Card Set Information

2013-12-12 14:26:30
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  1. cephalic
  2. cervical
  3. crural
  4. sural
  5. ventral
    • anterior
  6. ipsilateral
    on same side of midline
  7. contralateral
    opposite side of midline
  8. parietal
    • in regards to the cross-section of the thorax:
    • surface closest to the cavity wall; so the further away lining from the middle
  9. visceral
    • referring to a cross-section of the thorax
    • is the surface closest to the organ inside the cavity
    • lining on the organ itself
  10. 3 cardinal planes used to section the body
    • sagittal
    • transverse
    • frontal
  11. sagittal plane
    • dividing medial from lateral
    • *midsagittal and parasagittal
  12. midsagittal
    divides the body into two EQUAL, mirror image halves
  13. parasagittal
    • parallel to sagittal, but not through the midline
  14. transverse
    • horizontal
    • airplane
  15. frontal
    • coronal
    • cuts body into front and back
  16. oblique plane
    cuts diagonally
  17. dorsal cavity
    includes cranial cavity and vertebral cavity
  18. ventral cavity
    • includes Thoracic and abdominopelvic cavities. 
    • Divided by diaphragm
  19. thoracic cavity
    • includes pleural cavity (lungs), pericardial cavity, and mediastinum
    • *Mediastinum contains the pericardial cavity (heart)
  20. Electrons
    • negatively charged, small particles
    • give atom it's chemical properties
    • surround nucleus
  21. protons
    • positively charged, large particles
    • part of nucleus
  22. neutrons
    • no charge, large particles
    • part of nucleus
  23. Mass #'s
    the sum of an atoms protons and neutrons
  24. Isotopes
    • atoms of an element that have different numbers of neutrons and therefore different mass numbers
    • most are stable, meaning their nuclear structure doesn't change over time
  25. covalent bonds
    • result when atoms share electrons, nicely
    • covalent single bond usually indicated by a single line (H-H), same with double and triple bonds
    • Single covalent bond - two shared electrons
    • double covalent bond = four shared electrons
    • Triple covalent bond ☰ six shared electrons
  26. polar covalent bonds
    • water is an example
    • the sharing of electrons btwn two atoms is unequal - the nucleus of one atom attracts the shared electrons more strongly than the nucleus of the other
    • The resulting molecule has a partial negative charge near the atom that attracts electrons more stongely
  27. ions
    • an atom that has a + or - charge because it has unequal numbers of protons and electrons
    • Atoms that have given away an electron become cations
    • Atoms that have taken on an electron become anions
  28. ionic bonds
    • When atoms hang out together because they have opposite charges
    • they are not sharing electrons, but merely attracted by their opposite charges
    • easily disrupted by water
  29. hydrogen bond
    • a polar covalent bond btwn hydrogen atoms and other atoms, usually with oxygen, nitrogen and sulfur
    • results from the attraction of a partial negative and partial positive charge (partial + charge nearest hydrogens, partial - charge nearest O,N or sulfur)
  30. dipole
    • in a bond, where one end of bond is more negative, the other is more positive
    • *with hydrogen bonds: Oxygen, Nitrogen and sulfur nuclei are able to pull electrons much more strongly than the hydrogen nucleus. Thus, electrons are more likely to be found near Oxygen (or nitrogen or sulfur) nucleus, and less likely to be found near the hydrogen nucleus
  31. bond strength (from strongest to weakest)
    • triple covalent
    • double covalent
    • single covalent
    • ionic bond
    • hydrogen bond
  32. acid
    • a substance which dissolves in water to form one or more hydrogen ions (H+) as a cation (positive ion) and one or more anions  (negative ion)
    • HCl → H+ + Cl-
    • Because H+ is a single proton w 1 positive charge, an acid is also referred to as a proton donor
    • When mixed with a base, will form a salt
  33. base
    • a substance that dissolves in water to form one or more OH- ions (negative ions) and one or more cations (positive ions)
    • KOH → K+ + OH- 
    • Because it removes H+ from a solution, also called proton acceptor.When mixed with an acid, forms salt
  34. buffer
    • a function that can convert strong acids or bases into weak ones by removing or adding protons (H+)
    • Acts as a H+ and/or OH- "sponge" so that pH is kept relatively constant
  35. pH
    "negative logarithm of the hydrogen ion concentration"
  36. pH scale
    • used to express a solution's acidity or alkalinity (base)extends from 0 to 14, based on the concentration of H+ in moles per liter
    • Midpoint of pH scale is 7, where concentrations of H+ and OH- are equal
  37. 4 main kinds of biolobical molecules
    • carbs (sugars)
    • lipids (fats)
    • proteins
    • nucleic acids
  38. hexoses
    • 6 carbon sugars
    • most form 6 sided rings
  39. monosaccharides
    • single sugar molecules:
    • hexoses: glucose, fructose, and galactose
    • pentoses: deoxyribose and ribose
  40. disaccharides
    • formed when two hexoses combine; by dehydration synthesis (combo of 2 disaccharides w formation of water molecule)
    • the simplest kind of sugar polymers
    • include sucrose, lactose, and maltose
  41. sucrose
    • a disaccharide: table sugar
    • glucose + frutose
  42. lactose
    • a disaccharide: milk sugar
    • galactose + glucose
  43. maltose
    • a disaccharide
    • found in malt (fermented grain)
    • glucose + glucose
  44. dehydration synthesis
    • Combination of two monosaccharides w formation of a water molecule (separate, meaning water is a byproduct, dehydrates)
    • the bond btwn two hexoses occurs at a place where the -OH for one sugar finds the -H from another. 
    • As these two hexoses are combined, a water molecule (HOH) is formed.
