Bio - All Units Study Notes Review

Atom: the smallest whole unit of matter – compose of subatomic particles – protons and neutrons located in the nucleus, electrons located in energy shells surrounding the nucleus Element: pure substance composed of all of the same type of atom – eg. O2 Compound: made up of 2 or more atoms of different elements bonded together in a fixed ratio – pure substances because they have the same type of particles – eg. H2O form when atoms transfer electrons or share electron pairs Molecule: formed when atoms join together – could be either an element or a compound

Symbiosis: a situation in which two organisms live in close contact and at least one benefits

-­‐ Mutualism: a situation in which two organisms live in close contact and both benefit

-­‐ Parasitism: a situation in which one organism lives in or on another organism and feeds on that organism (eg. Lice)

-­‐ Commensalism: a situation in which two organisms live in close contact; one benefits and the other is not affected (eg. Ivy growing on tree trunk)

Invasive species: species introduced by humans into new environments with unforeseen consequences Monoculture: crops grown in large fields containing a single kind of plant Climate change: large quantities of greenhouse gases produced and emitted that trap thermal energy in the atmosphere Extirpation: habitat loss and pollution which can lead to the loss of a species from a particular region – isolated habitat loss Sustainability: how ecosystems support organisms, remain diverse and productive now, without compromising future generations’ use helps an ecosystem to be more resistant to change – more feeding relationships, more niches filled, more nutrient cycling Cytoplasm: jelly like fluid inside cells – surrounds organelles and contains a “soup” of important chemicals needed for cell processes Vacuole: membrane sacks – store food and water (and in plants, maintain cell shape) Lysosome: vacuole with digestive enzymes – breaks down food and involved in apoptosis (controlled cell death)

�1

Cell membrane: membrane filled with proteins and enzymes – control what goes in and what comes out of the cells, separates cell from external environment Endoplasmic Reticulum: system of tubes made from membranes – transports proteins and other material throughout the cell Ribosome: very small structures made of DNA and protein usually found on ER – make proteins by “reading” genetic code Golgi body: membrane tubes in a bundle with buds of membrane coming off – sorts, modifies, packages, and ships proteins Mitochondria: oval-shaped organelle with a double membrane – the “powerhouse” of the cell; produces energy from food (sugars) – performs cellular respiration Nuclear Membrane: membrane around the nucleus that is very porous – allows the genetic code to be communicated with the ribosomes and allows other materials in and out of the nucleus Nucleus: circular structure with a membrane – holds and protects the chromatin Nucleolus: circular structure inside nucleus – makes ribosomes Chromatin: DNA bundled in the nucleus with proteins – codes for proteins (genetic code) – chromosomes allow for DNA to be packaged Centriole (in animals only): two perpendicular bundles of tubes – involved in cell division Chloroplast (in plants only): oval-shaped organelle filled with stacks of protein – main site of photosynthesis (makes sugar to fuel mitochondrion) – chlorophyll in chloroplast allows cell to trap sun’s energy for photosynthesis Cell Wall (in plants only): thick, geometric, tough/hard outer covering of the cell – maintains structure of plant cell – separates cell from external environment Flagellum/cilia: whip-like tail – used for locomotion Cell cycle: entire period of a cell’s life, including: interphase, G1, G2, and mitosis Unicellular: organisms with one cell Multicellular: organisms with more than one cell Micro-organism: any organism of microscopic/small size (10^-6) – can be seen using a microscope – include bacteria (eg. E coli), fungi (eg. Yeasts), etc. – viewing organisms in magnified form allows us to see the structure, and then understand functions Hypothesis: a predicted, educated answer with a theoretical explanation to a testable question which the experiment attempts to answer – states the relationship between the dependent and independent variable(s) Independent variable: the variable which is manipulated – should only be ONE Dependent variable: the measured variable – responds to changes in the independent variable Controlled experiment: experiment that involves only ONE independent variable and multiple controlled variables, and also involves a control group to serve as a basis for comparison

�2

Chapter 1 Biological diversity: the number and variety of species and ecosystems on earth

-­‐ Species diversity: variety of different species – the quantity of each species contributes to overall diversity

-­‐ Structural diversity: variation in the types of ecosystems and habitats (size, shape, distribution)

-­‐ Genetic diversity: the genetic variability among organisms (usually referring to individuals of the same species)

Importance of Biodiversity: -­‐ more biodiversity = more resistant to change -­‐ More feeding relationships – ensures consistent food supply -­‐ More niches filled means more nutrient cycling -­‐ Maintenance of ecosystem services (eg. Water filtration, oxygen production,

pollination) -­‐ Natural beauty/fascination -­‐ Potential for new discoveries (eg. Medicines) -­‐ Economic benefits (ecotourism/exploitation)

Threats to biodiversity: -­‐ Habitat loss – changes in land use -­‐ Climate change -­‐ Over-exploitation -­‐ Invasive species -­‐ Pollution

Biological species concept: species: all organisms capable of breeding freely with each other under natural conditions and producing fertile offspring

-­‐ Disadvantages: some plants undergo hybridization: the cross-breeding of 2 different species, some organisms only reproduce asexually, if species are geographically separate they cannot mate, extinct species cannot mate

Morphological species concept: species: based on morphology-physical appearance and characteristics

-­‐ Disadvantages: significant variation can exist within a species Phylogenetic species concept: based on an organism’s evolutionary relatedness between and among species

�3

-­‐ Disadvantages: evolutionary histories are not known for all species, species can change over time and space (they evolve) - can result in the formation of a new species

Taxonomy: the science of classifying all organisms (living and fossil) -­‐ Challenges: different species can have very similar morphologies, individuals of

the same species can change during different phases of their life cycle, variation occurs between males and females (Sexual Dimorphism)

Dichotomous key: identification that uses a series of paired comparisons to sort organisms into smaller and smaller groups based on various characteristics until the organism is defined Carl Linnaeus: father of traditional taxonomy – based his groupings on similarities among organisms themselves as opposed to where they might live – first to practice Binomial Nomenclature: the formal system of naming species whereby each species is assigned a genus name followed by a specific species name either Greek or Latin, italics, Genus capitalized only Genus: a taxonomic level consisting of a group of species that share similar characteristics Morphology: the science of classifying organisms based on physical appearance and characteristics

-­‐ Advantages: simple and convenient to group based on appearance, cost-effective and efficient

-­‐ Disadvantages: more subjective, may overlook genetic relatedness Evolution: the scientific theory that describes changes in species over time and their shared ancestry Phylogeny: the study of evolutionary relatedness between, and among, species Evidence used to determine evolutionary relatedness:

• Anatomical characteristics homologous structures: biological features that have a common evolutionary origin

• Developmental comparisons stages of embryonic development • Biochemistry eg. Comparing proteins in organisms • DNA (a type of biochemistry) -­‐ Advantages: not limited to a set number of taxonomic ranks, accurate because

DNA is not influenced by the environment -­‐ Disadvantages: may require fossil analysis, in many cases the DNA of extinct

species is not available, expensive and may take long time Phylogenetic tree: a diagram depicting the evolutionary relationships between different species or groups Clade: a taxonomic group that includes a single common ancestor and all its descendants

�4

Cladogram: similar to a phylogenetic tree in that it shows evolutionary relatedness, but are more commonly hypotheses of evolutionary relatedness based on characteristics Hierarchy of Groups: Domain added only in 1996 by Carl Woese - Eubacteria, Archaea, Eukarya Kingdom Eubacteria, Archaea, Protista, Fungi, Plantae, Animalia Phylum Class Order Family Genus Species

Chapter 2

�5

Prokaryote: single-celled organism that does not contain membrane-bound organelles or a true nucleus – DNA present in nucleoid region – one circular chromosome – cells usually divide by binary fission (splitting in 2), asexually – mostly anaerobic Eukaryote: any organism whose cells contain membrane-bound organelles – some eukaryotic organisms are single-celled, other are multicellular – DNA in nucleus – multiple linear chromosomes – cells divide by mitosis – can reproduce sexually or asexually – mostly aerobic

Characteristics used to Group Taxon: -­‐ Cell type (eukaryote vs. prokaryote) -­‐ Nutrition (autotroph vs. heterotroph) -­‐ Number of cells (unicellular vs. multicellular) -­‐ Cell wall composition (peptidogylcan – positive or negative gram stain) -­‐ Type of reproduction (asexual vs. sexual) -­‐ Environment (with or without oxygen)

Archaea Eubacteria Pro.sta Fungi Plantae AnimaliaBody  form unicellular unicellular Uni  &  mul4 mul4 mul4 mul4Cell  wall Present  -­‐  

glycoproteinPresent  -­‐  pep4doglycan

Mostly  absent

Present  -­‐  chi4n

Present  -­‐  cellulose

absent

Feeder  type Auto  &  hetero Auto  &  hetero Auto  &  hetero

hetero auto hetero

Method  of  gaining  nutri.on

Absorp4on,  photo  or  chemosynth.

