GENERAL OVERVIEW:

TUESDAY 01-07-14

1: Glucose:

a: Food, what keeps you going... the energy that keeps you
alive. [true for all organisms]
b: one of the true beauties of Biochemistry is:
when we talk about the diversity of life, when we
start studying the enzymes, proteins, metabolic
pathways... they are all the same.
At the biochemical level, we are all on an equal
playing field
All anaerobic organisms [those that live on
oxygen] oxidize glucose to carbon dioxide and
water.

Huge heat releasing rxn.

the enthalpy of rxn. is very, very
favorable.
that heat, is basically dissipated
into the outside world and goes to
waste

 The trick of metabolism, is to

capture that energy to do something
useful with it.
Takes energy to make DNA,
proteins
To not waste energy as heat, what nature has
done is devised a way to break down glucose in a
bunch of little steps
each step releases a little bit of energy, and
so what the cell does, it captures that energy
in little packets and stores it as ATP.
[Taking heat energy and converting it to
chemical energy]
Do this in incremental steps it what
allows the cell to capture the heat
energy.

2: The whole science of thermodynamics, and Physical chemistry

is:
a: If you take any kind of energy yielding rxn. and you take
out the energy in little bitty pieces...
You get much more efficiency, then you would by
trying to capture the heat at the end. [ It's impossible
to capture all the heat and chemical energy at the end
of the rxn. but you capture a lot more if you do it in
little tiny packets]
3: Equate H atoms w/ Energy.
a: the more H atoms a molecule has, the more energy rich it

is.
b: Therefore glucose is a very energy rich molecule [ b/c it
has a lot of H atoms]
if you rip off all H atoms and give to Oxygen very
favorable rxn.

3: The Rxn. of molecular oxygen ( ) of any biological molecule

(amino acids, glucose, DNA, etc) is a very favorable rxn. [IT LIES
TO THE RIGHT]
a: Oxygen is a very powerful oxidizing agent, and what it
wants to do is take H atoms away from molecules
b: THINK ABOUT THIS:
We are made up of a whole bunch of H atoms within
our molecules, and we live in a atmosphere of about
20% oxygen; how is that possible that we don't
spontaneously ignite. Why arn't we burning up?
4: Where does the glucose come from?
a: We want to run the rxn. backwards... want to add H atoms
to Carbon Dioxide to make glucose [ takes a lot of energy to

do]
b: Where does the energy come from?
THE SUN PHOTOSYNTHESIS [the source of energy
on earth]
enables plants to take carbon dioxide and
combines it with H atoms to make glucose
we eat plants, animals eat plants, we eat
animals how we get glucose.

THE SOURCE OF ALL ENERGY IS THE SUN

5: We know that Entropy is associated with order and disorder, so
things tend to spontaneously disorder. That's what's happening
on earth this balance of order and disorder.
HOW IS IT POSSIBLE THAT WE KEEP ON DECREASING
ENTROPY IN THE BIOSPHERE (EVERYTHING BECOMES
MORE ORDERED), WHEN THE 2ND LAW OF
THERMODYNAMICS TELLS US THAT EVERYTHING MUST
SPONTANEOUSLY DISORDER??

The earth and everything around it has been looked at

as a "closed system" that is we have the earth,
atmosphere, and we are not exchanging energy with
anything else out there.
If you have a closed system has to
spontaneously disorder [ can't cause things to be
ordered, unless there is energy coming from the
outside forcing things to become ordered]
Where is that energy coming from?
The earth is not a closed system, we
are an open system. We are exchanging
with the universe, so what is providing
us with that energy to order things
around us?
THE SUN
when to sun goes, we become a
closed system and we all go bye
bye.
WHAT'S UNIQUE ABOUT BIOCHEMISTRY, COMPARED TO OTHER
CHEMISTRY CLASSES?
1: Working at room temperature, 37 C
2: Operating at neutral pH (life is not compatible outside of a very
narrow pH range)
A: Kinds of Molecules we are concerned with:
1: Macromolecules (big molecules)
a: Polysaccharides - energy storage

 sugar unit that repeats itself over and over again.

what starch, cellulose look like
b: Nucleic acids - genetic info.

c: Proteins - enzymes, structural

[What they all have in common, when they form a bond, water is
eliminated from the molecule in the process]
More efficient to store a polymer than each individual units
due to less Os and Hs in the polymer compared to each
individual units which have more Os and Hs that take up
space.

