Download Lecture 8. DNA AND THE LANGUAGE OF LIFE

DNA AND THE LANGUAGE
OF LIFE
NUCLEIC ACIDS STORE INFORMATION IN
THEIR SEQUENCES OF CHEMICAL UNITS
NUCLEIC ACIDS STORE INFORMATION IN
THEIR SEQUENCES OF CHEMICAL UNITS
• The Building Blocks of DNA
– Deoxyribonucleic acid (DNA) stores the
genetic information of organisms
– It is a polymer built from monomers called
nucleotides and is a nucleic acid as is
ribonucleic acid (RNA).
– There are four types of nucleotides, each with
three parts.
• A ring shaped sugar called deoxyribose
• A phosphate group (phosphorus surrounded by
NUCLEOTIDES
NUCLEIC ACIDS STORE INFORMATION IN
THEIR SEQUENCES OF CHEMICAL UNITS
four oxygen atoms.
– A nitrogenous base: single or double ring of
carbon and nitrogen atoms with functional
groups.
– Nitrogenous Bases
• The nucleotides differ only in their nitrogenous
bases.
– Pyramidines: single ring structures or thymine (T) or
cytosine (C)
– Purines: larger, double ringed of adenine (A) or guanine
(G)
NITROGENOUS BASES:
PURINES AND PYRAMIDINES
NUCLEIC ACIDS STORE INFORMATION IN
THEIR SEQUENCES OF CHEMICAL UNITS
– DNA Strands
• The nucleotides are connected by covalent bonds
that connect the sugar of one nucleotide to the
phosphate group of the next.
• The repetition of the sugar-phosphate is the sugarphosphate “backbone.”
• In a similar fashion to amino acid monomers
combining to form polypeptides, nucleotides of
nucleic acid polymers can combine in many
different sequences.
• The length of a nucleotide chain can vary from a
COVALENT BONDS BETWEEN
SUGAR AND PHOSPHATE
NUCLEIC ACIDS STORE INFORMATION IN
THEIR SEQUENCES OF CHEMICAL UNITS
few hundred to millions, allowing for an unlimited
number of sequences.
• DNA’s Structure
– In the early 1950s, Franklin and Wilkins
photographed DNA using a method called xray crystallography, which showed the basic
shape to be a helix.
– The Double Helix
• Watson and Crick used wire and tin to model the
DNA structure.
FRANKLIN & WILKINS,
WATSON & CRICK
NUCLEIC ACIDS STORE INFORMATION IN
THEIR SEQUENCES OF CHEMICAL UNITS
• They continued their work until Watson saw one of
Franklin’s photographs.
• The then created a new molecule of two strands of
nucleotides wound around each other, called a
double helix.
• Their model had the sugar-phosphate backbones
on the outside of the double helix and the
nitrogenous bases on the inside.
• They hypothesized that the bonds between the
bases were hydrogen bonds.
• They had constructed the actual DNA molecule!
NUCLEIC ACIDS STORE INFORMATION IN
THEIR SEQUENCES OF CHEMICAL UNITS
– Complementary Base Pairs
• They discovered that there were specific base
pairs between the purines and pyramidines:
– purine adenine with pyramidine thymine
– Purine guanine with pyramidine cytosine
• A is complementary to T and G is complementary
to C.
• The sequence on one strand can vary but the
bases on the second strand are determined by the
sequence on the first strand.
COMPLEMENTARY BASE
PAIRING
NUCLEIC ACIDS STORE INFORMATION IN
THEIR SEQUENCES OF CHEMICAL UNITS
• Each base must pair up with its complement.
• This was first reported by Watson and Crick in
1953, in the journal Nature. With them
subsequently receiving the Nobel prize for their
work.
REVIEW
1. What are the three parts of a nucleotide?
Which parts make up the backbone of a
DNA strand?
2. List the two base pairs found in DNA.
3. If six bases on one strand of a DNA
double helix are AGTCGG, what are the
six bases on the complementary section
of the other strand of DNA.
DNA REPLICATION IS THE MOLECULAR
MECHANISM OF INHERITANCE
• The Template Mechanism
– Dividing cells receive a complete set of
genetic instructions in each new cell.
