Molecular Biology
• Molecular biology is the study of DNA
– Its structure
– How it replicates (and assembles to create
genetically-distinct offspring)
– How it controls the cell by directing RNA and
protein synthesis
• How does DNA store genetic information,
copy it, and pass it along from one generation
to the next?
DNA and RNA
• DNA and RNA are nucleic acids consisting of
long chains of nucleotides (collectively called a
polynucleotide)
• There are 4 types of nucleotides that make up
DNA, each with a different nitrogenous base
– Adenine (A)
– Cytosine (C)
– Thymine (T)
– Guanine (G)
Sugar-phosphate backbone
Phosphate group
Nitrogenous base
Sugar
Nitrogenous base
(A, G, C, or T)
DNA nucleotide
Phosphate
group
Thymine (T)
Sugar
(deoxyribose)
DNA nucleotide
DNA polynucleotide
DNA and RNA
• RNA has the nitrogenous base Uracil (U),
instead of Thymine (T), and is usually singlestranded
• DNA is double-stranded and forms a double
helix
• The 2 sugar-phosphate backbones that form
the double helix run in opposite directions (5’
to 3’ and 3’ to 5’)
Each strand of DNA runs in opposite directions
Hydrogen bond
Base
pair
Ribbon model
Partial chemical structure
Computer model
DNA replication depends on specific
base pairing
• The specific pairing of bases in DNA is
evidence for a copying mechanism for the
genetic material
• Knowledge of the sequence of bases in 1
strand of DNA allows you to determine the
sequence in the second strand
• When 2 strands of DNA separate, each strand
serves as a template for the assembly of a
complimentary strand
DNA Replication
• The human genome (all genes collectively)
contains over 6 billion base pairs in 46
chromosomes (23 ‘homologou’s pairs)!
• Yet, DNA replication requires only a few hours
and is astonishingly accurate
• How does this process occur and what
controls it???
DNA Replication
• DNA replication requires more than a dozen
enzymes and other proteins (of course!)
• Replication of DNA begins at specific sites
called origins of replication
• Origins of replication consist of a specific
sequence of nucleotides where proteins
attach to the DNA and separate the strands
• Replication then proceeds in both directions
Origin of replication
Parental strand
Daughter strand
Bubble
Two daughter DNA molecules
DNA Replication
• Eukaryotic DNA has many origins of
replication shortening the overall time needed
for the replication process
• Replication occurs in “bubbles” of parental
(old) and daughter (new) DNA
• Eventually, all the “bubbles” merge yielding 2
completed daughter strands of DNA
Daughter strands (grey); Parental strands (blue)
DNA Replication
• The enzymes that link DNA nucleotides to a
growing daughter strand are called DNA
polymerases
• Remember that DNA’s sugar-phosphate
backbones run in opposite directions
• DNA polymerases add nucleotides only to the
3’ end, never to the 5’ end
• Thus, a daughter strand grows from 5’ to 3’
(Say what?!!?)
3 end
5 end
P
4
3
P
5
2
1
2
3
1
4
5
P
P
P
P
P
P
3 end
5 end
DNA polymerase
molecule
5
3
3
5
Parental DNA
3
5
Daughter strand
synthesized
continuously
Daughter
strand
synthesized
in pieces
• Since the 2 DNA strands run in opposite
directions, and replication always begins at
the 3’ end, the new daughter strand will be
laid down beginning at its 5’ end
• 1 daughter strand is synthesized continuously,
while the other must work outward from the
forking point
Formed 2nd
Formed 1st
Formed last
• The new strand is synthesized in short pieces
as the DNA strand opens up
• Another enzyme, called DNA ligase then links
the pieces together to form a single DNA
strand
Thank you, polymerases
• DNA polymerases also carry out a proofreading step to quickly remove any
nucleotides that have been paired incorrectly
during replication
• DNA polymerases and ligases are also involved
in repairing DNA damaged by harmful
radiation or toxic chemicals, including those
found in cigarette smoke!
DNA Replication
• DNA replication ensures that all cells in a
multicellular organism carry the same genetic
information
• DNA replication occurs during interphase!
