Chapter 1: Amino Acids, Peptides, and Proteins Flashcards
Amino acids contain what 2 functional groups?
- Amino group
- Carboxyl group
What is the formula for an amino group?
-NH2
What is a formula for a carboxyl group?
-COOH
What is an α-amino acid?
Amino group and carboxyl group are bonded to the same carbon, the α-carbon of the carboxylic acid
You can think of the α-carbon as the ____________ carbon of the amino acid.
central
In addition to the amino and carboxyl groups, the α-carbon also has what 2 other groups attached to it?
- A hydrogen atom
- A side chain (R group)
What determines the properites of amino acids?
The side chains
For most amino acids, the α-carbon is a ____________ center, as it has 4 different groups attached to it. This means that most amino acids are _______________ __________.
chiral/stereogenic
optically active
What is the only achiral amino acid? Why?
glycine; it has a hydrogen atom as its R group
All chiral amino acids are (L/D?)-amino acids, so the amino group is drawn on the ______ in a Fischer projection.
L; left
In the Cahn-Ingold-Prelog system, L (Fischer) translates to an (R/S?) absolut configuration for almost all chiral amino acids.
S
Even though it is an L-amino acid, this amino acid has an R absolute configuration because the –CH2SH group has priority over the –COOH group.
cysteine
____________ has a single hydrogen atom as its side chain and is therefore achiral.
Glycine
The smallest amino acid is ____________.
Glycine
Which four amino acids have alkyl side chains containing 1 to 4 carbons?
AVaIL = alkyl
- Alanine
- Valine
- Isoleucine
- Leucine
Which are the only 2 amino acids that have a sulfur atom in its side chain?
Methionine and cysteine
Since sulfur has a methyl group attached, it is considered relatively ____________. Why?
nonpolar; sulfur has approximately the same electronegativity as carbon
Which amino acid is the only cyclic AA?
Proline
In proline, the ________ ____________ becomes part of the side chain, forming a 5-membered ring. What does this do?
amino nitrogen; makes it less flexible, limits where it can be in a protein
3 amino acids have uncharged aromatic side chains. What are they?
Try PT
- Tryptophan
- Phenylalanine
- Tyrosine
Which is the largest amino acid with an aromatic side chain? What does it have?
tryptophan; has a double-ring system that contains a nitrogen
Which amino acid with an aromatic side chain is the smallest? What does it have?
phenylalanine; has a benzyl side chain
(benzyl = benzene ring + CH2)
Adding an -OH group to phenylalanine gives ____________.
tyrosine
While phenylalanine is relatively ____________, the -OH group makes tyrosine relatively ____________.
nonpolar; polar
What are the 5 amino acids whose R side chains are polar but not aromatic?
STNQC
- Serine
- Threonine
- Asparagine
- Glutamine
- Cysteine
________ and ____________ both have -OH groups in their side chains, which makes them highly polar. Can H bond.
(non-alipathic)
serine, threonine
____________ and ____________ have amide side chains.
Asparagine, glutamine
Unlike the amino group common to all amino acids, the ________ nitrogens do not gain or lose protons. What does this mean?
amide; There is no change in pH and they do not become charged.
The last amino acid with a polar side chain is ____________, which has a thiol (-SH) in its side chain.
cysteine
Because sulfur is larger than oxygen, the S-H bond is longer and weaker than the O-H bond. Sulfur is also more EN than oxygen. What does this mean for the thiol group in cysteine?
It is more prone to oxidation.
Only 2 of the amino acids have negative charges on their side chains at body pH. What are they and what other AA are they related to?
aspartate (aspartic acid) and glutamate (glutamic acid)
asparagine, glutamine
Unlike asparagine and glutamine, asparate and glutamate have ________________ (-COO-) groups in their side chains, rather than ________.
carboxylate, amide
Asparate and glutamate are the ____________________ forms of aspartic and glutamic acid.
deprotonated
What are the 3 amino acids with positively charged nitrogen atoms?
Stay positive, his lys aren’t real
- Histidine
- Lysine
- Arginine
________ has a terminal primary amino group
Lysine
____________ has 3 nitrogen atoms in its side chain
Arginine
Where is the positive charge on lysine?
It is delocalized over all 3 nitrogen atoms
____________ has an aromatic ring with 2 nitrogen atoms. This ring is an ________________.
histidine; imidazole
Histine’s side chain pKa is relatively close to 7.4, about 6, so at physiologic pH, one ________________ atom is protonated and the other isn’t.
nitrogen
Amino acids with long alkyl side chains are strongly hydrophobic and are more likely to be found in the interior of proteins. Which are they? Why are they in the interior?
