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Fall 2013 > BioChem Exam #2 > Flashcards

BioChem Exam #2 Flashcards

1
Q

What are the diseased states associated changes in the amounts of Hb SUBUNITS produced?

A

Abnormal Hb;
Alpha-thalassemia or Beta-Thalassemia;
Resulting in anemia due to decreased ability of RBC’s to transport O2 around the body

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2
Q

What disease results from changes in the Amino Acid sequence of Hb?

A

Sickle cell anemia;
Glu is replaced with Val (Non-conservative)
Changing structure changes the function!

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3
Q

What is the structure of normal Hb?

A

The OXY form has O2 bound to all subunits;

The DEOXY form exposes hydrophobic amino acids “greasy spot”on the alpha subunits, but they are inward (Glu)

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4
Q

What is the structure of Sickle Cell Hb?

A

The non-polar valine is exposed on the beta subunits and is unhappy because it is hydrophobic, so it wants to hide in the empty spots on the alpha subunits of other Hb;
Results in long chains of Hb;
These change the osmotic pressure and push water out of the RBC

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5
Q

What is Sickle Cell Crisis?

A

The collapsed cells clog up the arteries because they have formed aggregate chains;
More likely to occur in the “deoxy” state when O2 is missing because that is when the chains form;
Exercise, under anesthesia, anytime O2 is released from Hb

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6
Q

How does Sickle Cell help against malaria?

A

Malaria needs time to replicate in the body and as the spleen removes the “sick,” misshapen cells there is less time for the parasites to grow

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7
Q

How are proteins classified by FUNCTION?

A
  • Structural (collagen in connective tissue)
  • Transport (Hb moves Os)
  • Storage (Mb stores O2)
  • Defensive (Antibodies and immunity)
  • Catalytic (Enzymes)
  • Contractile (Actin/Myosin in muscles)
  • Receptor (Hormones and communication)
  • Regulatory (gene expression on/off)
  • Messenger (Hormones; carry all over body)
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8
Q

How are proteins classified by SHAPE?

A

Globular;

Fibrous

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9
Q

What are Globular Proteins?

A

Long polypeptide chain folded back on itself;
Usually DON’T have repeating sequences;
ENZYMES

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10
Q

What are Fibrous Proteins?

A

Usually do contain repeating sequences;
ONE type of secondary structure;
More organized and elongated

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11
Q

How are proteins classified by CHEMICAL COMPOSITION?

A

All proteins are composed of amino acids;
Some have additional components needed for biological activity (Non-amino acid);
EX: Hb needs heme group with iron

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12
Q

What is a CONJUGATED PROTEIN?

A

Amino Acid (Apoprotein) + Non-Amino Acid (Prosthetic group)

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13
Q

What are some common prosthetic groups?

A

Metal ion (creates metalloprotein)
Carb (creates glycoprotein)
Vitamins - Riboflavin (creates flavoprotein)

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14
Q

What are Enzymes?

A

Biological catalysts of metabolic processes;
All enzymes are globular, except ribozymes (RNA);
They change the structure of the substrate and so the function! – Lower the Activation Energy

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15
Q

Why is Catalysis by Enzymes so important?

A

Without catalysis, metabolic process would proceed too slow to support life

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16
Q

How do Enzymes catalyze reactions?

A

Increase the RATE;
Increase SPECIFICITY;
Increase CONTROL

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17
Q

How do Enzymes increase the RATE of the reaction?

A

The LOWER the activation energy needed to to reach the transition state of the reaction

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18
Q

How do Enzymes increase the SPECIFICITY of the reaction?

A

Reduce the amount of waste produced by bodily reactions;

They bind ONLY certain substrates as needed

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19
Q

How do Enzymes increase CONTROL of the reaction?

A

They can change shape and therefore control enzymatic reactions and pathways;
Some have the ability to alter themselves as needed by the body

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20
Q

Enzymes catalyze WITHOUT…

A
  • Altering the conditions within the cell (temp, pressure, pH, etc) - altering would denature the proteins;
  • Being consumed or irreversibly altered themselves (continually recycled)
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21
Q

What are Substrates?