Absorp4on,  photo  or  chemosynth.

Absorp4on,  photo  or  inges4on

Absorp4on  –  “Extracellular  diges4on”

photo inges4on

Mo.lity Present  in  some

Present  in  some

Present  in  some

Absent  -­‐  immo4le

absent Present  

Reproduc.on Asexual  (by  binary  fission  or  fragmenta4on  –  one  part  breaks  off)

Most  asexual  (binary  fission),  Some  sexually  by  conjuga4on

Asexual  &  sexual  (alterna4on  of  genera4ons

Sexual  and  asexual

Asexual  and  sexual  (alterna4on  of  genera4ons

sexual

Mitochondria absent absent present present present present

Nervous  System

absent absent absent absent absent present

Examples Methanogens,  extreme  thermophiles,  extreme  halophiles

E.  coli,  cyanobacteria

Euglena,  amoeba,  and  algae

Mushrooms,  bread  molds,  yeast

Ferns,  mosses,  flowering  plants

Sponges,  worms,  insects,  mammals

�6

Autotrophs: “self feeders” – synthesize their own food through photosynthesis or by breaking bonds in inorganic compounds

-­‐ Can add a prefix to further classify how an organism obtain energy: photo means using light (by performing photosynthesis) and chemo means using chemical compounds

Heterotrophs: “another” – consumes other organisms for nutrients Peptidoglycan: a chemical present in some cell walls that can be used to classify organisms – if a cell wall contains many layers of peptidogylcan it will stain positive and is called “Gram-positive” – thinner cell walls have little or no peptidogylcan, will have outer membranes, and do not show stain (“Gram-negative”) Aerobic: requires molecular oxygen for growth and development Anaerobic: do not require or live in oxygen

-­‐ Obligate anaerobes: die in oxygen -­‐ Facultative anaerobes: can grow in either condition

Types of Archaea

Characteristics of Bacteria cell: -­‐ Plasmids: small loops of DNA often found in prokaryotic cells that contain a

small number of genes – transferred in conjugation -­‐ Capsule: an outer layer on some bacteria, provides some protection for the cell

– reduces water loss, resists high temperatures, and helps keep out viruses and antibiotics

Shapes of Bacteria: Cocci: round resists drying Bacili: rod-shaped increased surface area for nutrient absorption Sprilli: spiral-shaped easier movement, locomotion Diplo = pair Strepto = chain Styphlo = cluster (like grapes)

Eubacteria Reproduction:

Methanogens Low  oxygen/anaerobic  –  high  methaneExtreme  halophiles High  salt/saline  environmentsExtreme  thermophiles Extremely  hot  environments  (70  to  90  C)

Psychrophiles Extreme  cold  (-­‐10  to  -­‐20  C)Acidophiles Very  acidic

�7

Binary fission (asexual): prokaryotic cell DNA replication cell elongation septum formation 2 identical daughter cells – advantages: exponential growth, one parent needed, conserves energy – disadvantages: no genetic diversity, higher risk for extinction, rapid reproduction leads to higher mutation rates and competition Conjugation (sexual): pilus forms between 2 cells, DNA is transferred from one cell to the other – increase likelihood that cells could adapt to changing conditions OR Transformation: when cell takes in DNA from environment and uses it OR Horizontal gene transfer: any process in which one species gets DNA from a different species advantages: allows for genetic variation which increases likelihood of species resisting change – disadvantages: slower, requires more energy, requires a partner, could obtain bad DNA Endospore formation (dormant phase): bacteria develop a small, seed-like structure consisting of a tough outer coating surrounding the DNA and a small amount of cytoplasm – in good conditions, endospore loses coat and bacteria returns to normal growth survive during favourable conditions advantages: likely have a longer lifespan, can resist unfavourable conditions – disadvantages: slow, no growth or reproduction

Serial Endosymbiosis: specifies the relationship between organisms which live on or within a mutually beneficial relationship – the process through which eukaryotic cells evolved Endosymbiont: the cell that lives within another/the host cell

-­‐ Ancestral prokaryote cell formed nucleus through infolding of plasma membrane -­‐ Mitochondria ancestor was an aerobic heterotrophic prokaryote, was engulfed

and became the endosymbiont within the larger anaerobic prokaryote -­‐ Chloroplast ancestor was a photosynthetic prokaryote that was engulfed and

became the endosymbiont Evidence of this:

-­‐ m & c have their own internal DNA (and its circular) -­‐ both have genes similar to those of bacteria, their ribosomes are similar too -­‐ both divide not by mitosis, but by binary fission like bacteria -­‐ both are appropriate sizes to be descendants of bacteria and both have

membranes -­‐ both move freely about the cell

Protista: extremely diverse characteristics, first eukaryotes, most aquatic organisms – organisms in the kingdom are classified as Protista mainly because they do not fit into any other Kingdoms – most unicellular, but some multicellular too - some pathogenic (eg. Malaria)

�8

-­‐ Protozoa: name means “first animals” – most organisms of this group engulf their food euglenoids, ciliates, and apicomplexa

-­‐ Algal protists: these are the eukaryotic algae – form the base of the food chain for most aquatic habitats – “plant-like” protists diatoms, red algae

-­‐ Fungus - like Protists: slime moulds and water moulds are not closesly related to other protists – slime moulds are decomposers in forested ecosystems, while water moulds decompose algae, leaves, etc. in aquatic ecosystems – some molds are parasitic and grown on other organisms’ skin slime moulds

Reproductive cycle of Protista -­‐ Life cycle consists of two generations which alternate between haploid: one set

of chromosomes (or genetic material) called a gametophyte, and diploid: 2 sets called a sporophyte

-­‐ Gametophytes fuse in fertilization and develop into sporophyte, then cycle repeats

Euglenoids -­‐ Unicellular  autotrophs  -­‐ 2  flagella  for  moving  -­‐ Outer  surface  covered  in  s4ff  proteins

Ciliates -­‐ Unicellular  heterotrophs  -­‐ Many  cilia  and  no  cell  walls

Apicomplexa -­‐ Unicellular  heterotrophs  -­‐ No  cell  wall  -­‐ All  are  parasites  of  animals

Diatoms -­‐ Unicellular  autotrophs  -­‐ Move  by  gliding  -­‐ Covered  by  glass-­‐like  silica  shells

Amoebas -­‐ autotrophs  -­‐ Some  have  hard  outer  skeletons  -­‐ Move  by  extensions  of  the  cytoplasm  called  pseudopods

Slime  Moulds -­‐ Heterotrophs,  decomposers  -­‐ Life  cycles  have  unicellular  and  mul4cellular  stages  -­‐ Move  with  flagella  or  pseudopods

Red  algae -­‐ Almost  all  mul4cellular  –  autotrophs  -­‐ No  cilia  or  flagella  -­‐ Cell  walls  made  of  cellulose

�9

Chapter 3 EVOLUTION FROM WATER TO LAND: archaea, bacteria and protists live in mostly aquatic environments - algal protists and fungi are multicellular in comparison to archaea, bacteria and other protists - fungi are multicellular and heterotrophic - plants are autotrophic and fungi are heterotrophic

Uses for fungi: major decomposers on earth, important in ecosystems for nutrient cycling – help plants obtain nutrients from soil – most terrestrial – more than 100,000 described species -some are pathogenic, cause animal and plant diseases – food production for humans eg. Mushrooms, bread, and alcohol – some used for medicines eg. Penicillin – symbiotic relationships

Phylums of Fungi

Advantage Disadvantage

Water sufficient moisture, no need to conserve water, moderate temperatures

gases must be dissolved, therefore lower concentration, lower light, danger of water freezing

Land higher available gas concentration, high light intensities

dry, requires waterproof coating (cuticle), greater temperature extremes, must be supported against gravity, embryo must be protected (seed/spore)

Chytridiomycota -­‐ Only  fungi  with  swimming  spores  -­‐ Most  are  saprophytes  -­‐ Can  be  single-­‐  or  mul4cellular

Zygomycota -­‐ Most  are  soil  fungi  -­‐ Many  parasi4c  –  some  have  commercial  uses  (eg.  Bread)

Glomeromycota All  form  symbio4c  rela4onships  with  plant  rootsAscomycota -­‐ Many,  such  as  yeast,  are  useful  to  humans  

-­‐ Some  cause  serious  plant  diseasesBasidiomycota -­‐ Include  mushrooms,  puballs  

-­‐ Most  decomposers  -­‐ Some  form  symbio4c  rela4onships  with  plants

�10

Characteristics: -­‐ Hypha: a thin filament that makes up the body of a fungus composed of long

tubes of cytoplasm containing many nuclei – cytoplasm is contained by a cell wall made of chitin – tubes separated into cell-like compartments by septa – contain large pores

