DNA: STRUCTURE AND REPLICATION

           DNA

           was known to be a chemical in cells by the end of the nineteenth century,

           has the capacity to store genetic information, and

           can be copied and passed from generation to generation.

           The discovery of DNA as the hereditary material ushered in the new field of molecular biology, the study of heredity at the molecular level.

 

DNA and RNA Structure

           DNA and RNA are nucleic acids.

            They consist of chemical units called nucleotides.

            A nucleotide polymer is a polynucleotide.

            Nucleotides are joined by covalent bonds between the sugar of one nucleotide and the phosphate of the next, forming a sugar-phosphate backbone.

 

Watson and Cricks Discovery of the Double Helix

           James Watson and Francis Crick determined that DNA is a double helix.

           Watson and Crick used X-ray crystallography data to reveal the basic shape of DNA.

           Rosalind Franklin produced the X-ray image of DNA.

           The model of DNA is like a rope ladder twisted into a spiral.

            The ropes at the sides represent the sugar-phosphate backbones.

            Each wooden rung represents a pair of bases connected by hydrogen bonds.

           DNA bases pair in a complementary fashion:

            adenine (A) pairs with thymine (T) and

            cytosine (C) pairs with guanine (G).

 

DNA Replication

           When a cell reproduces, a complete copy of the DNA must pass from one generation to the next.

           Watson and Cricks model for DNA suggested that DNA replicates by a template mechanism.

           DNA can be damaged by X-rays and ultraviolet light.

           DNA polymerases

            are enzymes,

            make the covalent bonds between the nucleotides of a new DNA strand, and

            are involved in repairing damaged DNA.

           DNA replication ensures that all the body cells in multicellular organisms carry the same genetic information.

           DNA replication in eukaryotes

            begins at specific sites on a double helix (called origins of replication) and

            proceeds in both directions.

 

THE FLOW OF GENETIC INFORMATION FROM DNA TO RNA TO PROTEIN

           DNA provides instructions to

            a cell and

            an organism as a whole.

 

How an Organisms Genotype Determines Its Phenotype

           An organisms genotype is its genetic makeup, the sequence of nucleotide bases in DNA.

           The phenotype is the organisms physical traits, which arise from the actions of a wide variety of proteins.

           DNA specifies the synthesis of proteins in two stages:

                transcription, the transfer of genetic information   from DNA into an RNA molecule and

                translation, the transfer of information from RNA into a protein.

           The major breakthrough in demonstrating the relationship between genes and enzymes came in the 1940s from the work of American geneticists George Beadle and Edward Tatum with the bread mold Neurospora crassa.

           Beadle and Tatum

            studied strains of mold that were unable to grow on the usual growth medium,

            determined that these strains lacked an enzyme in a metabolic pathway that synthesized arginine,

            showed that each mutant was defective in a single gene, and

            hypothesized that the function of an individual gene is to dictate the production of a specific enzyme.

 

           The one gene–one enzyme hypothesis has since been modified.

           The function of a gene is to dictate the production of a polypeptide.

           A protein may consist of two or more different polypeptides.

 

From Nucleotides to Amino Acids: An Overview

           Genetic information in DNA is

            transcribed into RNA, then

            translated  into polypeptides,

            which then fold into proteins.

           What is the language of nucleic acids?

            In DNA, it is the linear sequence of nucleotide bases.

            A typical gene consists of thousands of nucleotides in a specific sequence.

           When a segment of DNA is transcribed, the result is an RNA molecule.

           RNA is then translated into a sequence of amino acids in a polypeptide.

           Experiments  have verified that the flow of information from gene to protein is based on a triplet code.

           A codon is a triplet of bases, which codes for one amino acid.

 

The Genetic Code

           The genetic code is the set of rules that convert a nucleotide sequence in RNA to an amino acid sequence.

           Of the 64 triplets,

            61 code for amino acids and

            3 are stop codons, instructing the ribosomes to end the polypeptide.

