DNA and RNA Structure and Replication

• DNA and RNA are unbranched polymers composed of repeating monomers called nucleotides.
• Each nucleotide consists of a nitrogenous base, a pentose sugar, and one or more phosphate groups.
• RNA is single-stranded, while DNA is a double helix.

List of Nitrogenous Bonds

• Purines include Adenine and Guanine.
• Pyrimidines include Cytosine, Thymine, and Uracil.
• A repeating pattern of sugar-phosphate-sugar-phosphate forms the backbone, with bases hanging off.
• Phosphodiester bonds link the 5' carbon of one nucleotide to the 3' carbon of another.
• Hydrogen bonding connects nitrogenous bases and is easily disrupted.
• Chargaff's Rule:
  • In DNA, Adenine = Thymine (A=T) and Guanine = Cytosine (G=C).
  • In RNA, Adenine = Uracil (A=U).

DNA Replication

• Base pairing to a template strand underlies DNA replication.
• Since two strands of DNA are complementary, each acts as a template for building a new strand in replication.
• In DNA replication, the parent molecule separates, facilitated by Helicase which unzips the strand.
• Semiconservative Model: Watson and Crick's model predicts each daughter molecule has one old and one new strand after replication, with a remnant of the former molecule.

Steps of DNA Replication

• Initiation begins at the double helix.
• Single-strand binding protein stabilizes the single strands to prevent them from sticking together again.
• Topoisomerase relieves overwinding strain by breaking and rejoining DNA strands.
• An RNA primer, made of primase, is needed to start the nucleotide bases.
• Prokaryotes have one origin of replication, while eukaryotes have one or more.
• Elongation involves a continuous Leading Strand and a fragmented Lagging Strand that needs constant restarting.
• DNA Polymerase III adds nucleotides only to the free 3' end of a growing strand, elongating in the 5' to 3' direction.
• DNA Polymerase I changes or replaces the RNA primer.
• DNA Ligase glues the strand back together.
• The OKAZAKI Fragment is the gap in the lagging strand.
• DNA replication occurs bidirectionally.
• Termination happens when enzymes snip off a telomere/telos, shortening the strand.
• Nucleases proofread the new double helix structures and remove any mispaired bases.
• DNA Polymerase II replaces wrong nucleotide bases.

Transcription and Translation of Genes

• Central Dogma: DNA → RNA → Protein
• Overview:
  • Transcription:
    • RNA serves as a bridge between genes and proteins.
    • RNA copies information from DNA using RNA language.
    • Involves synthesizing RNA from DNA and adding nucleotides to bases.
    • Nucleus is the site of transcription.
  • Translation:
    • Synthesis of polypeptide using mRNA information.
    • RNA translates to protein at the ribosome.
    • Ribosomes are the site of translation.
  • Messenger RNA (mRNA) contains information transcribed from DNA.
  • Ribosomal RNA (rRNA) is where polypeptide chains are built during translation.
  • Transfer RNA (tRNA) delivers amino acids to the ribosome.

Main points for Transcription

• Enzymes use the nucleotide sequence of a gene to synthesize a complementary strand of RNA.
• RNA synthesis is catalyzed by RNA polymerase, which separates DNA strands and joins RNA nucleotides.
• RNA synthesis follows the base-pairing rules of DNA, except uracil substitutes for thymine.
• RNA Polymerase 2 separates and unwinds the double helix, making and base-pairing mRNA.

Process of Transcription

• Stage 1: Initiation - RNA polymerase II binds and starts transcription.
  • Promoter: region where transcription starts, including the DNA sequence where RNA polymerase attaches.
  • Transcription unit: stretch of DNA that is transcribed.
  • Transcription factors guide RNA polymerase II.
  • Transcription initiation complex consists of transcription factors, RNA polymerase II, and the promoter.
• Stage 2: Elongation - RNA polymerase II unwinds the DNA helix creating newly made RNA.
  • RNA polymerase II unwinds the DNA helix and moves along the DNA, untwisting the double helix by 10 to 20 bases at a time.
  • RNA polymerase II adds nucleotides to the 3' end of the growing RNA molecule, as it moves.
  • The newly synthesized RNA molecule peels away from its DNA template, and the double helix reforms.
• Stage 3: Termination - RNA polymerase II transcribes the polyadenylation signal sequence, releasing the RNA transcript.
  • Polyadenylation signal (AAUAAA) signals proteins to cut the RNA transcript from the polymerase.
  • Completed RNA transcript is altered from the DNA during copying.
• Post-Transcriptional Modifications: Enzymes in the eukaryotic nucleus modify pre-mRNA before dispatching genetic messages to the cytoplasm.
  • This includes the alteration of mRNA ends, where each end of a pre-mRNA molecule is modified.
  • The 5' end receives a modified nucleotide 5' cap, and the 3' end gets a poly-A tail (PolyAdenine Tail).
  • Split Genes and RNA Splicing: creates continuous mRNA molecules by removing some exons from RNA and splicing others together.
  • Spliceosome cuts out introns.
  • Introns are non-coding segments.
  • Exons are coding segments.
  • 5' cap + Poly-A Tail + Exons = mRNA

