BIO 120: Core Concepts

northern kentucky university college of arts and sciences
	BIO 120

	CORE CONCEPTS & TERMINOLOGY SPRING 2010 The following concepts and terms will be covered by all BIO 120 lecture instructors. Presentation of additional concepts is left to the discretion of the individual instructor. CHAPTER 1: INVITATION TO BIOLOGY A] TERMINOLOGY: Hypothesis Scientific theory Variable Control group Experimental group B] CONCEPTS: Hierarchical organization within an organism: (see Fig. 1.1: a-g) atom, molecule, cell, tissue, organ, organ system, multicelled organism Ecological hierarchy of life: (see Fig. 1.1: g-k): organism, population, community, ecosystem, biosphere Characteristics of life: All living things grow and reproduce with the help of DNA, energy, and raw materials. They sense and respond to their environment. The steps of the “scientific method” (7 steps listed on pg. 9) – a logical approach used to explain nature Scientists use the word “theory” differently than many in the general public to describe information that they are most sure of (but which still remains open to testing and revision) How to set up a controlled experiment CHAPTER 2: MOLECULES OF LIFE A] TERMINOLOGY: Atom Molecule Isotope Ion Hydrophilic Hydrophobic Solvent Solute pH Acid Base Organic compounds Denaturation B] CONCEPTS: The major subatomic particles (proton, electron, neutron) and their electrical charges The number of protons define the element The number of neutrons can vary somewhat (isotopes and radioactivity) The number of electrons can vary somewhat (ions) Opposite charges attract, like charges repel Some molecules have different electrical charges on different parts of the molecule (polar vs. non-polar molecules) Bonding of atoms and molecules by sharing electrons (covalent bonds) vs. weak electrical bonding (hydrogen bonds) Water States of matter: solid, liquid, gas & relation to temperature Unlike most matter, water is less dense as a solid Water as a polar solvent pH i. its relationship with hydrogen ions ii. Scale goes from 0-14 iii. 7 is neutral iv. below 7 is considered to be acid v. above 7 is considered to be basic (or alkaline) vi. the lower the pH, the more acidic the solution is vii. the higher the pH, the more basic the solution is Biological macromolecules and their building blocks - concept of monomers and polymers Carbohydrates Monosaccharides – the simplest carbohydrates and monomers (building blocks) for more complex carbohydrates (e.g. glucose & fructose) Disaccharides (e.g. sucrose & lactose) Polysaccharides i. Energy storage – starch (plants) & glycogen (animals) ii. Structural support – cellulose (plants) & chitin (animals) Lipids Different types of lipids - triglycerides (fats & oils), phospholipids, sterols and waxes Saturated vs. unsaturated fats & health implications Proteins Amino acids – the monomers (building blocks) for proteins Levels of protein structure – primary, secondary, tertiary, and quaternary structure The shape of a protein defines its biological activity Denaturation of protein molecules Nucleic Acids Nucleotides – the monomers (building blocks) of nucleic acids ATP – important energy molecule is a modified nucleotide DNA and RNA basic structure as polymers of nucleotides CHAPTER 3: HOW CELLS ARE PUT TOGETHER A] TERMINOLOGY: Cell Prokaryotic cell Eukaryotic cell Organelle B] CONCEPTS: Three parts of the cell theory Every organism consists of one or more cells A cell is the smallest unit with the properties of life Only living cells give rise to new cells (under current conditions) Similarities between all cells – plasma membrane, a region of DNA, and cytoplasm All plasma membranes consist of two layers of lipids (mainly phospholipids) and diverse proteins Similarities and differences between prokaryotic and eukaryotic cells Description and function of cellular organelles and cellular structures: Plasma membrane Cell wall Nucleus Mitochondria Ribosome Chloroplast Similarities and differences between plant and animals cells CHAPTER 4: HOW CELLS WORK A] TERMINOLOGY: Enzyme Substrate Active site B] CONCEPTS: First law of thermodynamics – energy cannot be created or destroyed Second law of thermodynamics – energy disperses spontaneously ATP/ADP cycle In general, making chemical bonds stores energy and breaking chemical bonds releases energy In chemical reactions, chemical bonds break and reform and atoms become rearranged into new molecules (same atoms that you begin with you end with, just rearranged) How enzymes make substances react The enzyme’s active site Lower energy required for reaction to occur CHAPTER 5: WHERE IT STARTS – PHOTOSYNTHESIS A] TERMINOLOGY: Pigment Photosynthesis Chlorophyll B] CONCEPTS: The visible light spectrum Shorter wavelength = higher energy Know in order (from shortest to longest wavelength) – violet, indigo, blue, green, yellow, orange, red Why do things appear different colors? Light absorbed