Genetic Material: Requirements and DNA

Genetic Material Criteria

• A molecule is considered genetic material if it meets certain criteria.
• It must store species-specific information.
• It must encode development, structure, and metabolic activities.
• The genetic material determines an organism’s genotype.
• It must be stable and replicated with high fidelity
• It must be transmitted from generation to generation.
• Replication, duplication, and transmission are key processes.
• Genetic material determines an organism’s phenotype.
• Genetic material is able to undergo rare mutations, or changes, able to provide the genetic variability required for evolution to occur.

DNA vs. Proteins as Genetic Material

• Proteins, made of 20 amino acids, were thought to be the genetic material
• It was thought they had plenty of capacity to store information.
• Nucleic acids, with only 4 nucleotides, were initially doubted as genetic material.
• DNA is the heredity molecule, despite its 4-base composition.
• This can be compared to Computers which use a binary code to store a lot of information
• Strong evidence supports DNA's role.
• Circumstantial evidence points to the nucleus containing DNA.
• Experimental evidence comes from Griffith, Avery, Hershey, and Chase.

Bacterial Transformation

• This is an evidence of genetic material.
• Streptococcus pneumoniae is a key bacterium in this process.
• S strain is smooth and deadly, while R strain is rough and not deadly.
• The R strain is transformed by a substance from the dead S strain.
• Oswald Avery's experiment confirmed this in 1943, as did the Hershey-Chase experiment in 1952.

Oswald Avery's Experiments

• Conducted research in the 1940s using DNase, RNase, and protease enzymes.
• DNase, which degrades DNA, prevents transformation.
• This supports the hypothesis that DNA is the genetic material.
• The smooth bacterial capsule is expressed by DNA, making bacteria deadly.
• Capsule is destroyed with a flame

Protein and RNA Experiments

• Degrading proteins does not affect the transforming substance.
• RNAase, an enzyme that digests RNA has no affect.
• This showed that neither protein nor RNA is the genetic material.

DNA Universality

• DNA is universal to all living organisms.
• Its bases are ACGT.
• DNA transcends barriers between Bacteria, Archea, and Eukaryotes.
• Synthetic biology demonstrates this with jellyfish DNA being expressed in bacteria and other species.

DNA Structure

• Nucleotides consist of a base, sugar, and phosphorus.
• Nucleosides consist of a base and sugar.
• DNA bases are ACGT.
• The sugar is pentose, specifically deoxyribose.
• Phosphorus (P) is also a key component.
• Purine nucleotides and pyrimidine nucleotides exist.
• The DNA molecule is double stranded with base pairing.

Chargaff's Rules

• The amount of ATCG varies from species to species.
• The amount of A equals T, and the amount of C equals G.
• The higher the CG component, the stronger the DNA molecule.

DNA Structure - X-Ray Diffraction

• Rosalind Franklin's X-ray diffraction provided key insights.

DNA Helix Structure

• The structure is a twisted ladder with 2 strands.
• Spacing is 2nm between strands.
• There is 0.34 nm between base pairs.
• A complete turn of the double helix is 3.4 nm.
• The strands are anti-parallel.

DNA and Base Pairing

• Strands are complementary and held together by hydrogen bonds between nucleobases.
• Adenine (A) pairs with thymine (T) by two hydrogen bonds.
• Cytosine (C) pairs with guanine (G) by three hydrogen bonds.
• Strands are anti-parallel and oriented in opposite directions.

DNA Replication

• 3 Models for DNA Replication; conservative, dispersive, or semi-conservative.
• The Meselson-Stahl Experiment in 1952 supported the Semi-Conservative model.

Leading vs Lagging Strand

• The leading strand undergoes continuous duplication.
• The lagging strand experiences discontinuous duplication with Okazaki fragments.

Enzymes Used in DNA Replication

• Helicase enzyme unwinds the double helix by opening it.
• Hydrogen bonds don't require boiling/high heat to be opened.
• DNA Polymerase is used for complementary base pairing (A with T, C with G) by adding nucleotides.
• Ligase is used for to join/ligation.
• The leading strand faces continuous duplication.
• the lagging strand faces Discontinuous duplication with Okazaki fragments.
• Topoisomerase enzyme is used for disentanglement.

Semi-Conservative Replication

• Replication is semi-conservative.
• It occurs through dehydration, synthesis, and condensation reactions.
• Polymerization occurs in DNA molecules between the 3'OH of the pentose and OH of phosphoric acid.
• Phosphodiester bonds/linkages, requires the release of Water

DNA Replication in Bacteria

• Each bacterium has 1 circular chromosome.
• Binary fission involves duplication into 2 chromosomes.
• Replication is bidirectional.
• The replication forks meet at the terminating site.
• Each daughter cell receives 1 chromosome.

RNA and Protein Synthesis

• Central Dogma: DNA is transcribed to RNA, which is translated to protein.
• DNA replicates itself and serves as a template for RNA (transcription).
• The leading strand of DNA guides the sequence of nucleotides in mRNA.
• In mRNA, Uracil (U) replaces Thymine (T).
• mRNA directs the sequence of amino acids in a polypeptide during translation.

