CH339K

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CH339K

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Lecture 1 * * * * * * * * * * * * * * * * * * * Thermodynamics (Briefly) Systems est divisa in partes tres Open Exchange energy and matter Closed Exchange energy only ... – PowerPoint PPT presentation

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Title: CH339K

1
CH339K

Lecture 1

2
Textbook

Mathews, C. K., van Holde, K. E., Appling, D. R.,
and Anthony-Cahill, S. J. (2012) Biochemistry,
4th Ed., Prentice Hall, New York
I believe there are copies in the Coop that will
probably cost an arm and a leg.
Its cheaper online.
If you already have a copy of Lehninger, you can
probably get by.

3
Grades

3 hourly exams
Final exam (cumulative)
Several problem sets assigned as homework
throughout the semester
All weighted equally
Drop your lowest grade

4
Final Exam

Cumulative, but a little shallower than the
hourly exams
No, you dont have to take the final if youre
satisfied with your grade.
Dont blame the instructor that the exams on a
Saturday.

5
Other Stuff

Since youve paid for this class, you can get a
temporary library card by presenting your fee
slip at the PCL
Science Library is on the second floor of the
tower.
Chemistry (Mallet) library is on the second
(ground) floor of Welch, in the old part of the
building.
Instructions for getting a UT EID are on your fee
receipt
Parking is catch-as-catch-can, and gets more and
more removed every semester.
Consider buying a N (36, evening surface) or
N (60, evening garage or surface) permit.
Drop dates
09/06/2013 at NOON. - Last day to drop with 50
refund.
09/13/2013. - Last day to drop with no signatures
required.
11/15/2013 - Last day a student may change
registration in a class to or from the pass/fail
or credit/no credit basis.
11/15/2013 - Last day a student may drop a class
except for urgent and substantiated, nonacademic
reasons - that is, at the Deans discretion,
which is pretty hard to come by compelling
reason is the key world
Your beloved professors salary is based on the
number of students in the class a couple of weeks
down the line. In the unlikely event that you
decide to drop (after the refund date), please
wait until I get paid for you.

6
Classroom Rules

Theoretically, youre not supposed to eat or
drink in here
This is an evening class I dont mind
Just no slurping, crunching, or overt drooling
No snoring
If anyone has a CHL It is illegal to carry in
the buildings on campus. Lock it in your car.
I will try to remember to post the lecture slides
on the website before class so people can
download if they wish.

7
For Those who Have been out of School for a
WhileMetric Units
Exponent Prefix Abb. Example
12 tera- T Total power output of human race is a couple of Terawatts
9 giga- G Intel's top processor (Q9650) runs at 3 gigaherz
6 mega- M Biggest bomb ("Tsar Bomba," 1961) ever made was about 60 megatons
3 kilo- k Average human male weighs about 70 kilograms.
2 hecta- h A mole of gas at STP occupies about 0.22 hectaliters
1 deca- da My yard (an acre) is about 2.5 decameters by about 7.5 decameters
0 A liter is about a quart.
-1 deci- da A cup of coffee is about 2 - 2.5 deciliters.
-2 centi- c The distance from the tip of your thumb to the knuckle is about 2.5 centimeters.
-3 milli- m The thickness of a dime is about 1 millimeter.
-6 micro- m A typical bacterial cell is a couple of micrometers long.
-9 nano- n Memory chip response times are measured in nanoseconds.
-12 pico- p Inkjet printer drop sizes range from 3 to 25 picoliters
-15 femto- f The radius of a lead nucleus is about 8 femtometers
8
Common Biochemistry Slang
Å Angstrom 10-10 m (0.1 nm) Used for atomic/molecular dimensions
ml milliliter mil
mg milligram mig
ml microliter l or lambda
mg microgram g or gamma
mg/ml milligrams per milliliter migs per mil Used for macromolecule concentrations
cal calorie 4.184 joules Older but common energy unit.
9
Logs

We dont use much calculus in this class (about
10 minutes if Im really bloviating) but we use
logarithms a lot!
Log (x) y where 10y x
Ln (x) y where ey x
e , the base of the natural logarithm, is defined
as
If x A x B, then log(x) log(A) log(B)
if x A / B, then log(x) log(A) log(B)
if x AB, then log(x) B x log(A)

10
Elemental Composition of E. Coli
Element By parts By mass Weight in Earths Crust Ppm by volume in atmosphere
H 63 10 0.2 0.55
O 25.50 64 46.1 209,460
C 9.50 18 0.03 390 (as CO2)
N 1.40 3 0.05 780,840
Ca 0.30 2 4.15
P 0.20 1 0.10
Cl- 0.08 0.50 0.05
K 0.06 2.09
S 0.05 0.05
Na 0.03 2.96
Mg 0.01 2.33
11
Elements Required for Life

