BIO 311C

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  1. Light Microscope (LM)
    visible light is passed through the specimen and then through glass lenses.

    These are microscopes that you are likely to use in any laboratory.

    The lenses refract (bend) the light in such a way that the image of the specimen is magnified as it is projected into the eye, onto photographic film or a digital sensor, or onto a video screen.
  2. Organelles
    membrane-enclosed compartments
  3. Electron Microscope (EM)
    focuses a beam of electrons through the specimen or onto its surface.
  4. Scanning Electron Microscope (SEM)
    especially useful for detailed study of the surface of the specimen.

    The electron beam scans the surface of the sample, which is usually coated with a thin film of gold.

    The beam excites electrons on the surface, and these secondary electrons are detected by a device that translates the pattern of electrons into an electronic signal to a video screen.

    The result is an image of the specimen’s topography. It has great depth of field, resulting in an image that appears three-dimensional.
  5. Transmission Electron Microscope (TEM)
    used to study the internal ultrastructure of cells.

    The TEM aims an electron beam through a very thin section of the specimen, similar to the way a light microscope transmits light through a slide.

    The image displays the pattern of transmitted electrons.
  6. Cell Fractionation
    a useful technique for studying cell structure and function, it takes cells apart and separates the major organelles and other subcellular structures from one another.

    The instrument used is the centrifuge, which spins test tubes holding mixtures of disrupted cells at various speeds
  7. Cytosol
    enclosed by the plasma membrane is a semifluid, jellylike substance called cytosol, in which organelles and other components are found
  8. Eukaryotic Cell
    most of the DNA is found in an organelle called the nucleus, which is bounded by a double membrane.

    The word eukaryotic is from the Greek eu, true, and karyon, kernel, here referring to the nucleus
  9. Prokaryotic Cell
    the DNA is concentrated in a region that is not membrane enclosed called the nucleoid.

    The word prokaryotic is from the Greek pro, before, and karyon, kernel, referring to nucleus.
  10. Nucleoid
    the region where the DNA is concentrated in a prokaryotic cell, not membrane enclosed.
  11. Cytoplasm
    interior of a prokaryotic cell, also used for the region between the nucleus and the plasma membrane of a eukaryotic cell
  12. Plasma Membrane
    located at the boundary of every cell.

    It functions as a selective barrier that allows sufficient passage of oxygen, nutrients, and wastes to service the entire cell.
  13. Nucleus
    contains most of the genes in the eukaryotic cell (some genes are located in the mitochondria and chloroplasts).

    It is generally the most conspicuous organelle in a eukaryotic cell, averaging about 5µm in diameter.
  14. Nuclear Envelope
    encloses the nucleus, separating its contents from the cytoplasm.

    It’s a double membrane.
  15. Nuclear Lamina
    a netlike array of protein filaments that maintains the shape of the nucleus by mechanically supporting the nuclear envelope
  16. Chromosomes
    structures that carry the genetic information
  17. Chromatin
    each chromosome is made of this.

    It is a complex of proteins and DNA
  18. Nucleolus
    a prominent structure within the non-dividing nucleus, which appears through the electron microscope as a mass of densely stained granules and fibers adjoining part of the chromatin
  19. Ribosomes
    complexes made of ribosomal RNA and protein, are the cellular components that carry out protein synthesis.

    Cells that have high rates of protein synthesis have particularly large numbers of ribosomes.

    For example, a human pancreas cell has a few million ribosomes
  20. Endomembrane System
    part of the membrane system in a eukaryotic cell, which carries out a variety of tasks in the cell.

    These tasks include synthesis of proteins and their transport into membranes and organelles or out of the cell, metabolism and movement of lipids, and detoxification of poisons
  21. Vesicles
    sacs made of membrane.

    The membranes of a particular system are related either through direct physical continuity or by the transfer of membrane segments as tiny vesicles.
  22. Endoplasmic Reticulum (ER)
    an extensive network of membranes that accounts for more than half the total membrane in many eukaryotic cells (endoplasmic means “within the cytoplasm,” and reticulum mean “little net.”
  23. Smooth ER
    its outer surface lacks ribosomes.

    • The functions of the smooth ER include:
    • synthesis of lipids, metabolism of carbohydrates, and detoxification of drugs and poisons
  24. Rough ER
    has ribosomes on the outer surface of the membrane and thus appears rough through the electron microscope.

    • The functions of the rough ER include:
    • protein synthesis by the ribosomes (secretory proteins), it is a membrane factory for the cell; it grows in place by adding membrane proteins and phospholipids to its own membrane, it also makes its own membrane phospholipids from precursors in the cytosol
  25. Glycoproteins
    mostly secretory proteins, proteins that have carbohydrates covalently bonded to them
  26. Transport Vesicles
    vesicles in transport from one part of the cell to another
  27. Golgi Apparatus
    many transport vesicles travel here.

    It’s a center of manufacturing, warehousing, sorting, and shipping.

    Here, products of the ER, such as proteins, are modified and stored and then sent to other destinations
  28. Lysosome
    a membranous sac of hydrolytic enzymes that an animal cell uses to digest macromolecules.

