All 20 amino acids with three-letter and one-letter codes and side chain classes: drill flashcards and a quiz. Free in your browser, no sign-up.
Subject: biology
At physiological pH (around 7.4), what is the predominant charge state of the amino and carboxyl groups in a free amino acid, and what is the resulting classification of the molecule?
Answer: The amino group is protonated (NH₃⁺), the carboxyl group is deprotonated (COO⁻), forming a zwitterion.
At physiological pH, the amino group of an amino acid gains a proton to become NH₃⁺, and the carboxyl group loses a proton to become COO⁻. This simultaneous presence of both positive and negative charges defines a zwitterion.
Which of the following best explains why proline is considered a 'helix breaker' in protein structures?
Answer: Its side chain forms a rigid five-membered ring that locks the backbone geometry and introduces kinks.
Proline's unique structure, where its side chain loops back and bonds to its own amino nitrogen, forms a rigid five-membered ring. This structure locks the backbone geometry, introduces kinks in the polypeptide chain, and prevents the nitrogen from participating in the hydrogen bonding required for alpha helix stability, thus disrupting them.
Considering their pKa values, why is histidine uniquely suited to act as a physiological buffer and participate in proton shuttling in enzyme active sites, compared to aspartate and lysine?
Answer: Histidine's side chain pKa (around 6) is close to physiological pH, allowing it to easily gain or lose a proton.
Histidine's imidazole side chain has a pKa around 6, which is very close to physiological pH (7.4). This proximity means that histidine can readily accept or donate a proton with small shifts in pH, making it an excellent physiological buffer and ideal for proton shuttling in enzyme active sites. Aspartate and lysine have pKa values further from physiological pH, making them less effective as physiological buffers.
How does the partial double bond character of a peptide bond primarily influence the overall structure of a protein backbone?
Answer: It makes the bond planar and prevents free rotation, constraining the shapes the backbone can adopt.
The partial double bond character of the peptide bond, due to electron delocalization, makes the bond planar and restricts rotation around it. This rigidity is crucial because it limits the conformational freedom of the polypeptide backbone, thereby influencing the overall three-dimensional structure of the protein.
Why is measuring UV absorbance at 280 nm a standard method for estimating protein concentration, and which amino acids are primarily responsible for this absorbance?
Answer: Proteins absorb UV light at 280 nm mainly because of aromatic amino acids, particularly tryptophan and tyrosine.
Aromatic amino acids (phenylalanine, tryptophan, and tyrosine) absorb ultraviolet light. Proteins absorb UV light at 280 nm primarily due to the aromatic rings of tryptophan and tyrosine, with tryptophan being the strongest absorber. This property allows for a quick estimation of protein concentration.
What is the one-letter code for Phenylalanine?
Answer: F
The one-letter code for Phenylalanine is F.
What is the one-letter code for Tryptophan?
Answer: W
The one-letter code for Tryptophan is W.
What is the one-letter code for Tyrosine?
Answer: Y
The one-letter code for Tyrosine is Y.
What is the one-letter code for Lysine?
Answer: K
The one-letter code for Lysine is K.
What is the one-letter code for Arginine?
Answer: R
The one-letter code for Arginine is R.
What is the one-letter code for Aspartate?
Answer: D
The one-letter code for Aspartate is D.
What is the one-letter code for Glutamate?
Answer: E
The one-letter code for Glutamate is E.
What is the one-letter code for Asparagine?
Answer: N
The one-letter code for Asparagine is N.
What is the one-letter code for Glutamine?
Answer: Q
The one-letter code for Glutamine is Q.
Which of the following amino acids is the only one that is achiral?
Answer: Glycine
Glycine is the only amino acid whose R group is a single hydrogen atom, meaning its alpha carbon is bonded to two identical groups (two hydrogen atoms), making it achiral.
Which class of amino acids primarily clusters in the interior of a folded protein, driven by the hydrophobic effect?
Answer: Nonpolar amino acids
Nonpolar amino acids have mostly hydrocarbon side chains, which are hydrophobic. In an aqueous environment, they tend to cluster together in the interior of a folded protein to minimize contact with water, a phenomenon known as the hydrophobic effect, which is a major driving force of protein folding.
What is the primary characteristic that defines an L stereoisomer in amino acids, and why is it significant in human proteins?
Answer: It indicates the specific configuration around the alpha carbon, and all amino acids in human proteins are this form.
The L stereoisomer refers to a specific spatial arrangement of the groups around the chiral alpha carbon in an amino acid. All amino acids incorporated into human proteins are exclusively the L stereoisomer, highlighting the stereospecificity of biological systems.
Which of the following best describes the formation of a peptide bond?
Answer: It is a condensation reaction between the carboxyl group of one amino acid and the amino group of another, releasing water.
A peptide bond forms when the carboxyl group of one amino acid reacts with the amino group of the next amino acid. This is a condensation reaction, meaning a molecule of water is released as the amide bond forms.
What is the significance of the N-terminus and C-terminus in a polypeptide chain?
Answer: They represent the ends of the chain with a free amino group and a free carboxyl group, respectively, defining its directionality.
A polypeptide chain has a distinct directionality. The N-terminus is the end with a free amino group, and the C-terminus is the end with a free carboxyl group. This directionality is fundamental to how proteins are synthesized and how their sequences are read and written.
