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Archibald Garrod (1890s)

• Credited as the first to establish a connection between genetics and biochemistry.

Rous

• Used RSV (Rous Sarcoma Virus) as a vector to deliver functional genes in treatments.

Miescher

• Discovered nuclein, a substance considered linked to heredity.

Fred Griffith

• "Transforming principle" can change harmless rough bacteria into virulent smooth bacteria:
• Injected mice with different forms of bacteria, leading to these results:
  • Virulent smooth bacteria: the mice died
  • Harmless rough bacteria: the mice lived
  • Heat-killed virulent smooth bacteria: the mice lived
  • Heat-killed virulent smooth bacteria + live harmless rough bacteria: the mice died; live and smooth bacteria were recovered.
• Suggested something from the dead virulent bacteria transformed the live harmless bacteria, making them virulent and carrying inheritance (S-transforming principal).

Oswald Avery

• Pointed towards DNA as the "transforming principle" that Griffith observed.

Alfred Hershey-Chase, Max Delbruck, and Salvador Luria

• "Waring Blender" experiment used bacteriophages to determine if protein or DNA carried genetic information using a radioactive tag.
• Grew E. coli in media with radioactive labels for either protein (³⁵S) or DNA (³²P).
• Infected the bacteria with phages grown in the environments created.
• A blender separated the phages from the bacteria after infection.
• Measured radioactivity in the bacterial pellet and supernatant.
• Phages inject their DNA into bacteria, proving that DNA, not protein, is the replicating genetic material.

George Beadle and Edward Tatum (1958)

• Used Neurospora crassa, a bread mold, as a model organism.
• Most mutations affected a single metabolic pathway, suggesting each gene produces a single enzyme.
• Proposed the "one gene-one enzyme" hypothesis, linking genes to specific protein functions.

Phoebus Levene

• Investigated the chemical structure of DNA and RNA.
• Discovered DNA and RNA comprise 4 nucleotides and a structural motif.
• Discovered the phosphodiester bond linking adjacent nucleotides between 3'C of one sugar and 5’C of another.

Albrecht Kossel (1910)

• Investigated the chemistry of DNA.
• Identified the four nitrogenous bases in DNA: adenine, guanine, cytosine, uracil, and thymine.
  • Purines: adenine and guanine have a 6-membered ring fused to a 5-membered ring.
  • Pyrimidines: cytosine, uracil, and thymine have a single 6-membered ring.
• Identified carbohydrates and phosphoric acid in DNA.
• Understood complex organic molecules are built from repeating building blocks, demonstrating polymers in biological molecules.

Erwin Chargaff

• Used chromatography to separate and quantify the different nitrogenous bases in DNA.
• Discovered that the number of T=A and the number of C=U, known as "Chargaff's Rule".

Rosalind Franklin

• Used X-ray crystallography to determine the structure of molecules.
• "Photograph 51" provided crucial evidence for the helical structure of DNA.

Linus Pauling

• Attempted to determine the structure of DNA.
• Proposed a triple helix model of DNA with phosphate groups in the center and bases sticking out.
• The model was flawed as it placed the negatively charged phosphate groups too close together, making the structure unstable.

James Watson and Francis Crick

• Collaborated to determine the structure of DNA.
• Discovered the double helix structure of DNA with antiparallel sugar-phosphate backbones and nitrogenous bases paired in the middle.
• Explained X-ray crystallographic data, Chargaff's Rules (A=T and G=C, with Cand G having a triple hydrogen bond and A and T having a double hydrogen bond), and how heredity occurs through complementary base pairing allowing each strand to serve as a template for the other.

Pharmacogenomics

• Study of how a person's genetic makeup influences drug responses.
  • Identifies genetic variations influencing drug metabolism and drug responses.
  • Identifies genetic biomarkers.

Gene Therapy

• Replaces faulty genes to cure diseases.
  • Uses viral vectors as delivery systems with gene editing (CRISP-Cas9).
  • Allows precise editing of specific genes and enables targeted corrections.

DNA and RNA

• Contain nitrogenous bases, a pentose sugar, and a phosphate group.
• DNA lacks OH at 2', making it more stable and less susceptible to hydrolysis and enzymatic degradation.
• RNA has OH at 2', making it more flexible for complex structures.

Differences Between RNA and DNA

• RNA is more reactive than DNA.
  • Participates in enzymatic reactions like splicing and protein synthesis and has catalytic activity.
• Nucleoside: nitrogenous base and pentose sugar.
• Nucleotide: nitrogenous base, pentose sugar, and phosphate group.
• Basis of heredity stemmed from a protein and was figured out by growing evidence, Chargaff's rule, X-ray crystallography, and Pauling's discovery.

Marshall Nirenberg / Holley / Khorana:

• Best known for work deciphering the genetic code.
• RNA sequence UUU coded for phenylalanine.

