Extra Biochem

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Extra Biochem
2015-05-12 17:40:04
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  1. difference between cofactor and coenzyme
    cofactor: inorganic molecules or metal ions; ingested as dietary minerals

    coenzymes: organic groups, mostly vitamins
  2. prosthetic groups
    tightly bound cofactors/ coenzymes that are necessary for enzyme funciton
  3. water soluble vitamins
    B complex vitamins and ascorbic acid (Vitamin C)
  4. fat-soluble vitamins
    • A
    • D
    • E
    • K
  5. Km
    substrate concentration at which half of the enzyme's active sites are full

    can be used to measure the affinity of the enzyme for the substrate

    high Km has lower affinity for substrate
  6. Lineweaver Burk plots

    x and y axis?
    x: 1/Km

    y: 1/Vmax
  7. How does temperature affect enzymes?
    double in velocity for every 10 degree C increase until optimum temp is reached
  8. feed-forward regulation
    enzymes are regulated by intermediates that precede the enzyme in teh pathway
  9. Lineweaver Burk plots

    - Competitive inhibition
    - Noncompetitive inhibition
    - Mixed inhibition
    - Uncompetitive inhibition
    CI: different 1/Km (increased value), same 1/ Vmax

    NI: same 1/Km, different 1/ Vmax (value decreases)

    MI: both are altered

    UI: parallel curves
  10. Difference between mixed and uncompetitive inhibition
    mixed binds to both ES and enzyme and can alter Km; vmax always decreases

    Uncompetitive just binds ES complex
  11. Role of kinesin
    aligning chromosoems during metaphose and depolymerizing microtubules during anaphase of mitosis
  12. Dynein function
    involved in the sliding movement of cilia and flagella
  13. Kinesins and dyneins are both important for?
    • vesicle transport
    • kinesins bring vesicles toward positive end of microtubule, while dyneins bring vesicles toward negative end
  14. CAMs
    cell adhesion molecules are proteins found on the surface of most cells that aid in the binding of the cell to the ECM or other cells

    they are all integral and include cadherins, integrins, and selectins
  15. cadherins
    group of glycoproteins that mediate Ca2+ dependent cell adhesion; hold similar cells together
  16. integrins
    group of proteins that all have two membrane spanning chains called alpha and beta

    important in cell signaling and promote cell division, apoptosis, etc. 

    others are used for WBC migration, stabilization of epithelium on its basement membrane, etc
  17. Selectins
    unique because they bind to carbohydrate molecules that project from other cell surfaces

    expressed on WBCs and endothelial cells that line BVs
  18. constant region of antibodies
    involved in recruitment and binding of other cells of the immune system
  19. What can binding of antibodies to antigens cause?
    • 1)neutralize antigen
    • 2)mark pathogen for destruction (opsonizatoin)
    • 3) clump together antigen and antibody into large insoluble protein complexes (agglutination)
  20. enzyme linked reeptors
    have 3 primary protein domains: a membrane spanning domain, a ligand binding domain, and a catalytic domain
  21. Three main types of G proteins
    Gs stimualtes adenylate cyclase, which increases cAMP in the cell

    Gi inhibits adenylate cyclase, which decreases cAMP in the cell

    Gq activates phospholipase C, which cleaves a phospholibipd from the membrane to form PIP2, which is cleaved into DAG and IP3, the latter of which opens calcium channels in the ER
  22. Charges of the anode and cathode.
    anode is positively charged

    cathode is negatively charged
  23. Proteins that are positively charged will migrate toward the __ and proteins that are negatively charged will begin migrating toward the __.
    • cathode
    • anode
  24. The amount of time a compound spends int he stationary phase of chromatography is __.
    retention time
  25. Edman degradation
    used for determining a.a. composition

    cleaves bonds to sequence sprotireins
  26. Bradford Protien assay
    protein mixed with blue dye

    protonated: dye is brown-green

    depronotated protein causes dye to turn blue
  27. How would you create a standard curve?
    • samples of known protein concentrations are reacted and then absorbance measured
    • unknown sample then exposed to same conditions
  28. ALdehyde carbons can participate in __.
    glycosidic linkages
  29. D-fructose
  30. d-glucose
  31. d-galactose
  32. d-mannose
  33. Difference between D and L sugars
    all D sugars have the hydroxide of the highest numbereed chiral center on teh right

