3D Structure of Proteins Flashcards
What is a Kinase
Protein that is going to phosphoralate a target
What is a Domain?
Functional unit in evolution that is preserved. A conserved part of a given protein sequence that can evolve, function and exist independently of the rest of the protein chain.
What is a phosphatase
Protein that is going to dephosphorelate a target
Kinase and phosphatase are examples of what part of a protein structure?
Domains
What defines a secondary structure?
Backbone H bonding defines the secondary structure elements
What creates backbone H bonding
Carbonyl oxygen bonding with an amide hydrogen. CO-NH
What is the sequence of the H bonding backbone?
Alpha-C, C, O, N, H, Alpha-C
What are characteristics of a peptide bond
They are uncharged bonds and almost all are trans peptide bonds.
What does a partial double bond cause?
No rotation - stays fixed in trans
What is another name for peptide bonds?
Amide bonds
What are the Phi 0 and Psi Y torsion angles?
Phi: N-C.alpha
Psi: C-C.alpha
What do the Phi and Psi torsion angles allow?
Allow proteins to fold in many different ways
What does the Ramachandrian Diagram show?
Shows the angles of Phi and Psi that are most commonly seen.
What is steric exlusion?
Two atoms cant be in the same place at the same time
True or False?
Around the torsion angles there can be complete rotation (360 degrees)
False
What is more stable? Alpha helix or beta sheets?
Alpha Helix
True or False?
Hemoglobin contains beta sheets?
False. Hemoglobin is all alpha helix
Why is Hemoglobin all helix?
Needs to be more stable. Red blood cells are bags of hemoglobin that remain in a harsh environment for 120 days
What is the average AA length of Alpha Helix
12 AA residues
What is the basic structure of a alpha helix
Slinky
What is the linear displacement along the axis of an Alpha Helix?
1.5 Angstroms
What is the Angstrom of one complete turn of Alpha Helix?
5.4 A
How many amino acids per turn around an Alpha Helix?
3.6 A.A
Around an Alpha Helix, how often will an amino acid with an R group be pointed out?
Every 100 degrees
What happens if an Alpha Helix is projected through a membrane?
There will be a cluster of alpha helices and hydrophobic R groups pointed out and hydrophilic R groups pointed inside.
What is a right handed helix?
When looking down the helix it will be curling in a right handed fashion
What are the torsion angles of Alpha Helix?
-60
What does the torsion angle of 60 do to the structure of the chain
Adds to the kinking of the chain to give it the alpha helix structure
What does Proline do to a secondary structure?
Develops a kink in the alpha helix because it no longer has an amide bonding to participate in the backbone h bonding.
What is the orientation of the H bonding to the axis of the helix?
H bonding is parallel to the axis of the helix
What is a 310 Helix?
It is like the alpha helix but wider and tighter. The 3rd amino acid is bonded and there are 10 atoms between the bondings
What is the major characteristic of beta strands?
Sticky
What is an example of a protein we would not want to be “sticky”? What is an example of something we would want to be “sticky”?
Not sticky - Hemoglobin - could cause sickle cell if so
Sticky - antibodies - they have beta strands
What is Amaloidoses disease?
Large sheets of beta strands formed together. Can cause diseases such as alzeimer’s
What are beta sheets?
At least two beta strands coming together. Form 22 average length
What is the orientation of the Backbone H bonding on a beta sheet? Where are the R groups?
Bonding is perpendicular to axis sheet and R groups projected up and down
What is a beta barrel?
Sheets that are not flat but rickedy and form a curl
Parallel Beta Sheets have oxygens that are ______
Lined up
What is the more stable form of beta sheets?
Antiparallel
*Opposite directions caused possibly by a kink made by proline
What is the torsion of beta sheets?
180
What causes the instability of Beta Sheets?
No tight packing and Sticky H Bonds
What are quaternary proteins?
They involve the clustering of several individual peptide or protein chains into a final specific shape.
What are the types of bonds found in quaternary structure?
Hydrogen, Salt bridges, and disulfide bonds
What are two major categories of proteins with quaternary structures?
Fibrous and globular
What is a fibrous protein compared to?
A baseball bat
What is a coiled-coiled protein?
Alpha keratin that is a fibrous protein. Found in skin, nails, and hair.
What is the structure of a coiled-coiled protein?
Modified alpha helix - 2 right handed alpha helices intertwined to form a left handed super helix. 3.5 residues/turn and every 2 turns we start identically where we started
What is the amino acid sequence of coiled - coiled alpha keratin?
Heptad sequence - same 7 sequence over and over again. (ends are complicated)
What is collagen triple?
It is a helix found in connective tissue/cartilage
How often is there a glycine and proline in Collagen triple?
Every third animo acid is a glycine and every second is a proline
Is collagen triple left handed?
It is right handed but each chain curls and wraps to the left
What is the structure of a Collagen triple?
Very strong rope. Gly is so small it can fit in the center of the triple helix. Has Proline kinks and no H bonds within the strand
What is Globular compared to?
Baseball
What type of structures can Globular proteins have?
They can have many combinations of both helix and sheets and are mostly clumped into a shape of a ball
What are major examples of globular proteins?
Insulin, Hemoglobin, and most enzymes
What are beta turns?
tight loop is formed when the carbonyl oxygen of one residue forms a hydrogen bond with the amide proton of an amino acid three residues down the chain. This hydrogen bond stabilizes the beta bend structure.
What two amino acids are commonly found in beta turns?
Proline and Glycine are frequently found in beta turns, proline because its cyclic structure is ideally suited for the beta turn, and glycine because, with the smallest side chain of all the amino acids, it is the most sterically flexible.
Why are H bonds sticky?
Hanging H bonds. H bonds are in the direction opposite of the axis of the strand. H bonds will want to interact with neighbor strands.