-­‐ Mycelium: a branched mass of hyphae -­‐ Chitin: a complex chemical found in the cell walls of fungi and in the external

coverings of insects and crustaceans such as lobsters and crabs

Extracellular digestion: Fungi grow next to their food source - release digestive enzymes into the environment – enzymes digest the food, then the fungi absorb the nutrients through the cell membranes of the hyphae Life cycle: nuclei are haploid, contain one set of chromosomes – spores contain a haploid nucleus, germinate and produce hyphae with single nuclei separated by septa – when 2 hyphae come into contact, cells can fuse forming a dikaryotic cell: containing 2 separate nuclei – cell then grows into a new mycelium, two haploid later fuse, forming a zygote – zygote undergoes meiosis: single cell gives rise to four haploid daughter cells (spores) – spores released into environment, germinate and the cycle continues

Mycorrhizae: a symbiotic relationship between a fungus and a plant root – hyphae grow around and within root cells of plant – fungus supplies plant with needed nutrients (eg. Phosphorus and copper) and plant provides fungus with energy-rich food molecules

3.2 The Plants

• Why are plants important? • Plants are producers of food • Give us oxygen • Without plants to supply food through photosynthesis there will be little life on earth • Classification and Phylogeny • Plants are thought to have evolved from charophytes (a group of green algae in the protist kingdom) • This is because both contain chlorophyl A and chlorophyl B and share pigments • Both types of organisms also start cytokinesis forming a cell plate • Characteristics • Multicellular eukaryotes • autotrophic, photosynthetic • immobile • Cell walls made of cellulose • Life cycles of plants are very different from animals

�11

•protected embryo Reproduction: alternation of generations - diploid generation is called sporophyte - haplid generation called gametophyte - gametophytes fuse in fertilization and develop into zygote, then cycle repeats Group 1 - Non-vascular plants: 3 phylum --> bryophytes (mosses), anthocerophytes (hornworts), and hepatophytes (liverworts) - no vascular tissues (no xylem or phloem) - transport nutrients via absorption - no roots - rhizoids: small root-like structure which develop from lower surface - produce swmming sperm in antheridia and eggs in archegonia Group 2 - Seedless plants: 4 phylum --> psilotophytes (whisk fern), lycopodophytes (club mosses), sphenophytes (horsetails), pteriophytes (ferns) - leaves, roots, stem, vascular tissues Group 3 - Gymnosperms (cone-bearing plants): 4 phylum --> conifers (pine, firs, spruce and cedars), cycadophytes, gnetophytes, ginkgophytes - seeds are exposed on cone scales (gymnosperm --> naked seed) - vascular system/specialized tissues Group 4 - angiosperms (flowering plants): 1 phlyum --> anthophyta - seeds protected within the body of a fruit - vascular system - reproduction relies on pollination - 2 larger classes based on cotyledon: monocots (1 seed leaf), and dicots (2 seed leaves) Human conditions that can threaten plants: climate change, overharvesting, pollution, urbanization

Animals: no cell wall - motile - sexual reproduction - most have tissues/organs - multicellular, specialized tissues - distinct body plan (symmetry) - to classify: most do not have feather, fur or scales - most do not have bones

-­‐ Germ layers: layers of cells in a developing embryo that gives rise to specialized tissues --> ectoderm (outer layer - produces skin, nerve and sensory organs), endoderm (inner layer - lungs, liver, pancreas, bladder and gut lining), and mesoderm (middle layer - muscles, blood, kidneys and reproductive organs)

-­‐ Classifying based on body symmetry: assymetrical OR radical symmetry: bodies organized equally around a central vertical axis OR bilateral symmetry: form mirror image along one vertical plane

-­‐ Invertebrates: no back bone - includes: sponges, cnidarians, mollusks, worms, anthropods and echinoderms

• PROTOSOMES (mouth forms before anus in embryo, bilateral symmetry) - • DEUTOROSTOMES (bilateral symmetry and anus forms before mouth in embryo) -

-­‐ Vertebrates: internal skeleton - includes: fish, amphibians, reptiles, birds and mammals

• Chordates: internal skeleton of bone and cartilage (contain notochord)

Viruses: -­‐ core: located in center of virus, contains DNA or RNA and proteins -­‐ Capsid: made of protein and form shell around core, protects DNA from enzymes

of host cell -­‐ Matrix: layer between capsid and envelope

�12

-­‐ Envelope: consists of lipids stolen from cell membrane of host cell --> not all viruses have capsid or envelope, but all have genetic information

• UNIT 2 Chromosome: DNA coiled/condensed around proteins – chromosomes are visible under the microscope by the end of prophase Centromere: a region on a chromosome (composed of DNA and proteins) – the centromere is a point of attachment for the spindle fibres and sister chromatids Chromatid: an identical copy of a chromosome attached to the “parent” chromatid at the centromere --> referred to as “sister chromatids” only when attached Centriole: a cellular organelle used during cell division – barrel-like structures that are used to form spindle fibres Spindle fibre: a protein component that attaches the centriole to the centromere Nuclear membrane: a membrane barrier that separates the nucleus from the cytoplasm – the nuclear membrane protects the DNA Nucleic Acids: contain the genetic code for life – cells and organisms use info. To code for protein, coordinate development, and determining individual characteristics of organism – hereditary information is contained in genetic code – variation in N-containing bases allows for this code – DNA stores information RNA is used as an intermediary, forms a complement/ template to the DNA code through complementary base pairing ribosomes read RNA and create proteins

-­‐ Nucleotide: composed of: 1) a phosphate group, 2) a pentose sugar, (which together alternate repeatedly to make up the sugar-phosphate backbone), and 3) a nitrogenous base N-containing bases of complementary nucleotides are bonded together by Hydrogen bonds in the interior of each strand

-­‐ Purines: Adenine and Guanine are double rings -­‐ Pyrimidines: Thymine/Uracil and Cytosine are single rings -­‐ A purine will always pair with a pyrimidine known as complementary base

pairing -­‐ DNA strands run in opposite directions to one another known as

“antiparallel” – ensures proper orientation and allows H-bonding to occur

Chromatin: genetic material in the nucleus that appears as an uncondensed long thin tangled mass of fibres DNA wrapped around histone proteins

DNA RNASugar  is  deoxyribose Sugar  is  riboseDNA  is  double  stranded RNA  is  single  strandedN-­‐containing  bases  are:  A,  T,  C,  G N-­‐containing  bases  are:  A,  U,  C,  GCodes  for  RNA Codes  for  protein

�13

Cell cycle: the entire cycle of a cell’s life Interphase: cell undergoes normal daily processes and growth – DNA in the form of chromatin - just before cell division, DNA is replicated – 90% of the cell cycle – made up of: 1) G1, phase 2) S phase, 3) G2 phase most active growth in interphase, and specifically, G1 G0 phase: “cell cycle arrest” – cell exists the cell cycle, most likely because there are not enough nutrients for growth or division can re-enter the cell cycle at any point G1 phase: “Gap 1” – cellular contents, excluding the chromosomes, are duplicated S phase: “DNA synthesis” – each of the chromosomes is duplicated by the cell G2 phase: “Gap 2” – cell double checks the duplicated chromosomes for error, making any needed repairs Mitotic phase: composed of mitosis and then cytokinesis Mitosis: cell division – prophase, metaphase, anaphase, and telophase Prophase: longest phase in mitosis – fluid transitions from early prophase to mid prophase to late prophase (prometaphase) – nuclear membrane and nucleolus disassemble, chromatin coils into strands called sister chromatids (joined by centromeres) – centrioles begin moving to poles and send out spindle fibers (beginning to form “centrosome” complex) Prometaphase: centrosome complex becomes more defined and elaborate – spindle fibers from both asters penetrate what used to be the nuclear region and attach to centromeres on sister chromatids via their kinetochore: a structure associated with specific sections of chromosomal DNA at the centromere – refers to the attachment Metaphase: chromatids line up along the equatorial plate of the cell Anaphase: sister chromatids separate and move to opposite ends of cell along spindle fiber tracks (now called chromosomes) Telophase: centrosome and spindle fibers disassemble – nuclear membrane and nucleolus reform – chromosomes uncoil to chromatin – cell membrane begins to pinch in Cytokinesis (not part of mitosis): process through which cell membrane pinches into two identical daughter cells cell then returns to Interphase

-­‐ Animal cell: cleavage furrow forms as cell membrane pinches in and cells separate

-­‐ Plant cell: cell plate (cell membrane & cell wall composition) forms between nuclei

Sexual Reproduction: fusion of 2 sex cells – genetic makeup is combination of both parents

-­‐ Disadvantages: takes long, requires more energy (finding parent, mating techniques, etc.)