vs. reflected General formula: 6 CO₂ + 12 H₂O + light energy ----à C₆H₁₂O₆ + 6 O₂ + 6 H₂O Photosynthesis is assisted by the pigment chlorophyll in the chloroplasts of green plant cells CHAPTER 6: HOW CELLS RELEASE CHEMICAL ENERGY A] TERMINOLOGY: Anaerobic Aerobic Fermentation Aerobic respiration B] CONCEPTS: General formula: C₆H₁₂O₆ + 6 O₂--------à 6 CO₂ + 6 H₂O + 36 ATP Aerobic respiration occurs in the cytoplasm and mitochondria, but most energy transferred to ATP in the mitochondria Energy is released from glucose when it is broken apart and the energy is transferred to molecules of ATP Alcoholic fermentation An anaerobic reaction Glucose converted to carbon dioxide and ethanol Only a net production of 2 ATP CHAPTER 7: HOW CELLS REPRODUCE A] TERMINOLOGY Mitosis Chromosome Meiosis Homologous chromosomes Fertilization Cancer Metastasis B] CONCEPTS Mitosis – Generalized overview of how it is accomplished with emphasis on: Exact replication of the cell’s chromosomes (genetic information) Daughter cells have the same genetic information as each other Daughter cells have the same genetic information as the parent cell Cytoplasmic division result in two cells from the original starting cell This process is the basis of body growth, cell replacements, tissue repair, and asexual reproduction in eukaryotes Chromosomes Composed of DNA and protein molecules There is a constant chromosome number within an organism’s body cells There is a constant chromosome number within a given species of organism Most eukaryotic multicellular organisms have their chromosomes occurring in pairs (homologous chromosomes) in their body cells Meiosis - Generalized overview of how it is accomplished with emphasis on: This process is the basis of gamete (sperm & egg) formation in sexual reproduction Daughter cells have half the normal number of chromosomes Daughter cells have one of each type of chromosome (no homologous pairs) Daughter cells can be different from each other (in terms of the genetic information they hold) and different from the parent cell Entails two division events and results in 4 cells from the original starting cell Fertilization – return to the normal number of chromosomes and homologous pairs of chromosomes (one set from each parent) leads to an increase in variation in organisms Cancer Results when cells lose control over their replication cycle, getting stuck in mitosis Tumor formation – benign vs. malignant CHAPTER 8: OBSERVING PATTERNS IN INHERITED TRAITS A] TERMINOLOGY Genetics Gene Allele Dominant allele Recessive allele Homozygous alleles Heterozygous alleles Genotype Phenotype Incomplete dominance Codominance Pleitropy Multiple alleles Polygenic inheritance Karotytpe Autosomes Sex Chromosomes Nondisjunction B] CONCEPTS Gregor Mendel’s contribution to genetics Monohybrid cross - Punnett square or probability to determine results of cross Dihybrid cross and independent assortment of alleles What a human karyotype looks like (46 total chromosomes; 22 homologous pairs of autosomes & 1 pair of sex chromosomes) Sex chromosomes (XY = male in humans) (XX = female in humans) Other patterns of inheritance Incomplete dominance Codominance (e.g. AB blood type) Multiple alleles (e.g. ABO blood groups) Pleitropy (e.g. multiple effects caused by mutation in DNA causing sickle-cell anemia or cystic fibrosis) Several genes sometimes control a single phenotypic trait (e.g. height & eye color) (= polygenic inheritance) The environment can affect how genes are expressed – the phenotype is the result of both genetics and the environment Continuous variation in traits of organisms usually shows a “bell curve” result X-linked recessive inheritance (e.g. color blindness & hemophilia) Nondisjunction – a problem caused by pairs of chromosomes which do not separate during cell division (e.g. Down syndrome) CHAPTER 9: DNA STRUCTURE AND FUNCTION A] TERMINOLOGY DNA DNA replication Cloning B] CONCEPTS The discovery of DNA as the genetic molecule The experiment with mice performed by Frederick Griffith The proof of DNA as the molecule involved with transforming nonvirulent bacteria (non-disease causing) to virulent form (disease causing) by Oswald Avery James Watson and Francis Crick discover the double helix structure of DNA and provide the mechanism for DNA exact replication and an explanation of its role as the hereditary molecule Structure of DNA Double helix Base pairing (A-T; C-G) The four nucleotides of DNA: adenine, thymine, guanine, cytosine Replication – DNA able to make an exact copy by having the two strands separate, each serving as the template for a new strand. Exact copying results due to the complimentary base pairing Cloning Identical twins and artificial twinning (embryo cloning) Nuclear transfer (technique used to clone an adult organism) CHAPTER 10: GENE EXPRESSION AND CONTROL A] TERMINOLOGY RNA Transcription Translation Codon Gene Ribosome Genetic code B] CONCEPTS