Week 2 - Biochemical bonds, Free energy, and biochemical reactions Flashcards
(28 cards)
Different forms of chemical bonds
1
concept of free energy
1
chemical reactions involve changes in free energy
1
ATP is the main source of energy in cells
1
Chemical bond?
attraction between atoms brought about by a sharing of electrons or a complete transfer of electrons between atoms
in aqueous solutions: strong bonds
covalent bond
in aqueous solutions: weak bonds
ionic bond
hydrogen bond
van der waals interaction
hydrophobic interaction
covalent bond
strong bonds
short
hold atoms close together
sharing of an electron pair (or multiple)
valence of an atom determines the number of covalent bonds it can form
covalent bonds and electrical polarity
polar; differences in electronegativity between two atoms bonded together; electrical dipole(polar bond); unequal sharing
non-polar; equal sharing
Covalent bond and rotation
single; allow rotation
double and triple; do not allow freedom of rotation
geometry of molecule; covalent bond
number and types of bonds determine the geometry of molecule
- bond angles determined to minimize the proximity of different atoms’ electrons to each other
non-covalent bond
ionic bond
hydrogen bond
hydrophobic interaction
van der waals attraction
ionic bond
electrostatic attraction between ions;
strongest of non-covalent interactions
dissociate in solution
* ionic bond very strong unless put in water
* weak acid and base are very strong bonded
hydrogen bond
formed between electronegative atom (N,O) and hydrogen atom (covalently attached to another atom; N,O)
stabilize biological molecules
- H+ covalently bonded to Carbon will NOT participate in hydrogen bond
- There is ONE hydrogen atom in a hydrogen bond
hydrophobic interaction
between hydrophobic molecules because they are repelled by water; between non-polar molecules
van der waals attraction
between all molecules as a result of permanent and transient dipoles (unequal distribution of electrons); random fluctuation induced transient dipoles
very weak force
non-specific attractive force
* 10A=weak van der Waals
* 5A = very strong attraction
* 4A = balanced by repulsive forces, owing to interpenetration of outer electron shells
pH dependent carboxyl group charge (ionization state)
depending on the pH of the solution,
acidic and basic groups may be protonated or deprotonated
* pH = measure of the [H+]
at its pKa, concentration of the two forms will be equal and there will be no net charge
Water and hydrogen bonding lattice
crystal molecules in regular fashion; tetrahedron; 육각수
multiple weak bonds
stabilize associations between macromolecules;
surface complementary
stable and less stable complex
specific interaction
complementary molecular surfaces
lock and key model; substrate has a fit shape
antibody-antigen interaction
enzyme and substrate complex
making and breaking chemical bonds, and energy
making - consume energy
breaking - release energy
strong bond - harder/ greater E
weaker bond - easier/ lesser E
free energy; G
amount of energy available for atoms and molecules to do work; ex. thermal energy
can interconvert between thermal energy (kinetic) and bond energy (potential)
delta G determine direction of chemical reaction
A+B -><0 is spontaneous; toward product
delta G = 0 is at equilibrium
activation energy
required for initiation of a reaction
leads to activated state
lowered by enzyme