    • *Ex: formation of sucrose, lactose, and maltose
  45. hydrolysis reaction
    • the opposite of dehydration: a water molecule is added to sucrose as it is broken into glucose and fructose
    • This happens inside our cells as table sugar in the diet is metabolized
  46. invertase
    • also called sucrase
    • Hydrolysis of sucrose is catalyzed by this enzyme
  47. peptide bond
    in proteins, the bond that holds amino acid monomers together which are formed from dehydration reactions
  48. lipid
    • hydrophobic substances / non-polar (not charged)
    • more carbon than water
    • divided into 4 categories
  49. 4 categories of lipids
    • Simple lipids: fats, oils, waxes
    • Compound lipids: phospholipids, sphingolipids
    • Steroids
    • Miscellaneous: Lipoproteins, fat-soluble vitamins
  50. polar vs non-polar molecules
    • polar = hydrophilic, charged ion
    • non-polar = hydrophobic, no charge (no ions)
  51. fatty acids
    • the basic building blocks of lipids
    • have carbon backbone
    • has a carboxyl acid at one end, rest of molecules is long chain made of carbon and hydrogen (making them very hydrophobic... since lack of oxygen)
  52. saturated fatty acids
    • fatty acids where all the carbons are filled, or saturated, with hydrogen bonds
    • Saturated = no double bonds = no kinks
  53. unsaturated fatty acid
    • when a double bond forms btwn two of the carbon atoms in the chain of carbon & hydrogen
    • "missing a hydrogen" cause the double bond This double bond puts a "kink" in the regular zigzag pattern of the carbon backbone
    • Monounsaturated = one double bond = one kink
    • Polyunsaturated = many double bonds = many kinks
  54. four levels of protein structure
    primary ,secondary, tertiary, and quaternary
  55. primary protein structure
    • where the protein structure starts
    • the order in which amino acids are strung together w peptide bonds
    • (the straight string of bonded molecules)
  56. secondary structure of a protein
    • how the sequence (primary protein structure) is folded, held together by hydrogen bonds
    • 2 types of folding:
    • helix - "spiral staircase",(α-helix) due to formation of hydrogen bonds btwn nitrogen of one amino acid to the oxygen of another located in another part of polypeptide chain
    • Sheet like: (β-pleated sheet) occurs due to hydrogen bonding btwn polypeptide chains lying side by side
    • Ex: hair; made from keratin. made of 3 α-helices twisted 2gether in cable
  57. tertiary structure of protein
    • The 3-dimensional arrangement of how these helix spirals and sheets are put together, forming a larger folded structure
    • Kinda looks like a pretzel
  58. quaternary structure of protein
    • the final 3 dim structure formed by all polypeptide chains making up the protein
    • in some proteins, two or more subunits (each w own 1st, 2nd, and 3rd structure) combine
    • *looks like globs of pretzels combines (w white chocolate :-)  )
  59. Types of atomic interactions leading to tertiary structure
    • Ionic bonds: formed when + & - charges attract each other
    • Hydrophobic: occur where non-polar groups snuggle up to each other, excluding water
    • Van der Waals - NOT WELL UNDERSTOOD, occur when "shapes" of molecules fit together like puzzle, 
    • Disulfide bridges: formed btwn cysteine (only amino acid with -SH group)
    • Hydrogen bonds: formed btwn H and O, N, S and adjacent O, N, or S atoms
  60. denaturation
    • when the interactions of a protein is disrupted while in it's secondary, tertiary, or quaternary structure, and the protein is unfolded, leaving the primary structure intact
    • *doesn't affect primary structure
    • So NOT EFFECTING THE PEPTIDE BONDS but are effecting the weaker interactions:
    • ex :hydrogen bonds
    • some proteins can reconfigure; so were temporarily denatured (warming milk)
  61. enzyme
    • type of proteins that speed up (catalyze) chemical reactions
    • They lower the amount of energy needed to start the reaction
    • They CANNOT - and do not - change the amount of energy lost or gained
    • are specific on what molecules it helps
  62. substrate
    the substance on which an enzyme acts on
  63. plasma membrane
    • a protective covering that regulates what comes into or leaves from the cell
    • "plasma" implying it's liquidity in nature
    • forms a link to other cells
    • "flies a flag" to identify the tissue or organ that the cell comes from, as well as the individual that cell belongs to
    • basically a "Lipid sea" with protein "icebergs" floating in it (either integral or peripheral proteins
    • *because of markers specific to individuals, is a challenge when transplanting organs
  64. fluid-mosaic model
    • the new model for cell membranes, proposed by Singer and Nicholson in 1973
    • Has lipid "sea" w protein "icebergs" floating in it
    • Proteins are integral or peripheral
  65. integral proteins
    • transmembrane proteins
    • embedded in bilayer, some can go from one side to the other (completely through the bilayer, allowing transport of other molecules into/out of the cell) 
    • span the membrane w hydrophobic amino acid residues hanging out w the lipid tails in the hydrophobic core of "sandwich"
    • "Integral proteins are present in the membrane"
  66. peripheral membrane proteins
    • loosely associated w cell membrane and lie completely inside or outside of cell
    • Inside: link cytoskeleton to membrane
    • Outside: link cell to connective tissue or to other cells
  67. permeability
    • tells us how easily a substance can cross the the plasma membrane
    • Gases can pass easily, since gas molecules are small and un-charged
    • Small fat-soluble molecules (butane and propane) can pass easily
    • Don't pass: charged ions & large, water-soluble molecules (ex: proteins)
  68. differential permeability
    • what defines a cell
    • *the cell lets some things pass (water and cell nutrients must be allowed into the cell)
    • *The cell doesn't let other things pass (the "guts" of the cell shouldn't leak out, toxic substances shouldn't leak in)
  69. entropy
    • the sum of random events
    • going from organized to disorganized (would go against nature to go from disorganized to organized, cause that takes energy)
    • High entropy = high disorder; low entropy = low disorder
    • diffusion is a kind of entropy
    • Ex: pile of toothpicks  just dropped, not likely to pile up neatly.
  70. Brownian motion
    • the random motion of small particles or even molecules in a liquid or gas
    • they just zip and bang around into each other, like billiards
  71. diffusion
    • Type of passive transport
    • 2 kinds: simple & facilitated
    • Molecules in a liquid of gas state tend to spread themselves out evenly throughout the volume of a container
    • move in Brownian motion
    • Affected by temp: the warmer it is, the more movement
    • Affected by molecular size: the smaller the molecule, the more movement
    • over time, the concentration of the substance will become equal in all parts of the system & they reach equilibrium
  72. simple diffusion
    Passive movement of a substance down it's concentration gradient through the lipid bilayer of the plasma membrane w/o help of membrane transport proteins
  73. Fick's first Law (of diffusion)
    molecules always diffuse from an area of high concentration (as in the unstopping of a perfume bottle) to an area of low concentration (the air in the room where the bottle is opened)
  74. facilitated diffusion
    • facilitates the diffusion , type of passive transport
    • passive movement of a substance down it's concentration gradient through the lipid bilayer by transmembrane proteins that function as channels or carriers
    • (remember, larger molecules and charged molecules have to be "escorted" even if the concentration is higher outside than inside)
    • Some channels are gated, meaning when open, it's specific molecule can move. When closed, it can not
    • Ex: diffusion of K+ & glucose
  75. *review
    solvent vs. solute
    • solvent = "dissolver"
    • solute = "dissolvee"
    • (think of a "Ute" football player being stomped to the ground, dissolving)
  76. Osmosis
    • type of passive transport
    • the passive movement of water across a semipermeable membrane
    • describes the diffusion of solvents across a semipermeable membrane
    • "If solute can't move, then solvent has to move"
  77. diffusion vs. osmosis
    • diffusion: solutes move
    • osmosis: solvents move
    • (in osmosis, solutes cannot move)
  78. osmotic pressure
    • the amount of force required to equalize volume
    • Ex: think of the U shaped tube, with water and sugar solution, separated by semi-permeable membrane; putting a plug on the sugar side to keep volume the same.
