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bio textbook notes
1.1 principles of biology
Biology is the study of life
The ancient civilizations of Greece, Romans, and Egyptians discovered that the bark of the white willow tree could be used to fight fever
The bark of white willow trees contains salicylic acid which was made into aspirin to treat fever and pain
12 principles tell whether something is alive. Out of the 12, the first 8 are used as criteria to determine the basic features of life.
Principle 1: cells are the simplest unit of life (organisms maintain organization and cells are the simplest units of organization)
Principle 2: living organisms use energy and are composed of matter (organisms need energy to maintain internal order)
Principle 3: living organisms interact with their environment ( organisms respond to changes in their environment) EX: a plant growing toward the light
Principle 4: Homeostasis (organisms regulate their cells/bodies to maintain stable internal conditions) EX: a bird maintaining its internal body temperature on a cold day
Principle 5: genetic material: organisms must reproduce, and genetic material gets passed down which gives offspring similar traits to their parents
Principle 6: Evolution: populations of organisms evolve from one generation to the other which results in traits that are important to survival
Principle 7: structure and function: the features of an organism determine its function. EX: webbed feet on ducks function as paddles for swimming
Principle 8: emergent properties: new properties of life emerge from complex interactions EX: our ability to see is an emergent property because of the interaction of many types of cells in the eye and the neurons that send signals to the brain
Principle 9: experimentation: biology is an experimental science and discoveries of biology are only made because of experiments
Experiments lead to theories that lead to biological principles
Principle 10: Quantitative analysis: Biology is a quantitative science. Biologists quantitatively analyze data and use mathematical approaches to make predictions
Principle 11: modeling: biologists use models to test prediction
Principle 12: biology and society: biology affects our society because many biological discoveries have had major societal impacts
Cell theory: states that all living things are made up of one or more cells, cells are the smallest unit of life, and new cells are created from existing cells by cell division
Metabolism: chemical reactions that are involved in the breakdown of cellular molecules - how organisms absorb energy
Deoxyribonucleic Acid (DNA): a blueprint for living things' organization, development, and function.
Ganes: segments of DNA that control characteristics/ traits of organisms
Ribonucleic acid (RNA): a messenger that transcribes genes
A hypothesis (a proposed explanation for a natural phenomenon) leads to an experiment that tests the validity of the hypothesis
Levels of organization: the organization of living organisms is analyzed at different levels of biological complexity. This starts with the smallest level to the biggest
Levels of organization from smallest to largest: Atoms, molecules/macromolecules, cells, tissues, organs, organ systems, organisms, population, community, ecosystem, biosphere
Atoms: the smallest unit of an element that has the chemical properties of the element
Molecules / Macromolecules: atoms bond with each other to form molecules. Smaller molecules bond together to form a large polymer called macromolecule
Cells: molecules and macromolecules associate with each other to form larger structures called cells
Tissues: many cells of the same type are associated with each other to form tissue
Organ systems: organs that are part of a larger interacting system
Organism: all living things are called organisms
1.2 biological evolution
Vertical evolution: new species evolve from pre-existing ones by the accumulation of mutations
Mutations: heritable changes in the genetic material of an organisms
natural selection: when a mutation causes a beneficial change in an organism to increase its chance of survival and reproduction
Horizontal gene transfer: the process by which an organism incorporates genetic material from another organism without being the offspring of that organism
1.3 classification of living things
Taxonomy: the field of biology that is concerned with the grouping and classification of species
All forms of life can be placed into 3 domains: Bacteria, Archaea, Eukarya
Bacteria: mostly unicellular prokaryotic that inhibit many diverse environments on earth
Domain archaea: unicellular prokaryotes that often live in extreme environments, such as hot springs
Domain Eukarya: unicellular/multicellular organisms having cells with internal components that serve various functions
Bacteria and Archaea are microorganisms whose cell structure is simple
Binomial nomenclature: two-part description used to provide species with a unique scientific name - the first word is the genus and the second word is the species descriptor
The genus name is capitalized but the specific epithet is not - both names are italicized
scientific names are usually Latinized: made to look like Latin words
1.4 biology as a scientific discipline
Model organisms: organisms studied by many researchers so that they can compare their results and determine scientific principles that apply more broadly to other species
Ecology: the study of organisms in their natural environment - considers populations, communities, ecosystems
Anatomy/physiology: the study of the structure and function of plants and animals
Cell biology: the study of cells and their interactions
Molecular biology: the study of the structure and function of the molecules of life
Hypothesis: a proposed explanation for a natural phenomenon
Predictions: expected outcomes that can be shown to be correct/incorrect
Chapter 2.1: Atoms
Matter: anything that has mass and occupies space (all organisms are composed of matter)
Matter can exist as solid, liquid, gas
Atoms: smallest functional units of matter that form all chemical substances and all organisms - cannot be broken down into other substances by ordinary chemical or physical means.
