonding and dipole-dipole interactions
What are features of S and T side chains?
they have hydroxyl (OH) group on the side chain, which is capable of forming hydrogen bonds.
these can also be phosphorylated (along with the OH of Tyrosine) by kinases, resulting in protein modifications.
What can happen to the OH group on serine/threonine/tyrosine side chains? What does this result in
?
The OH can be phosphorylated, which results in protein modifications
What are features of D and E side chains?
- contain a carboxyl group and therefore carry a negative charge at pH 7.0 (i.e. they are acidic)
True or false:
Aspartate and glutamate can be referred to as aspartic acid and glutamic acid.
True
The amino acids that carry a positive charge at pH 7.0 are called ______, ________ and they include ______, _______, _______
The amino acids that carry a positive charge at pH 7.0 are called polar, positively charged and they include lysine, arginine, histidine.
What does it mean when amino acids carry a pos/neg charge at pH 7.0?
If they carry a positive charge at pH 7.0 they are basic, if they carry a negative charge they are acidic
Match the side chain group (amino, guanidinium, or imidazole) with each of the following:
- Arginine
- Lysine
- Histidine
- Lysine: amino group
- Arginine: guanidinium group
- Histidine: Imidazole group
Where are charged amino acids usually located (on exterior or interior of protein) and why?
Charged amino acids are usually very hydrophilic and typically make ionic and hydrogen bonding interactions with H2O. Therefore they tend to be on the exterior of proteins, in contact with water.
These side chains are very hydrophilic, so they tend to be located in the active site of many enzymes, such as DNA polymerase:
Charged amino acid side chains
When an amino acid sequence is given, is it written and read from:
a) The C-terminus to the N-terminus, left to right
b) The N-terminus to the C-terminus, left to right
b) The N-terminus to the C-terminus, left to right
What is a buffer?
A solution with a pH that does not change very much when H3O+ or OH- ions are added.
It contains approximately equal amounts of a weak acid and its conjugate base
What does most of the energy required to unfold proteins go towards?
It goes mainly towards disrupting the stabilizing hydrophobic effect
What is an imino group?
C=N
