Biochem: Amino acids Flashcards
Aspartic Acid
One letter code, three letter code
Category: polar, non-polar, acidic, basic
Charge at physiological pH
D, Asp
acidic bc has carboxylic acid in R group
Aspartate - anionic (deprotonated) form of each molecule, which is how these amino acids are observed at physiological pH
Charge -1
Glutamic acid
One letter code, three letter code
Category: polar, non-polar, acidic, basic
Charge at physiological pH
E, Glu
acidic bc has longer chain than Asp but also has carboxylic acid in R group
Glutamate - anionic (deprotonated) form of each molecule, which is how these amino acids are observed at physiological pH
charge -1
Lysine
One letter code, three letter code
Category: polar, non-polar, acidic, basic
Charge at physiological pH
K, Lys Basic Amino Acids - pKa 10 cationic (protonated at biological pH) Looks like long CH2 chain Charge +1
Arginine
One letter code, three letter code
Category: polar, non-polar, acidic, basic
Charge at physiological pH
R, Arg
Basic Amino Acid- pKa 12
cationic (protonated at biological pH)
Charge +1
Histidine
One letter code, three letter code
Category: polar, non-polar, acidic, basic
Charge at physiological pH
H, His
Basic Amino Acid but can also act as Acidic Amino acid bc pKa value close to physiological pH - pKa 6.5
At pH of 7.4, histidine is unique in that it can either be protonated or deprotonated - so can act as acid too
Charge +1 (25%)
Glycine One letter code, three letter code Category: polar, non-polar, acidic, basic What does the R group look like? Charge at physiological pH
G, Gly
Hydrophobic [nonpolar] Amino Acids - repel water so often found on the interior of folding proteins
R group is just an H, aliphatic (alkyl) R group
0
Alanine One letter code, three letter code Category: polar, non-polar, acidic, basic What does the R group look like? Charge at physiological pH
A, Ala
Hydrophobic [nonpolar] Amino Acids - repel water so often found on the interior of folding proteins
R group is methyl group, aliphatic (alkyl) R group
0
Valine One letter code, three letter code Category: polar, non-polar, acidic, basic What does the R group look like? Charge at physiological pH
V, Val
Hydrophobic [nonpolar] Amino Acids - repel water so often found on the interior of folding proteins
R group looks like two methyl groups branching out from each other and 1C away from aa, aliphatic (alkyl) R group
0
Leucine One letter code, three letter code Category: polar, non-polar, acidic, basic What does the R group look like? Charge at physiological pH
L, Leu
Hydrophobic [nonpolar] Amino Acids - repel water so often found on the interior of folding proteins
R group looks like two methyl groups branching out from each other and 2C away from aa, aliphatic (alkyl) R group
0
Isoleucine One letter code, three letter code Category: polar, non-polar, acidic, basic What does the R group look like? Charge at physiological pH
I, Ile
Hydrophobic [nonpolar] Amino Acids - repel water so often found on the interior of folding proteins
R group looks like Leucine but extra methyl popping out of one of the branched methyl groups
0
Phenylalanine One letter code, three letter code Category: polar, non-polar, acidic, basic What does the R group look like? Charge at physiological pH
F, Phe
Hydrophobic [nonpolar] Amino Acids - repel water so often found on the interior of folding proteins
R group looks like hexagon popping out of side - aromatic side chain
0
Tryptophan One letter code, three letter code Category: polar, non-polar, acidic, basic What does the R group look like? Charge at physiological pH
W, Trp
Hydrophobic [nonpolar] Amino Acids - repel water so often found on the interior of folding proteins
R group looks like pentagon and hexagon attached, aromatic side chain
0
Serine One letter code, three letter code Category: polar, non-polar, acidic, basic What does the R group look like? Charge at physiological pH
S, Ser
Polar
R-group is polar enough to have hydrogen bonds with water but which does not act as an acid or base, they are hydrophilic and will interact with water whenever possible.
hydroxyl groups of serine, threonine, and tyrosine residues are often modified by the attachment of a phosphate group by a regulatory enzyme called a kinase and this regulates protein activity.
R group looks like methyl with OH at end
0
Threonine
One letter code, three letter code
Category: polar, non-polar, acidic, basic
Charge at physiological pH
T, Thr
Polar
R-group is polar enough to have hydrogen bonds with water but which does not act as an acid or base, they are hydrophilic and will interact with water whenever possible.
hydroxyl groups of serine, threonine, and tyrosine residues are often modified by the attachment of a phosphate group by a regulatory enzyme called a kinase and this regulates protein activity
0
Tyrosine
One letter code, three letter code
Category: polar, non-polar, acidic, basic
Charge at physiological pH
Y, Tyr
Polar
R-group is polar enough to have hydrogen bonds with water but which does not act as an acid or base, they are hydrophilic and will interact with water whenever possible.
hydroxyl groups of serine, threonine, and tyrosine residues are often modified by the attachment of a phosphate group by a regulatory enzyme called a kinase and this regulates protein activity.
