FOM Week 1

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FOM Week 1
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2010-08-24 16:13:27
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  1. Genome
    the complete set of genetic info encoded in base pairs
  2. Definition: Open Reading Frame (ORF)
    portion of the genome that codes for a protein
  3. Defintion: Regulatory Regions
    control gene expression of ORF
  4. Definition: Exons
    the coding portion of a gene tat produces a functional product (eg. mRNA)
  5. Definition: Introns
    DNA regions within a gene that is not translated into protein
  6. What is the central dogma of Omics?
    A DNA open reading frame has multiple introns and exons and can code for multiple RNAs via transcritpion. These RNAs can be translated into multiple proteins which can then undergo an array of post-translational modifications
  7. What was the previously believed central dogma of omics?
    1 gene--> 1 RNA--> 1 protein
  8. Definition: Omics
    study of the genome
  9. Definition: Transcriptome
    the complete set of RNA molecules produced in a given cell or organism-unlike the genome, it can vary with external conditions
  10. Definition: Proteome
    all the proteins present in a cell at any given time--more difficult to read than the transcriptome
  11. Definition: Polymorphism
    a mutation; a change in the sequence of DNA; a single nucleotide polymorphism (SNP) can lead to genetic variation; don't necessarily know the functional consquences of all polymorphisms; can be good/indifferent or bad
  12. When DNA is transcribed, what does a thymine residue code for?
    Uracil on the RNA
  13. What do A, T, C, and G stand for and to which base pair do they pair?
    • Adenine, thymine, cytosine, and guanine, respecitvely.
    • C and G pair together, A and T (U) pair together
  14. If the DNA sequence to be transcribed is ATCG, what will the mRNA sequence be?
    UAGC
  15. Schematically, on which side of a polypeptide chain is the N-terminus usually drawn?
    N-terminus is normally on the left while the C is on the right
  16. Which amino acids have positively charged side chains?
    Arginine, Histidine, Lysine
  17. Which amino acids have negatively charged side chains?
    Aspartic acid and glutamic acid
  18. Which amino acids have a polar, yet uncharged side chain?
    Ser, Thr, Asn, Gln
  19. The side chain of glycine is simply a hydrogen. Does this residue help/hinder alpha helices?
    Hinders. Glycine causes a kink in the alpha helix
  20. What is unique about the side chain of proline?
    The three carbons of the proline side chain covalently interact with the nitrogen that forms an integral part of the backbone, forming a ring
  21. Which amino acids have a hydrophobic side chain?
    Alanine, Isoleucine, Leucine, Methionine, Phenylalanine, Tryptophan, Tyrosine, and Valine
  22. What determines the primary structure of a polypeptide?
    The squence of a chain of AAs
  23. What are the two most common secondary structures?
    Alpha helices and beta sheets
  24. What does it mean to say that a beta sheet is antiparallel?
    The polypeptide interacts with itself so that strands forming the beta sheet are running opposite each other, such that N-termini and C-termini alternate
  25. What is a tertiary structure?
    It occurs when certain attractions are present between alpha helices and beta sheets; it is the overall 3D structure of a single polypeptide chain
  26. What is the difference between a domain and a motif?
    • A domain is a discrete portion of the same polypeptide that has a discrete function. It is generally larger and found in a class of proteins.
    • A motif can be determined from the primary sequence and is generally smaller. It's discrete function can be found in many proteins because it is more common, broad, and less specialized than a domain
  27. What is the difference between a quaternary structure and an aggregation?
    While a quaternary structure forms through controlled folding processes, an aggregation forms through an uncontrolled process of proteins sticking together and is usually pathological
  28. What organelle is hematoxylin stain used to identify?
    The nucleus; stains it blue
  29. What is the stain eosin used to identify?
    • Red blood cells (orange) and collagen fibers (pink)
    • It also stains the cytoplasm an intense pink when numerous mitochondria are present
  30. What tissue is Masson's trichrome most commonly used in?
    The connective tissue. It stains the cartilage blu-green and the muscle fibers red
