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Biochemistry and Molecular Genetics > Lehninger Ch 6 > Flashcards

Lehninger Ch 6 Flashcards

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Biology 101 flashcards
1
Q

Edward Buchner

A

1897
demonstrated cell-free yeast extracts could ferment sugar to alcohol
showed fermentation was promoted by molecules that continued to function when removed from cells

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2
Q

The Name Enzymes….

A

Was given by Frederick W. Kuhne to the molecules detected by Buchner

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3
Q

Enzyme

A

Most are proteins
With the exception of a few classes of catalytic RNA molecules known as Ribozyme
Catalytics activity depends on the integrety of the native protein conformation
Molecular weight: 12,000 to >1 million

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4
Q

Cofactor

A

1+ inorganic ions, such as Fe2+, Mg2+, Mn2+, or Zn2+

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5
Q

Coenzyme

A

Complex organic or metalloorganic molecule that act as transient carriers of specific functional groups

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6
Q

Prosthetic Group

A

Coenzyme or metal ion that is very tightly or covalently bound to the enzyme protein

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7
Q

Holoenzyme

A

Complete catalytically active enzyme together with its bound coenzyme and/or metal ions

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8
Q

Apoenzyme or apoprotein

A

the protein part of a holoenzyme(inactive)

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9
Q

Oxidoreductases

A

Transfer of electrons (hydride ions or H atoms)

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10
Q

Transferases

A

Group Transfer

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11
Q

Hydrolases

A

Hydrolysis (transfer of functional groups to water)

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12
Q

Lyases

A

Cleavage of C—C, C—O, C—N, or other bonds by elimination, leaving double bonds or rings, or addition of groups to double bonds

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13
Q

Isomerases

A

Transfer of groups within molecules to yeild isomeric forms

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14
Q

Ligases

A

Formation of C—C, C—S, C—O, and C—N bonds by condensation reactions coupled to cleavage of ATP or similar cofactor

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15
Q

Active site

A

The region of an enzyme surface that binds the substrate molecule and catalytically transforms it; also known as the catalytic site

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16
Q

What vitamin is the precursor for the CoA?

A

CoA, an activation-transfer coenzyme, is synthesized from the vitamin pantothenate

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17
Q

What vitamin is the precursor for the NAD+?

A

NAD+ is synthesized from niacin.

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18
Q

What vitamin is the precursor for pyridoxal phosphate?

A

Vitamin B6

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19
Q

Feed-forward type of regulation

A

In which something (toxin) activates the pathway. One of the most common ways this happens occurs. Is through the toxin acting to increase the amount of enzyme by increasing transcription of its gene.

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20
Q

Feedback regulation

A

The end product (ex thyroid hormone) directly controls its own rate of synthesis by suppressing earlier stimulating hormones. This is called a feedback loop.

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21
Q

Compartmentation regulation

A

Is a collection of enzymes within a specific compartment of the cell (eg. cytoplasm, peroxisome, lysosome, mitochondria)

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22
Q

Negative regulation

A

Refers to an inhibitor of an enzyme

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23
Q

Complementary regulation

A

Refers to several factors acting similarly (complementing each other) in regulating a pathway

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24
Q

What are coenzymes?

A

Most but not all, coenzymes in humans are synthesized from vitamins. They are neither proteins not carbohydrates but are complex organic molecules. They assist in the catalysis of a type of reaction, not just one reaction (coenzymes can associate with several different enzymes)

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25
Q

Substrate

A

The specific compound acted upon by an enzyme

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26
Q

Ground state

A

The starting point for either the forward reaction or the reverse reaction is called the ground state, the contribution to the free energy of the system by an average molecule (S or P) under a given set of conditions

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27
Q

Standard free-energy change

A

The free-energy change for a reaction occuring under a set of standard conditions: temperature, 298K; pressure, 1 atm (101.3 kPa); and all solutes at 1m concentration. ^G’ denotes the standard transformed free-energy change at pH 7.0 in 55.5 M water use by biochemists

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28
Q

Biochemical standard free-energy change

A

The free-energy change for a reaction occuring under a set of standard conditions: temperature, 298K; pressure, 1 atm(101.3 KPa); all solutes at 1 M concentration; at pH 7.0 in 55.5 m water. Also called standard transformed free-energy change

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29
Q

Transition state

A

An activated form of a molecule in which the molecule has undergone a partial chemical reaction; the highest point on the reaction coordinate

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30
Q

Activation energy

A

The amount of energy (in joules) required to convert all the molecules in 1 mol of a reacting substance from the ground state to the transition state

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31
Q

Reaction intermediate

A

A reaction intermediate is any species on the reaction pathway that has a finite chemical lifetime (longer than a molecular vibration)