  79. passive transport
    • Movement of substances down a concentration gradient until equilibrium is reached
    • NO ENERGY required
    • both diffusion and osmosis are examples
    • Ex: potassium ions, glucose
  80. Critical steps in facilitated diffusion of glucose
    • 1. glucose fits into "pocket" of glucose transporter (special protein in plasma membrane, specific for glucose)
    • 2. protein changes shape, closing glucose in pocket
    • 3. glucose transporter changes chape, forces glucose into cytoplasm
  81. active transport
    • always goes against gradient
    • used to move an ion against its concentration gradient
    • goes from low → high concentration
    • requires energy (ATP)
    • With sodium/potassium pump, moves both ions against their concentration gradients (so 3 Na+ moves out, 2 K+moves in), splits ATP for energy to do this (ATPase)
  82. electrogenic
    • referring to sodium/potass pump
    • since 3 positive charges are pumped out for every 2 allowed in, the cell is made more negative inside by the pump
  83. primary active transport
    active process in which a substance moves across the membrane against it's concentration gradient by pumps (carriers) that use energy supplied by ATP
  84. secondary active transport
    using the gradients we set up in primary active transport to move other ions/molecules against their concentration gradients
  85. Two unique types of transporters for (secondary) active transport
    • antiport system
    • symport system
    • This secondary active transport moves two or more molecules
  86. antiport system
    • move two or more molecules in opposite directions to drive the pump
    • Think of example of water "mill- wheel" (as in the Sodium/Calcium antiporters), as Sodium runs through will (turning it), Calcium can be "lifted" out of cell
  87. symport system
    • two or more molecules move in the same direction to drive the pump
    • again, think of example of water "mill" wheel, as the gate is opened for sodium to come into the cell, other molecules get "dragged in" w it or hitch a ride
  88. organelles giving structure
    • cytoskeleton 
    • centrosome
  89. cytoskeleton
    • "cell skeleton" ~ gives basic shape
    • Made up of structural proteins needed to move substances around the cell, as well as move cell around it's environment
    • a framework for cell to pull against to move or be moved
    • *made up of 3 different proteins: (from smallest to largest): Microfilaments, intermediate filaments, and microtubules
  90. microfilament
    • smallest structural protein in cytoskeleton
    • made of actin
    • it gathers together in microfilament strands (threads) to make up smallest structure of cytoskeleton
  91. intermediate filaments
    • medium sized structural protein in cytoskeleton
    • made up of keratin, vimentin, neurofilaments, lamins, and many other proteins
    • are thread like
  92. microtubules
    • largest of structural proteins in cytoskeleton
    • made up of the protein tubulin (alpha and beta), plus some microtubule-associated proteins (MAPs)
    • built like drinking straws, larger and more rigid than filamentous proteins
    • also used as "railroad tracks" in cell to move larger particles from place to place, especially in dividing cells & cells that move stuff over long distance such as nerve cells
  93. Lamellipodia
    • "extensions" that carry out functions which enable the cell to move from one place to another and enables cell to change shape
    • cell shape specialization supported by cytoskeleton
    • look like ruffles or sheets, can see them moving in real time
    • *recall endocytosis as active transport process (as phagocytosis & pinocytosis) ~ these rely on cell's ability to change shape
  94. microvilli
    • little shaggy hairs which increase the cells surface area
    • for cells that have an absorptive function, as in the intestine
    • each has microfilament core
    • on surface each has glycocalyx
    • cell shape specialization supported by cytoskeleton
  95. glycocalyx
    sugar-protein coat (shell) on surface of microvilli formed by digestive enzymes and cell "flags"
  96. centrosome
    • example of a microtubule-organizing center (MTOC) which are cell locations where microtubules are built (construction site)
    • represent origin of microtubules
    • Centrosome = centriole + pericentriolar material
  97. pericentriolar material
    the material around the centriole
  98. spindle apparatus
    • a rigid structure which lines up and then divides the chromosomes in cell division
    • formed from microtubules (which come from centrosomes)
  99. chromosomes
    • the packed genetic material that must be evenly split btwn two daughter cells
  100. organelles that provide synthesis
    • Ribosome
    • Rough ER
    • Smooth ER
    • Golgi comples
  101. ribosomes
    • the site of protein synthesis, makes proteins
    • are macromolecular assemblies (little factories) where proteins (+ some nucleic acids) gather together to do a job
    • a combination of RNA (Ribosomal ribonucleic acid), plus proteins
    • made of large subunit (60S) and small subunit (40S), when brought together forms ribosome
    • either found as free ribosomes or associated w membranes to make up the Rough ER
  102. endoplasmic reticulum
    • Comes in two types: Rough and smooth
    • Endoplasmic refers to "inside the cell"
    • "reticulum" is Latin for "network"
  103. Rough ER
    • (RER)rough endoplasmic reticulum = "rough inside cytoplasm network"
    • a collection of membrane bags w ribosomes arranged on surface
    • where we are making proteins and "dumping" them on the inside of the "sacks" or bags
    • Attached to Nuclear envelope of nucleus
  104. smooth ER
    • SER
    • three kinds (which all go by the same name): synthesis, storage and digestion
    • SER for lipid synthesis (because lipids are made differently than proteins, no ribosomes involved with SER)
    • SER for processing of toxins & cellular component
    • also for calcium storage in muscle (important for muscle cell function) (storage & digestion)
  105. mRNA
    • messenger RNA
    • the "instruction sheet"
  106. tRNA
    • transfer RNA
    • carrier for the raw materials of proteins (amino acids)
    • at the ribosome, amino acids are joined together by peptide bonds to form a protein chain
  107. Golgi complex
    • also called golgi apparatus
    • receives unprocessed proteins from rough ER and modifies them into their final form
    • Then it packages the proteins and "tags" them for export to final destination
    • Like "UPS pack and mail" store
    • is curved, functions are not distributed symmetrically
    • Think of Golgi's handle-bar mustache.. haha
  108. Who's going to Ace this test???
    Who's going to Ace this test???