CHON are the primary components, making up both
the water component as well as being the primary
ingredients of proteins and carbohydrates.
P, S, K, Na, Ca, Mg and Cl- are present
in significant amounts as electrolytes in the
body fluids and cytoplasm, as well as ingredients
of nucleic acids (P) and protein (S).
Other elements are present as trace elements,
required in mg or mg
Known essential
Fe, Zn, Cu, Mn, I, Mb, Se, Cr, Co.
Possibly essential
F, B, Al, Si, Br, Ni, Cd, As, Sn, V, W.
Not all organisms require all trace elements
Trace elements are most commonly metals used as
catalytic reactants in enzymes

12
Why Carbon?

In order to make big, functional molecules like
proteins, nucleic acids, and carbohydrates, you
need
Atoms that make several bonds
Atoms that make strong bonds
Atoms that arent too hard to come by
Only a few elements pull that off

13
Why Carbon?
Only a few common elements form 3 or more
covalent bonds
14

B Electron deficient element forms few stable
compounds, must be charged to reach octet.
N Lone pairs of electrons in adjacent nitrogen
atoms repel each other, resulting in low bond
energy.
Si, P Relatively large atom size destabilizes
chains, and P has the same problem as N.
SiO The silicon-oxygen bond is stable, but
interesting compounds dont form at earthly
temperatures, and those that do are frequently of
low solubility.

15
Typical Covalent Bond Energies
Bond Bond energy Bond energy
Bond kcal/mol kJ/mol
C - C 83.1 348
C - O 84 351
Si - Si 42.3 177
Si - O 88.2 369
N - N 38.4 171
P - P 51.3 215
16
Silicon-Based Life Form
Species Horta
Location Janus VI
Habitat Subsurface chemotroph
Discovered Stardate 3196
Its life, Jim but not as we know it
17
A Little O-Chem Review
Bleagghhh..
18
Macromolecules

Biochemistry is characterized by big molecules
Big biomolecules are almost exclusively polymers
These monomeric units are usually asymmetrical,
producing directional polymers.
Since each type of monomer can come in several
varieties, the sequence in which they are
assembled contains and can convey information.
Biomolecules contain codes.
Codes can carry instructions on how to make
something else, on how to fold and assemble into
a three-dimensional structure, or on how to
distinguish one individual organism from another.

Polymers Assembled from (monomers)
Polysaccharides Sugars (monosaccharides)
Proteins Amino Acids
Nucleic Acids Nucleotides
Big Lipids Fatty Acids, Polyalcohols, etc.
19
Proteins, for example
are condensation products of a-amino acids.
20
There are 20 amino acids that are incorporated
into proteins
Nature is, however, quite messy, and these can be
modified into a number of other non-standard
a.a.s.
You are going to have to learn them off
eventually, so you might as well do it now.
21
Cells

All living organisms (except viruses ) are
composed of cells - self-contained, more or less
self-sufficient units, which are the fundamental
entities of life.
The largest cells are 5 orders of magnitude
larger in diameter, translating to 15 orders of
magnitude greater in volume, than the smallest.
Size is limited at the lower end by the minimum
volume needed to contain and solvate the genome
and the macromolecules necessary for metabolism
and DNA replication.
At the upper end, size is limited by the
decreasing surface to volume ratio and the
increasing distance from the center to the
periphery.

Smallest Mycoplasmas (PPLOs) 0.1 - 0.2 um
Largest Thiomargarita (prokaryote) .75 mm
Ostrich egg 17 cm (cheating!!!!!!!!!)
Gromia sphaerica 38 mm
Xenophyophores 20 cm (cheating as well)
22
Mycoplasmas (really small cells)

Smallest self-replicating organisms
Smallest genomes (500 1000 genes)
Generally pathogenic
Mycoplasma causes pneumonia
Ureaplasma causes venereally transmitted
urethritis and salpingitis

23
Thiomargarita namibiensis

Lives on the Namibian continental shelf
Uses nitrate as an e- acceptor
Oxidizes H2S to elemental S

Modern Gromia sphaerica

565 MYA Fossil

25
Xenophyophores (really big cells)

20-cm xenophyophore (deposit feeder) from a deep
Atlantic hydrothermal vent region. Notice the
extremely convoluted surface of the critter,
maximizing surface area and minimizing the
distance from any part to the surface.
Subclass of amoebas (sensu lato). Definite
potential for a scifi movie.