    Lysosomal enzymes work best in the acidic environment found in lysosomes
  29. Phagocytosis
    A means of eating by engulfing smaller organisms or other food particles (phagein, to eat, and kytos, vessel).
  30. Food Vacuoles
    are membranous sacs formed by phagocytosis of microorganisms or particles to be used as food by the cell
  31. Contractile Vacuoles
    maintaining a suitable concentration of ions and molecules inside the cell
  32. Central Vacuole
    mature plant cells generally contain large central vacuoles. The central vacuole develops by the coalescence of smaller vacuoles, themselves derived from the endoplasmic reticulum and Golgi apparatus
  33. Mitochondria
    general sites of cellular respiration, the metabolic process that generates ATP by extracting energy from sugars, fats, and other fuels with the help of oxygen
  34. Chloroplasts
    found in plants and algae, are the sites of photosynthesis.

    They convert solar energy to chemical energy by absorbing sunlight and using it to drive the synthesis of organic compounds such as sugars from carbon dioxide and water
  35. Peroxisome
    an oxidative organelle that is not part of the endomembrane system, it imports proteins primarily from the cytosol, like the mitochondria and chloroplasts
  36. Cristae
    the outer membrane of the mitochondria is smooth, but the inner membrane is convoluted, with infoldings called cristae
  37. Mitochondrial Matrix
    enclosed by the inner membrane (second compartment), it contains many different enzymes as well as the mitochondrial DNA and ribosomes
  38. Plastids
    one of a family of closely related organelles hat includes chloroplasts, chromoplasts, and amyloplasts (leucoplasts), they are found in cells of photosynthetic organisms
  39. Thylakoids
    located inside the chloroplast as another membranous system in the form of flattened, interconnected sacs
  40. Granum
    in some regions the thylakoids are stacked like poker chips, each stack is known as a granum
  41. Stroma
    the fluid outside the thylakoid is the stroma, it contains the chloroplast DNA and ribosomes as well as many enzymes
  42. Peptidoglycan
    a network of modified-sugar polymers cross-linked by short polypeptides, contained by most bacterial cell walls
  43. Gram Stain
    developed by the nineteenth-century Danish physician Hans Christian Gram, scientists can classify many bacterial species into two groups based on differences in cell wall composition
  44. Gram-positive
    bacteria that have simpler walls with a relatively large amount of peptidoglycan
  45. Gram-negative
    are bacteria that have less peptidoglycan and are structurally more complex, with an outer membrane that contains lipopolysaccharides (carbohydrates bonded to lipids)
  46. Capsule
    a sticky layer of polysaccharide or protein that the cell wall of many prokaryotes is covered in
  47. Fimbriae
    some prokaryotes stick to their substrate or to one another by means of hair-like protein appendages called fimbriae
  48. Sex Pili
    appendages that pull two cells together prior to DNA transfer from one cell to the other
  49. Taxis
    many prokaryotes exhibit taxis, which is the movement toward or away from a stimulus (taxis=to arrange)
  50. Nucleoid
    prokaryotes chromosome located here, a region of cytoplasm that appears lighter than the surrounding cytoplasm in electron micrographs
  51. Plasmids
    in addition to a single chromosome, typical prokaryotic cells may also have much smaller rings of separately replicating DNA, most carrying only a few genes
  52. Endospores
    certain bacteria develop resistant cells called endospores when an essential nutrient is lacking
  53. Photoautotrophs
    photosynthetic organisms that capture light energy and use it to drive the synthesis of organic compounds from CO2 or other inorganic carbon compounds, such as bicarbonate (HCO3-).

    Cyanobacteria and many other groups of prokaryotes are photoautotrophs, as are plants and algae.
  54. Chemoautotrophs
    only need an inorganic compound such as CO2 as a carbon source.

    However, instead of using light as an energy source, they oxidize inorganic substances, such as hydrogen sulfide (H2S), ammonia (NH3), or ferrous ions (FE2+).

    This mode of nutrition is unique to certain prokaryotes
  55. Photoheterotrophs
    harness energy from light but must obtain carbon in organic form.

    This mode is unique to certain marine and halophilic (salt-loving) prokaryotes
  56. Chemoheterotrophs
    must consume organic molecules to obtain both energy and carbon.

    This nutritional mode is widespread among prokaryotes.

    Fungi, animals, most protests, and even some parasitic plants are also chemoheterotrophs
  57. Obligate Aerobes
    O2 for cellular respiration and cannot grow without it
  58. Obligate Anaerobes
    poisoned by O2, some live exclusively by fermentation
  59. Anaerobic Respiration
    when substances other than O2, such as nitrate ion (NO3-) or sulfate ions (SO42-), accept electrons at the “downhill” end of electron transport chains
  60. Facultative Anaerobes
    use O2 if it is present but can also carry out anaerobic respiration or fermentation in an anaerobic environment
  61. Nitrogen Fixation
    the conversion of atmospheric nitrogen (N2) to ammonia (NH3)
  62. Heterocytes
    specialized cells that only carry out nitrogen fixation
  63. Biofilms
    when metabolic cooperation between different prokaryotic species occurs in surface-coating colonies known as biofilms.