A

Reactant of an enzymatic reaction;

What the enzyme binds to and uses to create the product

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22
Q

What is Standard Free Energy change (Delta G)?

A

Final - Initial Energies;
(Products - Reactants);
*This product is basically fixed

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23
Q

Why is Standard Free Energy basically a fixed amount?

A

Because the substrates have one energy content and the products have another energy content no matter what;
The enzymatic difference is in how much energy it takes to TRANSFORM substrate to product

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24
Q

What is the Activation Energy?

A

Energy required to start a reaction;
Determines the rate of the reaction;
HIGH for UNcatalyzed;
LOWER for catalyzed

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25
Q

What is the Transition State?

A

Max on the curve between reactants and products;
Where there is necessary energy and atom arrangement to proceed to the products;
LOWER with ENZYME

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26
Q

What is Spontaneity of a Reaction?

A

The change in free energy (delta G);
Spontaneous, Exergonic - RELEASES energy (lower products);
Nonsponatenous, Endergonic - REQUIRES energy (higher products)

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27
Q

What is the Rate of a Reaction?

A

Amount of energy needed to reach the final product and how fast it gets there

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28
Q

What is the Transition State Species?

A

The enzyme-substrate complex;

They are bound together

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29
Q

How do Enzymes lower the activation energy?

A
  • Binding reactants in close proximity (readily react b/c they are close together);
  • Holding the reactants in the proper orientation (align the bonds)
  • Providing the right chemical environment and correct conditions to proceed
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30
Q

What is the Active SIte?

A

Area on the enzyme, usually a cleft/crevice in the protein and certain amino acids where the substrate BINDS by non-covalent interactions and CATALYSIS occurs

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31
Q

What is the First Step in Catalysis?

A

Bind the substrate to the enzyme with highly specific interactions between the substrate and side-chains and backbone groups of the amino acids of the active site

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32
Q

What is the Lock-and-Key Model?

A 
HIgh degree of similarity between the shape of the substrate and the geometry of the enzyme biding site;
Complementary shapes (puzzle pieces);
Does not account for protein conformational flexibility
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33
Q

What is the Induced-Fit Model?

A

Bind the substrate induces a conformational change in the enzyme causing a complementary fit after binding;
Binding site has a different 3-D shape before substrate binds;
Does account for protein conformational flexibility

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34
Q

What are the Steps in Enzymatic product formation?

A 
Enzyme and Substate Separate;
Enzyme + Substrate Complex;
Enzyme + Product Complex;
Enzyme and Product separates;
Enzyme Recycled and starts over
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35
Q

How can the Active Site be specific?

A

Absolute;
Group;
Linkage;
Stereospecificity

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36
Q

Absolute specificity

A

1 enzyme, 1 substrate = 1 product

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37
Q

Group specificity

A

Substrates have a common functional group;

Enzyme looks for that one common characteristic

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38
Q

Linkage specificity

A

Substates have a common type of chemical bond

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39
Q

Stereospecificity

A

Binding due to the match up of specific arrangement of the molecules

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40
Q

What is the role of the R-group at the active site?

A

Maintain overall structure of the protein (tertiary and quaternary);
Directly participate at the active site by binding and catalyzing;
*Very responsible for the success of the catalysis

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41
Q

What is an Enzyme Cofactor?

A

Additional help for the active site;
Apozenzyme (aa) + Cofactor (Non-aa) = Holoenzyme (active)
-Prosthetic groups or
-Coenzymes

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42
Q

What are Prosthetic groups?

A

Tightly bound cofactors that are permanently apart of the of the active site

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43
Q

What are Coenzymes?

A

Loosely bound cofactors;
Come in and out of the active site as needed;
Used over and over again with the enzyme;
Largely derived from Vitamins

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44
Q

What is an Enzyme “assay”?

A

Measuring the activity of an enzyme;

How much is present

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45
Q

How can you measure an enzymes assay?