Structure of RNA - single helix; ACGU nucleotides; similarities and differences to DNA DNA provides instructions on how to make protein molecules (carbohydrates and lipids produced by an organism are indirectly produced as a result of the action of protein molecules) Gene Expression – two steps needed to convert a gene into a protein Transcription – begins in nucleus when RNA strand copies the genetic information in the DNA molecule; the RNA can move from the nucleus into the cytoplasm and to the ribosomes Translation –where the information is translated from the nucleic acid sequence (language) of RNA to the amino acid sequence (language) of protein Special sequences of nucleotides on the DNA provides signals for the “start” of a gene and the “stop” point for RNA copying Translation is accomplished by translating a sequence of 3 nucleotide bases in mRNA (a codon) to a particular amino acid (the building blocks of proteins) Mutations and their relation to protein synthesis a. Base-pair substitutions b. Frameshift mutations caused by deletions or insertions Cells in a multicellular organism are able to control their genes – this allows cell differentiation CHAPTER 11: STUDYING AND MANIPULATING GENOMES A] TERMINOLOGY Restriction enzyme Plasmid Genome PCR DNA Sequencing Gel electrophoresis DNA fingerprint Tandem repeats Human genome project Gene therapy Genetic engineering Eugenics B] CONCEPTS Restriction enzymes were discovered in strains of bacteria – each particular type of enzyme cuts double stranded DNA at a particular nucleotide sequence (e.g. EcoRI cuts between the G and the A of the sequence GAATTC) Many of these enzymes leave single stranded tails or “sticky ends” on the cut fragments The use of plasmids to genetically modify bacteria cells An enzyme produced by certain types of viruses allows the construction of DNA from a molecule of RNA (the reverse of the normal process of transcription) – this is very useful to produce a piece of DNA that codes for a particular protein of interest Pieces of DNA can be isolated and mass produced by a technique called polymerase chain reaction (PCR) Gel electrophoresis – a technique that allows the separation of DNA fragments based on the size of the fragments DNA fragment moves through a gel due to an electric current DNA has a slight negative charge (remember: opposites attract & same charges repel) DNA fingerprints Reveals differences in the tandem repeats among individuals PCR can be used to make many copies of the tandem repeat areas of the DNA Human genome project Sequencing (finding the exact order of CGAT nucleotides) of human DNA About 21,000 genes have been identified for humans (although we are not sure what proteins all those genes code for) Mapping of chromosomes (what genes occur where) Comparing genes of humans with other organisms Potential for gene therapy Genetic engineering – examples of: Designer plants Bacteria Livestock Lab animals for medical research Ethical considerations Ethical considerations involved with genetic engineering of humans CHAPTER 12: PROCESS OF EVOLUTION A] TERMINOLOGY Evolution Natural selection Adaptation Gene pool Directional selection Stabilizing selection Disruptive selection Sexual selection (non-random mating) Genetic drift Gene flow B] CONCEPTS Jean Lamarck and evolution of living organisms through acquired characteristics Charles Lyell – geologist who stated that the Earth was much older than previously thought, that change occurred gradually over long periods of time, and that the same forces involved with change at present worked the same way in the past and will work the same way in the future Charles Darwin provides the idea of “descent with modification” and the mechanism that causes change over time – natural selection (he published his ideas in the book: On the Origin of Species) Natural selection Observation – organisms produce many more offspring than can survive Observation – organisms show variation in their structures and behaviors that are inherited Conclusion – Nature decides which variations are the best for survival and reproduction. Those with the “best” variations will survive and reproduce while those with less desirable variations will die and their undesirable variations will not be passed on to the next generation Remember – passing variations (genes or alleles) forward in time (reproductive success) is the key for being evolutionarily successful! Mutations function as the raw material for evolutionary change CHAPTER 13: EVOLUTIONARY PATTERNS, RATES, AND TRENDS A] TERMINOLOGY Radiometric dating Geologic time scale Plate tectonics Continental drift Comparative morphology Homologous structures Analogous structures Biological species concept Speciation Reproductive isolating mechanisms B] CONCEPTS Evidence of evolution – comes from biogeography, fossils, comparisons of body form, development, biochemistry, and DNA among/between different groups How