focus chapter 4 (protein structure)

Question 1

A peptide bond is a special type of amide bond formed by

Answer 1

condensation of the amino and carboxylic acid groups of neighboring amino acids.

Question 2

Water is released in the process of

Answer 2

forming the peptide bond

Question 3

peptide backbone

Answer 3

NCCNCCNCC

Question 4

The peptide backbone has hydrogen-bonding potential because of

Answer 4

the carbonyl groups and hydrogen atoms that are bonded to the nitrogen of the amine group

Question 5

Most proteins consist of

Answer 5

50 to 2000 amino acids

Question 6

Polypeptide chains are flexible yet

Answer 6

conformationally restricted

Question 7

The peptide bond is essentially

Answer 7

planar

Question 8

The peptide bond has partial double-bond character because

Answer 8

of resonance, and thus rotation about the bond is prohibited

Question 9

is the peptide bond charged or uncharged

Answer 9

uncharged

Question 10

Due to conformational restrictions, the two a-carbon atoms are in

Answer 10

trans

Question 11

Name the four levels of protein structure and describe the structural attributes of each level

Answer 11

primary, secondary, tertiary, quarternary

Question 12

Primary protein structure

Answer 12

 Linear Amino acid sequence
 Connected by peptide bonds
 Genes specify the unique amino acid sequence of proteins

Question 13

Secondary protein structure

Answer 13

 Folding into repeating pattern, A helix and b sheet, by hydrogen bonding
 Local structure of the polypeptide chain formed by hydrogen bonds between the carbonyl oxygen and amide hydrogen atoms in the polypeptide chain

Question 14

Tertiary protein structure

Answer 14

3D folding pattern and biologically active conformation of a protein due to side chain interactions

Question 15

The formation of compact, globular structures is governed by

Answer 15

the constituent amino acid residues

Question 16

Folding of a polypeptide chain is strongly influenced by

Answer 16

the solubility of the amino acid R-groups in water

Question 17

Hydrophobic R-groups orient

Answer 17

inwardly, away from water or polar solutes

Question 18

Polar or ionized R-groups

Answer 18

orient outwardly to contact the aqueous environment

Question 19

Forces stabilizing protein tertiary structure

Answer 19

• Hydrophobic interactions: the tendency of nonpolar groups to cluster together to exclude water (most important)
• Hydrogen bonding
• Ionic interactions: attraction between unlike electric charges of ionized R-groups
• Disulfide bridges between cysteine residues, leading to a cystine. The -SH (sulfhydryl) groups can oxidize spontaneously to form disulfides (-S-S-).

Question 20

Quaternary protein structure

Answer 20

 Interaction between different chains
 an assembly of two or more separate polypeptide chains that are held together by noncovalent interactions.
 the individual subunits alone are generally biologically inactive.
 stabilized by the same forces as tertiary structure

Question 21

two main types of protein secondary structure

Answer 21

beta sheet and alpha helix

Question 22

A-helix

Answer 22

 A coiled structure stabilized by intrachain hydrogen bonds
 R groups of the amino acids face outside the helix
 Hydrogen bonds occur between the carbonyl (C=O) of one amino acid and the amide hydrogen (NH) of another amino acid 4 residues away.
 all NH and CO groups are joined with H bonds except the first NH group and last CO groups at end of helix

Question 23

B-sheet

Answer 23

 composed of secondary structure elements that are distant from each other with respect to the protein’s amino acid sequence
 The b strands are located next to each other
 Hydrogen bonds can form between CO groups of one strand and NH groups of an adjacent strand

Question 24

Antiparallel b-sheet

Answer 24

Narrowly spaced hydrogen bond pairs that alternate between widely spaced pairs

Question 25

Parallel b-sheet

Answer 25

Evenly spaced hydrogen bonds that bridge at an angle

Question 26

B-turns and loops

Answer 26

Play an important role in the 3D structure of proteins, connecting together b-strands, b-strands to a-helices, or b-strands or a-helices to each other

Question 27

beta turns

Answer 27

o Position 2 typically proline
o Position 3 most often asparagine, glycine, arginine
o Hydrogen bond between the carbonyl of the amino acid in position #1 and the amino group of the amino acid in position #4

Question 28

beta loops

Answer 28

Variable amino acid sequence. Sequence may be conserved if a loop has some specific function.

Question 29

Secondary structures stabilized by

Answer 29

hydrogen bonding

Question 30

Tertiary and quaternary structures stabilized by

Answer 30

 Hydrophobic interactions
 Hydrogen bonding
 Ionic interactions
 Disulfide bridges