B: All of this is happening in water. (water - unusual properties)

C: Weak forces (really prevalent in biochemical systems)
1: What is the difference between a weak and a strong force?
a covalent bond between 2 atoms is a really strong
force.
Weak forces are non-bonding interactions that are
not covalent
2: Key factor that controls protein folding
3: How the double helix is formed
3 KEY CONCEPTS THAT REALLY SEPARATE BIOCHEMICAL
SYSTEMS FROM ORGANIC CHEMICAL SYSTEMS.
BIOENERGETICS, THERMODYNAMICS
A: EQUILIBRIUM CONSTANT:

Example:

2: If rxn. is favorable K > 1.0

(if a process is spontaneous, then rxn. is moving to the
right)
3: If rxn. is not favorable K

< 1.0

4: RULE OF THUMB: What you find in biological systems, a

protein and an enzyme bind together K for that kind of rxn.
is in the order of
roughly [ biology operates in equilibrium

constants in that range]

WE USUALLY DON'T TALK IN TERMS OF EQUILIBRIUM
CONSTANTS, WE INSTEAD TALK IN TERMS OF FREE ENERGY.
B: FREE ENERGY (G):
1: Another measurement of spontaneity of a rxn.
2: We can not normally measure the free energy of the reactant
or the product, but we can measure the change in free energy as
we go from reactants to products.

a: So if a rxn. is spontaneous:

3: What you don't want to mix up is free energy with things like
potential energy.
a: example - have a positive charge and a negative charge,
there's an energy of interaction between the two [NOT FREE
ENERGY CHANGE]
The free energy change is the measure of whether it
wants to be in one state vs. another.
Its the measure of the equilibrium constant, how far
to the left or right does the rxn. sit.
C: Relationship between K
energy)
1:

(equilibrium constant) and G (free

2: G = Standard state free energy

[rm temp, 1atm pressure, pH 6]
**not going to go away from this in this class. will
always be standard state free energy**
a: Basically tells us if, at equilibrium, a reaction lies to the
right or left.
3: G = Free energy under non-equilibrium conditions
a: inside living systems reactions, quite often operations in
biology
b: G 0
4: therefore...

5: Example:

a: Suppose we have 1mM Fructose-6-phosphate and 5mM

Glucose-6-phosphate. What is the free energy change?

D: you can couple unfavorable rxn. with favorable rxn. [Free energies
are additive]
1: This is how we drive rxns. that are unfavorable
2: example
Key rxn. to get glucose into metabolism, is to phosphorylate
Stick phosphate group on glucose, gets it ready for
further metabolism.

3: An enzyme can make a rxn. go faster, but it cant change G.

a: You can make rxn. go faster, but you cant change the
thermodynamics. [THE THERMODYNAMICS IS ABSOLUTE]
4: What nature has done is devised a way to couple these rxn.
a: So we are using the favorable rxn. of ATP hydrolysis and
coupling it with with the phosphorylation of Glucose to
drive the rxn.
So what the enzyme does is binds glucose and binds
ATP puts them together and the rxn. can go at the
active site. [in soln. nothing happens].
the thermodynamics hasn't changed, it is the
enzyme that allows the rxn. to happen.
THIS IS HOW BIOCHEMICAL RXNS. ARE
PUSHED.
E: ENTHALPY & ENTROPY:
1: The free energy (G) is not alone, it is defined by enthalpy
(H) & Entrophy (S).
G = H - T S
a: What this tells us is H is negative rxn. is favorable b/c
G will be more negative.
b: If S is positive rxn. is more favorable b/c we have a
minus a positive
c: If S is negative rxn. is an unfavorable process b/c a
minus times a minus become a positive.
2: ENTHALPY (H):
is the heat given off in a rxn.
H = H

-H

a: example:
You have water and drop HCl into the water, the
beaker gets hot.
H for the rxn is <0 (its negative)
if the heat of the rxn. is negative, then the
change in heat of the rxn. is negative. WHY
DID THE BEAKER GET HOT??
The beaker is not part of the rxn. it is
just holding the rxn.
In thermodynamics everything is
about the system. What defines the
system.
In this case the system is water &
HCl. The beaker doesn't count, it is
just the carrier. THEREFORE...
The beaker got hot, what that
means is the rxn. got cool.
meaning it gave off heat & the
heat had to go somewhere went
to the outside world meaning the
beaker.
b: Example 2:
Lets say we take urea (which is really soluble) and
dump it in water, the beaker gets really cold. It will
start to condense leading to little drippings on the side
of the beaker.
Is H positive or negative for that rxn?
H > 0 [ positive]
b/c the beaker got cold, the beaker was
giving heat to the rxn.

SO DON'T BE FOOLED BY WHAT THE RXN. FEELS LIKE B/C

IT IS NOT PART OF THE SYSTEM. THE SYSTEM ITSELF
WHICH IS ACTUALLY UNDER GOING THROUGH RXN. IS
CHANGING THE OUTSIDE WORLD.
c: IN GENERAL:
The making of bonds, is a favorable H. [H < 0]
When you break a bond, is an unfavorable H
[H > 0]
3: ENTROPY (S):
Is a measure of order in the system.
S = S

-S

In the purist turn is a measure of spontaneity.

a: It turns out that things spontaneously goes from higher
order to lower order (where concept of order and disorder
came from)
b: S > 0 is always favorable
[a spontaneous/ favorable process tends toward
disorder]
c: Classic example:

In order to go from disorder (large S) to order (small

S), energy must be applied. have to push down to
hold molecules together.