  31. What tissue is Mallory's Trichrome most commonly used in?
    Connective tissue; it stains keratin orange, cartilage blue, bone matrix a deep blue, and muscle fibers red
  32. What does PAS stand for, and what cellular structure is it most commonly used to identify?
    Periodic acid shift: The basement membrane and carbohydrates; it stains glycogen and other carbohydrates a magenta color; Used to stain sugars
  33. What is an antigen?
    most simply, it's the protein of interest
  34. Why are secondary antibodies used to identify antigens?
    The secondary antibody is a marker-coupled antibody that is directed against a primary antibody; it is used to amplify the signal
  35. What is the primary function of the nucleus?
    To maintain the integrity of the cell by regulating gene expression
  36. Histologically, what is the main difference between the nucelus and mitochondria?
    The nucleus may be the same shape and color as the mitochondria, but it will always be much bigger than the mitochondria
  37. What is the function of the rough endoplasmic reticulum?
    It forms an interconnected network of tubules in vesicles within cells; its primary function is to syntehsize proteins
  38. What is the function of the ribosomes?
    This is located on the RER and is the site of protein translation
  39. What are the function of the smooth ER?
    sythensizes lipids and steroids, metabolizes carbohydrates and steroids, reguates calcium concentration, drug detoxification, and attachment of receptors on cell membrane proteins
  40. What is the function of glycogen in the cell?
    Globs of protein are stored in the form of glycogen in the cell; stains very dark
  41. Histologically, how are lysosomes and peroxisomes different?
    Lysosomes are much darker in color than peroxisomes
  42. What is the function of lysosomes?
    They contain enzymes that break up materials within the cell and cellular debris
  43. What is the function of the golgi complex?
    It processes and packages macromolecules such as proteins and lipids after their synthesis and before they make their way to their destination
  44. What is the defining characteristic of GAs under the microscope?
    They are stacked complexes
  45. What is the function of the 2 centrioles in the cell?
    They are involved in the organization of the mitotic spindle and the completion of cytokinesis
  46. What is the function of the brush border located on cilia?
    To increased the surface area and absorption of microvilli
  47. What is the primary function of the peroxisomes?
    participates in the metabolism of fatty acids and rids the cell of toxic peroxides
  48. What is the primary function of the mitochondria?
    It generates most of the cell's ATP supply, although it is also involved in cel signaling, cellular diffusion, cell death and the control of the cell cycle and cell growth
  49. When vesicles are transported within the cell, which face of the GA do they enter?
    Enter in on the cis face and are transported out of the trans face
  50. What is the primary secretion of goblet cells?
    Mucin
  51. What is the pH of bile?
    8.0
  52. At what pH is blood considered to be in acidosis?
    below 6.9 (normal range is 7.35 to 7.45)
  53. What is the pH of the cytoplasm?
    7.2
  54. What is the pH of the lysosome and why?
    • 4.8 to 5.5
    • These are the optimal pHs for the enzymes within the lysosome
  55. What is the pH of the stomach?
    Anywhere from 1.0 to 4.0
  56. Which amino acid has a pKa between 6 and 6.5?
    Histidine
  57. Which amino acids have a pKa between 10 and 12?
    Lysine and Arginine
  58. What is the approximate pKa of both aspartate and glutamate?
    4.0
  59. What does the point pKa signify?
    The point at which 50% of the molecules are uncharged and 50% are charged
  60. Given that you know the pKa of a given compound, how would you draw the pH curve?
    First, plot the pKa on the x axis. Then use intuition to decide when the compound will be positively charged and when it will be negatively charged
  61. What are the 7 post-translational protein modifcations?
    • Formation of a disulfide bond
    • Acetylation
    • Glycosylation
    • Lipoylation
    • Proline Hydroxylation
    • Phosphorylation
    • Proteolysis
  62. What is acetylation?
    The addition of an acetyl group to either the N-terminus or amino residues
  63. What is glycosylation?
    The addition of a sugar residue to either a N or an O
  64. What is lipoylation?
    the addition of a lipid moiety onto a cysteine residue
  65. What enzyme is involved in proteolysis?
    Proteases cut the polypeptide backbone to produce a functional protein
  66. What residues would you add a phosphate group to if you wanted to promote cell signaling?
    Ser, Tyr, or Thr
  67. What happens to an alpha-helix when an alanine group is substituted in?
    • Nothing. Alanine is small and likes to be in alpha helices
    • Poly-Ala forms an alpha helix
  68. What happens to an alpha helix (or a beta sheet) when a proline is substituted in?
    • It is kinked. Proline is never found in an alpha helix or beta sheet. It is often found in random coils and turns.