 

           Because diverse organisms share a common genetic code, it is possible to program one species to produce a protein from another species by transplanting DNA.

 

Transcription: From DNA to RNA

           Transcription

            makes RNA from a DNA template,

            uses a process that resembles the synthesis of a DNA strand during DNA replication, and

            substitutes uracil (U) for thymine (T).

           RNA nucleotides are linked by the transcription enzyme RNA polymerase.

Initiation of Transcription

           The start transcribing signal is a nucleotide sequence called a promoter, which is

            located in the DNA at the beginning of the gene and

            a specific place where RNA polymerase attaches.

           The first phase of transcription is initiation, in which

            RNA polymerase attaches to the promoter and

            RNA synthesis begins.

RNA Elongation

           During the second phase of transcription, called elongation,

            the RNA grows longer and

            the RNA strand peels away from its DNA template.

Termination of Transcription

           During the third phase of transcription, called termination,

            RNA polymerase reaches a special sequence of bases in the DNA template called a terminator, signaling the end of the gene,

            polymerase detaches from the RNA and the gene, and

            the DNA strands rejoin.

 

The Processing of Eukaryotic RNA

           In the cells of prokaryotes, RNA transcribed from a gene immediately functions as messenger RNA (mRNA), the molecule that is translated into protein.

           The eukaryotic cell

            localizes transcription in the nucleus and

            modifies, or processes, the RNA transcripts in the nucleus before they move to the cytoplasm for translation by ribosomes.

 

           RNA processing includes

            adding a cap and tail consisting of extra nucleotides at the ends of the RNA transcript,

            removing introns (noncoding regions of the RNA), and

            RNA splicing, joining exons (the parts of the gene that are expressed) together to form messenger RNA (mRNA).

 

           RNA splicing is believed to play a significant role in humans

            in allowing our approximately 21,000 genes to produce many thousands more polypeptides and

            by varying the exons that are included in the final mRNA.

 

Translation: The Players

           Translation is the conversion from the nucleic acid language to the protein language.

Messenger RNA (mRNA)

           Translation requires

            mRNA,

            ATP,

            enzymes,

            ribosomes, and

            transfer RNA (tRNA).

Transfer RNA (tRNA)

           Transfer RNA (tRNA)

            acts as a molecular interpreter,

            carries amino acids, and

            matches amino acids with codons in mRNA using anticodons, a special triplet of bases that is complementary to a codon triplet on mRNA.

Ribosomes

           Ribosomes are organelles that

            coordinate the functions of mRNA and tRNA and

            are made of two subunits.

           Each subunit is made up of

            proteins and

            a considerable amount of another kind of RNA, ribosomal RNA (rRNA).

Ribosomes

           A fully assembled ribosome holds tRNA and mRNA for use in translation.

 

Translation: The Process

           Translation is divided into three phases:

                initiation,

                elongation, and

                termination.

Initiation

           Initiation brings together

            mRNA,

            the first amino acid with its attached tRNA, and

            two subunits of the ribosome.

           The mRNA molecule has a cap and tail that help the mRNA bind to the ribosome.

 

           Initiation occurs in two steps.

                An mRNA molecule binds to a small ribosomal subunit, then a special initiator tRNA binds to the start codon, where translation is to begin on the mRNA.

                A large ribosomal subunit binds to the small one, creating a functional ribosome.

Elongation

           Elongation occurs in three steps.

            Step 1: Codon recognition. The anticodon of an incoming tRNA pairs with the mRNA codon at the A site of the ribosome.

 

            Step 2: Peptide bond formation.

             The polypeptide leaves the tRNA in the P site and attaches to the amino acid on the tRNA in the A site.
             The ribosome catalyzes the bond formation between the two amino acids.

 

            Step 3: Translocation.

             The P site tRNA leaves the ribosome.
             The tRNA carrying the polypeptide moves from the A to the P site.

