Chapter 4

Question 1

The forces that stabilize protein structure are normally weak. What are the five things that contribute to stabilization? (four bonds and one interaction?

Answer 1

Hydrophobic interaction, H bonds, VdW, ion-ion, and disulfide bonds

Question 2

The _____ of a protein determines its _____

Answer 2

Structure
Function

Question 3

The peptide bond (between the carbon of the carbonyl and the nitrogen of the amide) is _____

Answer 3

Planar

Question 4

Why can’t the peptide bond be rotated?

Answer 4

Because the electrons from the carbonyl can delocalize and form a double bond between the carbon of the carbonyl and the nitrogen from the amide

Question 5

Although the peptide bond can’t rotate, the bonds containing ______ on either side can rotate

Answer 5

Alpha carbons (next to the carbon of the carbonyl and the nitrogen of the amide)

Question 6

Phi is the rotation between ____ and is usually ___ to ____ degrees

Answer 6

N-C

-45 to -180 degrees

Question 7

Psi is the rotation between _____ and is usually ___ to ___ degrees

Answer 7

C of carbonyl- C

-60 to +190 degrees

Question 8

What does a Ramachandran plot tell us?

Answer 8

The most common angles for Psi and Phi to take on, including the outer limits

Question 9

The alpha helix is stabilized by Van der Waal forces and has a hydrogen bond every ____ AA’s

Answer 9

Four (n of the carbonyl to the amide of n+4)

Question 10

What properties of R groups on the alpha helix can give increased stabilization?

Answer 10

Opposing charges. If negative and positive charges line up on the helix, it will be stronger

Question 11

Proteins are _____ not static. They have a native fold but also take on other cofigurations

Answer 11

dynamic

Question 12

What AA’s are the two “chain breakers” in an alpha helix?

Answer 12

Proline and glycine. Glycine bc it doesn’t have any substituents and cannot participate in VdW forces, and Proline because it has the wrong pitch angle, since the nitrogen is connected into the ring

Question 13

What is the difference between a parallel and antiparallel beta sheet?

Answer 13

The parallel beta sheet has loops, so the hydrogen bonds are directly across from each other. The antiparallel sheets have all chains facing the same way (all the R groups are going in the same direction), so the h bonds are at an angle

Question 14

Which is stronger: the parallel or antiparallel beta sheet?

Answer 14

Anti-parallel bc the distance between the H-bonds is less than that of the parallel

Question 15

Circular Dichroism is used to detect _____

Answer 15

The relative contributions to a proteins overall secondary structure. It gives a graph of alpha helix, beta sheet, and random coil

Question 16

What are the three kinds of secondary structures?

Answer 16

Alpha helix, beta sheets (parallel and antiparallel) and loops and turns

Question 17

How do secondary structures help proteins become more compact?

Answer 17

The secondary structures allow the protein to pile up on itself (from helixes and loops/turns) which decreases it’s overall size because it is no longer spread out like one long line

Question 18

Tertiary structures are formed when ____ structures fold together

Answer 18

Secondary

Question 19

What kinds of bonds stabilize tertiary structures (help them stay together)?

Answer 19

Disulfide bonds, hydrogen bonding, salt bridges, covalent bonding, and hydrophobic interactions

Question 20

A proteins lowest energy conformation, called its _______ is dominated by hydrophobic effects

Answer 20

Native conformation

Question 21

How is X-Ray crystallography used to determine protein structure? What are its pros and cons?

Answer 21

A crystallized molecule is bombarded with X-rays and rotated so that a picture can be taken from every angle. Those pictures are superimposed by foray calculations and create a very detailed 3D image

Can be used for any size molecule and is very detailed, but it requires a lot of sample and can take a while to precipitate (crystallize) the molecule

Question 22

How is NMR used to determine protein structure? What are its pros and cons?

Answer 22

After the backbone coupling is determined, NOE is used to determine the distance between protons in the protein. This is done multiple times to get an accurate model

Limited by size (molecules must be very small since large ones take longer to rotate), but this information can be gotten in solution, so no special prep is needed

Question 23

Cryo-electron microscopy is better than both X-ray crystallography and NMR. How does it work and what are the pros/cons?

Answer 23

An electron beam is passed through a sample and refracted to get 2D images. Those images are stacked on themselves to create a 3D picture

It is a solution technique, so no special prep is required. But the sensitivity limits the resolution of the pictures and there’s a lot of post-image processing needed to get the entire picture

Question 24

Fibrous proteins generally consist of ____ secondary structure (either alpha or beta) and are primarily used for ______ while globular proteins consist of a _____ of secondary structures and are used for _____

Answer 24

One, structure and support

Combination, enzymes or regulatory proteins

Question 25

Fibrous proteins are long and strand-like, _____ in water, and can be found in structural components of the body like keratin, skin, and ligaments

Answer 25

insoluble

Question 26

How is the structure of collagen different from an alpha helix?

Answer 26

Collagen are made up of 3 left handed helices twisted together. They have small side chain groups (alanine, glycine, proline) because that allows the helices to pack together tightly

Question 27

Why are proline and glycine bad for alpha helices?

Answer 27

Prolines pitch (from the ring in place of the amino group) is wrong for that of an alpha helix. Glycine doesn’t have any sidechains, so there are no forces that can help stabilize the helix

Question 28

What is the structure of beta-Keratin, and what gives it the ability to be perm-ed?

Answer 28

It is made up of 2 right handed alpha helices that are twisted into a left handed coil. They are composed of hydrophobic R groups that help the helices coil tightly, and have disulfide groups that contribute to strength and structure. (more disulfide bonds = harder and stronger)

Question 29

How is the globular protein set up so that it can be water soluble but still held together by hydrophobic interactions?

Answer 29

Like a micelle, the polar groups are on the surface and the non-polar groups are in the middle

Question 30

Large polypeptides fold into globular clusters called ______ that have multiple functions. They can bind substrates, or each section can have a different function

Answer 30

Domains

Question 31

The evolutionary relationships between proteins are better analyzed using _____ than AA sequence

Answer 31

Structure

Question 32

What is the advantage for a protein that is intrinsically disordered?

Answer 32

It is simply a domain, so it can move through space to find its ligand faster

Question 33

What did the Anfinsen experiment find in terms of disrupting a proteins native conformation?

A protein knows its native fold

Answer 33

If you denature a protein then remove the denaturing products before it can refold, the protein will return to its native conformation. If you let it refold and then remove the denaturation, it will become scrambled

Question 34

Chaperonins (chaperones) help facilitate folding by ______

Answer 34

Giving the protein the right environment it needs

Question 35

R groups are located on the _____ of alpha helices. They can stabilize each other through