9- Protein structure I

Question 1

what is the primary structure of a protein?

Answer 1

• sequence of amino acids in a protein
• a gene is a list of AA used to form a protein
• sequence of amino acid in gene is the same as final protein that is formed

Question 2

how do you read a primary sequence in a protein?

Answer 2

from the N-terminus to C-terminus

Question 3

what are 4 different types of secondary structure

Answer 3

• alpha helix
• beta sheet
• loop
• turn

Question 4

what determines the secondary structure?

Answer 4

the sequence of AA determine the secondary structure

Question 5

what are three things that influence the origin of the secondary structure?

Answer 5

• conformation restrictions between amide and alpha carbon
• interactions between amide bonds
• side chain interactions within a region of the chain

Question 6

why do amide bonds have double bond character?

Answer 6

between the carbon and nitrogen of the amide, a resonance hybrid can be formed. and both of these forms are major contributors, there is a higher deree of sp2 character for both C and N- therefore system behaves this way

Question 7

what is s-cis and s-trans conformations?

Answer 7

• s-cis is when two large groups are close together on same side (raises steric interference which raises energy of the conformation)
• opposite for s-trans (trans conformation is more stable)
• s stands for sigma

Question 8

describe the two spots that are rotatable in the backbone C-C bonds

Answer 8

1. alpha carbon and nitrogen of the AA in a peptide chain (left side phi) its a dihedral angle, can be conformed two different ways
2. connecting alpha carbon to the carbon of the amide bond (right side, sigh) its a dihedral angle, two different conformations

Question 9

why are large scale structures formed?

Answer 9

because of the side chain interactions

• negative charges attract positive charges
• hydrogen bonding between side chains and backbones
• non polar side chains interact with other non polar chains- sterics (phi and sigh main component is sterics)

Question 10

describe the alpha helix form

Answer 10

• alpha helical backbone
• hydrogen bonding between peptide bonds
• side chains hold it together, projecting out- sterics of these groups helps influence formation of alpha helix
• stabilizing- hydrogen bonding and hold backbone ribbon

Question 11

what does the ribbon diagram for alpha helixes look like?

Answer 11

flat chain of amide bond is the flat ribbon structure, formed in cylindrical shape
- point part is at top (C-terminus), square part at bottom (N-terminus)

Question 12

describe the beta structure forms

Answer 12

• beta strands -> backbone atoms are coplanar and flat
• several beta strands together= beta sheet
• large sheets curling around self= beta barrel
• they are s-trans
• rigid structures that can form bigger things

Question 13

explain the parallel and antiparallness of beta sheets

Answer 13

parallel: N -> C and N -> C for both strands that are attached by H bonds
antiparallel: N -> C and C

Question 14

describe the ribbon diagrams for beta structures

Answer 14

arrow at top (N), square bottom (C), yellow strands side by side or shown in barrel form (cylinder)

Question 15

what are loops

Answer 15

• areas with no defined secondary structure

- represented by spaghetti on ribbon diagrams

Question 16

what are turns

Answer 16

• several types
• may not be explicitly represented on ribbon diagrams
• look for areas where the chain changes direction by a large amount