Biochem Lecture 3 Flashcards
# Define the following terms for proteins: Primary Structure
Secondary Structure
Tertiary Structure
Quaternary Structure
Primary Structure: linear sequence of AA’s
Secondary Structure: LOCAL 3D folding (alpha helices or beta sheets via H bonds)
Tertiary Structure: 3D structure formed by condensation of secondary structure, stabilized by weak interactions.
Quaternary Structure: NONCOVALENT association of subunits into a multisubunit assembly
What form of a peptide bond is preferred?
TRANS confirmation is preferred (less steric bulk)
Draw the phi and psi angles for an AA
Look at graph
Secondary structure is generated by rotation___
Secondary structure is generated by rotation around phi and psi bonds.
What is the “native state” of a protein?
Native conformation is the stably folded and functional form of a biomolecule. (generally the confirmation with the lowest gibbs free energy)
How stable are proteins at room temperature?
The net effect of the weak forces allow proteins to only be marginally stable at room temp.
Rank the various types of bonds from strongest to weakest: Ionic, Covalent, Noncovalent, van der walls, hydrogen, hydrophobiv
Covalent> Hydrophobic> Hydrogen> Ionic> van der waals
The enthalpy change of protein folding is dominated by____.
Enthalpy change (delta H) is dominated by hydrogen bonds.
What two major roles does water play in modulating the strength of weak interactions?
Water plays two major roles:
- Interactions between polar groups contribute only the difference in enthalpy between groups when they are bonded to each other and the same groups when they are bonded to water.
- The contribution of water to the ENTROPY of a weak interaction is also considerable. HYDROPHOBIC EFFECT
Explain the first role water plays:
The interactions of water with H acceptors and H donors are often similar enthalpy to those that the groups can make to themselves. ENTHALPY is SMALL.
The dielectric constant of water is _____.
The presence of water _____ the electrostatic interaction between ions.
Dielectric constant of water is high
Presence of water weakens the electrostatic interaction between ions
What makes the largest contribution to delta G?
Hydrophobic effect
The solvent_____ entropy
The entropy in the polypeptide ____
Solvent increases in entropy
Polypeptide decreases in entropy
Driving force behind the hydrophobic effect?
GAIN IN SOLVENT ENTROPY
Explain van der Waals interactions
Distribution of electric charge around an atom
Increases as they come closer to each other, until they are seperated by van der Waals contact distance. At shorter distance, very strong repulsive forces become dominant because the outer electron clouds overlap
What is true of secondary structures in regards to bond angles?
Nearly all proteins adopt a confirmation in which the phi and psi angles of the backbone repeat in a regular pattern. (forming secondary structure)
Draw the Ramachandran plot. Label the axis and show shere the beta vs alpha regions are.
What is the simplest secondary structural element?
Beta turn (usually more than seven residues per turn)
Properties of the alpha helix:
What is the pitch?
How many AA’s per turn
The helix has a rise per residue of ___
- 4 angstroms is the pitch
- 6 AA’s per turn
Rise per residue of (5.4/3.6)= 1.5 angstroms
How do you calculate the rise per residue?
The pitch/ the residues per turn
In an alpha helix, what is hydrogen bonded to what and how far away are they?
The peptide planes are parallel/antiparallel with the helical axis.
The side chains point which direction?
The carbonyl is hydrogen bonded to the NH group every 4 residues away
The peptide planes are parallel to helical axis
Side chains point outwards and pointed up towards amino terminal end.
Why are there distortions in alpha helices?
- The packing of buried helices against other secondary structural elements
- Proline residues induce distortions of twenty degrees (lose two H bonds)
- Solvent…exposed helices point away from solvent
How are beta sheets structured?
Two or more strands align side by side and form hydrogen bonds between the strands
The strands are parallel or antiparallel (more stable)
Why are antiparallel beta sheets more stable?
They have a linear H bond
The parallel beta sheets have a nonlinear H bond
