Finals

• • Biology is the study of life
  • "Bio" means life
  • "Logy" is the study of
• Characteristics of living organisms

  • exhibit growth and development into highly ordered forms
  • unicellular and multicellular organisms
  • made of one or more cells
  • building instructions stored in DNA
  • maintain an optimal steady state despite changes in environment
  • homeostasis
  • require energy
  • reproduce on their own
  • evolve
  • die
• Life exhibits emergent properties

  • emergent properties are those that arise through interactions among smaller parts that alone do not exhibit such properties
  • in simple terms: it is a characteristic an entity gains when it becomes part of a bigger system
  • individual molecules become increasingly organized into larger, more complex structures
  • e.g., atoms - molecules - cells - tissues - organs - organisms
• Cells are the structural and functional units of life

  • prokaryotes
  • lack membrane-bound nucleus
  • e.g., bacterium and archaean
  • eukaryotes
  • membrane-bound nucleus
  • e.g., protist, algae, fungal cells, animal cells, plant cells
• viruses are not made of cells and they cannot grow and reproduce on their own

  • they need a host cell
  • some scientists believe that they are form of life
  • viruses do have DNA and RNA, and they can evolve and adapt
  • viruses being not a form of life is not universally accepted
• The molecules of life

  • water
  • it is the most predominant molecule of the cell
  • 70% of the cell is water
  • macromolecules
• Water

  • H2O is the solvent of life
  • dissolves more molecules than any other solvent
  • a polar molecule (i.e., opposite charges on either end)
  • dissolves other polar molecules
  • e.g., ammonia
  • dissolves charged molecules
  • i.e., ions - by binding with both anions and cations

  
• Information storage and retrieval in Earthlings

  • all earth life is based on DNA - RNA - Protein
  • they call this the "central dogma of molecular biology"
  • flows only in one direction, from DNA to RNA, to protein or RNA directly to protein
  • information is stored in DNA - the information in DNA is copied into RNA - the information in RNA guides the production of proteins

  
• The molecules of life - macromolecules

  • carbohydrates - polymers of sugars
  • e.g., cellulose, glycogen
  • lipids - not polymers
  • proteins - polymers of amino acids
  • nucleic acids - polymers of nucleotides

  these are all polymers except lipids
• Polymers

  • chains composed of molecules called monomers
• Polymer formation (i.e., polymerization)

  • monomers string together into polymers in a processes termed dehydration synthesis
  • the components of a water molecule are removed as subunits join into a larger molecule
  • OH's are hydroxyl group
  • hydroxy or hydroxyl group is a functional group with the chemical formula -OH and composed of one oxygen atom covalently bonded to one hydrogen atom
  • Hydrogens are example of protons (positively charged)

  
• monomers to polymers is called polymerization

  polymers to monomers is called depolymerization
• Polymer breakdown (i.e., depolymerization)

  • polymers are broken down via hydrolysis
  • the components of a water molecule are added as molecules are split into smaller subunits

  
• Enzymes make/hydrolyze polymers

  • enzymes catalyze the synthesis/hydrolysis of polymers
  • active site is where substrate binds and where catalysis and chemical reaction take place

  
• Most bio-polymers are not just straight chains of monomers

  • the chains arrange into varied levels of higher-order structure
  • examples:
  • DNA double helix
  • protein folding

  
• what determines a protein's structure?

  • the properties and order of the amino acids
• Amino acids

  • R = side chain
  • side chain define the chemistry of proteins

  A) side chain

  B) carboxyl group

  C) hydrogen

  D) amino groups

  
• non-polar side chains, polar side chains, and electrically charged side chains are examples of side chains
• Primary protein structure

  • amino acids are linked by covalent bonds called peptide bonds
  • covalent means electrons shared by atoms
  • peptide bonds means carboxyl group of one amino acid + amino group of another
  • proteins also known as polypeptides
  • polypeptides mean continuous, unbranched chain of amino acids joined by peptide bonds

  
• Secondary protein structure

  • hydrogen bonds between nearby amino acids cause the polypeptide to twist (alpha helix) or form sheets (beta sheets)