    Cells in a bioflim secrete signaling molecules hat recruit nearby cells, causing the colonies to grow.

    The cells also produce proteins that stick the cells to the substrate and to one another
  64. Extremophiles
    lovers of extreme conditions, include extreme halophiles and extreme thermophiles.

    The prokaryotes assigned to the domain Archaea live in environments so extreme that few other organisms can survive there
  65. Extreme Halophiles
    organisms living in highly saline environments, such as the Great Salt Lake, the Dead Sea, and Owens Lake
  66. Extreme Thermophiles
    organisms that thrive in hot environments.

    For example, archaea in the genus, Sulfolobus, live in sulfur-rich volcanic springs as hot as 90ºC.

    At temperatures this high, the cells of most organisms die b/c their DNA does not stay together in a double helix, and many of their proteins denature
  67. Methanogens
    a group of archaea named for the unique way they obtain energy: they use CO2 to oxidize H2, releasing methane as a waste product
  68. Decomposers
    chemoheterotrophic prokaryotes function as decomposers, breaking down corpses, dead vegetation and waste products, thereby unlocking supplies of carbon, nitrogen and other elements
  69. Symbiosis
    an ecological relationship in which two species live in close contact with one another.
  70. Host
    in general the larger organism in a symbiotic relationship is known as the host, serving as the home and food source for the smaller symbiont
  71. Symbiont
    in general the smaller organism in a symbiotic relationship is known as the symbiont, using the larger host as the home and food source for itself
  72. Mutualism
    an ecological interaction between two species in which both benefit
  73. Commensalism
    an ecological relationship in which one species benefits while the other is not harmed or helped in any significant way
  74. Parasitism
    an ecological relationship in which a parasite eats the cell contents, tissues, or body fluids of its host; as a group parasites harm but usually do not kill their host, at least not immediately
  75. Parasite
    an organism that feeds on the cell contents, tissues, or body fluids of another species (the host) while in or on the host organism.

    Parasites harm but usually do not kill their host
  76. Pathogens
    parasites that cause disease, many of which are prokaryotic
  77. Macromolecules
    A giant molecule formed by the joining of smaller molecules, usually by a condensation reaction.

    Polysaccharides, proteins, and nucleic acids are macromolecules
  78. Polymer
    A long molecule consisting of many similar or identical building blocks linked by covalent bonds, much as a train consists of a chain of cars
  79. Monomers
    The repeating units that serve as the building blocks of a polymer are these smaller molecules.

    Some of the molecules that also serve as monomers also have functions of their own.
  80. Condensation Reaction
    A reaction in which monomers are connected by a reaction in which two molecules are covalently bonded to each other through the loss of a water molecule.

    This can ALSO be known as a dehydration reaction, because water is the molecule being lost
  81. Enzymes
    Specialized macromolecules that speed up chemical reactions in cells
  82. Hydrolysis
    When polymers are disassembled to monomers.

    This is a process that is essentially the reverse of the dehydration reaction.

    Hydrolysis means to break using water
  83. Monosaccharides
    (monos=single, sacchar=sugar), generally, consisting of molecular formulas that are some multiple of the unit CH2O.

    Glucose (C6H12O6), the most common monosaccharide, is of central importance in the chemistry of life
  84. Disaccharide
    consists of two monosaccharides joined by a glycosidic linkage.
  85. Glycosidic Linkage
    A covalent bond formed between two monosaccharides by a dehydration reaction
  86. Polysaccharides
    are macromolecules, polymers with a few hundred to a few thousand monosaccharides joined by glycosidic linkages.

    1. Some polysaccharides serve as storage material, hydrolyzed as needed to provide sugar for cells.

    2. Others serve as building material for structures that protect the cell or the whole organism
  87. Starch
    Plants store starch, a polymer of glucose monomers, as granules within cellular structures known as plastids, which include chloroplasts.

    Synthesizing starch enables the plant to stockpile surplus glucose; and because glucose is a major cellular fuel, starch represents stored energy
  88. Glycogen
    Animals store this polysaccharide which is a polymer of glucose that is like amylopectin but more extensively branched.

    Humans and other vertebrates store glycogen mainly in liver and muscle cells.

    Hydrolysis of glycogen in these cells releases glucose when the demand for sugar increases
  89. Cellulose
    A polysaccharide polymer of glucose, which is a major component of the tough walls that enclose plant cells.

    • On a global scale, plants produce almost 100 billion tons of cellulose per year; it is the most abundant organic compound on
    • Earth
  90. Chitin
    A carbohydrate (polysaccharide) used by arthropods (insects, spiders, crustaceans, etc) to build their exoskeletons.

    An exoskeleton is a hard case that surrounds the soft past if an animal.

    Pure chitin is leathery and flexible, but it becomes hardened when encrusted with calcium carbonate, a salt
  91. Lipids
    The one class of large biological molecules that do not include true polymers, and they are generally not big enough to be considered macromolecules.

    These compounds are grouped together because they share one important trait: they mix poorly, if at all, with water (hydrophobic).
  92. Fat
    Constructed from two kinds of smaller molecules glycerol and fatty acids.