Translation

• Converts genetic information carried by mRNA into a new polypeptide chain (amino acid).
• RNA Transcript determines the sequence of amino acids.
• Codons are triplets of nucleotides—three nitrogenous bases arranged in order.
  • Each letter in nitrogenous bases equates to one codon, and one codon equates to one amino acid.
  • Gene to protein translation is based on a triplet code, which defines the three-nucleotide words of mRNA.
  • Chain of amino acids forms due to this process.

Process of Translation

• Stage 1: Initiation - completion of the Translation Initiation complex.
  • Includes a small ribosomal unit, methionine, and large ribosomal unit.
  • Start Codon = (AUG)
• Stage 2: Elongation
  • Starts with a start codon known as AUG.
  • tRNA carries amino acids.
  • Acceptance Site: tRNA enters.
  • Processing Site: Amino acid moves to the new tRNA with new peptide formation.
  • Exit Site
• Stage 3: Termination - Reaching one of three stop codons leads to dissociation of the translation initiation complex.
  • Stop Codon = (UAA UAG UGA).
• Primary Structure: the primary structure of a protein is its sequence of amino acids.
  • mRNA determines the sequence of amino acids.

Genetic Engineering

• Biotechnology involves using biological processes, organisms, or systems to improve the quality of human life.
• Genetic Engineering is the direct manipulation, or alteration, of genes found in DNA.
• Recombinant DNA combines one or more segments into another.
  • Plasmids are found only in bacteria or Prokaryotic Cells but can be injected into Eukaryotic Cells.

Classical vs Modern techniques

• Classical Breeding focuses on the mating of organisms with desirable qualities to create a new population with favorable traits applicable to food crops.
  • Objectives include improved food quality, increased yield, tolerances, resistance, and shelf life.
  • One example is crossing wild watermelon with modern watermelon.
  • This method's turnaround can be slow due to the randomness of meiosis.
• Modern Genetic Techniques allow scientists to insert desirable traits into organisms by altering the genes themselves for expression.
  • This allows scientists to introduce/insert new traits or enhance/disrupt an already existing gene.

Steps In DNA Recombination

• Step 1: Identify a trait of interest
• Step 2: Isolate the genetic trait of interest
• Step 3: Selection of an Appropriate Vector
  • Vectors are molecules (genes) that carry DNA to another organism.
  • Plasmids often carry genes conferring advantageous traits like antibiotic resistance, which are vital to an organism's survival.
  • Because of this Plasmids are great targets for genetic modification
• Step 4: Gene Modification
  • This involves cutting the desired gene by restriction enzymes (DNA scissors) and selecting an appropriate vector to propagate the desired gene.
  • Ligation involves joining the desired gene and the vector's gene, transforming it so it gets reproduced.
  • Following which the vectors that could contain the new gene are selected.
  • Sequencing is done to make sure it produced the proper product.
  • Restriction enzymes are crucial.

Introducing Desired Genes to Host Organisms

• Lipofection injects DNA into a lipid molecule (carrier), which then uses lipid carriers to deliver genes to host cells through endocytosis.
• Electroporation: uses electrical pulses to create and open up the pores in the cells of the plasma membrane.
• Microinjection: this involves injecting a small dosage under a microscope.
• Calcium Chloride (chemical transpection): preparing competent and mature cells to help DNA get in place, permeable, and stabilized.
  • This requires first an ice bath, then a hot water-heat shock treatment (thermal imbalance), widening the pores and allowing the DNA sequence to penetrate the cell.
• Biolistics involves a gene gun firing bullets made up of micro-particles of gold or tungsten coated with the desired DNA sequence.
• Plasmid as Vector: many plasmids contain genes that confer resistance to antibiotics, serving as selectable markers.
  • Only a small portion of cells take up the vector. Reporter genes then help select or identify host cells containing recombinant DNA

Human Insulin Production

• This involves using E. coli bacteria (humulin) or yeast (novolin).
• Bt-endotoxin kills pests when ingested and is non-toxic and safe to humans.

Evolution

• Key concepts to remember:
  • Evolution: Genetic change in a population over multiple generations.
  • Population: Interbreeding members of the same species.*
  • Allele: One or two or more alternative forms of a gene that arise by mutation and reside at the same locus on a chromosome.
  • Allele Frequency: The number of copies of an allele, divided by the total number of alleles for the same gene in the population.
  • Microevolution: Small, generation by generation changes to a population's gene pool (Genetic change within the population).
  • Macroevolution: Large scale evolutionary events, such as the appearance of new species.
• Evolution involves Charles Darwin whose theory is a genetic change in a population over multiple generations, with descent with modification.
  • Descent implies inheritance, while modifications refer to generational changes in traits.
  • Evolution can be inspected by examining their gene pool its entire range of genes and their alleles.
  • Can also be used in change in allele frequencies; and how much it varies in a population.

