Genetic Material and Nucleotides

Genetic Material

• Nucleic acids are used to store genetic information, serving as the cell's blueprint
• DNA is the main data storage molecule because of its chemical stability and double helical structure
• Some viruses use RNA as their genetic material
• Viruses are not living because they cannot undergo independent metabolism

Nucleotides

• Nucleic acids, the genetic material of cells, comprise nucleotides
• Nucleotides consists of a pentose sugar, a phosphate group, and a nitrogenous base
• Both the phosphate group and the nitrogenous base attach to the 5-carbon pentose sugar
• The nitrogenous base attaches to the 1' carbon atom
• The phosphate group attaches to the 5' carbon atom

Sugar-Phosphate Backbone

• Nucleotide monomers link into a single strand through condensation reactions, producing water as a byproduct
• A phosphodiester bond is a covalent bond between nucleotides, by the attachment of the phosphate group of one nucleotide to the sugar of another, at the 3'-hydroxyl position
• Successive condensation reactions lead to long polynucleotide strands
• The sugar and phosphate form the backbone, while the nitrogenous bases stick out from this strand

Nitrogenous Bases

• Nucleic acids have four nitrogenous bases
• Guanine and adenine are double-ringed purine bases
• Cytosine, thymine, and uracil are single-ringed pyrimidine bases
• Thymine is in DNA, uracil is in RNA
• Thymine and uracil molecules are chemically similar

RNA as a Polymer

• RNA expresses genetic instructions
• RNA is involved in protein synthesis
• Single-stranded RNA forms from a DNA template (gene) using nucleotide monomers via condensation
• Base pairing determines the order of nucleotide monomers
• The RNA sequence is complementary to the gene sequence
• Messenger RNA (mRNA) is the transcript copy of DNA instructions and encodes the protein sequence
• Transfer RNA (tRNA) carries protein subunits (amino acids) to the mRNA transcript
• Ribosomal RNA (rRNA) catalyses combining amino acids according to the mRNA sequence

DNA Double Helix

• DNA passes hereditary information between generations
• DNA also contains the set of instructions used to produce proteins via RNA and can therefore be considered the cell's ‘blueprint'
• Unlike RNA, DNA consists of two strands held by hydrogen bonding between base pairs
• Adenine pairs with thymine via two hydrogen bonds
• Guanine pairs with cytosine via three hydrogen bonds
• To ensure proper base pairing, the two DNA strands run in opposite directions (antiparallel)
• DNA has a ladder structure, with backbones forming the struts and base pairs acting as rungs
• Doubled-stranded DNA forms a double helix, containing approximately 10-15 bases per twist

DNA vs RNA

• DNA is more stable and serves as the master template for genetic instructions
• RNA is more versatile and transfers genetic information for coding
• DNA contains deoxyribose, uses thymine, and is double-stranded
• RNA contains ribose, uses uracil, and is single-stranded

Ribose and Deoxyribose

• RNA uses ribose to form nucleotides
• DNA employs a modified sugar with less oxygen at the 2'-position (deoxyribose)
• Ribose is also present in vitamins and coenzymes, like ATP

Complementary Base Pairing

• Different base sequences result in different instructions
• Nitrogenous bases pair up (purine to pyrimidine) through hydrogen bonding, creating a complementary sequence
• Guanine always pairs with cytosine, and adenine pairs with thymine (in DNA) or uracil (in RNA)
• Complementary base pairing is critical for its function as a genetic code
• One strand acts as a template for synthesizing a new strand, which allows genetic information to be replicated
• A complementary transcript is produced from a template, which allows genetic instructions to be expressed

DNA Base Sequence Diversity

• Genetic information is encoded in the nucleotide chain's base sequence
• A DNA strand of x length composed of four bases yields 4x different sequences
• Even a short sequence of 10 bases can create over 1 million combinations
• A median gene sequence length of roughly 24 kilobases allows for substantial base sequence diversity

DNA - Limitless Storage

• DNA is compact, stable, and has a virtually limitless capacity for storing information
• Scientists aim to encode digital data as genetic sequences

Genetic Code

• DNA stores instructions for protein production in triplets (codons)
• Each codon corresponds to a specific amino acid
• A gene sequence determines the order of amino acids in a polypeptide chain
• Combination of all codons and the amino acids they represent is known as the genetic code
• The genetic code is universal
• The conservation of the genetic code across life forms suggests all living organisms evolved from a universal common ancestor

RNA and DNA Directionality

• Each nucleotide has three components: a pentose sugar, a phosphate group, and a nitrogenous base
• The carbon atoms in the pentose sugar are numbered
• The base attaches to the 1'-carbon
• The phosphate attaches to the 5'-carbon
• Nucleotides form strands as the phosphate group of one nucleotide binds to the sugar of another at the 3'-hydroxyl position
• The 5' to 3' linkages in the sugar-phosphate backbone are used to assign directionality to the DNA strand
• DNA is antiparallel
• One strand runs from 5' to 3' and the other from 3' to 5'

DNA Helix Stability

• Pairing a double-ringed purine with a single-ringed pyrimidine stabilizes the DNA double helix
• Pairing two purines is unfavorable because they would be too close and repel
• Pairing two pyrimidines is unfavorable because they would be too far apart to form stable hydrogen bonds
• Purine-to-pyrimidine bonding ensures the sugar-phosphate backbones remain evenly separated

Nucleosome Structure

• In eukaryotes, DNA is compacted within the nucleus
• DNA associates with histone proteins, forming a nucleosome
• A nucleosome has DNA wrapped around eight histone proteins (an octamer)
• Negatively charged DNA binds to positively charged amino acids on histone proteins
• DNA coils around the histone octamer similar to thread wrapped around a spool
• Nucleosomes link via an H1 histone protein attached to linker DNA to create chromatin

Nucleosome Function

• Nucleosomes facilitate DNA supercoiling, protecting it from damage and regulating transcriptional activity
• Histone proteins possess N-terminal tails extruding from the nucleosome which affect how tightly the DNA is packaged
• The accessibility of genetic instructions is reduced when DNA is more tightly packaged

Hershey-Chase Experiment

• The Hershey-Chase experiment proved that DNA is the genetic material
• Eukaryotic chromosomes contain DNA and protein
• Viruses with only DNA and a protein coat can transfer their genetic material into hosts
• Alfred Hershey and Martha Chase grew viruses (T2 bacteriophage) in radioactive sulfur (35S) to label proteins and radioactive phosphorus (32P) to label DNA
• Viruses infected bacteria (E. coli)
• The virus and bacteria were separated via centrifugation
• The larger bacteria formed a solid pellet, while the smaller viruses remained in the supernatant
• The bacterial pellet was radioactive when infected by the 32P viruses (DNA) but not the 35S viruses (protein)
• Proved that DNA transfers to bacteria and is the genetic material

Chargaff's Data

• Chargaff's data refuted the tetranucleotide hypothesis with data on pyrimidine and purine bases across multiple life forms
• Nucleic acids are composed of nitrogenous bases
• Guanine and adenine are double-ringed purine bases
• Cytosine, thymine, and uracil are single-ringed pyrimidine bases
• Base sequence encodes genetic information
• Different base sequences make different genetic instructions and proteins
• An early theory suggested that DNA was composed of only 4 nucleotides per molecule with the four bases present in equal amounts and positioned externally
• Chargaff used UV spectrophotometry to measure each base amount, showing that the amounts were not consistent across all four bases
• DNA sequences were obtained from different species
• Different species had different base compositions
• Specific purines and pyrimidines occurred in equal ratios (i.e., A = T and G = C)