    Fats are not polymers, they are large molecules assembled from a few smaller molecules by dehydration reactions
  93. Fatty Acid
    Consists of a long carbon skeleton, usually 16 or 18 carbon atoms in length
  94. Triacylglycerol
    A fat consisting of three fatty acids linked to one glycerol molecule, aka triglyceride
  95. Saturated Fatty Acid
    A fatty acid in which all carbons in the hydrocarbon tail are connected by single bonds, thus maximizing the number of hydrogen atoms that are attached to the carbon skeleton
  96. Unsaturated Fatty Acid
    Consists of one or more double bonds, formed by the removal of hydrogen atoms from the carbon skeleton.

    The fatty acid will have a kink in its hydrocarbon chain wherever a cis double bond occurs
  97. Trans Fat
    An unsaturated fat containing one or more trans double bonds
  98. Phospholipids
    Essential for cells because they make up cell membranes.

    Their structure provides a classic example of how form fits function at the molecular level.

    SEE FIGURES 5.13 and 5.14 on PAGE 76-77
  99. Steroids
    Many hormones as well as cholesterol are steroids.

    Steroids are lipids characterized by a carbon skeleton consisting of four fused rings.

    Different steroids vary in the chemical groups attached to this ensemble of rings.
  100. Cholesterol
    A common component of animal cell membranes and is also the precursor from which other steroids are synthesized.

    In vertebrates, cholesterol is synthesized in the liver.
  101. Enzymes
    Life would not be possible without enzymes. Most enzymes are proteins.

    Enzymatic proteins regulate metabolism by acting as catalysts
  102. Catalysts
    Chemical agents that selectively speed up chemical reactions without being consumed by the reaction.

    SEE FIGURE 5.16 on PAGE 78
  103. Polypeptides
    Polymers of amino acids
  104. Protein
    Consists of one or more polypeptides, each folded and coiled into a specific three-dimensional structure
  105. Amino Acids
    All amino acids share a common structure.

    Amino Acids are organic molecules possessing both carboxyl and amino groups
  106. Peptide Bond
    The covalent Bond between the carboxyl group on one amino acid and the amino group on another, formed by a dehydration reaction
  107. primary structure (Levels of Protein Structure)
    its unique sequence of amino acids.

    The primary structure is like the order of letters in a very long word.

    2. Most proteins have segments of their polypeptide chains repeatedly coiled or folded in patterns that contribute to the protein’s overall shape

    These coils and folds are collectively referred to as the secondary structure
  108. secondary structure (Levels of Protein Structure)
    the result of hydrogen bonds between the repeating constituents of the polypeptide backbone

    Two main types of secondary structures are the α helix and the β pleated sheet

    Super imposed on the patterns of secondary structure is a protein’s tertiary structure
  109. α helix (Levels of Protein Structure)
    a delicate coil held together by hydrogen bonding between every fourth amino acid in the secondary structure
  110. β pleated sheet (Levels of Protein Structure)
    the structure with two or more regions of the polypeptide chain lying side by side are connected by hydrogen bonds between parts of the two parallel polypeptide backbones on the secondary structure
  111. tertiary structure (Levels of Protein Structure)
    the overall shape of a polypeptide resulting from interactions between the side chains of the various amino acids.

    One type of interaction is the hydrophobic interaction
  112. hydrophobic interaction (Levels of Protein Structure)
    One type of interaction in the tertiary structure

    • As a peptide folds into its functional shape, amino acids with hydrophobic side chains usually end up in clusters at the core
    • of the protein, out of contact with water.

    The shape of a protein may be reinforced further by covalent bonds called disulfide bridges.

    They form where two cysteine monomers, amino acids with sulfhydryl groups on the side chains are brought close together by folding of the protein.
  113. Quaternary structure (Levels of Protein Structure)
    the overall protein structure that results from the aggregation of polypeptide subunits.
  114. Denaturation
    In proteins, a process in which a protein unravels and loses its native shape, thereby becoming biologically inactive; in DNA, the separation of the two strands of the double helix.

    Denaturation occurs under extreme (noncellular) conditions of pH, salt concentration, and temperature
  115. Chaperonins
    Protein molecules that assist in the proper folding of other proteins.

    Chaperonins do not specify the final structure of a polypeptide.

    Instead, they keep the new polypeptide segregated from bad influences in the cytoplasmic environment while it folds spontaneously
  116. X-Ray Crystallography
    A method that is used to determine the 3-D structures of many proteins.
  117. Gene
    A unit of inheritance that programs the amino acid sequence of polypeptides
  118. Nucleic Acids
    A polymer consisting of many nucleotide monomers; serves as a blueprint for proteins and, through the actions of proteins, for all cellular activities.

    The two types are DNA and RNA
  119. DNA (deoxyribonucleic acid)
    Enable living organisms to reproduce their complex components from one generation to the next.

    Unique among molecules, DNA provides directions for its own replication.

    DNA also directs RNA synthesis
  120. RNA (ribonucleic acid)
    Controls protein synthesis
  121. Polynucleotides
    Nucleic acids that are macromolecules that exist as polymers.

