Download Lecture 4a (1/28/13) "Central Dogma"

Today’s lecture
• DNA makes RNA which makes Proteins
• Central Dogma of Molecular Biology Proteins
• DNA…How to measure its flexibility
Magnetic Traps.
Homework Schedule:
Turn in HW#1 now.
HW #2 Due Monday 2/4
There will be a TA from 11-11:15 in lecture
rm, 136 LLP to collect HW.
HW#3 will be assigned this Wednesday
1/13; Due Monday 2/11/13
Minimal knowledge about Nucleotides
Make up DNA (also RNA)
• 4 nucleotides: A,T,G,C (RNA: U replaces T)
• A=T ≈ 2kT two hydrogen bonds
G=C ≈ 4kT three hydrogen bonds
From Homework, you know that one or a
few A-T or G-C bonds will come apart, but
have a series of them, and the two halves
always stay together, i.e. are stable.
T A T G C C A G G T C A A C
|| || ||||||||
A T A C G G T C C A G T T G
_|_|_|_|_|_|_|_|_|_|_|_|_|_|_
Each strand
held together
by covalent bonds.
(Stable)
3.4 Å/base
If DNA is very long, and have to unzip DNA,
how does this happen?
An Enzyme which catalyzes
reaction and puts energy
(in uses ATP)
∆G+rev
∆G+forward
∆G
Your DNA
You have 3 billion base-pairs,
in 46 individual sections, called a chromosomes.
There are 23 pairs.
An X from mother; X or Y from father
(determines sex)
Slight shuffling of 1-23 chromosomes, called meiosis,
such that you are different than the average of your parents.
http://ghr.nlm.nih.gov/handbook/basics/howmanychromosomes
Total Length DNA: (3.4 Å)(3 x 109) = 1 meter in every cell!
Nucleus of Cell ≈ 5 mm long
What does this tell you about the flexibility of DNA?
Learn about Magnetic Traps to measure Persistence Length.
Most Biopolymers in Body are in Cells
Bacteria
Prokaryotes
(No nucleus)
1 mm
Eukaryotic cell (us)
(Has nucleus)
10-30 mm
10-100 mm
(Nucleus 3-10 mm)
 1014 (50-100 trillion!) cells in body…
…more stars than in Milky Way Galaxy.
Yet there are  200 different types of cells in
body. (Heart cell not equal to a brain cell…)
Each type of cell is diff. cause diff. parts of
DNA is turned on.
Every cell (except red blood
cells) contains a nucleus which
contains a copy of DNA– 1 meter
RBC: denucleated
DNA is 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.
DNA RNA Proteins
Central Dogma of Molecular Biology
DNA: linear series of 4 nucleotides (bases): A,T,G,C

Double-stranded
Transcription [DNA & RNA similar]
RNA: linear series of 4 nucleotides (bases): A,U,G,C

Mostly single-stranded
Translation [RNA & Proteins different]
Proteins: linear 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/
How to make nucleotide
Another Example of condensation reaction
Free H2O : lots of entropy gained
Reaction wants to go.
Covalent bonds holding
bases together —very
strong
3’
5’
If add salt to solution, what is effect on melting Temp?
Melting temp = Temp. at which DNA strands come apart.
DNA is twisted & antiparallel for base pairing
Thymine
Cytosine
Hydrogen Bonds
(2kT)
Guanine
Adenine
G-C more stable than A-T
Minor
grove
Major
grove
–  stacking keeps it together (Grease);
Phosphate negative charge makes it water soluble
(Sort of like soap)
DNA Replication
Chicken & Egg Problem
Have already shown that
If DNA is long and therefore very stable,
how can it replicate itself without an enzyme
(to lower the activation energy)?
(Nowadays, it uses DNA polymerase, which
is an enzyme, i.e. protein.)
The answer won a Nobel prize!
Involves RNA…
implications for the start of life on earth.
Difference between RNA and DNA
is the Sugar + 1 Base (T, U)
RNA is a string of nucleotides, just like DNA
 Larger groove (than DNA)—more
likely to be attacked by enzymes)
RNA substitutes Uracil for Thymidine
Uracil will base pair with
many groups.
Methyl group restricts uracil
(thymine) to pairing only with
adenine.
Thymidine greatly improves the efficiency of DNA replication,
by reducing the rate of mismatches, and thus mutations.
Also, methylation protects DNA from viruses.
RNA can be it’s own enzyme!
RNA can be a ribozyme –a
ribonucleic acid and enzyme–is an
RNA molecule with a well defined
tertiary structure that enables it to
catalyze a chemical reaction. It contains an
active site made completely of RNA. Can cut
either itself or another RNA.
http://en.wikipedia.org/wiki/Ribozyme
Used by nature! The ribosome, used to make
proteins from RNA, is itself a ribozyme
(involves RNA cutting by another RNA).
2009 Nobel Prize (Ramakrishnan, Cambridge;
Steitz, Yale; Yonath; Weizmann)
RNA solves the chicken & egg problem
From Nobel Lecture
The discovery of catalytic properties in RNA also gives us a new
insight into the way in which biological processes once began on
this earth, billions of years ago. Researchers have wondered
which were the first biological molecules. How could life begin if
the DNA molecules of the genetic code can only be reproduced
and deciphered with the aid of protein enzymes, and proteins can
only be produced by means of genetic information from DNA?
Which came first, the chicken or the egg? [Sid] Altman and [Tom]
Cech have now found the missing link. Probably it was the RNA
molecule that came first. This molecule has the properties
needed by an original biomolecule, because it is capable of being
both genetic code and enzyme at one and the same time.
Presentation Speech by Professor Bertil Andersson of the
Royal Swedish Academy of Science, December 10, 1989
RNA can be catalytic!
Life probably started with RNA (not DNA)
1989 Nobel Prize—Altman & Cech
(1967 Carle Woese suggested RNA can be catalytic—won the equivalent
of Nobel Prize)
It is now possible to make ribozymes that will specifically cleave any RNA
molecule. These RNA catalysts may have pharmaceutical applications. For
example, a ribozyme has been designed to cleave the RNA of HIV. If such a
ribozyme was made by a cell, all incoming virus particles would have their
RNA genome cleaved by the ribozyme, which would prevent infection.
Evidence that RNA have these properties?
The Ribosome is an RNA-based catalytic
machine– Big surprise!
Magnetic Traps
(see next section of slides)