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32
Q

Rate-limiting step

A

(1) Generally, the step in an enzymatic reaction with the greatest activation energy or with the transition state of highest free energy. (2) The slowest step in a metabolic pathway

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33
Q

Equilibrium constant (Keq)

A

A constant, characteristic for each chemical reaction, that relates the specific concentrations of all reactants and products at equilibrium at a given temperature and pressure

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34
Q

Rate Constant

A

The proportionality constant that relates the velocity of a chemical reaction to the concentration(s) of the reactant(s)

35
Q

Binding energy(^Gb)

A

The energy derived from noncovalent interactions between enzyme and substrate or receptor and ligand

36
Q

Specificity

A

The ability of an enzyme or receptor to discriminate among competing substrates or ligands

37
Q

Desolvation

A

In aqueous solution, the release of bound water surrounding a solute

38
Q

Induced fit

A

An enzyme conformation change in response to substrate binding that renders the enzyme catalytically active; also denotes a conformation change in any macromolecule in response to ligand binding, such that the binding site better conforms to the shape of the ligand

39
Q

Specific acid-base catalysis

A

Acid or base catalysis involving the constituents of water (hydroxide or hydronium ions)

40
Q

General acid-base catalysis

A

Catalysis involving proton transfer(s) to or from a molecule other than water

41
Q

Covalent catalysis

A

A transiet covalent bond is formed between the enzyme and the substrate. Formation and breakdown of a covalent intermediate creates a new pathway for the reaction, but catalysis results only when the new pathway has a lower activation energy than the uncatalyzed pathway. Both the new steps must be faster

42
Q

Enzyme kinetics

A

The oldest approach to understanding enzyme mechanisms, and one that remains very important, is to determine the rate of the reaction and how it changes in response to changes in experimental parameters

43
Q

Pre-steady state

A

In an enzyme-catalyzed reaction, the period preceding establishment of the steady state, often encompassing just the first enzymatic turnover

44
Q

Steady state

A

A nonequilibrium state of a system through which matter is flowing and in which all components remain at a constant concentration

45
Q

Steady state kinetics

A

As most of the reaction reflects the steady state, traditional analysis of reaction rates is referred to a steady-state kinetics

46
Q

Vo

A

Initial rate or velocity, the initial rate of a reaction

47
Q

Vmax

A

The maximum velocity of an enzymatic reaction when the binding site is saturated with substrate

48
Q

Michealis-Menten equation

A

The equation describing the hyperbolic dependence of the initial reaction velocity, Vo, on substrate concentration, [S], in many enzyme-catalyzed reactions: Vo= Vmax[S]/Km+[S]

49
Q

Steady-state assumption

A

The steady-state assumption is also known as the reactant stationary assumption. It’s based on the idea that the concentration of the enzyme-substrate complex (ES) will rapidly approach a steady state, meaning that its concentration won’t change significantly until a significant amount of substrate has been consumed

50
Q

Michaelis constant (Km)

A

The substrate concentration at which the enzyme-catalyzed reaction proceeds at one-half its maximum velocity

51
Q

Lineweaver-Burk equation

A

An algebraic transform of the michealis-menten equation, allowing determination of Vmax and Km by the extrapolation of substrate to infinity
1/v = (Km/Vmax[S]) + 1/Vmax.

52
Q

Michaelis-Menten kinetics

A

A kinetic pattern in which the initial rate of an enzyme-catalyzed reaction exhibits a hyperbolic dependence on substrate concentration

53
Q

Dissociation constant (Kd)

A

An equilibrium constant for the dissociation of a complex of two or more biomolecules into its components; for example, dissociation of a substrate from an enzyme

54
Q

Kcat

A

A more general rate constant to describe the limiting rate of any enzyme-catalyzed reaction a saturation
Kcat is equivalent to the rate constant for the limiting step

55
Q

Turnover number

A

The number of times an enzyme molecule transforms a substrate molecular per unit time, under conditions giving maximal activity at saturating substrate concentration

56
Q

Cleland nomenclature

A

A shorthand notation developed by W.W. cleland for describing the progress of enzymatic reactions with multiple substrates and products

57
Q

Reversible inhibition

A

Inhibition by a molecule that binds reversibly to the enzyme, such that the enzyme activity returns when the inhibitor is no longer present (also called competitive)

58
Q

Competitive inhibition (Km increases, Vmax stays the same)

A

Competes with the substrate for the active site of an enzyme, While the inhibitor (I) occupies the active site, the substrate is excluded, and vice versa. Many competitive inhibitors are structurally similar to the substrate and combine with the enzyme to form an unreactive E1 complex. Competing, Km increases while Vmax stays the same

59
Q

Uncompetitive inhibition(Vmax and Km decrease)