• The DNA genotype is expressed as proteins,
which provides the molecular basis for
phenotypic traits
– DNA dictates the synthesis of proteins which
determine the traits physically expressed by an
organism
DNA is transcribed into RNA and
translated into Protein
• A gene does not build a protein directly
• Instead, a gene dispatches its instructions for
building proteins in the form of RNA, which in
turn directs protein synthesis
• The transcription of DNA into RNA and the
subsequent translation of RNA into proteins is
considered the “central dogma” of molecular
biology
DNA
Transcription of DNA into RNA
RNA
Nucleus
Cytoplasm
Translation of RNA into Protein
Protein
DNA is life…the rest is just translation
• In eukaryotic organisms, DNA is stored in the
nucleus where it is transcribed into RNA; a
process called transcription
• RNA translates the information from DNA into
proteins in the cytoplasm (or to be more
precise, in the ribosomes… we’ll come back to
this); a process called translation
Genetic information written in codons is
translated into amino acid sequences
• A typical gene consists of hundreds or
thousands of nucleotides in a specific
sequence
• The sequence (and number) of these
nucleotides determines the protein produced
by this gene, and hence its resulting
phenotype
• DNA must first be re-written (transcribed) as a
sequence of RNA
Genetic information written in codons is
translated into amino acid sequences
• Translation then converts the nucleic acid
‘language’ into the polypeptide (protein)
‘language’
• The sequence of RNA nucleotides dictates the
sequence of amino acids of the polypeptide
being produced
• Thus, the RNA molecule acts as a messanger
carrying genetic information from DNA
DNA strand
Transcription
RNA
Codon
Translation
Polypeptide
Amino acid
Genetic information written in codons is
translated into amino acid sequences
• In order for translation to proceed, the
sequence of the 4 nucleotides in RNA (A,U,
C,G) must somehow specify the 20 amino
acids used to make up proteins
• The flow of information from gene to protein
is based on a triplet code; genetic instructions
for the amino acid sequences of a polypeptide
chain are written in DNA and RNA as a series
of 3-base ‘words’, called codons
The Genetic Code
• The genetic code is a set of instructions
indicating which codons are translated into
which amino acid
• The genetic code does not only specify which
codons code for which amino acids, but also
specify ‘start’ and ‘stop’ signals, which begin
and end protein synthesis, respectively
• For each of the 20 amino acids, there are 2-4
codons which code exclusively for them
Third base
First base
Second base
The Genetic Code
• The genetic code is nearly universal; humans
cells can translate bacterial RNA and vice versa
Transcription
• An enzyme called RNA polymerase attaches
to an area of one of the DNA molecules in the
double helix and moves along the DNA strand
‘reading’ the nucleotides
• It then selects complimentary nucleotides and
links them one by one via hydrogen bonds
• A nucleotide sequence called a promoter
serves as a “start” signal, while a terminator
sequence marks the end of transcription
RNA polymerase
DNA of gene
Promoter
DNA
Terminator
DNA
1
Initiation
2
Elongation
3
Termination
Completed
RNA
Area shown
in Figure 10.9A
Growing
RNA
RNA
polymerase
RNA nucleotides
RNA
polymerase
Direction of
transcription
Newly made RNA
Template
strand of DNA
Messenger RNA
• The type of RNA that encodes amino acid
sequences is called messenger RNA (mRNA)
• In eukaryotic cells, mRNA leaves the nucleus
where it had been transcribed and enters the
cytoplasm
• Before mRNA can leave the nucleus, it is
modified
– A ‘tail’ and ‘cap’ are added
– Introns are removed
A cap and
tail are
added to
protect the
mRNA
strand,
facilitate its
transport
out of the
nucleus and
to help
ribosomes
bind to it
Exon Intron
Exon
Intron Exon
DNA
Cap
RNA
transcript
with cap
and tail
Transcription
Addition of cap and tail
Introns removed
Tail
Introns are
intervening
sequences
of DNA
which do
not code for
amino
acids; must
be removed
Exons spliced together
mRNA
Coding sequence
Nucleus
Cytoplasm
Exons are
the coding
regions,
parts of the
gene which
remain and
are
translated
into amino
acids
Transfer RNA
• In order to convert the 3-letter codons of
nucleic acids into a single amino acid, a cell
must employ a molecular interpreter, transfer
RNA (tRNA)
• tRNA recognizes the codons in the mRNA
molecule and picks out the appropriate amino
acids for incorporation into the growing
polypeptide
Transfer RNA
• tRNA recognizes codons from mRNA via a
special triplet of bases called an anticodon,
which is complimentary to the codon on the
mRNA
• When the codon of mRNA complements the
anticodon of tRNA, the appropriate amino
acid is laid down at the other end of the tRNA
molecule
Amino acid attachment site
Hydrogen bond
RNA polynucleotide chain
Anticodon
Transfer RNA
• For each amino acid, there is a specific type of
tRNA that it will bind to
• And for each tRNA, there is a specific enzyme
which binds the amino acid to its specific
tRNA molecule
• How many enzymes (or tRNA molecules for
that matter) are there?
Translation
• mRNA leaving the nucleus enters the
cytoplasm where it binds to a ribosome
(Remember, all cells contain ribosomes…)
• Translation begins when the mRNA molecule
arrives at the ribosome
• While mRNA was being synthesized, tRNA
molecules were already uniting with their
specific amino acids
Translation
• The tRNA molecules then begin transporting
their amino acids to the ribosomes to meet
the mRNA molecule
• Ribosomes are made up of proteins and a type
of RNA called ribosomal RNA (rRNA)
• The ribosomes contain binding sites for both
mRNA and tRNA
tRNA-binding sites
Large
subunit
mRNA
binding
site
Small
subunit
Next amino acid
to be added to
polypeptide
Growing
polypeptide
tRNA
mRNA
Anticodon of tRNA
Codons of mRNA
New peptide
bond forming
Growing
polypeptide
4 Elongation
Codons
A succession of tRNAs
add their amino acids
to the polypeptide chain
as the mRNA is moved
through the ribosome,
one codon at a time.
mRNA
Polypeptide
5 Termination
Stop codon
The ribosome
recognizes a stop
codon. The polypeptide
is terminated and
released.