F: Enthalpy and Entropy in terms of Molecules:

1:
H < 0 [making of a chemical bond is usually a heat
generating process]
In going from 2 molecules to 1 molecule, the system has
become more ordered THEREFORE S < 0 [this opposes the
rxn]
You don't have one dominating over the other... has to be a
balanced between enthalpy and entropy.
VERY TYPICAL FOR ENTHALPY AND ENTROPY TO
BALCNE OR COMPENSATE FOR ONE ANOTHER.
2: Examples:
a: rxn. between oxygen and hydrogen to form water.

b:

G < 0 therefore favorable rxn.

H > 0 therefore not favorable
[reason: broken up a lot of bonds]
S > 0 therefore favorable
[reason: taken complex molecule, and busted it
up into 2 1/2 compounds]

WEAK FORCES
1: What makes weak forces so special in biology is that
everything occurs in water [water is a pretty strange molecule]
a: Water:

 is tetrahedral
has 2 H atoms
is a double headed molecule b/c it has 2 positive
poles and 2 negative poles
has 2 unpaired e-s
can do a lot of electrostatic interactions
HOW MANY HYDROGEN BONDS CAN A SINGLE
WATER MOLECULE FORM?
4 bonds
has a strong dipole moment

 The longer the vector, the stronger the dipole...

that means the stronger the charge separation on
the molecule.
2: DIPOLE MOMENT:
The ability of the molecule to reorient itself among another
molecule.
a: Other dipole example:

b: Most organic molecules don't have a dipole

ex: methane, ethane, benzene.
don't have a fixed dipole, they don't have a charge
separation
however, take 2 benzene and bring them
together, the e-s in that molecule will want to
redistribute (reorient) themselves so that the
positive end of one benzene is next to the
negative end of the other
[the e-s in one benzene molecule will slightly
redistribute themselves so there will be a
negative end, a positive end, and the one
next to it will have the same distribution but

flipped around ANTIPARALLEL. ]

Benzene molecule all by itself has no
dipole, but put it next to another organic
molecule, the e-s rearrange themselves to
give an INDUCED DIPOLE
REALLY IMPORTANT IN BIOLOGY B/C
THIS IS HOW NON POLAR
UNCHARGED MOLECULES INTERACT
WITH ONE ANOTHER.

c: Induced dipole has a special formulation

2 types of real energy
"Whats the energy of 2 atoms interacting with
each other?"
Have 2 molecules that are infinity apart, and
start to bring them together... there is going to be
an attraction between the 2
- dipoles are going to start inducing
- molecules are going to flip around and light
up
- distance at which everything is absolutely
perfect and everything is optimal.
[NEGATIVE ENERGY IS FAVORABLE]

- Take the two atoms and push them even

closer, the energy is going to start going
positive [ repulsive term]
OPTIMAL DISTANCE = REPULSIVE + ATTRACTIVE

Important in biology b/c when a

substrate interacts with an enzyme
a lot of them are non polar atoms that are
interacting with one another, so they don't
come into play until they are really close together
A: 3 Things Need to REMEMBER FOR THIS CLASS:
1: Dispersion (induced dipole)
involves mutual synchronization of fluctuating charges

2: Charge-Charge distribution
Longest-range force; nondirectional

If your bring 2 molecules together, first thing your going

to see is the charge difference.
opposite charges will start come together and we will get induced
dipoles, when the charges come together quite a bit closer, we get
charge- charge distribution.
3: Hydrogen Bond
Charge attraction + partial covalent bond

Special charge-charge interactions It is directional. \

a: The special thing about water, it can form 4 hydrogen

bonds.
Can interact with itself in multiple ways.

- water molecule keeps flipping around and

changing partners.
Doesn't just sit there... b/c it can do 4 H
bonds, it is always bonded to another one.
[Entropy is great... since it can flip around,
things are relatively disordered.. by
maintaining all the H bonds, enthalpy is
really favorable]

b: Different functional groups that do hydrogen bonding that

will be seen over and over again.

c: Though experiment:
What happens when you dissolve sodium chloride
(NaCl) in water?

 It dissolves in water, why is it so

soluble?
We have little water molecules
with great dipoles, so Hydrogen
orient themselves around the
negative chlorides, where as the
lone pairs on the oxygen can
orient themselves around the
positive sodium.
BUT... AT WHAT COST?
Sodium Chloride form very tight
interactions, so we have to break
up the +- interaction in order to
get the water molecules around
them [breaking up this
interaction is a very unfavorable
enthalpy thing to do H > 0]
HOWEVER WHEN WATER FORMS
AROUND THE ATOMS H < 0
So why is NaCl so soluble? why does it want to break
up? Driving force?
ENTROPY is the driving force.
Taking highly ordered crystal lattice of
salt, and breaking it up. [causing atoms to
become more free... we are creating a
more disordered system.]

How does this translate into proteins?

If you take two substates, and each has a charged
group, and put them on active site of a protein that
hydrophobic (nonpolar)... Those charge-charge
interactions are going to be really strong b/c there is
no water molecules to compete with it
This is why H bonds, why charge-charge
interactions all balance out.