26
There are, of course, even larger cells
27
Cell Structure - Bugs
28
Cell Structure - Critters
29
Cell Structure - Plants
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Living organisms (not counting viruses) can be
classified according to the similarities of their
genomes.Carl Woese (U. Illinois) proposed the
3 branches of life back in the 1970s.Archaea
and Bacteria are both prokaryotic in cellular
organization, but quite distinct genetically
Horizontal gene transfer among organisms of
different species complicates the matter rather
severely.
32
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33
A little thermodynamics

(which is probably more than anybody wants)

34
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35
Thermodynamics (Briefly)

Systems est divisa in partes tres
Open
Exchange energy and matter
Closed
Exchange energy only
Isolated
Exchange nothing

36
More Thermodynamics

Energy can be exchanged as heat (q) or work (w)
By convention
q gt 0 heat has been gained by the system from
the surroundings
q lt 0 heat has been lost by the system to the
surroundings
w gt 0 work has been done by the system on the
surroundings
w lt 0 work has been done on the system by the
surroundings

37
First Law of Thermo

?ESYSTEM q w or, alternatively, q ?E w

38
First law of Thermo (cont.)
Example Oxidation of a Fatty Acid (Palmitic)

C16H32O2 23O2 (g) ? 16CO2 (g) 16H2O (l)
Under Constant Volume
q -9941.4 kJ/mol.
Under Constant Pressure
q -9958.7 kJ/mol

39
First Law of Thermo (cont.)

Why the difference?
Under Constant Volume,
q ?E w -9941.4 kJ/mol 0 -9941.4
kJ/mol
Under Constant Pressure, W is not 0!
Used 23 moles O2, only produced 16 moles CO2
W P?V
?V ?nRT/P
W ?nRT (-7 mol)(8.314 J/Kmol)(298 K) -17.3
kJ
q -9941.4 kJ/mol (-17.3 kJ/mol) -9958.7
kJ/mol

40
Enthalpy

Technically speaking, most cells operate under
constant pressure conditions
Practically, theres not much difference most of
the time
Enthalpy (H) is defined as
H E PV or
?H ?E P?V
If ?H gt 0, heat is flowing from the surroundings
to the system and the process is endothermic
if ?H lt 0, heat is being given off, and the
process is exothermic.
Many spontaneous processes are exothermic, but
not all

41
Endothermic but spontaneous

Ammonium Nitrate spontaneously dissolves in water
to the tune of about 2 kg/liter
Ammonium nitrate has a DHsolution of 25.7
kJ/mol
Remember positive enthalpy endothermic
This is the basis of instant cold packs

42
Second law of Thermo

Any spontaneous process must be accompanied by a
net increase in entropy (S).
What the heck is entropy?
Entropy is a measure of the disorderliness of a
system (and/or the surroundings).
What the heck does that mean?
Better, it is a measure of the number of states
that a system can occupy.
Huh?...let me explain

43
Entropy

S k x ln(W) where
W is the number of possible states
k is Boltzmanns constant, R/N
Two states of 5 atoms in 50 possible slots.

State 1 State 2 etc
X
X
X

X X

X

X
X
X
X
44
What happens if the volume increases?

K
K

K K
K
Adding volume increases the number of slots,
therefore increasing W, the number of states,
thereby increasing entropy.
45

We can quantify that
Number of atoms dissolved Na
Number of original slots no
Number of original states Wo
Number of final slots nf
Number of final states Wf

Since Na ltlt Wo and Na ltlt Wf (dilute solution),
then

and

So we can simplify the top equations to

and
46

Okay, so what (quantitatively) is the change in
entropy from increasing the volume?

Substituting and solving

So DS is logarithmically related to the change in
the number of slots.
47

Lets make the assumption that we are dealing
with 1 mole (i.e. N atoms) of solute dissolved in
a large volume of water.
Since Boltzmanns constant (k) R/N, our
equation resolves to

Since the number of slots is directly related
to the volume

And since the concentration is inversely related
to the volume

48
Entropy (cont.)

Entropy change tells us whether a reaction is
spontaneous, but
Entropy can increase in the System, the
Surroundings, or both, as long as the total is
positive.
Cant directly measure the entropy of the
surroundings.
HOWEVER, the change in enthalpy of the system is
an indirect measure of the change in entropy of
the surroundings an exothermic reaction
contributes heat (disorder) to the universe.

49
Gibbs Free Energy

We can coin a term called the Free Energy (G) of
the system which tells us the directionality of a
reaction.
G H TS
?G ?H - T ?S
If ?G lt 0, free energy is lost ? exergonic
forward rxn favored.
If ?G gt 0, free energy is gained ? endergonic
reverse rxn favored.

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Different ?Gs

?G is the change in free energy for a reaction
under some set of real conditions.
?Go is the change in free energy for a reaction
under standard conditions (all reactants 1M)
?Go is the change of free energy for a reaction
with all reactants at 1M and pH 7.

52
Partial Molar free Energies

The free energy of a mixture of stuff is equal to
the total free energies of all its components
The free energy contribution of each component is
the partial molar free energy