    L sugars have it on teh left
  34. epimers
    a special subtype of diastereomers are those that differ in configuration at exactly one chiral center
  35. six-membered rings with oxygen
    pyrannose rings
  36. five membered rings with oxygen
  37. lactone
    cyclic ester with a carbonyl group persisting on the anomeric carbon
  38. Which reagents are used to detect the presence of reducing sugars?
    Tollens: uses Ag(H3)2 as an oxidizing agent because aldehydes reduce Ag+ to metallic silver

    Benedicts reagent: aldehyde group is oxidized causing a red precipitate
  39. Difference between beta-amylase and alpha-amylase
    beta cleaves at the reducing end of the polymer

    alpha cleaves anywhere to yield shorter polysaccharides
  40. What is the relationship between a Fischer projection and a Haworth projection?
    all the groups on the right in the Fischer projection go on the bottom of hte HP, and all the groups on the left go up top
  41. What does glycerol form?
    phosphoglyceries and glycerophospholipids
  42. Sphingolipids have what?
    a sphingosine backbone
  43. glycerophospholipids
    those phospholipids with a cglycerol backbone bound by ester linkages to two fatty acids and a phosphiodiester linkage to a highly polar head group

    ex: phosphatidylcholine, phosphatidylethanolamine
  44. True or False: all phospholipids are glycerophospholipids
    all phospholipids are glycerophospholipids is false

    all glycerophospholipids are phospholipids
  45. Sphingomyelins are major components of what?
    plasma membranes of cells producing myelin (Schwann and oligodendrocytes)

    they have a phosphodiester bond and are thus phospholipids
  46. Sphingolipids
    have no phosphodiester bond and are not phospholipids
  47. terpenes
    metabolic precursors to steroids and other lipid signaling molecules

    class of lipids built from isoprene moieties

    a single terpene unit has two isoprene units (C5H8)
  48. prostaglandin
    regulate synthesis of cAMP
  49. vitamin
    essential nutrient that cant be made by body and must be consumed in diet
  50. Vitamin A
    imp. in vision, growth and development, and immune funcition
  51. Vitamin D
    • consumed or formed
    • in liver and kidneys, it is converted to calcitriol, which increases calcium and phosphate uptake in the intestines
  52. Vitamin E
    associated with tocopherols, which are biological antioxidants
  53. Vitamin K
    vital to posttranslational modifications reuired to form prothrombin
  54. saponification
    the ester hydrolysis of triacylglycerols using a strong base
  55. characteristics of aromaticity
    • 1) the compound is cyclic
    • 2) the compound is planar
    • 3) the compound is conjugated
    • 4) the compound has 4n+2 pi electrons (Huckel's rule)
  56. B-DNA

    B: right handed helix

    Z: left handed helix
  57. What can denature DNA?
    • heat
    • alkaline pH
    • chemicals like formaldehyde and urea
  58. DNA pol III vs. I
    III: synthesizes strand by adding dNTPs, releasing a free pyrophosphate (PPi)

    I: replaces the RNA in the primer with DNA
  59. DNA pol alpha and delta
    synthesis of DNA
  60. RNase H
    removes RNA primers
  61. DNA pol delta
    replaces RNA with DNA
  62. tumor suppressor genes
    p53, Rb (retinoblastoma0

    called antioncogenes bc they stop tumor progression by inhibiting the cell cycle
  63. nucleotide excision repair
    recognizes distortion of double helix, such as by formation of thymine dimrs, and cuts it out 

