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 sugar-phosphate “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 x-ray 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 Process1. 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.