Transcript Lecture 2 (1/25/10) "The Language of Life"

Homework
Read Chapter 1 of ECB
Due week from this Wednesday.
(extra time for books to come)
Homework Set #1 on web
Due at start of class next Monday
Due to your requests:
Lecture on :
Evolution
Protein folding
What is Physics 498Bio?
Biophysics or Biological Physics?
Mathematician Stanislaw Ulam:
“Ask not what physics can do for biology, ask what
biology can do for physics. The first is biophysics, the
second biological physics.
Biological physics is a subset of physics.
Wolfgang Pauli:
“The history of physics is a history of making
concepts.”
The idea in biological physics is to untangle
the incredibly complex of biology in terms of
so-called simple ideas of physics. Eventually,
one gets a greater understanding and new
technology.
Biological physics : under the mantle of complex physics, where
the complexity comes from biology. But it can’t be too
complicated, otherwise you never get anywhere. At present, to
deal with biological systems in their living environment is much
too complex. Eventually, it might not be so, but for now it is.
Protein Folding—good example of Biological
Physics
Biological Physics
“Good” Problem: Protein Folding
Unfolded
Inactive

Folded

Active
Hans Frauenfelder ,
founder of
biological physics.
Wolynes, PNAS, 1998
Energy/ Entropy Landscape of Protein Folding
(More later…)
Biophysics
vs.
Biological Physics
We’ll studying both,
but emphasis on biophysics
– get new biology by applying new physics…lasers,
x-rays, microscopes
The Language of Life
What things are alive?
“I know it when I see it.”
-- Justice Potter Steward
in a 1964 Supreme Court case on pornography
Qualities we associate with living being:
—it moves, it reproduces, it eats.
prerequisite for living
Trees don’t move,
A person can be alive even if they are unable to move.
People are certainly alive if they’re born sterile, or
become so.
Viruses can’t reproduce by themselves
—they high-jack apparatus of their bacterial hosts
to do the job.
Is a virus alive? People disagree.
Eating –yes, although the must include trees:
drinking (water) and taking in energy via sunlight.
Living defined at the
molecular level
At the molecular level, the definition,
surprisingly, becomes somewhat less
complex.
All living organism consist of complex,
heterogeneous macromolecules
Necessary, but not sufficient.
A bag of starch, mixed in with other polymers, is
clearly not alive—but is does appear to be necessary.
All living organisms consist and make
complex, heterogeneous
macromolecules.
They do this by ingesting them and making
them from simple compounds.
Amazingly, through evolution, organism have
survived by making only 4 macromolecules
What do you make?
The 4 essential macromolecules
Much of discussion from “Physical Biology of the
Cell”, by R. Phillips, Jane Kondev, and Julie Theriot
Protein
(Branched)
carbohydrate
Lipid
(cell membrane)
(Fat)
DNA
Each macromolecules, made from small pieces.
(A) DNA made up of nucleotides, (B) Proteins, made up of amino acids;
(C) Lipid molecule from fatty acids (generally hydrophobic), often in
cell membrane, (D) Branch carbohydrate from the simple sugars.
Two Great Polymer Languages
(via Francis Crick)
Nucleic Acid alphabet = 4 nucleotides
Proteins alphabet = 20 amino acids
Few # of alphabets
diverse polymers
Length of a polymer can vary enormously--from
a single one to 100 million or so
--hence the number of possible combinations
that make up the polymer, is enormous.
In biology, polymer –106-108 monomers long.
Let’s say N equals 15--a very short polymer. So for this
short polymer, and alphabet = 4, that’s 415 = 230 =
1,073,741,824 or over a billion different combinations.
Adding more complexity : Isomers
Two Polymers : made up of the exactly the same type of
monomers and have the same order of monomers, there can be
an enormous variation in their physical placement, known as
isomers.
An isomer is where you have the same number of atoms in the two
polymers, but the arrangements of these atoms are different. For
example, each monomer can be connected to another monomer either
straight or bent fashion. Then there is 2n4n = 8n = 23n= 245 =
35,184,372,088,832 or over 35 trillion different polymers of length
N=15.
So, from a relatively simple set, one can get
tremendous diversity.
Get to know your neighbors
You will have to report to the whole class
immediately afterwards! –so listen up!
With a partner (who you don’t know)…
Tell your name, your year (undergrad, vs. grad.)
What you want to be when you “grow up”
Tell one thing that’s surprising about yourself.
An example (me):
This is Paul. He’s a senior citizen. (Ph.D. 1990,
Physics, but really Biophysics)
When he grows up (in the next stage of his life),
I want to be a ski instructor.
Something surprising about myself:
6 years ago I had an unfortunate incident while
in San Diego hitting a car head-on while riding
my bicycle. After months of hospitalization and
rehab, I can do most things, but have trouble
with my leg and arm.
Been arrested multiple times.
DNA is made up of A,T,C,G in a
double helix of anti-parallel
strands
3.4 Å
3.4 nm per
~10 base-pairs
= 1 turn (360º)
Must come apart for bases to be read.
Anti-parallel has interesting interpretation for way DNA is made.
One enzyme that read 5’ 3’ or two, with another reading 3’ 5’?
Structure of DNA
A-T, G-C bond, line up
Two strands are oppositely oriented
Form a minor and major groove
U RNA
U
6Å
12 Å
Every 3 base pairs encode for one amino acid
DNA RNA Proteins
Central Dogma of Biology
DNA: series of 4 nucleotides (bases): A,T,G,C