    • Poly-Pro forms a PPII helix
  69. What does Poly-gly form?
    random coils
  70. When insulin is first formed, before it is activated, what is it called?
    Preproinsulin
  71. How many modifications must preproinsulin undergo before it becomes a functional insulin molecule?
    2. First the leader signaling sequence must be cleaved and the disulfide bonds must be formed, then the C chain must be removed
  72. Which is faster acting, an insulin dimer or an insulin hexamer?
    An insulin dimer. The insulin hexamer is longer-lasting
  73. Definition: Fibrillar proteins
    Repeating globular units (alpha and beta) of tubulin producing long twisted fibers
  74. What is a protofilament?
    The "vertical" line of tubulin heterodimers. 13 of these come together to forma microtubule with a hollow center (lumen) that is approximately 10 nm thick
  75. What is the lumen?
    The hollow center of the microtubule
  76. Where are you most likely to find the hydrophobic portion of an integral membrane protein?
    On the outside of the protein, facing the plasma membrane
  77. What are the defining characteristics of an intrinsically disordered protein?
    • no predictable secondary structure
    • No hydrophobic core
    • A high net carge (causes the different parts of the strand to repulse each other)
    • Long repetitive sequences (ie >50 Gly)
    • Easily chopped up into small fragments by proteolysis
    • Many of these are transcription factors
    • Make up 30% of proteins in eukaryotes
  78. What are 5 ways to classify proteins based on function?
    • Chemistry (enzymes that catalyze reactions)
    • Signaling (produce cellular responses to the environment)
    • Structure (provide support and organization to cells)
    • Transport (either move molecules in and out of the cells or circulate in the blood)
    • Storage (allow cells to utilize oxygen, nutrients, and energy)
  79. What are some conditions that denature proteins?
    Changes in pH, ionic strength, pressure, temeprature, osmotic pressure, and urea (in the kidneys)
  80. What is the most common definition of a quaternary subunit?
    A single polypeptide that encodes on mRNA
  81. Proteins are constantly in motion. Both their small side chains roate and domains can move on hinges. What is the best method to see these motions?
    • NMR, but only for small proteins.
    • recently computer simulations have been working on it
  82. What are the different ways that proteins can be grouped together and classifed?
    Proteins can be grouped by common structural properties, common sequence, common function, common ligand, or common post-translational modification
  83. Fibrillar proteins, integral membrane proteins, and intrinsically disordered proteins make up apprixmately 75% of all proteins in the body. What are the other 25%?
    Standard soluble, globular proteins; these are the ones we think of most often
  84. What is the primary amino sequence repeated several times in collagen?
    • Pro-X-Gly
    • (Note that proline and glycine don't like to be in normal secondary structures very often)
  85. What protein best fits the description "inside-out globular proteins"?
    Integral membrane proteins
  86. In which technique do you line up specific primary sequences of proteins and do a "best possible fit" to identify similarities?
    Bioinformatics
  87. What are traditional protein families defined by?
    Sequence alignment
  88. What is an isoform of a protein?
    A protein with a similar general function, but with crucial differences. An example is liver pyruvate kinase and muscle pyruvate kinase
  89. What is a ligand?
    Something that binds to a protein
  90. What does it mean to say that proteins are modular?
    The protein is made of several different domains, but these domain usually have different functions
  91. What does it mean to say that a protein is moonlighting?
    The protein has more than one function
  92. Describe the biochemistry of Tau
    Normal cells have microtubules that are phosphorylated and dephosphorylated in steady state equilibrium. In patients with Tau, a pathogenic Tau kinase is present that phosphorylates these filaments and drastically alters the equilibrium. The filaments aggregate to from paired helical filaments. Tau tissue contains no microtubules. This is often seen in patients with traumatic head injuries (athletes) and Alzheimer's patients
  93. Describe the biochemistry behind mad cow disease in humans
    Prion proteins occur in normal conditions. Upon ingesting infected cow meat, a spontaneous mutation occurs in the the prion precursor. This mutation causes uncontrolled prion aggregation to form prion fibrils (amyloids). These elongate and then you've got problems
