L7- Protein Structure

Question 1

What kind of bond links the amino acid residues of a protein to one another?

Answer 1

Peptide bond.

Question 2

What is a polypeptide?

Answer 2

A polypeptide is a chain of amino acids linked together by peptide bonds.

Question 3

What is meant by primary, secondary, tertiary, and quaternary structure of a protein?

Answer 3

Primary: the amino acid sequence. Secondary: helices, beta sheets, and turns. Tertiary: the way the secondary structure elements come together in 3D space. Quaternary: the way multiple proteins come together to form a complex.

Question 4

What determines most of the structural and functional properties of a protein?

Answer 4

The protein’s amino acid side chains, which are also called R-groups.

Question 5

Which amino acids are positively charged at neutral pH?

Answer 5

Arginine, lysine, and histidine.

Question 6

Which amino acids are negatively charged at neutral pH?

Answer 6

Aspartate and glutamate.

Question 7

Which of the 20 standard amino acids are aromatic?

Answer 7

Phenylalanine, tryptophan, and tyrosine.

Question 8

The amino acid R-groups of water soluble proteins that face the exterior of the protein are usually ________ (hydrophobic/hydrophilic), and those that face the interior of the protein are usually ________ (hydrophobic/hydrophilic).

Answer 8

Hydrophilic, hydrophobic.

Question 9

Regions of proteins that interact with DNA are usually ___________ (positively/negatively) charged.

Answer 9

Positively charged because DNA carries a negative charge.

Question 10

What technique can a scientist use to measure the purity of a protein in a sample?

Answer 10

SDS PAGE.

Question 11

Define specific activity of a protein.

Answer 11

It is the activity per amount of protein.

Question 12

A scientist inserts a sample of protein in a spectrophotometer and calibrates the instrument to detect absorbance of the sample at a wavelength of 280nm. What is the scientist measuring?

Answer 12

The content of tryptophan and tyrosine residues in the protein. Absorbance at 280nm is frequently used to determine protein concentration of a purified protein.

Question 13

How may the activity of a DNA-binding protein be determined?

Answer 13

By the ability of the protein to band-shift DNA.

Question 14

What type of bond has the most significant influence on how proteins fold?

Answer 14

Weak non-covalent bonds. The energy contribution from each individual bond is small, but the net contribution from all the non-covalent interactions is large.

Question 15

What is a molten globule?

Answer 15

It is a type of protein folding intermediate.

Question 16

What is the role of chaperone proteins in protein folding?

Answer 16

They catalyze folding of some proteins.

Question 17

Name two common secondary protein structure elements.

Answer 17

Alpha-helix and beta-sheet.

Question 18

Describe the hydrogen bonding pattern between amino acid residues in an alpha-helix.

Answer 18

Hydrogen bonds in an alpha-helix occurs between the oxygen of a carbonyl group and the HN of an amino acid that is four residues down the polypeptide chain.

Question 19

Which amino acid cannot fit in an alpha-helix? This amino acid has a five-member ring and is referred to as the ‘helix breaker.’

Answer 19

Proline.

Question 20

Describe the hydrogen bonding pattern between amino acid residues in a beta-sheet.

Answer 20

In a beta-sheet, hydrogen bonding occurs between backbone atoms within stretches of amino acid residues. At least two (and frequently more) extended polypeptide chains are involved.

Question 21

What does the drug Kalydeco do?

Answer 21

It is a treatment for CF patients with a particular mutation (G551D). This mutation appears in 4-5% of patients.

Question 22

Which amino acid has the smallest side chain?

Answer 22

Glycine. Its side chain is a hydrogen atom.

Question 23

Describe the pathogenesis of inherited Creutzfeldt-Jakob disease.

Answer 23

The disease is caused by a single amino-acid mutation. This mutation causes prion proteins to switch their conformation from soluble alpha-helices to insoluble beta-sheets. The insoluble beta-sheets can form aggregates that in turn lead to neurological symptoms.

Question 24

Proteins make a significant contribution to the buffering capacity in cells and plasma. What part of proteins allows them to act as buffers?

Answer 24

Titratable groups on the amino acid side chains. Note that the pKa of these groups differ depending on the side chain. Also, since the protein concentration in cells and plasma is quite high, proteins have a considerable buffering capacity.

Question 25

Define pKa.

Answer 25

The pKa is the pH at which the concentration of the acid form of a molecule is equal to the concentration of the base form of the same molecule. In other words, half the molecules are in the acid form, and half are in the base form.

Question 26

Define pI (isoelectric point).

Answer 26

The pI is the pH at which a molecule is electrically neutral.

Question 27

At what pH will a buffered solution be most resistant to changes in the pH after the addition of acid or base?

Answer 27

At the pKa of the buffer.

Question 28

Which amino acid is capable of forming disulfide bonds?

Answer 28

Cysteine. Disulfide bonds are most often found in oxidizing environments such as outside of the cell.

Question 29

What is the main buffer in blood?

Answer 29

Carbonic acid/bicarbonate (H2CO3/HCO3-).

Question 30

What is the main buffer inside cells?

Answer 30

Phosphate ions.

Question 31

At pH values lower than the pKa, the ________ (acid/base) form of the molecule predominates. At pH values higher than the pKa, the ________ (acid/base) form of the molecule predominates.

Answer 31

Acid, base.

Question 32

Aspirin is a weak acid at low pH and has a pKa of 3.5. Per unit surface area, will more aspirin be absorbed in the stomach (pH 1.5) or in the intestine (pH 6.5)?

Answer 32

At a pH below its pKa, aspirin will be in its acid form (RCOOH). At a pH above its pKa, aspirin will be in its base form (RCOO-). Since non-ionized molecules cross cell membranes passively whereas ionized molecules do not, more aspirin will be absorbed in the stomach than in the intestine.