BMS 527 1: Protein and Amino Acid Practice Flashcards

Sixty-five fill-in-the-blank practice flashcards covering amino acids, protein structure levels, peptide bonds, and denaturation from Lecture 1.

Proteins are the primary molecules that carry out "__________" in living organisms.

work

All proteins are polymers consisting of smaller, repeating units called __________.

monomers

A __________ is defined as a polymer consisting of more than one "flavor" of monomer.

heteropolymer

Amino acids are linked together by __________ bonds to create long chains.

peptide

All amino acids are organic compounds containing both an amino- and a __________ functional group.

carboxyl

Only specific amino acids, known as __________ amino acids, are used to make proteins.

proteinogenic

In proteinogenic amino acids, the amino and carboxylic acid groups are bonded to the central __________.

α-carbon

There are __________ "classic" proteinogenic amino acids for which at least one codon exists in the genetic code.

20

The __________ method is used to represent amino acids and distinguish between L and D enantiomers.

CORN

Most proteinogenic AA contain a __________ α-carbon, except glycine.

chiral

The one-letter code for the AA Tryptophan is __________.

W

The three-letter code for the AA Glutamine is __________.

Gln

The one-letter code for the AA Aspartic acid (aspartate) is __________.

D

The one-letter code for the AA Lysine is __________.

K

The three-letter code for the AA Asparagine is __________.

Asn

In the hierarchy of protein structure, the term hydrophobic literally means "__________."

water hating

In the hierarchy of protein structure, the term hydrophilic literally means "__________."

water loving

The __________ carbon is on the backbone, while the __________ carbon is the first carbon of the AA side chain.

α; β

The only AA that is not chiral is __________.

glycine

Aliphatic side chains are non-polar and their hydrophobicity increases with the number of __________ atoms.

C

Aromatic side chains, such as those in Phenylalanine (F) and Tryptophan (W), absorb light in the __________ spectrum.

near-UV

Tyrosine (Y) is often considered a debatable case for hydrophobicity because it contains an aromatic ring and a __________ group.

phenolic

The amino acid __________ can form a covalent disulfide bond with its R group.

cysteine

According to the Bronsted-Lowry definition, an acid is a molecule that __________ a proton ($H^+$).

donates

Bronsted-Lowry base __________ a proton when the environment is below its pKa.

accepts

The degree to which an acid gives up its proton is represented by the dissociation constant __________.

$K_a$

At a pH = pKa, a functional group is __________ protonated and 50% deprotonated.

50%

At physiological pH ($7.4$), the AA backbone exists as a __________, carrying both + & - charges.

zwitterion

The pKa of the backbone α-carboxyl group is approximately __________.

$2$

The pKa of the backbone α-amino group is approximately __________.

$9$ to $10$

The __________ (pI) is the specific point at which a protein carries no net charge.

isoelectric point

For AA with non-ionizable side chains, the pI is the halfway point between __________ and __________.

$pKa_1$; $pKa_2$

To calculate the pI of a + charged AA, take the halfway point b/w the side chain pKa and the __________ pKa.

amino

To calculate the pI of a - charged AA, take the halfway point b/w the side chain pKa and the backbone __________ pKa.

COOH

__________ structure is defined as the linear sequence of covalently bonded AA.

Primary

__________ structure refers to the local arrangement of the polypeptide backbone in space, often stabilized by H-bonds.

Secondary

__________ structure describes the overall 3D structure and global fold of a single polypeptide chain.

Tertiary

__________ structure is the structure of proteins composed of 1+ subunit or polypeptide chain.

Quaternary

The covalent peptide bond is formed through a __________ rxn that releases a water molecule.

condensation

The lone pair of electrons on the amide nitrogen is delocalized, giving the peptide bond __________ character.

partial dbl bond

By convention, peptide sequences are read from the __________ terminus to the __________ terminus.

N; C

The __________ conformation of a peptide bond, where Cα atoms are on the same side, is rare due to steric hindrance.

cis

In proteins, about __________ of Proline residues participate in a cis peptide bond configuration.

10%

The torsion angle representing rotation around the N-Cα bond is known as the __________ angle.

$\Phi$ phi

The torsion angle representing rotation around the Cα-C bond is known as the __________ angle.

$\Psi$ psi

Allowed torsion angles for AA in a polypeptide are visualized using __________ plots.

Ramachandran

The AA __________ is conformationally very flexible, while __________ is rigid and restricted.

glycine; proline

One of Pauling's principles for secondary structure is that the __________ group must remain planar.

amide

An alpha (α) helix is a common secondary structure that contains __________ AA per helical turn.

3.6

In an alpha helix, hydrogen bonding occurs b/w a carbonyl oxygen and an amide hydrogen __________ residues down the chain.

four

The side chains of AA in an alpha helix point __________ from the helix.

outward

In __________ beta sheets, the neighboring polypeptide chains run in opposite directions.

antiparallel

Beta sheets are localized secondary structures that adopt a __________ structure.

pleated

Glycine is considered a "secondary structure breaker" because it lacks a __________ carbon.

beta

Because of their cyclic side chains, __________ introduce kinks and rarely participate in alpha helices.

prolines

Folded proteins are broadly categorized into __________ (long fibers) or globular (round) types.

fibrous

Tertiary structure is held together by hydrogen bonds, ionic bonds, dipole-dipole interactions, and __________ interactions.

hydrophobic

Disulfide bonds are strong covalent linkages formed b/w sulfur-containing side chains of two __________.

cysteines

The AA __________ cannot form disulfide bonds because it contains a methyl group.

methionine

The oxygen-transport protein __________ is the classic example of quaternary protein structure.

hemoglobin

The free energy ($G$) of a protein __________ as folding increases, making the native state energetically favorable.

decreases

When a protein unfolds and loses its native shape, the process is called __________.

denaturation

The process of breaking peptide bonds using enzymes is known as __________.

hydrolysis

Protein denaturation involves weakening the bonds holding the structure together but does not necessarily break __________ bonds.

peptide

The cooking of egg white albumin, which involves heat-induced aggregation, is an example of __________ denaturation.

irreversible