General Biology 2

• Friedrich Miescher isolated "nuclein" from pus cells, which later became known as DNA
• DNA and RNA serve as primary genetic material in organisms
• DNA stores genetic information, replicates and passes on traits during cell reproduction
• DNA provides avenues for genetic mutation and diversity

Nucleotides

• Subunits of nucleic acids are called nucleotides.
• Nucleotides consist of a nitrogenous base, pentose sugar and a phosphate group
• A nucleoside is a complex of a sugar and a base.
• Nucleotides in DNA are named after their nitrogenous base
• These are: Adenine, Guanine, Cytosine, and Thymine.
• The sugar in DNA is deoxyribose

Polynucleotide Chain

• Uniqueness lies in the sequence of nitrogenous bases, read from 5' to 3' direction

Tautomers of Nitrogenous Bases

• Cyclic bases are classified as purines and pyrimidines.
• Pyrimidines include amino and imino forms.
• Purines include keto and enol forms.

DNA Helix

• Two DNA polynucleotide chains are bound via complementary base pairing
• The DNA strands are antiparallel, running in opposite directions (5'→3′ and 3'→5′)
• DNA is a double-stranded nucleic acid

Contributions to Understanding DNA Structure

• Rosalind Franklin and Maurice Wilkins used X-ray crystallography to analyze DNA structure.
• Erwin Chargaff determined that adenine and thymine, and guanine and cytosine have equal quantities
• Watson and Crick, building on Franklin, Wilkins, and Chargaff's work, proposed that DNA's uniformity in size comes from complementary base pairing
• These pairings possess specificity in hydrogen bond formation.
• DNA structure is helical, resembling a twisted ladder.

DNA Acronyms

• PuAG (Purine, Adenine, Guanine) and PyCT (Pyrimidine, Cytosine, Thymine) aid in remembering base classifications

Genetic Stability

• Base pairs are organized inside the helix through base stacking, contributing to overall thermodynamic stability

DNA Helical shape

• DNA possesses a right-handed double helical nucleic acid

DNA Grooves

• DNA helix has major and minor grooves due to the deoxyribose's angle of protrusion

DNA Conformations

• DNA has A, B, and Z conformations, differing in formation, base pairs per turn, and helix shape

Comparison of Three DNA Conformations

• B DNA forms at 92% relative humidity, A DNA at 70% relative humidity, and Z DNA at low and high salt concentrations
• Base pairs per turn: B DNA has 10 bp, A DNA has 11 bp, and Z DNA has 12 bp
• Dexterity: B DNA and A DNA are right-handed, while Z DNA is left-handed
• Helical diameter: B DNA is 20 Å, A DNA is 23 Å, and Z DNA is 18 Å
• Complete turn: B DNA is 33.2 Å, A DNA is 24.6 Å, and Z DNA is 45.6 Å

Eukaryotic DNA

• Eukaryotic DNA is linear with telomeres
• Organized as chromatin (DNA + proteins)
• Packed through histones into nucleosomes, 30-nm fibers, and metaphase chromosomes.

The RNA Molecule.

• RNA, is single-stranded.
• Contains uracil instead of thymine
• Contains ribose instead of deoxyribose.
• It is a product of transcription of DNA
• RNA molecules can assume enzymatic functions

RNA enzymatic function

• Ribozymes are catalytic RNA molecules
• RNase P is a ribozyme that catalyzes tRNA synthesis.

Amino Acids.

• Amino acids are the subunits/monomers of proteins
• Each possesses a carboxyl group (COOH), an amino group (NH2), a proton, and a varying R group

Levels of Protein Structure.

• Amino acids organize into polypeptides/proteins via primary, secondary, tertiary, and quaternary levels

Primary Protein Structure.

• Formed by peptide bonds between amino acids

Secondary Protein Structure.

• Secondary protein structures include helix or pleated sheets

Tertiary Protein Structure.

• Tertiary structures consist of polypeptides, helices and sheets

Quaternary Protein Structure.

• Multiple folded protein subunits form a single complex for greater functionality

Protein Data Bank (PDB).

• The Protein Data Bank (PDB) is a collection of experiments on the structure of DNA, RNA, and proteins
• PDB enables viewing 3D structures of proteins.

