Download The Discovery, Structure, and Function of DNA

The Discovery,
Structure, and
Function of DNA
The Link from Function to Form
1869: Friedrich Meischer isolates DNA (“nuclein”) from fish sperm and human pus.
1900: Hugo de Vries, Carl Correns, and Erich
von Tscermak rediscover Mendel’s ratios.
The big debate: Can Mendelian mechanics measure evolutionary change? Problems with
replicating Mendel’s simple rules using different organisms and traits lead to a renewed interest in locating the “gene” and
describing its physio-chemical dynamics.
1919: Thomas Morgan demonstrates conclusively that genes are physical units lying
along chromosomes, which in turn lie inside every cell of every organism.
1943: Oswald Avery isolates deoxyribonucleic
acid (DNA) as the chemical manifestation of heredity.
Discovery of DNA: The Players
James Watson: Fresh Indiana U. PhD, starts
postdoc at Cambridge’s Cavendish Labs
under the direction of Sir Lawrence Bragg
Francis Crick: Currently working at Cavendish
on X-ray diffraction of proteins
Maurice Wilkins, Rosalind Franklin: Working
at X-ray diffraction of DNA at London’s
King’s College
Linus Pauling: Working at Caltech on the structure of proteins
Discovery of DNA: The Game
The Sides: Those who believed that proteins
held the key to genetic traits and that
these traits were transferred biologically,
and those who believed that DNA held
these traits, and the transfer was chemical.
1951: Pauling predicts alpha-helix structure of
collagen proteins, using model-building techniques. Wilkins shows X-ray diffraction
pictures of DNA.
DNA is known to be
• crystalline (regular repeating structure)
• acidic (electron accepting)
• contains one or more a sugar-phosphate
backbones
• backbone attached to bases composed
of adenine (A), cytozine(C), guanine(G), and thymine(T), with A-T
and G-C pairs appearing in approximately equal quantities.
But how is it constructed?
Discovery of DNA: The Play
1952: Watson and Crick set out specifically to
win the Nobel prize by finding the structure of DNA.
Main questions: How many backbone strands
are there, and are they centrally located
or on the outside of the molecule?
Solution technique: Make molecular models
out of metal, try to fit the components
of the molecule together to satisfy X-ray
diffraction data.
First try: Three central strands in a helical
shape.
Wilkins&Franklin observe that resulting water content is too far off. Back to the
drawing board.
Discovery of DNA: The Chase
1953: Pauling postulates similar 3-chain central strand model for DNA. Watson&Crick
observe chemical discrepencies.
Visit to Wilkins&Franklin confirms outside helix model.
Watson&Crick begin on outside chain helix,
choose 2-strand model.
Problem with outside model: How do you fit
the ACGT molecules inside the helix, and
still satisfy the correct molecular distances
in the backbone?
Second try: 2-strand outside model, with AA, C-C, G-G, T-T matching along the inside. Problems with fit.
Final form: A-T, G-C pairing satisfies chemical laws, X-ray data, and are symmetric.
February 28, 1953: Crick announces to a Cambridge pub that they had “found the secret of life”.
Structure and Function of DNA
DNA (deoxyribonucleic acid): Found in every cell in an organism in exact copies (except for the gametes)
The Structure of DNA: Two helically intertwined backbones made up of alternating phosphate and deoxyribose (sugar)
molecules supporting internal base pairs
adenine (A) paired with thymine (T)
cytosine (C) paired with guanine (G)
The pairs can occur in any combination and
order as necessary to define the organism.
The Structure of DNA
Replication of DNA During Cell
Division: Mitosis (Interphase)
1. Enzymes unzip the DNA molecule between
its base pairs, leaving two complementary
single strands.
2. DNA polymerase matches the bases in each
strand, attaching new complementary strands,
creating two new copies of DNA.
3. The two strands separate and go to each
copy of the replicated cell.