0
Asparagine
One letter code, three letter code
Category: polar, non-polar, acidic, basic
Charge at physiological pH
N, Asn
Polar
R-group is polar enough to have hydrogen bonds with water but which does not act as an acid or base, they are hydrophilic and will interact with water whenever possible
0
Glutamine One letter code, three letter code Category: polar, non-polar, acidic, basic What does the R group look like? Charge at physiological pH
Q, Gln
Polar
R-group is polar enough to have hydrogen bonds with water but which does not act as an acid or base, they are hydrophilic and will interact with water whenever possible.
0
Cysteine One letter code, three letter code Category: polar, non-polar, acidic, basic What does the R group look like? Charge at physiological pH
C, Cys Polar (slightly) Sulfur containing Amino Acid Contains a thiol (also called a sulfhydryl - like an alcohol with an S atom instead of O atom) 0
Methionine One letter code, three letter code Category: polar, non-polar, acidic, basic What does the R group look like? Charge at physiological pH
M, Met
Fairly nonpolar
Contains a thioether (like an ether that has an S instead of O atom)
0
Proline One letter code, three letter code Category: polar, non-polar, acidic, basic What does the R group look like? Charge at physiological pH
Unique because its amino group is covalently bound to its nonpolar side chain, creating a secondary alpha-amino group and makes a distinctive ring structure
0
Essential aa’s are…
Very heavy milk wtf - VH MILK WTF
Amino acids are amphoteric
Amino acids can act as acid (carboxylic acid group) and bases (amino group)
Pka of carboxylic groups and amino groups
Amino groups - 9 or 10
Carboxylic acid - 2
When the pH of the solution is less than the pKa of an acidic group, the acidic group will mostly be in its protonated/deprotonated form?
protonated
When the pH of the solution is greater than the pKa of an acidic group, the acidic group will mostly be in its protonated/deprotonated form?
deprotonated
What is charge on glycine at pH of 6?
-1
The pH at which a molecule is uncharged or ______ is referred to as its isoelectric point (pI) implying that an amino acid
Zwitterionic
How to calculate the isoelectric point?
Take the average of the two pKa’s (surrounding the neutral charge)
Name two common types of covalent bonds between amino acids in proteins:
peptide bonds that link amino acids
disulfide bridges between cysteine R groups
Peptide bond formation and other word for this
peptide bond formed between carboxyl group of one amino acid and the alpha group of another amino acid with loss of water
Peptide bonds formed amino to carboxyl end
What is proteolysis or proteolytic cleavage?Proteolytic enzyme or protease?
Hydrolysis of a protein by another protein. The enzyme that does the cutting
What kind of bond is a disulfide bond? What do you need to make it/examples?
Tertiary structure
Covalent between reactive thiol groups (sulfhydryl, SH) of cysteines
Need oxidizing agents to make this disulfude bond but
need reducing agents like BME beta mercaptoethanol, DTT, etc. to breal disulfide bonds
What is cystine?
When cysteine residue is disulfide bonded to another cysteine
Denaturation does not touch peptide bonds. What can proteins be denatured by?
Proteins denatured by urea (disrupts H-bonding), extreme pH, extreme temperature, changes in salt concentrations (tonicity)
What 2 aa do we not see in alpha helix?
Proline and glycine found in beta turns instead
Proline - no hydrogen atom available for backbone hydrogen bonding and makes kink in backbone
What can urea do to protein?
Urea break hydrogen bonds (break secondary and tertiary structure) but not disulfide bridges
Secondary structure stabilized by
Hydrogen bonds between backbone NH and CO groups
alpha helices always right handed
Tertiary Structure
Include Van der Waals forces between non polar side chains, hydrogen bonds between polar side chains, disulfide bonds between cysteine residues, and electrostatic interactions between acidic and basic side chains
Driven by interactions between R groups and with solvent (water)
Hydrophobic effect:
Hydrophobic side chains fold into the interior of the protein, away from the solvent (water) while hydrophilic R groups tend to be exposed to the water on surface of protein
If you denature by adding urea and then take the urea away what will happen?
If you add reducing agent, then denature with urea, then remove the reducing agent, then and then removed?
a) protein spontaneously reform
b) Protein will not be same bc when denatured, you removed reducing agent to disulfide bonds formed in bad spot they were in
Tertiary structure
Forces stabilizing quaternary structure are generally the same as those involved in tertiary structure - van der Waals forces, hydrogen bonds, disulfide bonds, and electrostatic interactions
Forces between different polypeptides
Peptide bonds NOT involved in quaternary structure
