Download Nucleic Acids and the Encoding of Biological Information

Nucleic Acids
and the
Encoding of
Biological
Information
Chapter 3
GRIFFITH’S EXPERIMENT ON THE NATURE
OF THE GENETIC MATERIAL
In 1928, Frederick Griffith demonstrated that
molecules can transfer genetic information from one
organism to another.
AVERY, MACLEOD, AND MCCARTY’S EXPERIMENT ON
THE NATURE OF THE GENETIC MATERIAL
Virulent bacteria (killed)
DNA is extracted from
heat-killed virulent cells,
along with trace amounts
of RNA and protein.
Nonvirulent
bacteria
Virulent and
nonvirulent
Nonvirulent bacteria only
bacteria
The untreated extract can
transform nonvirulent cells into
virulent cells.
Only extracts treated with the
enzyme that destroys DNA
were unable to transform
nonvirulent bacteria.
Replication:
Process of copying the genetic information (DNA)
THE CENTRAL DOGMA
CARBON ATOM
THE CENTRAL DOGMA
We learned in Chapter 1 of the central dogma—DNA is
transcribed into RNA and that RNA is translated into protein.
The processes of transcription and translation are regulated,
meaning that they can be turned on or off according to the
needs of the cell function and or cell type (i.e., muscle cells).
In prokaryotes, both transcription and translation occur in the
cytoplasm.
In eukaryotes, transcription occur in the nucleus and translation
occur in the cytoplasm
NUCLEOTIDE STRUCTURE
THE FOUR BASES
Sugar + Base = Nucleoside
Sugar + Base + Phosphate = Nucleotide
PHOSPHODIESTER
BONDS
5’-AGCT-3’
THE DNA DOUBLE HELIX
A
B
HYDROGEN
BONDING
%A = %T
%G = %C
HYDROGEN BONDS + BASE STACKING
DNA REPLICATION
SUPERCOILING
1.DNA molecules in cells have a length far greater than the diameter of the
cell itself.
2.In prokaryotic cells, the DNA is circular.
3.It forms supercoils in which the circular molecule coils upon itself, much
like what happens when you twist a rubber band between your thumb and
forefinger.
4. Supercoiling relieves the strain caused by topoisomerases that cleave,
partially unwind, and reattach a DNA strand.
5. In doing so, supercoils also preserve the 10 base pairs per turn in the
double helix.
6
Chromatin
Condensed chromatid
1400 nm in diameter
5
Coiled coil
700 nm in
diameter
4
Coiled
chromatin fiber
300 nm in
diameter
2
Nucleosome
fiber 10 nm in
diameter
3
Histone
proteins
Nucleosome
1
Chromatin
fiber 30 nm
in diameter
DNA duplex 2
nm in diameter
CHROMATIN
1.In eukaryotes, the DNA in the nucleus is linear, and
each molecule forms one chromosome.
2.Again, there is a packaging problem because a
chromosome is thousands of times longer than the
diameter of the cell.
RNA WORLD HYPOTHESIS
1.Many scientists believe that RNA, not DNA, was the
original information storage molecule in the earliest
forms of life on Earth.
2.The reasons for thinking this are:
a.RNA is used in key cellular processes, including
DNA replication, transcription, and translation.
b.Experiments have shown that RNA can evolve
over time and act as a catalyst.
3.Why do cells now use DNA?
• Because RNA is a much less stable molecule.
DNA VS. RNA
DNA
RNA
Sugar
Deoxyribose
Ribose
Bases
A, T, C, G
A, U, C, G
5’ end
Monophosph
ate
Triphosphate
Size
Very large
Smaller
Strands
Double
Single
TRANSCRIPTION
Template strand
RNA transcript
Nontemplate strand
TRANSCRIPTION
1.The general process of transcription is
straightforward.
2.As a region of DNA unwinds, one strand is
used as a template for the RNA transcript to be
made.
3.The only difference is that T’s are replaced
with U’s.
4.The enzyme responsible is RNA polymerase.
5.The new strand grows in the 5′ 3′ direction,
which means the template DNA strand is in the
3′  5′ direction.
INITIATION AND TERMINATION OF
TRANSCRIPTION
TATA
TATA
TATA
TATA
INITIATION AND TERMINATION OF
TRANSCRIPTION
1.RNA polymerase and associated proteins bind to
the DNA duplex at promoter sequences.
2.Eukaryotic and archaeal promoters contain a
sequence similar to TATAAA, which is known as a
TATA box.
3.The first nucleotide to be transcribed is usually
positioned about 25 base pairs from the TATA box.
4.RNA polymerase moves along the template strand
in the 3′  5′ direction.
5.Transcription will continue until RNA polymerase
encounters a terminator.
INITIATION AND TERMINATION OF
TRANSCRIPTION
Transcription is regulated:
1.Genes that are needed all the time in all cells
(housekeeping genes) are transcribed all of the
time,
but
2.Most genes are transcribed only at certain times,
in certain conditions, or in certain cell types.
Eukaryotic Promotor Recognition
1
General transcription
factors bind to the
promoter, and
transcriptional
activator proteins
bind to enhancers.
Enhancer sequences
Promoter
3'
5'
Transcriptional activator proteins
3'
5'
Transcriptional
start site
5'
3'
DNA
General
transcription
factors
5'
3'
EUKARYOTIC PROMOTOR RECOGNITION
Eukaryotic Promotor Recognition
1.In bacteria, promoter recognition is mediated by a
protein, sigma factor.
