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Molecular Biophysics Test 2
A set of Molecular Biophysics for test 2 for Dr. Kathy Schegg
38
Biochemistry
Undergraduate 4
02/25/2015

Additional Biochemistry Flashcards

 


 

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Term
Secondary Structure
Definition

 

The secondary structure of a protein is the local conformation of its backbone.


 

To understand secondary structure, one must first consider the nature of the peptide bond.

 

 

Term
Character of the Peptide Bond
Definition

the peptide bond has a rigid, planar structure.

The rigid, planar structure is a consequence of the resonance interactions that give the peptide bond ~40% double bond character.


Term

 

Peptide bonds – trans vs cis

 

Definition

 

The 2 amino acids that make up the peptide bond are almost always trans to each other; that is, successive α C’s ( and R groups) are on opposite sides of the peptide bond connecting them.


A planar, fully extended all-trans conformation would appear to be optimum for proteins to minimize steric interactions.

 

Term

 

Trans and Cis conformations of Proline

 

Definition

 

A few peptide bonds will have a cis configuration, especially when the peptide bond is followed by a  Pro.

 

Term
Torsion Angles
Definition

 

 the bonds on either side of the peptide bond are regular single bonds and they are capable of twisting.

These 2 bonds are known as:

 

 

 

C α – C bond - 

 

psi torsion angle (ψ)

 

 

 

N - C α bond –

 

phi torsion angle (φ)

 

 

Term

 

Rotation Nomenclature

 

Definition

psi and phi angles are defined as +180° when the polypeptide chain is in its planar, fully extended all-trans conformation and all peptide groups are in the same plane.

If psi or phi angles rotate clockwise, there is an increase in their ψ or φ values.
If psi or phi angles rotate counterclockwise, there is an decrease  in their ψ or φ values.

 

Term
Role of Steric Interference
Definition

 

However, only certain combinations of ψ and φ will work because other combinations produce steric interference.

 

Term
Ramachandran Plots
Definition
The plot shows ψ and φ angles and the combinations of these angles that will not cause groups to invade each other’s van der Waals space
Term
Main Types of Secondary Structure
Definition

 

Regular    

 

  A regular structure occurs when ψ and φ angles remain the same or nearly the same throughout the segment.

 

Nonrepetitive

 

  A nonrepetitive structure has varying ψ and φ angles

 

Term
Characteristics of Secondary Structure
Definition

 

Secondary structures elements are rarely associated with specific functions

 

Term
Most Common Regular Structure: Helices
Definition
a polypeptide chain is twisted by the same amount about each of its αC atoms, it assumes a helical conformation
Term
p (pitch)
Definition

 

distance the helix rises per turn

 

Term
n (number)
Definition

number of amino acids per helical turn

 

Positive n – right-handed helix

Negative n – left-handed helix 

Term
Properties of Probable Helices
Definition

 

must be allowed on the Ramachandran plot

 

must allow for maximum bonding interactions

 

must allow for H bonding between the

 

  –NH of a backbone amino acid and the C=O of another amino acid. 

 

Term
The α – Helix
Definition

 

The α-helix is the only helical polypeptide conformation which has both:

 

  an allowed conformation 

 

  a favorable H bonding pattern

 

Term
α-Helix for L-amino acids
Definition

 

 

Most common type of secondary structure.  Is found in both globular and fibrous proteins.

Characteristics:

  Is right-handed

  ψ  = - 47°, φ  =  - 57° (note: angles are both negative, so peptide chain continuously circles)

  n  =  3.6 residues per turn

  p  =  5.4 Å

Each –C=O hydrogen bonds to the –NH four amino acids away.

 

 

 

Term
R Groups of Alpha Helicies
Definition

 

R groups all project out and backwards, perpendicular to the helix axis, at 100° intervals.

 

Term
Properties of an average α-helix
Definition

 

Inglobular proteins, the average stretch of α-helix has:

 

  ~12 residues

 

  3 helical turns

 

  length of 18Å

In actual proteins, and ψ and φ angles may deviate slightly from the theoretical values.  This produces important subtle bends and kinks.

 

 

Term
Propensity of amino acids to be part of an α-helix
Definition

 

Depends on the R group:

 

  Ala – greatest tendency

 

  Leu, Lys, Met – strong helical formers

 

  Ile, Gln, Glu– pretty good

 

    Asn, Ser, Thr, Cys  -  bulk and shape   destabilize α-helix – too much crowding

 

  Gly and Pro – the worst

 

Term
Location of α- helices
Definition

 

α-helices are found within protein structures, often buried within the protein.

They are common in the lipid bilayers of membranes. 

