BIOCHEM EXAM 1

1st Law of Thermodynamics

energy is conserved (neither created or destroyed; converts from one form to another)

2nd Law of Thermodynamics

entropy is constantly increasing; the tendency of any process in nature is to increase disorder

3rd Law of Thermodynamics

Entropy of a system approaches zero as the temperature reaches absolute zero (0 Kelvin); entropy is dependent on temp of the system

open system

allow for exchange of energy and matter ex. living organisms

closed system

allows energy to be exchanged only ex. boiling water w/ lid on

isolated system

no exchange of energy or matter ex. perfect thermos

characteristics of living organisms

• open system

• never at equilibrium (take nutrients and expel waste)

• in steady-state- constant flow of total input and output (so whole system remains constant)

Enthalpy

• heat

• ΔH= 𝛴H(bonds broken)-𝛴H(bonds formed)

endothermic reaction

• +ΔH

• heat is absorbed by system

• new bond are less stable

• not enthalpically favorable

exothermic reaction

• -ΔH

• heat is released by system

• new bond are more stable

• enthalpically favorable

positive entropy (+ΔS)

• more disorder

• less complex products

• entropically favorable

negative entropy (-ΔS)

• more order

• more complex products

• entropically unfavorable

-ΔG

• spontaneous/favorable

• exergonic

• process occurs without energy input

• from high energy to low energy

+ΔG

• nonspontaneous/unfavorable

• endergonic

• needs energy input for rxn

• low every to high energy

What are the overall favorable conditions for Free Energy?

-ΔH & +ΔS

-ΔH & +ΔS

spontaneous at all temperatures

-ΔH & -ΔS

spontaneous at low temperatures

+ΔH & +ΔS

spontaneous at high temperatures

+ΔH & -ΔS

nonspontaneous at all temperatures

Free Energy Change under non-standard conditions

ΔG= ΔG°+RTlnQ

R

gas constant= 8.314 J/mol*K

Biochemical Free Energy Change

ΔG= ΔG°’+RTlnQ

• removed the involvement of pH and water conc.

equilibrium constant

K_eq=([C_eq]^c[D_eq]^d)/([A_eq]^a[B_eq]^b)

Q

([C_i]^c[D_i]^d)/([A_i]^a[B_i]^b)

Gibbs Free energy at equilibrium

ΔG°= -RTlnK_eq

K_{eq >1}

• large -ΔG

• product favored/made

• spontaneous in forward direction

K_{eq <1}

• large +ΔG

• reactant favored/made

• non spontaneous in forward direction

K_{eq =1}

• ΔG=0

• equilibrium

• no driving force for reaction

pH of cell

7.4

How to calculate kelvin:

add 273.15 to the Celsius value

structure of water

• covalent bond between 1 electronegative oxygen & 2 electropositive hydrogen

• bent conformation (b/c 2 electron clouds

• polar (has dipole moment)

properties of water

• hydrogen bonding when water interacts with each other (can create large networks and rapidly fluctuate allowing for biochemical events)

• excellent solvent (b/c ability for fast interactions)

• interactions with dictate structures and functions of macromolecule

• participates in non-covalent bond interactions

hydrophobic effect

the tendency of water to minimize its contacts with hydrophobic molecules

sphere of hydration

water molecules form a “cage” around the hydrophobic solute

aggregation

the process where individual molecules, particles, or proteins clump together to form larger clusters or complexes, driven primarily by their interactions with surrounding water molecules (water takes the more favorable conformation and thermodynamically favorable)

ionization

the process where an atom or a molecule gains or loses electrons to become a charged particle called an ion; changes the acid and conj. base concentrations therefore pH and biochemical processes

pH

• measure of [H⁺] (acidity) in any solution

• = -log[H⁺]

• 1-6 pH= acidic

• 14=pH+pOH

pOH

=-log[OH^-]

acid

proton donor

base

proton acceptor

acid dissociation constant

K_a= [H₂O]+K_eq= [H₃O⁺][A^-]/[HA]

• tells us the strength of acid/ability to transfer a proton to water

pKa

=-log[K_a]

• works like pH (lower the # the stronger the acid

Henderson-Hasselbalch Equation

pH= pK_a+log[A^-]/[HA]

How is pH change of a solution determined?

• pK_a of the acid/base pair (how likely to donate proton)

• concentration on pair (how many available)

inflection point

point in titration which enough base has been added to neurtalize 50% of the acid (pH=pK_a)

equivalence point

point in titration at whcih enough base had been added to exactly neutralize the acid

buffering capacity

ability to resist pH changes on addition of an acid or base; when pH=pK_a and within 1 unit of the pK_a

primary amino group

• basic and ionizable

• on N-terminal side

• pka~9

carboxylic acid group

• acidic and ionizable

• on c-terminis side

• pka~2

dipolar ion

molecules that contain charged groups of opposite polarity (positive and negative charge)

zwiterions

• net charge= zero

pH< pKa

• acidic/protonated state prefered

• pH is lower than pka of group

• [A^-]<[HA]

pH>pKa

• deprotonated/basic state preferred

• pH is higher than pKa

• [HA]<[A^-]

characteristics of amino acid ionization

• all amino acids are weakly polyprotic acids

• at low pH, all ionizable groups will be protonated (+)

• ionizable groups start deprotonated based on pH compared to pKa

categories of amino acids

non-polar aliphatic (hydrophobic), uncharged polar, aromatic, negatively charged, and positively charged

non-polar side chains

non-ionizable, interact with each other (nonpolar) not water or other polar/ionic molecules, hydrophobic

polar side chains

• interact with surrounding water molecules and polar/ionic molecules (hydrogen, ionic, dipole)

• the pKa determines chemical properties of amino acid and resulting protein

aromatic groups

• bulky

• Phe & Trp= non-polar

• Try= polar & uncharged (can do hydrogen bonding)

uncharged groups

• uncharged at pH=7.4 (have partial charges)

• hydrophilic

• participate in hydrogen bonds b/c of thiols, hydroxyls, and amides

• serine, threonine, cystine, asparagine, glutamine

nonpolar aliphatic amino acids

• have 2 pKa values (carboxyl and amino)

• glycine, alanine, proline, valine, leucine, isoleucine, methionine

negatively charged groups

• negative charge when pH=7.4

• participate in ionic interactions with positively charged molecules

• can be hydrogen bond accepters

• aspartate & glutamate

positively charged groups

• participate in ionic interactions with negatively charged molecules

• can be hydrogen bond donors

• lysine, arginine, histidine (ionizes at pH=7.4)

importance of Histidine

• pka=6 meaning ionizable at pH=7.4

• can be protonated (+1) or neutral (0) at physiological pH

• important in catalytic in enzymes

isoelectric point

• pH at which the molecule has zero net charge

• molecules are at least soluble point

• pI=(pK_i+pK_j)/2

hydropathy

• measure combined hydrophobicity and hydrophilicity of an amino acid

• indicates where likely to find (interior/exterior)

• interior- +2.8-+5, high hydrophobicity (nonpolar amino acids)

• exterior- -1- -5, highly hydrophilic (charged/polar)

• throughout- -1-+2.8, slight; hydrophilic

asp

3.7

glu

4.3

His

6

Cys

8

Tyr

10

Lys

10

Arg

12

Thr

13

Ser

13

Carbonyl in peptide

3.5

Amino in peptide

8.5