Biochem Protein Lecture 6 Flashcards Preview

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Flashcards in Biochem Protein Lecture 6 Deck (65):

Protein ___ can be described as the spatial arrangement of atoms in a protein



These changes achieve spatial arrangements without breaking covalent bonds

Conformational changes


There are 100s of theoretical conformations possible. Do most of them predominate?

No, one or a few underbiological conditions predominate


A few stable conformations under a given set of conditions are necessary because some conformational changes must take place in proteins as they bind to other molecules

Those conformation which occur are the ones that are thermodynamically

Most stable (lows Gibbs free energy)


The actual resonance structure of peptide bonds is a hydrid of the two resonance forms. How much does the resonance stabilize the peptide bond?

The six atoms of the peptide group lie in a single plane with the O atom of the carbonyl group and the H atom of the amide N trans to each other

Are the peptide C-N bonds able to rotate freely? Why or why not?



Partial double bond character


Can rotation occur about N-Cα and Cα-C bonds?

Are cis and trans peptide bond formations possible?

What form are the peptides in proteins? Why?

What is the exception?

Yes (Look at diagrams)



There is less steric interference between the R groups of adjacent aa

X-Pro sequence, X can be any other aa and cis conformation is favored


These are proteins in a functional, folded conformation

The tendency to maintain this conformation is

Native Proteins



Is the native conformation of proteins very stable or slightly?

What stabilizes native conformation?

Slightly (20-65kJ/mole)

Disulfide bonds
Weak, noncovalent interactions (H-bonding, hydrophobic interactions and ionic interactions)


What range of energy is require to break a single covalent bond?

What range is required to disrupt weak interactions?

200-460 kJ/mol



If weak interactions are so much weaker than strong, why do they predominate at stabilizing structure?

Therefore, the protein with the lowest or highest G is the one with the greatest number of weak interactions?

There are many of them

Lowest G


When water surrounds a hydrophobic molecule, a highly structured cell of water forms called

Solvation layer


Entropy actually increases or decreases with a solvation layer? Why?


Hydrophobic groups cluster together and only part of their surface exposed to surface.?


_____ Interactions are very important in stabilizing protein conformations



When hydrophobic residues are buried in the protein interior away from water, what does that do to the number of H-bonds and ionic interactions within the protein?

Maximizes them


This bond also makes an important contribution to protein conformation

How many bonds separate the alpha carbons of adjactent aa residues in a protein?

Peptide Bond

3 covalent bonds


What did X-ray diffraction studies off aas, dipeptides and tripeptides reveal regarding bond length of C-N in each structure?

The C-N peptide bond is shorter than the C-N bond in a simple amine


Atoms associated with peptide bonds are



The bond angles of the alpha carbon atoms correspond to ____ hydrid orbitals



The 3σ bonds associated with each of the carbonyl C and N atoms involve ______ hybrid orbitals. The axes are planar, and the bond angles are ______ degrees


120 degrees


The C-N peptide bond distance is in between C-N single and double bonds.

Can partial C-N double bonds rotate?




Why is there a shorter bond in peptide bonds?

Due to resonance or partial sharing of 2 pairs of electrons between carbonyl oxygen and amide nitrogen.. A small dipole results


Be able to draw the hybrid of the two resonance forms of peptide bonds.

How much does the resonance stabilize the peptide bond in kcal/mol

The six atoms of the peptide group lie in a single plane with the atom of the carbonyl group and the H atom of the aminde N _____ to each other

Slide 10.

21 kcal/mole



Is rotation permitted about N-C alpha and C-C alpha bonds?

Yes. Even though the arrangement of atoms in the peptide bond is planar and rotation about the peptide bond is restricted, cis and trans peptide bond conformations are possible


The peptide in proteins is in the _____ form because there is less steric interference between the R groups of adjacent aa

What is the exception?


Proline, favors cis because of ring.


In terms of protein conformations, rotation about the single bonds to the ________ results in a range of protein conformation

Alpha carbon


Bond angles from rotation about the N-Cα are labeled _____ and for rotation about the Cα-C theyre___

Bond angles from rotation about the N-Cα are labeled φ (phi) and for rotation about the Cα-C they're labeled ψ (psi)


Study positive and negative rotation (slide 14)



Allowed values for ψ and φ are graphically shown in a

Ramachandran Plot


What do the darkly shaded areas of Ramachandran Plots reflect?

What about moderately shaded regions?

What about the lightly shaded regions?

What about the yellow regions?

Fully allowed conformations

Conformations allowed at the extreme limits for unfavorable atomic contacts

Permissible conformations if a little flexibility is allowed in the bond angles

Not allowed


This term refers to the local conformation of some part of a polypeptide

Common, regular folding patterns of polypetide backbones include

The simplest arrangement a polypeptide can assume it a

Secondary Structure

Alpha helix and Beta conformations

Helical Structure


If the Al ψ and φ angles are constant throuhghout a polypeptide chain, the polypeptide will have a

Helical shape

The given set of angles of ψ and φ determine the type of helix


What protrudes out from the helical backbone of polypetide helical structures?



