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Biochemistry > Biochem Protein Lecture 7 > Flashcards

Biochem Protein Lecture 7 Flashcards

1
Q

The major proteins of hair and wool

A

α-keratins

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2
Q

Molecules are constructed primarily from

A

α-helices

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3
Q

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?

A

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

Conformations of protein molecules

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4
Q

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

Are they right or left handed?

A

Intermediate filament proteins

Right

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5
Q

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

A

β-Conformation

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6
Q

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

A

Zigzag structure

β-sheet

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7
Q

How are the H bonds different in beta sheets?

A

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

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8
Q

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

A

Parallel

Antiparallel

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9
Q

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

A

Perpendicular

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10
Q

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

The repeat period period is shorter for which one?

What else is different?

A

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

H-bonding patterns

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11
Q

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

A

Yes, folding

Yes.

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12
Q

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

A

φ = -119 and ψ =113

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13
Q

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

A

φ = -139 and ψ =135

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14
Q

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?

A

Small

Gly and ala

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15
Q

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

A

Gly and ala

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16
Q

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

A

Antiparallel

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17
Q

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

A

1/3

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18
Q

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

A

Link segments of α -helix and β sheet

19
Q

When are β turns especially common?

A

When they connect two adjacent segments of an antiparallel β sheet

20
Q

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

A

Type I

21
Q

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?

A

Type I

No

22
Q

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

A

Gly

23
Q

Which two aas are often found in β turns?

A

Gly and Pro

24
Q

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?

A

cis

Right turns

Small and flexible

25
Q

Where are β turns found?

A

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

26
Q

A less common turn than a β turn

how many residues per turn?

where is the H bond?

A

γ turn

3 aa per turn

between 1st and 3rd residues

27
Q

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

A

Collagen

28
Q

What is the most abundant protein in vertebrates?

A

Collagen

29
Q

The collagen triple helix is what category structure?

A

Secondary structure

30
Q

Is the collagen triple helix right or left handed?

A

Left handed

31
Q

What are the bond angles of the collagen triple helix?

A

φ = -51 and ψ = 153

32
Q

What is n and p for the collagen triple helix?

A

n=3.3 residues/turn

p= 10 A

33
Q

These two structure are the major secondary structures in proteins

A

α helix and β conformation

34
Q

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?

A

gly, it is small and flexible

35
Q

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

A

Pro and gly

36
Q

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?

A

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

37
Q

What is the equation for Pα?

A

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

38
Q

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

A

!

39
Q

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

A

propensities

Check out the table

40
Q

This is a method for assessing common secondary structure

A

Circular Dichroism

41
Q

What does circular dichroism measure?

A

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

42
Q

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

A

Structural asymmetry

43
Q

What is the light absorbing energy for proteins?

What region does it occur?

A

The peptide bond

Far UV region (190-250nm)

44
Q

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

A

Wavelength

Biochemistry (27 decks)

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