Amino Acids in Proteins
What is the name of the carbon adjacent to the carbonyl carbon?
What are the two groups of an amino acid involved in peptide bond formation?
the carboxyl group and the amino group
What is the approximate pKa of the carboxyl group?
pKa ~ 2
What is the approximate pKa of the amino group?
pKa ~ 9-10
All amino acids except glycine are L-amino acids or R-amino acids?
In order to form a peptide bond, does water need to be removed or added?
removed; dehydration synthesis
What are the amino acids found in the nonpolar, aliphatic group?
Glycine, alanine, leucine, isoleucine, valine, and proline
True or False? Because of proline's cyclic conformation, it is known as a helix disruptor?
Which amino acids are considered aromatic?
Phenylalanine, tyrosine, and tryptophan
What amino acids are considered polar but uncharged?
asparagine, glutamine, serine and threonine
What are the sulfur-containing amino acids?
Methionine and cysteine
Methionine is often involved in what type of modification?
Cysteine is involved in what kind of bonds?
Serine and threonine are often involved in what kind of linkages and additions?
glycosidic linkages and phosphorylation
What types of environments see the use of disulfide bonds?
highly oxygenated environments
In the endoplasmic reticulum, which amino acid is recognized most frequently for protein modification?
Which amino acids are considered positive (basic)?
Arginine, lysine, histidine
Which amino acids are considered negative (acidic)?
Aspartate and glutamate
What is pKa?
the point at which their is an equal number of protonated and unprotonated species
What is the Henderson-Hasselbalch Equation?
pH = pKa + log([A-]/[HA])
What is the isoelectric point?
the point at which an amino acid has a net neutral charge
What kind of interactions occur between amino acid R-groups?
2. hydrogen bonding
3. disulfide bond formation
4. Salt bridges
What three things can affect salt bridges?
3. ion concentration
What is the primary structure?
the sequence of amino acids
What is the pKa of Asp?
What is the pKa of Glu?
What is the pKa of His?
What is the pKa of Cys?
What is the pKa of Tyr?
What is the pKa of Lys?
What is the pKa of Arg?
What determines the sequence of amino acids?
The codon sequence of a mRNA
True/False? Why? Hemoglobin is a gene ortholog of myoglobin?
False; Hemoglobin is a paralog because they are descended from the same gene. Generically they are know as orthologs.
What is conservative substitution?
Replacing one amino acid for one that is similar i.e. leucine for valine or aspartate for glutamate
What is meant by "hidden variations"?
amino acid sequences can be altered but this does not critically change the structure or function
In general, a non-conservative substitution can lead to what with regards to structure and function?
1. increased activity
2. decreased activity
3. altering of structural integrity
What is a polymorphism?
sequence variations in an allele within a population
What is an isoform?
A protein isoform is one of several different forms of the same protein. Isoforms often occur because of tissue specificity.
What is an isozyme?
Enzymes with same function but different structure.
Why is species-specific insulin use the most optimal choice for treating diabetes in humans?
Species variations can lead to an immune response by the immune system
What happens to insulin when it complexes with zinc?
When insulin complexes with zinc, it precipitates out.
According to lecture, what are two kinds of carbohydrate addition?
O-glycosylation and N-glycosylation
What amino acid(s) and functional group are involved in O-glycosylation?
Ser, thr, and tyr; -OH
What amino acid(s) and functional group are involved in N-glycosylation?
What is palmitoylation?
The addition of palmitic acid (C16) to the -SH of cys
What is myristoylation?
The addition of myristic acid (C14) to the NH of N-terminal glycine
What is phenylation?
fatty acid addition to the SH of cys
Which amino acid(s) and functional group are involved in phosphorylation?
OH of ser, thr, and tyr
Which amino acid(s) and functional group are involved in acetylation?
NH2 of lysine, terminus
ADP-ribosylation involves which amino acid(s) and functional group(s)?
N of arg and gln, S of cys
Which amino acid(s) are involved in oxidation?
pro and lys
Which amino acid(s) are involved in carboxylation?