Lectures 1, 2 + tutorial 1 Flashcards
What are the four types of noncovalent interactions?
- Electrostatic attractions: Between fully or partially charged atoms.
- Van der Waals attractions: weak, nonspecific attractions when two atoms are in close proximity.
- Hydrogen bonds
- Hydrophobic force: not actually a bond, but a nonspecific attraction between two hydrophobic molecules in an aqueous environment.
What are the three kinds of molecular motion?
- Translational motion: the movement of a molecule from one place to another
- Vibrations
- Rotations
What does it mean when the free energy (delta G) is positive? And when it’s negative?
If delta G is positive: energetically unfavourable, if it’s negative: energetically favourable.
What is the formula for the free energy change of a reaction (delta G)?
Delta G = Delta G0 + RTln(keq)
Why does the formation of ADP from ATP yield so much energy?
- The release of the terminal phosphate group removes an unfavourable repulsion between adjacent negative charges.
- The phosphate ion released is stabilized by resonance and by favourable hydrogen-bond formation with water.
NAD+/NADH is mainly used in…
NADP+/NADPH is mainly used in…
catabolic reactions, anabolic reactions
What is electronegativity?
Electronegativity is the tendency of the nucleus to pull on the outer shell electrons (only the valence electrons). There’s an increase in electronegativity from large elements to small ones, because the distance between the nucleus and the electrons is smaller in small elements, therefore the electronegativity is higher.
What is the difference between an ionic bond and a covalent bond?
An ionic bond is the complete exchange of valence electrons between elements.
A covalent bond is the sharing of valence electrons between elements. (Forms an electron pair)
What is a big and important difference between amines and amides?
Amines in water combine with H+ to become positively charged, whereas an amide remains uncharged in water.
Which two things determine wheter a chemical group acts as an acid or a base in water?
- On the pKa (acid dissociation constant)
- The PH of the environment
What does it mean when a substance has a low pKa? And a high pKa?
- Low pKa: stronger acid, because the acid releases protons readily, making it a strong acid.
- High pKa: weak acid, because the acid holds onto its proton more tightly, making it a weaker acid.
If the PH > pKa, then …
If the PH < pKa, then …
- If the PH > pKa: the acid is mostly deprotonated (A- form).
- If the PH < pKa: the acid is motly protonated (HA form).
What is the definition of the pKa?
The pKa is a measure of the tendency of a molecule to hold onto its proton.
High pKa: holds onto proton tightly, weak acid.
Low pKa: easily lets proton go, strong acid.
What does an atom need to have in order to be able to act as a base?
To act as a base, an atom needs to have a lone electron pair.
What happens when the pKa matches the PH?
When the pKa matches the PH, there will be an equal amount of protonated and deprotonated forms present in solution.
Give the definition of catabolism and anabolism.
*Catabolism: breakdown of complex molecules into simple molecules by oxidation.
* Anabolism: synthesis of complex molecules from single molecules, through reduction reactions.
What is oxidation? What is reduction?
- Oxidation is the loss of electrons, the loss of C-H bonds, and sometimes the loss of O-H bonds.
- Reduction is a gain of electrons, a gain of C-H bonds, and sometimes a loss of O and a gain of OH bonds.
In what ratios are NADH/NAD+ and NADPH/NADP present in the cell and why are these ratios important?
- NADH/NAD+ «_space;1, so WAY more NAD+ present in the cell. This is to drive the oxidation of food molecules, so it serves as electron acceptor for the breakdown (oxidation) of food molecules.
- NADPH/NADP»_space;1, so WAY more NADPH in the cell, to donate protons and electrons for biosynthesis (anabolic reactions).
B-type vitamins are precursors for several activated carriers/cofactors in metabolism. Name three B-type vitamins and what they are precursors for.
- B5: precursor for coA
- B3: precursor for NADH
- B2: precursor for FADH2
What does it mean when delta S (entropy) < 0?
And when delta S > 0?
When delta S < 0, it means there is a decrease in order, so the reaction will not happen spontaneously/be favourable.
When delta S >0, it means the disorder increases, and it’s a spontaneous process.
What is the formula for G using entalpy and entropy?
G = delta H - T * delta S
* G= Gibbs free energy
* delta H = enthalpy (heat)
* delta S = entropy (disorder)
What is the definition of G? (Gibbs free energy)
Gibbs free energy (G) is a measure of the maximum amount of useful work that a system can perform at constant temperature and pressure. It determines whether a process is spontaneous based on the balance of enthalpy and entropy.
Why is cysteine a special amino acid?
Because the SH group gives the side chain slightly polar properties, but the amino acid is predominantly hydrophobic.