-­‐ Advantages: more genetic diversity

�14

Trait: inherited characteristics – parents give their offspring information in form of hereditary units called genes: a specific sequence of DNA that codes for a trait tens of thousands of genes inherited from our parents make our genome Hereditary units: humans have 46 chromosomes in all Somatic (body) cells – 23 chromosomes in each Gamete (sex cell) – one chromosome contains hundreds of thousands of genes, each of which is a specific region on the DNA molecule Locus: a gene’s specific location along the length of a chromosome Life cycle: viewing history of an organism from conception to the production of its own offspring Homologous Chromosomes: chromosomes that make up a pair, and share: same length, same centromere position, same staining pattern (same types of genes) one homologous chromosome from each pair is contributed from each parent

-­‐ * Exception - Sex chromosomes: females have X and X – males have X and Y -­‐ All chromosomes other than sex chromosomes are called autosomes

Gametes: sex cells, or sperm or egg cells – each has 22 autosomes and one X or Y chromosome – haploid cells (n = 23) – union of gametes, one from male and one from female, forms a zygote: first cell of new organism; a fertilized egg – zygote is a diploid Meiosis: also known as “reduction division” – is the process of reducing chromosome set from diploid to haploid and producing gametes (sex cells) – preceded by Interphase (S phase, and G1 and G2) - divided into Meiosis I and Meiosis II Prophase I: chromatin begins condensing to chromosomes – in a process called synapsis, homologous chromosomes, each made up of 2 chromatids, come together as pairs – each chromosome is now visible as a tetrad, a complex of 4 chromosomes – crossing over: at many places along their length, chromatids of homologous chromosomes are crisscrossed – chromosomes separate and rejoin, transferring some DNA from paternal chromosome to maternal – microtubules penetrate what used to be nuclear region and interact with chromosomes Metaphase I: chromosomes arrange in the middle of the cell randomly (independent assortment), still in homologous pairs – spindle fibres attach to centrosome complex, are responsible for this relocation Anaphase I: homologous pairs are pulled apart to opposite poles, sister chromatids still attached at centromere Telophase I: homologous chromosomes reach opposite poles – cell splits cytoplasm in two and meiosis II begins Prophase II: centrioles are at opposite ends, spindle fibres attach at centromeres Metaphase II: chromosomes align at middle of cell, with each sister chromatid attached to spindle fibres from each pole Anaphase II: centromeres of sister chromatids separate, chromatids are now individual chromosomes which move toward opposite poles

�15

Telophase II: nuclei begin to form at opposite poles of cell and cytokinesis occurs there are now 4 haploid daughter cells Characteristics responsible for genetic variation in each generation:

-­‐ Crossing over -­‐ Independent assortment (when homologous chromosomes line up and

separate, they do so independent of one another, so each cell is a mixture of maternal and paternal in different proportions)

-­‐ *Fertilization ( a 3rd mechanism that can cause variation) Spermatogenesis: creation of sperm cells in males diploid cell begins as spermatogonium: a cell that has not yet received the signal to undergo meiosis – divides, produces spermatocytes – spermatocytes (2n) undergo meiosis and become 4 highly specialized sperm cells (n):

-­‐ “Head” for fertilization of egg cell with DNA -­‐ Lots of mitochondria to produce energy to move -­‐ Flagella for motility -­‐ Very small so can easily be motile

Oogenesis: creation of ova/egg cells – oocytes (2n) undergo meiosis I and form a large secondary oocyte (n), attached to a smaller polar body secondary oocyte undergoes fertilization – meiosis II occurs, then 2 other polar bodies produced, deteriorate, and one large egg cell is produced:

-­‐ No structures for movement, makes it easy for sperm to locate and fertilize -­‐ Very large egg cell as mitosis of a zygote to form an embryo requires lots of

energy and nutrients -­‐ Only ONE cell, because it is not advantageous for humans to have multiple

offspring at once

Nondisjunction disorders: failure of the homologous chromosomes to separate and move to opposite poles during meiosis – results in an abnormal number of chromosomes in the daughter cells

-­‐ Trisomy: 3 homologous chromosomes in place of a pair

Spermatogenesis OogenesisEven  division  of  cytoplasm,  4  sperm  cells  created

Uneven  division  of  cytoplasm,  single  egg  cell  created

Meiosis  can  occur  in  testes  con4nuously  à  unlimited  number  of  sperm  cells

At  birth,  an  ovary  contains  all  cells  it  will  ever  have  that  will  develop  into  eggs

Meiosis  in  males  occurs  con4nuously Long  rest  period  –  at  birth,  meiosis  I  occurs,  and  not  un4l  puberty  do  the  egg  cells  enlarge  and  enter  Prophase  II

�16

-­‐ Monosomy: a single chromosome in place of a pair -­‐ Triploidy: 3 sets of DNA (3n) -­‐ Polyploidy: extra sets of DNA

Chapter 5

Mendelian genetics: Gregor Mendel studied pea plant – “father of genetics” – pea plants are capable of self-fertilization – Mendel could control fertilization by removing the male parts (stamen – gamete: pollen), would already know parents of the new seeds – female reproductive parts: pistil – gamete: ovule easy to use pea plants, b/c:

-­‐ Grow quickly -­‐ Capable of cross and self-fertilization -­‐ Cheap -­‐ Many varieties -­‐ Plants exhibit only one characteristic, never a combination of two

Character: heritable feature that varies among individual plants (eg. Flower colour) Trait: a possible variant for a characteristic (eg. Purple or white flowers) Alleles: alternative versions of genes – account for variations in inherited characteristics for each character, an organism inherits two alleles, one from each parent – the two alleles for each character separate during gamete formation Dominant alleles: if present, they are always expressed – represented by capital letter in Mendelian notation Recessive alleles: only expressed when dominant alleles are not present – lower-case letter Homozygous: an organism that has a pair of identical alleles for a character – these organisms can only pass on ONE allele Heterozygous: organism that has two different alleles for a character – are not “true-breeding” – can produce gametes with one OR the other of the alleles Genotype: the genetic make-up of alleles (eg. GG) Phenotype: the outward expression of the genotype (eg. Green seed)

Mendel’s experiments: created strains of pure-bred plants – mated or “crossed” two pure-bred pea varieties, purple-flowered and white-flowered plants known as the “P Generation” – all offspring, “F1 Generation” had purple flowers (the dominant characteristic) then crossed the heterozygous purple-flowered plants and created the “F2 Generation” produced a 2PP: 2Pp: 1pp genotypic ratio OR a 3 purple: 1 white phenotypic ratio

�17

Monohybrid cross: a cross involving only 2 alleles for a character Test cross: used to find out the genotype of a parent with the dominant trait present – mate the unknown parent with a homozygous recessive parent and the offspring will reveal the genotype (involves 2 crosses 1) homozygous dominant AND 2) heterozygous with homozygous recessive) Mendel’s First Law/Law of Segregation: organisms inherit two copies of genes, one from each parent each allele in a pair separates into a different gamete during meiosis, organisms only pass on one copy of each gene

Mendel’s dihybrid cross: illustrates the offspring genotypes possible when parents differing in two characteristics are crossed Mendel experimented with true-breeding parents of round-seeded, yellow pea plants (RRYY), and wrinkled-seeded, green pea plants (rryy) to create F1 heterozygous plants (RrYy – all round and yellow) F2 phenotypes: 9 yellow/round : 3 green/round : 3 wrinkled/yellow : 1 wrinkled/green Conclusions: characteristics are NOT LINKED (inheritance of seed shape had no influence on inheritance of see colour) Mendel’s Second Law/Law of Independent Assortment: if genes are located on separate chromosomes, they will be inherited independently of one another

Product law: the probability of 2 independent events both occurring is the product of their individual probabilities Discontinuous variation: either/or traits allow for Mendelian patterns of variation to be observed Continuous variation: observed when genes are affected by other gene products (can be additive or negate) often several genes and chromosomes are involved to create an additive effect, so final phenotype is the result of contributions from each allele

Incomplete dominance: a pattern of inheritance where neither allele is dominant over the other one – if both alleles present, blending of traits will appear as an intermediate expression (eg. Red X white flowers will produce pink flowers) - *still supports law of independent assortment* Co-dominance: occurs when both alleles for a trait are dominant – both variations expressed equally if present (eg. A brown AND white-spotted cow) – eg. Sickle cell anemia – HbSHbS have C-shaped sickle cells, HbAHbA have normal cells and people with HbAHbS have some normal, some sickle-shaped so they are immune from malaria

Multiple alleles: result in non-Mendelian patterns of inheritance– when a trait is controlled by multiple alleles, the gene exists in several allelic forms (each individual will still only have 2 alleles of the many possibilities)

�18

-­‐ Eg. ABO blood groups – 3 alleles: A, B, O – individual will only have 2/3 possible alleles

Multifactorial traits/Continuous variation: results in a gradient of variation for a trait – occurs when a trait is controlled by 2 or more pairs of alleles (alleles can be located on many different pairs of chromosomes) – dominant allele is usually additive

Pedigree: uses symbols that identify males (squares) and females (circles), individuals affected by the trait being studied, and family relationships to represent genetic inheritance graphically Autosomal recessive disorders: genetic disorders caused when individuals have TWO recessive alleles for a trait on autosomes (non-sex chromosomes) – inherit one from each parent- eg. Cystic fibrosis – if heterozygous, are considered a “carrier” of the disorder Autosomal dominant genetic disorders: occurs when individual has AT LEAST ONE dominant allele for a trait – must inherit one from at least one parent – eg. Huntington’s disease

