FII - Lecture Slides 45 - 82 Flashcards
How many amino acid residues are there per turn of the alpha helix?
3.6 Amino Acids
What is the distance between each turn of the alpha helix?
5.4 A
What is the distance along the helix per amino acid?
1.5 A (5.4/3.6)
What does the #1 C = O line up with to form hydrogen bonds that make the alpha helix stable?
It lines up with #5 H = C
What are antiparallel Beta Sheets?
Where the N and C terminus are alternating down the sheet
What is better in antiparallel beta sheets?
The hydrogen bonds align better
What are parallel beta sheets?
The N terminus and C-terminus are not alternating
What is the major pattern in antiparallel Beta Sheets?
7 A
What is the major pattern in parallel Beta Sheets?
6.5 A
How do antiparallel beta pleated sheets make maximum space?
They have space available for awkward and bulky side chains
What amino acids prefer a Beta Pleated Sheet Structure?
WYF
VIT
C
What Amino Acids prefer Alpha Helices?
ARQ
GHL
KMF
What determines the secondary structure form?
The local majority of the alpha helixes or beta pleated sheet.
What is a secondary structure breaker?
It has a chain that disrupts the secondary structure
What are the secondary Structure Breakers?
GPNDS
What do you need in order for these secondary structure breakers to work
You need 2 of these Amino Acids in the span of four
GAPR (two in span of four)
What do secondary structure breakers form?
They form a “turn” or “loop” allowing the polypeptide chain to turn drastically.
What is the “Native State”
It is a proteins 3D tertiary structure that is required for their function.
What is Denaturation?
Unfolding of the protein where the function of the protein is lost, typically irreversible
How can denaturation happen?
- Heat
- Harsh Detergents (SDS)
- Disruptive Solvents
What is tertiary structure?
Tertiary Structure is the overall pattern of folding of the whole polypeptide chain.
What is the simplest possible tertiary structure?
The continuous secondary structure
What is the total pattern of a-keratin?
Alpha Helixes
What is the total pattern of b-keratin?
Beta pleated sheets
What is the total pattern of collagen?
Unique triple helix structure, with three repeating units of amino acids -Gly-Pro-X
What is unique about proline and Glycine?
They are globular: they have the ability to fold back onto themselves
What is the major driving force of protein folding?
The hydrophobic effect
What does the hydrophobic effect deduce about the protein folding?
The non-polar amino acids will be in the interior (core)
The polar amino acids will be on the surface/outer layer as they are able to interact with H2)
How do close contact forces attract?
Through Van Der Waals forces (aka. London Dispersion forces)
What is a London Dispersion force?
A weak attraction between molecules that is typically temporary
(Partial Positive and Partial Negatives)
What are the limited number of tertiary structure patterns?
- Majority alpha helical segments
- Majority B-sheet segments
- Alternating A-helical and B-strand segments
What do majority alpha helixes form?
Alpha Bundles
What are the characteristics of Alpha Bundles?
- Secondary Structure breakers sets the limit of each helix.
- Non-polar Amino Acids every 3 to 4 places in the helix forming a non-polar patch.
What is an example of an alpha helix bundle?
Myoglobin.
What tertiary structure do majority B-sheets always take on?
Anti-parallel beta sheet structure due to its strength and alignment of hydrogen bonds
What are the two structures majority Beta-Sheets take on?
Greek Key Motif
Beta Barrel
What is a Greek Key Motif?
Antiparallel Structure with alternating C and N-terminus and alternating polarity amongst amino acids
What is a Beta Barrel?
Antiparallel beta sheets that wrap all the way around (typically made with 6 - 8 sheets)
The interior is nonpolar and the surface is polar.
What tertiary structure does alternating A and B form?
Parallel B sheet
aB Barrel
aB Sandwich
What is a Parallel B sheet made up entirely of
Non-polar amino acids and must be away from water.
What is the aB Barrel?
The Beta Sheet forms the central barrel and the alpha helices surround it.
Non-Polar on inside and polar on outside
What is the aB sandwich?
Non-polar B Sheet between two layers of alpha helices, will see a twist in the B-sheet (middle)
What do larger proteins fold up into?
Domains (10-20kDA)
What are large proteins often called?
Modular: they consist of two or more receptive domains
What is the hydrophobic effect?
Non-polar amino acids are kept within the core of the protein
What are Van Der Waals attractions?
Dipole-diplole interactions (weak interaction between molecules that is often temporary and helps to limit atom-atom close contact)
What are H-Bonds?
Form between donors and acceptors that line up in a folded protein
Ion pairs
An electrostatic attraction between a negative side chain and a positive side chain
What are Disulfide bonds?
When pairs of Cysteine - SH group reacts with O2 releasing water, making a strong bivalent bond.
What was the experiment using ribonuclease?
Ribonuclease (enzyme) was denatured when placed into urea.
Once it was removed, it was able to renature itself to its “native” state
This showed how the amino acid sequence required all the information necessary to fold a chain