Francis Crick

• Determined the codon length using bacteriophages in a plaque assay.
  • Found that only the addition or deletion of three nucleotides, or multiples of three, restored the phage's function.
  • Showed that the genetic code was read in groups of three nucleotides, confirming how it would be based on a triplet codon.

George Gamow

• Was involved in understanding genetic code and contributed to its discovery.

Severo Ochoa

• Severo Ochoa contributed to understanding the genetic code.

Direction of genetic code:

• PNPase: production of RNA oligonucleotides is used for genetic coding.
• mRNA is read in the 5' to 3' direction.
• Start codon: AUG.
• Stop codons: UGA, UAA, UAG.

DNA Folding and compaction:

• Informational tape to encode sequence, contain both coding info, and physicochemical properties of RNA and proteins.
• Enable replication and transfer.
• Direct readout: bases individually make specific contact with a protein between exposed chemical groups.
• Indirect readout: binding depends on recognition of a structure influenced by DNA sequence.
  • DNA must be condensed to fit in the nucleus while accessible for cellular processes.
  • Achieved through involving histones, nucleosomes, and higher-order chromatin structures.

DNA Grooves:

• The major and minor grooves of the DNA double helix enable DNA-protein interactions involved in replication, transcription, repair, and gene regulation by providing accessibility for enzymes, non-catalytic proteins, and modifications of DNA.
• Grooves contribute to DNA-protein interactions through noncovalent (HB and van der Waals) and covalent modifications of DNA and histones.
• The major groove is wider and carries more sequence information.

B-form DNA:

• Type of DNA form that has 10.5 bp (helical).
• It is right-handed and has bases perpendicular to the axis.
• It is packed in the helix center and is a cylinder that is preferable for packaging as it is the most stable type of DNA.

A-form DNA:

• Type of DNA form that has 11 bp (helical).
• It is right-handed and has bases tilted 20° with respect to the axis.
• It is shifted to the helix periphery.
• As the groovess are not as deep, at lower humidity B-DNA converts to A-form and becomes less accessible for proteins and may form upon protein for certain proteins to DNA
• RNA-DNA and RNA-RNA duplexes form this thicker version of the DNA structure.

Z-form DNA:

• Type of DNA form that is left-handed.
• It uses sequences capable of forming it are common around transcription initiation sites to get the structure.
• This is the DNA structure type contains one deep, narrow groove.

DNA melting and renaturation:

• DNA Replication: localized denaturation allows DNA pol to synthesize a new strand.
• Transcription: DNA in the promoter local denaturation allows binding of txn factors and RNA pol.
• DNA Repair: the damaged DNA region is locally denatured, facilitating the recognition and repair.
• DNA-Protein Interactions: proteins often require localized DNA melting to access specific DNA sequences or binding sites.
• Factors Affecting DNA Melting: G-C Content, Length of DNA Salt Concentration and Temperature.
• Denaturation is reversible.
  • Renaturation/Annealing: separated strands reunite, reforming the double helix when the temperature dips below the Tm (melting temp).
• A technique employing repeated cycles of denaturation, annealing (where primers bind to the separated strands), and extension (DNA polymerase synthesizes new strands) to amplify specific DNA sequences.
  • In vitro Applications can include PCR, DNA Sequencing and DNA Hybridization

DNA as a molecule:

• The use of dsDNA as a template allows it to be deciphered the nucleotides' precise order.
• Can be used for complementary strands originating from different sources to anneal to form hybrid molecules, which finding applications in various diagnostic and research endeavors..
  • Hyperchromic Effect: dsDNA absorbs less UV light at 260 nm compared to ssDNA due to base-stacking interactions as DNA denatures, absorbance increases, indicating DNA is versatile.
  • Its flexible and dynamic polymer is capable of assuming various forms is DNA is essential for packaging and accessibility making it more important that be compacted into small volume.

Chromosome Structure:

• DNA must be compacted to fit inside the nucleus as they are very long and thin.
• DNA-binding proteins found in eukaryotic chromosomes can be either histone or are non-histone proteins leading to regular spacing being present aomg the DNA.
• Chromatin is the complex of both classes of proteins and nuclear DNA.

Nucleosomes:

• A barrel-shaped core octamer of eight histone proteins is barrel-shaped core consist of H2A, H2B, H3, and H4 for eukaryotes.
• DNA complex is stabilized by electrostatic interactions between (+) amino acids of histones and (-) charged phosphate backbone of DNA, and joined by linker DNA.
• H1 helps stabilize the nucleosomes between DNA's entry and exit sites with the Function of organizing and damage to maintain it within the nucleus: - Provide structural stability and enabling DNA and gene expression. - positioning and accessibility to txn factors/ regulatory proteins which can modify its position, facilitating gene activation or