DNA and RNA: Structure and function

• DNA and RNA are nucleic acids in living systems.
• DNA is genetic material for most organisms.
• RNA mainly functions as a messenger, adapter, structural, or catalytic molecule, and is genetic material in some viruses.
• Genomics is a new era following the sequencing of the human genome.
• DNA structure is important to understand, and later understand it's relationship to RNA

DNA Structure:

• The length of DNA is determined by the number of nucleotide or base pairs it has
• Bacteriophage φX174 contains 5386 nucleotides.
• Bacteriophage lambda contains 48502 base pairs.
• Escherichia coli contains 4.6 x 10^6 base pairs.
• Human DNA (haploid) contains 3.3 x 10^9 base pairs.
• A polynucleotide chain consists of a nitrogenous base, a pentose sugar, and a phosphate group.
• Purines (adenine and guanine) and pyrimidines (cytosine, uracil, and thymine) are nitrogenous bases present in DNA and RNA.
• Cytosine is present in both DNA and RNA.
• Thymine is only present in DNA, and Uracil is present in RNA.
• A nitrogenous base plus a 1' carbon pentose sugar forms a nucleoside, linked by N-glycosidic linkage
• Nucleosides can include adenosine, deoxyadenosine, guanosine, deoxyguanosine, cytidine, deoxycytidine, uridine or deoxythymidine.
• A phosphate group linked to the 5' carbon of a nucleoside makes a nucleotide, via a phosphoester linkage
• Two nucleotides are linked by a 3'-5' phosphodiester linkage, forming a dinucleotide.
• A polynucleotide chain is formed as more nucleotides join.
• A free phosphate group is found at the 5' end of the sugar, and a free OH is found at the 3' end of the sugar.
• The sugar and phosphates form the backbone with nitrogenous bases projecting from it.
• RNA has an additional -OH group at the 2' position of the ribose and uracil instead of thymine.
• Friedrich Meischer first identified DNA as an acidic substance in the nucleus.
• In 1953, James Watson, Francis Crick, Maurice Wilkins, and Rosalind Franklin together proposed the Double Helix model.
• The Double Helix model is the base pairing between the two strands.
• Erwin Chargaff determined ratios between Adenine and Thymine and Guanine and Cytosine are constant and equal to one.
• Complementarity is a unique property from base pairing where knowing one sequence is enough to determine the other
• Each strand from a parental DNA acts as a template to produce two identical daughter DNA strands, which is called genetic implication.

Features of the Double Helix structure:

• Two polynucleotide chains form the double helix, with the sugar-phosphate backbone on the outside and the bases projecting inward.
• The polarity of the two chains are anti-parallel: 5'→3' in one, and 3'→5' in the other.
• Bases pair through hydrogen bonds: Adenine to Thymine (two bonds) and Guanine to Cytosine (three bonds).
• A purine always pairs with pyrimidine, for uniform distance between the double helix strands.
• The two chains are coiled in a right-handed fashion, and the helix pitch is 3.4 nm with roughly 10 base pairs per turn
• The distance between a base pair in a helix is approximately 0.34 nm.
• Bases stack over one another within the double helix to add stability.
• Francis Crick proposed the central dogma of molecular biology: genetic information flow is DNA→RNA→Protein.

DNA Helix Packaging:

• The calculated length of a DNA double helix in a mammalian cell is 2.2 meters, however the typical nucleus size if only 10^-6
• E. coli. DNA is 1.36 mm
• DNA must be packaged so it can fit into cells
• In prokaryotes (E. coli), DNA is negatively charged, held by positive proteins and organized in large loops in an area in the cell called a nucleoid.
• To create a DNA nucleosome in eukaryotes, negatively charged DNA wraps around positively charged histone octamer proteins.
• A typical nucleosome includes 200 base pairs of DNA helix.
• Nucleosomes are the repeating unit of chromatin, and appear as ‘beads-on-string’.
• Chromatin fibers form after beads-on-strings are packaged and are further coiled and condensed into chromosomes in metaphase
• This packaging requies Non-histone Chromosomal (NHC) proteins
• Euchromatin is chromatin that is loosely packed, stains light, and is transcriptionally active.
• Heterochromatin is chromatin that is densely packed, stains dark, and transcriptionally inactive.

Genetic Material:

• DNA structure, and what material acts as genetic information
• Discovery of “nuclein” (DNA) happened parallel to Mendel’s inheritance law, but it took a long time
• The molecular level of genetic inheritance was determined by 1926 after previous discoveries by other scientists
• It was unknown whether DNA or some other molecule was the genetic material

Transforming Principle:

• Frederick Griffith's experiments with Streptococcus pneumoniae in 1928 demonstrated bacterial transformation.
• Streptococcus pneumoniae come in S and R strains
• The S strain is lethal and causes pneumonia
• Living bacteria can change physical form
• S strain bacteria forms smooth shiny colonies, while R strain forms rough colonies due to a mucous coat
• Mice with the S strain died
• Mice with the R strain lived
• Heat killed S strain injected into mice did not kill them
• A mix of heat-killed S and live R strains injected into mice killed them
• Living S bacteria was recovered from the dead mice.
• Living R strain bacteria transformed into virulent S strain bacteria.
• A 'transforming principle' from the heat-killed S strain enabled the R strain to synthesize a smooth coat and become virulent.
• The biochemical nature of the genetic material was undefined, and unknown whether the material was proteins

Transforming Principle Characterization:

• Genetic material was thought to be protein prior to Oswald Avery, Colin MacLeod, and Maclyn McCarty's work (1933-44)
• Experiment by Oswald Avery, Colin MacLeod, and Maclyn McCarty was to determine the biochemical nature of ‘transforming principle’ in Griffith's experiment.
• DNA alone from S bacteria transformed R bacteria to S bacteria after biochemicals (proteins, DNA, RNA, etc.) were purified.
• Proteins and RNA are ruled the the transforming substance because protein-digesting enzymes (proteases) and RNA-digesting enzymes (RNases) did not affect transformation
• DNA transformation was inhibited after Digestion with DNase.
• DNA is considered the hereditary material, but not all biologists were convinced.