• This protein associates with RNA polymerase
and facilitates its binding to specific promoters
to initiate transcription.
2.In eukaryotes, transcription initiation requires the
combined action of at least six proteins (general
transcription factors).
EUKARYOTIC PROMOTOR RECOGNITION
Enhancer sequence
5'
3'
Mediator
complex
2
Through looping of DNA,
transcriptional activator
proteins, mediator
complex, RNA Pol II, and
general transcription
factors are brought into
close proximity, allowing
transcription to proceed.
DNA
5'
3'
Promoter
RNA polymerase
complex (Pol II)
Promoter region
EUKARYOTIC PROMOTOR RECOGNITION
Eukaryotic Promotor Recognition
1.These factors recruit RNA polymerase II (Pol II) to
the site for transcription.
2.In addition, proteins bound to an enhancer
sequence need to recruit a mediator complex that in
turn interacts with the Pol II complex.
RNA POLYMERASE II ADDS NUCLEOTIDES
TO THE 3’ END
RNA Polymerase II Adds Nucleotides
RNA
transcript
Template
DNA strand
RNA–DNA duplex
RNA
polymerase
complex (Pol II)
RNA Polymerase II Adds Nucleotides
1.Transcription takes place in what looks like a
bubble that is about 14 base pairs in length.
2. The RNA-DNA duplex in the bubble is about 8
base pairs in length.
POLYMERIZATION REACTION
POLYMERIZATION REACTION
The details of the polymerization reaction:
1.The incoming ribonucleotide triphosphate is recognized by
the RNA polymerase and joined to the growing transcript if it
base pairs correctly.
• In this case, the A in the DNA strand would need to be
paired with a U in the transcript.
2.The RNA polymerase orients the oxygen in the hydroxyl group
at the 3’ end of the growing strand into a position from which
it can attack the innermost phosphate of the triphosphate.
3.The 3’-OH of the growing strand attacks the high-energy
phosphate of the incoming ribonucleotide, providing the
energy for the reaction to take place.
RNA POLYMERASE IN PROKARYOTES
RNA POLYMERASE IN PROKARYOTES
The complex in prokaryotes also forms a
transcription bubble.
1.The RNA polymerase is able to separate the DNA,
allow an RNA-DNA duplex to form, elongate the
transcript nucleotide by nucleotide, release the
finished transcript, and restore the original DNA
double helix.
2.The RNA polymerase contains separate channels
for the entry of the trinucleotides and DNA to be
transcribed, and for the exit for the RNA transcript
and transcribed DNA.
PRIMARY TRANSCRIPT IN PROKARYOTES
PRIMARY TRANSCRIPT IN PROKARYOTES
1.The RNA transcript that comes off the template
DNA strand is known as the primary transcript.
• It contains the information of the gene that was
transcribed.
2.For protein-coding genes, the primary transcript
includes the information needed to direct the
ribosome to produce the protein.
3.The RNA molecule that combines with the
ribosome to direct protein synthesis is called
mRNA.
PRIMARY TRANSCRIPT IN PROKARYOTES
1.In prokaryotes, this relationship is simple because
the primary transcript is the mRNA.
• Both processes occur in the cytoplasm and there is
no nuclear envelope to separate transcription
spatially from translation.
2.It is also common in prokaryotes for the primary
transcripts to contain the information for more than
one gene.
• The mRNA is then said to be polycistronic mRNA.
PRIMARY TRANSCRIPT IN EUKARYOTES
5’ Cap on Eukaryotic
mRNA
PRIMARY TRANSCRIPT IN EUKARYOTES
Eukaryotic cell
Exon
Intron
DNA
Poly(A) tail
5' cap
Primary transcript
(RNA)
The 5' end is modified by a
special nucleotide called the
5' cap.
mRNA
Polyadenylation adds a
poly(A) tail to the 3'
end.
Spliced exons
Introns are excised from the RNA strand
and exons are spliced together.
PRIMARY TRANSCRIPT IN EUKARYOTES
1.In eukaryotes, there is a barrier between
transcription and translation (the nuclear
membrane).
2.The primary transcript undergoes a complex
process of chemical modifications known as RNA
processing.
3.Three types of chemical modification occur
before the mRNA is translated by the ribosome.
Modification 1
1. The first is the addition of a 5’cap consisting of 7methylguanosine to the 5’ end of the primary transcript.
With the addition of the 5’ cap, the ribosome would not
recognize the mRNA and translation could not occur.
Modification 1
5′ Cap on Eukaryotic mRNA
7-Methylguanosine
5'-to-5'
phosphate
linkage
The 5’ cap consists of a modified
base linked by its 5’ carbon to the
5’ end of the primary transcript by
a bridge composed of three
phosphates.
5' end of RNA
transcript
Modification 2
2. The second major modification is the addition of about 250
consecutive adenines to the 3’ end of the mRNA. This
process is known as polyadenylation.
This modification plays an important role in transcription
termination as well as the export of the mRNA to the
cytoplasm of the cell.
Both the 5’ cap and the polyA tail help to stabilize the RNA
transcript since single-stranded nucleic acids can be unstable
and susceptible to breakdown by enzymes.
Modification 2
Modification 3
3. The third modification of the primary transcript is the
excision of certain sequences known as introns, leaving
intact the exons. This process is known as RNA splicing.
Intron removal is catalyzed by a complex of RNA and
protein known as the spliceosome:
About 90% of all human genes contain at least one intron
Modification 3
ALTERNATIVE SPLICING
One primary transcript can code for multiple genes; which gene is
formed depends on how the transcript is spliced.