Biochem Protein Lecture 7 Flashcards
The major proteins of hair and wool
α-keratins
Molecules are constructed primarily from
α-helices
X-ray diffraction studies of proteins were conducted by William Astbury in the 1930s, what did he demonstrate about α-keratins?
What did Pauling and Corey use this information and their data on the peptide bond to determine?
It has a regular structure that repeats every 5.15 to 5.2 A
Conformations of protein molecules
The α-keratins are part of a broader family of proteins called
Are they right or left handed?
Intermediate filament proteins
Right
Pauling and Corey preidcted a second type of repetitive structure called ___, its a more extended conformation of polypeptide chains
β-Conformation
In the β conformation, the backbone of the polypeptide chain is extended into a
The chains can be arranged side to side to form a series of pleats, this arrangement is called a
Zigzag structure
β-sheet
How are the H bonds different in beta sheets?
The H-bonds are formed between adjacent segments in the polypeptide chain
The adjacent polypeptide chains can be either parallel or anti parallel
This means the same amino to carboxyl terminal orientations
This means opposite amino to carboxyl orientations
Parallel
Antiparallel
In the Beta-sheet, the H bond are approximately ____ to th elong axis of the polypeptide chains
Perpendicular
The parallel/antiparallel beta sheets are similar but with some differences.
The repeat period period is shorter for which one?
What else is different?
Parallel repeat period (6.5A) is shorter than antiparallel (7A)
H-bonding patterns
The individual segments of a polypeptide chain that form a beta sheet are usually nearby on a polypeptide chain
Can they be distant?
Can they come on different polypeptide chains
Yes, folding
Yes.
What are the φ and ψ conformations for the parallel beta sheet?
φ = -119 and ψ =113
What are the φ and ψ conformations for the antiparallel beta sheet?
φ = -139 and ψ =135
When two or more beta sheets are closely layered together within a protein, the R groups of those aa residues on the interacting surfaces must be large or small?
The content of which two AAs is high, then?
Small
Gly and ala
B keratins like silk firbroin and firboin of spider webs are packed very close together, and therefore have __ and ___ alternating over large areas of the sequence
Gly and ala
Fibroin consists of closely packed, parallel/antiparallel B sheets?
Antiparallel
In globular proteins, what proportion of aa residues are in turns or loops where the polypeptide chain changes direction?
1/3
What do β turns in globular proteins do for the protein structure?
Link segments of α -helix and β sheet
When are β turns especially common?
When they connect two adjacent segments of an antiparallel β sheet
This is the more common β turn type, occurs twice as much
Type I
This β turn is a 180 degree turn involving 4 aa residues; the carbonyl of the 1st aa bonds with the amino group of the 4th aa residue
Do residues 2 and 3 participate in H bonding?
Type I
No
Type II β turns have the same type of H bonding as Type I β turns, but which aa is always the third residue?
Gly
Which two aas are often found in β turns?
Gly and Pro
For pro, peptide bonds invlolving its imino N readily assume a ____ configuration
This configuration is good for left or right turns?
Why is gly often found in β turns?
cis
Right turns
Small and flexible
Where are β turns found?
Near surface of a protein where peptide group of central two aa residues can H bond to water
A less common turn than a β turn
how many residues per turn?
where is the H bond?
γ turn
3 aa per turn
between 1st and 3rd residues
This is a major protein component of tendons, cartilage, the organic matrix of bones, and the cornea of the eye
Collagen
What is the most abundant protein in vertebrates?
Collagen
The collagen triple helix is what category structure?
Secondary structure
Is the collagen triple helix right or left handed?
Left handed
What are the bond angles of the collagen triple helix?
φ = -51 and ψ = 153
What is n and p for the collagen triple helix?
n=3.3 residues/turn
p= 10 A
These two structure are the major secondary structures in proteins
α helix and β conformation
In the Ramachandran plot of the AAs in the bovine trypsin inhibitor, most of the data falls within allowed regions. Which aa is the exception?
gly, it is small and flexible
These two AAs are relatively common in β turns and relatively absent in α helices
Pro and gly
From an analysis of known structures of a number of proteins, tables have been put together to show the relative frequency of finding an AA in a particular common secondary structure
What do the variables Pα, Pβ, and Pt represent?
α helices (Pα), β sheets (Pβ) and turns (Pt)
What is the equation for Pα?
Pα= fα/, aka the frequency of finding an AA divided by the average frequency for all AAs
AA residues can range from strong formers of a particular structure to weak formers to breakers of a particular secondary structure
!
Chou and Fasman have established rules to predict the secondary structures of proteins from the sequence by using the observed ___ of AAs
propensities
Check out the table
This is a method for assessing common secondary structure
Circular Dichroism
What does circular dichroism measure?
Differences in absorption of left handed vs right handed plan polarized light resulting from structural assymetry
What do differences is aborption of plane polarized light between left and right handed helices result from?
Structural asymmetry
What is the light absorbing energy for proteins?
What region does it occur?
The peptide bond
Far UV region (190-250nm)
Molar extinction coefficient differences for left and right handed plane polarized light are plotted as a function of
Wavelength
