Question 1

LYSINE HAS PKA VALUES OF ABOUT 2.2 (ALPHA-CARBOXYL), 9.0 (ALPHA-AMINO) AND 10.5 (SIDE CHAIN). WHAT IS ITS NET CHARGE AT PH 7.4?

Accepted Answer

+1. At pH 7.4 the carboxyl group is deprotonated (-1), while both amino groups sit below their pKa and stay protonated (+1 each). Adding them gives -1 + 1 + 1 = +1.

Question 2

GLYCINE HAS PKA VALUES OF 2.34 AND 9.60 AND NO IONIZABLE SIDE CHAIN. WHAT IS ITS ISOELECTRIC POINT?

Accepted Answer

5.97. With only two ionizable groups, the pI is the average of the two pKa values: (2.34 + 9.60) / 2 = 5.97. At that pH the zwitterion dominates and the net charge is zero.

Question 3

FOUR AMINO ACIDS ARE RUN IN AN ELECTRIC FIELD AT PH 7. WHICH ONE MOVES TOWARD THE POSITIVE ELECTRODE?

Accepted Answer

ASPARTATE. Only a negatively charged species is pulled toward the positive electrode. Aspartate's extra carboxyl group gives it a net charge of -1 at pH 7, lysine and arginine are +1, and glycine is neutral overall.

Question 4

GLYCINE IS DISSOLVED IN A SOLUTION AT PH 1. WHAT IS ITS NET CHARGE?

Accepted Answer

+1. At pH 1 the pH is below both pKa values, so both groups hold their protons. The carboxyl is neutral (COOH) and the amino group is NH3+, giving a net charge of +1.

Question 5

IN SICKLE CELL DISEASE, GLUTAMATE AT POSITION 6 OF THE HEMOGLOBIN BETA CHAIN BECOMES VALINE. WHY DOES THIS ONE CHANGE MATTER SO MUCH?

Accepted Answer

IT PUTS A HYDROPHOBIC PATCH ON THE SURFACE THAT MAKES DEOXYGENATED HEMOGLOBIN STICK TOGETHER. A charged, water-loving residue on the protein surface is swapped for an oily one. In the deoxygenated state that sticky patch binds a pocket on a neighbouring hemoglobin, so the molecules polymerize into fibres that distort the red cell.

Question 6

RIBONUCLEASE IS UNFOLDED WITH UREA AND A REDUCING AGENT, THEN BOTH ARE SLOWLY REMOVED. THE ENZYME REGAINS FULL ACTIVITY. WHAT DOES THIS SHOW?

Accepted Answer

THE AMINO ACID SEQUENCE CONTAINS THE INFORMATION NEEDED TO FOLD. Nothing but the chain itself was left once the chemicals were removed, yet it returned to its working shape. This is the classic evidence that a protein's sequence specifies its three-dimensional structure.

Question 7

IN A SOLUBLE GLOBULAR PROTEIN, WHERE WOULD YOU MOST EXPECT TO FIND LEUCINE AND VALINE SIDE CHAINS?

Accepted Answer

BURIED IN THE INTERIOR, AWAY FROM WATER. Leucine and valine have nonpolar hydrocarbon side chains. Folding packs them into the core, where they avoid water, while charged and polar residues face the solvent.

Question 8

A MUTATION PLACES PROLINE IN THE MIDDLE OF A LONG ALPHA HELIX. WHAT IS THE MOST LIKELY RESULT?

Accepted Answer

THE HELIX IS KINKED OR BROKEN AT THAT POINT. Proline's ring ties its side chain to the backbone nitrogen. That removes the N-H the helix needs for its hydrogen bond and locks the backbone angle, so the helix bends or ends there.

Question 9

WHEN AN EGG IS BOILED, WHICH LEVEL OF STRUCTURE IN ITS PROTEINS SURVIVES?

Accepted Answer

PRIMARY. Heat breaks the weak hydrogen bonds and hydrophobic interactions that hold the folded shape. The covalent peptide bonds linking the amino acids in sequence are untouched, so only the primary structure remains.

Question 10

ON SDS-PAGE A PROTEIN RUNS AT 100 KDA WITHOUT A REDUCING AGENT AND AT 50 KDA WITH ONE. WHAT DOES THIS TELL YOU?

Accepted Answer

IT IS TWO 50 KDA SUBUNITS LINKED BY A DISULFIDE BOND. SDS alone already pulls apart subunits held by noncovalent forces. A pair that only separates once a reducing agent is added must be joined covalently, which in proteins means a disulfide bond between cysteines.

Question 11

TWO CYSTEINES 80 POSITIONS APART IN ONE CHAIN END UP SIDE BY SIDE AFTER FOLDING AND FORM A DISULFIDE BOND. WHICH LEVEL OF STRUCTURE DOES THIS BOND STABILIZE?

