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 NucleotidesMake 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.

_|_|_|_|_|_|_|_|_|_|_|_|_|_|_A T A C G G T C C A G T T G

T A T G C C A G G T C A A C||||||||||||

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 catalyzesreaction and puts energy (in uses ATP)

∆G+forward

∆G

∆G+rev

Your DNAYou 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) =

What does this tell you about the flexibility of DNA?Learn about Magnetic Traps to measure Persistence Length.

1 meter in every cell!Nucleus of Cell ≈ 5 m long

Bacteria Prokaryotes(No nucleus)

Eukaryotic cell (us)(Has nucleus)

1 m10-30 m 10-100 m

(Nucleus 3-10 m)

Most Biopolymers in Body are in Cells

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.

1014 (50-100 trillion!) cells in body……more stars than in Milky Way Galaxy.

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

Must come apart for bases to be read.

3.4 Å 3.4 nm per ~10 base-pairs= 1 turn (360º)

DNA RNA ProteinsCentral Dogma of Molecular Biology

http://learn.genetics.utah.edu/units/basics/transcribe/

DNA: linear series of 4 nucleotides (bases): A,T,G,C

RNA: linear series of 4 nucleotides (bases): A,U,G,C

Transcription [DNA & RNA similar]

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 ValineProteins are 3-D strings of linear amino acids

Do everything: structure, enzymes…

Double-stranded

Mostly single-stranded

How to make nucleotideAnother Example of condensation reaction

Free H2O : lots of entropy gained

Reaction wants to go.

Covalent bonds holding bases together —very strong

If add salt to solution, what is effect on melting Temp?Melting temp = Temp. at which DNA strands come apart.

3 ’

5 ’

DNA is twisted & antiparallel for base pairing

Minor grove

Major grove

Hydrogen Bonds

(2kT)

– stacking keeps it together (Grease);

Phosphate negative charge makes it water soluble

(Sort of like soap)

G-C more stable than A-T

Thymine

Guanine

Cytosine

Adenine

DNA ReplicationChicken & 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

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.

Larger groove (than DNA)—more likely to be attacked by enzymes)

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.

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)

http://en.wikipedia.org/wiki/Ribozyme

RNA solves the chicken & egg problemFrom 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)