secondary structure of proteins

Question 1

secondary protein structure

Answer 1

regular repetitive patterns in short sections of the polypeptide chain

Question 2

polypeptide chain backbone

Answer 2

linked by C-C and C-H single bonds which are flexible due to bond rotation

Question 3

Chain flexibility

Answer 3

• arises from bond rotation not bond bending
• single bonds allow for rotation about bond axis
  -normal 109 and 12- degree bond angles are present

Question 4

conformations

Answer 4

state of molecule that can be interconverted by bond rotations without breaking covalent bonds
(different shapes of polypeptide chain)

Question 5

configurations

Answer 5

can be interchanged by breaking covalent bonds, not by bond rotation
(cis and trans forms of a molecule)

Question 6

X-ray diffraction

Answer 6

• measures repeating patterns on molecular scale
• measured in angstrom units
  1 Å= 1x10^-10 meter

Question 7

resonance forms of the peptide bond

Answer 7

one with a C-N single bond and one with a C=N double bond
- peptide bond is rigid fixing in trans-geometry because it behaves more like a double bond than a single bond

Question 8

rigid planes

Answer 8

alpha amino and carboxylate are locked in rigid planar peptide bonds and only 2 bonds to alpha carbon can rotate freely

Question 9

restricted bond rotation

Answer 9

limits freedom of motion so only limited structures can form - 2 possible repeating patterns
1. helical shape - every alpha-carbon turns the same direction
2. extended shape - the alpha carbon turn in alternating directions

Question 10

the alpha helix

Answer 10

forms when amino acids all have the same orientation and alpha-carbons turn same direction

Question 11

the beta sheet

Answer 11

strands in the same direction make parallel b-sheet
- H-bonds connect strand to strand
strands in opposite directions make antiparallel b-sheet
- H-bonds align better in antiparallel mode

Question 12

amino acids preferring beta configurations

Answer 12

W,Y,F,V,I,T,C
- these AAs are either large, have a branch or large S atom

Question 13

amino acids preferring alpha configurations

Answer 13

M,F,L,K,H,A,R,E,Q
- this is the default behaviour of amino acids

Question 14

what determines secondary structure form

Answer 14

local majority of amino acids that prefer alpha or beta

Question 15

secondary structure breakers

Answer 15

G,P,N,D,S
- disrupts secondary structure by forming a turn or loop allowing polypeptide chain to change direction up to 180 degrees
- 2 breakers in a group of 4 amino acids interrupts the secondary structure