Lecture 5: Protein Structure and Function

Question 1

Amino acids and structure

Answer 1

• Amino acids have distinct side chains that contribute to a protein structure
• Linear chains of amino acids fold to form 3D chains

Question 2

Levels of protein structure

Answer 2

• Primary: Linear sequence of amino acids encoded by DNA(peptide bonds)
• Secondary: Periodic regular structures(alpha-helix, beta-strands, beta-turns)(hydrogen bonds)
• Tertiary: Secondary structures folded into motifs and domains
• Quaternary: Assembly of distinct polypeptides into multi-subunit structures

Question 3

Themes of protein structure

Answer 3

• Must be flexible enough to function properly
• Stable enough to not convert to another conformation
• Exposed amino acids must be compatible with environments where protein functions

Question 4

Peptide bond

Answer 4

• Condensation reaction: Condenses two molecules into one releasing an H2O molecule
• Release H2O to form bond between carboxyl carbon and amine nitrogen
• Polar, uncharged bonds
• Experience resonance, providing characteristics of a double bond
• Rigid and planar

Question 5

Primary structure

Answer 5

• Amino acids are joined in a condensation reaction
• Chain has directionality: amino terminal end is beginning of polypeptide chain
• Backbone consists of peptide bonds and alpha carbons of each amino acid

Question 7

Alpha helices

Answer 7

• Intra-strand hydrogen bonds form between peptide backbone
• C=O group from one amino acid residue forms a hydrogen bond with the N-H group 4 residues away
• 3.6 residues per 360 turn
• Right sided helix with side chains pointing out

Question 8

Proline

Answer 8

• The only amino acid not normally present in an alpha helix is proline
• Proline is very rigid and doesnt allow for proper phi and psi angle to form
• No hydrogen present on nitrogen of the peptide bond to form a hydrogen bond

Question 9

Beta strands and sheets

Answer 9

• Hydrogen bonding links nearby or distant portions of the polypeptide to beta strands to form beta-sheets
• Hydrogen bonding occurs between the carbonyls and amines in the peptide backbone
• Strands can run parallel or antiparallel

Question 10

Beta turns

Answer 10

• 4 residue segment that allows the peptide chain to turn 180
• Found on surface of globular proteins, connecting secondary structures
• Hydrogen bonds form between carbonyl oxygen and amine hydrogen
• Pro is common at position 2
• Gly, Asn, and Ser are frequently seen in turns

Question 11

Tertiary structures

Answer 11

• Secondary structures come together to form stable 3D tertiary structures
• Non-covalent interactions bring regions together to form distinct structures within a protein
• Electrostatic interactions
• Hydrogen bonds
• Hydrophobic interactions(grouping of non-polar amino acids)
• Disulfide bonds can stabilize both tertiary and quarternary structures

Question 12

Protein folding

Answer 12

• Secondary structures form due to favorable hydrogen bonding
• Non-covalent interactions and disulfide bonds play role in tertiary and quarternary structure
• Hydrophobic effect is primary diriving force in protein folding

Question 13

Quarternary structure

Answer 13

• Involves arrangement of multiple subunits of distinct polypeptide chains
• Multi-subunit proteins may consist of identical or non-identical polypeptides held covalently or non-covalently
• Larger macromolecular structures can form due to interactions between polypeptide chains

Question 14

Post-Translational Modifications

Answer 14

• Modify amino acids within a protein
• Alter interactions between amino acid and change tertiary/quarternary structure

Question 15

Protein Degradation

Answer 15

• Protein strucure is held together by numerous weak forces
• Denaturation is disruption of forces by external stresses
• Results in loss of structure and function