A

Measure the rate of DISAPPEARANCE of the Sub;

Measure the rate of the APPEARANCE of the Product

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46
Q

What type of curve is an enzyme energy profile?

A

Hyperbolic;
Linear - activity taking place at a constant rate;
Leveling off - all enzymes is combined to a substrate (equilibrium between formation and breakdown of E+P complexes and recycling)

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47
Q

Why do we only measure the INITAL rate of enzymes?

A

Only linear!!;
Not necessary to consider the reverse reaction;
Not necessary to consider change int eh substrate concentration;
Not necessary to reach equilibrium (then we cannot view the enzyme activity)

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48
Q

What are the units for expressing enzyme activity?

A

Rate of Reaction is used to quantitate enzymes (how much sub. is being converted to products);
International Units

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49
Q

How can Enzymes be used to diagnose disease?

A
  • Direct measurement of the Enzyme concentration in the blood (The presence of Plasma specific vs. non-plasma specific enzymes) OR
  • Detection/Measurement of the concentration of the substrate
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50
Q

What are Non-Plasma Specific Enzymes?

A

Present in the blood due to damaged or destroyed cells

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51
Q

What can be diseases are found by DIRECTLY measuring the enzyme concentration?

A
  • Detect disease or organ damage (heart enzymes in blood after a heart attack determine damage)
  • Monitoring Drug Effects (see if drug is damaging and causing release of non-specific enzymes)
  • Detect predisposition to genetic diseases
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52
Q

What disease is diagnosed by the concentration of the Substrate? (Indirect enzyme measurement)

A

The measurement of the concentration of glucose in the blood

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53
Q

How are Enzymes used to treat disease?

A

Directly by injection;

Aiding in drug design

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54
Q

What enzymes treat by direct injection?

A

Streptokinase and tPA (breakdown blood clots; heart attack and stroke);
Asparaginase (destroys asparganine and limits tumor growth)

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55
Q

Whats problems are associated with injecting enzyme?

A
  • Easily degraded;
  • Allergic reactions (proteins);
  • Cannot be absorbed into the bloodstream (not digested) so must be injected - not readily available to patients
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56
Q

How do enzymes help drug design?

A

They allow for the replication of specific inhibitors;

Targeting individual rates of metabolism

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57
Q

What is a biochemical pathway?

A

A series of linked reactions;

Enzymes causing the formation of one product which becomes the reactant of the following reaction and so on

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58
Q

What regulation of biochemical pathways is required?

A
  • Maintaining order of the reactions;
  • Responding to changes in the environment;
  • Conserving and directing energy use to make them efficient
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59
Q

How are pathways regulated?

A

Control of the Enzyme activity that drives the rxn:

  • Change the ACTIVITY level of the enzyme present (change structure)
  • Change the AMOUNT of enzyme present
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60
Q

What are the Factors that influence Enzyme activity?

A
  • Temperature
  • pH
  • Enzyme concentration
  • Substrate concentration
  • Presence of inhibitors
  • Allosteric
  • Feedback inhibition
  • Regulation of Enzyme synthesis
  • Location within the cell
  • Isozymes
  • Covalent modification
  • Zymogens
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61
Q

How does TEMP affect enzyme activity?

A

Raising the temp increases the available energy to a point and reaching transition faster;
But too much heat denatures the enzymes and slows/stops the reaction

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62
Q

How does pH affect enzyme activity?

A
  • Overall enzyme structure (denatures);
  • Affecting the charged R-groups at the active site (altering substrate binding and catalysis);
  • Change the charge on the substrate and how it interacts with the R-groups at the active site (can’t bind right)
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63
Q

How does Increasing Enzyme concentration effect the activity?

A

[Sub] remains constant, [E] increases;
Enzyme doesn’t work as hard as it can;
When all substrate is bound to reactants, can no longer see activity because no more substrate to bind;
No sub, No rxn, so enzyme can’t change anymore even though there is plenty (rain gauge)

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64
Q

What does the graph look like when the [S] is CONSTANT and ENZYME is INCREASING?