Sex-linked traits: traits controlled by genes on the sex chromosomes X-linked Recessive disorders: a single recessive allele on a male’s X chromosomes is expressed in his phenotype, but a female must have two recessive alleles to be affected men have Y chromosome, so no potential to mask recessive allele on x-chromosome - females have two X-chromosomes, if they are heterozygous they are a carrier more males than females affected Point mutation: a small-scale change in the nitrogenous base sequence of a DNA – mutation may be beneficial, harmful or neutral (having no effect on organism)

-­‐ Base-pair substitution: one nucleotide replaced by a different nucleotide -­‐ Insertion: a nucleotide is added to sequence -­‐ Deletion: one nucleotide is eliminated

Chromosome mutation: an error that involves an entire chromosome or a large part of a chromosome – eg. Non-disjunction disorders]

-­‐ Deletion: gene/part of chromosome deleted

Genotype  (superscripts) Cell  appearance Phenotype

IAIA  or  IAIO Triangle  an4gens Type  AIBIB  or  IBIO Circular  an4gens Type  BIAIB Circle  and  triangle  an4gens Type  AB

IOIO No  an4gens Type  O

�19

-­‐ Inversion: part of chromosome flipped/reinserted backwards -­‐ Translocation: part of chromosome spliced out and reinserted at different loci -­‐ Duplication: segment is repeated

Spontaneous mutation: a mutation that is not caused by any outside factors; occurs randomly – occurs in mitosis or meiosis when replicating DNA Induced mutation: a mutation that occurs because of exposure to an outside factor – eg. Second-hand smoke increases the chance of developing lung cancer, UV rays increase chance of skin cancer Antibiotic resistant: describes strains of bacteria that are no longer susceptible to the effects of antibiotics; are sometimes called “superbugs” and are prevalent to hospital settings might occur because a mutation in the gene that produces a bacterium’s cell wall allows the antibiotic to bind to the cell wall and renders it useless against the bacteria Transposons: segments of DNA that can move along or between the chromosomes Transposition: the process of moving a gene sequence from one part of the chromosome to another part of the chromosome

Unit 3 – Evolution

Evolution: a scientific theory that describes changes in species over time and shared ancestry (history of life on Earth) Theory: attempts to explain observations in the natural world – can be used to explain past/future events – based on evidence – has been repeatedly tested and is widely accepted amongst scientific community – should be able to account for new evidence and be open to revisions as new evidence brought forward On the Origin of Species by Means of Natural Selection or the Preservation of Favoured Races in the Struggle of Life: title of Charles Darwin’s work publishing theory of evolution in 1859

-­‐ Controversial because it differed greatly from the conventional wisdom that species were immutable (unchanging) and created by G-d

Aristotle: proposed unpopular idea of a changing world – ranked species from least perfect to most perfect and called this “Scala Naturae” – proposed that variability was a “mistake” in copying the ideal form Georges Buffan (1707-1788): was puzzled by anatomical features in animals that seemed to serve no purpose – led him to hypothesize that changes occur over time (but he had no way to prove this) James Hutton (1726 – 1797): developed the theory of Gradualism – stems from the suggestion that mountains were formed from slow geological processes over eons of

�20

time – Gradualism states that change on Earth is the cumulative product of slow but continuous processes Georges Cuvier (1769-1832): developed theory of Catastrophism: states, based on rock and fossil evidence, that a series of environmental catastrophes (eg. Noah’s Ark Flood) occurred and that each local catastrophe resulted in the extinction of existing organisms and changes in Earth – noticed that different rock layers (strata) contained different fossils older strata located at the bottom contained older, simpler organisms and younger strata were higher and contained more complex organisms, but the fossils of simple organisms were found in all depths – rock layers contain fossils of many species not above or below them Fossils: remains or traces of organisms from the past – most are found in sedimentary rocks – layers of sand and mud at bottoms of seas, etc. cover over one another, creating layers of rock called strata – erosion may eventually carve through younger strata and reveal fossils

-­‐ Whole/plant animal: relatively rare as preservation of soft and hard body parts is rare

-­‐ Petrification: remains of organisms turned to rock – organic substances decay but water containing minerals soak into the cavities and pores of the hard structures water slowly dissolves original hard parts and replaces with minerals

-­‐ Imprints: outlines of leaves, feathers, footprints, etc. – significance of footprints: depth, size, and distance between provide info about weight, length and bone structure

-­‐ Mould/casts: living organisms buried in mud/clay which hardens (eventually to rock) – body dissolves away, leaving a cavity within the hard material – cavity is filled with stone in shape of original creature

Charles Lyell (1797-1875): developed theory of Uniformitarianism: Earth has been changed by the same processes in the past that are occurring in the present – geological change is slow and gradual rather than fast and catastrophic – natural laws that influence these changes are constants, they operated in the past the same as they do today

-­‐ Also related concept of “artificial selection” in plants and animals (humans choose)

J. Baptiste Lamarck (1744-1829): developed MECHANISMS OF EVOLUTION: thought that new species of more “complex” form progressed from previously existing “lower” forms – did not believe in a common origin but rather that simpler forms mutated to more complex forms due to the environment 2 mechanisms: Use and Disuse: many structures modified because there were not needed/used – Acquired characteristics: characteristics resulting from Use and Disuse were passed on to individual’s offspring now know his theory is flawed, because most features do not

�21

change in response to use, and things which do change are not heritable (eg. Vision) – no alteration of DNA Darwin – why was he so special???

-­‐ Linked ideas from paleontology, geology, geography, and biology with own observations

-­‐ Gave evolution a mechanism: NATURAL SELECTION -­‐ Wealth of evidence since Darwin’s time has supported variants of theory of

evolution -­‐ Other theories were limited because the age of the Earth was thought to be much

younger Beneficial mutation: mutation which increases the reproductive success of an organism; beneficial mutations are favoured by natural selection and accumulate over time create variation within a species, traits passed on through inheritance, change over time Neutral mutation: a mutation that does not result in any selective advantage or disadvantage create variation within species – over time may become advantage or disadvantage Harmful mutation: any mutation that reduces the reproductive success of an individual and is therefore selected against; harmful mutations do not accumulate over time, because these individuals die off, traits are NOT inherited Darwin’s Voyage

-­‐ When 22 years old in 1831, left England and set sail on HMS Beagle as a naturalist to circle globe for 5 years

-­‐ First went to Brazil, collected and recorded species – amazed by rainforest -­‐ Viewed species as part of an unchanging, divine plan created by G-d

Uruguay: looked for living animals and fossils, examined strata of cliffs – discovered bones of huge creatures, the Glyptodon which is a cousin of the armadillo, and Megatherium which is a cousin of the ancient ground sloth – saw similarities between bones and living animals – species were unique to South America – proof of extinction of species Argentina: discovers large rheas (birds) in North, and smaller rheas in the South, wonders if they are 2 species, are very similar – birds do not overlap, one replaces the other, possibly because of competition – also noticed penguins who use wings as fins, steamers who use wings as paddles, and rheas use wings to “sail”/float all flightless, but use wings for different purposes Andes Mountains: inland and 5000 feet above sea level, rocks filled with seashells – all fossils are of water inhabitants – impacted by Lyell’s theory, witnessed an earthquake raise land 3m up - theorized that geological processes like earthquakes had lifted the land upward over time – said earth’s crust is unstable and constantly changing –

�22

because of the 3 m rise for one earthquake, hypothesized the earth must be at least 1 million years old Galapagos: September 1835 – discovers what he thinks are warblers, finches and grosbeaks – are actually all finches with distinct beaks – fascinated by mockingbirds and differences between birds on different islands – seals and big tortoises seem to have no fear of predators Volcanic Islands: keen to explore coral atolls (rings of coral reefs in middle of ocean) – only living coral grows at tops, grows over old coral – said these were volcanic islands that were sinking - realized there was high biodiversity underwater and low species diversity on land – hypothesized this is due to the fact that only a few species could travel to islands (via water or air) Return to England: studies mockingbirds from different islands – some long, curved, some short, straight beaks – different species from different islands – tortoises, finches, etc. as well – wonders if they had changed over time, got to islands from mainland of South America – reads Malthus’s paper on population, understands more offspring are produced than will survive, results in competition for resources – those that do not survive are less suited to environment – Darwin now believed that species can and DO change over time – comes up with mechanism for evolution called natural selection – publishes in 1859 Natural selection: traits that confer an advantage for survival/reproduction become better represented in future generations - Traits that are not advantageous become less represented in future generation because these organisms would not have survived to reproduce

-­‐ 1. Must be inherited variation if there are no differences, which organisms reproduce will be just random chance

-­‐ 2. Environment must favour certain traits over others selection pressures from environment may result from a number of biotic/abiotic factors (eg. Disease, climate, food, predators, etc.)

