learning objective 2.1 Flashcards
What is a bronsted-lowry base & acid?
A bronsted-lowry base is a proton acceptor
A bronsted-lowry acid is a proton donor
What is a lewis acid & base?
A lewis acid is an electron pair acceptor
A lewis base is an electron pair donor
Activation energy (Ea)
The energy required to produce the transition state. Ea determines if a rxn will proceed
Gibbs free-energy change (delta)G equation
(delta) G = (delta)H - T(delta)S ;
- depends on the concentrations of reactants and products
Explain favorable and unfavorable reactions in regards to (delta)G
When (delta)G = (-), the reaction is spontaneous/favorable and therefore does not require outside energy.
- The reaction proceeds forward when it is spontaneous
- The reaction is also exergonic, meaning it releases energy
When (delta)G = (+), the reaction is nonspontaneous/unfavorable and therefore requires outside energy.
- The reaction favors the reactants when it is nonspontaneous
- The reaction is endergonic, meaning it absorbs energy
What is a buffer?
A solution that resists changing the pH when a small amount of acid or base is added
- it is made with a weak acid and its conjugate base or a weak base and its conjugate acid in equal concentrations.
- Ex.) bicarbonate buffer system
What is a calorie?
The amount of heat required to raise the temperature of 1 gram of H2O from 14C to 15.5C.
1 cal = 4.184 J
1 J = 0.239 cal
J = Joule
What does a catalyst do?
- it lowers the Ea of a rxn without changing the (delta)G or gibbs free-energy change.
- it does this by stabilizing the transition to make it more favorable
- it is not consumed in a rxn. instead it is regenerated with each rxn cycle.
- enzymes are catalysts
compare standard free-energy change and Gibbs free-energy change and explain how they are useful in considering chemical reactions.
- Standard free-energy change is used to indicate distance of standard state from equilibrium
- Gibbs free energy change is used to indicate the distance from equilibrium at a particular Q (reactants/products)
- when [products]=[reactants], then standard free energy= gibbs free energy
How are activation energy and catalysis related to each other in terms of reactions?
Activation energy is the energy required to push through the transition state to make the reaction take place.
- Because the Ea is usually very big, this causes the reaction to take a long time to occur.
- Catalysts lower the Ea without changing the rxn by stabilizing the transition state so that rxn can proceed faster at lower energy. The catalysts are not consumed in the rxn.
The first law of thermodynamics
the law of conservation of energy: says that energy can not be created nor destroyed, only changed from one form to another.
The second law of thermodynamics
says that disorder, or entropy, of the universe increase
The properties of water that are essential for biochemistry
- a polar molecule with a permanent dipole
- has a high melting pt, boiling pt, and high heat of vaporization
- easily dissolves polar and charged molecules
- highly cohesive b/c of hydrogen bonds. it is highly ordered in ice
- the most abundant substance in living organisms
- the solvent most used in biochemical reactions.
Compare covalent and non-covalent
Covalent bonds: when atoms share an electron pair between them.
- can be single, double, and triple covalent bonds in polar and nonpolar molecules.
Noncovalent bonds: bonds formed either by completely exchanging or not exchanging at all
- strong noncovalent bonds: ionic bonds
- weak noncovalent bonds: hydrogen bonds, van der Waals interactions
compare polar and nonpolar
polar bonds: when electrons are shared unequally between atoms.
- happens when there is a difference in electronegativity of atoms. there’s a partial positive charge and a partial negative charge
non-polar bonds: when electrons are shared equally
What is a redox reaction?
A chemical reaction where electrons are transferred between reactants. One is oxidized while the other is reduced
characteristics of a polar bond?
- when electrons are shared unequally between atoms
- form between atoms of different electronegativity (ability to attract electrons)
- creates dipoles
- net dipole moment depends on bond geometry
(u) dipole moment = partial charge x distance
ENDothermic
(delta)H = (+), reactions that require an input of heat
ENDergonic
(delta)G= (+), reactions where energy is added
EXergonic
(delta)G= (-), reactions where energy is released
EXothermic
(delta)H= (+), reactions that produce or release heat
Equilibrium
The point where the rate of rxn in the forward direction equals the rate of rxn in the reverse direction.
