Biochem Protein Lecture 1 Flashcards
Proteins are polymers of
Amino Acids
Each amino acid residue is joined to its neighbor by a specific type of covalent bond:
Peptide Bond
How many different amino acids are commonly found in proteins?
Are there many less common ones?
20
Yes
What does each amino acid have?
The amino acids differ from each other in their
1) A carboxylic acid group
2) An amino group bonded to the same carbon atom (α carbon)
Side Chains (R-groups
Amino acids are grouped into 5 main classes based on their
R-Group Properties
Which R-Group property of AAs is particularly important?
Polarity
AAs vary from nonpolar and hydrophobic to polar and hydrophilic
This amino acid is the simplest structure of the aliphatic non-polar R-group.
Glycine
These nonpolar, alkyl groups tend to cluster together within proteins and stabilize proteins through hydrophobic interactions
Alanine, Valine, Leucine, and isoleucine
This amino acid is a non-polar aliphatic and is one of two sulfur containing AAs and has a nonpolar thioether group in its side chain. Note that the electronegativity of sulfur is similar to carbon
Methionine
This AA has nonpolar aliphatic side chain with cyclic structure; it’s secondary amino (imino) group is held in rigid conformation, which reduces flexibility of polypeptides containing proline
Proline
T/F: Aromatic R groups are relatively nonpolar and hydrophobic
TRUUUUUEEEE
This is the 1st aromatic R group
Phenylalanine
This aromatic R-Group has a bicyclic ring (indole), it contains an NH group which can form H bonds
Tryptophan
This aromatic R-group contains an OH group which can H-bond
Tyrosine
Why are tyrosine and tryptophan more polar than phenylalanine?
Because of their H-bonding ability
All aromatic aa’s absorb UV light, especially
What absorbance is characteristic of most proteins?
tryptophan
280nm
This group of R groups is hydrophilic, contain functional groups that H-bond with water (O and/or N), and the side chains are polar because of large differences in electronegativities between these atoms.
Polar, Uncharged R Groups
These polar uncharged R groups contain hydroxyl groups in their side chains
Serine and Threonine
This polar uncharged R group contains a sulfhydryl group and is readily oxidized to form a covalently linked dimeric AA called Cystine (two cysteine molecules joined by a disulfide bond)
Disulfide linked residues are strong hydrophilic or hydrophobic?
Cysteine
Hydrophobic (nonpolar)
These polar uncharged R groups contain amide groups in their side chains; and differ from each other by a methylene unit (CH2)
Which has an extra methylene unit?
Asparagine and Glutamine
Glutamine
Asparagine and glutamine are the ____ of aspartate and glutamate
Amides
This group of R groups is very hydrophilic and has a significant positive charge at pH of 7.0
Because they’re basic, they associate with H+ in solution to form positively charged groups
Positively Charged (Basic) groups
This positively charged basic R group has a second primary amino group on the epsilon carbon atom
Lysine
This positively charged basic R group has a positively charged guanidino group
Arginine
This positively charge basic R group has an imidazole group and is the only aa having an ionizable chain with a pKa near neutrality
Histidine
The imidazole group of histidine is less or more basic than amino or guanidino groups.
At pH 7, its prredominately unprotonated or protonated
Less
Unprotonated
In many enzyme catalyzed reactions, His (histidine) facilitates the reaction by serving as a
Proton donor/acceptor
This group of R groups has a net negative charge at pH of 7 and is very hydrophilic
Negatively Charged (Acidic) R groups
Both of these negatively charged acidic R groups have a second carboxyl group. They are acidic and dissociate to give H+ and COO- at pH of 7
The carboxyl groups are referred to as beta and gamma carboxyl groups because they’re attached to the beta and gamma carbons
Aspartate
Glutamate
Relative to strong acids like HCl and H2SO4, amino acids are
Weak acids undergo ____ over a wide pH range
Weak acids
What are the equations for Keq and pKa?
Keq = [H+][A-]/[HA] = Ka
pKa= -log Ka
A proton donor and its corresponding proton acceptor make up the
Conjugate acid-base pair
what is the example of titration of AA with two ionizible groups
What groups are they
Glycine
COOH and NH3+
As pH increases, which group of glycine ionizes first?
Why?
What is the name of the ion form at pH 6 when all of the carboxylic acid has ionized
The carboxylic acid ionizes first because it is a stronger acid than the acid form of amine
Zwitterion Form
The pKas of the ionizing groups for glycine are 2.34 for COOH and 9.6 for NH3+. Is this lower or higher than what is typically observed of these groups?
Lower
The titration data for glycine shows that glycine has two regions of _______. In these regions, adding base produces relatively small changes in pH
Buffering power
This is the only AA providing significant buffering power near neutral pH
Histidine
The relationship between an AAs net ____ and the pH of the solution is also obtained from the titration curve
Net Electric Charge
At pH 5.97, glycine is present predominately as its dipolar form, does it have a net electric charge?
The characteristic pH at which the net electric charge is zero is called the
No.
Isoelectric Point
Note: amino acids with nonionizable R-Groups have similar, though not identical, pKa values
!
The ratio of the existence of the acidic or basic form of an R group in a solution at a particular pH can be determined from a knowledge of the ____ of the R group and applying the Henderson-Hasselbach equation
What is that equation?
pKa
pH=pKa + log[A-]/[HA]
