Levels of Protein Structure

Briefly describe each level of protein structure and what interactions hold them together

• primary - sequence of amino acids; covalent peptide bonds between amino acids

• secondary - areas of contigous local structure; hydrogen bonds between H of amine and Oyxgen of carbonyl

• tertiary - overall 3D shape, noncontinugous sections arranged; hydrophobic affect, sometimes ionic or disulfide

• quaternary - multiple polypeptide chains coming together

Describe primary strucutre, inlcuding:

• what changes happen to the atoms

• how the esequnece is written

• and how the partial double-bond character of peptide affects orientation

• lose H on OH of carboxylic acid on first amino acid and lose H of amine as N joins with the carbonyl

• written N terminus to C terminus

• partial double bond character of peptide

What direction do amino acid chains run?

N terminus to C terminus

What is the partial double-bond character of a peptide bond and what does it cause?

• resonance form of amide created in peptide bond

• partial double bond limits rotation on the Nitrogen to only the Hydrogen and R groups

• creates a more planar molecule

Describe secondary structure, including:

• what they are

• what interactions hold them together

• types and their general info

• H bonds between contiguous amino acids

• maintained by Hydrogen bonds

• alpha helix - coil or spring; right handed helix with side chains facing outward

• beta sheets - extended structure with 2 strands, backbone in same place and side chains alteranting between above or below plane

• beta turns - 4 amino acids long, change direction of polypeptide chain by 180 degrees, often between beta sheets

Describe alpha helixes, including their hydrogen bonding, left/right handedness, and common amino acids

• most stable secondary structure

• each peptide involved in 2 hydrogen bonds (increases stability), neutralizes polarity in each bond and occurs only on backbone

• hydrogen bond between adjacent NH (h donor) and carbonyl (H acceptor) of each peptide bond on backbone

• coil or spring shaped

• Right handed helix (coils to the right)

• side chains face outwards

• Prole (unflexible) is a helix breaker at end of alpha helix; glycine sometimes

Describe hydrogen bonding on alpha helixes

• 2 hydrogen bonds on each amino acid

• H bond between NH (h donor) and carbonyl (H acceptor) of adjacent amino acids

• neutralizes polarity of protein core

• h-bonding occurs ONLY on backbone

Describe beta sheets, including their structure, hydrogen bonding, orientation, common uses, and types

• extended structure with wide space per aa

• 2 stranded, held together by Hydrogen bond between the backbone NH (h donor) and carbonyl (H acceptor) of other strand

• both strands of backboen in same plane, side chains alternate betwen above and below the plane

• can form a “barrel” for a pore for ions to pass through; requires a nonpolar and polar side side of molecule (done by alternating Polar and nonpolar amino acids in sequence)

• antiparallel, parallel, and mixed

Describe the types of beta sheets

• antiparallel - run N to C, then C to N, etc. ; stronger hydrogen bonds

• parallel - run N to C, go back to do some other stuff, N to C, etc. Weaker h bonds

• mixed - parallel and antiparallel; run N to C, C to N, go back to do some stuff, C to N, etc.

Describe beta turns, inclduing their length, hydrogen bonds, uses, and common amino acids

• 4 amino acids long

• Hydrogen bonds between carbonyl of amino acid and NH of next amino acid on backbone

• change direction of polypeptide chain by 180, often between beta sheets

• often have proline (naturally has a turn) and glycine (conformationally flexible)

Briefly describe tertiary structure, including what it is, what interactions drive it, and how its organized

• overall folding/3D shape

• driven by hydrophobic effect

• organizes so nonpolar side chains are inside and polar side chains are outside to reduce interactions with H2O and increase entropy

What is the most stable secondary protein structure?

alpha helix

In primary protein structure, what isomer of the partial double bond at the amide is more stable?

trans isomer (R group and amino acid opposite)