  109. cis face
    • also called entry face
    • part of Golgi Complex which receives transported material from the rough ER
  110. trans face
    • also called exit face
    • opposite side at entry (duh)gives rise to secretory vesicles to transport material
  111. Protein processing in Golgi Complex
    • 1. protein is synthesized in Rough ER
    • 2. Transport vesicles carry "raw", unprocessed proteins to Golgi
    • 3. Transport vesicles fuse w cis face of golgi
    • 4. As proteins are processed, they are moved from one golgi stack to the next by transfer vesicles (in stacks, unused parts are removed by one set of enzymes &, if a glycoprotein is being produced, the branched sugar groups are added here)
    • 5. Last transfer vesicle fused w the trans face of Golgi
    • 6. the processed, completed protein is packages into vesicle which is shed from exit face
  112. Once protein is shed from exit face of Golgi, where does it go?
    • can go one of three places:
    • If a secretory protein, is packaged into vesicle and released from cell by exocytosis
    • If a membrane protein (or glycoprotein), packaged into a membrane vesicle which fuses w cell membrane. The protein or glycoprotein then becomes part of cell surface
    • If protein is defective or not needed, packaged into vesicle which is directed to lysosome for breakdown and recycling
  113. organelles that provide energy
  114. What is ATP?
  115. What is metabolism
    • Basically all the chemical reaction that go within our body
    • The process of metabolism has two components: building (also called synthesis or anabolic)  and  if we are "tearing down) (catabolic)
  116. anabolism
    • the buildup of smaller molecules into larger ones
    • Is endergonic 
    • we put energy in, energy goes "en-to" and is stored in bonds
    • consume ATP and release waste energy as heat (making it exothermic)
    • ADP + P + energy = ATP
  117. endergonic reactions
    reactions which require energy(ergon- is Greek for energy; so energy goes "en-to" bonds)
  118. exergonic reactions
    reactions in which energy is released (or extracted from bonds)
  119. catabolic
    • the breakdown of large molecules into smaller ones
    • energy is released from bonds, making it an exergonic bond (energy is extracted from bonds); get more energy out than what we put in
    • create ATP and also release waste energy as heat (making it exothermic)
    • ATP ⇒ ADP + P + energy
  120. When ATP is broken down....
    • ATP → ADP + P + energy (+ heat)
    • Starting with simple molecules such as glucose, amino acids, glycerol and fatty acids
    • Anabolic reaction takes place, which transfers energy from ATP to create complex molecule such as glycogen, proteins and triglycerides
  121. Creating ATP....
    • ADP + P + energy = ATP + heat
    • Involves catabolic reaction
    • If complex molecules are broken down (such as glycogen, proteins, and triglycerides), the catabolic reaction transfers energy from them back into ATP (also releases heat as byproduct) breaking back down to glucose, amino acids, glycerol, and fatty acids.
  122. exothermic
    heat releasing reactions
  123. How does ATP play central role in metabolism
    • What we eat (proteins, carbs and lipids) is broken down into amino acids, sugars and fatty acids.
    • The bonds of these molecules are then broken, creating energy (catabolism)
    • The energy released is stored as ATP (more correctly, IN ATP)
    • Then, the energy from ATP's bonds is recaptured (anabolism) as cellular structures are built from amino acids, sugars and fatty acids.
  124. Metabolism vs Burning
    Metabolism is a controlled burning process. Energy is released in smaller, controlled steps, storing energy in ATP as you go.In burning, all energy is released in one step.
  125. How do organ systems interact to maintain energy homeostasis?
    • Digestive system absorbs nutrients from food
    • Respiratory system brings O2 in, blows  CO2 out
    • Circulatory system brings nutrients and O2 to cells, carries waste & CO2 away
    • Excretory System rids body of waste (urea from proteins in the urine, feces, etc)
  126. Dephosphorylation
    • Simply taking a phosphate away
    • ATP → ADP + P
  127. Phosphorylation
    • simply adding a phosphate 
    • ADP + P (+energy) = ATP
  128. C6H12O6
    The main nutrient we use for energy = glucose
  129. remember ability of an acid
    can be a proton donor
  130. Think of metabolism as a theatrical production
    • Starring Role: Glucose
    • Supporting Cast: Pyruvic acid, Lactate acid, Coenzyme A (CoA)
  131. Pyruvic acid
    • "pyruvate" in ion form, when acid donates a proton
    • "supporting role" in metabolism
    • a 3 carbon molecule that is important intermediate in metabolism
  132. Lactic acid
    • "Lactate" in ion form; when acid donates a proton
    • "supporting role" in metabolism
    • has 3 carbons, but represents a metobolic "dead end"
  133. CoA
    • Coenzyme A: two-carbon carrier
    • is a sulfur-containing molecule that acts as a carbon carrier
    • Think of this as the "shovel" that can hold only two-carbon "lumps of coal"
    • Two-carbon "lumps of coal" units are acetate groups
    • *fact that only two carbon units can fit into the Krebs cycle "furnace" is important to keep in mind!!!
    • When it is carrying an acetyl group, it's called acetyl - CoA Actually a B vitamin
  134. cofactor in a chemical reaction
    a substance which participates in the chemical reaction, but is not consumed by the chemical reaction, but serves specific function
  135. gene
    region of DNA that codes for a protein
  136. mRNA
    • messenger RNA ~ the final edited version
    • carries the code for a primary sequence of amino acids in protein
    • responsible for being copied and carrying that information out of the nucleus, into the cytoplasm, where the ribosomes can act on it.
    • Leaves nucleus through nuclear pores
  137. 4 bases involved with DNA
    • Adenine, Cytosine, Guanine, Thymine (DNA only)
    • Reading order: A,G,C,T (5′ to 3′) ~ where A -T only bind to each other, and G - C only bing to each other.