    Each polynucleotide consists of monomers called nucleotides.
  122. Nucleotides
    Composed of 3 parts: a nitrogenous base, a five carbon sugar (pentose), and a phosphate group
  123. Pyrimidine
    One of two types of nitrogenous bases found in nucleotides, characterized by a six-membered ring.

    Cytosine(C), Thymine (T), and Uracil (U) are pyrimidines
  124. Purines
    • One of two types of nitrogenous bases found in nucleotides, characterized by a six-membered ring fused to a five-membered
    • ring.

    Adenine (A) and Guanine (G) are purines.
  125. Ribose
    The sugar component of RNA nucleotides
  126. Deoxyribose
    The sugar component of DNA nucleotides, having one fewer hydroxyl group than ribose, the sugar component of RNA nucleotides
  127. Double Helix
    The form of native DNA, referring to its two adjacent antiparallel polynucleotide strands wound around an imaginary axis into a spiral shape
  128. Antiparallel
    The opposite arrangement of the sugar-phosphate backbones in a DNA double helix
  129. Selective Permeability
    The plasma membrane exhibits selective permeability; that is it allows some substances to cross it more easily than others.
  130. Amphipathic
    A phospholipid is an amphipathic molecule, meaning it has both a hydrophilic region and a hydrophobic region
  131. Fluid Mosaic Model
    The currently accepted model of cell membrane structure, which envisions the membrane as a mosaic of protein molecules drifting laterally in a fluid bilayer of phospholipids
  132. Evolution
    the process of change that has transformed life on Earth from its earliest beginnings to the diversity of organisms living today
  133. Biology
    the scientific study of life
  134. Emergent Properties
    properties that were not present at the proceeding level; they are due to the arrangement and interactions of parts as complexity increases
  135. Systems Biology
    the goal is to construct models for the dynamic behavior of whole biological systems
  136. Eukaryotic Cell
    a cell that is subdivided by internal membranes into various membrane-enclosed organelles
  137. Prokaryotic Cell
    a cell where the DNA is not separated from the rest of the cell by enclosure in a membrane-bounded nucleus.

    They also lack the other kinds of membrane-enclosed organelles that characterize eukaryotic cells
  138. DNA
    (deoxyribonucleic acid) genetic material
  139. Genes
    the units of inheritance that transmit information from parents to offspring
  140. Genome
    the entire library of genetic instructions that an organism inherits
  141. Bioinformatics
    the use of computational tools to store, organize, and analyze the huge volume of data that result from high-throughput methods
  142. Negative Feedback
    the most common form of regulation in which accumulation of an end product of a process slows that process.

    Ex. The cell’s breakdown of sugar generates chemical energy in the form of a substance called ATP.

    When a cell makes more ATP than it can use, the excess ATP “feeds back” and inhibits an enzyme near the beginning of the pathway.
  143. Positive Feedback
    regulation in which an end product speeds up its production.

    Ex. When a blood vessel is damaged, structures in the blood called platelets begin to aggregate at the site.

    Positive feedback occurs as chemicals released by the platelets attract more platelets.
  144. Domains
    bacteria, archaea (both prokaryotic), and eukarya (eukaryotic)
  145. Discovery Science
    describes natural structures and processes as accurately as possible through careful observation and analysis of data
  146. Data
    recorded observations. Qualitative (data in the form of recorded description), Quantitative (data recorded as measurements)
  147. Inductive Reasoning
    discovery science can lead to important conclusions based on types of logic called inductions.

    Ex. “the sun always rises in the East.”
  148. Hypothesis
    a tentative answer to a well-framed question—an explanation on trial
  149. Deductive Reasoning
    the logic flows in the opposite direction, from general to specific.

    From general premises we extrapolate specific results.

    Ex. If all organisms are made up of cells (premise), and humans are organisms (premise), then humans are composed of cells (deductive prediction)
  150. Theory
    (1) much broader in scope than an hypothesis,

    (2) is general enough to spin off many new, specific hypotheses that can be tested,

    (3) compared to any one hypothesis, a theory is generally supported by a much greater body of evidence
  151. Models
    can take many forms: diagrams, graphs, 3-D objects, computer programs, mathematical equations
  152. Technology
    applies scientific knowledge for some specific purpose.

    Biologists speak of discoveries, technologists speak of inventions
  153. Element
    a substance that cannot be broken down to other substances by chemical reactions.

    Today chemists recognize 92 elements occurring in nature (oxygen, gold, carbon, etc).
  154. Compound
    a substance consisting of two or more different elements combined in a fixed ratio.

    Ex. Table salt, is sodium chloride (NaCl), a compound composed of the elements sodium (Na) and Chloride (Cl) in a 1:1 ratio
  155. Trace Elements
    those required by an organism in only minute quantities.

    Some trace elements, such as iron, are needed by all forms of life; others such as iodine are needed by vertebrates as it is an essential ingredient of a hormone produced by the thyroid gland
  156. Atom
    smallest unit of matter that still retains the properties of an element.