A 
Y = Initial velocity;
X = [E];
Hyperbolic;
Levels off as the Sub becomes limiting;
Only linear part can be used to determine enzyme concentration and activity
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65
Q

How is the concentration of the Enzyme dependent upon the substrate?

A

As the substrate is limited, No more conversion of enzyme;

CANNOT determine activity because it is measured by the conversion of substrate to product

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66
Q

How does Increasing Substrate concentration effect the enzyme activity?

A

Enzyme must work as hard as it can to keep up with the increasing substrate;
Enzyme eventually become limiting because all of it is bound to a substrate;
Every time a product is released, binds another substrate

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67
Q

What does the graph look when the [E] is CONSTANT and the [S] is INCREASING?

A

Y = initial velocity;
X = [S];
Hyperbolic;
Levels off as the Enzyme becomes limiting (all bound in ES);
Vmax occurs as the asymptote to enzyme concentration
*Michaelis-Menten!

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68
Q

What is Vmax?

A

the maximum reaction rate;
How fast the enzyme can convert to products;
# of substrate molecules turning to products per unit of time for a fully saturated enzyme

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69
Q

What is the Saturation Point for an enzyme?

A

When all enzymes are apart of the enzyme-substrate complex;

Steady state situation

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70
Q

What is the Michaelis-Menten equation?

A

Expresses the effect of [S] on the initial velocity;

Initial velocity = (Vmax [S]) / (Km + [S])

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71
Q

What is Km?

A

Ratio of rate constants;
Measure of the binding capacity of the ES;
Characteristics of a particular enzyme and a given substrate;
Enzyme with 2 or more subs may have different Km for each;
Enzymes that act on many different substrates may have a range of Km values

72
Q

What is the Km equation?

A

(Breakdown of ES/Formation of ES);

[k-1/ k1]

73
Q

What is the relationship between Km and binding capacity?

A

HIGHER Km = Weaker/Less binding;
LOWER Km = Stronger binding;
Inverse relationship

74
Q

Where is Km found on the M-M graph (increasing sub, constant enzyme)?

A

Half the Vmax (Vmax/2) corresponds to the Km;
Vmax on the Y, Km on the X;
On linear portion (steady state)

75
Q

How does the concentration of Substrate related to Km?

A

[S] within the cell is usually close to the Km;

The conc. of the Sub regulates the reaction

76
Q

What is the Lineweaver-Burk Double Reciprocal Plot?

A

Relates the concentration of the Substrate to the initial velocity and Km with a LINEAR Curve;
Uses y = mx+b

77
Q

Linear L-B Curve equation

A

(1/initial velocity) = { (Km/Vmax) X (1/[S]) } + (1/Vmax);

  • Y = (1/initial velocity)
  • MX = { (Km/Vmax) X (1/[S]) }
  • B = (1/Vmax)
78
Q

Why is K2 (formation of E+P) NOT considered in the Km?

A 
Rate Limiting Step;
Conversion of the ES to the product;
Too slow to really make a difference;
Don't worry about the reverse reaction;
Km is BINDING enzyme to sub;
PRODUCT does NOT matter
79
Q

What is at the Y-intercept of the L-B reciprocal graph?

A

1/Vmax

80
Q

What is at the X-intercept of the L-B reciprocal graph?

A

-1/Km

81
Q

What is the equation for the conversion of Enzyme to product?

A

E + S ES –> E + P

82
Q

What part of the equation represents the Km value?

A

First part;
E + S ES;
BINDING and K2 doesn’t matter

83
Q

What part of the equation represents the Vmax value?

A

Second part;
ES –> E + P;
How fast the enzyme is converting to products so K2 matters (rate limiting)

84
Q

Why is K2 so slow compared to K1 and K-1?

A

Because K2 is the actual conversion the substrate into the product with required chemical transformation;
K1/K-1 are just simple binding

85
Q

What is the relationship of Vmax to product output? (ES to E+P)

A

HIGH Vmax = HIGH conversion to product;

LOW Vmax = LOW conversion to product

86
Q

What are Inhibitors?