  94. What are some small molecules that can assist with protein folding?
    Pro, Ala, Taurine, Polyols (sorbitol and glycerol) and methylamines (TMAO and betaine)
  95. What are the 2 types of chaperones?
    Heat shock proteins and chaperonins
  96. What is the function of a heat shock protein?
    Folds new and misfolded proteins (small ones)
  97. What is the function of a chaperonin?
    It is a protein folding machine. It folds large proteins using ATP. The unfolded protein binds to the chaperonin and using magic, the chaperonin produces a perfectly folded protein
  98. What is the function of ubiquitin?
    It attaches to misfolded/old proteins, which signals a proteasome to come degrade them
  99. If a positively charged matrix is used in column chromotography, what will be the charge on the first fraction collected?
    Positive
  100. Does protein gel electrophoresis separate proteins based on charge or size?
    • Size, with the smaller proteins moving faster and farther
    • The proteins are not separated based on charge because the polyacrylamide gel swamps the charge; makes it irrelevant
  101. When using mass spec, will unique masses be found for each primary sequence or for post-translational modifications?
    Both
  102. Where are epithelia found in the body?
    lining cavities, body surfaces, and tubes
  103. What is the name of the membrane that epithelial cells lie on?
    Basal lamina (basement membrane works too)
  104. What is the primary function of epithelia?
    To absorb, secrete, transport, excrete, protect, and sensory reception
  105. When naming an epithelial cells, what must you take into account?
    The number of cell layers and the shape of the cells
  106. Definition: Simple Epithelia
    Single layer of cells found at surfaces involved in selective diffusion, absorption, and secretion
  107. Definition: Pseudostratified Epithelia
    all cells rest on the basement membrane, but the nuclei are at different levels giving it the appearance of having different layers; found in the repiratory tract and the male reproductive system
  108. Definition: Simple Squamous Epithleium
    a single layer of cells characterized by folat, scale-like cells; nuclei are flat
  109. Definition: Cuboidal Epithelium
    epithelial cells that have a cube-like shape; their width is approximately equal to their height; may exist in single layes or multilayers depending on their location in the body
  110. Definition: Stratified Epithelium
    Epithelial cells arranged in layers upon a basement membrane where only one layer is in contact with the membrane while other layers adhere to one another; named by the most superficial layer of cells (the layer closest to the surface)
  111. Definition: Columnar epithelium
    epithelia whose height are at least 4 times their width; divided into simple and stratified
  112. Definition: Transitional epithelium
    lines the surfaces of hollow organs such as the kidney, urinary bladder and accessory organs: transitional cell carcinoma of the urinary system arises from this type of tissue
  113. Where would you be most likely to find simple squamous epithelium?
    lining blood vessels, air sacs of the lungs; it permits the exchange of nutrients, wastes, and gases
  114. Where would you be most likely to find simple cuboidal epithelium?
    lining the kidney tubules and glands; it secretes and reabsorbs water and small molecules
  115. Where would you be most likely to find simple columnar epithelium?
    lining most digestive organs; it absorbs nutrients and produces mucus; often found near goblet cells
  116. Where would you be most likely to find stratified squamous epithelium?
    on the outer layer of the skin, mouth, and vaginal tract; it protects against abrasion, drying out, and infection
  117. Where would you be most likely to find stratified cuboidal epithelium?
    Lining the ducts of sweat glands; it secretes water and ions
  118. Where would you be most likely to find stratified columnar epithelium?
    Lining the epididymus, mammary glands, and the larynx; it secretes mucus
  119. What is the difference between microvilli, cilia, and stereocilia?
    • Microvilli are short projections of luminal membrane containing actin filaments. They function to increase surface area of the GI tract
    • Cilia are motile (ATP dependent) and much larger than microvilli
    • Seterocilia are really long microvilli with a filamentous actin core and are found in the reproductive tract