    • Dana Aint Gonna Catch Trust
  138. 4 bases involved w RNA
    • Adenine, Cytosine, Guanine, uracil (RNA only)
    • For reading order: A, G, C, U (5′ to 3′) ~ 
    • where A-U only bind together, and G - C only bind together
    • Think of "R U Dana Thelander?"  (RNA)
  139. How is mRNA made?
    • In the DNA sequence of the gene, it has both exon and intron sections.
    •  We take several of these exon regions and, through RNA processing (editing), cut them out and splice them together to form the final mRNA which is translated into a polypeptide or protein
    • After which, the mRNA can pass through the nuclear membrane into the cytoplasm and be translated.
    • **Note that although introns were transcribed, they will not be translated.
  140. RNA Editing
    • An RNA/protein particle (small nuclear ribonucleo-protein = snRNP, pronounced "snurp")
    • it removes introns (part of DNA not made into protein and edited out) by forming lariats
    • The it cuts and splices exons together (portion of DNA that is made into protein)
  141. 3 types of RNA that are players in protein synthesis
    • mRNA ~ messenger RNA
    • rRNA ~ ribosomal RNA (makes ribosomes)
    • tRNA ~ transfer RNA (trucks amino acids to ribosome)
  142. mRNA
    • messenger RNA ~ carries coded message from nucleus to ribosome
    • very unstable, allows for transcriptional control of protein production
    • made by RNA polymerase II
  143. rRNA
    • ribosomal RNA ~ w proteins, forms ribosomes (protein factories); small and large subunits
    • more stable than mRNA, (mostly) made by RNA polymerase I
  144. tRNA
    • transfer RNA ~ "trucks" to bring amino acids to the growing protein strand
    • supplies ribosomes w correct amino acid
    • each has a unique anticodon
    • RNA folded up into a cloverleaf-shaped: one loop of RNA forming a "leaf" (anticodon) matches the mRNA message (codon)
    • The acceptor arm "stem" carries an amino acid shape held together by hydrogen bonds
    • Notice each tRNA has a particular pairing of anticodon and amino acid
    • more stable, made by RNA polymerase III
  145. anticodon
    • one of the loops of the "clover leaf" shape of the tRNA
    • has a set of three ribonucleotides, which will bind to the mRNA (by it's codon)
    • pared w a specific amino acid which binds to an acceptor arm
  146. codon
    three base pairs on mRNA, coding for an amino acid, matches up with tRNA (at anticodon)the sequence in mRNA which codes for a protein
  147. acceptor arm
    • the "stem" part of the "clover-leaf" shape of tRNA
    • carries the amino acid
  148. start codon
    • 5′-AUG-3′ is always the start codon for mRNA translation
    • matches up to anticodon (5′-CAU-3′) on tRNA
  149. terminator code
    • in translation
    • UAA, UAG OR UGA  means STOP
  150. Steps in Translation
    • 1. Ribosome attaches to mRNA
    • 2. AUG start codon matches up to tRNA- which is carrying methionine (in parking spot P, parking spot A is empty)
    • 3. Next tRNA-amino acid arrives (pulls into parking spot A)
    • 4. Peptide bond forms (the two amino-acids in the parking spots decide they should bond. synthesis begins)
    • 5. Ribosome shifts three mRNA bases (met-tRNA is released to bonded amino-acid, leaves parking spot P so other tRNA in parking spot A can now park in P, and empty parking A can be occupied by new amino acid - tRNA
    • 6. Process continues, polypeptide is growing
    • 7. stop codon is reached, polypeptide is released
  151. Cell Cycle
    • Mitosis and interphase
    • takes approx. 24hr to complete
  152. Interphase
    • part of cell cycle, period btwn cell division
    • DNA is in euchromatin form
    • Consists of 3 stage when cell is not actively dividing-G1 (also called "growth-1" or "gap-1")-S (replication of DNA)-G2 (growth-2 or "gap-2")
  153. G1
    • happens after mitosis, first growth (or gap) phase; called "Gee-one"takes 8 - 10 hours to complete
    • Cell duplicates organelles and cytoplasmic components
    • In order to enter S phase, cell must pass "checkpoint"
  154. "checkpoint" in interphase
    • btwn G1 and S, also btwn S and G2
    • Similar to going through customs at airport... hitting many checkpoints
  155. quiescent
    a resting state, cell is incapable of cell division, parked in cell cycle called G0
  156. G0
    • pronounced "Gee-zero"
    • If cell cannot pass the G1/S checkpoint, or is quiescent (not actively dividing) remains in G0
    • where cell exits cell cycle, gets "off merry-go-round"
    • *G0 Lock happens when a cell never comes out, or never divides again.
    • Like neurons spend lifetime here
    • Other cells (like liver, kidney) may wait here for up to several years but can prepare for division if needed
  157. S
    • phase in interphase, stands for "synthesis" (for DNA)
    • replication of DNA so it can divide equally btwn daughter cells (went from 46 to 92 chromatids)
    • takes 8 hours
  158. G2
    • last part of interphase, finalizes it's preparations for mitosis
    • Cell now carries double amount of normal DNA
    • Duplication of centromeres, now has 92 DNA molecules
    • Second checkpoint must be crossedtakes 4 - 6 hours
  159. chromosome #'s
    • called "n"
    • Each daughter cell must have appropriate amount of DNA: two copies of each gene, called a diploid # (2n)
    • Cells which have only one copy of each chromosome are called haploid (sperm or egg)
  160. DNA replication
    • process by which DNA molecules increase to 92
    • these 92 molecules are packed into 46 chromosomes and when chromatids are ripped apart at anaphase, each daughter cell gets 46 DNA molecules. 
    • *since dna is only synthesized in one direction (5′ to 3′), this creates problem since strands are antiparall.
  161. Mitosis vs. Cytokinesis
    • Mitosis: process of nuclear division. Genetic material must be parcelled equally btwn cells, chromosomes form, get pull apart, dissolve
    • Cytokinesis: process of cell division (happens at end of mitosis, in cytoplasm & organelles). plasma membrane of cells tightens like rubber band and pinches off two cells. Separates genetic material cytoplasm and organelles into two equal daughter cells.
  162. cytokinesis
    "cell motion"how daughter cells move apart.