A

substances that slow down or block enzyme activity;
Irreversible;
Reversible (Noncompetitive, Competitive, or Uncompetitive)

87
Q

What are Irreversible Inhibitors?

A

Reacts with the enzyme through a covalent bond with the important functional group;
Enzyme is NO LONGER functional

88
Q

Nerve Gas - Irreversible Inhibitor Examples

A

Acetylcholinersterase inhibitors prolong the neurotransmitter acetylcholine;
Actions on the neuromuscular junction will result in prolonged muscle contraction and paralysis

89
Q

What are Competitive Inhibitors?

A

Similar structure to the substrate;
Binds at the active site and blocks the substrates access to it and doesn’t allow binding;
Vmax is the SAME;
INCREASES Km value (decreased binding);
Reversible by increased [S] (can’t compete)

90
Q

What are Noncompetitive Inhibitors?

A

Binds the enzyme at ANOTHER SITE than the active, so the structure of the enzyme changes;
Substrate can still bind, but the change in structure means NO MORE CATALYSIS;
Km (binding) is the SAME;
Vmax DECREASES (no conversion);
Not reversible by increased [S]

91
Q

What are Uncompetitive Inhibitors?

A

Inhibitor binds only AFTER the substrate binds;
Binds to the ES complex;
Does not compete for binding, but altering the structure doesn’t allow conversion to products;
Km DECREASES (binding increases):
Vmax DECREASES

92
Q

How do Uncompetitive Inhibitors shift the equilibrium causing Km to increase?

A

Binding shifts the equilibrium to the RIGHT so there is more binding, but bound complexes cannot covert to product so Vmax will decrease;
Graph is parallel to an uninhibited enzyme

93
Q

What are Allosteric Enzymes?

A

Have one or more binding sites OTHER THAN the active site which are specific for binding effector molecules;
Generally larger and more complex than other enzymes

94
Q

What is the key to Allosteric Behavior?

A

The existence of multiple forms of quaternary structure;

COOPERATIVITY

95
Q

What is Cooperativity?

A

Binding of one substrate or molecule makes the subsequent binding EASIER;
Changes the shape allowing other substrate to bind more readily

96
Q

What are Allosteric Effectors?

A

Bind to the enzyme at another SPECIFIC area than the active site (;
NOT the substrate;
Modifies quaternary structure and behavior of the enzyme

97
Q

What are the effects of Effectors?

A
  • Positive = Speed up

- Negative = Slow down

98
Q

What do Effectors do to the graph?

A

Sigmoidal (S curve);
Positive = Shift to the Right;
Negative = Shift to the Left
*Velocity changes a lot with a little change in [S]

99
Q

What are Homotropic Allosteric Interactions?

A

Several identical molecules binding to the enzyme;

Several substrates are different sites

100
Q

What are Heterotropic Allosteric Interactions?

A

Different ligands (such as a substrate + inhibitor) binding to an enzyme

101
Q

What are Allosteric Effector Regulatory Roles (moment-to-moment regulation)?

A
  • Very sensitive to the [S] (Homotropic effect)
  • Effector allow change in activity w/o change in [S] (Heterotropic effect);
  • Effectors don’t have to resemble [S] (can respond to other paths)
  • Effectors bind in equilibrium
102
Q

How do Effectors bind in equilibrium?

A

More Unbound, Bind effectos more;

Less Unbound, Release effectors and loose effect

103
Q

What is Feedback Inhibition?

A

Short-term control that uses Allosteric Enzymes;
End product of a metabolic pathway acts as an allosteric inhibitor of enzymes earlier the path after a BRANCH POINT (commitment step);
Only blocks the path directly to that product

104
Q

What drives Feedback Inhibition?

A

Having excess product will act as an inhibitor to keep from continually making too much of that product

105
Q

What is the Regulation of Enzyme Synthesis for enzyme control?

A

On/Off mechanism;
Expression of gene repressed or induced to needs of the cell/organism;
Change in the AMOUNT of enzyme present, not just if it is active;
Long-Term Regulation b/c requires completely making more enzyme to turn back on

106
Q

What are the different Organizations in the cell that can effect enzyme activity?

