Comprehensive Study Notes: Biology – Key Concepts from Transcript (Levels of Organization through CHEMICAL Foundations)
Levels of Biological Organization
- Order: highly ordered structure that characterizes life (example: sunflower).
- Evolutionary adaptation: reproductive success of individuals with heritable traits best suited to their environments (example: camouflage).
- Response to the environment: organisms respond to environmental stimuli quickly (example: Venus flytrap closing on insects).
- Regulation: regulation of blood flow through vessels to maintain constant body temperature by adjusting heat exchange with the environment.
- Energy processing: obtaining fuel and using chemical energy stored in food to power movement and other work.
- Growth and development: inherited information carried by genes controls growth and development patterns.
- Reproduction: ability to reproduce your own kind.
Hierarchy of Biological Organization
- The biosphere: all environments on Earth inhabited by life; includes most regions of land, bodies of water, and the atmosphere; visible from space near continents and oceans.
- Ecosystems: environments such as forests, grasslands, coral reefs, deserts; includes all living and nonliving things that life interacts with.
- Communities: entire array of organisms in a particular ecosystem; each form of life is a species.
- Populations: all individuals of a species living within a specified area.
- Organisms: individual living things.
- Organs and organ systems: a body part consisting of two or more tissues (examples: stems, leaves, roots as major plant organs).
- Tissues: require a microscope; have cellular structure; each tissue type is a group of similar cells.
- Cells: life’s fundamental unit of structure and function; unicellular and multicellular forms; lowest level of organization that can perform all life activities.
- Molecules: chemical structure consisting of two or more atoms (example: chlorophyll).
More on Ecosystems
- All organisms interact continuously with their environment.
- Both organism and environment are affected by their interactions.
Ecosystem Dynamics
- Two major processes:
- Cycling of nutrients: minerals acquired by plants eventually return to the soil.
- Flow of energy: from sunlight to producers to consumers.
- Producers: photosynthetic organisms that convert light energy to chemical energy.
- Consumers: organisms that feed on producers or other consumers.
Energy Conversion in Ecosystems
- Moving, growing, reproducing require work; work depends on a source of energy.
- Exchange of energy between an organism and its surroundings involves transforming one form of energy to another.
- Sometimes energy is converted to thermal energy (heat).
- Energy flows through an ecosystem; usually enters as light and exits as heat.
Cells and Heritable Information
Chromosomes: partly made up of deoxyribonucleic acid (DNA); the substance of genes.
Each chromosome has a very long DNA molecule with many genes arranged along its length.
Genes: units of inheritance that transmit information from parents to offspring.
In each cell, the genes along DNA encode information to build the cell’s components and other molecules.
DNA directs development and maintenance of the entire organism.
DNA is a double helix; each link in the chain is made from four nucleotides: A, T, C, G.
Nucleotides make up genes.
Genes program the cell's production of proteins; the sequence of nucleotides in a gene codes for specific proteins with unique shapes and functions (e.g., enzymes catalyze specific chemical reactions).
DNA provides instructions; proteins are responsible for actually building and maintaining the cell.
Genome: the entire library of genetic instructions that an organism inherits.
Two main forms of cells:
- All cells have a membrane that regulates passage of materials and use DNA.
- Prokaryotic cells and Eukaryotic cells:
- Bacteria and Archaea are prokaryotes.
- All other forms of life are eukaryotes.
Eukaryotic cells: contain membrane-enclosed organelles such as chloroplasts; nucleus is the largest organelle (contains DNA).
Prokaryotic cells: smaller and simpler; DNA is not separated into a nucleus; lack membrane-enclosed organelles.
Emergent properties of systems:
- Emergent properties arise from the arrangement and interactions of parts as complexity increases.
- Everything is co-dependent, and everything belongs for a reason.
Power and Limitations of Reductionism
- Reductionism: reducing complex systems to simpler components to make them easier to study.
Systems Biology
- Looks toward development and maintenance of cells and organisms.
- Goal: model the dynamic behavior of whole biological systems.
- Predict how a change in one or more variables affects other components and the whole system.
- Basics of systems strategy:
- Inventory as many parts as possible.
- Investigate how each part behaves in relation to others in the system.
- Pool data from many research teams with computers and software.
- Requires: high-throughput technology, bioinformatics, and interdisciplinary teams.
Feedback Regulation
- Regulation resembles a supply-and-demand economy: the output or product of a process regulates that same process.
- Negative feedback: accumulation of an end product slows the process (example: ATP excess feeds back and inhibits an enzyme near the beginning).
- Positive feedback: the end product speeds up its production (example: during energy demand, sugar consumption in muscle cells increases; during rest, different reactions convert surplus sugar to storage fuels).
- Enzymes: different enzymes catalyze different chemical reactions.