- Alanine
- Isoleucine
- Leucine
- Valine
- Phenylalanine
Away from water
All amino acids with charged side chains are (hydrophobic/hydrophilic?), along with the amides, which are ________________. What are the amino acids with charged side chains.
Positively charged:
1. Histidine
2. Arginine
3. Lysine
Negatively charged:
1. Glutamate
2. Aspartate
Amides:
1. Asparagine
2. Glutamine
Amino acids are ________________ species, as they can either accept a proton or donate a proton; how they react depends on the pH of their environment.
amphoteric
Ionizable groups tend to (lose/gain?) protons under acidic conditions and (lose/gain?) them under basic conditions.
gain; lose
The pKa of a group is the pH at which, on average, ____________ are deprotonated.
half of the molecules of that species
[deprotonated] = [protonated] or [HA] = [A-]
If pH < pKa, a majority of an AA species will be ________________.
protonated
If pH > pKa, a majority of an AA species will be ____________________.
deprotonated
Because all amino acids have 2+ groups that can be deprotonated, they all have at least (how many?) pKa values?
2
The first pKa, pKa1 is for the ____________ group and is usually around ____.
carboxyl; 2
For most amino acids, the second pKa value, pKa2, is the pKa for the ____________ group, which is usually between ____ and ____.
amino; 9 and 10
Under very acidic conditions, the amino group will be fully ____________ and will be ____________ charged. What is its formula?
protonated; positively; -NH3+
Under very acidic conditions, the carboxyl group will also be fully ________________ and will be ________________. What is its formula?
protonated; neutral; -COOH
At the physiologic pH, the carboxylic acid is ________________ and the amino acid is ________________. What are their formulas?
deprotonated; protonated
-COO- and -NH3+
At physiologic pH, an amino acid has both a positive and negative charge. This means it is electrically ____________ and is referred to as a ________________, which is a dipolar ion.
neutral; zwitterion
exist in water as internal salts
At very basic conditions, the carboxylate group and amino group are ________________. The carboxylate is ____________ charged and the amino is ____________.
deprotonated; negatively charged, neutral
Titration of amino acids looks like that of 2 ________________ acids, with 2 curves. It could also be 3 if the ________ ____________ is charged.
monoprotic; side chain
When pH is close to pKa value of a solute, the solution acts as a ________, and the titration curve is relatively ________.
buffer; flat
protonated and zwitterion concentrations are equal
When you start adding base where pH = pKa, the carboxylate group goes from half-protonated to fully protonated. Once 1.0 equivalent of base is added, the AA is only in zwitterion form. Every molecule is electrically ____________, and thus the pH equals the ________________ point of the AA.
neutral; isoelectric point
The ________________ ________ is the pH at which the molecule is electrically neutral.
isoelectric point
For neutral amino acids, you can calculate the isoelectric point how?
Average the 2 pKa values for the amino and carboxyl group
When 1.5 equivalents of base have been added to a solution of neutral amino acid, the concentration of ____________ form equals the concentration of the fully ____________________ form (because amino acid has started to deprotonate).
zwitterion, deprotonated
When 2.0 equivalents of base have been added to a solution of neutral amino acid, the amino acid has become fully ________________.
deprotonated
____________ are composed of amino acid subunits, sometimes called ____________.
Peptides; residues
____________ consist of 2 amino acid residues; ____________ have three.
dipeptides; tripeptides
The term ____________ is used for relatively small peptides, up to about 20 residues, while longer chains are called ____________.
oligopeptide; polypeptide
The residues in peptides are joined together through ________ ________, a specialized form of an amide bond, which form between what?
peptide bond; forms between the COO- group of one amino acid and the NH3+ of another amino acid.
What functional group is formed in a peptide bond?
-C(O)NH-
Peptide bond formation is an example of a ________________ or ________________ reaction, because it results in the removal of a water molecule.
condensation; hydration
Peptide bond formation can also be viewed as an ________ ________________ reaction, which can occur with all carboxylic acid derivatives.
acyl substition
When a peptide bond forms, the ____________ carbonyl carbon on the first amino acid is attacked by the ____________ amino group on the second amino acid. After that attack, the ____________ group of the carboxylic acid is kicked off.
electrophilic; nucleophilic; hydroxyl
Because amide groups have delocalizable pi electrons in the carbonyl and lone pair on the amino nitrogen, they can exhibit ________________.
resonance
See Figure 1.11
Rotation of the protein backbone around its C-N amide bonds is restricted, which makes the protein more ________.
rigid
When a peptide bond forms, the free amino end is known as the ________ terminus or ____-terminus. The free carboxyl end is known as the ________ terminus or ____-terminus.
amino, N; carboxy, C
To break down peptide bonds, this requires ________________. This can be catalyzed by hydrolytic enzymes like trypsin or chymotrypsin.
hydrolysis
Trypsin cleaves at the carboxyl end of ____________ and ________, while chymotrypsin cleaves at the carboxyl end of ________________, ____________ and ________.
arginine and lysine; phenylalanine, tryptophan, and tyrosine
High yield
How do trypsin and chymotrypsin catalyze hydrolysis?