  163. mitosis
    • M phase ~ the actually, active process of cell division
    • takes about 30 minutes
    • 4 stages: prophase, metaphase, anaphase, telophase
    • "please meet aunt teresa"
  164. prophase
    • first phase of mitosis
    • DNA is tightly packed into chromosomes
    • nuclear envelope breaks down
    • mitotic spindle forms
  165. metaphase
    • middle phase of mitosis, everything in parent cell lines up in middle
    • chromosomes (formed in prophase) move to middle of parent cell and microtubules of mitotic spindle attach to anchors (centromeres) 
    • phase used to create karyotype
  166. anaphase
    • the phase of mitosis where the contents of the two daughter cells move backwards, away from each other
    • chromatids are torn apart in two equal pieces
  167. telophase
    mitosis is complete ("telo: end")cleavage furrow appears, cell split
  168. alleles
    • One copy of a gene inherited from the mother, and one copy of a gene inherited from the father.
    • each child has 50/50 chance of getting each allele
    • *In modern molecular genetics, these are the same as polymorphisms
  169. Dominant alleles
    • those where inheriting one copy of the gene, or getting the DNA, which will give you a condition or disease
    • Only takes one gene to have disease
  170. Recessive alleles
    those where inheriting one copy of a gene makes you a carrier, inheriting two copies will give you a condition or disease
  171. punnett squares
    • used to analyze genetics
    • Use capital letter for dominant allele
    • Use small letter for recessive allele
    • *if disease is dominant, then individuals with AA or Aa will have disease, while those w/ aa will not
    • *if disease is recessive, than individuals w AA or Aa will not have disease, but individuals w aa will
  172. Albinism
    • lacking of skin pigment
    • an autosomal recessive genetic disease
  173. sickle cell anemia
    • mutation during transcription
    • causes overall structure of red blood cells to change from biconcave disk to ragged, sickle shaped which is susceptible to damage as it passes through narrow capillaries
  174. 3 major shapes or morphological types of bacteria
    • 1st: cocci
    • 2nd: bacilli = coccobacilli - vibrios
    • 3rd: spirillia and spirochetes
  175. Cocci/Coccus
    • singular: coccus
    • ("berry, grain") spherical bacterial cells, non-motile
    • subcategories: diplo (pair), strepto (chain), staphylo (irregular cluster) and tetra (group of four)
  176. bacilli
    • Singular: bacillus
    • rod-shaped bacteria, ("little rod, wand")
    • Included coccobacilli and vibrios
    • Ex: e coli
  177. coccobacilli
    • those bacteria shaped btwn a cocci and bacilli
    • are oval shaped
    • Coccus ("berry, grain") + bacillus ("little rod, wand") = coccobacillus
  178. vibrios
    • the bacteria shaped btwn cocci and bacilli
    • exhibit a comma-shape
    • *their single flagellum makes them appear to vibrate under the microscope, hence the name
    • Ex: Causes cholera
    • "collars and vibraters"
  179. spirilla
    • Singular: spirillium
    • either loosely-coiled or wavy
    • division of one of "third" main bacterial shapes, are long, thin, spiral, rigid rod-shaped cells
    • "Will-ya spill em, hold tight!"
  180. spirochetes
    • division of one of "third" main bacterial shapes
    • are tightly coiled, corkscrew-shaped rods, non-rigid
    • hard to see
    • Ex: syphilis"phyllis cheats (chetes), uncork the wine n unwind"
  181. diplococci
    cocci found in pairs
  182. streptococci
    • cocci which form chains
    • strepto- = chains of
    • -cocci = round bacteria
    • "Steps have straight lines, like chains are straight lines"
  183. staphylococci
    • cocci which form grape-like clusters
    • staphylo- = clusters of
    • -cocci = round
    • "like when you bang a staph on the ground, round circles in irregular patterns..."
  184. binary fission
    • term used to describe cell division in bacteria
    • process of growth and division continues as long as favorable environmental and adequate nutritional conditions exist
    • also known as transverse fission
  185. Bacterial cell division
    • do not have cell cycle
    • are continuously dividing and replicating their DNA, as long as their are in favorable and nutritional conditions
    • Phases: Lag Phase and Log Phase
  186. Phases of bacterial Cell Division
    • Lag Phase
    • Log Phase
    • Stationary phase
    • Decline (death) phase
  187. Lag Phase
    • The "gear-up" phase
    • not greatly increasing in #, but metabolically active (growing, synthesizing enzymes, and producing large amounts of ATP)
    • do not reproduce in significant #'s during this phase
  188. Log Phase
    • the period of rapid, exponential growth
    • generation time: genetically determined period of logarithmic growth
    • will continue as long as there are sufficient nutrients and environment has suitable conditions for synthesis of ATP
  189. generation time
    • how long it takes a bacteria to divide
    • the genetically determined period of logarithmic growth which varies by bacterial species from minutes to hours
    • Most are under 10 hrs
  190. Stationary phase
    • "leveling off" period, the phase of bacterial growth in which non-replicating cells (those dying off) are about the same in #'s as those still reproducing new cells
    • Cells are running out of nutrients
  191. Decline (Death) phase
    • happens once the essential atmospheric, temp and nutritional conditions for log phase are depleted
    • The # of cells dying is greater than # of new cells arising from division
    • cells lose their ability to maintain metabolic funtions
  192. Symbiosis
    • means "living together"
    • bacteria may form 3 different symbiotic relationships w a living host:
    • Mutalism, parasitism, and commensalism
  193. Mutalism
    • type of symbiotic relationship, both members of association benefit
    • Ex: Escherichia coli (E. coli) in large intestine of humans. We provide nice, warm environment; we benefit from Vit. K produced from E. coli, which is essential for clotting process. Also ward off disease-causing organisms and help digest cell walls of plants. So, beneficial.
  194. Parasitism
    • one organism, the parasite, benefits from the relationship and the other organism, the host, is harmed.
    • Many types
    • Ex: malaria and tapeworms
  195. Commensalism
    • one organisms benefits and the other neither benefits or is harmed.
    • Ex: bacteria which live on our skin
  196. Two classes of bacteria that must be intracellular to survive:
    Chlamydia and Rickettsias
  197. Chlamydia
    • Obligate intracellular organisms
    • The most common STD in the US; causing pelvic inflammatory disease (PTD) in women & urethritis in men.
    • Another variant causes epidemic conjunctivitis in newborns acquired during passage through the birth canal
    • Require a eukaryotic cell for replication
    • Ex: Chlamydia trachomatis causes a variety of human infections
  198. Chlamydia trachomatis
    • A complex organism that has multiple serological variants which cause a variety of human infections.