RNA Types

• Ribosomal RNA (rRNA) makes ribosome units for protein synthesis.
• Transfer RNA (tRNA) moves amino acids to the ribosome.
• Messenger RNA (mRNA) copies a gene and transfers the message to the ribosome which is where it is translated into protein.
• Nucleotides- ATP, CTP, GTP, UTP, dATP, dGTP, dTTP, dCTP

RNA Structure

• RNA is single stranded.
• The sugar is ribose.
• RNA is an exact copy of the DNA's leading strand
• Uracil (U) replaces thymine (T) in mRNA.
• Uracil is a pyrimidine.

Transcription Requirements

• This stage requires DNA which contains the gene.
• RNA Polymerase and a sigma factor are needed to recognize the promoter.
• Free nucleotides ATP, GTP, UTP, and CTP are also needed.
• Promoter and terminator sequences on the DNA are essential.
• The lagging strand is transcribed.
• The RNA sequence mirrors the leading strand, with T replaced by U.
• rRNA, tRNA, and mRNA are transcribed.
• Prokaryotic mRNA transcripts can be monocistronic (one gene) or polycistronic (multiple genes).
• Proteins encoded on polycistronic messages often have related functions.

Replication vs. Transcription

• Replication uses DNA polymerase, while transcription uses RNA polymerase.
• DNA replication uses dNTPs (ATGC), while transcription uses NTPs (AUGC).
• DNA replication occurs for both strands, while transcription only uses one strand based on ATG and the promoter.
• Helicase unwinds DNA for replication; it is not needed for transcription.
• Replication replicates the whole entire DNA strand, transcription only transcribes parts, or segments, of the DNA.
• Transcription starts at the promoter and ends at the polyA tail, which has no similar process in replication.
• Replication results in 2 DNAs, while transcription leads to many RNAs.

Translation - the Genetic Code

• Translation requires a code.
• If each of the 4 bases codes for 1 amino-acid, then the code will cover only 4 amino-acids.
• If each combination of 2 bases codes for 1 amino-acid, then the code will cover only 16 amino-acids.
• Triplet code or Codons, if each combination of 3 bases codes for 1 amino-acid, provides 64 combinations.
• The codon nature of the Genetic Code is Degenerate/Redundant.
• The Genetic Code has no ambiguity, each codon corresponds to one amino-acid.
• Amino acids, Algorithm, and code are all major components

The players for Protein Synthesis Translation

• The Ribosome comprises ribosomal, or rRNA and is also called the Protein Polymerase Complex.
• Large (50S) and small (30S) subunits constitute a large number The large subunit has 3 locations
• E site: Exit site
• P site" Peptidyl site
• A site: Acceptor or Aminoacyl site

tRNA in Translation

• Aminoacyl-tRNA synthetase
• This transfers amino acids to their corresponding tRNA

Translation - Chemical Reactions

• tRNA brings amino acids for protein synthesis.
• Amino acids form polypeptide chains.
• Peptide bonds join together strings of amino acids between the Amino group and Carboxyl group.
• Protein Synthesis Chemical Reaction is Anabolic,
• Releases water through Dehydration,
• and Stores energy through Endergonic process
• Translation stages are: initiation, elongation and termination

Initiation in Translation

• Initiator tRNA moves amino acid Methionine to Start Codon AUG
• mRNA joins the small subunit of the protein By complementarity in between codon and anticodon,
• Initiator tRNA which has anticodon UAC, corresponds With the mRNA, at the start codon AUG . Ribosomal subunits, which assemble into a ribosome The initiator tRNA resides in the P site
• A-site then prepared to get the next tRNA and amino-acid

Elongation in Translation

• tRNAs bring more amino-acids for Polypeptide synthesis with Dehydration
• The next tRNA enters occupies the A-site.
• A chemical peptide is synthetized between the first amino acid Methionine and the next amino acid forming a dehydration process at where the P site is located with the help of peptide bond.
• Methionine transfers the tRNA into the E-site.
• By relying on the complementarity in between codon and anticodons, the synthesis continues (tRNA).

Termination in Translation

• The process concludes Once the codon stop Is met.
• A Release Factor occupies The A-Site.
• By hydrolysis, that newly synthetized Polypeptide Chain gets expressed, separating from the last tRNA
• and then, a new protein synthesis will be created via The ribosomal units disassemble

Mutations and types

Changes that may arise from new and existing nucleotide sequences.

vertical gene

• through transfer organisms that may adapt and change in the event of the environmental change.

horizontal gene transfer

• that is a movement from which one organism to another passes the changes from progeny

Types of Mutations

• Point Mutation, point Mutation are examples of Mutations 1 in which can undergo a point or base substitution
• Sense
• Missense
• Nonsense that = 3 nucleotides and may consist of 1 Amino Acid

Types of Mutation - Frameshift

mutations such as Deletions and Insertions which equal 3 nucleotides and may be 1 amino acid

Genetic bacterial transfer and recombination

• Bacteria is transferred though bacteria though their genes.

With being transferred by:

• Transformation
• Conjugation
• Transduction which involves A virus known as Bacteriophage

Recombination involves

• Crossing Over of the dna within the and in between that that are being or have cells The transferring Of course can take over when is that a dna has been fragmented Or a small amount plasmid