Development of Evolutionary Thought

• Aristotle believed species are identical and unchanging.
• Buffon believed that as species move locations they change.
• Lamarck believed that frequently used traits enhance, new species come from existing ones through environmental forces, and posited 'theory of use and disuse'.
• Lyell believed that all changes in nature are gradual. _Darwin and Wallace believed that species arise through the process of individuals varying in a given population through natural variation -Darwin's Voyage to the Galapagos Islands provided evidence of evolution -His five-year voyage, beginning in 1831, included a five-week stay in the Galapagos Islands

Patterns of Descent with Modification:

• All life on Earth shares a common ancestor an ancestral organism shared by two or more descent lineages
• Through the process of descent with modification, this common ancestor gave rise to the diverse species documented in the fossil record around us today.
• Offspring inherit traits from their parents and those traits may be modified/changed. Malthus's Idea on Populations:
• Food availability, disease, and war limit the size of a human population and other organisms may face similar limitations, explaining why more individuals are produced than survive.
• Environmental challenges would eliminate poorly equipped variants.

Origins of Evolutionary Thought

• Lyell's writings influenced Wallace who wrote to Darwin about evolution by natural selection and presented his writing to the Linnean society.
• The concept of Natural Selection involves a fundamental process or mechanism through which organisms with advantageous traits are more likely to pass on their genes.

Natural Selection

• The environment exerts selective pressures, favoring certain traits over others.
• It requires variation, heredity, differential survival and reproduction, selective pressure, and time -- all of which is defined by natural selection.
• Natural selection is a term to describe “this preservation of favorable variations and the rejection of injurious variations."

Mechanisms of Evolution

• Natural Selection: The most important mechanism of evolution
• Survival of the Fittest: Reproductive success across multiple generations, an ability to survive and reproduce in its specific environment.

Modes of Natural Selection:

• Directional Selection favors one extreme phenotype allowing it to be more fit, causing many environments to choose that trait.
• Disruptive Selection favors two or more extreme phenotypes evolving towards a bimodal distribution, decreasing frequency and leading to speciation.
• Stabilizing Selection favors average traits causing there to be more intermediate averages.

Other Mechanisms of Evolution:

• Mutations: A change in an organism's DNA sequence causing it to mutate and form an allele for the new population, however traits can be neutralized or be beneficial. -Gene Flow: Migration is the movement of individuals into or out of a population, but does not require the movement of entire individual Non-random mating: A mechanism of evolution that occurs when individuals within a population choose mates based on specific traits rather than randomly. -Assortative Mating - occurs when individuals preferentially mate with partners who have similar phenotypic or genotypic traits. -Disassortative Mating - occurs when individuals preferentially mate with partners who have dissimilar phenotypic or genotypic traits. Genetic Drift: A change in allele frequencies that occurs purely by chance, tending to eliminate alleles in a population -Founder effect: Occurs when a small group leaves, its home and isolates as a new settlement -Bottleneck Effect- Happens when a population's size drops rapidly over a short period

Evidences of Evolution:

• Fossil - Is any remnant that is preserved in earth.
• Relative Dating - Places into sequences
• Radiometric Dating - Dating that uses radioactive isotopes as a clock. Radiometric isotopes are a form of absolute dating.
• Plate Tectonics; Plates come together and cause the rise of mountain ranges.
• Anatomical Comparisons has aspects like Homologous with similarities that show common ancestry and Vestigial showing features that dont serve a purpose
• Embryonic Development with its many physical traits that they produce traits

TAΧΟΝΟΜY & PHYLOGENETICS

• Taxonomy is the discipline identifying, naming, and classifying organisms. It involves the practice of naming, describing, identifying, and specimen preservation. Classification + Nomenclature = Taxonomy
• Systematics involves the study of evolutionary relationships which studies phylogenies and diversification. Governs the evolutionary history and phylogenetic relationships in addition to taxonomy. Taxonomy + Phylogeny = Systematics
• Aristotle developed the system of dividing organisms into plant or animal, divided by the the color of their blood and the location they come from.
• Carolus Linnaeus developed the nomenclature naming species with with two words as the name is based.
• The names contain the genus or a species
• The first word is capital and if the species should be in small letters.
• If you were to write the name it should be underlined

Evolution and classfication:

• descent with modification
• tree branching on their taxonomic categories
• nested categores serve as filters
• the things are placed in the came class even thought they may separate
• the three domain system included archaea, bacteria, and eukaryote, its used ot clssify based on rRNA.