– One generation passes genetic instructions to
the next generation.
– Before DNA was discovered as the genetic
material, it was proposed that gene-copying
was based on the template mechanism.
DNA REPLICATION IS THE MOLECULAR
MECHANISM OF INHERITANCE
– Like reproducing pictures from negatives, the
negative of DNA is used to make more DNA.
– Applying the complementary base rule allows
you to pair the specific base with its
complement: A to T, C to G.
– Using enzymes, the double helix separates
with each “negative” producing a new
complementary strand.
– Enzymes link the nucleotides together to form
DNA REPLICATION
DNA REPLICATION IS THE MOLECULAR
MECHANISM OF INHERITANCE
two new DNA strands, called daughter
strands.
– This process of copying the DNA molecule is
called DNA replication.
• Replication of the Double Helix
– There are more than one dozen enzymes
involved in DNA replication.
– DNA polymerases also act to make the
covalent bonds between the nucleotides of
the new strand.
DNA REPLICATION IS THE MOLECULAR
MECHANISM OF INHERITANCE
– The replication begins at specific sites called
origins of replication and the copying
proceeds outward in both directions, creating
replication bubbles.
– Eukaryotic DNA molecules has many origins
where replication starts at the same time.
– Eventually all the bubbles merge, yielding two
double stranded DNA molecules, each with
one original strand and one new strand.
REPLICATION OF THE DOUBLE HELIX
DNA REPLICATION
REPLICATION BUBBLE
DNA REPLICATION IS THE MOLECULAR
MECHANISM OF INHERITANCE
– DNA replication occurs before cells divide,
ensuring that all the cells contain the same
genetic information.
– The same mechanism produces DNA copies
that subsequent generations inherit from their
parents during reproduction.
REVIEW
1. Describe how DNA replicates by using a
template.
2. List the steps involved in DNA replication.
3. Under what circumstances is DNA
replicated.
A GENE PROVIDES THE INFORMATION
FOR MAKING A SPECIFIC PROTEIN
• One Gene, One Polypeptide
– The genotype of an organisms is it’s genetic
makeup, or the sequence of nucleotide bases
in its DNA.
– The phenotype, or the organism’s specific
traits, is found in proteins and their wide
variety of functions.
– Beadle and Tatum, in the 1940s found the
relationship between genes and proteins
A GENE PROVIDES THE INFORMATION
FOR MAKING A SPECIFIC PROTEIN
working with the orange bread mold
Neurospora crassa.
– They found that mutant strains of the mold
could not grow on the usual medium and they
lacked a single enzyme to produce the mold.
– They attributed this to a single gene; hence,
the one gene, one enzyme hypothesis.
– This hypothesis states that the function of an
individual gene is to dictate the production of
a specific enzyme.
ORANGE BREAD MOLD
A GENE PROVIDES THE INFORMATION
FOR MAKING A SPECIFIC PROTEIN
– Since that time, it has been learned that
genes dictate the production of a single
polypeptide that make up part of an enzyme
or another protein, now changing the one
gene, one enzyme to one gene, one
polypeptide.
• Information Flow: DNA to RNA to Protein
– RNA is the messenger between DNA and
proteins.
RIBONUCLEIC ACID (RNA)
A GENE PROVIDES THE INFORMATION
FOR MAKING A SPECIFIC PROTEIN
– Ribonucleic acid (RNA) has a ribose as the
sugar instead of a deoxyribose, only one
strand instead of two, and uracil instead of
thymine.
– Several types of RNA molecules play a part in
the intermediate steps from gene to protein.
– As you already know, the language of genes
is written as a sequence of bases along the
length of a DNA chain.
TRANSCRIPTION
TRANSCRIPTION
TRANSCRIPTION AND TRANSLATION
A GENE PROVIDES THE INFORMATION
FOR MAKING A SPECIFIC PROTEIN
– The RNA is the messenger from the DNA to
the ribosome for the construction of the
polypeptide chain.
– DNA’s nucleotide sequence in converted to
the single strand RNA molecule by
transcription.
