CH339K

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CH339K

• Lecture 1

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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.

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Grades

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

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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.

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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.

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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.

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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
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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.
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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)

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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
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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

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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

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Why Carbon?
Only a few common elements form 3 or more
covalent bonds
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• 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.

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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
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Silicon-Based Life Form
Species Horta
Location Janus VI
Habitat Subsurface chemotroph
Discovered Stardate 3196
Its life, Jim but not as we know it
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A Little O-Chem Review
Bleagghhh..
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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.
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Proteins, for example
are condensation products of a-amino acids.
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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.
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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)
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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

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Thiomargarita namibiensis

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

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• Modern Gromia sphaerica

• 565 MYA Fossil

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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.

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There are, of course, even larger cells
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Cell Structure - Bugs
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Cell Structure - Critters
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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.
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A little thermodynamics

• (which is probably more than anybody wants)

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Thermodynamics (Briefly)

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

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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

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First Law of Thermo

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

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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

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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

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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

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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

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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

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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
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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.
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• 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
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• 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.
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• 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

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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.

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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.

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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

• Where

• In dilute (i.e. biochemical) solutions,
• the activity of a solute is its concentration
• The activity of the solvent is 1

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Free Energy and Chemical Equilibrium

• Take a simple reaction
• A B ? C D
• Then we can figure the Free Energy Change

Rearranging
Combining Factoring
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Freee Energy and Equilibrium (cont.)

• Hang on a second!
• AB is the product of the reactant
  concentrations
• CD is the product of the product
  concentrations
• Remembering Freshman Chem, we have a word for
  that ratio.

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Free Energy and Equilibrium (cont.)

• SO ?Go for a reaction is related to the
  equilibrium constant for that reaction.
• ?Go -RTlnKeq
• Or
• Keq e-?Go/RT
• If you know one, you can determine the other.

Note things profs highlight with colored arrows
are probably worth remembering
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Real Free Energy of a Reaction

• As derived 2 slides previously
• DG is related to DGo, adjusted for the
  concentration of the reactants

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Example
Glucose-6-Phosphate ? Glucose Pi ?Go -4
kJ/mol At 100 µM Glucose-6-Phosphate
5 mM Phosphate 10 mM Glucose
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Measuring H, S, and G

• We know
• ?G ?H - T ?S
• And
• ?Go -RTlnKeq
• So
• ?H - T ?S -RTlnKeq
• Or

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Measuring H, S, and G

• This is the vant Hoff Equation
• You can control T
• You can measure Keq
• If you plot ln(Keq) versus 1/T, you get a line
• Slope -?Ho/R
• Y-intercept ?So/R

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Vant Hoff Plot

• ?Ho -902.1 8.315 -7500 J/mol
• ?So 3.61 8.315 30 J/Kmol