Transcript DNA double helix: Many weak (H

Basic Biology
& some calculations
[Read Chpt 1 of Berg et al.: lots of
important things about Molecular
Binding, Central Dogma, Entropy, DG]
1. Living is made up of complex polymers
organized in one or more cells.
2. Central Dogma of Biology
DNA RNA Proteins
2a. Why “junk” DNA become hot.
3.How to calculate stability of DNA
4. What introns and exons lead to
tremendous genetic variability
At the molecular level,
the definition of life becomes
somewhat simpler.
All living organisms consist and make
complex, heterogeneous macromolecules.
They do this by ingesting the necessary
substituents and make them from simple
compounds. It has a way of reproducing itself,
although any one member of the species need
not be able to reproduce.
4 Large [Macro]Molecules
(from small molecules)
Biological polymers (Large molecule
made from many smaller building block)
•
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DNA & RNA  Nucleotides
Proteins  Amino Acids
Carbohydrates  Sugars
Lipids (Fats) Fatty acids
Each is used to:
a. Make macromolecules/structural
b. Energy Source
c. Information– Storage/signaling
Example:
a.Make Proteins, Enzymes, Hair…
b. Break down yields energy;
c. amino acids used as nerve impulses (your
brain largely runs on a.a. glutamate.)
Major Classes of Macromolecules
Hemoglobin
(protein)
DNA
fragment
(nucleic
acid)
Polysaccharide
(carbohydrate)
0.34 nm
between
base pairs
Lipid
An atomic scale representation of each
Atoms: What are we made of?
Campbell
We are mostly made of water (H2O): ≈75%
C —very versatile: everything made of:
Nucleic acids, Proteins, Lipids (fat),
Carbohydrates. (Remember these families)!
O —bonding, proteins, fats, nucleic acids
N — proteins, genetic material
Ca, P — bones
The Fundamental Unit of Life is
the Cell
3 types (not two!)
http://bio1903.nicerweb.com/
Locked/media/ch25/25_18Tr
eeOfLife.jpg
Archea and Bacteria most ancient: without a nucleus
(special place to put its genetic material, DNA).
Otherwise bacteria and archea look a lot alike.
Eukaryotes have a nucleus.
Here at U of Illinois, Carl Woese in the 1970s made
claim that 3 branches of life based on RNA
What caused split? Don’t know but…Possibly the
ingestion of a bacteria to become a mitochondria
(specialized to make energy—ATP)
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 (100 billion!) 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…)
Nucleus contains DNA
Blueprint of cell
Every cell (which has nucleus) has identical DNA
[A few types, like red blood cells,
are made with a nucleus but gets
de-nucleated.]
Each cell type expresses only a part of
information in DNA
(Brain cell differs from a heart cell….)
How much DNA? 3 billion base pairs
1 meter
In humans 46 pieces: chromosomes
So a meter of DNA must be packed in 3-10 mm!
What does this tell about bendability of DNA?
Highly flexible. Persistence Length = 50 nm (~150 bp.)
What is persistence length? Walk in one
direction: how long headed in that direction
(Yet can unwind and very robust in storing genetic
information over a lifetime)
How this is measured? Use magnetic tweezers
DNA is a double helix of anti-parallel strands
DNA uses a 4 letter sequence, A, T, G, C
3.4 Å 3.4 nm per
~10 base-pairs
= 1 turn (360º)
Must come apart for bases to be read.
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.
We’ll calculate this in a few minutes.
(Boltzman constant.)
• To unzip, takes energy, ATP and proteins
that act like a wedge.
• Also takes proteins that act to unwrap the
DNA and then act like a wedge
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
Note: Student mentioned metallic bonds
Metallic bonding is the bonding within metals. It involves the delocalized sharing of
free electrons between a lattice of metal atoms. Thus, metallic bonds may be
compared to molten salts.
e.g. Iron (Fe)... Why is it so strong? Of course, metallic bonding.
Metal atoms typically contain a small amount of electrons in their valence shell
compared to their period or energy level. These become delocalised and form a Sea
of Electrons surrounding a giant lattice of positive ions.
Metals seem to have higher boiling and melting points which might suggest stronger
bonds between the atoms.
Metallic bonding, as with covalent bonding is non-polar, in that there is no (for pure
elemental metals) or very little (for alloys) electronegativity difference among the
atoms participating in the bonding interaction, and the electrons involved in that
interaction are delocalized across the crystalline structure of the metal.
The metallic bond accounts for many physical characteristics of metals, such as
strength, malleability, ductility, conduction of heat and electricity, and luster. See also
chemical bond.
Metallic bonding is the electrostatic attraction between the metal atoms or ions and
the delocalised electrons. This is why atoms or layers are allowed to slide past each
other, resulting in the characteristic properties of malleability and ductility.
Metallic bond are different from chemical bonds. Ionic and covalent bonds are
chemical bonds.
Covalent bonding is a common type of bonding, in which the electronegativity
difference between the bonded atoms is small or non-existent. In the latter case, the
bond is sometimes referred as purely covalent. See sigma bonds and pi bonds for
current LCAO-explanation of non-polar bonds.
e.g. CH4 (methane)
Ionic bonding is type of electrostatic bond between atoms which have an
electronegativity difference of over 1.6 (this limit is a convention). These form in a
solution between two ions after the excess of the solvent is removed.
e.g. NaCl (common salt). https://answers.yahoo.com/question/index?qid=1006020202026
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 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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Say the unbound case has E= 0
The bound case therefore has E = 2kT. (Notice that the energy is
negative, i.e. it’s more stable if a
bond is formed)
Zipped vs. unzipped
What if just one bond? Bond/unbound?
e2 ~ 8
What if 10 weak bonds? e 20
Many base pairs, essentially completely stable.
We note that these numbers are completely unrealistic because our
calculation doesn’t include the entropy. That is, it should be based on the
free-energy (DG), not the energy, but the trend we see here, is still
qualitatively correct. Still have end-fraying, but probability that whole
thing comes apart– essentially zero.
DNA RNA Proteins
Central Dogma of Molecular Biology
DNA: linear series of 4 nucleotides (bases): A,T,G,C