  120. What are the primary functions of the basal lmaina/BM?
    • to provide structural support
    • to act as a filter
    • to establish polarity
    • to control growth and differentation
  121. What is the function of hemidesmosomes?
    to link epithelial cells to the basal lamina; specifically, it links the intermediate filament proteins inside the cell to the BM
  122. What are the anucleated epithelial cells on the outermost layer of our skin called?
    Keratin
  123. What is the primary function of basal infoldings?
    To increase surface area and thereby increase transport; they are associated with cells involved in active transport
  124. What is the primary function of the zonula occludens?
    to form a barrier at the apical surface of the epithelial cells
  125. Where can the zonula occludens be found?
    Connecting two epithelial cells at their most apical surface; forms a ring all the way around the cell
  126. What is the primary function of the zonula adherens?
    Links to actin cytoskeleton of 2 separate cells
  127. What is the zonula adherins formed by?
    Cadherins
  128. What is the primary function of desmosomes?
    To link intermediate filaments; these are spot welds and do not form a continuous barrier around the cell
  129. What forms the desmosomes?
    cadherins
  130. Definition: Gap junction
    a direct connection between 2 cells that allows for the movement of molecules and ions between the cells
  131. Definition: endothelium
    the thin layer of cells that lines the interior surface of blood vessels
  132. Which epithelial cell are you most likely to find lining the interior surface of blood vessels?
    Simple squamous
  133. What part of the cell can rearrange very quickly, be stbale and provide structure, and can asseble and disassemble in a dynamic equilibrium?
    the cytoplasm
  134. In both actin and microtubule filaments, which end are monomers most likely to be added?
    • The positive end
    • They come off of the negative end of actin and the positive end of microtubules
  135. What is the function of the GTP cap?
    to stabilize microtubules and keep them from shrinking and falling apart
  136. On a microtubule, which is more stablizing, GTP or GDP?
    GTP. When the GTP cap is removed, the GDP-tubulin dimers immediately fall apart
  137. In terms of energy molecules utilized, what is the difference between actin and microtubules?
    Microtubules use GTP wile actin uses ATP
  138. Definition: Intermediate filaments
    the third group that makes up the cytoskeleton (actin and microtubules); provide much structural support
  139. What are the subunits that comprise an intermediate filament?
    start with a protein with open N-terminus and C-terminus and lengthy alpha-helical region; 2 proteins form a coiled coil; these find another coiled coil and form a staggered tetramer (one of the coiled coils flips so that N-terminus is facing the opposite way); two tetramers pack together; 8 of these tertramers twist into a ropelike filament which is about 10 nm in diameter
  140. What is the defect in epidermoylsis?
    one of the keratin proteins has a mutation: keratin 5/14 leads to e. bullosa (fatal); keratin 1/10 leads to e. hyperkeratosis; keratin 9 leads to e. plantopalmar
  141. Why does the defect in keratin in epidermolysis lead to severe blistering?
    the defective keratin network cannot form strong ropes, rendering the hemidesmosomes incapable of doing their job; the layers of skin simply fall apart
  142. What is the diameter and basic structure of the microfilament that makes up actin?
    6 nm; double helix
  143. What are the 6 major types of intermediate filaments and where are they found?
    • Vimentin (mesenchyme)
    • Glial fibrillary acidic protein (glia)
    • Neurofilament (neurons)
    • Keratins (epithelia)
    • Nuclear lamins
    • Desmin (muscle)
  144. What is the diameter and basic structure of a microtubule?
    23 nm; 13 protofilaments forming a hollow tube
  145. What is the function of cofilin?
    To tighten and hold together the actin filaments (from 74 nm to 57 nm)
  146. Specifically, what structure is profilin bound to?
    The formin whiskers
  147. What does profilin do?
    It binds actin monomer and helps it bind ATP; the formin whisker then pulls the complex toward the site of the next actin addition, where profilin releases it and moves back to the original position
  148. What does the formin dimer do?
    It puts the actin monomer in the right conformational position to bind to the actin filament, thereby increasing actin buildup
  149. How does the centrosome contribute to microtubule stability?
    The negative ends bidn to the centrosome complex at the core and are stabilized while the positive ends radiate out and continue growing; the negative end is capped with gamma tubulin and accessry proteins in a gamma tubulin ring complex