    • Ex: Trachoma, STD's and conjunctivitis in newborns acquired during birthing process
  199. Trachoma
    an eye infection caused by Chlamydia trachomatis  One of the leading causes of blindness in the world
  200. Rickettsia
    • obligate intracellular parasites with complex life cycle
    • normally inhabit arthropod vectors (such as ticks, lice, fleas, etc.)
    • Transmission to humans is through a bit
    • most prevalent in US is Rocky Mtn. Spotted Fever
    • Lime Disease
    • *Utah doesn't have tick that causes these diseases
  201. Mycoplasmas
    • the tiniest free-living organisms
    • unique in the bacterial world cause they do not have a cell wall ~ therefore have no set shape
    • diverse in nature, especially in many animal & bird species
    • Some species actually make up normal respiratory and urogenital microflora of humans
  202. Mycoplasma pneumoniae
    attaches to surface epithelial cell sites and causes a respiratory disease primary atypical pneumonia (walking pneumonia)
  203. General nature of viruses
    • are obligate intracellular parasites
    • need a host cell; virus provides the RNA or DNA to replicate, takes over genetic machinery of host cell
    • Contain RNA or DNA (NOT BOTH)
    • RNA viruses also contain code for reverse transcriptase, enzyme which makes DNA from RNA
    • Are DNA viruses OR RNA virusesOver half of all human infectious processes are due to viruses
  204. Why is it hard to target viruses?
    they change their antigens frequently, so they are continually changing
  205. Viral classification
    in general, viruses are broadly classified as either RNA or DNA viruses based on the make-up of their genome
  206. Viral structure
    • Nucleic acid (RNA or DNA)
    • Capsid
    • envelope
  207. Nucleic acid of virus
    • A virus contains either a single or double strand of DNA or RNA
    • in nuclear region
    • differing among viral groups
  208. Capsid (viral structure)
    • protective coating enveloping the nucleic acid in viral cell
    • determines the shape of the virus
    • Composed of capsomeres
    • can be helical, polyhedral (multi-sided), or in some cases bullet-shaped
  209. capsomeres
    the individual protein subunits which make up capsids
  210. nucleocapsid
    the combined capsid/nucleic acid arrangement (viral structure)
  211. Viral envelope
    • when present, are external to the capsid & are acquired from the combo's of proteins, lipids and carbs found in host cell
    • many viruses have glycoprotein spikes
    • These structures account for high degree of both host, and host cell, specificity of viruses
    • many also serve to "hide" virus from being attacked by host's immune system
  212. Viral replication process
    • also referred to viral progeny
    • 5 step replication cycle:
    • ~1 Adsorption
    • ~2 Penetration
    • ~3 Synthesis
    • ~4 Maturation
    • ~5 Release
    • "A Penis Soothes My Rages"
  213. virion
    a single, complete virus unit
  214. Adsorption
    • Step 1 in 5-step viral replication cycle
    • Attachment of the virus to host cell
    • W/ enveloped viruses, the glycoprotein spikes attach to specific matching sites on hosts cell wall
    • W/ naked (non-enveloped) viruses, attach to specific molecular sites on cell surface
  215. Penetration
    • Step 2 in 5-step viral replication
    • follows quickly after adsorption, process by which virus enters host cell via endocytosis or fusion w cell membrane of host
    • Once inside, virus uncoats
    • free strand of nucleic acid then moves to host cell's nucleus
    • "Sexual penetration requires no clothes"
  216. uncoating of virus
    upon entering host cell, virus immediately loses envelope and capsid
  217. Synthesis
    • Step 3 in 5-step viral replication
    • produces new genetic material and varies btwn RNA and DNA viruses
    • W/ DNA viruses, the DNA is synthesized in orderly manner in nucleus, using viral enzymes in transcription
    • Proteins are synthesized in cytoplasm using host cytoplasmic enzymes and by using the host cell ribosomes and Golgi organelles
  218. Maturation
    • Step 4 in 5-step viral replication
    • the assembly, or "packaging" of the newly synthesized molecules into complete virions (new little baby viruses)occurs as soon as abundance of viral nucleic acid, enzymes and proteins have been synthesized
    • some viruses are capable of inserting viral genetic material into host's genome permanently, which is then capable of producing new viruses.
    • Can occur years after infection
  219. Release
    • Step 5 in 5-step viral replication
    • the departure of the new virions from the host cell
    • is this final cycle of viral reproduction that may be the cause of symptoms in host
    • Some viruses rupture host cell releasing virions; others release viruses and host cell remains intact in process called budding
    • enveloped viruses form their envelopes from host cell membrane as they exit the cell
  220. Viral Pathogenicity
    • viruses are very specific about which animal/animal cell they target for infection
    • nature of infection depends on type of virus, system affected and host response
    • Several types of viral infections that fall into two main categories: acute and latent (persistent)
  221. Acute viral infections
    • Disease cycle is relatively short
    • Host cell rupture and virus spreads to neighboring cells
    • After sufficient cellular damage, symptoms rapidly appear in infected host. 
    • It's up to host's immune defenses to eradicate viral invaders, as well as provide measure of protection from future exposure to viral agent
    • Ex: common cold (rhinovirus), influenza (types A and B), hepatitis viruses
  222. Latent/persistent viral infections
    • vary widely in scope
    • once in cell, infection proceeds by replication of essential enzymes and proteins, but viral material (also called provirus) remains in host and replicates new virions when "triggered"virus becomes relatively inactive but reemerges
    • provirus remains in host cell
    • Replicates new virions when triggered by some external event (stress, fever, etc.)