Molecule: when two or more atoms are bonded together
Element: a pure substance made up of only one kind of atom
Atomic nucleus: protons and neutrons are confined
Electrons: Found in regions at various distances from the nucleus
Protons have a positive charge
Electrons have a negative charge
Neutrons are electrically neutral
Orbitals: The region surrounding an atom's nucleus where the probability of finding a particular electron is high.
Electron shell: composed of one or more orbitals
valence electrons: An electron in the outer shell of an atom that is available to combine with other atoms. Such electrons allow atoms to form chemical bonds with each other.
Atomic number: the number of protons in an atom
Atomic mass: An electron in the outer shell of an atom that is available to combine with other atoms. Such electrons allow atoms to form chemical bonds with each other.
Radioisotopes: An isotope found in nature that is inherently unstable and usually does not exist for long periods. Such isotopes decay and emit energy in the form of radiation.
2.2 chemical bonds/molecules
covalent bonds: A chemical bond in which two atoms share a pair of electrons.
Structural formula: A chemical formula in which each covalent bond between atoms is represented by a line indicating a pair of shared electrons.
Electronegativity: A measure of an atom’s ability to attract electrons to its outer shell from another atom.
nonpolar covalent bond: A strong bond formed between two atoms of similar electronegativities in which electrons are shared equally between the atoms.
polar covalent bonds: A covalent bond between two atoms with different electronegativities; the shared electrons are closer to the higher electronegativity atom than the lower electronegativity atom. This distribution of electrons around the atoms creates a polarity, or difference in electric charge, across the molecule.
Hydrogen bond: A weak chemical attraction between a partially positive hydrogen atom of a polar molecule and a partially negative atom of another polar molecule.
Van der Waals dispersion forces: Attractive forces between molecules in close proximity to each other, caused by the variations in the distribution of electron density around individual atoms.
Ion: An atom or a molecule that gains or loses one or more electrons and acquires a net electric charge.
Ionic bond: The bond that occurs when a cation binds to an anion.
2.3 chemical reactions
Chemical reaction: A process in which one or more substances are changed into other substances by the making or breaking of chemical bonds and/or the removal or addition of electrons.
2.4 properties of water
Solute: A substance dissolved in a liquid.
Solvent: The liquid in which a solute is dissolved.
Hydrophilic: Refers to ions and molecules that contain polar covalent bonds and will dissolve in water.
Hydrophobic: Refers to molecules that do not have partial charges and therefore are not attracted to water molecules. Such molecules are composed predominantly of carbon and hydrogen and are relatively insoluble in water.
Amphipathic: Molecules containing a hydrophobic region and a hydrophilic region.
Micelle: The sphere formed by amphipathic molecules when they are mixed with water. In animals, micelles aid in the absorption of poorly soluble products during digestion.
H2O exists as a solid, liquid, and gas
Roles of water:
Homeostasis
Water participates in chemical reactions
Water provides support
Water is used to eliminate soluble wastes
Evaporation helps some animals dissipate body heat
The cohesive force of water molecules aids in the movement of water against gravity in plants
Water in saliva serves as a lubricant while eating
2.5 PH and Buffers
Hydroxide ions: An anion with the formula OH–.
Ch.3 organic molecules
Organic molecules: A carbon-containing molecule, so named because they are found in living organisms.
3.1 the carbon atom
The carbon atom can form multiple covalent bonds with other atoms, including other carbon atoms
Carbon atoms most commonly form covalent bonds with other carbon atoms and with hydrogen, oxygen, nitrogen, and sulfur atoms
Hydrocarbons: Molecules with predominantly hydrogen-carbon bonds.
Functional groups: A group of atoms with chemical features that are functionally important. Each functional group exhibits the same properties in all molecules in which it occurs.
3.2 synthesis and breakdown of organic molecules
Monomers: An organic molecule that can be used to form larger molecules (polymers) consisting of many repeating units of the monomer.
Polymers: A large molecule formed by linking many smaller molecules called monomers.
Condensation reaction: A chemical reaction in which two or more molecules are combined into one larger molecule by covalent bonding, usually with the loss of a small molecule.
Dehydration reaction: A type of condensation reaction in which a molecule of water is lost.
hydrolysis reaction: A chemical reaction that utilizes water to break apart molecules.
3.4 carbohydrates
Carbohydrates: An organic molecule, often with the general formula C(H2O); a carbon-containing compound that includes starches, sugars, and cellulose.
Monosaccharides: A simple sugar.
Isomers: Two molecules with an identical molecular formula but different structures and characteristics.
Glucose is very water soluble and circulates in the blood or body fluids of animals where it is transported across cell membranes then the glucose is broken down by enzymes into smaller molecules, releasing energy that was stored in the glucose’s chemical bonds. This energy is then stored in the bonds of adenosine triphosphate (ATP) which is then turned into an energy source
Disaccharides: A carbohydrate composed of two monosaccharides.(two sugars)
Glycosidic bond: A bond formed between two sugar molecules.
