1. Oxidoreductase
    • Enzymes that catalyze oxidation-reduction reactions. In other words, the transfer of electrons in biological processes.
    • -reductant: electron donor
    • -oxidant: electron acceptor

    Normally have dehydrogenase of reductase in the name. Oxidase means that oxygen is normally the final acceptor.
  2. Transferases
    Catalyze the movement of a functional group from one molecule to another.
  3. Kinases
    A type of transferase that transfers a phosphate group (like ATP) to another molecule.
  4. Hydrolases
    Catalyze breaking of a compound into two molecules using water addition.

    • Normally named after the substrate bond they cleave:
    • -phosphatase
    • -peptidases
    • -nucleases
    • -lipases
  5. Lyases
    Catalyze cleavage of a single molecule into two products. Sometimes they can synthesize two molecules.
  6. Isomerases
    Catalyze rearrangement of bonds in molecules (in stereisomers and constitutional isomers)
  7. Ligases
    Involved in addition and synthesis reactions of large molecules.
  8. In what way do enzymes affect the thermodynamics and kinetics of a reaction?
    They do not affect the thermodynamics. ΔG or ΔH do not change.

    They do affect the rate of the reaction by increasing it massively.
  9. Lock and Key Model vs Induced Fit Model
    • Lock and Key: the substrate comes into an enzyme with a solid state that does not change (like a lock and key)
    • Induced Fit Model: (most scientifically based) enzyme uses energy to change to the substrate as it approaches, and releases energy as substrate leaves, going back into the original shape
  10. Coenzymes and Cofactors (proteins dealing with them)
    • Nonprotein molecules that bind to enzyme active site to participate in catalysis. They are kept at low concentrations.
    • Coenzyme: organic
    • Cofactor: inorganic

    • Apoenzymes: enzymes without cofactors
    • Holoenzymes: enzymes with cofactors
    • Prosthetic Groups: tightly bound cofactors or coenzymes are necessary for enzyme function
  11. B1
  12. B2
  13. B3
  14. B5
    Pantothenic Acid
  15. B6
    Pyridoxal Phosphate
  16. B7
  17. B9
    Folic Acid
  18. B12
  19. Proteinogenic Amino Acids
    20 amino acids our body needs and produces. They contain two functional groups (-NH2 and -COOH) and are joined by peptide bonds.
  20. Stereochemistry of Amino Acids
    All amino acids are chiral except glycine since the R group is a hydrogen.

    They all have an L configuration (so R group drawn to the right, amino group to the left, carboxyl group up, H bottom).

    They all have S absolute configuration except cysteine that is R but still L
  21. Nonpolar, Nonaromatic Side Chains
    • Complete Alkyl Side Chains:
    • Glycine
    • Alanine
    • Leucine
    • Valine
    • Isoleucine

    • Other
    • Methionine (S atom)
    • Proline (cyclic amino acid)
  22. Aromatic Side Chains
    • Tryptophan (largest)
    • Phenylaline (smallest)
    • Tyrosine (relatively polar from OH)
  23. Polar Side Chains
    • -OH Side Chains
    • Serine
    • Threonine

    • Amide Side Chains
    • -Asparagine
    • -Glutamine

    • Other
    • -cysteine (thiol group; -SH)
  24. Negative Side Cahins
    • Aspartic Acid => Aspartate anion
    • Glutamic Acid => Glutamate anion
  25. Positive Side Chains
    • Arginine
    • Lysine
    • Histidine
  26. If the enzymes are saturated with substrate, what determines the rate?
    Maximum velocity (maimum velocity of enzyme at work; vmax) depends on the concentration of enzymes. If you increase [enzymes], you increase vmax. This can be done by inducing transcription of enzymes.

    Once the vmax is reached - adding substrate would not affect the rate of the reaction.
  27. Michaelis-Menten Equation dependent on what reaction (rates too)
    E + S (k1)⇆(k2) ES (k3)→ E + P

    • E: enzyme
    • S: substrate
    • ES: enzyme substrate
    • P: product

    • Each k represents the start of the arrow, and the rate of that reaction.
    • k1: ES complex form at that rate
    • k2: ES comples dissociates at that rate
    • k3: turns in E & P at that rate
  28. Michaelis-Menten Equation
    Relates rate of reaction to enzyme concentration.

    v = (vmax[S]) / (Km+[S])

    Km: Michaelis Constant; it is concentration of substrates when (1/2) enzyme active sites filled
  29. (vmax)/2 = ...
    (vmax[S]) / (Km+[S])
  30. vmax (Km+[S]) = ...
    2 (vmax[S])
  31. Km + [S] = ....
  32. Km (rates too)
    Michaelis Constant; it is concentration of substrates when (1/2) enzyme active sites filled.

