biochem terms exam 1

dipole

relationship between positive and negative charge

hydrogen bond donor

hydrogen bond attached to electronegative atom (O or N)

hydrogen bond acceptor

electronegative atoms with available lone pairs

• C-H methyl group is NOT polar enough to be a donor

hydrogen bonds

• individually weak, but many is stronger

• pay attention to type of hydrogen bond

nonpolar groups exposed to water

• water surrounding becomes more ordered —> less entropy (less randomness)

nonpolar groups buried together

releases ordered water —> increased entropy (more randomness)

entropy

“randomness” or “disorder”

• high entropy —> more randomness

• low entropy —> less randomness/more ordered

hydrophobic effect in protein core

Ala, Val, Leu, Ile, Phe

stereoisomers

bonds NEED to be broken to be stereoisomers

• if you can rotate a bond so both molecules look the same —> NOT stereoisomers

enantiomers

• type of stereoisomers

• mirror images

diastereomers

• type of stereoisomer

• NOT mirror images

• cis —> trans

• trans —> cis

• R —> S

• S —> R

geometric isomers

• type of stereoisomer

• cis —> trans

• trans —> cis

closed system

ONLY energy exchange w the surroundings

open system

exchanges energy AND matter w the surroundings

• organisms are open systems

homotropic allosteric modulator of hemoglobin

oxygen

heterotropic allosteric modulator of hemoglobin

• proteins

• CO2

• BPG

BPG

• increases oxygen delivery to tissues at high altitudes

• stabilizes T state by binding in the central cavity

  • enabling more effective release of oxygen in tissues

How does CO2 stabilize the T state of Hb?

by binding / reacting w its N-terminal amino group

enzymes

catalysts that speed up a rxn

• helps reach equilibrium faster

• most are proteins

how fast does cyclophilin speed up a rxn?

10^5

how fast does carbonic anhydrase speed up a rxn?

10^7

how fast does triose phosphate isomerase speed up a rxn?

10^9

how fast does carboxypeptidase A speed up a rxn?

10^11

how fast does phosphoglucomutase speed up a rxn?

10^12

how fast does Syccinyl-CoA transferase speed up a rxn?

10^13

how fast does urease speed up a rxn?

10^14

how fast does orotidine monophosphate decarboxylase speed up a rxn?

10^17

catalytic perfection

when enzyme works at maximum efficiency

• every encounter w enzyme and substrate leads to a rxn

catalytic efficiency

Kcat / Km

• shows how well an enzyme converts a substrate into a product

• high Kcat and low Km —> most efficient

specificity constant

Kcat / Km

turnover number

Kcat

Michaelis Constant

Km

• when Vo = ½ Vmax

Maximum Velocity

Vmax

• max speed or rate at which an enzyme can catalyze a rxn when fully saturated w substrate

Initial Velocity

Vo

Vo = (Vmax • S) / (Km + S)

is the rxn faster or slower w high activation E

slower

is rxn faster or slower w low activation E

faster

does adding an enzyme increase or decrease activation E

decrease

kinetics

• rxn rate

• enzymes affect kinetic E

thermodynamics

• reaction —> product

• point of equilibrium

• NOT affected by enzymes

entropy equation

ΔS = S final - S initial

enthalpy

• H

• number and kinds of bonds

free energy equation

ΔG = ΔH - TΔS

• temp on Kelvin (degrees celsius + 273)

ΔH < 0

releases heat (exothermic)

• breaks bonds

ΔH > 0

absorbs heat (endothermic)

• creates bonds

ΔS > 0

more randomness (increase entropy)

ΔS < 0

less randomness (decrease entropy)

• more order

ΔG < 0

happens spontaneously (exergonic)

ΔG > 0

NOT spontaneous (endergonic)

equilibrium equation

Keq = product / reactant

Standard Gibbs Free Energy

ΔG°

• when temp is 298K, solutes at 1M, and pressure is 1atm

Standard Gibb’s Free Energy Equation

ΔG° = -RT ln Keq

Free Energy Change of Standard Energy

ΔG = ΔG° + RT ln (products / reactants)

what orientation is hydrogen bonding strongest in?

straight line

electrostatic force equation

F = (k Q1 Q2) / εr²

F —> electrostatic force

Q1 and Q2 —> magnitude of charge

r —> distance between Q1 and Q2

ε —> constant

k —> Coulomb’s constant (1/4𝜋ε₀)

Coulomb’s Constant

k = 1 / 4𝜋ε₀

ε of vacuum

1

ε of air

1.00059

ε of water

80

Amphipathic

polar charged + nonpolar regions

nonpolar groups are hydro_____

phobic

polar groups are hydro_____

philic

when water reacts w nonpolar molecules, what happens to entropy?

it is decreased

hydrophobic effect

amphipathic molecules (polar + nonpolar)

• nonpolar clusters together in center

Van Der Waals

• partial positive reacts w partial negative (attracts)

osmotic pressure equation

Π = iMRT

i = Van Hoff factor (# of particles a solution splits into)

M = molarity (mols / L)

R = gas constant (0.08206)

T = temp in K

osmolarity equation

osmolarity = iM = (Π / RT)

Kw of water at 25C

1.0 × 10^-14

Kw equation

Kw = [H+] [OH-]

H+ when pH = 7

1 × 10-7

pH when [H+] = 1.0 × 10^-7

7

pH ion product equation

pH = -log[H+]

pH relationship

logarithmic

• log 10 = 1

• log 100 =2

• log 1000 =3

acid dissociation constant

Ka

Ka = [(H+)(A-)] / [HA]

is larger Ka stronger or weaker acid?

stronger (K > 1)

is low pKa stronger or weaker acid?

weaker (<7)

is lower Ka stronger or weaker acid?

weaker (K < 1)

is larger pKa stronger or weaker acid?

stronger (>7)

Henderson Hasselbach equation

pH = pKa + log (A- / HA)

Glycine

Gly

Alanine

Ala

Proline

Pro

Valine

Val

Leucine

Leu

Isoleucine

Ile

Methionine

Met

Phenylalanine

Phe

Tyrosine

Tyr

Tryptophan

Trp

Serine

Ser

Threonine

Thr

Cysteine

Cys

Asparagine

Asn

Glutamine

Gln

Lysine

Lys

Histidine

His

Arginine

Arg

Asparatate

Asp

Glutamate

Glu

Glycine

G

Alanine

A