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Saturday, April 25, 2009

BASIC PRINCIPLES OF BIOLOGY

  1. Biology: the study of life
    1. Characteristics of life include:
      1. metabolism
      2. reproduction
      3. growth
      4. movement
      5. responsiveness
      6. complex organization
    2. Evolution of life
      1. Natural Selection
        1. survival of offspring best adapted to living conditions
        2. more offspring produced than could survive
        3. offspring most often are not identical; show variations based on gene differences
        4. survivors (able to adapt) to age of reproduction pass genes to next generation
        5. nature selects offspring; shapes evolution of species
      2. Artificial Selection
        1. humans select traits for domesticated animals and farm crops
  2. Cytology: The study of cells
    1. All living things are composed of cells; come from cells
      1. cell size: small to maximize surface area to volume ration; regulate internal cell environment
      2. cell (plasma) membrane: fluid-like phospholipid bilayer, proteins, and glycoproteins
      3. cell wall: outside of cell membrane in some organisms (composed of carbohydrate [e.g., cellulose or chitin] or carbohydrate derivitive [e.g., peptidoglycan]
      4. cytoplasm: material outside of nucleus
        1. site of metabolic activity
        2. cytosol: solutions with dissolved substances such as glucose, CO2, O2, etc.
        3. organelles:membrane-bound subunits of cells with specialized functions
      5. cytoskeleton: supportive and metabolic structure made of microtubules, microfilaments, and intermediate filaments
    2. Eukaryotic Cells: complex organization with membrane-bound organelles including:
      1. Nucleus -DNA/chromosomes, control cellular activities via genes
      2. Nucleolus - located within nucleus; site of ribosome synthesis
      3. Rough endoplastic reticulum- involved in protein synthesis with ribosomes
      4. Smooth endoplastic reticulum- involved in lipid synthesis without ribosomes
      5. Golgi apparatus- packaging center for molecules; carbohydrate synthesis
      6. Lysosome- contains hydrolytic enzymes for intracellular digestion
      7. Peroxisome- involved in hydrogen peroxide synthesis and degradation
      8. Chloroplast- site of photosynthesis
      9. Chromoplast- non-green pigments
      10. Leukoplast- stores starch
      11. Mitochondrion- ATP production
      12. Vacuole- general storage and space-filling structure
    3. Prokaryotic Cells: simple cellular organization with no nucleus or other membrane-bound organelles
  3. Cell Reproduction -- Mitosis & Cytokinesis
    1. Reproduction Steps
      1. Mitosis - four stages of division of nuclear material
        1. Prophase - chromosomes condense and organize; nuclear membrane and nucleoli disappear; spindle apparatus assembles and attaches to centromeres of duplicated chromosomes
        2. Metaphase - spindles line up duplicated chromosomes along equator of cell, one spindle to each half or chromatid of duplicated chromosome
        3. Anaphase - centromere of each duplicated chromosome is separated and sister chromatids are pulled apart
        4. Telophase - chromosomes uncoil; nucleoli reappear; cytokinesis occurs and the two genetically identical daughter cells are produced
      2. Cytokinesis - division of remaining cellular contents of cytoplasm
    2. Cell Reproduction Cycle -- 4 stages
      1. G1 -active growth and metabolism
      2. S -DNA synthesis and duplication
      3. G2 -synthesis of molecules in preparation for cell division
        1. Stages G1, S, & G2 are collectively referred to as Interphase. Interphase chromosomes are referred to as chromatin, a diffuse, loosely scattered arrangment of chromosomes.
      4. Mitosis & Cytokinesis
        1. Mitotic chromosomes in the Mitosis/Cytokinesis stage are highly condensed and coiled; distinct.
  4. Organismal Reproduction -- Meiosis
    1. Sexual Processes
      1. Sexual reproduction - fusion of genetic material (gametes) from two parental organisms
      2. zygote (fertilized egg) must have proper chromosomal numbers; each gamete must have half or haploid (N) of original diploid (2N) amount of DNA
      3. Meiosis - reduces chromosome number by half and results in new genetic combinations in the gametes
    2. Meiosis -- 2 stages preceded by Interphase; many meiotic events similar to mitosis
      1. Meiosis I
        1. Prophase I -chromosomes condense and organize; matched or homogeneous chromosomes (one maternal and one paternal in each pair) are physically paired. Segments of chromatids can cross over within each chromosome pair
        2. Metaphase I - homologues line up at equator
        3. Anaphase I - homologues separated into two groups, each group having a mixture of maternal and paternal chromosomes
        4. Telophase I - new haploid nuclei forming for two new daughter cells
        5. Interkinesis - no replication of DNA occurs because each chromosome is still duplicated and consists of two chromatids (although crossing over results in some chromatids with maternal and paternal segments)
      2. Meiosis II
        1. Prophase II - chromosomes condense
        2. Metaphase II - chromosomes line up at equator
        3. Anaphase II - chromatids of each chromosome are separated
        4. Telophase II - each daughter cell from meiosis I will form two more two more cells for a total of four cells
    3. Faunal/Floral game to genesis
      1. Animals - meiosis occurs in germinal tissues; called spermatogenesis in males and oogenesis in females. each results in a gamete
      2. Plants - process is similar except mitotic divisions may follow meiosis to produce gametes