new species evolve – disruption of gene flow, genetic divergence, speciation and the development of reproductive isolation CHAPTER 14: EARLY LIFE A] TERMINOLOGY Virus Antibiotics B] CONCEPTS Origin of life – experiments show that organic molecules that serve as the building blocks of life can form spontaneously, as can cell-like structures (first steps toward the origin of life) What the Earth was like when life first formed Stanley Miller’s experiment on forming complex organic molecules from simple inorganic molecules Prokaryotic life was the first type of life on the planet Photosynthesis and the addition of oxygen to the Earth’s atmosphere The oxygen enriched atmosphere put an end to the further spontaneous chemical origin of life Viruses Structure Viral reproduction – lytic pathway vs. lysogenic pathway Some with DNA & others with RNA as the genetic information molecule How antibiotics work and why they are not useful for viral infections HIV and AIDS [NOTE: most of this is not in the textbook] What the initials HIV and AIDS stand for Difference between being HIV positive and having AIDS Timeline involved with HIV infection and development of AIDS What causes death How HIV is spread from one person to another Ways to stop HIV transmission from person to person No cure or vaccine is currently available HIV as a pandemic disease CHAPTER 18: POPULATION ECOLOGY A] TERMINOLOGY Ecology Population Exponential growth Carrying capacity Logistic growth B] CONCEPTS During a specified interval, population size is generally an outcome of births, deaths, immigration and emigration With exponential growth, population size increases by a fixed percentage of the whole in each interval Its reproductive base gets larger and larger over time A graph of population size against time produces a J-shaped growth curve This type of growth cannot continue indefinitely – sooner or later required resources for life are used up and the population will crash Resources in short supply put limits on population growth Carrying capacity may change in an environment as resource availability changes The world’s human population has surpassed 6.6 billion Through expansion into new habitats, cultural intervention and technological innovation, the human population has temporarily skirted environmental resistance to growth Human growth curve (see Fig. 18.12) Birth rates fall as nations become more industrialized, but their per capita consumption of resources increases. CHAPTER 19 (29): COMMUNITY STRUCTURE AND BIODIVERSITY A] TERMINOLOGY Community Habitat Niche Mutualism Predation Parasitism Symbiosis Coevolution Predator Prey Mimicry Ecological succession Biodiversity Endangered species B] CONCEPTS The structure of a community is determined by physical factors and by the interactions among species within it. Close interactions between species can lead to coevolution Competition has negative effects on both participants The competitive exclusion principle - what is it & how does this relate to invasive introduced species in our environment? Species that have dissimilar resource requirements are more likely to coexist than those having similar needs Predators and prey exert selective pressure on one another By the process of ecological succession, one array of species replaces another in a sequential fashion Primary succession occurs in habitats more or less devoid of life Secondary succession occurs in areas where an existing community has been severely disturbed The current range of global biodiversity is an outcome of an overall pattern of extinctions and slow recoveries For the past forty years, human activities have raised rates of extinction through habitat losses, species introductions, overharvesting and illegal wildlife trading CHAPTER 20: ECOSYSTEMS A] TERMINOLOGY Ecosystem Primary producers Consumers Trophic levels Food chain Food web Biological magnification Greenhouse effect Global warming B] CONCEPTS In an ecosystem energy flows in one way through organisms while nutrients are cycled among organisms An organism’s trophic level describes how many steps it is from the ecosystem’s energy source With each energy transfer, some of the energy is lost as heat. These losses limit the number of trophic levels in ecosystems Ecologists measure the amount of energy and nutrients that enter an ecosystem, the amounts captured, and the proportions stored in each trophic level Atmospheric concentrations of greenhouse gases trap heat and keep Earth warm enough for life Fossil fuel burning and other human activities add to greenhouse gases and lead to global warming CHAPTER 21: THE BIOSPHERE A] TERMINOLOGY Ozone CFCs (chlorofluorocarbons) B] CONCEPTS Ozone in the upper atmosphere is declining, exposing Earth’s surface to higher levels of dangerous UV radiation A class of human made chemicals called CFCs are the main destroyers of the ozone layer
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