• RNA is a different form of the DNA message.
– In the next step, translation takes place,
converting nucleic acid language to amino
acid language.
TRANSLATION
TRANSLATION
A GENE PROVIDES THE INFORMATION
FOR MAKING A SPECIFIC PROTEIN
– This is done based on codons for the flow of
information from gene to protein.
– The codon is a three base word that codes
for a specific amino acid.
– Each codon brings forth an amino acid that
translates into a polypeptide.
• The Triplet Code
– Nirenburg, an American biochemist, began
cracking the codes in the early 1960s.
A GENE PROVIDES THE INFORMATION
FOR MAKING A SPECIFIC PROTEIN
– He found that by putting just UUU on an RNA
molecule and putting this in a test tube
containing all 20 of the amino acids, a
polypeptide containing only phenylalanine
(Phe) was made.
– He and other scientists, using this method,
concluded the other amino acids represented
by each codon.
– There are 64 sequences (4³) with start and
stop codes.
CODON CODES
CODON WHEEL
A GENE PROVIDES THE INFORMATION
FOR MAKING A SPECIFIC PROTEIN
• Almost all organisms share the same
coding system.
• In experiments, genes can be transcribed
and translated after being transferred from
one species to another.
REVIEW
1. How did Beadle and Tatum’s research in
the “one gene-one polypeptide”
hypothesis?
2. Which molecule completes the flow of
information from DNA to protein?
3. Which amino acid is coded for by the
RNA sequence CUA?
4. List two ways RNA is different from DNA.
THERE ARE TWO MAIN STEPS
FROM GENE TO PROTEIN
• Transcription: DNA to RNA
– There are three types of RNA involved in
making proteins from the instructions carried
in genes.
• Messenger RNA (mRNA) is transcribed from the
DNA template.
– This resembles replication but only one strand is
produced from the template.
– The two DNA strands separate at the place where
transcription will start and then the RNA bases pair with
complementary DNA bases.
TRANSCRIPTION
THERE ARE TWO MAIN STEPS
FROM GENE TO PROTEIN
– The only difference between this and DNA replication is
that the base pairing is different-uracil instead of thymine
pairs with adenine.
– RNA polymerase, a transcription enzyme, links the RNA
nucleotides together telling the polymerase where to
begin and end the transcribing process.
• Editing the RNA Message
– In prokaryotes only, the mRNA transcribed
from a gene directly serves as the messenger
molecule that is translated into a protein.
EDITING THE RNA TRANSCRIPT
EDITING THE RNA TRANSCRIPT
THERE ARE TWO MAIN STEPS
FROM GENE TO PROTEIN
– In eukaryotes, the RNA transcribed is
modified or processed before it leaves the
nucleus as mRNA to be translated.
– Certain regions on the RNA are noncoding
regions called introns.
– Exons are the coding regions of the RNA
transcript (those parts of the gene that remain
in the mRNA) and are, therefore, translated,
or ‘expressed.”
THERE ARE TWO MAIN STEPS
FROM GENE TO PROTEIN
– Introns are removed and exons spliced
together before the RNA leaves the nucleus,
a process called RNA splicing.
• Translation: RNA to Protein
– Translating the nucleic acid language to
protein language requires enzymes, ATP,
ribosomes, and transfer RNA (tRNA).
THERE ARE TWO MAIN STEPS
FROM GENE TO PROTEIN
– The Players
• An interpreter is needed to translate the message
from mRNA to the polypeptide chain, that
interpreter being tRNA.
• Transfer RNA (tRNA) translates the three letter
codons of mRNA to the amino acids that make up
proteins.
• This process involves:
– the tRNA becoming bound to the appropriate amino
– recognizing of the appropriate codon in the mRNA
– A different version of tRNA molecule per codon
TRANSFER RNA (tRNA)
THERE ARE TWO MAIN STEPS
FROM GENE TO PROTEIN
• One end of the tRNA has a specific triplet of bases
called an anticodon which are complementary to
a specific codon on the mRNA.
• During translation, the anticodon on tRNA
recognizes a particular codon on mRNA according
to the base pairing rules.