    excision enonuclease makes nicks in backbone to remove it
  64. deamination
    loss of amino group from cytosine resulting in uracil
  65. How is deamination corrected?
    • base excision repair
    • 1) base is recognized and removed by a glycosylase enzyme, leaving an AP site, recognized by AP endonuclease
  66. hnRNA
    heterogeneous nuclear RNA; mRNA is derived from this after posttranscriptionl modifications
  67. Initiation of translation in prokaryotes relies on
    the Shine-Dalgarno sequence
  68. prenylation
    addition of lipid groups to certain membrane bound enzymes
  69. Transcription factors have two domains. What are they?
    DNA binding domain and an activation domain
  70. histone acetylation
    decrease postive charge on tails and weakens interactions, resulting in an open chromatin conformation
  71. DNA methlation
    add a methyl group to silence genes
  72. coding strand
    this DNA is not used as a template during transcription; it is identical to the mRNA transcript except that all the thymine nucleotides in DNA have been replaced with uracil in the mRNA molecule
  73. lipid rafts
    aggregates of specific lipids in the membrane that function as attachment points ofr other biomolecules and play roles in signaling
  74. Sphingolipids do not contain __.
  75. gap junctions
    allow direct cell-cell communication and are often found in small buches together

    called connexons and are formed by alignment and interaction of pores composed of six molecules of connexin

    fx: permit movement of water and some solutes directly between cells
  76. tight junctions
    prevent solutes from leking into the space between cells via a paracellular route
  77. desmosomes
    bind adjacent cells by anchoring to their cytoskeletons

    formed by interactions between transmembrane proteins associated with intermediate filaments inside adjacet cells
  78. hemidesmosomes
    main function to attach epithelial cells to underlying basement membranes
  79. primary active transport
    uses ATP to directly transport molecules across a membrane
  80. Secondary active transport
    uses energy to transport molecles across the membrane; in contrast to primary, there is no direct coupling to ATP hydrolysis; instead, it harnesses energy released by one particle going down its electrochemical gradient to drive a different particule up its gradient
  81. resting potential for cell membranes
    -40 and -80 mV
  82. depolarization
    35 mV
  83. Nernst equation
    can be used to determine membrane potential from intra- and extracellular concentrations of various ions

    E= RT/ zF ln [ion outside]/[ion inside]
  84. Goldman-Hodgkin-Katz voltage eqation
    Vm=61.5 log[ (Permeability of Na)(Concentraiton of Na outside)+ (Permeability of K)(Concentration of K outside)+ (Permeability of Chloride)(Concentration of Cl inside)]/(opposite of the inside)
  85. outer mitochondrial membane
    highly permeable due to many large pores that allow for the passage of ions and small proteins
  86. normal glucose concentration in peripheral blood
    5.6 mM
  87. GLUT 2
    in hepatocytes and pancreatic cells

    capture excess glucose for storage

    low affinity for glucose (high Km)
  88. GLUT 4
    in adipose tissue and muscle

    insulin causes movement of more GLUT4 transporters

    Km normal
  89. Hexokinase and Glucokinase
    • they phosphorylate glucose, trapping it in the cell
    • hexo: in tisues and inhibited by product
    • gluco: stimulated by insulin
  90. PFK1
    rate limiting enzyme

    F6P is phosphorylated to F16BP

    inhibited by ATP and citrate; activated by AMP

    insulin stimulates it; glucagon inhibits it
  91. PFK2
    insulin activates it

    found in the liver

    converts F6P into F26BP, which activates PFK1, allowing glycolysis to continue
  92. Glyceraldehyde-3-phosphate dehydrogenase
    catalyzes oxidation and addition of inorganic phosphate to its substrate, G3P
  93. 3-phosphoglycerate kinase
    transfers the high-energy phosphate from 1,3-bisphosphoglycertae to ADP, forming ATP adn 3-phosphoglycerate
  94. pyruvate kinase
    catalyzes substrate level phosphorylation; activated by fructose-1,6-bisphosphate
  95. lactate dehydrogenase
    in fermentation