Protein Resolution.

• Data on protein structures are quantified via protein resolution
• The smallest distance (in Å) between two distinguishable features identified through x-ray diffraction

Protein Structure Bonds

• Peptide bonds: hold amino acids together.
• Hydrogen bonds: form helices and sheets.
• Tertiary structures: stabilized by covalent and weak non-covalent interactions.
• Quaternary structures: require more complex molecular interactions.

Nucleic acid types

• DNA is primary genetic material
• RNA is the second type
• The basic nucleotide comprised of a 5-C sugar, a phosphate group, and a nitrogenous base

Nitrogenous Bases

• DNA's nitrogenous base may be adenine, guanine, thymine, or cytosine
• RNA has uracil instead of thymine.
• DNA possesses deoxyribose, while RNA has ribose.
• Prokaryotic DNA is circular and organized into domains in the nucleoid region. - Eukaryotic DNA is organized into nucleosomes, 30-nm chromatin fiber, and metaphase chromosomes

Protein monomers

• Amino acids are the monomers of proteins, consisting of a central carbon with four branches

Recombinant DNA Applications

• Agriculture, Bioremediation, Pharmaceuticals, Gene Therapy and Genetic Testing

Agriculture: Golden Rice

• Produces beta carotene in its grains, contains phytoene synthase gene from corn also approved by the Department of Agriculture. Also addresses vitamin A deficiency

Agriculture: Glyphosateresistant Soybeans .

• Glyphosate herbicide can't distinguish crops from weeds.
• it interferes with amino acid synthesis
• Foreign resistance gene from A. tumefaciens produced by Monsanto.

Agriculture: FLAVR SAVR Tomatoes

• Addresses early tomato ripening/rotting
• Genetically Modified crop with extended shelf-life, it prevents polygalacturonase expression. Can be ripened using ethylene

Agriculture: Bioreactor Cows.

• Application in biopharming involving cows
• Cows with foreign genes from humans
• These cows produce human proteins allowing therapeutic properties

Agriculture: AquAdvantage Salmon.

• Exhibits improved growth rate and growth hormone gene from Chinook salmon
• Additional promoter gene from ocean pout
• Growth duration throughout the entire year
• They are not related to the prevalence of autism

Bioremediation.

• Uses microbes to degrade contaminants and considered cost-effective and noninvasive
• Improves microbes' bioremediation capacity via Pseudomonas fluorescens, Bacillus subtilis

Pharmaceuticals

• Use of non-virulent E. coli to produce human insulin to treat diabetes
• Replaces extraction from cows and pigs
• Humulin was the first commercialized form
• Other proteins include clotting factors and Hgh

Genetic Testing.

• Detects genetic disorders, especially at birth
• Applicable to asymptomatic and late-onset disorders.
• Uses DNA probes/polymerase chain reaction (PCR)
• Detects Huntington's disease.

Gene Therapy

• Treats genetic disorders by introducing normal genes into viruses
• Viruses are used as vectors to introduce the genes/ is also applied to the treatment of hemophilia

Issues with Genetic Engineering

• Includes health and biodiversity concerns, and ethical considerations by campaigns lead by Greenpeace, and potential depression for genetic conditions

Potential Health Effects.

• Includes, toxic effects, allergic reactions, compromised immunity, or cancer; also loss of nutrition

National Academies of Sciences, Engineering, and Medicine (2016).

• No toxicity difference between GM and non-GM crops, no negative effects in kidney and digestion, and does not related to cancer, obesity, or autism

Potential Effects on Biodiversity.

• Horizontal gene transfer, loss of wild, invasion of GMOs is possible with decline in variation and biodiversity

Ethics.

• Includes concerns of corporate exploitation, and going against "natural" genetic modifications

Classical and Modern Breeding Techniques.

• Breeding is controlled sexual reproduction of two parent organisms to produce offspring

Objectives of Plant Breeding.

• Includes increased yields, resistance from pests, diseases, and stress. As well as improved processing, and nutrient quantity

Objectives of Animal Breeding.

• includes Increased production of milk, eggs, meat, wool and resistance against diseases with improved less aggression

Captive Breeding.

