The Basics: A general review of
molecular biology:
DNA
Transcription
RNA
Translation
Proteins
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The answer is "yes"
Polymers
A polymer is a big molecule composed of smaller
molecules linked together with similar bonds.
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Synthetic polymers: nylon, kevlar, polyethylene
Are these the secret of life?
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Natural polymers: Cellulose, starch, chitin rubber
Are these the secret of life?
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No. The secret of life lies
in a special kind of
polymer.
SUPER POLYMERS.
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Super polymers
are just like regular polymers, except
1. They are composed of more than
one subunit but linked by the same
type of bonds
2. The subunits are arranged in a
specific order
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3
’
5’
Now, if all the elephants were the same, this
would be a regular polymer.
In DNA, one kind of SUPER POLYMER, there are four
kind of elephants with the names: A, C, G, and T
A
5’
C
G
Note the backbone is the same for each one
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T 3
’
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5’
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3
’
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How would you design a monomer so that branched
polymers could result?
A. Monomers would have two
tails
B. Monomers would have two
trunks.
C. Both a or b
D. Neither a nor b
E. I'm going to tell the
PETA that you want to
genetically modify
elephants!
One Trunk/Tail
Two Tails
Two Trunks
5’
3’
3’
3’
All SUPER POLYMERS are made by adding one
unit at a time on to the tail end of the chain
(the 3` end).
In the chain above, synthesis is said to
proceed 5` to 3`
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3’
5’
3’
3’
3’
3’
Here's another question: Assume a
large field with thousands of A, C, G,
and T elephants. At the sound of bell,
all the elephants form chains
(remember they always grab on to
the tail of another elephant).
How could you make sure that all the
chains stopped with an "A" elephant?
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5’
3’
3’
3’
How could you make a polymer that
always stopped growing at “A”?
A. Cut off the tails of all A elephants
B. Cut off the tails of all non-A
elephants
C. Cut of the trunks of all A
elephants
D. Cut off the trunks of all non-A
elephants
E. DON’T TOUCH THESE
ELEPHANTS!
3’
SUPER POLYMERS fall into two categories
1. Some act primarily to carry instructions. They
are said to be "informational" or "instructional"
2. Some are best at performing operations. They
are said to be "operational". They are molecular
machines.
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DNA (deoxy-ribonucleic acid) is the genetic material
It is an informational super polymer
-think of it as the blueprint
DNA structure-- a polymer of nucleotides
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Nucleotides have :
2) a ring-shaped
nitrogen base
3) a phosphate group
1) a 5 carbon sugar
Can you identify each of the units in your models?
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Things to notice about the sugar:
--sugars can circularize by eliminating an H20 molecule
and forming a bond between hydroxyl groups
--the carbons in the sugar are given numbers in standard
Nomenclature, designated as “prime” to distinguish from
carbons on the nitrogen base
these numbers are used to distinguish critical sites in
The nucleotide and in the DNA strand.
5'
O
HOH2C
OH
1'
4'
H
H
H H
3'
2'
OH
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OH
5'
O
HOH2C
OH
1'
4'
H
H
H H
3'
2'
OH
H
Ribose
Deoxyribose
RNA
DNA
ribose is a
5-carbon sugar
2’-deoxy-ribose is different from ribose in that it
lacks a hydroxyl group (-OH) on the 2’ carbon
DNA-2’-deoxy-ribose
RNA-ribose
5'
O
HOH2C
OH
1'
4'
H
H
H H
3'
2'
OH
OH
Ribose
The chemical difference
associated contributes
significantly to the
differences between DNA
and RNA biochemistry
5'
O
HOH2C
OH
1'
4'
H
H
3'
OH
H H
2'
H
Deoxyribose
Identify the 5' and 3' groups on your sugar molecule
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The OH groups on the 5’ and 3’ carbons are the
reactive groups through which nucleotides become
joined
a nucleotide includes one phosphate group joined at the
5’ position…..
PO4
5'
O
HOH2C
OH
1'
4'
H
H
H H
3'
2'
OH
OH
Ribose
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5'
O
HOH2C
OH
1'
4'
H
H
3'
OH
H H
2'
H
Deoxyribose
Add the phosphate group to your sugar rings
5'
What to knowHOH
about
theO phosphate:
OH
2C
1'
4'
H
1) linked at 5’ carbon
H
3'
H H
2'
PO4
5'
O
HOH2C
OH
1'
4'
H
H
H H
3'
2'
2) can have 1, 2, or
residues OH
OH 3 phosphate
OH
H
(nucleotide mono-phosphate,
Ribose nucleotide di-phosphate
Deoxyribose ,
nucleotide tri-phosphate)
3) ***the oxygens of the phosphate group are negatively
charged at physiological pH.
