Biochem Important Areas

Overall Biochemistry Topics
1. Course Starts Here
  1. PROTEINS!
    1. Enzymes do things
      1. Reactions
        Km / Vmax
        Lineweaver Burke
        Straight line - INtercept @ X = -1/kM, Intercept at Y = 1/Vmax
        1/V = km / Vmax * 1/S + 1/Vmax
        Michaelis Menten plots
        Curve that has an asymptote. NOT straight line
        v = km/vmax (S) + kM
        Dixon.. thing with Inhibitors
        Km is a measure of DISassociation
        Vmax is a measure of the maximum rate
    2. Proteins are made up of amino acids!
      1. There are 20 amino acids
        Basic AA
        Acidic AA
        Polar AA
        Aromatic AA
        Non-polar
      2. AA are joined by Dehydration Synthesis
        Dehydration Synthesis - Removes H2O to make a covalent bond
        Dehydration synthesis also joins Carbs, lipids, and Nucleic Acids
      3. Amino acids have two "Key" bonds that determine relative angles - Phi and psi
        Phi and Psi combinations are predicted by the Ramachandran Plot
        Has 3 major areas occupied - Right handed Alpha helices, Beta Sheets, & left handed alpha helices
        Basically, only glycine, because it has the smallest R group (just an H) can adopt other conformations
      4. AA can fold into alpha helices or beta sheets
        Secondary structures form motifs - Motifs build into domains
    3. Protein Structure
      1. Why Do enzymes do things??
        Energy needs to be released - NEGATIVE delta G
        Gibbs Free energy = negative is spontaneous (positive is not)
        Exergonic reactions Drive Endergonic reactions
        The value of Delta G is measured by either!
        Delta G = delta H -TdeltaS
        Delta S is entropy - disorder of a system
        Increased when proteins fold BECAUSE the water increases in entropy
        Delta G = -RTlnK
        K is the equilibrium constant ( products / Reactants, raised to exponents)
2. Second area
  1. Lipids
    1. Types of Lipids!
      1. Glycerophospho lipids
      2. Sphingo Lipids
      3. Triacyl Glycerides
      4. Steroids / Cholesterol
    2. Chemical Reactions of Lipids
      1. Synthesis
        Dehydration Synthesis to join Fatty Acids to Glycerol. Usually Ester Linkage
        Synthesis from Acetyl CoA to a Palmitate
      2. Breakdown
        Usually Hydrolysis
        Breakdown from a Fatty acid like Palmitate
3. Third Area
  1. Carbohydrates
    1. General formula CnH2nOn
      1. Most commonly have 6 carbons and called HEXOSES
        Aldoses - Aldehyde groups
        Aldehyde is a C=O at the END of a carbon chain
        Ketoses which have ketone groups
        Ketone is a C=O in the middle of a Carbon chain
        Cyclic Forms
        Ketal vol semi Metal
        Acetal vs. Hemiacetal
        Chair Conformations
        Linear Forms
      2. identification of D vsl L
    2. What are Examples with the following descriptions?
      1. Monosaccharides
      2. Multiple Subunits
        Disaccharides
        Polysaccharides
        Alpha vs. Beta Linkage
    3. Feeder Pathways of Sugars FOR glycolysis
      1. Sucrose - Lactose - Trehalose - Glycogen - Galactose - Mannose
4. Fourth Area
  1. Glycolysis
    1. Stage 1- Investment of Energy
      1. tage 2 - Chop up and Isomerize to 2x 3C
        Stage 3 - Extract Energy and make Pyruvate
        Fate of pyruvate?
        Pyruvate Dehydrogenase to make Acetyl CoA for CAC or FA syntheis
        Ethanol Fermentation
        Lactic Acid Fermentation
    2. GlucoNeoGenesis
      1. Making Glucose from molecules that were not glucose!
        Opposite of Glycolysis
      2. Important Steps
    3. Regulation of Glycolysis
      1. PFK1 enzyme Regulation
        Effect of Citrate
        Effect of ATP
        Effect of Fructose 2,6 bisphosphate
      2. Hexokinase Regulation
        Effect of G6P
        Hexokinase IV
        Sequestration of Hexokinase IV
5. Fifth area!and beyond!
  1. Related to Sugars and Breakdown/ Buildup
    1. Glycogen Synthesis. Start at Substrate - move CCW
      1. Substrate for it
        Synthesis of glycogen by adding sugar to which end? ( Reducing or non reducing)
        What does Branching mean?
      2. Liver and Skeletal muscle differences
      3. Red blood cell contribution
      4. Enzymes
        Purpose of each glycogen synthase
        Purpose of each glycogen phosphorylase
        What does T vs. R state refer to?
      5. Hormonal control of Glycogen synthesis
  2. Energy Generation and Related
    1. Oxidative Phosphorylation
      1. Where does it happen in Eukaryotes? in Prokaryotes?
      2. Where is the electron transport chain found?
      3. What is the name and purpose of Complex 1
        What is the name and purpose of Complex 2
        What is the name and purpose of Complex 3
        What is the name and purpose of Complex 4 ?
        What provides this complex with e-? What molecule takes the e- from this complex?
        What provides this complex with e-? What molecule takes the e- from this complex?
        Which complexes or ETC members directly transport H+ to form the H+ ion gradient?
        What provides this complex with e-? What molecule takes the e- from this complex?
        What provides this complex with e-? What molecule takes the e- from this complex?
      4. In what membrane is ATP synthase found?
        Which way does it allow diffusion of H+ ions?
        how many subunits does it have?
      5. What is the yield of ATP per Glucose?
        What is the yield of ATP per 16C Palmitate (a Fatty acid)
    2. The Krebs CYcle AKA the Citric Acid Cycle
      1. What are the inputs?
        How is Acetyl CoA made? (at least two possibilities)
        in detail - How does the Pyruvate Dehydrogenase complex work? - specifically referring to each Coenzyme - TPP, Lipoic acid, CoA
        How does each of the following regulate the PDC? Why?
        Acetyl CoA - high concentration
        NADH - high concentration
        kinase / phosphatase activities to add/remove phosphate to PDC
        Check out the Purple area if you arent sure for way #2
        What other pathways / methods can put molecules INTO the Citric acid cycle
      2. What steps are irreversible? Why are they irreversible?
      3. When is CO2 produced?
      4. When is NADH produced?
    3. Glyoxylate Cycle
      1. What does it make? From what starting material?
        Why is it important for Seeds to be able to use the Glyoxylate cycle? (Think storage material of seeds)
      2. What organisms CAN use it?
      3. What organisms CANT use it?

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Biochem Important Areas

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	Created by Chris Kornak-Bozza over 7 years ago