    oxidizes NADH to NAD+
  96. DHAP (dihydroxyacetone phosphate)
    formed from fructose 1,6-bisphosphate and can be isomerized to Glycerol-3-phosphate, which can be converted to glycerol
  97. How do erythrocytes get energy?
    anaerobic glycolysis
  98. Adaptation to high altitudes (low pO2) involves six things. What are they?
    increased respiration

    increased oxygen affinity for hemoglobin

    increased rate of glycolysis

    increased [2,3-BPG] om NRNC

    normalized oxygen affinity for hemoglobin restored by the increased level of 2,3-BPG

    increased hemoglobin
  99. pyruvate dehydrogenase is inhibited by?
    acetyl CoA, causing pyruvate to be converted into oxaloacetate (to enter gluconeogenesis)
  100. glycogenesis
    synthesis of glycogen granules, beginning with a core preotein called glycogenin

    glucose addition to a granule begins with glucose 6-phosphate, which is converted to glucose 1-phosphate. It then is coupled to UDP, which permits its integration into the glycogen chain by glycogen synthase, which is the rate limiting enzyme of glycogen synthesis and forms alpha-1,4-glycosidic bonds
  101. glycogen synthase is stimulated by __ and inhibited by __
    insulin and glucose 6-phosphate

    epinephrine and glucagon
  102. glycogenolysis
    process of breaking down glycogen

    rate limiting enzyme is glycogen phsophorylase, which breaks alpha-1,4-glycosidic bonds
  103. glycogen phosphorylase is activated by __ and inhibited by __
    glucagon in the liver and AMP and epinhephrine in the skeletal muscle

  104. Gluconeogenesis
    production of glucose from other biomolecules; carried out by the kidneys and liver

    promoted by glucagon and epinephrine and inhibited by insulin
  105. Important substrates for gluconeogenesis are:
    glycerol 3-phosphate (from triacylglycerols)


    glucogenic amino acids
  106. glucogenic amino acids
    all except leucine and lysine; can be converted into intermeidates that feed into gluconeogenesis
  107. ketogenic amino acids
    can be converted into ketone bodies; can be used as an alternative fuel during periods of prolonged starvation
  108. What is not possibe with acetyl CoA
    it is not possible to covert it back to glucose
  109. four major enzymes of gluconeogenesis
    pyruvate carboxylase: activated by acetyl coA that is derived from fatty acids; to provide glucose int eh liver during gluconeogenesis, fatty acids must be burned to provide this energy

    phosphoenolpyruvate carboxykinase (PEPCK): induced by glucagon and cortisol; converts OAA to PEP; activated by glucagon and cortisol

    fructose-1,6-bisphosphatase: RLS of gluconeogenesis; hydrolyzes phosphate from fructose 1,6-bisphosphate to produce fructose 6-phosphate; activated by ATP and inhibited by AMP

    glucose-6-phosphatase: only in ER; transported into ER
  110. Gluconeogeesis requires expenditure of ATP that is provided by __.
    beta-oxidation of fatty acids

    hepatic gluconeogenesis is always dependent on beta-oxidation of fatty acids in the liver
  111. Although acetyl-CoA from fatty acids cannot be converted into glucose, it can be converted into __.
    ketone bodies as an alternative fuel for cells, including the brain
  112. Pentose phosphate pathway
    serves two functions: production of NADPH and serving as source of ribose 5-phosphate for nucleotide synthesis
  113. Difference between NADPH and NADH
    NAD+: high energy electron acceptor from a number of biochemical reactions

    NADPH: primarily acts as an electron donor in a number of biochemical reactions; potent reducing agent because it helps other molecules be reduced
  114. What determies whether the CAC will be activated or inhibited?
    ratios of ATP/ADP and NADH/NAD+
  115. Where is the CAC located?
  116. pyruvate dehydrogenase kinase
    phosphorylates pyruvate dehydrogenase to inhibit acetyl CoA
  117. Pyruvate dehydrogenase phosphatase
    reactivates PDH by removing a phospate
  118. what are the controls of the CAC?
    citrate cynthase: inhibited by ATP, NADH, citrate, and succinyl CoA

    isocitrate dehydrogenase: ATP and NADH

    alpha ketoglutarate: succinyl CoA, NADH; ATP
  119. What are the steps for the Pyruvate dehydrogenase complex?
    PDH: pyruvate is oxidized, yielding CO2