Replication of DNA during mitosis
Replication of DNA to Produce
Gametes: Meiosis
Steps of meiosis:
1. Before meiosis, the nucleus contains two copies of
each chromosome, a maternal and a paternal copy.
This is called a homologous chromatid pair.
2. In the nucleus, the chromosome pairs separate, and
each side replicates itself exactly. The identical
copies join to form two pairs, called sister chromatids, of each chromosome.
3. The two pairs line up, and may swap pieces of chromosome between either of the maternal and paternal members. This exchange is called crossing
over. This is the first way of realizing of Mendel’s
law of independent assortment.
4. Each pair of a chromosome is then drawn to opposite sides of the nucleus, and the nucleus splits into
two nuclei, each with complete paired copies of the
genome. Which pair goes to which nucleus is the
second way of realizing Mendel’s law of independent assortment.
5. The paired chromosomes in each nucleus now separate and are drawn to opposite sides of the new
nucleus. The nucleus splits again, forming four gametes, each containing one copy of each chromosome. This is the way of realizing Mendel’s law of
independent segregation.
Steps of Meiosis
More on Crossing Over
Two different halves of the replicated chromosome (called cromatids) swap genetic material by the following steps :
1. They are cut at the same place on the DNA
molecule.
2. A section of DNA from each member of
the sister pair crosses over to match with
the same section of DNA from the homologous chromatid, forming a connected pair
of homologous chromatids called a Holliday junction. This will involve some “repairing” of mismatched base-pairs in order
to make complementary copies across the
new DNA molecule.
3. One of the two appropriate backbone strand
pairs are then cut at the opposite ends of
the crossing region, and reconnected to the
matching backbone of the DNA strand that
it will now become part of.
This creates two new complete chromatids. It
can be done a number of times, and then the
chromatids are matched with a mixed or nonmixed partner in the meiosis process.
Reconnect
Repair these
mismatched
sections
cross over in
this section
cut at these
two points
original chromatid pair
.
I
OR
II
resulting chromatid pair (choose one)
The Crossing Over Process
I:these
OR
II: these
A T
T A
G C
T A
A T
A T
A T
T A
G C
T A
A T
A T
A T
T A
G C
T A
A T
A T
G C
C G
A T
C G
A T
A T
G C
C A
A A
C G
G T
T T
GC
T A
AT
CG
AT
AT
G C
A T
T A
C G
G C
A T
G C
A T
T A
C G
G C
A T
G C
A T
T A
C G
G C
A T
A T
T A
G C
A T
T A
T A
I
GC
T A
AT
A T
T A
T A
G C
A T
T A
G C
T A
T A
A T
T A
T A
A T
T A
G C
G C
C G
T A
II
A T
T A
G C
GC
T A
AT
G C
A T
T A
I
GC
TA
TA
G C
C G
T A
A Small Example
OR
GC
TA
TA
G C
C G
T A
II
GC
T A
AT
G C
A T
T A
Proteins
Proteins are the basic functional units in any
organism. They are made up of a single carbonnitrogen backbone with docking points each
supporting one of 20 amino acids. Amino
acids can occur in any combination and order
as necessary to define the protein.
From DNA to Protein
• The protein amino acid sequence is coded
in a specific piece of the DNA called a
gene.
• The gene is made up of triples of base
pairs, called codons, each of which corresponds to a specific amino acid.
• Each gene has associated with itself a promoter sequence of DNA upstream of the
gene sequence, and a termination sequence
downstream, which identifies its location in
the genome.
• The gene sequence may also have intron
portions which do not code any part of the
protein, and must be removed before protein production starts.
The 20 Amino Acids
amino acid
alanine
arginine
aspartic acid
asparagine
cysteine
glutamic acid
glutamine
glycine
histidine
isoleucine
leucine
lysine
methionine
phenylalanine
proline
serine
threonine
tryptophan
tyrosine
valine
3-L abbrev.