-­‐ 3. Must be more offspring than can survive, and competition between members of the same species for this to occur, must be limits on resources, maters, predators, etc.

-­‐ 4. Long length of time required Key Ideas: used “descent with modification” rather than “evolution” in book – present forms of life have arisen by descent and modification from an ancestral species – process of modification occurs by natural selection – as populations moved to different habitats, they slowly changed as they adapted to their environment Adaptation: a characteristic or feature of a species that makes it better able to survive and reproduce (pass on genetic information) in its environment Limits to Darwin’s theory:

-­‐ No mechanism for inheritance known

�23

-­‐ No mechanism for variation known -­‐ Actual age of earth still not proven to be 4.5 BYO -­‐ Fossils seemingly “misplaced” or “missing”

Modern Evolutionary Synthesis: combination of Darwin’s theory and the new information about DNA and heredity – mutations recognized as source of variation (new genes) Fossils as evidence:

-­‐ Appear in chronological order – possible ancestors in older rocks (eg. Fish, then amphibians, reptiles, birds, mammals)

-­‐ Transitional fossils exist – shows “intermediates” between species (eg. Archaeopteryx – between birds and reptiles)

-­‐ All organisms do not appear in fossil record simultaneously -­‐ Fossils show relatedness between species, and allow for observation of change

Radiometric dating: used to obtain precise estimates about age of earth/fossils – radioisotopes decay at constant half-life, look at ratio of parent to daughter isotopes to determine age of rocks – relates to evolution by: placing species around certain times, showing age of earth Homologous structures: body parts in different species that have same evolutionary origin but serve different functions (eg. Wings in rheas, steamers and penguins) show relatedness between species, and common ancestors, and change over time

-­‐ Eg. Embryology: during fetal development, similarities between embryos can be seen – the more closely related two organisms are, the more similar their development

-­‐ Eg. Homologous genes: comparative biochemistry provides the strongest support for evolution because it is quantitative, physical evidence and removes environmental factors – the more closely related two organisms are, the more similar their biochemical make-up – more closely related, more homologous genes and more similar genes

Analogous structures: have a common function between species but entirely different structures (eg. Butterfly vs. bat wing) show natural selection (favouring of traits) Vestigial structures: structures that serve no useful purpose in a living organism, but may have served a purpose in the past or does serve a purpose in a related organism (eg. Whales have pelvic bones) show change over time and common ancestry – eg. Pseudogenes: a vestigial gene that no longer codes for a functioning protein Artificial selection: Darwin knew breeders and farmers could choose organisms with desirable traits to produce offspring – through selective breeding, extraordinary diversity can be seen in species shows inheritance of traits, change over time and serves as a parallel to natural selection (selection of traits)

�24

Chapter 8

Microevolution: a change in the frequencies of alleles within a population over time – smallest scale evolution Hardy-Weinberg Principle: the frequencies of alleles in the gene pool will remain constant unless acted upon by other agents – describes genetics of non-evolving populations – provides a method for calculating expected allele frequencies from one generation to the next – provides a reference point with which to compare the frequencies of alleles of natural populations whose gene pools may be changing

-­‐ P2 + 2pq + q2 = 1 -­‐ P = frequency of dominant allele -­‐ P2 = frequency of individuals with homozygous dominant -­‐ q = frequency of recessive allele -­‐ q2 = frequency of individuals with homozygous recessive

p + q = 1 Hardy-Weinberg Equilibrium: populations whose allele frequencies are not changing are NOT currently evolving – for this equilibrium to be maintained, there must be: 1) random mating, 2) no mutations, 3) isolation from other populations, 4) large population size, 5) no natural selection most populations do NOT meet these requirements, so populations are changing Other factors that can contribute to evolution:

-­‐ small populations are more vulnerable to changes in allele frequencies due to random chance events

-­‐ mating is NOT random and preferred mates are more likely to pass their genes on

-­‐ genetic mutations and horizontal gene transfer can occur -­‐ gene flow, (immigration/emigration) can disrupt the occurrence of alleles -­‐ when natural selection occurs, certain alleles are more likely to be passed on to

the next generation than others Selection pressures: selection pressures include predators, food availability, climate, disease, mates (special case), etc. – can vary and result in different patterns of selection Stabilizing selection: favours the intermediate phenotype and acts against the extremes – reduces variation, but improves adaptation to more constant features of a consistent/stable environment (eg. Birth weight in babies) Directional selection: favours the phenotype at one extreme end over the other – results in the distribution of the phenotype shifting in that direction (eg. Pepper moth)

�25

Disruptive selection: takes place when extremes of a phenotypic range are favoured relative to the intermediate – as a result, the intermediate phenotypes can be eliminated from the population (eg. Darwin’s finches’ beaks) Sexual selection: evolution favours small sperm and large eggs because sperm only need to carry genetic information while eggs must have energy for cell division and growth of the embryo – both sexes develop ways to attract a mate – when males and females of the same species look different, we call this sexual dimorphism – many distinct features that we see in animals do not help them to survive, but rather, to help them find a mate and reproduce sexual reproduction, although it requires lots of energy, evolved because it creates variation (BIODIVERSITY) and makes species more resistant to change sexual selection can act: during processes that lead to acquiring mating opportunities (Pre-copulatory - eg. Excluding competitors, attracting and selecting mates, etc.) and during and after mating (post-copulatory – eg. Fertilization choices)

-­‐ Intra-sexual selection: competition between members of the same sex (usually males) for access to mates usually responsible for evolution of male characteristics (eg. Deer antlers, beetle horns, large body size) that provide males with an advantage to fight off competition

-­‐ Intersexual selection: members of one sex, (usually females) choose members of the opposite sex responsible for evolution of elaborate behavioural displays and morphological and behavioural traits (eg. Peacock’s tail)

-­‐ Female parental care: variance in male reproductive success will be large, because female offspring care will not be immediately available for further reproduction and competition for females will increase among males

-­‐ Biparental care: variance in male reproductive success will be lower, since males are engaged more in parental care and will not be pursuing mating opportunities sexual monomorphic species usually arrive, since males and females behave in similar ways

-­‐ Male parental care: variance in reproductive success among females is high – females may evolve secondary sexual characters, to try and monopolize access to one or more males to care for their offspring

Genetic drift: in small populations, the frequency of particular alleles can be changed dramatically by chance alone – genes can drift in or out of a population, however most natural populations are large enough to be unaffected by genetic drift/random chance

-­‐ Bottleneck populations: populations that near extinction as a result of natural disaster or human interference can change the gene pool of a population – bottleneck is a situation in which, as a result of chance, certain alleles are over-represented and others are under-represented – results in reduced variation in the surviving population

�26

-­‐ Founder effect: occurs when small numbers of individuals colonize a new area, the new colony has reduced variation based on founders of the colony alleles carried by the founders are by random chance – in new environment, colony will experience different selection pressures than original parent population did

Gene flow: at different points in history, genes have flowed between populations at a greater or lesser frequency – for example, today global travel and inter-racial relationships are much more common – when continents were joined (Pangaea), genes flowed much more easily than after they divided – gene flow can act to increase the variability of alleles Non-random mating: mating is almost never random – plants and animals much more likely to mate with a partner that is: close by, the same species, and has desirable features

Speciation: formation of a new species from existing species – the formation of a new species is also called Macroevolution can identify new species using the biological-species concept, but also considering: anatomy, physiology, biochemistry, behaviour, genetics, and so, morphological and phylogenetic species concepts also considered Reproductive isolating mechanisms: when two populations becomes reproductively isolated, there is little or no gene flow between them – reproductive isolating mechanisms are either pre- or post-zygotic Pre-zygotic mechanisms: mechanisms which prevent reproduction before a zygote is formed

-­‐ Prevention of mating: -­‐ Ecological isolation – different habitats -­‐ Temporal isolation – different reproductive cycles, seasons, etc. -­‐ Behavioural isolation - different mating signals -­‐ Prevention of fertilization : -­‐ Mechanical isolation – structural differences in reproductive organs -­‐ Gametic isolation – no molecular recognition of sperm and egg

Post-zygotic mechanisms: mechanisms which prevent speciation after zygote is formed

-­‐ Prevention of Hybrids: -­‐ Hybrid inviability/mortality: no embryos develop to maturity (no mitosis) -­‐ Hybrid sterility: baby is sterile – reproductive isolation still exists, genes die out -­‐ Hybrid breakdown: baby viable and can mate with others or parent species, but

next generation produces weak/sterile individuals that do not usually survive Allopatric speciation: evolution of populations into separate species, as a result of geographic isolation – geological processes can fragment a population into two or more allopatric populations (having separate ranges) – eg. Emergence of mountain ranges, movement of glaciers, formation of land bridges, subsidence of large lakes OR small

