Transcript Lecture 2 (1/16/13) "Introduction and the 4 Macromolecules of Life"

Today’s lecture #2
Quick things
• Close the door (thanks anonymous
person)
• Web cite:
http://people.physics.illinois.edu/Selvin/PRS/
PRS.html
(my web site…click on Physics 475 Sp13)
http://people.physics.illinois.edu/Selvin/inde
xSP13.html
• Kind of rushed today cause want to get to
protein structures for Klaus Schulten’s
lecture
01/15/2013
Questions from last Lecture
• Liked King Kong
• Could he have existed? No
• Quantum Mechanics
Not really relevant,
Although Heisenberg Uncertainty Principle
and theory of fluorescence/light is somewhat relevant.
• Topics of written/oral
--you choice, although most likely should be from
Science, Nature, Cell.
See handout on Web page.
Today’s lecture
•
•
•
•
Temperature of earth: Greenhouse Effect
What is Life?
∆G and ∆E stability of molecules
The 4 types of macromolecules
Nucleic Acids, Proteins, Carbohydrates, Lipids
• Central Dogma of Molecular Biology
• DNA
• Protein Structure
Is there water-based life on other planets?
Example of physical limits to life.
Idea: For water-based life, 0º < Tave < 100ºC
Can we calculate Tave of planets in our solar system?
Earth
What determines (surface) temp?
Answer: Heat (photons) from sun
How much light?
Ie= 1.35 kW/m2
1 meter
1 meter
How many (flood)lights?
# Floodlight ~ 30 (1 meter away)
(Incandescent light 3% efficient)
Why determines earth temperature?
Why can life exist?
Temp of earth constant
Heat in = Heat out
Heat In (Absorbed)
=
(1-a)IepRe2
a= reflectivity of object
aearth ≈ 0.3

= Heat Out
= aσ T4 x (surface area)
σ = const (=5.7 x 10-8 W/m20k4)
T = absolute Temp.
(Stefan-Boltzmann Law)
Kittel, Thermal Physics pg 91-96
(1-a)IepRe2 =
(aσT4)(4pRe2)
(1- a )I e
4s
Heat out
Heat in
[Note: Re2 cancel]
é (1- 0.3)1350W /m 2 ù
ú = Te
4ê
-8
2 4
= T ë (4)(5.7 ´10 w/m k ) û
1/4
= 253° K = -15
˚C
Too cold! Actual <Te> = 288 ° K = 15 ˚C
If Earth had no atmosphere the global average surface
temperature would be -15˚C. With an atmosphere, temp is
actually would be ≈15˚C.
Conclusions of calculations
Temp of earth primarily determined by
sun’s photons, not earth’s mantle.
Calculation off because of
Greenhouse effect: earth has an atmosphere.
Heat out
Heat in
Sun
Earth
You calculate
what temperature
should be!
Boltzmann factor & Degeneracy
• Generalize the definition of the free energy to include
degeneracy. Like flipping a deck of cards twice.
• Each energy level may be populated with several
molecules, i.e. have many accessible states. We define
the multiplicity Wi as the number of accessible states
with energy Ei. For example:
W=3
W=2
W=3
W=2
3

