Biochem Protein Lecture 7

Question 1

The major proteins of hair and wool

Answer 1

α-keratins

Question 2

Molecules are constructed primarily from

Answer 2

α-helices

Question 3

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?

Answer 3

It has a regular structure that repeats every 5.15 to 5.2 A

Conformations of protein molecules

Question 4

The α-keratins are part of a broader family of proteins called

Are they right or left handed?

Answer 4

Intermediate filament proteins

Right

Question 5

Pauling and Corey preidcted a second type of repetitive structure called ___, its a more extended conformation of polypeptide chains

Answer 5

β-Conformation

Question 6

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

Answer 6

Zigzag structure

β-sheet

Question 7

How are the H bonds different in beta sheets?

Answer 7

The H-bonds are formed between adjacent segments in the polypeptide chain

Question 8

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

Answer 8

Parallel

Antiparallel

Question 9

In the Beta-sheet, the H bond are approximately ____ to th elong axis of the polypeptide chains

Answer 9

Perpendicular

Question 10

The parallel/antiparallel beta sheets are similar but with some differences.

The repeat period period is shorter for which one?

What else is different?

Answer 10

Parallel repeat period (6.5A) is shorter than antiparallel (7A)

H-bonding patterns

Question 11

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

Answer 11

Yes, folding

Yes.

Question 12

What are the φ and ψ conformations for the parallel beta sheet?

Answer 12

φ = -119 and ψ =113

Question 13

What are the φ and ψ conformations for the antiparallel beta sheet?

Answer 13

φ = -139 and ψ =135

Question 14

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?

Answer 14

Small

Gly and ala

Question 15

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

Answer 15

Gly and ala

Question 16

Fibroin consists of closely packed, parallel/antiparallel B sheets?

Answer 16

Antiparallel

Question 17

In globular proteins, what proportion of aa residues are in turns or loops where the polypeptide chain changes direction?

Answer 17

1/3

Question 18

What do β turns in globular proteins do for the protein structure?

Answer 18

Link segments of α -helix and β sheet

Question 19

When are β turns especially common?

Answer 19

When they connect two adjacent segments of an antiparallel β sheet

Question 20

This is the more common β turn type, occurs twice as much

Answer 20

Type I

Question 21

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?

Answer 21

Type I

No

Question 22

Type II β turns have the same type of H bonding as Type I β turns, but which aa is always the third residue?

Answer 22

Gly

Question 23

Which two aas are often found in β turns?

Answer 23

Gly and Pro

Question 24

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?

Answer 24

cis

Right turns

Small and flexible

Question 25

Where are β turns found?

Answer 25

Near surface of a protein where peptide group of central two aa residues can H bond to water

Question 26

A less common turn than a β turn

how many residues per turn?

where is the H bond?

Answer 26

γ turn

3 aa per turn

between 1st and 3rd residues

Question 27

This is a major protein component of tendons, cartilage, the organic matrix of bones, and the cornea of the eye

Answer 27

Collagen

Question 28

What is the most abundant protein in vertebrates?

Answer 28

Collagen

Question 29

The collagen triple helix is what category structure?

Answer 29

Secondary structure

Question 30

Is the collagen triple helix right or left handed?

Answer 30

Left handed

Question 31

What are the bond angles of the collagen triple helix?

Answer 31

φ = -51 and ψ = 153

Question 32

What is n and p for the collagen triple helix?

Answer 32

n=3.3 residues/turn

p= 10 A

Question 33

These two structure are the major secondary structures in proteins

Answer 33

α helix and β conformation

Question 34

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?

Answer 34

gly, it is small and flexible

Question 35

These two AAs are relatively common in β turns and relatively absent in α helices

Answer 35

Pro and gly

Question 36

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?

Answer 36

α helices (Pα), β sheets (Pβ) and turns (Pt)

Question 37

What is the equation for Pα?

Answer 37

Pα= fα/, aka the frequency of finding an AA divided by the average frequency for all AAs

Question 38

AA residues can range from strong formers of a particular structure to weak formers to breakers of a particular secondary structure

Answer 38

!

Question 39

Chou and Fasman have established rules to predict the secondary structures of proteins from the sequence by using the observed ___ of AAs

Answer 39

propensities

Check out the table

Question 40

This is a method for assessing common secondary structure

Answer 40

Circular Dichroism

Question 41

What does circular dichroism measure?

Answer 41

Differences in absorption of left handed vs right handed plan polarized light resulting from structural assymetry

Question 42

What do differences is aborption of plane polarized light between left and right handed helices result from?

Answer 42

Structural asymmetry

Question 43

What is the light absorbing energy for proteins?

What region does it occur?

Answer 43

The peptide bond

Far UV region (190-250nm)

Question 44

Molar extinction coefficient differences for left and right handed plane polarized light are plotted as a function of

Answer 44

Wavelength