    Dihydroproply transacetylase: oxidizes 2-carbon attached to TPP and transfers to lipoic acid-> acetyl CoA via transfer of acetyl

    Dihdropropyl dehydrogenase: reoxidizes lipoic acid, forming FADH2, which is converted to NADH
  120. amino acid catabolism
    lose amino group via transamination
  121. ATP production via the CAC
  122. Complexes in the ETC
    NADH CoQ oxidoreductase: NADH catalyzed; FMN and Fe-S units

    Succinate-CoQ oxidoreductase: receives from succinate

    Cyt C oxidoreductase: Q cycle

    Cyt C oxidase
  123. How does NADH in the cytosol get to the natrix
    Glycerol 3 phosphate shuttle: NADH oxidized while fomring glycerol 3 phosphate from DHAP; glycerol 3 phosphate dehydrogenase then accepts and transfers to FADH2

    malate-aspartate shuttle: OAA converted to malate, while NADH is converted to NAD+; once in matrix, process is reversed
  124. Bile
    emulsifies fats; contains bile salts, pigments, and cholesterol
  125. What does the pancreas release to digest fats?
    pancreatic lipase, colipase, cholesterol esterase
  126. In the postabsorptive state, what are fats doing?
    fatty cids are released from adipose tissue and used for energy
  127. LPL
    lipoprotein lipase; necessary for metabolism of chylomicrons and VLDL
  128. Explain the densities of lipoproteins
    least dense: chylomicrons (highest fat-to-protein ratio)

    VLDL: slightly more dense

    IDL: intermediate density


  129. chylomicron
    transport dietary triacylglycerols and cholesterol from intestine to tissues
  130. VLDL
    transports triacylglycerols from liver to tissues
  131. IDL
    picks up cholesterol from HDL to become LDL; picked up by the liver
  132. LDL
    delivers cholesterol to cells
  133. HDL
    • picks up cholesterol accumulating in BV
    • delivers cholesterol to liver and steroidogenic tisues
    • transfers apolipoprotiens to other lipoproteins
  134. citrate shuttle
    carries mitochondrial acetyl-CoA into the cytoplasm where cholesterol synthesis occurs
  135. HMG COA reductase
    involved in the synthesis of cholesterol; rate limiting enzyme
  136. Relationship between cholesterol and insulin
    insulin promotes synthesis of cholesterol
  137. LCAT
    transfers a fatty acid to cholesterol, producing soluble cholesteryl esters
  138. which two fatty acids are important?
    alpha linoleic and linoleic acid; both are polyunsaturated
  139. Where does fatty acid synthesis occur?
    in the liver; fatty acids stored in adipose tissue
  140. triacylglycerols
    storage form of fatty acids
  141. What must be done to unsaturated fatty acids?
    they meed to undergo rearragement of the cis bonds to trans to isolate the double bond within the first three carbons
  142. In the fasting state, the liver converts excess acetyl-CoA from beta oxidation of fatty acids into the __ and __.
    ketone bodies acetoacetate and 3-hydroxybutyrate
  143. ketogenesis
    occurs in mitochondria of liver cells when excess acetyl CoA accumulates in the fasting state
  144. HMG-CoA Synthase __ and HMG CoA lyase __
    forms HMG-CoA

    breaks it down into acetoacetate
  145. What is the relationship between 3-hydroxybutyrate and acetoacetate?
    3 hydroxybutryate is oxidized to acetoacetate
  146. Absorption of amino acids and small peptides through the luminal membrane is accomplished by _
    secondary active transport linked to sodium
  147. What must occur before amino acids can be used for energy?
    trans or deamination
  148. glucogenic v. ketgenic
    glucogenic: can be converted into glucose through gluconeogenesis

    ketogenic: can be converted into acetyl-CoA and ketone bodies
  149. Why is constant deamination/ transamination bad?
    it auses a build up of amino groups; but the urea cycle occurs in the liver to remove excess nitrogen from teh body
  150. What are physiological conditiosn
    • 1 M concentration
    • pressure of 1 atm