For the α polypeptide helix the repeating unit is a single turn of the helix which extends ______ A along the long axis

Each helical turn is ____ aa residues

What are the aa residue conformations with φ and ψ?

Is it right or left handed?

5.4 A

3.6 residues

φ = - 60°

ψ = - 45 to - 50°

Right handed


What percent of all aa resiudes in polypeptides are α-helices?

What do internal (intrachain) H-bonds do to the α-helix?

Where are the H bonds in fig 4.4a?



H bonded to N of peptide linkage and carbonyl oxygen of fourth aa on the amino-terminal side chain of the peptide bond


With the α helix, every peptide bond except those close to the helix participates in

All H bonds combined impart lots of ___ to the helical structure

H-bonding (?)



Can the alpha helix form with both D and L amino acids at the same time?

Can the naturally occurring L -amino acids form right and left handed helices?

No, it must be all L or all D

Yes, they can form both


Which helix formed by L-amino acids is less stable and has not been observed in proteins?

Left handed


In defined helices, this is the distance parallel to axis in which the helix makes one turn

Pitch (p)


In defined helices, the distance parallel to the axis from one residue to the next is the

Rise (h)


In defined helices, the number of amino acid residues is



In defined helices, this is the distance parallel to the axis in which the structure directly repeats itself. It contains an integral (m) number of polymer residues


The number of polymer residues is m


Is the α-helix one of the idealized helices?

Why is it 3.6 residues per turn?

What is the rise of the α-helix?

What is the pitch?


It repeats after 18 residues, which amounts to 5 turns

1.5 A/resiude

p=nh, p=3.6*1.5 = 5.4 A


In the alpha helix, if we include the H bond, a loop of ___ atoms is formed



Polypeptide helices are described as nN helices where

this is the number of residues per turn

this is the number of atoms in the hydrogen bonded loop

So what are the values for the α helix?



n=3.6 N = 13


How much is each successive turn of the αhelix bonded to adjacent turns, resulting in significant structural stability?

3-4 H-bonds


What are the two other possible helical structures of polypeptide chains?

3(10) helix

π helix


This other helix is observed in some proteins, and is less common the α helix. It is right handed, and frequently found within α helical proteins

What is an example of an α helical protein it is found in?

3(10) helix



how many atoms are in the H loop of a 3(10) helix?

10 (duh)


Which other helix is not observed in proteins? It has 16 atoms in the H loop with 4.4 residues/turn

π helix


If a polypeptide had all of its residues in a particular secondary structure, like α helix, the points for all residues would

Many values of φ and ψ are prohibited by _____ between atoms in the polypeptide backbone and AA side chains


Steric interference


The AA residues in this helix have φ and ψ conformations of ψ = -45 to -50 and φ = -57 to -60

In contrast, this helix results from φ and ψ conformations of -49 and -26, respectively

α helix

3(10) helix


Ramachandran has calculated the distances between atoms in a ________ for all sets of φ and ψ angles. He wanted to determine which angles are sterically forbidden based on distances less than the sume of the van der Waals radii of the atoms

Tripeptide of L-ala


No two atoms should approach each other more closely than is allowed by their

van der Waals radii


You might have to know minimum contact distances between atoms and which angles are allowed. Ask the prof



Is the Ramachandran plot symmetric?

What does this mean?


left and right handed helical regions have different areas of stability


What is the fact that left and right handed helical regions have different areas of stability a consequence of?

All AAs are in the L form


Steric interference between the side chains and the backbone of the helix is less with a ___ handed helix

What could affect the allowed regions even more?

Right handed

Bulkier or less bulky (gly) AAs.


Are β-sheet structures of polypeptide chains found?



Not all polypeptides can form an α helix. What five things prevent it from occurring

1) A long block of glu residues

20 Many adjacent lys/arg residues

3) Asn, ser, thr, and cys residues that are close together

4) Pro and gly are part of the polypeptide chain

5) Identity of aa residues near the α helical segment


Why does A long block of glu residues prevent alpha helices?

There can be no alpha helix at pH 7 because of negative charges repelling one another


Why do many adjacent lys/arg residues prevent the formation of an alpha helix

There can be no alpha helix at pH 7 due to positive charges repelling one another


Why do Asn, ser, thr, and cys residues that are close together prevent the formation of an alpha helix

They are bulky and their shape


The twist of an alpha helix insures critical interactions between aa side chains _______ residues away from each other

3-4 residues away from each other


Why are pro and gly rarely found in alpha helices?

N is part of a rigid ring in pro, so rotation about N-C α bond is not possible, which introduces a kink in an α helix. There is also no H on N for H bonding

Gly has a lot of conformation flexibility resulting in coiled structure


Why can the identity of aa residues near the end of a polypeptide chain prevent the stability of an alpha helix?

A small dipole exists in each peptide bond. Net dipole increases with helix length. The four aa at each end of the helix do not participate fully in helix H bonds. Neg. charged aa found near the amino terminus (STABILIZE + CHARGE). Positively charged aa found near the carboxy terminus