Ala
Arg
Asp
Asn
Cys
Glu
Gln
Gly
His
I le
Leu
Lys
Met
Phe
Pro
Ser
Thr
Trp
Tyr
Val
1-L abbrev.
A
R
D
N
C
E
Q
G
H
I
L
K
M
F
P
S
T
W
Y
V
Map of Codons to Amino Acids
Each mRNA triple codes for either an amino
acid or a stop codon (TC).
first
base
U
C
A
G
second base
U
C
A
G
Phe Ser Tyr Cys
Phe Ser Tyr Cys
Leu Ser TC TC
Leu Ser TC Trp
third
base
U
C
A
G
Leu
Leu
Leu
Leu
Pro
Pro
Pro
Pro
His
His
Gln
Gln
Arg
Arg
Arg
Arg
U
C
A
G
Ile
Ile
Ile
Met
Thr
Thr
Thr
Thr
Asn
Asn
Lys
Lys
Ser
Ser
Arg
Arg
U
C
A
G
Val
Val
Val
Val
Ala
Ala
Ala
Ala
Asp
Asp
Glu
Glu
Gly
Gly
Gly
Gly
U
C
A
G
The Central Dogma
DNA → RNA → protein
Perhaps the most important process in cellular
biology is the process that changes a gene into
a protein. This process is called the expression of that gene, and the process by which
this is done is call the central dogma.
RNA: Intermediary in the copying of DNA to
either itself (replication) or to proteins
The structure of RNA: A single sugar-phosphate backbone with single bases attached.
The bases are the same, except that thymine
is replaced by uracil (U), which likewise
matches with a T in replication.
The Production of a Protein
Initiation: The production of a protein begins when a
protein called a transcription factor binds onto a
promotor site of the DNA.
Transcription: RNA polymerase then goes to work at
the promoter site, and moves along the DNA strand,
producing a complementary strand of messenger
RNA (mRNA), except that U matches with A.
When the process reaches a certain termination
sequence, the process halts and the mRNA is passes
out of the nucleus to be translated into a protein.
(The original strand may have to be additionally
processed to remove blocks of introns that do not
contribute to the protein.)
Translation: A rhibosome (rRNA) matches each codon
in the mRNA to a transfer RNA (tRNA) structure, which contains
• at one end an anticodon complementary to the
mRNA triple, and
• at the other end an amino acid which corresponds to the codon indicated by the original
DNA triple.
The rhibosome brings in the tRNA in succession as
it moves down the mRNA strand, hooking the new
amino acid to the ever-growing protein.
Termination: When the terminator triple is reached (which
may not necessarily be the end of the mRNA strand!),
the rhibosome lets go of the protein, and it is free
to do its assigned job.
The Central Dogma
Example
Suppose a protein is to be made from a strand
of DNA with the following base pairs:
−→
GGAATDGATCGGCGTCATTTTTGTGCAAGTCTA
TAGACTTGCACAAAAATGACGCCGATCGATTCC
←−
The arrows indicate the opposite direction in
which the bases will be searched on each strand.
The protein is identified by promoter site TTGCACA
and terminator site ATTCC. This is found on
the bottom strand, and the mRNA is produced
from that point on. The resulting mRNA strand
is
UUU|UAC|UGC|GGC|UAG|(C)
with the | marking the (complementary) codons
of the mRNA strand, and the stop (complementary) codon UAG indicating the end of the
protein. (Note that there may be more letters
after the stop codon; these are ignored by the
protein production process.)
The triples in this sequence now match with
tRNA structures with paired anticodon-amino
acid pairs
AAA---Phe, AUG---Tyr, ACG---Cys, CCG---Gly
and so the new protein has amino acid residues
phenylalanine, tyrosine, cysteine, and glycine,
in that order.
Note that if the RNA polymerase had slipped
one base-pair in the start of the transcription,
we would have had mRNA
UUU|ACU|GCG|GCU|AGC|UAA
which would have produced the protein with
amino acids phenylalanine, threonine, alanine,
alanine, and serine.