DNA is the Genetic Material:

• Alfred Hershey and Martha Chase proved that DNA is genetic material (1952) by working with bacteriophages that infect bacteria
• Bacteiophages attach to and inject gentic material into bacteria
• Viral genetic material that treats viral material as bacteria manufactures more virus particles
• Hershey and Chase tested if protein or DNA entered bacteria from viruses.
• Viruses were grown in media with radioactive phosphorus and radioactive sulfur.
• Proteins do not contain phosphorus, and DNA contains phosphorus
• Viruses grown in the presence of radioactive phosphorus contained radioactive DNA
• Viruses grown in the presence of radioactive sulfur contained radioactive protein
• DNA did not contain sulfur.
• Viruses are allowed to attach to E. Coli.
• The virus coats were removed by agitating them in a blender as the infection proceeded
• The separating of virus particles from bacteria happened by spinning them in a centrifuge.
• Bacteria w/ radioactive DNA became radioactive, showing that DNA passed from virus to bacteria
• DNA is passed from virus to bacteria because proteins werent radioactive which means they never entered the bacterica
• Proteinsts vs DNA debate over resolution as genetic material has resolved unequivocally

Genetic Material (DNA versus RNA):

• RNA (some viruses) is genetic material.
• Dynamic messenger functions of RNA is why DNA is the predominant genetic material.
• The differences between chemical structures of the two nucleic acid molecules may explain why
• A molecule that is genetic material must generate replicas, and be chemically and structurally stable
• A molecule that is genetic material 'Mendelian Characters' and be able to provide scope for slow changes for evolution
• Nucleic acids (DNA and RNA) can direct duplication by base pairing and complementarity
• A proteins cannot fulfill first criteria
• genetic material cannot change with with different stages of life cycle
• Stability showed that heat killed bacteria and did not destroy some genetic material in Griffith’s experiment.
• Complementary strands being heated and separated come together by appropriate conditions if explained
• 2'-OH is reactive making RNA easily degradable and labile
• That DNA better gengeric material because DNA is structurally more stable
• Presence of thymine increases stability, replacing uracil
• DNA and RNA able to mutate
• RNA mutates faster, being unstable
• RNA genomes evolve faster and mutates for viruses that have shorter likespans
• RNA synthesies proteins directly, expressing characters
• The synthesis of proteins depends on DNA through RNA
• Protein production is based on RNA

RNA World:

• RNA genetic material that is first for genetics
• RNA for essential life processes for genetics evolved around RNA
• Genetic and catalytic material of RNA functions catalyst
• For catalyzing biochemical reactions in living systems use what, catalyze with RNA but use proteins
• Reactive and unstable material catalyst
• The evolution of RNA to DNA required chemical modifications
• For undergoing changes, DNA needed stability by double being stranded, using complementary strand.

Replication:

• Watson and Crick proposed in 1953 a possible copying mechanism following structure
• Watson and Crick stated: “It has not escaped our notice that the specific pairing we have postulated immediately suggests a possible copying mechanism for the genetic material”
• Two strands act a template that separate for synthesis
• Each new DNA molecule would have a newly synthesized and parental strand molecule after replication
• Semiconservative DNA replication termed
• Experiments have proven that DNA replicates semiconservatively.
• It was shown first in Escherichia coli and subsequently in higher organisms, such as plants

Testing DNA Replication:

• Matthew Meselson & Franklin Stahl performs following experiment 1958 to test and prove this
• E. coli grown a medium that isotope of nitrogen contains (15NH4CL) only as source for nitrogen many generations
• Newly synthesized DNA was 15N
• Normal DNA molecule distinguished this centrifugation.
• Note with 15 N, can separate this isotope radioactively with 14N.
• (after various definite intervals cells multiplied, samples was took.) The transferred cell DNA and extracted the medium
• Separated independantly density to measure double stranded gradients independently
• Understand molecule with density sediment faster or molecule
• The results

Enzymes:

• catalysts and enzymes the process needs
• Template the DNA polymerase to catalyze the of deoxynucleotides main enzyme
• Catalysis has high polymerisation to enzymes efficient, have to time short fast
• (humans whose e. coli that has 4.6 x 106 bp) rate complete ( 6.6 x 109bp) time with complete diplod
• Per every of have also be accurate to reaction they cataluze as polymerase will also mutations also degree high not only polymerize

Transcription

• Genetic information is copied from one strand of DNA into RNA that is termed as transcription
• Process is complementarity with adenosine forming base pairing with uracil
• DNA segment and one of the strands is copied into RNA unlike in replication.

Transcription Unit:

• It needs defining boundaries so it can demaracate strand of DNA used to transcribed
• It would be a simple answer because it complicates information transfer
• Transcription unit three regions: promoter, terminator, gene,
• Definition when defining, two structural strands needs structural unit of transcription
• Polymerase the also direction direction

Types of RNA and the Process

• Bacteria, RNAs are transferred(tRNA) protein cell rRNAs (rRNA) transfer (mRNA) ribosome needed type the All codes the (mRNA) RNA that there RNA is the translation translation catalys transciption catalyzation polymerase transcription
• The processes of translation requites polymers
• Nucleotides don’t form bonds, for the genetic proposition that can direct amino sequences for the proteins