A

Soluble Enzymes;
Membrane-bound Enzymes;
Compartmentalization

107
Q

Organizations of Soluble Enzymes in the Cell

A
  • Non-associated (randomly bump into each other, no organization)
  • Loosely associated (hand product from enzyme to enzyme)
  • Multienzyme complexes (group of enzymes that always function together, all-or-nothing)
108
Q

Organization of Membrane-Bound Enzymes

A

Facilitate multi-enzyme pathways by keeping them all close together and correctly oriented;
Hydrophobic membrane regulates enzyme activity

109
Q

Organization by Compartmentalization

A

Different concentrations of substrate in different “compartments” of the cell drive reactions certain ways;
EX: Mitochondria can have enzyme that converts X to Y, but cytoplasm will convert Y to X

110
Q

What are Isozymes?

A

Enzymes that occur in multiple forms in the same species, tissue, or cell which carry out the same reactions with different kinetic properties, effectors, etc;
Different Km and Vmax values

111
Q

What do Isozymes reflect?

A
  • Different metabolic patterns in different organs
  • Different locations and roles of a given enzyme in cell
  • Differentiation and development
  • Differential fine-tuning of metabolic rates through differing responses to allosteric effects
112
Q

Example of Isozymes

A

Muscles convert Pyruvate to Lactic Acid;
Liver converts Lactic Acid to Pyruvate;
-2 enzymes that interconvert between the same substances, but prefer one direction over the other due to differing properties

113
Q

What is Covalent Modification?

A

Enzyme activity altered due covalent insertion/removal of a small functional group;
Reversible;
Adding PO4 turns enzyme On OR Off (totally one or the other);
More long-term than Allosteric, but shorter than Reg. of Synthesis

114
Q

Mechanism for Covalent Modification

A

ATP and a Modification Enzyme (protein kinase) add PO4 to the enzyme;
Will either make a Less active, More active (ON) or
a More active, Less active (OFF);
Each enzyme will only have one effect either way

115
Q

How can Covalent Modification be reversed?

A

Must have Phosphotase enzyme to hydrolyze the PO4 from the enzyme

116
Q

What are Zymogens?

A

Enzymes that are originally synthesized as INACTIVE Precursors;
Irreversible conversion to the active form through the hydrolysis of one or more peptide bonds;
Will remain active its entire life cycle;
Used for Storage and Transport

117
Q

Why are Zymogens used for Storage?

A

Because there needs to be a constant available supply to use upon immediate need;
EX:
-Digestive enzymes in the pancreas need to be readily available when we eat, but not always active;
-Insulin is inactive in the blood stream until needed to regulate blood glucose levels

118
Q

Why are Zymogens used for Transport?

A

Do not want enzymes functioning while in transport or in a part of the body that they shouldn’t be;
EX: Don’t want early activation of digestive pancreatic enzymes while being sent through the blood stream to other organs

119
Q

What is Metabolism?

A

ALL chemical processes occurring within a cell;

Making and Breaking chemical bonds

120
Q

What are the 2 types of Metabolic Processes?

A

Extracting energy from the environment (Light and chemical);

Using that energy

121
Q

How is energy extracted from the environment?

A

Light energy is taken in by photosynthetic organisms and converted to sugars (starch);
Other organisms then break the bonds of the sugars to release Chemical energy

122
Q

How is energy used?

A
  • Chemical bond energy to break sugar bonds and synthesize proteins, nucleic acids, and lipids;
  • Electrical (eels);
  • Light (fireflies);
  • Mechanical (muscles);
  • Thermal (excess is lost as heat to regulate body temp)
123
Q

What are the 2 classes of Metabolic Pathways?

A

Catabolic (break);

Anabolic (make)

124
Q

Catabolism

A

Breakdown of complex nutrients into simpler, usable molecules;
RELEASES energy;
Oxidative process

125
Q

Anabolism

A

Synthesis of complex cell constituents from simple molecules;
USES energy from catabolism;
Reduction process

126
Q

What is Bioenergetics?