    • Ex: herpes virus, Epstein-barr Virus, HIV
  223. herpes viruses
    • classic example of virus causing both acute and latent/persistent viral infection
    • Cold sores are acute phase of herpes infection
  224. Epstein-Barr virus
    • infectious mononucleosis
    • immune system virus
  225. oncogenic viruses
    • cancer-producing viruses
    • possess oncogenes that cause uncontrolled and abnormal division of host cells by altering cell cycle "checkpoints"
    •  Ex: hepatitis B, Hepatitis C, Human Papilloma virus
  226. oncogenes
    cancer-causing genes which cause the uncontrolled and abnormal division of host cells
  227. human papillomavirus
    virus which has been directly linked to cervical cancer in women
  228. treatment of viral infections
    • MOST EFFECTIVE means of preventing many viral diseases is through use of vaccines
    • very few effective therapies; antibiotics are ineffective since they act on bacterial cell components not found in viruses
    • Some antiviral drugs do slow down attachment of virus to host cell
    • Some simply suppress, do not cure, viral infection
    • Vaccines targets at viruses include polio vaccine, Gardasil for cervical cancer, and the hepatitis vaccines
  229. the kingdom of Fungi
    • important for decomposition and recycling of organic material
    • include mushrooms
    • medically important
    • divided into two groups: yeasts and molds
    • some are human pathogens, some are toxic and hallucinogenic
  230. Mold
    • produces spores whose arrangement and appearance depend on fungal species
    • some cause opportunistic infections, especially among those w compromised immune systems
    • Many affect respiratory system due to inhalation of spores from environment
  231. Pathogenicity of molds
    • varies, but are usually limited to infections of the hair, nails and skin
    • includes infections as athlete's foot, jock itch and ringworm
    • other infections, usually found in tropical regions, cause moderate to serious infections
  232. Yeasts
    unicellular fungi; important in bread, beer & alcohol production, and other applicationsSeveral species exist as normal flora, especially on mucus membranes and GI tract
  233. Pathogenicity of yeast
    • Some species are opportunistic pathogens of humans which take advantage of weakened defenses
    • Most common caused by Candida albicans  which causes thrush (infection of mouth and pharynx) & vaginitis
    • Those w diabetes & compromised immune systems most susceptible, systemic infections do occur
  234. Parasitic organisms, classification
    • two large groups: single-celled protozoa & multi-celled helminths (worms)
    • Protozoa are in kingdom Protista
    • Helminths, like humans, are in kingdom Animalia
  235. parasite
    • an organism that lives at the expense of another organism
    • transmitted to humans by vectors ~
    • biologically, ex: mosquito transmitting malaria. mechanically, Ex: transmission of parasite eggs to food by flies & other insects
    • epidemic to much of worlds population, especially in underdeveloped countries
    • account for up to 20 million deaths per year, either from parasitic disease itself, or from complications from disease
  236. Protozoa
    • single-celled, in kingdom Protista
    • in general, 2 stages: trophozoite & cyst stage
  237. Trophozoite stage
    protozoa stage which is infective;  the motile, invasive form of the organism
  238. Cyst stage
    protozoa stage which allows the organism to survive in a dormant state in the external environment
  239. Giardia lamblia
    • very common protozoan disease for humans, found worldwide
    • Humans become infected by ingesting the cysts in water contaminated by animal carriers
    • a flagellated protozoan causing intense gastrointestinal distress & diarrhea
    • can be treated w antibiotics
  240. Cryptosporidium
    • common protozoan pathogenic for humans
    • become more prevalent
    • causes self-limiting GI symptoms
    • Infected individuals can become chronic carriers, potentially have ability of infecting others
    • associated with recreational water use (public swimming pools)
  241. Plasmodium
    • common pathogenic protozoan for humans, who are intermediate hosts
    • causes malaria
    • first goes after liver, next generation affects red blood cells
    • causes over 1 million deaths per year, most are young children in Africa
    • several species, all transmitted by Anopheles mosquito
    • organism invades RBC's during asexual phase of life cycle
  242. Helminths
    • (Worms)
    • come in four groups: flukes, tapeworms, roundworms and tissue parasites (which can be a roundworm, larval form or tapeworm)
    • hosts are definitive or intermediate, or accidental
  243. definitive hosts
    host for helminth which harbor the parasite when it reproduces by sexual reproduction
  244. intermediate hosts
    hosts for helminth which harbor the parasite at some developmental stage in it's life cycle
  245. Accidental hosts
    • hosts for helminth which are not part of the normal life cycle of the infectious parasite
    • most are also 'dead end' hosts, they do not transmit the infection further
  246. Examples of helminths
    tapeworms and roundworms
  247. tapeworms
    • segmented worms that contain a head (scolex) and many segments (proglottids)
    • are hermaphroditic, containing both ovaries and testes
    • infective stage is larvae found in cattle and swine
  248. roundworms
    • intestinal, found throughout world.Adults live in lumen of intestinal tract
    • human infection occurs either by ingestion of mature egg (ovum) or by penetration of skin by larval stages found in warm, moist soil.
  249. Enterobius
  250. Ascaris
    the giant intestinal roundworms"helminths"
  251. hookworms
    can penetrate skin
  252. Strongyloides
    common intestinal worm
  253. Streptococcus pyogenes
    • bacteria that causes pharyngitis"strep throat"upper respiratory tract infection
    • common in winter
  254. Haemophilus influenzae
    • one of top 3 bacterial organisms which can cause pneumonia
    • contain a capsule virulence factor
    • involved in lower respiratory tract infection (lungs)
  255. Klebsiella pneumoniae
    • one of top 3 bacterial organisms which can cause pneumonia
    • contain a capsule virulence factor
    • involved in lower respiratory tract infection (lungs)
  256. Streptococcus pneumoniae
    • one of top 3 bacterial organisms which can cause pneumonia
    • contain capsule virulence factor
    • involved in lower respiratory tract (lungs)
  257. Salmonella
    • type of bacterial organism which infects the GI tract
    • acquired from contaminated food or water
  258. Shigella
    • type of bacterial organism which infects GI tract
    • acquired from contaminated food or water
  259. Staphylococcus aureus
    • type of bacterial organism which can infect GI tract
    • acquired from contaminated food or water
  260. E. coli 0157:H7
    • a specific type of E.coli organism, bacterial
    • common in intestinal tract of cattle, has been linked to contaminated meats and veggies
  261. Haemophilus Influenzae
    • ype of bacterial organism which infects the cerebrospinal fluid and meninges
    • particularly in young children
    • vaccine is available
  262. Neisseria meningitidis
    • type of bacterial organism with infects the cerebrospinal fluid and meninges particularly in young adults
    • vaccine is available
  263. Clostridium botulinum
    • botulism
    • secretes toxins
    • bacterial
  264. Clostridium tetani
    • tetanus
    • secretes toxins
    • bacterial
  265. Staphylococcus aureus
    • toxic shock syndrome
    • secretes toxins
    • bacterial
  266. Candida albicans
    • species of yeast that cause the most common yeast infections
    • causes thrush in the mouth and vaginitis