3. Protein Structures Flashcards
(41 cards)
What do protein primary structures give rise to ?
They give rise to complex proteins or to their 3D fold
True/False: Proteins balance multiple factors to adopt conformations that minimize the free energy of the system.
True
What is the primary structure of proteins?
The sequence of amino acid residues
They are the basis, ultimately decide the teritary structure and the function of the protein.
What is the secondary structure of proteins?
Alpha helicies and beta sheets
About the local structures in the phi and psi bonds
Localized conformation of the polypeptide backbone based on the phi and psi torsion angles (local bonds).
What are the teritary structures of a protein?
Three dimensional structure of an entire polypeptide, including all its side chains’
Teritary sturctures will fold onto each other to make quaternary structures
What are the Quaternary structures of a protein?
Spatial agreenment of polypeptide chains in a protein with multiple subunits
The noncovalent interactions with tertiary structures give rise to quaternary structures
What are the thermodynamic principles of protein folding?
Gibbs free energy (delta G) dictates the directionality of a process.
- if delta G < 0 the reaction occurs spontaneously which makes it exergonic
- *if delta G > 0 then the reaction is endergonic and is nonspontaneous
- *if delta G = 0 then the reaction is at equilibrium (where the concentration of A and B are the same)
GIBBS FREE ENERGY PROVIDES NO INFORMATION ABOUT THE RATE OF THE REACTION!!!! The sign of delta G can show a reaction if its spontaneous or non spontaneous, but it does not show the rate
What is free energy defined as?
Gibbs free energy is essentially an accounting tool to keep track of entropy changes of both the system and the surrounding
- it is determined through enthalpy and entropy
H is a measure of the heat of the system
S is a measure of disorder of the system
Free energy is a state function therefore the delta G of a reaction is independent of the mechanism of the transformation (it is the proces of a reaction/ the steps)
*DOES NOT PROVIDE INFORMATION ON THE KINETICS OF THE REACTION**
Describe the spontaneous formation of liposomes of glycerophospholipids
Due to its spontaneity, that means delta G is negative which is favorable entropy and enthalpy conditions
- heat is released so enthalpy is reduced, it is not absorbed (small delta H)
- Water is released to increase the disorder of the system so entropy is increased
Enthalpy needs to be less than entropy to show that delta G is less than 0, which means that the reaction is under favorable enthalpy and entropy conditions
- The sign dictates if a reaction is spontaneous
- if it is a spontaneous formation then delta G is negative
Describe the secondary structure of proteins
Contains primary structures that are made of the sequence of amino acid residues
Also based on the localized conformations of the psi and phi bonds
True/False: proteins balance multiple factors to adopt conformations that minimize the energy of the system
True; they are entropy and enthalpy favored so delta G is less than 0
The most common secondary structures in proteins are right - handed alpha helix sheets and beta pleated sheets
Each protein has their own ramachadan diagram which determines how much of beta strands and alpha helix strands ther are which shows the allowed angle combinations of the local bonds in these strands.
What is the phi and psi angle range for alpha helix sheets?
Phi angle: -70 - -60 (C alpha to N)
Psi angle: - 50 - -40 (C alpha to C’)
* right handed (L - amino acids)
The carboxylate group of the residue (n) is hydrogen bonded to the NH group of the residue n +4
- The direction of the H - bonds are parallel to the long axis of the alpha helix EXCEPT for the amino acids at the ends of the helix, the carboxylate and the NH groups are hydrogen bonded.
How do you find the H bonding?
If you’re starting with an NH, you count +4 above the chain (or to the right)
If you’re starting with a C=O, you count below the chain (or to the left)
True/False: Geometrical structures of the helix dictate any transmembrane properties.
True
How many degree’s is the turn per residue?
100 degrees
Residue per turn is
..?
3.6
Rise per residue …?
1.5 A
Rise per turn is…?
Residue (rise) = rise per turn
(3.6) [residue per turn] x (1.5) [rise per residue] = 5.4
True/False: Core of the helix is tightly packed due to van der waal interactions/extensive H bond formation?
True; it gives rise to repetitive structures
True/False: the side chains of a helix points inward?
False; the side chains of a helix points outward to avoid sterics with the backbone and the other side of the chain and give rise to the structure and stability
Why do the side chains radiate away from the helical axis?
Because the center of the alpha helix has backbone atoms that are closely packed due to them being bonded with hydrogen bond interactions (close enough to form H bonds)
It also allows side chains to interact with another helix or beta strand to give rise to teritary structures
- the R groups engage in noncovalent interactions for higher order structure formation
True/False: alpha helixes are tightly wound by covalent interactions and therefore do not cover as much space as compared to beta sheets
True, they participate in both covalent and non covalent interactions
Describe beta strands
- Extended structure because the distance between residues is much larger
- The distance between an adjacent amino acid along a beta strand is about 3.5 A in contrast to a distance of 1.5 A on an alpha helix
- The side chains of the adjacent amino acids are pointed in OPPOSITE directions to reduce sterics
- The beta sheets is formed by linking two or more strands lying next to one another through hydrogen bonds
What are the phi and psi angles of beta strands?
Phi - - 150 - -100 (alpha C to N)
Psi - +120 - 160 ( alpha C to C’)