Polysaccharides: Many monosaccharides are linked to form long polymers. (many sugars)
Polysaccharides in living organisms include: Starch: Found in plant cells, Glycogen: present in certain types of animal cells, Cellulose: found in the cell walls of plant cells, Peptidoglycans: Found in the cell walls of certain bacteria, Chitin: found in the cell walls of fungi, and the exoskeletons of arthropods, glycosaminoglycans: polysaccharides found in connective tissue and surrounding cells in animals
A monosaccharide contains a ring structure that includes carbons and ONE oxygen
Nucleotides have 3 parts: phosphate group, sugar, base
Amino acids do not have a ring and are named based on functional groups they contain — amino group, acid group
4.1 origin of living cells
Prebiotic soup: before life
Prebiotic soup: formed by the slow accumulation of organic molecules in the early oceans over a long period of time formed the prebiotic soup
Bacterial Cells: Simple structures without membrane-bound organelles, containing DNA in a nucleoid region and a plasma membrane.
Eukaryotic Cells: More complex with organized compartments and organelles (e.g., nucleus, mitochondria) that carry out specialized functions.
Plant Cells: Have unique structures like chloroplasts for photosynthesis, central vacuole for storage, and a sturdy cell wall for protection.
Polymers and Protobionts
Polymerization: Occurs when monomers (nucleotides, amino acids) are joined together, which requires a structure or scaffold to enable this process.
Protobionts: Early life-like structures that emerged from organized polymers.
Coacervates: Solid droplets of organic molecules surrounded by water.
Liposomes: Spherical structures with a lipid bilayer that compartmentalize biological molecGene Expression and Cell Types
All cells in multicellular organisms share the same genome but express different subsets of genes corresponding to their specialized functions (proteomes).
Housekeeping Genes: Common genes that are necessary across all cell types for basic cellular functions.
Proteome vs. Genome:
Genome: The complete set of DNA (genes) in an organism.
Proteome: The unique set of proteins expressed by a cell based on its specific functions.
Cellular Structures and Functions
Bacterial Cells: Simple structures without membrane-bound organelles, containing DNA in a nucleoid region and a plasma membrane.
Eukaryotic Cells: More complex with organized compartments and organelles (e.g., nucleus, mitochondria) that carry out specialized functions.
Plant Cells: Have unique structures like chloroplasts for photosynthesis, central vacuole for storage, and a sturdy cell wall for protection.
ules, representing a step towards cellular organization.
4.3
Plasma membrane: a double layer of phospholipids and embedded proteins that forms a barrier between the cell and its external environment
Cytoplasm: the region of the cell contained within a plasma membrane
Nucleoid: the location of the genetic material (DNA). the nucleoid is not a membrane-bound compartment
Ribosomes: cell components involved in polypeptide synthesis
Cell wall: A relatively rigid, porous structure located outside the plasma membrane of prokaryotic, plant, fungal, and certain protist cells; provides support and protection.
Glycocalyx: An outer viscous covering surrounding a bacterium that traps water and helps protect bacteria from drying out. 2. A carbohydrate-rich zone on the surface of animal cells; also called a cell coat.
Pili: hairlike projections that allow cells to attach to surfaces and to each other
Flagella: long appendages that provide prokaryotic cells with a way to move, also called motility
4.4
Motor proteins: A category of cellular proteins that use ATP as a source of energy to promote movement; consists of three domains called the head, hinge, and tail.
Head: the site where ATP binds and is hydrolyzed to adenosine diphosphate (ADP) and inorganic phosphate (Pi)
Hinge: the site that bends in response to ATP binding and hydrolysis. This bending is what causes movement to occur
Tail: an elongated region that is attached to other proteins or to other kinds of cellular molecules. Together, the hing and tail make up a structure called the lever arm
The cytoskeleton: made up of microtubules, intermediate filaments, actin filaments
Actin filaments: microfilaments that are the smallest cytoskeletal filaments and are important in muscle contraction
Proteins belong to amino acids
Carbohydrates are part of monosaccharides
Nucleic acid belongs to the nucleotide
Theory: A well-supported explanation encompasing all living things
Hypothesis: a proposed explanation that applies to a specific phenomenon or observation
One dalton is approximately the mass of one proton or hydrogen atom
A mole of a substance contains the same number of particles are there is in 12g of carbon
Nitrogen and phosphorus have the same number of electrons in their outermost shells
Carbon and nitrogen have 2 electron shells
The outermost electron shell of helium and argon are full
Hydrogen and helium have one electron shell
Sodium and chlorine have 3 electron shells
Polar covalent bond: bonded atoms have an unequal pull on the shared electrons so that the electron spends more time around one atom than the other
PH Measure: the amount of hydrogen ions in a solution
DNA/RNA: nucleotide
Double bonds found in unsaturated fats form structures that stop tightly bound formations
NOT a characteristic of the DNA double helix: the two strands are held together by covalent bonds between bases
DNA: double-stranded, housed within the nucleus of an animal cell, nitrogenous bases A, T, G,C
RNA: single-stranded, ribose sugar within backbone, nitrogenous bases, A, U, G, C
Phospholipids: composed of 3 fatty acids and 1 glycerol, the entire molecule is either saturated or unsaturated, and has a backbone of 4 fused carbon rings