• Crocodylus mindorensis is critically endangered Philippine crocodile with facility at Silliman University
• Pithecophaga jefferyi is an endangered Philippine eagle with center located in Davao City

Historical Progress of Plant Breeding.

• Historical figures include: Gregor Mendel, Pioneer Company, Norman Borlaug and Joseph Koelreuter amongst

Classical Plant Breeding Methods.

• Includes selective breeding and crossbreeding

Mass Selection.

• It improves crop qualities by selecting good quality offspring every generation and open pollinates (both self and cross).

Pure-line Selection

• Aims to establish a homozygous breed for particular trails where self-pollination is applicable.

Clonal Selection.

• Used for good quality hybrids that asexual and vegetative traits
• Select initial crop, and acquire the vegatative structures determine the superior traits, perform vegetative structure reproduction.

Crossbreeding or Hybridization.

• Prevents self-pollination by removing stamens, and combines two superior traits from species.
• Eliminates some inferior traits but can be labor intensive due to emasculation.

Classical Animal Breeding Methods .

• Includes inbreeding and crossbreeding.

Inbreeding.

• Accumulates superior traits of a male and female
• May be mating superior with offspring or with related individuals
• Reinforces a trait to a animal group.

Crossbreeding.

• Breeds 2 individuals from different breeds.
• they must have be reproductively compatible
• used to combine desirable traits among animals

Modern Plant Breeding Methods.

• Somatic hybridization, mutation breeding, artificial reproductive technologies, and genetic engineering

Somatic Hybridization.

• Fuses protoplasts from 2 plants with desirable traits

Mutation Breeding.

• Used to introduce crops such as soybeans to mutate via radiation

Artificial Reproductive Technologies.

• Where cattle are artificially inseminated using semen

Genetic Engineering.

• It can be used as a classical method to create and introduce new genes from any organism.

Genetic Engineering Techniques

• Genetic engineering involves direct manipulation of genes for desired traits which includes adding, deleting, under or over expressing existing genes. Recombinant DNA Technology: Recombinant DNA technology, which is the primary tool used to genetically engineering organisms
• Scientists associated with the Genetic Engineering Techniques include: Cohen and Boyer, Rudolf Jaenisch, Genentech Bevan

Recombinant DNA Technology principles

• To determine whether the introduction will make or break DNA, the proteins that act like phenotypic determners should be identified, and introduce the foreign gene

Genetic Identification

• Used to determine genes such as the Bt gene or cry1Ab from B. thuringiensis, that produce the cry protein, a protein to destroy corn
• It involves isolation via Werner Arber's study of the restriction enzymes, and Daniel Nathans elucidating the ability of restriction endonucleases to cut DNA at specific sites

Genetic Engineering Techniques:

• Introduction can be done via microprojectile bombardment, electroporation/Agrobacterium tumefaciens mediated transformation

Genetic Engineering Animals and Bacteria

• Human cells extractd with human insulin can introduce the recombinant DNA into fermentation tanks and the extraction becomes genetic extraction for analysis

Steps To Produce Transgenic Crops

• 1. determination of the selected gene
• 2. isolation using restriction enzymes and gel electrophoresis
• 3. location using recombinant DNA
• 4. bacteria tranformation through cultured recombinant enzyme ligation
• 5. introducing a bacterial cell
• 6. allowing that bacteria to affect the surrounding plant cells.
• 7. Regenerating the cultured plant cells

History of Life on Earth During the 1800s.

• The timeline of the appearance of life is:
• 4.6-3.8 BYA where the earth formed by ziricon
• 3.5 BYA Life form called protokaryes begins.
• 3.0 BYA photosynthetic organisms begin.
• 2.0 BYA the appearance of eukaryotes
• 250 TYA Multicellular organisms begin
• 500 MYA Cambrian and Ordovician sea animals begin to appear
• 251-6555 MYA - Dinousaurs appear for the Mesozoic Era. The evidence is fossils of ancient sea life, and many layers of layered lithosphere showing the history of the earth

Earth formation

• The universe is about 4.6 billion years old
• Earth life only began 3.5 - 4.0 billion years ago.
• Fossils show how it emerged and the common ancestor were prokaryotic
• Oxygen was scare creating am anaerobic atmosphere
• Eukaryotic cells evolved from prokaryotic cells and earth environments suitable for life forms

Evolution of Life

• Brought by geologic climate and geological changes. Earth changes has made a form for winder variet of life

4 theories of special creation.