    Km = [S] when reaction at (1/2) vmax

    • Km < [S] reaction rate increases slowly as substrate is added
    • Km > [S] reaction rate increases quickly as substrate is added
  33. X and Y intercept of a Linweaver Burkman Plot
    (1/V) vs (1/[S]) - a double reciprocal graph of the Michaelis-Menten equation

    • X-intercept: 1/km
    • Y-intercept: 1/vmax
  34. A Michaelis-Menton Plot (v vs [S]) forms a hyperbola. Sometimes the enzyme makes it form an S shape. Why?
    • Sigmoidal Curve
    • This is caused by enzymes with multiple subunits and multiple active sites. They have two possible states:
    • -low affinity tense state: [T]
    • -high affinity relaxed state: [R]
  35. What is going on with substrate and enzyme in the following state for an enzyme that creates a sigmoidal curve? [T]⇆[R]
    • Low affinity tense state: [T]
    • High affinity relaxed state: [R]

    • Substrate binds to the enzyme encouraging other substrates to bind.
    • [T]⇆[R]
    • Enzyme loses substrate encouraging more substrates to unbind.
  36. How how do you differentiate between hydrophilic and hydrophobic side chains?
    • Hydrophobic
    • These side are normally have long carbon chains that uncharged and nonpolar

    • Hydrophilic
    • Side chains that are charged, as well as amides aspargine and glutamine

    In the creation of a protein, everything else generally lies in the middle of the protein with hydrophilic on the outside, and hydrophobic on the inside.
  37. Ball park pKa values for amino acids that are monoprotic
    • pKa1: around 2; the carboxyl group is the first to lose a proton
    • pKa2: around 9/10; the amino group is more likely to lose a proton

    (+) - 2 - (neural) - 9 - (-)
  38. How does temperature affect enzyme activity (include rates)?
    An enzyme activity doubles in velocity for every 10 degree increase. Once an optimal range is reached, the enzyme immediately drops in activity after degree increase because enzyme denatures.

    Optimal body temp for enzymes: 37 C
  39. How does pH affect enzyme activity?
    • Certain enzymes work bast at certain pH levels. This allows for further selectivity. For example:
    • stomach pH: 2
    • blood pH: 7.35
    • optimal enzyme pH: 7.4
    • pancreas enzymes: 8.5
  40. How does salinity affect enzyme activity?
    Increasing level of salt disrupts hydrogen and ionic bonding causing partial charges on enzymes or quartionary changes and sometimes denaturation.
  41. Feed Forward Regulation
    When an enzyme is affected by intermediate in it's furtur pathway. This causes the enzyme to negatively affect or positively.
  42. Negative Feedback
    When an enzyme is shut down by a product that has reached it's wanted concentration.
  43. Four types of reversible inhibition
    • -competitive
    • -noncompetitive
    • -mixed
    • -uncompetitive
  44. Competitive Inhibition (reversible inhibition)
    • The enzyme would have two molecules binding to active site: a substrate and inhibitor. The inhibitor prevents the substrate from binding to the enzyme until the substrate reaches a high enough concentration that the enzyme wants the substrate more.
    • vmax: same
    • Km: larger because more substrate needed to reach (1/2)vmax
  45. Noncompetitive Inhibition (reversible inhibition)
    • The inhibitor binds to the allosteric sit of the enzyme (not the active site), changing the conformation of the enzyme and removing activity.
    • vmax: decreases because there are less enzymes working
    • Km: same (no amount of substrate can remove inhibitor)
  46. Mixed Inhibition (reversible inhibition)
    • It can bind to enzyme or enzyme-substrate complex, but has different affinities for each (same would mean it is noncompetitive inhibitor)
    • vmax: decreases (allosteric)
    • Km: depends: enzyme preferred - increases, enzyme substrate complex preferred - decreases
  47. Uncompetitive Inhibition (reversible inhibition)
    • Inhibitor binds only to the enzyme-substrate complex at the allosteric site, locking the ezyme and substrate into place.
    • vmax: decreases
    • Km: decreases
  48. Irreversible Inhibition
    Permanently altering an enzyme from working.
  49. Molecules that bind to allosteric site (2)
    allosteric activators or allosteric inhibitors
  50. Covalent Modification vs Transient Modification
    Covalent Modification: enzymes that can activated or deactivated by phosphorylation or dephosphorylation.

    Transient Modification: modification of an enzyme that is short term (allosteric activation and inhibition)
  51. Glycosylation
    It can tag enzymes for transport within a cell or modify protein activity and selectivity.
  52. Zymogens
    Regulatory domain of the enzyme must be removed or altered to expose active site. Normally end in -ogens.
  53. Structural Proteins
    • Proteins that provide intracellular support, and tissue support via extracellular matrix.
    • -tendons
    • -ligaments
    • -cartilage
    • -collagen
    • -elastin
    • -keratin
    • -actin
    • -tubulin

    • Structure Type
    • Motif: repetitive organization of secondary structure giving tissue a fiberous nature.
  54. Collagen
    (Structural Protein) Found in extracellular connective tissue. It provides strength and flexibility to tissue.

