Biochem Protein Lecture 6

Question 1

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

Answer 1

Conformation

Question 2

These changes achieve spatial arrangements without breaking covalent bonds

Answer 2

Conformational changes

Question 3

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

Answer 3

No, one or a few underbiological conditions predominate

Question 4

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

Answer 4

Most stable (lows Gibbs free energy)

Question 5

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?

Answer 5

21kcal//mol

No

Partial double bond character

Question 6

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?

Answer 6

Yes (Look at diagrams)

Yes

Trans

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

Question 7

These are proteins in a functional, folded conformation

The tendency to maintain this conformation is

Answer 7

Native Proteins

Stability

Question 8

Is the native conformation of proteins very stable or slightly?

What stabilizes native conformation?

Answer 8

Slightly (20-65kJ/mole)

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

Question 9

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

What range is required to disrupt weak interactions?

Answer 9

200-460 kJ/mol

4-30kJ/mol

Question 10

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?

Answer 10

There are many of them

Lowest G

Question 11

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

Answer 11

Solvation layer

Question 12

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

Answer 12

Increases

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

Question 13

_____ Interactions are very important in stabilizing protein conformations

Answer 13

Hydrophobic

Question 14

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?

Answer 14

Maximizes them

Question 15

This bond also makes an important contribution to protein conformation

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

Answer 15

Peptide Bond

3 covalent bonds

Question 16

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

Answer 16

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

Question 17

Atoms associated with peptide bonds are

Answer 17

Coplanar

Question 18

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

Answer 18

sp3

Question 19

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

Answer 19

sp2

120 degrees

Question 20

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

Can partial C-N double bonds rotate?

Answer 20

!

No.

Question 21

Why is there a shorter bond in peptide bonds?

Answer 21

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

Question 22

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

Answer 22

Slide 10.

21 kcal/mole

trans

Question 23

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

Answer 23

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

Question 24

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?

Answer 24

Trans

Proline, favors cis because of ring.

Question 25

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

Answer 25

Alpha carbon

Question 26

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

Answer 26

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

Question 27

Study positive and negative rotation (slide 14)

Answer 27

!

Question 28

Allowed values for ψ and φ are graphically shown in a

Answer 28

Ramachandran Plot

Question 29

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?

Answer 29

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

Question 30

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

Answer 30

Secondary Structure Alpha helix and Beta conformations Helical Structure

Question 31

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

Answer 31

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

Question 32

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

Answer 32

R-groups

Question 33

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?

Answer 33

5. 4 A 3. 6 residues φ = - 60° ψ = - 45 to - 50° Right handed

Question 34

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?

Answer 34

1/4 Stabilize H bonded to N of peptide linkage and carbonyl oxygen of fourth aa on the amino-terminal side chain of the peptide bond

Question 35

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

Answer 35

H-bonding (?) Stability

Question 36

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?

Answer 36

No, it must be all L or all D Yes, they can form both

Question 37

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

Answer 37

Left handed

Question 38

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

Answer 38

Pitch (p)

Question 39

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

Answer 39

Rise (h)

Question 40

In defined helices, the number of amino acid residues is

Answer 40

n

Question 41

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

Answer 41

Repeat The number of polymer residues is m

Question 42

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?

Answer 42

No. It repeats after 18 residues, which amounts to 5 turns 1.5 A/resiude p=nh, p=3.6*1.5 = 5.4 A

Question 43

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

Answer 43

13

Question 44

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?

Answer 44

n N n=3.6 N = 13

Question 45

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

Answer 45

3-4 H-bonds

Question 46

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

Answer 46

3(10) helix π helix

Question 47

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?

Answer 47

3(10) helix myoglobin

Question 48

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

Answer 48

10 (duh)

Question 49

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

Answer 49

π helix

Question 50

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

Answer 50

Superimpose Steric interference

Question 51

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

Answer 51

α helix 3(10) helix

Question 52

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

Answer 52

Tripeptide of L-ala

Question 53

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

Answer 53

van der Waals radii

Question 54

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

Answer 54

!

Question 55

Is the Ramachandran plot symmetric? What does this mean?

Answer 55

No left and right handed helical regions have different areas of stability

Question 56

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

Answer 56

All AAs are in the L form

Question 57

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?

Answer 57

Right handed Bulkier or less bulky (gly) AAs.

Question 58

Are β-sheet structures of polypeptide chains found?

Answer 58

Yes

Question 59

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

Answer 59

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

Question 60

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

Answer 60

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

Question 61

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

Answer 61

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

Question 62

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

Answer 62

They are bulky and their shape

Question 63

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

Answer 63

3-4 residues away from each other

Question 64

Why are pro and gly rarely found in alpha helices?

Answer 64

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

Question 65

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

Answer 65

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