• Special generation form from nonliving organisms
• Biogenesis form living organisms
• Cosmogenesis from other parts
• Speccial creation from religious points of view. non living organisms.

Time Period Events Leading to Evolution.

• 3850 Oldest known rocks and fossils
• 2700 Atmospheric oxygen concentration increases
• 1600 oldest animal fossils
• Paleozoic Era, breakup and Glaciation

Francesco Redi

• The Italian physician
• Redi was able to prove that organisms do not just come to life spontaneously and disprove to special generation

John Needham and the verification of microbial growth

• John Needham, an English priest proved that special generation to occur in an appropriate contidion
• Needham concluded that the the correct conditions made it necessary to heat to make organisms even smaller and prove the existence of growth through air and boiling the substance. This disproves special generation

Lazzaro Spallanzani

The Italian scholar the conducted a experiment to verify Lazzaro's setup.

• Needham that had not the sealed broth enough to kill all organisms in it, where microorganisms was growth disproving special origin.

Louis Pasteur

• Louis Pasteur's experiment convinced most scientists that it was a new origin
• Pasteur's idea was to test and set up that vital element from air was necessary for life to emerge

Phanerozoic Time

• Phanerozoic a time scale when rock was cut
• There would be microbial contamination
• 88% of earth transformed to liquid and dust

Life and single celled organisms

• Became more conducive to single celled
• Cynoboacteria to exit a source in Australia

The Cryogenian Period

• The the animal life that predates the Ediacaran period

The latter part of Precambrian life

• Proterozoic was affected by tectonic plate movement that causes supper continent rodiria and brought the about the ice ages.

The geologic processes

• Began with Rodinia which was a supercontinent and split and caused glaciation

Towards the latter

• Paleoziotic era was wiped by extinct life forms when sea land changed

Era of 180 Years

• split pangea and reduced climates but caused events by comets impacting

Mountains and mammal ages

• Where mammals evolved with different enviroenemtons.

Natural Selction

• The Brussels that cause the species in a group that can lead in to species
  • First lineage.

Species Survival over a long period

• Can lead to a community that is species

Species that lead to genetic selection

• Includes selection and traits and is artificial

A species has genetic structure

• Allelles can have difference in structures that can decrease a genetic potential
• All species have a reproductive potential
• Genetypes have traits of genes Phenotypes have characterisitic of traits

High Genetic Strucutre -

• Has a mutatation over time
• Genetic drift with change

Generates New Popoulatoin

• Founder effect, when wiped from the environment
• Botleneck effect can be change by random
• New population with segments

General Zoology -

• Asks key question about evolution 5.1: the evolution or population of living forms changes over time.
• Is an ongoing event or humans are the final products of the evolutionary system but rather a continuous and competing for reproduction

Species - As reproductively isloated.

• Reproductive system isolate organisms where certain sites are isolated based on mechanisms for speciation

Mechanisms for isolating pre-and post-zygotic

• Prevent before and after fertilization, includes gamete and fertilization.
• Incompatible systems may be involved in after the reproduction of the species

Other Isolation

• Temporal or seasonal isolation, behaviorial

Genetic Isolation of groups that are evolved.

• Allo - allo patric patriction of 1st and 2nd species where only the species are maintained.
• Sym - sym patric systems that involves genetic changes that create unique systems of number
• Para - para patric with small amounts of generatrns

Key People and Observations in Evolution

• Charles Darwin, explained natural process with variation, that resulted in competition and survival of useful events/offspring Voyage for beagles showed the results, and published theory of evolultion by "Descent of Modification, this involves the ability of traits that can change species that evolves.
• Jean Baptist Lamark, traits are transferred, with darwin struggling for existence and not all offspring can be reproduce

Modern Selction

• can be of artificial forms, where traits and charactersitics are well adapted for the species, from thhe theory of decesnt