What does the primary structure of a protein refer to?
Answer: The specific sequence of amino acid residues in the polypeptide chain.
The primary structure of a protein is defined as the unique linear sequence of amino acid residues linked by peptide bonds in a polypeptide chain. This sequence dictates all higher-order structures of the protein.
What is the one-letter code for Alanine?
Answer: A
The one-letter code for Alanine is A.
What is the one-letter code for Asparagine?
Answer: N
The one-letter code for Asparagine is N.
What is the one-letter code for Cysteine?
Answer: C
The one-letter code for Cysteine is C.
What is the one-letter code for Glycine?
Answer: G
The one-letter code for Glycine is G.
What is the one-letter code for Histidine?
Answer: H
The one-letter code for Histidine is H.
What is the one-letter code for Isoleucine?
Answer: I
The one-letter code for Isoleucine is I.
What is the one-letter code for Leucine?
Answer: L
The one-letter code for Leucine is L.
What is the one-letter code for Methionine?
Answer: M
The one-letter code for Methionine is M.
What is the one-letter code for Proline?
Answer: P
The one-letter code for Proline is P.
What is the one-letter code for Serine?
Answer: S
The one-letter code for Serine is S.
What is the one-letter code for Threonine?
Answer: T
The one-letter code for Threonine is T.
What is the one-letter code for Valine?
Answer: V
The one-letter code for Valine is V.
Every amino acid is built around a central carbon atom called the {0}.
Answer: alpha carbon
The alpha carbon is the central carbon atom in an amino acid to which the amino group, carboxyl group, hydrogen atom, and R group are attached.
The identity and chemical behavior of each amino acid comes entirely from its variable side chain, known as the {0}.
Answer: R group
The R group is the variable side chain that distinguishes one amino acid from another.
A molecule that carries both a positive and a negative charge at the same time, like free amino acids at physiological pH, is called a {0}.
Answer: zwitterion
At physiological pH, amino acids exist as zwitterions, with a protonated amino group (NH₃⁺) and a deprotonated carboxyl group (COO⁻).
In 19 of the 20 amino acids, the alpha carbon acts as a {0} because it carries four different groups.
Answer: chiral center
A chiral center is a carbon atom bonded to four different groups, which is true for the alpha carbon in all amino acids except glycine.
All amino acids incorporated into human proteins are the {0}.
Answer: L stereoisomer
Amino acids in human proteins exclusively exist as the L stereoisomer.
Glycine, alanine, and valine are examples of {0} because their side chains are mostly hydrocarbon and avoid water.
Answer: nonpolar amino acids
Nonpolar amino acids have hydrocarbon side chains that are hydrophobic and tend to cluster in the interior of folded proteins.
Serine, threonine, and cysteine are classified as {0} because their side chains can form hydrogen bonds but carry no net charge at physiological pH.
Answer: polar uncharged amino acids
Polar uncharged amino acids have side chains capable of hydrogen bonding but do not have a net charge at physiological pH.
Aspartate and glutamate are considered {0} because they have carboxyl groups in their side chains that are deprotonated and negatively charged at physiological pH.
Answer: acidic amino acids
Acidic amino acids have carboxyl groups in their side chains that are negatively charged at physiological pH.
Lysine, arginine, and histidine are categorized as {0} due to their nitrogen-containing side chains that can accept a proton.
Answer: basic amino acids
Basic amino acids have nitrogen-containing side chains that can accept a proton, making them positively charged at certain pH values.
The clustering of nonpolar side chains in the interior of a folded protein, away from water, is a major driving force of protein folding known as the {0}.
Answer: hydrophobic effect
The hydrophobic effect describes the tendency of nonpolar molecules to avoid water, leading to their clustering in an aqueous environment.
The {0} is the pH at which a molecule carries no net charge.
Answer: isoelectric point
The isoelectric point (pI) is the specific pH at which a molecule, such as an amino acid or protein, has an overall net charge of zero.
The {0} is the pH at which a functional group is 50% protonated and 50% deprotonated.
Answer: pKa
The pKa value indicates the pH at which an ionizable group is half protonated and half deprotonated.
Amino acids that the human body cannot synthesize and must obtain from the diet are called {0}.
Answer: essential amino acids
Essential amino acids are those that the body cannot produce and must be consumed through diet.
Amino acids that the body can synthesize are referred to as {0}.
Answer: nonessential amino acids
Nonessential amino acids are those that the body can synthesize on its own.
Amino acids link into chains through {0}, which are amide bonds.
Answer: peptide bonds
Peptide bonds are amide linkages that connect amino acids in a protein chain.
The formation of a peptide bond involves a {0}, which releases one molecule of water.
Answer: condensation reaction
A condensation reaction involves the joining of two molecules with the release of a small molecule, such as water, as seen in peptide bond formation.
A chain of amino acids starts at the {0}, which is the end with the free amino group.
Answer: N-terminus
The N-terminus is the beginning of a polypeptide chain, characterized by a free amino group.
A chain of amino acids ends at the {0}, which is the end with the free carboxyl group.
Answer: C-terminus
The C-terminus is the end of a polypeptide chain, characterized by a free carboxyl group.
The sequence of amino acid residues in a polypeptide chain is known as the protein's {0}.
Answer: primary structure
Primary structure refers to the linear sequence of amino acids in a protein.
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