Chapter 4 Flashcards
The forces that stabilize protein structure are normally weak. What are the five things that contribute to stabilization? (four bonds and one interaction?
Hydrophobic interaction, H bonds, VdW, ion-ion, and disulfide bonds
The _____ of a protein determines its _____
Structure
Function
The peptide bond (between the carbon of the carbonyl and the nitrogen of the amide) is _____
Planar
Why can’t the peptide bond be rotated?
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
Although the peptide bond can’t rotate, the bonds containing ______ on either side can rotate
Alpha carbons (next to the carbon of the carbonyl and the nitrogen of the amide)
Phi is the rotation between ____ and is usually ___ to ____ degrees
N-C
-45 to -180 degrees
Psi is the rotation between _____ and is usually ___ to ___ degrees
C of carbonyl- C
-60 to +190 degrees
What does a Ramachandran plot tell us?
The most common angles for Psi and Phi to take on, including the outer limits
The alpha helix is stabilized by Van der Waal forces and has a hydrogen bond every ____ AA’s
Four (n of the carbonyl to the amide of n+4)
What properties of R groups on the alpha helix can give increased stabilization?
Opposing charges. If negative and positive charges line up on the helix, it will be stronger
Proteins are _____ not static. They have a native fold but also take on other cofigurations
dynamic
What AA’s are the two “chain breakers” in an alpha helix?
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
What is the difference between a parallel and antiparallel beta sheet?
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
Which is stronger: the parallel or antiparallel beta sheet?
Anti-parallel bc the distance between the H-bonds is less than that of the parallel
Circular Dichroism is used to detect _____
The relative contributions to a proteins overall secondary structure. It gives a graph of alpha helix, beta sheet, and random coil
What are the three kinds of secondary structures?
Alpha helix, beta sheets (parallel and antiparallel) and loops and turns
How do secondary structures help proteins become more compact?
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
Tertiary structures are formed when ____ structures fold together
Secondary
What kinds of bonds stabilize tertiary structures (help them stay together)?
Disulfide bonds, hydrogen bonding, salt bridges, covalent bonding, and hydrophobic interactions
A proteins lowest energy conformation, called its _______ is dominated by hydrophobic effects
Native conformation
How is X-Ray crystallography used to determine protein structure? What are its pros and cons?
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
How is NMR used to determine protein structure? What are its pros and cons?
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
Cryo-electron microscopy is better than both X-ray crystallography and NMR. How does it work and what are the pros/cons?
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
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 _____
One, structure and support
Combination, enzymes or regulatory proteins
Fibrous proteins are long and strand-like, _____ in water, and can be found in structural components of the body like keratin, skin, and ligaments
insoluble
How is the structure of collagen different from an alpha helix?
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
Why are proline and glycine bad for alpha helices?
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
What is the structure of beta-Keratin, and what gives it the ability to be perm-ed?
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)
How is the globular protein set up so that it can be water soluble but still held together by hydrophobic interactions?
Like a micelle, the polar groups are on the surface and the non-polar groups are in the middle
Large polypeptides fold into globular clusters called ______ that have multiple functions. They can bind substrates, or each section can have a different function
Domains
The evolutionary relationships between proteins are better analyzed using _____ than AA sequence
Structure
What is the advantage for a protein that is intrinsically disordered?
It is simply a domain, so it can move through space to find its ligand faster
What did the Anfinsen experiment find in terms of disrupting a proteins native conformation?
A protein knows its native fold
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
Chaperonins (chaperones) help facilitate folding by ______
Giving the protein the right environment it needs
R groups are located on the _____ of alpha helices. They can stabilize each other through