    They are so small that it would take about 1 million of them to stretch across the period printed at the end of the sentence
  157. Neutron
    an electrically neutral particle
  158. Electron
    an electrically negatively charged particle
  159. Proton
    an electrically positively charged particle
  160. Atomic Nucleus
    the protons and neutrons are packed together tightly at the center of a dense core at the center of an atom
  161. Dalton
    for atoms and subatomic particles (and for molecules) we use this unit of measurement, in honor of John Dalton, the British scientist who helped develop the atomic theory around 1800.

    The Dalton is the same as the atomic mass unit (amu).
  162. Atomic Number
    the number of protons, which is unique to the element.

    This is written as a subscript to the left of the symbol for the element.

    Ex. 2He, tells us that an atom of the element helium has 2 protons in its nucleus
  163. Mass Number
    we can deduce the number of neutrons from this second quantity, which is the sum of protons plus neutrons in the nucleus of an atom.

    The mass number is written as a superscript to the left of an element’s symbol.

    Ex. 42He, because the atomic number tells us how many protons there are we can deduce the number of neutrons by subtracting the atomic number from the mass number (4-2=2 neutrons)
  164. Atomic Mass
    because neutrons and protons each have a mass very close to 1 dalton, the mass number is an approximation of the total mass of an atom.

    Ex. 42He, so we might say the atomic mass of helium is 4 daltons
  165. Isotopes
    all atoms of a given element have the same number of protons, but some atoms have more neutrons than other atoms of the same element and therefore have greater mass.

    Ex. There are three forms of carbon that have an atomic number of 6, i.e. 6 protons, 126C (6 neutrons), 136C (7 neutrons), 146C (8 neutrons).
  166. Energy
    the capacity to cause change, for instance, by doing work
  167. Potential Energy
    is the energy that matter possesses because of its location or structure.

    Ex. Water in a reservoir on a hill has potential energy because of its altitude.

    When the gates of the reservoir’s dam are opened and the water runs downhill, the energy can be used to do work, such as turning generators.
  168. Electron Shells
    electrons are found in these shells, each with a characteristic average distance and energy level
  169. Valence Electrons
    outer electrons that are found in the electron shell
  170. Valence Shell
    the outermost electron shell
  171. Orbital
    the 3-dimentional space where an electron is found 90% of the time
  172. Chemical Bonds
    atoms staying close together, held by attractions
  173. Covalent Bond
    the sharing of a pair of valence electrons by 2 atoms
  174. Molecule
    two or more atoms held together by covalent bonds
  175. Single Bond
    a pair of shared electrons
  176. Structural Formula
    a type of molecular notation in which the constituent atoms are joined by the lines representing covalent bonds
  177. Molecular Formula
    a type of molecular notation representing the quantity of of constituent atoms, but not the nature of the bonds that join them
  178. Double Bond
    a double covalent bond; the sharing of two pairs of valence electrons by two atoms.
  179. Valence
    the bonding capacity, usually equals the number of unpaired electrons required to complete the atom’s outermost (valence) shell
  180. Electronegativity
    the attraction of a particular kind of atom for the electrons of a covalent bond
  181. Nonpolar Covalent Bond
    a bond in which electrons are shared equally
  182. Polar Covalent Bond
    one atom is bonded to a more electronegative atom, the electrons of the bond are not shared equally
  183. Ion
    a charged atom (or molecule), 2 types-cation and anion
  184. Cation
    when an atom is positively charged
  185. Anion
    when an atom is negatively charged
  186. Ionic Bond
    because of their opposite charges, cations and anions attract each other
  187. Ionic Compounds, or Salts
    compounds formed by ionic bonds.
  188. Hydrogen Bond
    forms when a hydrogen atom covalently bonded to one electronegative atom is also attracted to another electronegative atom
  189. Vander Waals interactions
    weak bonds that occur only when atoms and molecules are very close together
  190. Chemical Reactions
    the making and breaking of chemical bonds, leading to changes in the composition of matter
  191. Reactants
    the starting materials in a chemical reaction
  192. Products
    the end materials in a chemical reaction
  193. Chemical Equilibrium
    the point at which the reactions offset one another exactly
  194. Polar Molecule
    two ends of the molecule have opposite charges, unequal distribution of electrons
  195. Cohesion
    when the hydrogen bonds hold the substance (water) together
  196. Adhesion
    the clinging of one substance to another
  197. Surface Tension
    a measure of how difficult it is to stretch or break the surface of a liquid.

    Water has a greater surface tension than most other liquids
  198. Kinetic Energy
    the energy of motion
  199. Heat
    a form of energy, for a given body of matter, the amount of heat is a measure of the matter’s total kinetic energy due to motion of its molecules; thus heat depends in part on the matter’s volume
  200. Temperature
    a measure of heat intensity that represents the average kinetic energy of the molecules, regardless of volume
  201. Celsius Scale
    at sea level, water freezes at 0oC and boils at 100oC. Human body averages 37oC, and comfortable room temp is 20-25oC
  202. Calorie
    a unit of heat.