- no net change in concentrations. they stay the same
- Kf[A][B] = Kr[C][D]
Oxidation
- Loss of electrons
- Loss of hydrogen atoms
- Gain of oxygen atoms
[Oil Rig] Oxidation is losing. Reduction is gaining
** becomes more positive (+)
Reduction
- Gain of elections
- Gain of hydrogen atoms
- Loss of oxygen atoms
[Oil Rig] Oxidation is losing. Reduction is gaining
**becomes more negative (-)
Reaction rate
How fast a reaction proceeds
Vforward=Kforward[A][B] ; Kforward= constant
Vreverse=Kreverse[C][D] ; Kreverse= constant
What are the different types of non-covalent interactions
Ionic interactions, hydrogen bonds, van der Waals interactions, hydrophobic effect
Describe hydrogen bonds and how it is affected by water
- interaction of partially charged proton(H+) with an O,N, I, or F. Most commonly bonded to O and N in biomolecules
- an electrostatic interaction
- A weak interaction. Longer bonds than covalent bonds
- most stable when straight
- low energy bonds (4-20 KJ/mol or 1-5 Kcal/mol in water)
- Affected by water: competition in water for forming Hydrogen bonds
Describe ionic interactions and how it is affected by water
- Electrostatic interactions can happen between partially charged atoms and fully charged ions
- the strongest interaction is between fully charged ions. These are called salt bridges
- they do not have direction
- they create a uniform electrical field
- there is no specific geometry
- interaction is impacted by the distance between atoms
Affect by water:
- they are very strong in the absence of water b/c of the crystal formation that occurs in solid form. - water greatly reduces its strength through partial neutralization of the charges.
- *the atoms are hydrated upon dissolving in water, meaning water bonds with the atoms
- Energy of hydration > the energy stabilizing crystal
Describe van der waals interactions and how it is affected by water
- attractive forces due to the movement of electrons around atoms
- creates electrostatic attraction b/w atoms through dipoles
- a weak force
- very abundant in molecules
- need to be close in distance
- help create cohesion between nonpolar and polar molecules. (which is important for interaction of nonpolar molecules in H2O)
- temporary partial charges in molecule. affects electron clouds in other atoms by inducing temporary dipoles
Affect by water: NOT affected by water
Hydrophobic effect
- Not a bond, due to repulsive forces between molecules such as polar and nonpolar
- drives the aggregation of nonpolar molecules to reduce the number of caged water molecules
What is alkalosis
when blood ph > 7.35
- metabolic alkalosis is the retention of HCO3- or ingestion of bases
- respiratory alkalosis is hyperventilation
What is an amino acid?
- Monomers
- Building blocks for proteins
- 2 or more bonded amino acids are a polypeptide.
- form a peptide bond that produces water. it is a condensation reaction
- amino group of one amino acid is bonded to the carboxyl group of the neighboring amino acid
- strings of unbranched amino acids are folded into 3D shapes/conformations
What is acidosis?
- when blood ph <7.35
- metabolic acidosis is excess production of organic acids (lactate, ketone bodies) or loss of HCO3-
- respiratory acidosis is the retention of CO2
What is a carbohydrate?
- as monomers carbohydrates are simple sugars
- Carbon : water is 1:1
- carbohydrates are energy sources [glycogen, starch, both are polysaccarhides], [glucose, a monomer]
- carbohydrates give mechanical support in some organisms [ cellulose, chitin]
- Carbohydrates also help with communication [ glycoproteins, glycolipids]
what is chemical potential energy?
Stored energy in bonds that can be turned into kinetic energy
What is cholesterol?
- Cholesterol is a sterol. Which is a form of a lipid
- It has a polar head group
Configuration
- Bonds change/rearrangements
- same types and number of atoms and bonds
- cannot be interconverted w/o breaking and reforming covalent bonds
- can have cis and trans configurations
- different arrangements have different biological activity
conformation
spatial rearrangements, but bonds are not broken. just rotated.
dissociation constant
Kd= 1/ka= [reactants]/[products]
- indicates the affinity of complex
- the lower the Kd the stronger the bond/affinity
- kd is stronger in the allosteric (substrate) binding site than in the catalytic site
- molecule
fatty acids
contain hydrocarbon chains with COOH group
have different lengths
can be saturated [does not have C-C double bonds]
can be unsaturated [has C=C bonds]