 

Approximately 20 amino acids in an α-helix formation are needed to span a membrane.

 

 

Term
α-Helix for D-amino acids
Definition

 

All properties are opposite from the α-helix with L-amino acids:

 

  Left-handed 

 

  ψ  = + 57°  φ  =  + 47°

 

  n  =  - 3.6 residues per turn

 

  p  =  5.4 Å

 

Is very rare since D-amino acids are very rare.

 

Term
Left-handed α-helix with L-amino acids
Definition

 

Left-handed α-helices are occasionally seen in proteins. 

 

Term
Stability of an α-helix depends on
Definition

 

a.Intrinsic propensity of amino acids to form an α-helix

 

b.Interactions between R groups

 

c.Bulkiness of R groups

 

d.Occurrence of Pro and Gly

 

e.Interactions of groups at C- and N-termini of helix

 

Term
Nomenclature for helices
Definition

 

nm helices:

 

n  =  number of residues / turn

 

m  =  number of atoms, including H, in the ring that is closed by the H bond

 

An α-helix is 3.613

 

Term
 2.27 Ribbon
Definition

 

Right-handed

 

n  =  2.2 residues per turn

 

Φ and ψ combinations are forbidden in the Ramachandran plot. Has strongly forbidden conformation angles.

Has never beenobserved

Term
310 Helices
Definition

 

Right-handed

 

n  =  3.0 residues per turn

 

p  =  6.0 Å  (thinner than α-helix; rises steeply)

 

R groups are not well staggered and experience some interference

 

Only occasionally observed in proteins.

 

Most 310 helices often occur as a single-turn transition at one end of an α-helix. 

 

Term
Polyproline Helix
Definition

 

There is no H on the Nof the peptide bond. (No H bonding occurs.)

 

The cyclic pyrrolidone side chains cause conformational constraints.

 

Polyproline I is an all cis right-handed conformation.  It is very compact.

 

Polyproline II is an all trans, left-handed conformation.  It is very extended and much more favorable.

 

Ψ = 150°

 

Φ = -79°

 

Term
All Trans Polyproline Helix
Definition

 

Left-handed

 

  n  =  -3.0 residues per turn

 

  p  =  9.4 Å

 

The pitch is very large.  The extended conformation permits Pro side chains to avoid each other. 

 

Term
Polyglycine Helix
Definition

 

Since glycine has no side chain, polyglycinecan assume ψ, φ angle combinations that no other polypeptide can tolerate. 

 

The helix can be either right-handed or left-handed.  

 

The type II helix is trans, n = 3,

 

  p = 9 Å

 

Term
Where are the helices on the Ramachandran Plot?
Definition

 

α = α helix

 

αL = left-handed α helix

 

3 = 310 helix

 

2 = 2.27 ribbon

 

π = π helix

 

II = left-handed polyglycine II and polyproline II helices

 

Term
β Structures
Definition

 

The ψ  and φ angle combinations in β structures are in an allowed region of the Ramachandran plot.

  They also fully utilize the H binding capacity of the –NH and O of peptide bonds

H bonding is not within the immediate chain

 

Each individual segment of the polypeptide chain is referred to as a β strand.

 β strands H bonded to one another to form βsheets

itself, but between neighboring polypeptide chains (H bonds are perpendicular to helical axis).

 

Term
Two Types of β-Pleated Sheets
Definition

 

Antiparallel

 

Neighboring H bonded chains run in opposite directions

 

Carbonyl oxygens and amine groups are optimally aligned

Parallel

Neighboring H bonded chains extend in the same direction.

 

Parallel and antiparallel strands can be mixed within a sheet.

 

 

Term
Characteristics of polypeptide strands in β-pleated sheets
Definition

 

 

Parallel: ψ  =  113°  φ  =  -119°

 

Antiparallel: ψ  =  135°  φ  =  -139°

Two residue distance is 7.0 Å (antiparallel) and 6.5 Å (parallel).

Amino acids are in trans configuration

 

 

 

 

Term
Where are β Sheets on the Ramachandran Plot?
Definition

 

↑↓    Antiparallel β sheets

 

↑↑   Parallel β sheets

 

Term
 Display of β strands
Definition

 

 

In 3-D structures of proteins, each β strand is shown as a ribbon with an point.

 

 The arrow points from N-terminus to C-terminus.

 

For parallel sheets, arrows point in the same direction.  For antiparallel strands, arrows point in opposite directions.

 

 

 

Term
Display of β strands and α helices
Bovine carboxypeptidase A
Definition

 

β-pleated sheets in globular proteins usually have a right-handed helical twist.

 

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