�27

populations may become geographically isolated when individuals from the parent population travel to new locations Sympatric speciation: evolution of populations within the same geographic area into separate species – this type of speciation is more common in plants – can occur quickly (in one generation) if a genetic change results in a reproductive barrier between the mutants and parent populations – most commonly results from chromosome changes (polyploidy) that change the reproductive barrier between the parent and next generation – can also occur in animals but it is less common because it results from random mating

Evolutionary theory must explain: -­‐ How adaptations evolve in populations -­‐ Origin of new species which results in biological diversity

Pathways of evolution (once new species exists, natural selection will continue to act on that population): Divergent evolution: large-scale evolution of a group into many forms – happens when a population is under different selection pressures – disruption and natural selection continue, resulting in different traits – acts to INCREASE BIODIVERSITY – eg. Vertebrate limbs Adaptive radiation: divergent evolution occurs so quickly or simultaneously from a common ancestral population (or several populations) that a number of distinct but more closely related species are produced – possible as each new species will fill a different ecological niche – adaptive radiation usually occurs as new resources become available – acts to INCREASE BIODIVERSITY – eg. Galapagos finches Convergent evolution: the evolution of similar traits in distantly related species – similar selection pressures and natural selection produces these similarities – eg. Bat, falcon and pterodactyl Co-evolution: one species evolves in response to the evolution of another species (particularly when two species are dependent on one another for survival) – pronounced in symbiotic relationships Speed of evolution Theory of Gradualism: views evolutionary change as slow and steady, before and after a divergence (speciation event) – the thought (pre-1972) was that big changes occur as an accumulation of many small changes – evident in some species in the fossil record (transitional fossils) but there are often instances of new species appearing “suddenly” Punctuated equilibrium: a model of evolution that views evolutionary history as long periods of stasis (no change) that are interrupted by periods of divergence – was suggested by Niles Eldredge and Stephen Jay Gould – suggests most species undergo most of their morphological changes when they first diverge from the parent species – after that, they change relatively little, even as they give rise to other species – explains

�28

why we often see few transitional fossils – speciation will often occur in small isolated populations – this model is more in line with the fossil record

è Both models considered valid – can be applied in different situations, depending on type of speciation event and type of reproductive isolation

Macromolecules

Macromolecule: large polymer made up of many smaller sub-units (monomers) -­‐ Disassembling and assembling of molecules almost always involves enzymes –

proteins that make the process quicker, often referred to as catalysts -­‐ Assembling: anabolic reaction (general type of reaction that involves polymers) –

dehydration synthesis reaction: water is formed from the removal of the functional (hydrogen) group of one of the monomers and the hydroxyl (OH) group of the other monomer – results in a covalent bond between the subunits that possesses an oxygen in the attachment – called an ester bond

-­‐ Disassembling: catabolic reaction (makes monomers) – in the breaking down of large molecules into smaller monomer units – in the presence of water, ester bond is broken (with the help of enzymes) and water is split into components H, and OH – called a hydrolysis reaction

Complex carbohydrates: polysaccharides – made of simple sugar subunits – body’s primary source of immediate energy – excess of carbohydrates are stored in body for later use – can be recognized by “ose” ending – produced by the process of photosynthesis carried out by plants, cyanobacteria, algae potatoes, bread, pasta, fruits

-­‐ primary carbohydrate in living things for energy storage is glucose (monosaccharide – made from photosynthesis) – two other common monosaccharides are fructose and galactose

-­‐ disaccharide: two monosaccharides chemically bond together – form by dehydration synthesis (aka condensation) in which water is produced as the reaction takes place

-­‐ Polysaccharide: carbohydrates can form long chains of monosaccharides bonded together – can be used for energy storage or as structural molecules (in cell walls – cellulose)

Proteins: polypeptides – made up of amino acids – have an amino group on one end and a carboxyl group on the other – there are 20 different side (R) groups making 20 different amino acids – your body can make all but 8 amino acids, these must come from food – Essential amino acids: amino acids your body cannot make from simpler products – combine by dehydration synthesis – small chain of amino acids is called a oligopeptide or dipeptide – amino acids fold in intricate ways, bonding between side

�29

chains – the amino acid sequence is what determines the structure and function of the protein – denaturation: unfolding of 3d structure of protein, causes protein to lose function – can occur when hydrogen bonds broken by temperature and pH changes – most important group of proteins called enzymes: serve as catalysts, help facilitate and speed up chemical reactions in the body eg. Hair, finger nails, blood clots, etc. Lipids: fats, oils, waxes, phospholipids and steroids

-­‐ Fats and oils (triglycerides): hold much more chemical energy than carbohydrates – fats used to store energy in adipose tissue (fat tissue made of adipose/fat cells) – excess macromolecules are converted and stored as fat in adipose cells 2 components: glycerol and fatty acid chains – fatty acid attaches to each hydroxyl group on the glycerol molecule by dehydration synthesis – process releases 3 molecules of water per triglyceride – triglycerides are hydrophobic

-­‐ Waxes: often used by plants and animals as a water-proof coating (waxy cuticles on leaves)

-­‐ Phospholipids: the main component of the cell membranes in the human body – structure is similar to triglycerides – have hydrophilic end that is soluble in water, fatty acid tails in middle, and hydrophobic polar head

-­‐ Steroids: made of 4 carbon rings and a side chain – often used as chemical signalling molecules (hormones) – HGH (anabolic steroids) used to promote

Bonds FaIy  acids  shape

Stacking,  state  and  MP

Examples

Saturated single linear Easily  stacked,  packed  4ghtly  together  –  par4cles  close  together  -­‐  solid  at  room  temperature  –  mel4ng  point  generally  high

Buher,  cheese

Unsaturated  &  Polyunsaturated

Double  bonds Bent/kinked Not  as  4ghtly  packed  –  par4cles  further  apart  -­‐  liquid  at  room  temperature,  lower  mel4ng  point

Vegetable  oil,  canola  oil

�30

muscle gain – cholesterol is an essential component of cell membranes (cell signalling) as well, but too much leads to heart disease

-­‐ Nucleic acids (see nucleic acids in genetics unit notes) Digestive System Alimentary canal = gastrointestinal tract = digestive tract

-­‐ Animals: tube within a tube design – “inner tube” is the digestive tract -­‐ Starts with mouth and ends with anus -­‐ Food is processed along the way so as to: 1) obtain nutrients from food as well

as, 2) energy Nutrient: any chemical compound required to sustain life

-­‐ Macronutrients: carbohydrates, lipids, proteins, and nucleic acids – required in large amounts

-­‐ Micronutrients: minerals and vitamins – required in small amounts -­‐ All come from food

Four components of digestion: 1) ingestion taking in nutrients 2) digestion breaking down organic (carbon-containing) compounds 3) absorption smaller nutrients absorbed into bloodstream 4) egestion waste that is not absorbed is removed from body 5 main organs involved in digestion (food passes through):

-­‐ Stomach -­‐ Mouth -­‐ Esophagus -­‐ Large intestine -­‐ Small intestine

3 accessory organs (food does not actually enter): -­‐ Liver -­‐ Gallbladder -­‐ Pancreas

Types of digestion: Mechanical digestion: chewing, grinding food into smaller pieces Chemical digestion: use of many different digestive enzymes to obtain nutrients from food

Homeostasis: the internal balance or equilibrium maintained by the body despite internal or external changes relates to digestion because the system requires specific conditions for proper functioning – chemical digestion relies on enzymes which work best at very specific temperatures and pH values – body needs energy to maintain homeostasis, energy comes from food Ingestion & Digestion: The Mouth

�31

Incisors: 4 top, 4 bottom teeth – used for biting, nibbling and holding food Canines and Bicuspids: ripping, tearing and piercing Molars: grinding and chewing action of chewing stimulates salivary glands Salivary glands: produce saliva, composed of: 1) enzymes (salivary amylase) which breaks down starches, 2) H2O, solvent that dissolves food particles and lubricates (moistens and softens), and 3) mucous, lubricates food for easier passage in esophagus Mouth: tongue helps roll mashed up food into ball called a bolus – when swallowing, epiglottis ensures bolus does not go into trachea, but rather, esophagus Esophagus: waves of rhythmic contractions push food down into the stomach – 2 types of muscles: Longitudinal muscles, and circular ring muscles circular squeeze inward, and longitudinal push downward contractions called peristalsis The Stomach Sphincters: circular muscles that regulate movement of food into and out of the stomach

-­‐ Gastroesophageal sphincter: food coming in -­‐ Pyloric Sphincter: food going out – thickened muscle region at the junction of

the stomach and duodenum Gastric juices: 3 layers of muscles in the stomach lining continue to physically digest your food – gastric glands produce the gastric juices – stomach contains: 1) acid (HCl), which denatures proteins, 2) mucous, which protects the lining of the stomach, and 3) enzymes (pepsin – needs a low pH to function), which hydrolyzes (breaks down) proteins into smaller polypeptides some absorption of alcohol, medicines and water into the bloodstream occurs directly in stomach Small intestine: divided into 3 regions – main site of chemical digestion and absorption of nutrients large surface area (length and villi: infolding), and enzymes mix of food, water and gastric juices which enters small intestine is called chyme – secretes digestive enzymes: maltase: breaks down maltose into glucose (monosaccharide), and peptidase: breaks down oligopeptides into amino acids