2

1

0
Assume that a more general formula for the probability
P(Ei, Wi) = (Wi/Z) e-Ei/kT
of finding a molecule with energy Ei, with the multiplicity factor Wi.
Using Wi = exp[ln Wi] ; and later define S= kln[Wi]; G= E-TS
P(Ei, Wi) = (Wi/Z) exp(-Ei/kT) = (1/Z) [exp(lnWi)] exp(-Ei/kT)
= (1/Z) exp -(Ei – kTlnWi)/kT
Define S= kln[Wi]
P(Ei, Wi) = (1/Z) exp -(Ei – TS)/kT = = (1/Z) exp –(Fi )/kT
where F = Helmholtz free energy which is same as Gibb’s
Free Energy for liquids (non-gasses).
Note: ∆G because always energy w.r.t. some zero (like E,
∆E); define E and S. Typically, 1M concentration.
Equilibrium
How stable is one state over
another?
A  B
Probability of being in B = Z-1exp(-GB/kT)
Probability of being in A = Z-1(exp-GA/kT)
Keq = B/A = exp (-GB/kT+ GA/kT)
= exp –([GA- GA]/kT)= exp –(∆G/kT)
∆G = -kTlnKeq
Stability and thermal activation
Both systems are stable because they
have activation energy to convert!
All chemical reactions involve changes in energy.
Some reactions release energy (exothermic) and
others absorb it (endothermic).
Keq= [B]/[A]
[Says nothing about
∆G+rev/forward]
∆G+forward
∆G+rev
Keq = f(∆G)?
Keq = exp(-∆G/kT)
∆G
∆G = -kT ln (Keq)
Enzymes
(Catalyst)
∆G+rev
∆G+forward
∆G
If Activation Energy < kT, then rxn goes forward. If not,
need to couple it to external energy source (ATP).
Breaking down a polymer
How you get energy/ Why you eat.
(b) Hydrolysis: breaking down a polymer
High energy
Einitial
1
2
3
4
Hydrolysis adds
a water molecule,
breaking a bond.
Low(er) energy
1
Efinall
2
Gives (free)
Energy
(Efinal < Einitial;
Sfinal > Sinitial)
3
Carbohydrate—polymer
You eat food, break it down
into smaller pieces and you gain energy
Both systems are stable cause they have
activation energy to convert!
Forming/breaking down a polymer
(a) Dehydration reaction: synthesizing a polymer
1
2
3
Short polymer
Unlinked monomer
Dehydration removes
a water molecule,
forming a new bond.
1
2
3
4
Takes (free)
Energy (ATP)
(Efinal> Einitial;
Sfinal< Sinitial)
Longer polymer
Efinal= Einitial + ATP + heat
You live by taking some energy (in the form
of a small molecule ATP, Adenosine TriPhosphate, whose energy ultimately comes
from food, which gets energy from the Sun)
and building up polymers.
Need to know Chemical Bonding
4 types
1. Covalent – 100kT. Sharing of electrons. C-H
Is light enough to break covalent bond?
1um =1eV; kT=1/20eV. 1um= 20kT: close (yup)
2. Ionic - varies tremendously, 100kT to few kT.
+ and – attract, but depends on solvent.
Na+ Cl- = few kT (break up easily)
3. Hydrogen – few kT, up to 5kT
1. Hydrogen attached to a very
electro-negative elements, (O, N)
causing the hydrogen to acquire a
significant amount of positive
charge.
2. Lone pair– electrons in relatively
small space, very negative.
Result is H is (+) and O is (-). Will
bind to other molecules
4. Van der Waals –kT (weakest, but many of them
together--significant). Two neutral atoms have
instantaneous dipoles, and attract.
Neon: -246°C; Xenon: 108°C
www.chemguide.co.uk/atoms/bonding/hbond.html#top
Break time!
Somebody wrote:
“It’s very funny to meet random
people in class”
so do like last time…
4 minutes (2 min per person)
With someone you don’t know,
Find out their:
1.Name, Year, undergrad vs. grad.
2.Why you’re taking the course.
3.Tell one thing that’s surprising.
A few people will have to report!
4 Large [Macro]Molecules
(from small molecules)
Biological polymers (Large molecule
made from many smaller building block)
•
•
•
•
DNA & RNA  Nucleotides
Proteins  Amino Acids
Carbohydrates  Sugars
Fats (also called Lipids) Fatty
acids
Each is used to:
a. Make macromolecules/structural
b. Energy Source
c. Information– Storage/signaling
DNA & RNA ; ATP; Genetic Information
Proteins; break down yields energy;
nerve impulses.
:
The 4 types of macromolecules
Proteins
DNA
(RNA)
Lipids (Fat)
Carbohydrates
Protein Structu
• Primary
--20 different
amino acids
• Secondary
• Tertiary
(single polypep
Quaternary–
multiple polypeptides
Myoglobin- 1
Linear sequence of ~ 20 amino acids
Can get enormous diversity and
function with Proteins
Figure 5.20b
4 Different layers of Protein
Structure
Tertiary
structure
Secondary
structure
Quaternary
structure
a helix
Hydrogen bond
 pleated sheet
( arrow toward
carboxyl end)
 strand
Hydrogen
bond
Transthyretin
polypeptide
Transthyretin
protein
Minimal knowledge about Nucleotides
• 4 nucleotides: A,T,G,C
• A=T ≈ 2kT two hydrogen bonds
G=C ≈ 4kT three hydrogen bonds
[More Next time]
Homework #1 Assigned!
Due at beginning of class
Jan. 23, 2013
[also read Chpt 1 of Phillips et al.
Evaluate class
1. What was the most interesting thing you
learned in class today?
2. What are you confused about?
3. Related to today’s subject, what would
you like to know more about?
4. Any helpful comments.
Put your name in upper right-corner.
Then tear off your name before turning in.
(That way you can be brutally honest!)
Answer, and turn in at the end of class.
(I’ll give you ~5 minutes.)