Accepted Answer

TERTIARY. The bond connects side chains from distant parts of the same polypeptide, holding its overall three-dimensional fold. Bonds between separate chains would count as quaternary instead.

Question 12

SAILORS WITH SCURVY HAD FRAGILE BLOOD VESSELS AND BLEEDING GUMS. WHICH PROTEIN DEFECT EXPLAINS THIS?

Accepted Answer

COLLAGEN CANNOT FORM A STABLE TRIPLE HELIX WITHOUT VITAMIN C TO HYDROXYLATE PROLINE. The enzyme that converts proline to hydroxyproline in collagen needs vitamin C. Without hydroxyproline, the three collagen chains cannot hold their triple helix firmly, so connective tissue in vessel walls and gums weakens.

Question 13

WHICH SUBSTITUTION IN THE HYDROPHOBIC CORE OF A PROTEIN IS LEAST LIKELY TO DISRUPT ITS FOLD?

Accepted Answer

LEUCINE TO ISOLEUCINE. Leucine and isoleucine are both nonpolar and almost the same size, so the core stays oily and well packed. The other swaps bury a charged side chain where there is no water to stabilize it.

Question 14

AT PH 7.4, AN AMINO ACID'S ALPHA-AMINO GROUP (PKA ABOUT 9) IS MOSTLY ___.

Accepted Answer

PROTONATED. The pH is well below the group's pKa, so protons are plentiful and the group holds on to one as NH3+. Each pH unit below the pKa makes the protonated form ten times more common.

Question 15

SILK IS STRONG BUT FLEXIBLE BECAUSE ITS FIBROIN PROTEIN IS BUILT FROM STACKED, EXTENDED STRANDS ARRANGED IN BETA ___.

Accepted Answer

SHEETS. Fibroin's extended strands line up side by side and hydrogen bond to each other across the strands. Stacking many of those flat layers gives a fibre that resists stretching yet bends easily.

Question 16

EVERY THIRD RESIDUE IN COLLAGEN'S TRIPLE HELIX MUST BE ___, BECAUSE NO OTHER SIDE CHAIN IS SMALL ENOUGH TO FIT WHERE THE THREE CHAINS MEET.

Accepted Answer

GLYCINE. Where the three collagen strands pack together there is only room for a hydrogen atom as a side chain. Mutations that replace one of these glycines cause brittle bone disease, osteogenesis imperfecta.

Question 17

AT PH 7.4, A GLUTAMATE SIDE CHAIN WITH A PKA NEAR 4.1 CARRIES A ___ CHARGE.

Accepted Answer

NEGATIVE. The pH is more than three units above the pKa, so the side-chain carboxyl has lost its proton and exists as COO-. That is why glutamate can form salt bridges with lysine.

Question 18

WHEN THE PH EQUALS A GROUP'S PKA, ___ OF THOSE GROUPS ARE PROTONATED.

Accepted Answer

HALF. By the Henderson-Hasselbalch equation, pH = pKa makes the log term zero, so the ratio of deprotonated to protonated forms is exactly 1. Each form makes up 50 percent.

Question 19

IN THE TRIPEPTIDE ALA-GLY-SER, THE FREE ALPHA-AMINO GROUP BELONGS TO ___.

Accepted Answer

ALANINE. Peptide sequences are written from the N-terminus to the C-terminus. The first residue listed keeps the free amino group, and the last, serine, keeps the free carboxyl group.

Question 20

A FRIED EGG WHITE TURNS OPAQUE AND FIRM BECAUSE HEAT HAS LEFT ITS ALBUMIN PROTEINS ___.

Accepted Answer

DENATURED. Heat unfolds the albumin chains and exposes their hydrophobic interiors, which clump together and scatter light. The amino acid sequences are unchanged; only their folded shapes are lost.

Question 21

A PERM USES A REDUCING AGENT TO BREAK THE ___ BONDS IN HAIR KERATIN, THEN AN OXIDIZER TO RE-FORM THEM IN NEW POSITIONS.

Accepted Answer

DISULFIDE. Keratin is cross-linked by sulfur-sulfur bridges between cysteines. Reducing them lets the strands slide while the hair sits on a curler, and oxidizing them afterwards locks in the new shape.

Question 22

HEMOGLOBIN, BUILT FROM TWO ALPHA AND TWO BETA CHAINS, HAS A LEVEL OF STRUCTURE THAT SINGLE-CHAIN MYOGLOBIN LACKS: ___ STRUCTURE.

Accepted Answer

QUATERNARY. Only proteins with more than one polypeptide subunit have this level. The way hemoglobin's four chains shift against each other is what lets it bind oxygen cooperatively, which myoglobin cannot do.

Amino Acids and Protein Structure