    The amount of heat it takes to raise the temperature of 1g of water by 1oC
  203. Kilocalorie
    1000 calories, the quantity of heat required to raise the temperature of 1 kilogram of water by 1oC (the calories on food packages are actually kilocalories)
  204. Joule
    1 joule equals 0.239 cal; one calorie equals 4.184 joules
  205. Specific Heat
    specific heat of a substance is defined as the amount of heat that must be absorbed or lost for 1g of that substance to change its temperature by 1oC.

    Water has relatively high specific heat
  206. Heat of Vaporization
    the quantity of heat a liquid must absorb for 1g of it to be converted from the liquid to the gaseous state.

    Water has a high heat of vaporization
  207. Evaporative Cooling
    when the hottest molecules, those with the greatest kinetic energy, are the most likely to leave as gas
  208. Solution
    a liquid that is a completely homogenous mixture of two or more substances
  209. Solvent
    the dissolving agent of a solution
  210. Solute
    the substance that is dissolved
  211. Aqueous Solution
    is a solution in which water is the solvent
  212. Hydration Shell
    the sphere of water molecules around each dissolved ion
  213. Hydrophilic
    from the greek word hydro, water, and philios, loving.

    Any substance that has an affinity for water
  214. Colloid
    a stable suspension of fine particles in a liquid
  215. Hydrophobic
    from the greek phobos, fearing.

    Substances that are nonionic and nonpolar (or for some reason cannot form hydrogen bonds) actually seem to repel water
  216. Molecular Mass
    the sum of the masses of all the atoms in a molecule.

    Ex. sucrose, C12H22O11, has a molecular mass of 342 daltons. The mass of carbon is 12, hydrogen 1, and oxygen 16
  217. Mole
    this represents an exact number of objects, 6.02 x 1023, which is called Avogadro’s number
  218. Molarity
    the number of moles of solute per liter of solution, it is the unit of concentration most often used by biologists for aqueous solutions
  219. Hydrogen Ion
    (H+), a single proton with a charge of 1+ .
  220. Hydroxide Ion
    (OH-), the water molecule that lost a proton, which has a charge of 1-
  221. Hydronium Ion
    (H3O+), when the proton binds to the other water molecule which makes it a hydronium ion
  222. Acid
    a substance that increases the hydrogen ion concentration of a solution.

    Ex. when HCl is added to water, hydrogen ions dissociate from the chloride ions: HCl ---> H+ + Cl-
  223. Base
    a substance that reduces the hydrogen ion concentration of a solution.

    Ex. when ammonia (NH3) acts as a base when the unshared electron pair in nitrogen’s valence shell attracts a hydrogen ion from the solution resulting in an ammonium ion (NH4+): NH3 + H+ ---> NH4+
  224. pH
    the pH of a solution is defined as the negative logarithm (base10) of the hydrogen ion concentration (pH = -log [H+]).
  225. Buffers
    substances that minimize changes in the concentrations of H+ and OH- in a solution.

    They do so by accepting hydrogen ions from the solution when they are in excess and donating hydrogen ions from the solution when they have been depleted.
  226. Acid Precipitation
    refers to rain, snow or fog with a pH lower (more acidic) than pH 5.2
  227. Organic Chemistry
    compounds containing carbon are said to be organic and the branch of chemistry that specializes in the study of carbon compounds is called organic chemistry
  228. Hydrocarbons
    organic molecules consisting of only carbon and hydrogen
  229. Isomers
    compounds that have the same numbers of atoms of the same elements but different structures and hence different properties
  230. Structural Isomers
    differ in covalent arrangements of their atoms
  231. Geometric Isomers
    have the same covalent partnerships, but they differ in their spatial arrangements.

    The differences arise from the inflexibility of double bonds.

    Single bonds allow the atoms they join to rotate freely about the bond axis without changing the compound
  232. Enantiomers
    isomers that are mirror images of each other
  233. Functional Groups
    in the example of sex hormones, different chemical groups contribute to function by affecting the molecule’s shape.

    In other cases, the chemical groups affect molecular function by being directly involved in chemical reactions
  234. Adenosine Triphosphate or ATP
    a complicated organic phosphate, an adenine-containing nucleoside triphosphate that releases free energy when its phosphate bonds are hydrolyzed.

    This energy is used to drive endergonic reactions in cells
  235. Levels of Biological Organization (from biggest to smallest)

    "Big Earl Can't Play On Our Tennis Court On Mondays"
    • Biosphere
    • Ecosystems
    • Communities
    • Populations
    • Organisms
    • Organs and Organ systems
    • Tissues
    • Cells
    • Organelles
    • Molecules
  236. Linnaean system (most specific to most general)

    "Does King Philip Call Our Family German Spies"
    • Domain
    • Kingdom
    • Phylum
    • Class
    • Order
    • Family
    • Genus
    • Species
  237. Image Upload
    Amino: (-NH2) consists of a nitrogen atom bonded to two hydrogen atoms and to the carbon skeleton

    Functional properties: acts as a base; can pick up an H+ from the surrounding solution (water, in living organisms); ionized, with a charge of 1+, under cellular conditions

    Name of compounds: amine
  238. Image Upload
    Carbonyl: (>CO) consists of a carbon atom joined to an oxygen atom by a double bond

    • Compounds
    • Ketones: if the carbonyl group is within a carbon skeleton
    • Aldehydes: if the carbonyl group is at the end of the carbon skeleton