Transcription [DNA & RNA similar]
RNA: series of 4 nucleotides (bases): A,U,G,C

Translation [RNA & Proteins different]
Proteins: series of 20 amino acids: Met-Ala-Val-…
each coded by 3 bases  amino acid
AUG Methionine; GCU  Alanine; GUU Valine
Proteins are 3-D strings of linear amino acids
Do everything: structure, enzymes…
http://learn.genetics.utah.edu/units/basics/transcribe/
DNA  RNA  Amino acids
Transcribe
Genetic code
translate (1 codon = 3 bases)
U is a slightly altered T
Central Dogma of Biology
Minimal knowledge about Nucleotides
• 4 nucleotides: A,T,G,C
• A=T ≈ 2kT two hydrogen bonds
G=C ≈ 4kT three hydrogen bonds
• Many weak bonds…very strong overall
structure. DNA is stable.
• Requires enzyme/ATP to split apart, to do its
thing: replicate, transcribe.
• ATP– universal food source of all cells.
≈ 25 kT ≈ 100pN-nm.
DNA: A-T 2 H bonds; G-C 3 H bonds
Thymine
Cytosine
Hydrogen Bonds
(2kT)
Guanine
Adenine
G-C more stable than A-T
–  stacking keeps it together (Grease);
Phosphate negative charge makes it water soluble
(Sort of like soap)
Boltzman factor + Partition function
(review of basic Stat. Mech. – see Kittel, Thermal Physics
E1
Temp, T
E0
If T = 0 ºK, what proportion of particles will be in E1, Eo?
Answer: pop(Eo) = 1
pop(E1) = 0
If T > 0 ºK, what proportion of particles will be in E1, Eo?
P  Ei    const. e Ei / kT
P  E1 
- E1 -E 0  kT
 e
e-(E -Eo)/kBT
P  E 0  Boltzman factor
1
P E   1
i
const.=
1
N
e
 1/ Z
J= represents jth state
-E j / kT
j=0
Z = partition function
N
 e
j=0
1
P  E i   e  Ei |kT
z
-E j / kT
Partition Function for 2-state system
- 1 E1
- o
Eo
e -E1/kT
P  E1  = -E o /kT
e
+e -E1/kT
Simple case: Ball in gravitational field.
Thermal fluctuations, finite probability of being at height, h.
E = ??
E = mgh
Eo h = 0
E1 h =(mg)(h meter)
P(h)
=
P(0)
e-mgh/kT
As ball gets smaller, probability gets smaller / larger ?
“Ball” the size of O2? Why can you breathe standing up?
What is 1/e height for O2?
For O2, 1/e height is ~10 km ~height of Mt. Everest.
(10 km is “death zone”)
Probability of dying if you go over 20,000 ft is 10% for every
trip!!
Two states
A – B bonded: E ~ -5 kT (a few H-bonds)
A , B not bonded: E = ?? 0
A+B  A–B