Termination

           Elongation continues until

            a stop codon reaches the ribosomes A site,

            the completed polypeptide is freed, and

            the ribosome splits back into its subunits.

 

Review: DNA RNA Protein

           In a cell, genetic information flows from

            DNA to RNA in the nucleus and

            RNA to protein in the cytoplasm.

 

           As it is made, a polypeptide

            coils and folds and

            assumes a three-dimensional shape, its tertiary structure.

           Transcription and translation are how genes control the structures and activities of cells.

 

Mutations

           A mutation is any change in the nucleotide sequence of DNA.

           Mutations can change the amino acids in a protein.

           Mutations can involve

            large regions of a chromosome or

            just a single nucleotide pair, as occurs in sickle-cell disease.

 

           Mutations within a gene can be divided into two general categories:

            nucleotide substitutions (the replacement of one base by another) and

            nucleotide deletions or insertions (the loss or addition of a nucleotide).

           Insertions and deletions can

            change the reading frame of the genetic message and

            lead to disastrous effects.

 

Mutagens

           Mutations may result from

            errors in DNA replication or recombination or

            physical or chemical agents called mutagens.

           Mutations

            are often harmful but

            are useful in nature and the laboratory as a source of genetic diversity, which makes evolution by natural selection possible.

 

VIRUSES AND OTHER NONCELLULAR INFECTIOUS AGENTS

           Viruses share some, but not all, characteristics of living organisms. Viruses

            possess genetic material in the form of nucleic acids wrapped in a protein coat,

            are not cellular, and

            cannot reproduce on their own.

 

Bacteriophages

           Bacteriophages, or phages, are viruses that attack bacteria.

           Phages consist of a molecule of DNA, enclosed within an elaborate structure made of proteins.

           Phages have two reproductive cycles.

            In the lytic cycle,

              many copies of the phage are produced within the bacterial cell, and
              then the bacterium lyses (breaks open).

 

            In the lysogenic cycle,

              the phage DNA inserts into the bacterial chromosome and
              the bacterium reproduces normally, copying the phage at each cell division.

 

Plant Viruses

           Viruses that infect plants can

            stunt growth and

            diminish plant yields.

           Most known plant viruses have RNA rather than DNA as their genetic material.

           Many of them, like the tobacco mosaic virus, are rod-shaped with a spiral arrangement of proteins surrounding the nucleic acid.

           Viral plant diseases

            have no cure and

            are best prevented by producing plants that resist viral infection.

 

Animal Viruses

           Viruses that infect animals cells

            are a common cause of disease and

            may have RNA or DNA genomes.

           Many animal viruses have an outer envelope made of phospholipid membrane, with projecting spikes of protein.

           The reproductive cycle of an enveloped RNA virus can be broken into seven steps.

 

HIV, the AIDS Virus

           The devastating disease AIDS (acquired immunodeficiency syndrome) is caused by HIV (human immunodeficiency virus), an RNA virus with some special twists.

           HIV is a retrovirus, an RNA virus that reproduces by means of a DNA molecule.

           Retroviruses use the enzyme reverse transcriptase to catalyze reverse transcription, the process of synthesizing DNA on an RNA template.

           The behavior of HIV nucleic acid in an infected cell can be broken into six steps.

           HIV infects and eventually kills several kinds of white blood cells that are important in the bodys immune system.

           While there is no cure for AIDS, its progression can be slowed by two categories of medicine that interfere with the reproduction of the virus.

 

Viroids and Prions

           Two classes of pathogens are smaller than viruses.

1.  Viroids are small, circular RNA molecules that infect plants.

2.  Prions are misfolded proteins that somehow convert normal proteins to the misfolded prion version, leading to disease.

           Prions are responsible for neurodegenerative diseases including

            mad cow disease,

            scrapie in sheep and goats,

            chronic wasting disease in deer and elk, and

            Creutzfeldt-Jakob disease in humans.