  150. What does ARP stand for?
    Actin related proteins (2 and 3)
  151. What does the ARP do?
    ARP 2 and 3 combine with an activating factor (unknown) and actin monomers associate with it to form the nucleated actin filament; the ARP complex then binds to another actin filament at a 70 degree angle to form an actin meshwork
  152. Does formin move the actin when adding actin monomers?
    Negative. It simply puts the actin in the good place to bind; does this using a wobbling motion
  153. How is capping used to cap filament length?
    Uncapped filaments groaw at plus and minus ends; the capped population of filaments grows at the minus end only
  154. What are the different types of bundling that filaments can do in a cell?
    • Contractile bundling (anti-parallel) is seen in stress fibers of the cells
    • Gel-like networking (no real order) is seen in the cell cortex
    • Tight parallel bundling is seen in the filopodium
  155. What is a filamin dimer?
    two associated L-shaped proteins that sit on top of the actin meshwork to further stabilize it
  156. Which proteins are used tos tabilize actin bundles?
    • fimbrin (monomer); alpha-actinin (dimer); spectrin (tetramer); and filamin (dimer)
    • each of these connects actin, and spaces them differently according to where they are in the body
  157. Is mysoin II more likely to enter a contractile bundle or a parrallel bundle?
    More likely to enter the contractile bundle. The tight packing of parallel bundles prevents myosin II from entering
  158. How does fimbrin help stabilize the actin filaments?
    Crosslinks the actin filaments (seen in the microvilli)
  159. What connects the actin filaments to the plasma membrane of the microvilli?
    calmodulin and myosin-I act as the lateral side arms
  160. What are the cytoskeletal elements of a neuron?
    neurofilaments and microtubules
  161. What are the top three leading causes of death in the US and Kansas?
    Heart disease, cancer, and stroke
  162. What's the leading cause of death in children under the age of 1?
    Congenital anomalies
  163. What's the leading cause of death in children ages 1-4?
    Unintentional injuries and congenital anomalies
  164. What's the leading cause of death in children age 5-14?
    unintentional injuries, cancer and homicides
  165. What's the leading cause of death in young adults ages 15-24?
    unintentional injuries, suicide, and homicide
  166. What's the leading cause of death in adults, ages 25-44?
    Unintentional injuries, cancer, and suicide
  167. What's the leading cause of death in adults, ages 45-64?
    cancer, heart disease and unintentional injuries
  168. What's the leading cause of death in adults, ages 65 and older?
    Heart disease and cancer
  169. What is healthy people 2010?
    A set of health objectives for the nation to achieve over the first decade of the new century
  170. What is Healthy people 2010 based on?
    Initiatives pursued over the past two decades and the surgeon generals 1979 report
  171. What is a protein binding site?
    a well-defined region that binds ligands, can stabilize folded proteins and can change protein conformation; this region has a specific AA sequence that allows the binding to occur
  172. What are the results of a mutation in the primary AA sequence of a binding site?
    a change in affinity and specificity
  173. Definition: Affinity
    How tightly a ligand is bound
  174. What is Kd?
    The dissociation constant; the point at which 50% of the protein/enzyme is bound to substrate
  175. What is the equation for Kd?
    • Kd=[A][B]/[AB]
    • given in M
  176. What are the units for the association constant?
    M^-1
  177. When [A]=[AB], what can we say about Kd?
    Kd=[B]
  178. What is the equilibrium constant equation?
    Keq=[prod.]/[react]
  179. What can we say about the affinity of a protein for a ligand if the Kd shifts to the right?
    • The affinity is weaker
    • If it shifts to the left, it's stronger
  180. Definition: Negative Cooperativity
    • binding one ligand makes subsequent binding more difficult;
    • A protein exhibiting negative cooperativity will NEVER reach 100% saturation (bound)
    • On the log curve, also a less steep slope because binding is slower
  181. Will the curve of an enzyme exhibiting positive cooperativity by steeper or more shallow than one not exhibiting this?
