Chapter 1: Amino Acids and Protein Structure

Question 1

L - amino acid chemical classifications

Answer 1

• Aliphatic
• Aromatic
• Sulfur-containing
• Alcohols
• Bases
• Acids
• Amides

Question 2

Post-translational modifications

Answer 2

• Modified amino acids

- Occurs after they have been incorporated into the primary structure of a peptide or protein

Question 3

Hydroxyproline

Answer 3

• Post-translationally modified in collagen structures

Question 4

Gamma Carboxyglutamate

Answer 4

• Post-translationally modified in clotting factors and protein C

Question 5

Prosthetic groups

Answer 5

• Covalently bound accessory components

Question 6

Weak Acids

Answer 6

• Allows side chain functional group of amino acids to donate or accept (act as a base) protons as environmental pH fluctuates

Question 7

Covalent peptide bonds (amide bonds)

Answer 7

• Formed between α-amino acids
• Bonds formed by condensation reactions and use energy
• Trans bonds that are stable
• Unionized at physiological pH
• Coplanar, exist in linear orientation

Question 8

Primary structure

Answer 8

• Linear sequence of amino acids
• Connected by peptide bonds
• Determines functional 3D shape

Question 9

Insulin

Answer 9

• Synthesized in the pancreatic ß-cells

Question 10

Proteolytic cleavage

Answer 10

• Releases C-peptide and biologically active hormone

Question 11

Hemoglobin

Answer 11

• Transport protein

- Bind with oxygen to transport it through the blood

Question 12

Edman Degradation

Answer 12

• Historically used to determine the primary structure of a protein
• Amino terminal residue is labeled with a phenylisothionate at pH 9.0
• Forms a phenylthiocarbamoyle derivative
• Derivative cyclized under mild acidic conditions
• Released from peptide, leaving remaining bonds intact

Question 13

Secondary enzyme

Answer 13

• Partially digests the parent peptide to generate overlapping peptides

Question 14

Denaturation

Answer 14

• Achieved by diothreitol and alkylation with iodoacetate
• Prevents bonds from reforming
• Also may be achieved by treatment with 2-mercaptoethanol

Question 15

Secondary structure

Answer 15

• Local spontaneous repeated folding of a protein/polypeptide
• Stabilized predominantly by H-bonds

Question 16

Alpha helix

Answer 16

• Stabilized by H-bonds between NH and CO groups of amino acids 4 residues
• Can extend up to 650 residues in length
• Distinct polar and non-polar sides of the chain
• Spiral molecule

Question 17

Beta pleated sheet

Answer 17

• Fully extended polypeptide chains
• Linked together by interchain H-bonds between CP and NH groups
• Composed of up to 10 polypeptide strands lying adjacent to each other
• Can run parallel in the N > C direction or antiparallel in the opposite N > C direction

Question 18

Tertiary structure

Answer 18

• Energetically favored conformation
• Folding of protein/peptide into a 3D conformation that remains flexible and dynamic
• Contains multiple domains or sections
• Stabilized by variety of bonds

Question 19

Tertiary structure bond types

Answer 19

• Ionic linkages
• Hydrogen bonds
• Hydrophobic interactions
• Van de Waa’ls forces

Question 20

Quaternary structure

Answer 20

• Spatial organization of of monomeric subunits

- Stabilized predominantly by hydrophobic interactions, hydrogen bonds, and Van der Waal’s forces

Question 21

Oligomeric proteins

Answer 21

• Multi subunit proteins
• Possess multiple interacting polypeptide chains
• Only types of proteins that possess a quaternary structure

Question 22

Hemoglobin

Answer 22

• Alpha 2 Beta 2 tetramer

- Quaternary structure stabilized by non-covalent interactions

Question 23

Thalassemias

Answer 23

• Insufficient amounts of subunits are produced

- Occurs as a consequence of gene deletion or defects during transcription/translation

Question 24

Protein denaturation

Answer 24

• Occurs with the disruption or dismantling of the active three dimensional protein configuration
• Most often happens with extreme heat
• pH and ionic strength that may dismantle the non-covalent interactions that stabilize the protein structure

Question 25

Primary structure review

Answer 25

• Linear sequence of amino acids connected by the peptide bonds
• Determines its functional three dimensional shape

Question 26

Edman degradation procedure review

Answer 26

• Can be used to determine the primary structure of a protein
• Specific cleavage of peptides into shorter fragments improves the reliability and usability of the technique

Question 27

Secondary structure review

Answer 27

• Local recurring arrangement of a protein
• Wide variety of structures has been identified
• Alpha helix and beta pleated sheet most familiar and important confirmations

Question 28

Tertiary structure review

Answer 28

• Spatial organization of amino acids that are far apart in the protein’s primary structure
• Stabilized by non-covalent interactions between the amino acid side chains

Question 29

Quaternary structure review

Answer 29

• Proteins that are composed of multiple subunits

- Interaction between side chains in separate polypeptide chains

Question 30

Denaturation review

Answer 30

• Reversible

- Occurs by extremes of pH, temperature, heavy metals, detergents, and organic solvents