    Temp of 25 degrees Celsius

    dG=dGo+RTlnQ, where Q is the reqaction quotient
  151. what does creatine phosphate do
    it is used for direct phosphorylation of ATP in muscle
  152. postprandial state (absorptive/ well-fed state)
    greater anabolism than catabolism 

    blood glucose levels rise and stimulate release of insulin, which affects the liver, muscle, and adipose tissue

    glycogen is synthesized in the liver and muscle; and excess glucose is converted to fatty acids and triacylglycerols
  153. Which two cells are insensitive to insulin?
    • nervous tissue
    • red blood cells
  154. Postabsorptive state (Fasting)
    glycogen degradation and the release of glucose is stimulated

    glycogenolysis begins immediately; and gluconeogenesis takes a while longer

    glucagon, cortisol, epi and norepi, and GH are released

    the reelase of amino acids from skeletal muscle and fatty aids from adipose tissue are stimulated by the decrease in insulin and increase in epineprine
  155. Prolonged fasting (starvation)
    levels of glucaon and epinephrine are elevated; glycogen stores are rapidly degraded; gluconeogenesis activity continues

    after about 24 hours, gluconeogenesis is the predominant source of glucose

    lipoolysis is rapid, resulting in excess acetyl-CoA for the synthesis of ketone bodies

    muscle tissue uses fatty acids as fuel adn brain adapts to using ketones
  156. Tissues in which glucose uptake is not iaffected by insulin are :
    • nervous tissue
    • kidney tubules
    • intestinal mucosa
    • red blood cells
    • beta-cells of the pancreas
  157. The tissues that require insulin are?
    adipose and skeletal muscle
  158. What else does insulin do?
    amino acid uptake by muscle cells, threby increasing levels of protein synthesis and decreasing breakdown of essential proteinsincreases LPL activity and triacylglycerol synthesis
  159. Insulin decreases
    triacylglycerol breakdown

    formation of ketone bodies
  160. Increased ATp promotes __
    exocytosis of insuin through several ion and voltage gated channels
  161. Glucagon does what?
    increases liver glycogenolysis

    increass liver gluconeogenesis

    increases lvier ketogenesis and decreased lipogenesis

    increased lipolysis
  162. Glucocorticoids
    • released from adrenal cortex
    • responsible for stress response

    ex: cortisol promotes mobilization of energy stores; inhibits glucose uptake; enhances activity of glucagon, epinephrine, etc.
  163. What produces catecholamines
    adrenal medulla
  164. What does the adrenal cortex produce?


    sex hormones
  165. What do thyroid hormones do?
    they increase the basal metabolic rate, as evidenced by increased O2 consumption and heat secretion

    • T4 increase in metabolic rate
    • T3 produces a more rapid increase in metabolic rate and has a shorter duration of activity
  166. What happens to __ during well fed and fasting? 

    wel fed: glucose and amino acids used

    fasting: fatty acids
  167. What happens to __ during well fed and fasting? 

    resting skeletal muscle
    WF: glucose

    fasting: fatty acids, ketones
  168. What happens to __ during well fed and fasting? 

    cardiac muscle
    WF: fatty acids

    fasting: fatty acids and ketones
  169. What happens to __ during well fed and fasting? 


    fasting: fatty acids
  170. What happens to __ during well fed and fasting? 

    well fed: glucose

    fasting: glucose (ketones in prolonged fast)
  171. What happens to __ during well fed and fasting? 

    well fed: glucose

    fasting: glucose
  172. respiratory quotient
    CO2 produced/ O2 consumed
  173. Ghrelin
    secreted by stomach in response to signals of impending meal; increase appetite and stimulates orexin secretion
  174. Orexin
    further increases apetite adn is involved in alterness and hte sleep wake cycle
  175. leptin
    decreases appetite by suppressing orexin production