Translation
• Translation begins with a ‘start’ codon, and
ends with a ‘stop’ codon
• The amino acid methionine (Met) is always
translated by the start codon (AUG)
• What would the anticodon look like?
• Stop codons (UAA, UAG, and UGA) do not
code for amino acids but instead act only as
signals to end translation
Review
• Describe the differences between mRNA,
tRNA and rRNA
• What bases are found in DNA? In RNA?
• Which molecule has codons? Anticodons?
• What is transcription? Translation? Which
happens first and where does each occur in
the cell?
Mutations
• A single change in the amino acid coded for by
a gene can lead to mutation
• …and a single change to a single nucleotide
can lead to a change in amino acid!
• Mutations can be caused
by a nucleotide addition,
deletion or substitution
• Insertions or deletions are
the most disastrous
www.milehive.com/.../x-men-origins-wolverine.jpg
Mutations
• The production of mutations can occur
spontaneously during DNA replication or by a
mutagen, a physical or chemical agent such as
X-rays and ultraviolet light (physical)
• What would happen if a mutation occurred in
an intron? An exon?
http://www.ninjaturtles.com/
Viruses
• A virus is a fragment of nucleic acid
surrounded by a protein coat
• Viruses are infectious; they are parasites that
can reproduce only inside living cells
• The host cell provides most of the
components necessary for replicating,
transcribing and translating the viral DNA!
You can run, but you can’t hide…
• Viruses infect bacteria, archaea,
protists, plants and animals, and
are found in nearly every
ecosystem on Earth!
• Viruses contain genes made of
DNA or RNA
• The protein coat (or membrane
in some cases) allows the virus to
penetrate the host cell
Viral DNA
Viruses
• Viruses cause illness because they attach to a
cell, and inject their DNA into it
• The host cell is then ‘instructed’ by the viral
DNA to produce more copies of itself and to
translate proteins, which together serve to
assemble more viruses!
• Eventually the cell lyses and releases an army
of viruses
Lytic cycle of viruses
Phage attaches
to bacterial cell.
Phage injects DNA.
Phage DNA directs host
cell to make more phage
DNA and protein parts.
New phages assemble.
Cell lyses and
releases new phages.
Viruses
• The common cold is caused by viruses
containing RNA, as are measles, mumps, AIDS
and polio
• DNA viruses cause hepatitis, chicken pox and
herpes
• Glycoproteins on the virus’s outer coat enable
it to attach to receptor proteins on the host
cell’s plasma membrane (very specific!)
Got NyQuil?
• The amount of harm caused by viruses
depends largely on how quickly an organism’s
immune system responds to fight the
infection, and also on the ability of the
infected tissue to repair itself
• Our respiratory tract can efficiently replace
damaged cells by mitosis and we usually
recover quickly from colds, but damage done
to nerve cells by the Poliovirus is permenant
How do viruses spread?
• Ever wonder why we sneeze and cough when
we’re sick???
• Cold sores, herpes, chicken pox…..
Viral DNA may become part of the
host chromosome
• Viruses reproduce via the host cell as
previously described in the lytic cycle
• But viruses can also reproduce via an
alternative route called the lysogenic cycle
• During a lysogenic cycle, viral DNA is
replicated without destruction of the host cell
• In this case, viral DNA is incorporated into the
host cell’s DNA and is replicated every time
the host cell prepares to divide
Lytic and Lysogenic viral cycles
Phage
1
Attaches
to cell
Bacterial
chromosome
Phage DNA
Cell lyses,
releasing phages
Phage injects DNA
7
2
Many cell
divisions
4
Lytic cycle
Lysogenic cycle
Phages assemble
Phage DNA
circularizes
Prophage
5
3
Lysogenic bacterium reproduces
normally, replicating the
prophage at each cell division
6
OR
New phage DNA and
proteins are synthesized
Phage DNA inserts into the bacterial
chromosome by recombination
Viruses
• The bacteria that cause diphtheria, botulism
and scarlet fever would be harmless were it
not for the viral DNA encoded into their DNA!
• Mutations of existing viruses are a constant
source of new, emerging viruses
• RNA viruses are usually the culprit; errors in
replication are not subject to the types of
proofreading mechanisms that help reduce
mutations in DNA replication
Question of the day (or century,
millennium, etc ….)
•
•
•
•
Are viruses alive????
Do they reproduce?
Do they grow and develop?
Do they take in energy and process it to
perform their activities?
• Do they respond to their environment?
• Do they adapt?
Want to learn more?