Transcription [DNA & RNA similar]
RNA: linear series of 4 nucleotides (bases): A,U,G,C

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/
DNA RNA
Must uncoil the DNA, separate the strands, and use
one of strands as a template to make a RNA strand.
RNA: uses U instead of T, uses ribose instead of
deoxyribose
U
U
U
The RNA that codes for proteins are called
messenger RNA is an exact copy of DNA.
RNA  Proteins
3 nucleotides codes for 1 amino acid. Proteins are
made up for a linear string of 20 different amino
acids.
Histidine 
U
U
Cysteine
Glycine 
U
Gene = sequence of DNA (or RNA) that makes a protein
Also need to know where to start making the
protein, and where to stop making the protein.
If you can sequence all your DNA, how
can you tell how many genes are there?
Linear sequence of ~ 20 amino acids
Can get enormous diversity and
function with Proteins
If 3 bases make a codon, how
many amino acids might there be?
Answer: 43 = 64
Have redundancy, typically in the last nucleotide
The Central Dogma of Biology
nucleus
nucleus
cytoplasm
cytoplasm
Each time a cell divides, entire DNA gets replicated.
For us, that’s 3 billion base pairs.
Splicing is fundamental for Gene
Expression
Splicing is fundamental for
Gene Expression
Alternative Splicing
Adds Complexity
1 Gene, many proteins
Down Syndrome Cell Adhesion Molecule
DSCAM = 1 pre-mRNA = 38,000 potential
mRNAs
Now you understand why we’re not
just a tiny worm.
Why little worm (19,735 genes, 97
MB) has as many genes as a human
(~21k, 3,000 MB = 3 GB)!
A lot of “genes” are alternatively
spliced, can produce more than one
protein.
Until very recently, used to call DNA which
didn’t code for a protein “junk DNA”
1 mm____
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.