3- Introduction to Proteins

Question 0

What are some functions that proteins serve?

Answer 0

Structurally - involved in contractile structures
Transport - of oxygen, Co2, other molecules
Unique binding properties

Question 1

What are proteins and peptides made of, and what is unique about the bond that connects these components?

Answer 1

Proteins are composed of amino acids joined by peptide bonds. Peptides are chains of amino acids joined by amide linkages (i.e. peptide bonds).

Peptide bonds are rigid due to tautomerism, but has free rotations around other bonds. These bonds are shorter than C-C bonds and can be biologically active.

Question 2

Describe the general solubility properties of protein.

Answer 2

Usually soluble.

Question 3

What is a primary structure?

Answer 3

Amino acid sequence of a protein.

Question 4

What is a secondary structure?

Answer 4

bonding of primary structure to form more rigid structures.

Ex.Alpha Helix, Beta pleated sheet, beta-turns, random coil arrangement.

Question 5

What is a tertiary structure?

Answer 5

Folded secondary structures for the purpose of compacting the protein

Question 6

What is a quaternary structure?

Answer 6

Proteins with two or more polypeptide chains held together by non-covalent forces

Question 7

What are commonly occurring modifications of amino acids found in some proteins?

Answer 7

1) Acetylation: N-terminal residue is terminated giving resistance to degradation
2) Carboxylation
3) Hydroxylation (hydroxylated proline further stabilizes collagen fibers)
4) Glycosylation
5) Phosphorphylation (cellular process regulation switch)
F) Disulfide linkages

Question 8

What amino acids are sometimes found to be phosphorylated in proteins?

Answer 8

Serine, Threonine and Tyrosine

Question 9

Describe alpha helix

Answer 9

• tightly coiled formation stabilized by hydrogen bonding between imido N-H groups and the oxygen atom of carbonyl groups of the main chain.
• 3.6 amino acids residues per turn.
• Found in globular and fibrous proteins

Question 10

Describe beta pleated sheets

Answer 10

hydrogen bonding between neighboring chains or long regions of the same chain are formed. H-bonds are perpendicular to the long axis of polypeptide chain.

Question 11

Describe Beta-turns

Answer 11

Structures that cause reversals in the direction of peptide chains b/c carbonyl oxygen of residue #N is involved in a hydrogen bond with N-H residue of #N+3

Question 12

Describe random coil arrangements

Answer 12

unorganized secondary structure

Question 13

What stabilized higher order structures in protein?

Answer 13

Electrostatic attraction of charged residues (salt bridges); internal hydrogen bonds; van der waals and London dispersion forces; Entropy driven hydrophobic effects

Question 14

What amino acids are likely to carry charges on side chains at neutral pH?

Answer 14

Aspartic acid, glutamic acid
(+) : Lysine, arginine, and histidine
(-): Tyrosine and Cysteine

Question 15

What are zinc fingers?

Answer 15

A zinc ion is complexed to four amino acids (usually cysteines or histidines) causing a loop of ~12 aminoa acids to protrude.

Question 16

What are kringle domains?

Answer 16

conserved sequences that fold large loops stabilized by 3 disulfide linkages

Question 17

What are leucine zippers?

Answer 17

arrangements of leucines along one side of an alpha helix chain in two proteins so proteins can form dimers leaving basic amino acid regions to bind DNA (facilitates the transcription process and protein-protein interaction)

Question 18

How can proteins be denatured?

Answer 18

Detergents, Chaotropic agents; High temperatures (50-60 degrees higher); drastic pH changes; organic solvents

Question 19

What is the hydrophobic effect?

Answer 19

The major tendency of nonpolar substances to aggregate in aqueous solutions or fold inward in proteins