A

Binds as the site distinct from the substrate active site and, unlike a competitive inhibitor, bind only to the ES complex. Thus lowers the Vmax and apparent Km also decreases because the substrate required to reach 1/Vmax decreases by a factor of a^1. Because the enzyme is inactive when the uncompetitive inhib. is bound but the inhibitor is not competing with the substrate for binding, the inhibitor effectively removes some fraction of the enzyme molecules from the reaction (two or more substrates)

60
Q

Mixed inhibition (lowers Vmax, Km can increase or decrease)

A

The reversible inhibition pattern resulting when an inhibitor molecule can bind to either the free enzyme or the enzyme-substrate complex (not necessarily with the same affinity) Usually effects both Km and Vmax. Lowering Vmax and either increasing or decreasing Km depending of E or ES (two or more substrates)

61
Q

Noncompetitive Ihibition

A

a=a’ special case, affect the vmax but not the km

62
Q

Irreversible inhibitors

A

Bind covalently with or destroy a functional group on an enzyme that is essential for the enzymes activity, or they form a highly stable noncovalent association. Formation of a covalent link between an irreversible inhibitor and an enzyme is a particularly effective way to inactivate an enzyme

63
Q

Suicide inactivator

A

Undergoes the first few chemical steps of the normal enzymatic reaction, but instead of being transformed into the normal product, the inactivator is converted to a very reactive compound that combines irreversibly with the enzyme, they hijack the normal enzyme reaction mechanism to inactivate the enzyme

64
Q

Transition state analog

A

A stable molecule that resembles the transition state of a particular reaction and therefore binds the enzyme that catalyzes the reaction more tightly than does the substrate in the enzyme-substrate complex

65
Q

Serine proteases

A

One of four major classes of proteases, having a reaction mechanism in which an active-site Ser residue acts as a covalent catalyst,

66
Q

Retrovirus

A

An RNA virus containing a reverse transcriptase

67
Q

Regulatory enzyme

A

An enzyme with a regulatory function, through its capacity to undergo a change in catalytic activity by allosteric mechanisms or by covalent modification

68
Q

Allosteric enzyme

A

A regulatory enzyme with catalytic activity modulated by the noncovalent binding of specific metabolite at a site other than the active site

69
Q

Allerosteric Modulator

A

The modulators for allosteric enzymes may be inhibitory of stimulatory. The modulator can be the substrate itself; regulation in which substrate and modulator are identical is referred to as homotropic

70
Q

Regulatory protein

A

Protein whose function is to regulate the activity of another protein or enzyme by binding to it.

71
Q

Homotrophic

A

Describes an allosteric modulator that is identical to the normal ligand

72
Q

Heterotrophic

A

Describes an allosteric modulator that is distinct from the normal ligand

73
Q

Protein Kinases

A

Enzymes that transfer the terminal phosphoryl group of ATP or another nucleoside triphosphate to a Ser, Thr, Tyr, Asp, or His side chain in a target protein, thereby regulating the activity of other properties of that protein

74
Q

Protein phoshatates

A

Enzymes that hydrolyze a phosphate ester or anhydride bond on a protein, releasing inorganic phosphate, Pi. Also called phosphoprotein phosphatases

75
Q

Zymogen

A

An inactive precursor of an enzyme; for example, pepsinogen, the precursor of pepsin

76
Q

Proproteins (proenzymes)

A

Proteases are not the only proteins activated by proteolysis. In other cases, however, the precursors are called not zymogens but more generally proproteins. For example, the connective tissue protein collagen is initially synthesized as the soluble precursor procollagen

77
Q

Regulatory cascade

A

A multistep regulatory pathway in which a signal leads to activation of a series of proteins in succession, with each protein in the succession catalytically activating the next, such that the original signal is amplified exponentially

78
Q

Platelets

A

Small, enucleated cells that initiate blood clotting; they arise from the blood marrow cells called megakaryocytes. Also known as thrombocytes

79
Q

Fibrin

A

A protein factor that forms the cross-linked fibers in blood clots

80
Q

Fibrinogen

A

The inactive precursor protein of fibrin

81
Q

Thromboxane

A

Any of a class of eiconsanoid lipids with a six-membered ether-containing ring; involved in platelet aggregation during blood clotting
-Activation leads to the presentation of anionic phospholipds on the surface of each platelet and the release of the signaling molecule such as –

82
Q

Thrombin

A

Peptide removal is catalyzed by the serine protease thrombin

83
Q

Intrinsic pathway

A

Blood Clotting= As all components of this pathway are found in the blood plasma, it is called the intrinsic pathway

84
Q

Extrinsic pathway

A

The second path is the tissue factor, or extrinsic pathway. A major component of this pathway, the protein Tissue Factor(TF) is not present in the blood

Biochemistry and Molecular Genetics (14 decks)

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