    • Steeper
    • Figured this out by taking the weighted average of the low affinity and high affinity sites
  182. When does cooperativity occur?
    When a single polypeptide chain has identical binding sites, and the binding of one ligand changes the affinity of the next ligand binding
  183. Definition: Positive cooperativity
    When the binding of one ligand causes the second to bind more tightly
  184. Does allostery affect the Kd?
    Yes, it shifts it, depending on whether the allostery is positive or inhibitory
  185. When does allostery occur?
    When a protein has binding sites for 2 different types of ligands, and the binding of one ligand changes the affinity for the other
  186. What happens to the Kd with inhibitory allostery?
    It shifts to the right because the affinity for the second ligand becomes weaker
  187. Definiton: Inhibitory Allostery
    Neither ligand wants to bind as much when the other ligand is already bound
  188. What happens to the Kd with enhancing allostery?
    It shifts to the left because the affinity is strengthened by the binding of the first ligand
  189. Why does nature need allostery?
    REGULATION! it allows the cell to adapt to changing conditions
  190. How is allostery used in metabolism?
    Changing nutrients allows the reaction rates to be turned up or down
  191. How is allostery used in DNA transcription?
    Can change transcriptome/proteome in response to the environment
  192. What is the key difference between allostery and cooperativity?
    Allostery involves 2 different ligands (one is usually an effector) at 2 different binding sites; cooperativity involves identical binding sites and the same ligands
  193. Does cooperativity affect the Kd?
    No, it merely changes the slope
  194. Definition: Incidence
    the rate of NEW cases of disease in a susceptible population in a given period of time
  195. What is the equation to determine incidence?
    incidence=(# New cases of disease)/(# at risk in population in a given time period)
  196. Definition: Prevalence
    ALL cases of disease (new and old) in a susceptible population; depends on incidence and duration of disease
  197. What is the equation to determine prevalence?
    prevalence= (# new and old cases of disease)/(#people in pop. at that point in time)
  198. What is the equation to determine mortality rate?
    (total # deaths in a period)/(# of people in pop. mid-period)
  199. Definition: Standard Deviation
    How spread out things (data points) are in a population
  200. Definition: Standard Error of the Mean
    How spread out is the sample mean
  201. What kind of hypothesis do you use in statistics?
    Null hypothesis--assume that the opposite of what you wish to prove is true; the hypothesis of no difference
  202. What is the p-value?
    A measure of how likely it is that what we have observed could occur randomnly; use a p-value of 0.05
  203. If you have a normal distribution and continuous data, what type of test should you run to disprove your hypothesis?
    t-test
  204. If the data is categorical and the distribution is not normal, what type of test should you run to disprove your hypothesis?
    Chi-square test
  205. Definition: t-test
    statistical test used to compare the mean values between 2 different groups
  206. Definition: chi-square test
    statistical test used to compare proportions between 2 different groups
  207. Definition: Confidence intervals
    A range of plausible values for the difference; if a 95% confidence interval for a difference does not contain 0, then the p-value is less than 0.05
  208. If a 95% CI for a ratio does not contain 1, what do we know about the p-value?
    it is less the 0.05
  209. How similar are the primary sequences of hemoglobin and myoglobin?
    • ~18% identical and ~38% similarity
    • Secondary and tertiary structures are very similar; they bind the same prosthetic group (heme) and the same ligand
  210. How are hemoglobin and myoglobin's quaternary structure different?
    • Mb is a monomer
    • Hb is a tetramer with 2 alpha subunits and 2 other subunits (usually beta, but doesn't have to be)
  211. Which has the greater affinity for oxygen and why?
    Mb does, needs to steal it from Hb to take to muscles
  212. What happens to the oxygen binding curve at high altitudes?
    There is a reduction in the amount of oxygenated blood leaving the lungs; more of it is reduced
  213. What happens to the oxygen binding curve during exercise?
    There is an increase in the gaseous pressure of oxygen in the reduced blood returning from the tissues; becoming acidotic
  214. What happens to the oxygen binding curve in methemoglobinemia?
    There is a decrease in the percent saturation of the oxygenated blood leaving the lungs
  215. What is methemoglobinemia?
    A disorder characterized by the presence of higher than normal level of methemoglobin (metHb) in the blood. This metHb has an extremely high affinity to oxygen, resulting in almost no oxygen delivery to the tissues

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