Properties of Biological Molecules Flashcards
First Law of Thermodynamics
Law of Conservation of Energy
- Energy is neither created nor destroyed
Second Law of Thermodynamics
Law of Thermodynamics
- Entropy always increases that’s in an isolated system and not in thermal equilibrium.
2 facts from Thermodynamics velocities:
- Thermodynamics is not indicative of velocity
- Reaction velocity is increased by a catalyst
What is Gibbs Free Energy?
Energy required to do work; a thermodynamically property of a chemical rxn
Gibbs Free Energy under Standard conditions:
G°’ = -RT ln Keq
Gibbs Free Energy under Nonstandard Conditions
Delta G° = delta G’ + RT ln [products]/[reactants]
- More products = less (-) = less spontaneity
- More reactants = more (-) = greater spontaneity
Explain the concept of Chemical Equilibrium
Le Chatelier’s Principle
- Energy input; coupled rxns, Free energy parameters are additive
What are the 3 bond properties?
- Van der waals Interactions - distribution of electronic charge around an atom flunctuates w/ time.
- Electrostatic Interactions - opposite charges attract
- H-Bonding
What is Coloumbs Law?
E = kq1q2/Dr
- The principle that the force of attraction or repulsion between two point electric charges is directly proportional to the product of the charges and inversely proportional to the square of the distance between them.
Properties of Water
- Polar
- Cohesive in nature
- Bent
- Asymmetrical distribution of charge
- Hydrophobic effect
What are the two types of metabolic processes?
- Acid-Base Rxns
- Redox Rxns
Weak acid and weak base properties & equation for acid/base rxns
- Weak bases dissociate in water w/ it’s conjugate base
- Weak acids dissocite in water forming conjugate acid
- Keq = [OH-][H+]/[H2O]
K = 1.8 x 10-16
What occurs in Redox Rxns
Transfer of electrons
- Electron donor - reducing agent
- Electron acceptor - oxidizing agent
What is the equilibrium constant for acid dissociation
Ka = [H][A]/[HA]
What is the Henderson-Hasselbalch equation
pH = pKa + log [A-]/[HA]
What are the two torsion angles:
Phi (90°) and Psi (-90°)
Both are disfavored
Sub-structures of Secondary Protein structure
- alpha-helix
- beta-helix
- beta-turns
Alpha-helix Characteristics
- Stabilized via H-bonds
- R-groups stick out
- 3.6 aa/turn (5.4/1.5)
- Right-handed double helix
Beta-Strand/Sheet Characteristics
- Parallel - H-bonds within one aa
- Anti-Parallel - H-bonds amongst two aa
3° Structure Characterisitcs
- 3D conformation
- Mostly globular or spherical
- Hydrophobic interactions (covered by chaperone proteins to avoid aggregations forming)
- Disulfide bonds
- Metal ions
- H-bonding
What is a fibrous protein, and examples
- Polypeptide chains arranged in a parallel fashion along a single liner axis forming a tough, water-insoluble fiber/sheet
- Collagen, Keratin
What is a globular protein and example
- Ellipsoid/Spherical shape
- Enzymes (serum albumin most abundant)
What are the features of quaternary protein structure
- Multiple subunits that are held together by non-covalent interactions
- H-bonds, Hydrophobic Interactions, Van der Waals forces, Salt Bridges
- Hemoglobin
Collagen characteristics
- Repeating triplet sequence with Glycine (assist in turns)
- 20% Pro or Hyp
- Triple helix - individual chain twisted left, chains together twisted right
How can collagen be modified?
With hydroxyl groups
Globular Protein Examples:
- GADPH - enzymatic rxns
- Myoglobin - contain pockets (in this case containing heme)
- Porins - water-fill hydrophobic channel, hydrophobic exterior