    Stucture - three helical fibers composed of α-helices forming a secondary helix)
  55. Elastin
    (Structural Protein) An important component of the extracellular matrix connective tissue. Provides stretch such that it it can also recoil back and return to original shape.
  56. Keratins
    (Structural Protein) Intermediate filament proteins found in epithelial cells (skin). They contribute to molecular integrity of cell and function as regulatory proteins. (hair and nails)
  57. Actin
    (Structural Protein) Protein that makes microfilaments and thin filaments. It has a positive and negative side allowing it to slide unidirectionally.
  58. Tubulin
    (Structural Protein) Protein that makes microtubules responsible for chromosome separation, structure, and intracellular transportation with kinesin and dynein.
  59. Myosin
    (motor protein) Interacts with actin. Involved in cellular transport. Movement of neck is responsible for power stroke of sarcomere contraction.
  60. Kinesin and Dyneins (similarities and differences)
    (motor proteins) They has two heads, in which one is attached to tublin at all times.

    • Similarities
    • Vesicle transport
    • -kinesin: moves vesicle to (+) end of microtubule
    • -dynein: moves vesicle to (-) end of microtubule

    • Neurotransmitter vesicle transport
    • -kinesin: moves neurotransmitter vesicle to (+) end of neuron (synase)
    • -dynein: moves waste and recycled neurotransmitter vesicle to (-) end of neuron (soma)

    • Differences
    • Kinesin: role in aligning chromosomes during metaphase and depolymerizing microtubules during anaphase
    • Dyneins: responsible for sliding of cilia and flagella
  61. Binding Proteins
    Proteins that have a high affinity for certain molecules. They serve a stabilizing function and a transport function (but for those the affinity differs at different environments)
  62. Cell adhesion molecules (CAMs)
    • Proteins found on most cells and aid in binding of cell to extracellular matrix. There are 3 main types:
    • -cadherins
    • -integrins
    • -selectins
  63. Cadherins (Cell Adhesion Molecule)
    They are responsible for holding similar cells together (like skin).

    Group of glycoproteins that mediate calcium dependent cell adhesion.
  64. Integrins (Cell Adhesion Molecule)
    Bind a cell to extracellular matrix.

    Group of proteins made up of 2 membrane spanning chains called α and β.

    These chains are important and binding and communicating, promoting cell division, apoptosis, etc.
  65. Selectins (Cell Adhesion Molecule)
    Bind cells to carbohydrate molecules that project from the cell surfaces.

    They play an important role in host defense, including inflammation and white blood cell migration.
  66. Antibodies (immunoglobins)

    What are the three ways it destroys it's target?
    Proteins produced by B-cells that function to neutralize targets in the body by recruiting other proteins to eliminate threat.

    • 1) Neutralize antigen such that pathogen or toxin can't exert effect on body.
    • 2) Opsonization: marking a pathogen for destruction by other white blood cells.
    • 3) Agglutinating: clumping together with the antigen; this clump can then be phagocytized and digested by macrophages.
  67. Structure of Antibodies (immunoglobins)
    They are Y-shaped proteins with 2 identical heavy chains and 2 identical light chains held by disulfide linkage.

    At the tip of the Y, they have an antigen-binding region that has polypeptide sequence that binds to a specific antigenic sequence (antigen: targets of antibody)
  68. Biosignalling
    Process in which cells receive and act on signals. The proteins can have functions in substrate binding and enzymatic activity.
  69. Ion Channels (3 types)
    Proteins that create a pathway specidic for charged particles via facilitated diffusion (a form of passive transport that allows ions cross bilipid layer through a channel based on a concentration gradient)

    • Three Channels
    • Ungated Channel: channel always open
    • Voltage-Gated Channel: regulated by a membrane potential (normally closed until a certain voltage is met)
    • Ligand-Gated Channel: channels that open only when a ligand binds to them
  70. Enzyme-Linked Receptor (3 parts)
    • A receptor with catalytic activity in response to a ligand, It has 3 parts:
    • Membrane-Spanning Domain: anchors receptor to cell
    • Ligand Binding Domain: a ligand binds to here that causes a conformational change
    • Catalytic Domain: from a confirmational change, it causes a second messanger cascade (responsible for phosphorylating enzymes)
  71. G-Protein Coupled Receptors (GPCRs)
    -What protein does it use?
    -What can increase receptor affinity to protein?
    -What happens when G-Protein binds?
    -What is the structure?
    • What protein does it use?
    • They are involved in signal transduction. To transmition a signal, they use heterotrimeric G protein (uses GTP;active and GDP;inactive).

    • What can increase receptor affinity to protein?
    • A ligand binding to the receptor causes G protein to increase affinity to receptor.

