L7- Protein Structure Flashcards Preview

Biochemistry Exam 1 > L7- Protein Structure > Flashcards

Flashcards in L7- Protein Structure Deck (32):

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

Peptide bond.


What is a polypeptide?

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


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

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.


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

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


Which amino acids are positively charged at neutral pH?

Arginine, lysine, and histidine.


Which amino acids are negatively charged at neutral pH?

Aspartate and glutamate.


Which of the 20 standard amino acids are aromatic?

Phenylalanine, tryptophan, and tyrosine.


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).

Hydrophilic, hydrophobic.


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

Positively charged because DNA carries a negative charge.


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



Define specific activity of a protein.

It is the activity per amount of protein.


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?

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


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

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


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

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.


What is a molten globule?

It is a type of protein folding intermediate.


What is the role of chaperone proteins in protein folding?

They catalyze folding of some proteins.


Name two common secondary protein structure elements.

Alpha-helix and beta-sheet.


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

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.


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.'



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

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.


What does the drug Kalydeco do?

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


Which amino acid has the smallest side chain?

Glycine. Its side chain is a hydrogen atom.


Describe the pathogenesis of inherited Creutzfeldt-Jakob disease.

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.


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

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.


Define pKa.

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.


Define pI (isoelectric point).

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


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

At the pKa of the buffer.


Which amino acid is capable of forming disulfide bonds?

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


What is the main buffer in blood?

Carbonic acid/bicarbonate (H2CO3/HCO3-).


What is the main buffer inside cells?

Phosphate ions.


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.

Acid, base.


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)?

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.