• On the other end of tRNA is the site where a
particular amino acid attaches.
• There is an enzyme specific for each amino acid
that recognizes both the tRNA and the amino acid
and then links them together, using energy from
ATP.
TRANSLATION
TRANSLATION
THERE ARE TWO MAIN STEPS
FROM GENE TO PROTEIN
• The ribosome is the coordinating structure
between the two RNAs.
• This ribosome is made up of two subunits, made of
proteins and another type of RNA called
ribosomal RNA (rRNA).
• The ribosome has a binding site for mRNA and two
binding sites for tRNA, the “P” site for the tRNA
carrying the growing polypeptide chain and an “A”
site that holds the tRNA carrying the next amino
acid.
“P” AND “A” SITES
TRANSCRIPTION AND TRANSLATION
TRANSCRITION AND TRANSLATION
TRANSLATION
THERE ARE TWO MAIN STEPS
FROM GENE TO PROTEIN
– The Process
1. Translation brings all the parts together: mRNA,
the first tRNA, two subunits of the ribosome.
2. The starting codon (AUG) tells us where
translation will begin.
3. New amino acids are added to the chain until a
stop codon (UAA, UAG, UGA) is reached.
4. When a new amino acid does not arrive at the
“A” site, translation stops.
5. The completed polypeptide is set free by
hydrolysis from the tRNA.
TRANSLATION
TRANSLATION
THERE ARE TWO MAIN STEPS
FROM GENE TO PROTEIN
• A single ribosome can make polypeptide chains in
less than a minute.
• Review of Protein Synthesis
– The chain of command originates with the
DNA of the gene, which serves as the
template in transcription of mRNA, which
specifies the sequence of amino acids in a
polypeptide chain, assisted by tRNA and
rRNA on the ribosome.
REVIEW
1. What kind of nucleic acid is made during
transcription ?
2. How do introns and exons relate to RNA
splicing?
3. List the three RNA types involved in
transcription and translation, and describe the
role of each.
4. Briefly describe the steps of protein synthesis.
MUTATIONS CAN CHANGE
THE MEANING OF GENE
• How Mutations Affect Genes
– Mutations are any changes in the nucleotides
sequences of DNA.
– They can involve large regions of
chromosomes or a single base, as in sickle
cell disease or Tay-Sachs disease.
– Sometimes the substitution of a base causes
no problem or can be fatal.
– There is more than one codon for some
amino acids.
BASE SEQUENCE CHANGES
LEADING TO MUTATIONS
MUTATIONS CAN CHANGE THE
MEANING OF GENE
– If the mutation is to a codon that codes for the
same amino acid, it is known as a silent
mutation.
– Sometimes the amino acid picked up, while
wrong, is so similar to the original that, again,
no changes ensue.
– Insertions or deletions of nucleotides are the
most disastrous.
– Adding or subtracting nucleotides can alter
MUTATIONS
MUTATIONS
MUTATIONS CAN CHANGE THE
MEANING OF GENE
– Triplet groupings and those nucleotides
subsequent to the “mistake” can be regrouped
into different codons, coding for different
amino acids resulting in a different protein.
• What Causes Mutations?
– Mutations occur during DNA replications or
meiosis.
– Mutagens are physical or chemical agents
that can cause mutations.
MUTATIONS CAN CHANGE THE
MEANING OF GENE
– High energy radiation, x-ray or ultraviolet, can
cause mutations.
– There are chemicals that are similar to DNA
bases but cause incorrect base pairing.
– Some mutations can be beneficial such as in
butterflies.
– Mutations can be passes on to future
generations through gametes and are the
ultimate cause of genetic diversity.
MUTATIONS
MUTATIONS
REVIEW
1. Explain why a base substitution is often
less harmful than base deletion or
insertion.
2. Describe how a mutation can be helpful
rather than harmful.
3. Give an example of a mutagen.
BIOLOGISTS CAN ENGINEER BACTERIA
TO MAKE USEFUL PRODUCTS
• Engineering Bacteria: An Introduction
– Many bacteria contain plasmids, which are
small, circular DNA molecules that are
separate from the larger bacterial
chromosome.