    • What happens when G-Protein binds?
    • When the G protein binds, it changes the intracellular pathway of receptor (inhibiting or activating it)

    • Structure
    • Seven membrane spanning α-helices.
  72. What are the three main types of G-Proteins?

    (involved in G-coupled receptors that transduce signals)
    • Gs: stimulates adenylate cyclase which increases levels of cAMP
    • Gi: inhibits adenylate cyclase which decreases levels of cAMP
    • Gq: activates phospholipase C (cleaves phospholipid from PIP2

    Three part (α, β, γ) => all 3 with GDP => activation of receptor makes it with GTP => α breaks of with GTP and activates proper enzyme (inactivates) and become GDP => returns to receptor
  73. How do transport kinetics differ from enzyme kinetics?
    They have a km and vmax value and can be cooperative but they have no Keq values, nor do they use a catalyst.
  74. Electrophoresis
    Subjecting compounds to an electrical field, that moves the compound in accordance with net charge and size.

    • Anions travel to anode (-)
    • Cations travel to cathode (+)

    Made up of a porous polyacrylamide gel that allows small charged particles to quickly pass through.
  75. Migration Velocity (Electrophoresis)
    Velocity of the migration of particles during electrophoresis.

    v = Ez/f

    • E: electrical field strength
    • z: net charge of molecule
    • f: frictional coefficient (depending on mass / shape of molecule)
  76. How does polyacrylamide gel electrophoresis work? (Analyzing Method)
    • Analyzing Method
    • It is used to differentiate close massed particles by charge. It is limited by mass-to-charge and mass-to-size ratio.
  77. How does sodium dodecyl sulfate (SDS) polyacrylamide gel electrophoresis work? (Analyzing Method)
    • Analyzing Method
    • It is used to analyze different masses by neutralizing the proteins.

    A detergent is used that disrupts all noncovalent bonds by having large (-) chains bind to the protein; neutralizing and denaturing it.
  78. Isolectric focusing in gel electrophoresis
    The molecules travel on the basis of the isolectric point (where the protein or amino acid are neutral).

    A pH gradient is created in the gel with the acid at the anode (+), and base at the cathode (-). As the molecule travels, it reaches a point where no protons are binding to it, making it neutral and stuck at pH = pI.
  79. When is chromatography preferred of electrophoresis?
    When having to separate large proteins.
  80. Elute
    Running a mobile phase through the stationary phase and allowing the sample to run through the stationary phase.
  81. Partitioning (Chromatography)
    Separation of sample components in stationary phase.
  82. What matters in the protein and what shortens retention time in column chromatography?
    Column Chromatography: a column filled with silica or alumina beads (absorbent) uses gravity to move solvent down, separating compounds as they drip out.

    As a solution flows size and  polarity matter. The less polar the compound, the faster it moves (smaller retention time).
  83. Ion Exchange Chromatography
    Beads in a column are coated with charged substances that increase retention time of opposite charged molecules.

    Those stuck in the column can be removed by salt gradient.
  84. Size-Exclusion Chromatography
    Column beads have tiny pores where small molecules get trapped so large particle elute through faster.
  85. Affinity chromatography (methods of protein removal)
    A column is made with beads tha are coated in recptors that have a strong affintiy for the protein of interest. This causes proteins to be retained.

    • Obtaining Protein
    • The column is then elluted with:
    • 1) antibody that competes for receptor protein binds to
    • 2) an elutant with a pH that disrupts bonds of the protein to receptor
  86. 2 ways of determining protein structure
    • 1) X-Ray Crystallography: measures electron density on an extremely high -resolution scale by examining the crystallized protein
    • 2) Nuclear Magnetic Resonance (NMR) Spectroscopy
  87. Edmand Degradation
    Used to figure out the primary structure of a protein by sequentially and selectively removing N-terminal amino acid of the protein for analysis via mass spec.
  88. How is the primary structure of larger proteins determined?
    They are digested with chymotrypsin, trypsin, and cyanogen bromide at specific sites of amino acids.

    Smaller fragments are then measured by electrophoresis and Edman degredation.
  89. How is the activity of the protein determined?
    By monitering a known reaction with a known concentration of substrate and comparing it with a standard. Activity is related to concentration.
  90. How can concentration of a protein purified be determined?
    Almost exclusively it can be determined via spectroscopy but UV Spectroscopy but it is prone to contamination.

    • So they can also be determined through the changes in color via certain reaction like:
    • Bicinchoninic acid (BCA) assay
    • Lowry reagent assay
    • Bradford protein assay (most common)
  91. Bradford protein assay (for protein concentration determination)
    A mixture of protein and Coomasie Bradford blue dye is used.

    • Protonated Dye = Green brown
    • Deprotonated Dye = blue color

    The more the protein, the more of the blue color.
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