PA B
e 5 kT / kT
5


e
 148
 o / kT
PA, B
e
149 molecules
148 will be A - B
1 will be A, B
DNA double helix: Many weak (H-bonds),
makes for very stable structure.
If you have many weak bonds (e.g. each bond
only few kT) you can get a biomolecule that
will not fall apart.
H bonded ~ 2 kT
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|
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Zipped vs. unzipped
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What if just one bond? Bond/unbound?
e -2 ~ 1
8
What if 10 weak bonds? e -20
Many base pairs, essentially completely stable.
Still have end-fraying, but probability that whole thing
comes apart– essentially zero. [Need enzymes to separate.]
With proteins, lots of hydrogen and weak bonds
– have conformational dynamics, but rarely fall apart!
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.)
Cyrus
Eric
Josh
Matthias
Pengfei
Wylie
Charles
Alireza
Thuy (Vietnamese)
Kiran
Xin
Anthony
Pavel
Vishel
Anne (my TA)
Size Scales of DNA (+ Protein)
Chromatin = Complex of DNA +
Protein (histones + non-histones)
Nucleotides
[4 Diff. types,
A,T,C,G]
8/17/06
3 x 109 = 3 billion
~ 1 meter
Flexibility of DNA?
~ 1 meter packed in
3-10 mm (size of nucleus)
# chromosomes?
46 (ca. 50)
Length/chromosomes?
~ 1/50 meter = 2 cm!
Cell Size
Bacteria - 1 mm
1 mm
Eukaryotic cell – 10-100 mm
10-100 mm 
10-30 mm
(Nucleus 3-10 mm)
How much DNA inside of every single cell?1 meter
So a meter of DNA must pack 3-10 mm!
What does this tell about bendability of DNA?
Like spaghetti, uncooked or cooked?
See how this is measured using magnetic tweezers
Interesting factoids:
1.  1014 cells in body…
…more stars than in Milky Way Galaxy.
2.  200 different types of cells in body.
You are what you eat
You get virtually all of the energy and the stuff which makes you,
from the food that you eat.(You get a tiny bit from sunlight.)
Energy (food) Energy (body can use) = Adenosine triphosphate, ATP
(most important)
+ NADH (More later)
+ glucose (sugar)
ADP+ Pi  ATP
with the human body turning over its own weight in ATP each day
ATP