– Plasmids may carry genes and can make
copies of itself.
– When it replicates, one copy can pass from
one bacterial cell to another, resulting in gene
sharing between the bacteria.
PLASMIDS
BIOLOGISTS CAN ENGINEER BACTERIA
TO MAKE USEFUL PRODUCTS
– The plasmids engage in gene transfer that
can spread traits that aid the bacterial cells to
survive, such as antibiotic resistance.
– The plasmid can be used for good purposes
such as gene cloning.
• The plasmid is removed from the bacterial cell.
• A desired gene from any cell is inserted into the
plasmid, resulting in recombinant DNA, a
combination of the original DNA and the new DNA.
• The plasmid is returned to the bacteria, where
GENE CLONING
GENE CLONING
BIOLOGISTS CAN ENGINEER BACTERIA
TO MAKE USEFUL PRODUCTS
replication can produce many copies of the
desired genes.
• “Cutting and Pasting” DNA
– How do biologists remove a gene from one
molecule and put it into another?
• The desired DNA is cut from a much longer DNA
molecule.
• Restriction enzymes are the tools that are used
to cut this DNA.
• These are found in bacteria and protect it from
intruding DNA from other organisms and phages.
BIOLOGISTS CAN ENGINEER BACTERIA
TO MAKE USEFUL PRODUCTS
• The enzymes cut the DNA into small pieces.
– The cuts are staggered leaving single-stranded DNA
hanging off the ends of the fragments.
– These are called the sticky ends and can bind to any
sequence that is complementary to it.
• Two ends of DNA fragments can join together by
base pairing with the use of DNA ligase, that
pastes the sticky ends together.
RESTRICTION ENZYMES
RESTRICTION ENZYMES
RESTRICTION ENZYMES
CLONING OF A HUMAN GENE
BIOLOGISTS CAN ENGINEER BACTERIA
TO MAKE USEFUL PRODUCTS
• Cloning Recombinant DNA
– Libraries of Cloned Genes
• What is produced is many different clones, not just
the desired gene, each containing different
portions of the source DNA.
• Why?
– The restriction enzymes make cuts all over the source
DNA with the result being many genes that are cloned.
• All the cloned DNA fragments make up the
genomic library.
GENOMIC LIBRARY
GENOMIC LIBRARY
BIOLOGISTS CAN ENGINEER BACTERIA
TO MAKE USEFUL PRODUCTS
• The plasmid contains DNA fragments big enough
to carry one or a few genes but together all the
plasmids in the library contain the entire genome of
the organism from which the DNA came.
– Indentifying Specific Genes With Probes
• Biologists have tools that allow them to locate
specific genes.
• In one method, you must know part of the
nucleotide sequence.
• Then, using a nucleotide labeled with a radioactive
isotope, a complementary strand is produced.
BIOLOGISTS CAN ENGINEER BACTERIA
TO MAKE USEFUL PRODUCTS
• The complementary radioactive strand is called a
nucleic acid probe.
• After this, the DNA being searched is treated with
chemicals or heat to separate the two DNA
strands.
• The probe pairs with the complementary strand on
the DNA molecule.
• Following this identification, the bacterial cells with
this DNA are allowed to multiply and produce large
quantities of the desired gene.
NUCLEIC ACID PROBE
NUCLEIC ACID PROBE
BIOLOGISTS CAN ENGINEER BACTERIA
TO MAKE USEFUL PRODUCTS
• Useful Products From Genetically
Engineered Microorganisms
– Some bacteria with recombinant DNA can
break down chemicals, clean up toxic waste
sites, produce useful chemicals (pesticides to
drugs), and plastics.
– In medicine, recombinant DNA can produce
pure insulin, and vaccines such as for
hepatitis B.
GENETIC ENGINEERING
REVIEW
1. How can a biologist use plasmids to produce
bacteria that carry a specific gene?
2. Explain how the “sticky ends” that result from
the action of restriction enzymes can be useful.
3. Explain how a nucleic acid probe enables
researchers to identify a specific gene.
4. Give an example of a use of recombinant DNA
technology in medicine.