Grouping Species and Taxonomy
- Levels:
1) Species
2) Genus
3) Family
4) Order
5) Class
6) Phylum
7) Kingdom
8) Domain - Three Domains:
- Domain Bacteria
- Domain Archaea
- Domain Eukarya: includes Protists, Kingdom Plantae, Kingdom Fungi, Kingdom Animalia
Evolution and Inquiry
Charles Robert Darwin: two main points
- Succession of ancestors → descent with modification
- Mechanism for descent with modification → natural selection
Natural selection: the environment ‘selects’ for propagation of certain traits; can lead ancestral species to split into two or more descendant species
Inquiry: search for information and explanation often focusing on specific questions
Two main processes:
- Discovery science: describing nature via observations; qualitative vs quantitative data; inductive reasoning to derive general conclusions from many observations.
- Hypothesis-based science: explaining nature; hypothesis is a tentative answer to a well-framed question; makes predictions that can be tested; must be falsifiable; often expressed as If … then … (deductive reasoning).
Theories: scientific theories are broader than hypotheses and usually supported by more evidence.
Science and Technology: technology applies scientific knowledge; science and tech are interdependent; inventions help discoveries and vice versa.
11 Themes that Unify Biology
- 1) The cell
- 2) Heritable information
- 3) Emergent properties of biological systems
- 4) Regulation
- 5) Interaction with the environment
- 6) Energy and life
- 7) Unity and diversity
- 8) Evolution
- 9) Structure and function
- 10) Scientific inquiry
- 11) Science, technology, and society
CHP Two: Elements and Compounds
- Organisms are composed of matter: anything that takes up space and has mass.
- Matter is made up of elements.
- Element: substance that cannot be broken down to other substances by chemical reactions.
- 92 elements total.
- Compound: substance consisting of two or more different elements in a fixed ratio.
- 25 of the 92 natural elements are essential to life.
- Major elements: C, O, H, N make up 96% of living matter.
- Minor elements: P, S, Ca, K and other elements make up 4%.
- Trace elements: required by an organism in only minute quantities (e.g., Iron is needed by all forms of life).
- Atom: smallest unit of matter that retains the properties of an element.
- Subatomic particles: neutrons, protons, and electrons.
- Neutrons + protons form the atomic nucleus; electrons form a cloud around the nucleus.
- Atoms are electrically neutral overall; electrons carry negative charge, protons carry positive charge.
- Atomic mass unit (dalton): mass units for atoms; neutrons and protons are ~1 dalton; electrons are negligible in mass for total atomic mass.
- Atomic number Z: number of protons (subscript to the left of the symbol).
- Mass number A: total number of protons and neutrons (A = Z + N).
- Isotopes: same number of protons (Z) but different number of neutrons; have different masses.
- Radioactive isotopes: nucleus decays spontaneously, emitting particles and energy; changes the number of protons and thus the element.
- Energy: the capacity to cause change; potential energy is energy due to location/structure.
- Electron potential energy: increases as electrons move farther from the nucleus; energy levels are defined by electron shells.
- Absorbing energy moves an electron to a higher shell; losing energy moves it to a lower shell.
- Electron configuration determines chemical behavior.
- First shell: 2 electrons; Second shell: 8 electrons (max in second shell).
- Valence electrons: electrons in the outermost shell; determine chemical behavior and bonding potential; atoms with completed valence shells are inert.
- Electron orbitals: 3D space where an electron is 90% of the time; each shell has a specific number of orbitals; first shell has one spherical orbital (max 2 electrons); second shell has one large spherical orbital and three dumbbell-shaped p orbitals (max 8 electrons).
- Covalent bonds: sharing a pair of valence electrons between atoms; a molecule is formed by covalent bonds; double bonds share two pairs of electrons.
- Bonding capacity (valence): number of unpaired electrons in the valence shell.
- Electronegativity: attraction of an atom for electrons in a covalent bond; more electronegative atoms pull shared electrons more strongly.
- Nonpolar covalent bonds: electrons shared equally.
- Polar covalent bonds: electrons not shared equally.
- Ionic bonds: transfer of electrons from one atom to another, creating ions; cation = positively charged, anion = negatively charged.
- Environment affects the strength of ionic bonds.
- Dry salt crystals: strong bonds; dissolved salt crystals: bonds become weaker.
- Hydrogen bonds: attraction between a hydrogen atom covalently bonded to a highly electronegative atom and another electronegative atom.
- Van der Waals interactions: nonpolar regions create transient charges due to uneven electron distribution; allows weak interactions when atoms/molecules are very close.
- Molecular shape and function: the shape and size of a molecule affect its function; geometry determines how molecules recognize and respond to each other; complementary shapes allow binding via weak bonds (e.g., endorphins resemble similar molecules with related effects).
- Chemical reactions: making and breaking chemical bonds; written as reactants → products with coefficients indicating the number of molecules; atoms must be conserved (example: photosynthesis: ).
- Rate of reaction: influenced by reactant concentrations; higher concentrations generally increase rate until equilibrium is reached.
- Chemical equilibrium: forward and reverse reactions occur at the same rate; concentrations of reactants and products no longer change.