Therefore DNA carries a large net negative charge!
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The polynucleotide chain
To form the polynucleotide chain, the oxygen of the 3' hydroxyl group on the
chain “attacks” the phosphate of a nucleotide triphosphate eliminating H2O and
releasing the two outermost phosphate residues.
The
phosphodiester
bond
**Notice that the DNA chain is synthesized in a 5’ to
3’ direction.Build a 4 unit backbone chain
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Is this a super polymer?
5’ end
***There is an asymmetry to the
DNA chain!
5’ end--phosphate group
3’ end--free hydroxyl group
3’ end
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Break the chain back into monomers
There are 4 bases (units) in DNA:
N H2
C
N1
6
5
C
H
4
3
C
N
7
N
C
C
C
H2N
C
N
H
Ad e n i n e
A
C4
H
N
H
Gu a n i n e
G
N3
H
C H3
C
H
N
C
H
9
N
C
H
N
8
C
2
H
O
2
6
C
1
N
C
O
Cy t o s i n e
C
C
H
5
N H2
H
O
C
C
N
N
C
H
O
Th y m i n e
T
Adenine and Guanine have 2 rings--purines
Cytosine and Thymine have 1 ring--pyrimidines
Which base do you have?
Add the base to your sugar
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C – Black
N – Blue
O - Red
DNA is double-stranded--two polynucleotide chains
Hydrogen bonds between bases hold these together
1
Guanine
Cytosine
G and C have 3 H-bonds
5
Adenine
A and T make 2 H-bonds
H-bond your base with your partner
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Thymine
DNA strands are arranged in an anti-parallel manner
5’
3’
Complementary
(Not “complimentary”)
5’
3’
Reassemble the single strand of DNA
Then anneal (form base-pairs) to make double-stranded
DNA
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Build a helix competition!!!
One side of the room against the other!
First side to build their entire double
helix wins a prize!
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DNA strands are arranged in an anti-parallel manner
3'
5'
3'
5'
5'-TCGTCA-3'
3'-AGCAGT-5'
"Flipped"
5'-TGACGA-3'
3'-ACTGCT-5'
Written as: TCGTCA or TGACGA
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Clicker Question: What is the
complementary sequence of the
sequence 5'-GGAATCG-3'?
3’-CCTTAGC-5’
A. 5’-GCTAAGG-3’
B. 5’-CCTTAGC-3’
C. 5’-CGATTCC-3’
CG
-3
’
0%
’-G
GA
AT
GA
TT
CC
-3
’
0%
5’
-C
CT
T
5’
-C
’-G
CT
AA
GG
-3
’
D. 5’-GGAATCG-3’
0%
AG
C3’
0%
Clicker Question #5: Which DNA
would be harder to denature
(separate the two strands)?
A) ATTA
TAAT
D) GCGCGC
CGCGCG
B) GCGC
CGCG
E) AGCGCT
TCGCGA
C) AATATA
TTATAT
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Clicker Question #5: Which DNA
would be harder to denature
(separate the two strands)?
A. ATTA
B. TAAT
C. B) GCGC
D.
CGCG
E. C) AATATA
A. TTATAT
D) GCGCGC
CGCGCG
E) AGCGCT
TCGCGA
Critical Properties of DNA
1) Negative charge (will move toward a + electrode!)
2) DNA can be denatured and renatured (nucleic acid
Hybridization).
3) DNA is soluble in water.
4) DNA absorbs UV light.
5) DNA can be stained and amounts of DNA can be
Measured using ethidium bromide.
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Ethidium bromide intercalates into the DNA double helix
EthBR fluoresces under UV light, enabling us to “see” DNA
no fluorescent
color…
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fluorescent
Genes, chromosomes and genomes
Gene: DNA devoted to making one specific polypeptide
Genes are housed on chromosomes
All DNA of an organism makes up its genome
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Central dogma
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Protein synthesis: translation (mRNA to protein)
Proteins have catalytic and structural functions
Proteins with catalytic functions are enzymes
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Video
http://www.youtube.com/watch?v=41_Ne5mS2ls
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Link to YouTube Videos for an excellent review of
the process of transcription and translation
http://www.youtube.com/watch?v=41_Ne5mS2ls
http://vcell.ndsu.edu/animations/transcription/movi
e-flash.htm
http://vcell.ndsu.edu/animations/mrnaprocessing/mo
vie-flash.htm
http://vcell.ndsu.edu/animations/translation/movieflash.htm
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