BCHM-3050 Lecture Notes - Lecture 7: Hydroxylysine, Collagen, Globular Protein

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26 Jun 2018

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Chapter 6: 3D Structure of Proteins

4 Levels of Protein Structure

Primary Structure: amino acid (polypeptide) sequence that makes up the protein. Is the direct end result

of mRNA translation. Only the peptide bond is present between individual amino acid monomers.

oThe other 2 bonds on the main chain of the polypeptide will have rotational capabilities, but the

other bond between the carbonyl group does not have rotation.

o6 atoms are fixed – free rotation is allowed only about the Carbon atom only.

oNitrogen to Carbon = phi

oCarbonyl Carbon and Nitrogen = peptide bond

Secondary Structure: local areas of the REPEATING main chain structure. There are hydrogen bonds,

and have formed local regions of patterned sub-structures (helixes/sheets).

oBond Angles & Bond Lengths – amide groups must remain planar, and no 2 atoms should

approach more closer than any intermolecular force allows. Noncovalent bonds (hydrogen

bonds) help to stabilize 3D structure.

oIncreases in atomic radii lead to an increase in H+ bond distances

Tertiary Structure: overall 3D arrangement or interactions between the secondary structural elements in

a polypeptide chain.

oHydrophobic amino acids move to the interior of the structure, and hydrophilic amino acids are

towards the exterior.

oCofactors – non protein elements that are part of the structure, and require the 3D shape to hold

them there.

Quartnary Structure: spatial arrangement and non-covalent reactions of multiple polypeptide chains to

form a multi-subunit complex. You need 2+ polypeptide chains.

oVery similar to tertiary, but just has more polypeptide chains.

Secondary Structures in Proteins

Alpha Helix: side chains radiate OUT from the helix axis, and the H+ bonds are nearly parallel to the

axis.

oAmphiphilic – have both hydrophilic and hydrophobic faces

oCould be completey hydrophobic

Beta Pleated Sheets: stabilized by side chain H+ bonds and alternate sides of the sheet. Can be parallel

or anti-parallel based on the polypeptide alignment of the N & C termini.

310 Helix: meets Pualin criteria, but not freuqnetly found. Had 2’ helices.

Parameters:

oResidues per Turns

oRise

oPitch

Steric Interactions

Phi and Psi angles cause steric clashes, where atoms are closer than their Van der Waals radii, and these

conformations are NOT ALLOWED. They are made from the Cis form.

Ramachandran Plot: shows sterically allowed phi and psi angles. The size of the side chain; bigger the

side chain, less room to move around.

Side Chains in Beta Sheets

Side chains are located on opposite faces, and are stabilized by main-chain hydrogen bonds between

adjacent B-strands.

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Document Summary

Primary structure: amino acid (polypeptide) sequence that makes up the protein. Is the direct end result of mrna translation. Secondary structure: local areas of the repeating main chain structure. There are hydrogen bonds, and have formed local regions of patterned sub-structures (helixes/sheets): bond angles & bond lengths amide groups must remain planar, and no 2 atoms should approach more closer than any intermolecular force allows. Noncovalent bonds (hydrogen bonds) help to stabilize 3d structure: increases in atomic radii lead to an increase in h+ bond distances. Quartnary structure: spatial arrangement and non-covalent reactions of multiple polypeptide chains to form a multi-subunit complex. You need 2+ polypeptide chains: very similar to tertiary, but just has more polypeptide chains. Alpha helix: side chains radiate out from the helix axis, and the h+ bonds are nearly parallel to the axis: amphiphilic have both hydrophilic and hydrophobic faces, could be completey hydrophobic.

Related Questions

1. A sequence of amino acids in a certain protein is found to be â Ser â Gly â Pro â Gly â

The sequence is most probably part of a(n):

a. beta turn

b. antiparallel beta sheet

c. alpha-helix

d. parallel beta-sheet

e. alapha-sheet

2. Which statement about peptides bonds is NOT TRUE?

There is perfectly free rotation about the peptide bond.

The peptide bond has partial double-bond character.

The peptide bond is shorter than a normal carbon-nitrogen single bond.

The peptide bond usually has a trans configuration with respect to the alpha-carbons of the two amino acids involved in the peptide bond.

Peptide bonds are made via condensation of an amine and a carboxylic acid with loss of water.

3. Which of the following statements about proteins is FALSE?

	Active proteins are generally very loosely structured.
	In water-soluble proteins, hydrophobic amino acid residues are generally buried and not exposed to water.
	Primary structure determines tertiary structure.
	Secondary structure is regular, recurring arrangements in space of nearby amino acid residues in a polypeptide.
	Quaternary structure involves the interaction of subunits in a protein with more than one polypeptide chain.

maroonwallaby335

a)If you have 14 amino acids in a polypeptide chain, how manypeptide bonds are there in the polypeptide chain?

b) T/F R groups affect peptide bond formation.

c)What is unique about the peptide bond and how does thischaracteristic affect the length of the bond?

d)What are the 3 Greek torsion angles and between what atoms arethey located?

e)What is the dominant peptide bond conformation and why is thisso? What amino acid exhibits the other conformation?

e)If you have 10 different amino acids and want to make apolypeptide chain of 6 amino acids, how many theoreticalcombinations of amino acids could you make?

f)If the molecular weight of a protein is 2000 Da, how many aminoacids are in the protein?

1. The level of protein structure that is stabilized primarilyby non-covalent interactions between the side chains within asingle polypeptide chain is refered to as its:

A) primary structure

B) secondary structure

C) tertiary structure

D) quaternary structure

E) none of the above

2. Collagen, a strong fibrous protein found in connectivetissue, bone, and the extracellular matrix, has a structure inwhich three left-handed helices wind around each other to form aright-handed triple helix. The primary structure of collagen has arepeat unit of -(Gly-X-Pro)- Which of the following bonds stabilizethe collagen triple helix? (mark all that apply)

A) Hydrogen bonds between hydroxyproline residues

B) Hydrogen bonds between N-H and C=O

C) Ionic bonds between amino acid side chains

D) Hydrogen bonds between charged amino acids

3. The non-covalent forces that stabilize the Beta-strandconformation of peptides include:

A) H-bonds between amide C=O and amide NH

B) Van der Waals packing between the peptide backbone atoms

C) Van der Waals packing due to side chain interdigitation

D) Only A and B above

E) None of the above

4. What is the approximate length difference of a 22-kDasingle-stranded ?-helical protein segment vs. a 22-kDasingle-stranded ?-strand protein segment? Assume a mean residuemass of 110 Da. Show work.

5. Circular dichroism measurements have shown that the peptidebackbone of poly-l-lysine (KKKKKKK) adopts a random coilconformation at pH 7.0, but becomes ?-helical as the pH is raisedabove 10. This observation is known as the

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BCHM-3050 Lecture Notes - Lecture 7: Hydroxylysine, Collagen, Globular Protein

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