  5. Molecular Genetics
    1. Genes, DNA & Nucleic Acid
      1. Gene functions:
        1. To be preserved and transmitted.
        2. To control various biological functions through the production of proteins (i.e., large, complex sequences of amino acids) and RNA.
      2. Gene structure: -two types of nucleic acids:
        1. Deoxyribonucleic acid (DNA)
        2. Ribonucleic acid (RNA)
      3. Nucleotides: - the components of necleic acids -- three subunits:
        1. Sugar (deoxyribose in DNA; ribose in RNA)
        2. Phosphate
        3. Nitrogenous base (5 possible bases)
          1. In DNA, the nucleic acid of chromosomes, four nitrogenous bases are found: adenine (A), guanine (G), cytosine (C), and thymine (T).
          2. RNA consists of similar bases, except uracil (U) replaces thymine (T).
        4. DNA is double helix molecule: -(similar to a spiral staircase or twisted ladder), with the sides formed by repeating sugar-phosphate groups from each nucleotide, and the horizontal portions (the steps) formed by bonds involving A with T or C with G.
    2. The Central Dogma
      1. Replication
        1. DNA is copied from other DNA, by unzipping the helix and paring new nucleotides with the proper bases (i.e., A with T and C with G) on each separated side of the original DNA
      2. Transcription
        1. Messenger (m)RNA is copied from DNA, by unzipping a portion of the DNA helix that corresponds to a gene.
        2. Only one side of the DNA will be transcribed, and nucleotides with the proper bases (A with U and C with G) will be sequenced to build pre-mRNA.
        3. Sequences of nucleotides call introns are removed and the remaining segments called exons are spliced together.
        4. The mature mRNA leaves the nucleus to be transcribed by the ribosomes.
      3. Translation
        1. Proteins are synthesized from (m)RNA by ribosomes (which are composed of ribosomal (r)RNA and proteins) which read from a triplet code (i.e., codons that is universal
        2. The ribosomes instruct transfer (t)RNA's to bring in specific amino acids in the sequence dictated by the mRNA, which in turn was built based on the sepuence of nucleotides in the original gene portion of the DNA.
    3. Mutations
      1. Any random, permanent change in the DNA molecule
      2. Many are harmful; Some have no effect; A few benefit the organism
      3. Nature selects those that are beneficial or adaptive in organisms to help shape the course of evolution.
  6. Population Genetics
    1. Populations vs Individuals
    2. Hardy-Weinberg Law
    3. Hardy-Weinberg & Natural Populations
  7. Mendellian Genetics
    1. Introduction
    2. Law of Segregation of Alternate Factors
    3. Law of Independent Assortment
    4. Mendel Updated
    5. Chromosomes and Sex Determination
    6. Sex-Linked Traits
  8. Energy and Life
    1. Our sun - Organisms directly or indirectly use sun's energy to become and remain in an organized state
      1. Metabolism - series of chemical reactions involved in storing (anabolism) or releasing (catabolsim) energy
      2. Enzymes - biological catalysts; facilitate metabolic chemical reactions by speeding rates and lowering heat requirements
      3. Adenosine Triphosphate (ATP) - A high-energy molecule. Energy stored in ATP is released by breaking phosphate-to-phosphate bonds and creating adenosine diphosphate (ADP). ATP is recycled by adding back phosphate groups using energy from the sun.
    2. Photosynthesis -- Sunlight or radiant energy is captured by chlorophyll and carotenoid photopigments (in cytoplasm of prokaryotes and chloroplasts of eukaryotes) in two main steps:
      1. Light-dependent reactions -- captured light energy is transferred to electrons that come from H2O; O2 is a by-product
      2. Light-independent reactions -- energized electrons are transferred to CO2 (reduction reactions) to form glucose (Calvin-Benson cycle).
    3. Cell respiration -- highly energized electrons stored temporarily in glucose are removed (oxidation reactions) in a step-wise fashion to maximize energy capture at each step:
      1. Glycolysis: - anaerobic process in cytoplasm in which glucose, a six-carbon compound, is oxidized to two pyruvates, which are both three-carbon chains
      2. Krebs Cycle: - aerobic process that oxidizes pyruvates to CO2
      3. Chemiosmotic Phosphorylation: - energized electrons released during the previous steps are used to concentrate hydrogen ions in one area (of the cell membrane in prokaryotes; of the mitrochondrion in eukaryotes) to create a chemical gradient between positively and negatively charged ions (i.e., a battery). The potential energy resulting from this osmotic gradient isused to resynthesize ATP from ADP and AMP. After electrons have been used, they must be transferred to O2.
  9. Cell Transportation -- how substances enter and leave
    1. Passive
      1. Relies on thermal energy of matter -- the cell does not do work
        1. Diffusion - movement from an area of high to low concentration
        2. Facilitated diffusion - a permease, or membrane enzyme, carries substance
        3. Bulk flow - mass movements of fluids; affected by pressures and solutes
        4. Osmosis - diffusion across a semi-permeable membrane
    2. Active
      1. Relies on cell providing energy supply
        1. Membrane pumps - Permease used to move substance, usually opposite the direction of diffusion
        2. Endocytosis - materials are bought into a cell via:
          1. Phagocytosis - solids
          2. Pinocytosis - liquids
        3. Exocytosis - expel materials from the cell
source : uni.edu

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