Lec 4: RNA (and Proteins)
Homework
HW#2: Due Monday
Reading, ECB, Chpt 2: Due Wednesday.
Quiz next Wednesday
A vs. B vs. Z-DNA
B “normal” configuration;
A,Z- unusual, not-normal configuration”
Figure 3-B-3. The normal right-handed "double helix" structure
of DNA, also known as the B form.
In a solution with higher salt concentrations or with alcohol
added, the DNA structure may change to an A form, which is
still right-handed, but every 2.3 nm makes a turn and there are
11 base pairs per turn.
Another DNA structure is called the Z form, because its bases
seem to zigzag. Z DNA is left-handed. One turn spans 4.6 nm,
comprising 12 base pairs. The DNA molecule with alternating GC sequences in alcohol or high salt solution tends to have such
structure.
http://www.web-books.com/MoBio/Free/Ch3B3.htm
http://www.tulane.edu/~biochem/nolan/lectures/rna/DNAstruc2001.htm
Major vs. Minor Axis of DNA
Major axis more likely to be accessible to proteins
Sequence-specific DNA-binding proteins generally interact with
the major groove of B-DNA, because it exposes more functional
groups that identify a base pair.
Cro protein complex with DNA
Lambda repressor protein bound to
a lambda operator DNA sequence
http://en.wikipedia.org/wiki/DNA
http://commons.wikimedia.org/wiki/File:Cro_prot
ein_complex_with_DNA.png
Major vs. Minor Axis of DNA
Structural proteins that bind DNA are well-understood examples
of non-specific DNA-protein interactions. Within chromosomes,
DNA is held in complexes with structural proteins.
These proteins organize the DNA into a compact structure called
chromatin.
DNA that is not n x 3 bases in length?
“There *must* be. For example, many
stretches of DNA code for RNAs -including ribosomal RNAs, tRNAs,
newly discovered microRNAs, and
many many others. All of these have
particular requirements for what the
RNA is -- including conservation of
many of their bases -- yet these will not
in general have lengths = 3*n.
--Jonathon Widom, Northwestern Univ.
RNA has 3 different uses, called 3
different names, (mRNA, tRNA, rRNA)
1. Messenger RNA (mRNA)
[~copy of DNA]
2. transfer RNA (tRNA)
[binds to amino acid and
codon for mRNA]
3. ribosomal RNA (rRNA)
[Makes up Ribosome, along
with protein. Has catalytic
activity– can form peptide
bond. RNA is catalytic!]
http://en.wikipedia.org/wiki/Messenger_RNA
Why is RNA & DNA different?
Probable Answer: RNA came first.
RNA is capable of storing
information (though not great
cause of U) and can catalyze
reactions.
Later, split off—Long-term storage
given to DNA because it’s more
stable. (T instead of U)
Catalysis mostly given to
proteins—more diverse, efficient.
What is a Catalyst/Enzyme?
Z
X+ Y 
For now just pretend that ΔG is equal to ΔE.
(In-fact ΔG= ΔH- TΔS ≈ ΔG ≈ ΔE- TΔS)
The starting and final reaction energies
are the same,
but the activation barrier is lowered.
If Ea low enough (≈ kT), it will happen
spontaneously
Ribozyme
(ribonucleic acid + enzyme)
Example of a biocatalyst,
i.e. an enzyme
http://en.wikipedia.org/wiki/Ribozyme
RNA can be catalytic!
1989 Nobel Prize—Altman & Cech
RNA is likely predecessor of
DNA
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 Sciences,
December 10, 1989
Evidence that RNA have these properties?
The Ribosome is an RNA-based catalytic
machine– Big surprise!
Ribosome, i.e. Translation, is RNA catalyzed!
Proteins;
23S rRNA;
5S rRNA (at
the top)
A-site tRNA
P-site tRNA
T. Steitz, 2000, Science
A ribosome's true colors. (Top) The large subunit of the ribosome seen
from the viewpoint of the small subunit. (Bottom) The peptidyl transfer
mechanism catalyzed by RNA (2). The general base (adenine 2451 in
Escherichia coli 23S rRNA) is rendered unusually basic by its environment
within the folded structure; it could abstract the proton at any of several
steps, one of which is shown here.
RNA is an enzyme!
Nobel Prize 2009: Atomic Structure of Ribosome
(Steitz, Ramakrishnan, Yonath)
RNA is made from DNA
Introns vs. exons in Eukaryotes
In prokaryotes
(messenger)
prokaryotes introns
are only found in
tRNA and rRNA
In eukaryotes
intron –”non-coding region” deleted
1993 Nobel Prize in Medicine to Phillip Allen and Richard J. Roberts
http://en.wikipedia.org/wiki/Intron
What is siRNA?
Small interfering RNA (siRNA), sometimes known as
short interfering RNA or silencing RNA, is a class of
double-stranded RNA molecules, 20-25 nucleotides in
length, that play a variety of roles in biology. Most
notably, siRNA is involved in the RNA interference (RNAi)
pathway, where it interferes with the expression of a
specific gene. dsRNA can also activate gene expression
(RNAa). MicroRNAs (miRNA) tend to be ssRNA…Long
dsRNA cleaved by Dicer….
http://en.wikipedia.org/wiki/Small_interfering_RNA
siRNAs can also be exogenously (artificially) introduced
into cells by various transfection methods to bring about
the specific knockdown of a gene of interest. Essentially
any gene of which the sequence is known can thus be
targeted based on sequence complementarity with an
appropriately tailored siRNA. This has made siRNAs an
important tool for gene function and drug target
validation studies in the post-genomic era.
2006 Nobel Prize on RNA interference
Fire and Mello
What is Entropy?
∆S
Qualitative: Degree of disorder
Gas will expand from a bottle at finite
temperature because there are more
accessible states available to it, than
staying put.
(Temperature gives molecules a little
bit of energy to access states)
Quantitative:
∆S = kBln W
where W = # accessible states.
Reaction that produces H2O, which, in
general, is free to diffuse everywhere,
is highly favorable.
How to make nucleotide
(Example of condensation reaction,
like amino acids & peptide bonds)
Free H2O : lots of entropy gained
Reaction wants to go.
Amino acids
<a.a.> ~110 grams/mole
(or about 100g/mole)
hydrophilic
R=CH3
Fairly hydrophilic
Hydrophobic
Amino Acids undergo condensation
reaction to form peptides
Free H2O : lots of entropy gained
Linear sequence of ~ 20 amino acids
Can get enormous diversity and
function with Proteins
Secondary Structure
a-helix, b-sheets
a-helix, b-sheets depends on specific amino acids
Typical size of genes & proteins
Class evaluation
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.
Answer, and turn in at the end of class.