  
• Tertiary protein structure

  • chemistry between side chains causes higher-order folding
  • the bonds that occur in this structure are ionic bonds, disulfide linkage, hydrogen bonds, and hydrophobic interactions

  
• Quaternary structure is the association of several protein chains or subunits into a closely packed arrangement

  • assembling the other proteins into a complex structure

  
• Proteins are the most diverse type of macromolecules that we find in the cell
• Polymer examples: carbohydrates

  • below are all polymers of glucose, but in different forms:
  • amylose (a component of starch)
  • cellulose
  • chitin
  • small differences lead to big differences in the resulting higher order structures

  
• amylose

  • plant cells store carbohydrates in the form of amylose

  cellulose

  • major component of the cell wall

  chitin

  • found in the exoskeleton of many arthropods animals

  they have differences in structure organization thus differences in functions
• Amylose and cellulose structure

  • amylose has an a-(1-4) glycosidic bonds
  • hydroxyl group is on the opposite side of the alcohol group
  • cellulose have a b-(1-4) glycosidic bonds
  • hydroxyl group is on the same side of the alcohol group

  
• Chitin has a b-(1-4) glycosidic bonds but with different side chains

  
• Cell Theory

  By the mid-19th century, microscopic observations had yielded three generalizations, which constitute the cell theory:

  1. all organisms are composed of one or more cells
  2. the cell is the basic structural and functional unit of all living organisms
  3. cells arise only from the division of preexisting cell
• First observations of cells using microscopes - 1600's

  • Robert Hooke (1635-1703) looked at cork cells
  • Anton Van Leeuwenhoek (1663-1732) made a better microscope and saw "many very little animacules" (i.e., microbes, archaeans)
  • father of microbiology
• Establishment of cell theory - 1800's

  • Theodore Schwann, Mattias Schleiden
  • all living organisms are made of cells
  • Rober Remark, Rudolph Virchow
  • proposed that all cells come from previous cells
  • Louis Pasteur
  • Confirmed above hypothesis by demonstrating that the long-standing theory of spontaneous generation (a.k.a. abiogenesis) was bunk
• Size of cells

  • most cells are microscopic
  • size of the cell is not related to body size, but related to its function
  • below 0.1 mm isn't visible to the human eye
• Why do cells tend to be small?

  • surface area must be sufficient to allow exchange of materials between the cell and its surroundings
  • larger volumes require more surface area
  • larger volume, larger metabolic reactions it can sustain
  • larger volumes require more structural support

  
• Trade-off between cell surface area and volume

  • the problem is that as volume increases, the surface area does not increase proportionately
  • volume increases by a factor of 3 (V=a^3)
  • area increases by a factor of 2 (A=6a^2)
• Cell size is limited by surface area to volume ratio

  • if the surface area is not large enough to meet the demands of cell volume, the cell will stop growing
• How can we observe cells?

  Microscopy: higher resolution, magnification, and contrast

  • resolution - the ability of a microscope to distinguish two objects as being separate
  • higher magnification increases resolution
  • magnification = observed size / actual size
  • higher contrast gives more detail, but can't increase resolution
  • high contrast = high depth, clarity, and details

  
• Light (Optical) Microscopes

  • use lenses to bend light and magnify images by a factor of roughly 100-fold
  • can be used to view living specimens in natural colour
  • chemical dyes and fluorescent labelling may be applied to resolve specific structures
• Types of Light Microscopes

  • bright field
  • dark field
  • phase-contrast
  • differential interference contrast (Nomarski)
  • these microscopes, except bright field, are contrast-enhancing methods
  • they also use the light-scattering (refractive) properties of specimens
  • variations in specimen thickness and density influence how light passes through it
• Contrast-enhancing method - dark field

  • illuminates sample at an angle so light does not hit the objective lens directly (obliquely)
  • only light that is scattered upwards by the sample reaches the objective lens

  
• Contrast-enhancing methods - phase contrast

  • this method creates slight phase shifts in the illuminating light, which manifest as higher detailed images
  • phase shift is converted into change in amplitude/intensity of light
• Contrast enhancing methods - differential interference contrast (Normarski)

  • similar to phase-contrast
  • but, more powerful and sophisticated
  • gives a pseudo-3D appearance
  • the specimen doesn't have to be thin
  • more depth