-­‐ Duodenum: U-shaped, shortest and widest region – pancreatic and bile ducts secrete here

-­‐ Jejunum: contains more folds and intestinal glands than the duodenum, breaks down remaining proteins and carbohydrates

-­‐ Ileum: contains fewer and smaller villi – absorbs nutrients and pushes remaining material into large intestine

è Villi: the small intestine, a system of tubes, is covered in millions of these tiny finger-life projections – even individual cells have projections called microvilli – small intestinal glands occupy the spaces between these villi and secrete intestinal juices – each villus has a blood supply (venules and arterioles) that

�32

allow for absorption into bloodstream – lymph vessels (called lacteals) transport materials (mainly fat particles) to the body

Pancreas: produces sodium bicarbonate (a base) to raise the pH of chyme and prevent it from destroying the small intestines – secretes digestive enzymes:

-­‐ Lipase: breaks down lipids (triglycerides) into glycerol and fatty acid chains -­‐ Pancreatic amylase: breaks down starches into maltose -­‐ Trypsin (same as pepsin): breaks down proteins into oligopeptides different

from pepsin in its conditions – pepsin is in acidic stomach, Trypsin is in basic stomach

Liver: produces bile (an emulsifier which dissolves fats) which is stored in the gallbladder – bile salts mechanically break down fats into smaller clusters – lipases can now break the fats down faster into glycerol and fatty acids Large intestine: composed of ascending colon, transverse colon, and descending colon – parts of food which are indigestible make it to large intestine – absorbs water and dissolved minerals from any undigested food – bacteria assist in this as well as produce vitamins K and B12 and some amino acids – remaining material is feces which passes out of the body through the rectum and anus – cellulose is the main component of feces

Nasal passages: tiny hairs and mucus filter out trap dust and particles - entry point for air - warms and moistens air so that gases may be dissolved, and to prevent damage to delicate tissue of respiratory membrane of lungs - capillaries inside warm air Oral cavity: saliva and mucus warm and moisten air to prevent damage to lung tissue and to dissolve gases - entry/exit point for air Pharynx: air travels through - connects/joins oral and nasal cavities (empty space) to larynx (first part of trachea) Epiglottis: small muscular flap in pharynx - closes when digesting food, remains open when breathing so air flows into trachea - glottis is the opening Larynx: vocal chords - thin, flexible membranes which vibrate - make noise/sound Trachea: semi rigid tube of soft tissue wrapped around C-shaped bands/rings of cartilage which make sure trachea does not collapse and airways remain open - lined with mucus-producing cells and cilia which protect lung from foreign matter - passageway for air Bronchus: two main tubes of trachea that lead toward lungs - air travels through to bronchioles - branching increases surface area Bronchiole: small tubes - branching increases surface area - air travels through to alveoli alveoli: cluster of tiny sacs one cell thick surrounded by a network of capillaries - moist membrane filled with fluid, dissolves gases and protects lining, sacs stay full - oxygen diffuses into bloodstream, carbon dioxide diffuses from blood into alveolus Diaphragm: large sheet of muscle located beneath the lungs Purpose of respiration: cellular respiration --> process that occurs in cells that gives/creates cellular energy from glucose

�33

oxygen + glucose ---> energy + wastes (carbon dioxide and water) Respiratory system: gas exchange system - other types: gills in fish, skin exchange in amphibians, spiracles in insects, lungs in mammals - in conjunction with circulatory system, allows oxygen to get to cells of body while getting rid of carbon dioxide waste External respiration: breathing (inspiration and expiration) Internal respiration: production of energy through cellular respiration (make ATP from glucose inside cells) Gas exchange: transfer of gases (CO2 and O2) across a respiratory membrane - CO2 from cells --> blood --> environment - O2 from air --> lungs --> blood --> cells - diffusion: movement of material from areas of high concentration to areas of low

concentration - gases must diffuse across a thin, (for increased efficiency) and moist (to dissolve gases) membrane

- rate of diffusion depends on: - concentration of gases/the concentration difference - larger surface area will increase diffusion speed - thickness of membrane (diffusion can only occur through maximum of a few cells)

Inspiration: diaphragm contracts (moves down) which has the effect of creating more space in the chest cavity - external intercostal muscles contract (while internal intercostal muscles relax), allowing rib cage to expand - lung volume is increased which creates a low pressure environment - low pressure environment in lungs compared to high pressure of air draws outside air into lungs Expiration: diaphragm relaxes (moves up) which creates less space - intercostal muscles allow rib cage to depress (move down and in) - lung volume is decreased which creates a high pressure environment - high pressure in lungs compared to environment pushes air out of the lungs Tidal volume: the volume of gas inspired or expired in a normal unforced breath Inspiratory reserve volume: the maximum volume of gas that can be inspired from the end of a tidal inspiration Expiratory reserve volume: the maximum volume of gas that can be expired beyond the end of a tidal expiration Residual lung capacity: the volume of gas that remains in the lungs after a maximum expiration - not exchanged - kept in lungs to keep them inflated Vital lung capacity: The maximum volume of gas that can be expired after a maximum inspiration (i.e. the biggest volume of air that can be inspired and expired)

Circulatory system: transport system of macronutrients (e.g. glucose), micronutrients, and special nutrients (e.g. oxygen, CO2 and water) - 4 chambers, closed system - transport nutrients, transport wastes - transport oxygen and CO2 to/from lungs - transports immune system products (white blood cells, antibodies) and hormones

(chemical messengers) - maintains body temperature Pulmonary circuit: right side of circulatory system - blood flows from right atrium to right ventricle to the lungs

�34

Systemic circuit: left side of system - blood flows from left atrium to left ventricle to the body

1) blood is oxygenated in the lungs 2) the heart pumps oxygenated blood to the body through arteries 3) the body uses oxygen 4) deoxygenated blood returns to the heart through veins 5) the heart pumps deoxygenated blood to the lungs

Cardiovascular system: blood vessels and heart muscles - heart beat is actually a double pump (lub-dub sound is valves opening and closing) - both atria relax, fill with blood --> called diastole - first pump pushes blood from atria into the ventricles - valves between the atria and ventricles prevent the back-flow of blood - second pump is stronger, because muscle wall is thicker to pump blood further -

pushes blood from ventricles to the lungs and body --> called systole - valve in the pulmonary artery and one in the aorta prevent blood from flowing back into

the ventricles when heart relaxes after each pump --> called semi-lunar valves

1) Right atrium 2) tricuspid A-V valve 3) right ventricle 4) pulmonic semi-lunar valve 5) pulmonary arteries (to lungs) 6) Pulmonary capillaries of right and left lung 7) Pulmonic veins 8) Left atrium 9) bicuspid A-V valve 10) left ventricle 11) aortic semi-lunar valve 12) aorta 13) arteries 14) arterioles 15)capillaries 16) venules 17) veins 18) superior and inferior vena cavas (back to right atrium)

Blood pressure: the force of blood pushing on the walls of the arteries - keeps blood flowing in one direction - measured using a sphygmomanometer which reads two numbers: - systolic pressure: value on the gauge when blood enters top atria - diastolic pressure: value on the gauge when blood enters ventricles

Arteries: carry oxygenated blood away from heart --> exception: pulmonary artery: carries deoxygenated blood from the heart to the lungs

�35

Veins: carry deoxygenated blood towards heart --> exception: pulmonary vein: carries oxygenated blood from lungs to heart - thin walls, large circumference - are valves in veins which work together with muscles to prevent back flow of blood along pathway Capillaries: smallest vessels - materials exchanged between blood and body - arteries branch off into networks of extremely thin vessels to deliver nutrients and oxygen and take in wastes like carbon dioxide - networks called capillary beds/capillary networks

plasma: fluid medium through which solid blood components along with dissolved gases, nutrients, wastes and hormones are transported throughout the body - contains dissolved proteins (e.g. protein for blood clotting) erythrocytes (red blood cells): contain hemoglobin, molecule that enables the cell to bind oxygen molecules - do not have nucleus in mature stage, allow to carry more hemoglobin leukocytes (white blood cells): protect body against invading microorganisms and toxins - much fewer in number than red blood cells - contain nucleus - different types - some produce antibodies, others engulf and digest microorganisms using enzymes platelets: small fragments of larger cells produced from cells in bone marrow - initiate blood clotting - irregularly shaped - move through smooth blood vessels when resting - become active and rupture if they encounter a sharp edge/cut in blood vessel - when membrane breaks, releases substance that reacts with proteins in plasma to create a mesh of fibers that prevents further blood flow - eventually contract and close wound in blood vessel

�36