    Functional properties: a ketone and an aldehyde may be structural isomers with different properties, as is the case for acetone and propanal; these two groups are also found in sugars, giving rise to two major groups of sugars: aldoses (containing an aldehyde) and ketoses (containing a ketone)

    Name of compounds: ketone and aldehydes
  239. Image Upload
    Carboxyl: (-COOH) the entire assembly of atoms when an oxygen atom is double-bonded to a carbon atom that is also bonded to an -OH group

    Functional properties: has acidic properties (is a source of hydrogen ions) because the covalent bond between oxygen and hydrogen is so polar; found in cells in the ionized form with a charge of 1- and called a carboxylate ion

    Name of compounds: carboxylic acid or organic acid
  240. Image Upload
    Hydroxyl group: (-OH), a hydrogen atom is bonded to an oxygen atom, which in turn is bonded to the carbon skeleton of the organic molecule

    Functional properties: is polar as a result of the electrons spending more time near the electronegative oxygen atom; can form hydrogen bonds with water molecules, helping dissolve organic compounds, such as sugars

    Name of compounds: alcohols
  241. Image Upload
    • Methyl group: consists of a carbon bonded to three hydrogen atoms. The methyl group may be attached to a carbon or to a different atom
    • Functional properties: addition of a methyl group to DNA, or to molecules bound to DNA, affects expression of genes
    • Name of compounds: methylated compounds
  242. Image Upload
    Phosphate group: a phosphorus atom is bonded to four oxygen atoms; one oxygen is bonded to the carbon skeleton; two oxygens carry negative charges. The phosphate group (-OPO32-, abbreviated (P)) is an ionized form of a phosphoric acid group (-OPO3H2; note the two hydrogens).

    Functional properties: contributes negative charge to the molecule of which it is a part (2- when at the end of a molecule; 1- when located internally in a chain of phosphates); has the potential to react with water, releasing energy

    Name of compounds: organic phosphates
  243. Image Upload
    Sulfhydryl group: consists of a sulfur atom bonded to an atom of hydrogen; resembles a hydroxyl group in shape

    Functional properties: two sulfhydryl groups can react, forming a covalent bond. This "cross-linking" helps stabilize protein structure; cross-linking of cysteines in hair proteins maintains the curliness or straightness of hair. Straight hair can be "permanently" curled by shaping it around curlers, then breaking and re-forming the cross-linking bonds

    Name of compounds: thiols
  244. Which domains have membrane-bound subcellular compartments?

    NOT Prokaryotes (Archaea and Bacteria)
  245. Shared characteristics of Archaea and Bacteria
    Prokaryotic, single-celled, microscopic
  246. Unique characteristics not shared between Archaea and Bacteria
    Genetics and environment
  247. Eukarya kingdoms
    Protists, plants, animals, fungi
  248. A scientific hypothesis must always have to important qualities:
    It must be testable and falsify-able
  249. Four classes of large macromolecules
    Carbohydrates, proteins, lipids, and nucleic acids
  250. Polymers are synthesized by
    condensation reactions
  251. Polymers are broken down by
    hydrolysis reactions
  252. Fat consists of
    fatty acid and glycerol
  253. Fat molecule is made of
    three fatty acids attached to a glycerol through an ester linkage
  254. What determines if the fat is saturated or unsaturated?
    Hydrocarbon chain...saturated if there are no double bonds, and unsaturated if there's one or more double bonds
  255. Phospholipids are composed of
    two fatty acids, a phosphate group, and glycerol
  256. Steroids are composed of
    carbon skeleton with four fused rings
  257. Compare and contrast the following lipids: fats, phospholipids, and steroids
    Fats are composed of three fatty acid chains attached to a glycerol

    Phospholipids are composed of two fatty acids, a phosphate group, and glycerol

    Steroids are composed of carbon skeleton with four fused rings
  258. What functional groups are present in fats?
    hydroxyl and carboxyl
  259. What characterizes an amino acid?
    side chains (R groups) and
  260. Amino acids in proteins are linked by
    peptide bonds
  261. Functional groups in amino acid backbones
    amino and carboxyl
  262. Three parts of a nucleotide
    Sugar, phosphate group, and nitrogen
  263. Features common to all cells
    All organisms are made of cells

    Bound by a lipid bilayer (plasma membrane)

    Have cytosol (internal fluid)

    Have ribosomes

    Synthesize organic molecules

    Have chromosomes (DNA to store information)
  264. bacteria cell walls
  265. archaea cell walls
    polysaccharides and proteins
  266. Eukarya cell walls
    cellulose or chitin
  267. Parts of an animal cell (7)
    • Nucleus
    • Ribosomes
    • ER
    • Mitochondria
    • Centriole
    • Golgi Apparatus
    • Plasma membrane
  268. Parts of a plant cell (9)
    • Nucleus
    • Ribosomes
    • ER
    • Mitochondria
    • Golgi Apparatus
    • Vacuole
    • Chloroplast
    • Plasma membrane
    • Cell wall

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BIO 311C
2010-09-27 06:42:02

Exam 1
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