Cleave
get 100 pN-nm
http://tuberose.com/Dighttp://tuberose.com/Digestion.html
Need to know Chemical Bonding
4 types: what are they?
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 electronegative 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
In singulo Biophysics
Single molecules, single cells,
single species, single planets…
Heterogeneity is the norm
Men vs. women: height, sex organs
Important to understand (prostate cancer,
ovarian cancer
It is only in last 10 (20) years that single
molecule detection has been possible!
Fig. **. The rate of growth of single
molecules has doubled every 2.2 years.
RNA vs. DNA
Life probably began as an RNA world
• RNA more flexible than DNA
(lack of an OH-bond in RNA!),
can do catalysis as well as store
information.
• RNA not as stable as DNA,
therefore not as good at genetic/
information storage.
• Life probably began based on
RNA.
Simple Lipids
triglycerides
http://lipidlibrary.aocs.org/Lipids/whatlip/index.htm
Carbohydrates
Carbohydrates is the primary source of energy.
Carbohydrates, which as the name implies, contains carbon
and “hydrates,” that is, water. It’s formula is (CH2O)n,
where n = 3-8 (Fig. **). As you can see from Fig. **, a
carbohydrate also contain two or more –OH groups, and
contains a C=O (known as an aldehyde or a ketone) The
simplest case, where the carbohydrate cannot be broken
down into simpler carbohydrates, is known as
monosaccharides (from the Greek “mono” = one; “sacchar”
meaning sugar). A polysaccharide consists of many
monosaccharides.
Carbohydrates are the most common source of energy for
the human body. Protein and fats build tissue and cells,
although people can live healthy lives without
carbohydrates. This is because (excess) proteins and fats can
be turned into an energy-source. Nevertheless,
carbohydrates are the most straightforward way to get
energy. People in the U.S. typically get 40% to 60% of their
energy from carbohydrates, although 55% to 75% is
considered more ideal.
(http://simple.wikipedia.org/wiki/Carbohydrate)
Proteins
DNA, Carbohydrates. Lipid have
isomers
i.e. can have identical mass, but different
spatial Arrangements.
Note that virtually all
have isomers. For
example, in DNA can be
made of A- or B- or some
more bizarre types of
structures; Carbohydrates,
shown in (D), can have
the exact same chemical
make-up, but the order
can be arranged, leading
to different branches.
Chemical Bonds. All chemistry can be boiled
down to plus and minus attracts, and plus and
plus or negative and negative repel. You get
negative charge from having more electrons
than protons, and positive charges from having
more protons than electrons. Within this general
truism, chemists define 4 different types of
chemical bonds. They are covalent bonds, ionic
bonds, hydrogen bonds, and Van der Waal
bonds. Covalent bonds are ones in which two
atoms share an electron(s)
Proteins have a fair amount of complexity, but not
too much.
Proteins are made of 20 monomers, called amino
acids, which are strung together in a linear
arrangement to form a biopolymer. Amino acids can
be thought of as letters, and a protein as the word.
Each amino acid varies only in their side-group; the
straight-on part which is involved in connecting
them to another amino acid on either end is the
same. The biopolymer folds up in its native three
dimensional structure and performs its function,
whether that be mechanical support, being a truck to
transport things, or being a catalyst to make
reactions happen on a reasonable time-scale.
Frauenfelder wanted to know whether there were
any principles behind the mechanism of its folding.
**But is this new physics??** **What about nonpoissonian behaviour in cell growth?/** In a famous
paper, where he studied the binding of carbon
monoxide to myoglobin, he discovered the proteinfolding landscape {Austin, 1973 #3357; Alberding,
1976 #3355}. While undoubtedly famous, it has
been a mixed blessing. It has led people on the
complex path to actually calculate how proteins
folds, for which there has been consider progress.
On the other hand, it has been a process which has
taken four decades, with a long way to go!
Biological physics : under the mantle of complex physics, where the
complexity comes from biology. But it can’t be too complicated,
otherwise you never get anywhere. At present, to deal with biological
systems in their living environment is much too complex. Eventually, it
might not be so, but for now it is. One system which is amenable to
quantitative reasoning, is the study of protein folding, a field Hans
Frauenfelder , former Professor of Physics and founder of biological
physics: became famous for.
Here proteins have a fair amount of complexity, but not too much.
Proteins are made of 20 monomers, called amino acids, which are strung
together in a linear arrangement to form a biopolymer. Amino acids can
be thought of as letters, and a protein as the word. Each amino acid
varies only in their side-group; the straight-on part which is involved in
connecting them to another amino acid on either end is the same. The
biopolymer folds up in its native three dimensional structure and
performs its function, whether that be mechanical support, being a truck
to transport things, or being a catalyst to make reactions happen on a
reasonable time-scale. Frauenfelder wanted to know whether there were
any principles behind the mechanism of its folding. **But is this new
physics??** **What about non-poissonian behaviour in cell growth?/**
In a famous paper, where he studied the binding of carbon monoxide to
myoglobin, he discovered the protein-folding landscape {Austin, 1973
#3357; Alberding, 1976 #3355}. While undoubtedly famous, it has been
a mixed blessing. It has led people on the complex path to actually
calculate how proteins folds, for which there has been consider progress.
On the other hand, it has been a process which has taken four decades,
with a long way to go!
Organism have developed an amazing ability, fine tuned over a
billion or-so of years of evolution, to make macromolecules. In
fact, there are just a few types of macromolecules and each type
of macromolecule is made from only a few types of monomers.
This makes it fairly easy to learn them. But the length of a
polymer can vary enormously--from a single one to 10 million or
so, and hence the number of possible combinations that make up
the polymer, is enormous. What adds to the complexity is that
even if two polymers are made up of the exactly the same type of
monomers and have the same order of monomers, there can be
an enormous variation in their physical placement, known as
isomers. Hence, from this simple alphabet, comes an incredibly
complex story that is life. For example, imagine if an organism
consists of just 4 different letters, or monomers. From this it can
make a polymer—the word which is formed from the monomer
alphabet. A polymer of N length can have 4N different polymers.
In biology, the polymer can be a million monomers long, but let’s
just say N equals 15--a very short polymer. So for this short
polymer, and very simple language (English has 26 letters) that’s
415 = 230 = 1,073,741,824 or over a billion different combinations.
And the range is actually much bigger because there are isomers
of these polymers. An isomer is where you have the same
number of atoms in the two polymers, but the arrangements of
these atoms are different. For example, each monomer can be
connected to another monomer either straight or bent fashion.
Then there is 2 n4n = 8n = 23n= 245 = 35,184,372,088,832 or over 35
trillion different polymers of length N=15. So, from a relatively
simple set, one can get tremendous diversity.
What’s a (Bacterial) Cell made of ?
It is mostly water and macromolecules
Water is absorbed without any processing
(as is inorganic ions and certain simple carbohydrates).
Structure of DNA
A-T, G-C bond, line up
Two strands are oppositely oriented
Form a minor and major groove
U RNA
U
6Å
12 Å
Structure of DNA
A-T, G-C bond, line up
Two strands are oppositely oriented
Form a minor and major groove
U RNA
U
DNA: A-T 2 H bonds; G-C 3 H bonds
Thymine
Cytosine
Hydrogen Bonds
Adenine
(2kT)
Guanine
G-C more stable than A-T
Minor
grove
Major
grove
–  stacking keeps it together (Grease);
Phosphate negative charge makes it water soluble
Biological Physics
“Good” Problem: Protein Folding
Unfolded
Inactive

Folded

Active
Hans Frauenfelder ,
founder of
biological physics.
Wolynes, PNAS, 1998
Main driving force : 1) Shield hydrophobic (black spheres)
residues/a.a. from solvent/ water; 2) Formation of intramolecular
hydrogen bonds. Probably forms a-helices and b-sheets (a lot of
H-bonds) along pathway.
Protein folding Landscape: Spend 4 centuries on it!