They break apart the amide bond by adding a hydrogen atom to the amide nitrogen and an OH group to the carbonyl carbon.
________ are polypeptides that range from just a few amino acids in length up to thousands.
proteins
The ____________ structure of a protein is the linear arrangement of amino acids coded in an organism’s DNA. It’s the sequence of amino acids from N-terminus to C-terminus.
primary
What stabilizes primary structures?
The formation of covalent peptide bonds between adjacent amino acids
The primary structure of a protein is determined by ____________ (either the protein or DNA).
sequencing
A protein’s ________________ structure is the local structure of neighboring amino acids. They are the result of ____________ bonding between nearby amino acids.
secondary; hydrogen
What are the 2 most common secondary structures?
alpha-helices and beta-pleated sheets
The ____-____________ is a rodlike structure in which the peptide chain coils clockwise around a central axis.
alpha-helix
What stabilizes the alpha-helix?
intramolecular hydrogen bonds between a carbonyl oxygen atom and an amide hydrogen atom 4 residues down the chain
The alpha-helix is an important component in the structure of ____________, a fibrous structural protein found in skin, hair, and nails.
keratin
The ____-________ sheets, which can be parallel or antiparallel, have peptide chains that lie alongside one another, forming rows or strands.
beta-pleated
What holds beta-pleated sheets together?
intramolecular hydrogen bonds between carbonyl oxygen atoms on one chain and amide hydrogen atoms in an adjacent chain
Why do beta-pleated sheets have pleats?
to accommodate as many hydrogen bonds as possible
The R groups of amino acids point where in the plane of the beta-pleated sheet?
Above and below
Because of its rigid cyclic structure, ________ will introduce a kink in the peptide chain when it is found in the middle of an alpha-helix. Thus, they are rarely found in alpha-helices, unless they cross the cell membrane. Also rarely found in the middle of pleated sheets.
proline
Where is proline often found?
- In turns between the chains of a beta-pleated sheet
- The residue at the start of an alpha-helix
Proteins can be broadly divided into ________ proteins (structures that resemble sheets or long strands) and ________ proteins (that tend to be spherical). What are examples of each?
fibrous, collagen; globular, myoglobin
A protein’s ____________ structure is its 3D shape. What determines this?
tertiary; hydrophilic and hydrophobic interactions between R groups of amino acids
Hydrophilic N-H and C=O bonds found in the polypeptide chain get pulled in by hydrophobic residues found in the protein’s interior. What do these hydrophilic residues do?
They stabilize the protein from the inside through electrostatic interactions and hydrogen bonds
As a result of hydrophobic interactions, most amino acids on the surface of proteins have ____________ R groups.
hydrophilic
If a protein loses its tertiary structure, it loses its function. This is called ____________________.
denaturation
Whenever a solute dissolves in a solvent, the nearby solvent molecules form a ________________ ________ around that solute.
solvation layer
When a hydrophobic side chain is placed in an aqueous solution, the water molecules in the solvation layer cannot do what? What happens instead?
Cannot form hydrogen bonds with the side chain; the nearby water molecules have to rearrange themselves into specific arrangements to maximize hydrogen bonding
Putting hydrophilic residues on the exterior of a protein allows nearby water molecules to have more latitidue in their positioning, thus (decreasing/increasing?) their entropy.
increasing
____________ structures only exist for proteins that contain more than one polypeptide chain. These structures are an aggregate of smaller globular peptides, or ____________, and represent the functional form of the protein. Example?
Quaternary; subunits
Example is hemoglobin, which has 4 distinc subunits
Quaternary structures have 4 possible roles. What are they?
- Stabilize by reducing surface area
- Reduce amount of DNA needed to encode
- Bring catalytic sites close together (less travel for intermediates)
- Induce cooperativity or allosteric effects (one subunit can undergo conformational change to enhance/reduce other subunits’ activity)
____________ proteins derive part of their function from covalently attached molecules called ____________ groups.
Conjugated; prosthetic
Denaturation is often irreversible. Unfolded proteins cannot catalyze reactions. What are the 2 main causes of denaturation?
Heat and solutes
When the temperature of a protein increases, its average kinetic energy increases. When temperature gets high enough, what can happen to the protein?
The hydrophobic interactions that hold the protein together can be overcome, causing the protein to unfold
Solutes can denature proteins by disrupting what?
The forces that hold the protein together, e.g. disulfide bridges, hydrogen bonds, noncovalent bonds etc.