A

The study of processes involved in extraction and transfer of chemical energy

127
Q

What is Gibbs Free Energy (G)?

A

Energy that could be used or made available to do useful work’
Intrinsic energy present in the chemical bonds of a molecule

128
Q

What is the energy content within a cell?

A

Sum of:

  • making chemical bonds
  • muscle contraction
  • nerve impulse transmission
  • transport across membranes
129
Q

What is Delta G?

A

Free energy CHANGE in a reaction;

Difference in energy content of products and reactants (constant temp and pressure)

130
Q

What are the 2 classes of Reactions?

A

Spontaneous, Exergonic;

Nonspontaneous, Endergonic

131
Q

Spontaneous, Exergonic

A

Energy RELEASED;
“Downhill” from high to low energy content;
NEGATIVE Delta G

132
Q

Nonspontaneous, Endergonic

A

REQUIRES added energy;
“Uphill” from low to high energy content;
POSITIVE Delta G

133
Q

For a reaction that RELEASES energy (Spontaneous), Delta G…

A

It the MAX amount of energy that will be produced

134
Q

For a reaction that REQUIRES energy (Nonspontaneous), Delta G…

A

Is the MINIMUM amount of energy needed for the reaction to run

135
Q

What influences Delta G values?

A

Temp,
Pressure
Concentration

136
Q

What Standard Conditions do we use for Delta G?

A

at pH=7;
T=25C;
P=1atm;
conc=1M

137
Q

What is Energy Coupling?

A

The linking of reactions that PRODUCE energy to reactions that REQUIRE energy

138
Q

What is Direct Coupling?

A

Delta G values are ADDITIVE for reactions that are directly linked in a pathway;
Sum of the overall pathway must be NEGATIVE for it to occur

139
Q

What is Energetic Energy Coupling?

A

Uses HIGH ENERGY INTERMEDIATES to transfer energy from a reaction that PRODUCES energy to a reaction that REQUIRES energy

140
Q

What is ATP?

A

Adenosine triphosphate

141
Q

What is the base of ATP?

A

Adenine

142
Q

What is the Sugar of ATP?

A

Ribose

143
Q

What is a Nucleotide?

A

Base + Sugar + PO4 (for ATP)

144
Q

What is the Nucleoside of ATP?

A

Adenine + Ribose = Adenosine

145
Q

How does ATP provide energy?

A

Single phosphate removed (orthophosphate, Pi);

2 phosphates removed (pyrophosphate, PPi)

146
Q

What is the energy release by removing a SINGLE phosphate (Orthophosphate)?

A

-7.3 kcal/mole

147
Q

How much energy is released by taking off 2 phosphates at one time? (pyrophosphate, PPi)

A

Almost twice as much removing a single phosphate

148
Q

Why is ATP such good energy source?

A
  • Required for the synthesis of genetic material (We can easily make it)
  • Relatively stable at pH 7
  • Energy released is in the range needed for biosynthetic reactions
149
Q

Why is Phosphoenolpyruvate (PEP) not as good of an energy source?

A
  • We can make it;
  • NOT stable at pH 7;
  • Releases too much energy (wasteful and damaging)
150
Q

Why is Glucose-6-phosphate not as good of an energy source?

A
  • We can make it;
  • Stable at pH 7
  • Too little energy released
151
Q

How is energy from Phospoenolpyruvate and Glucose-6-phosphate used?

A

Direct use in pathways;

Transfer their energy to ATP (Storage and transport within the cell)

152
Q

What is an Oxidation-Reduction Reaction?

A

The transfer of ELECTRONS;
Typically in pairs;
ALWAYS acts together

153
Q

What is Oxidation?

A

LOSS of electrons;

Catabolism

154
Q

What is Reduction?

A

GAIN of electrons;

Anabolism

155
Q

What happens to the SUBSTRATE in Oxidation-Reduction?

A

The substrate starts reduced and becomes OXIDIZED as it is broken down into another molecule;
LOSES electrons

156
Q

What is reactant is REDUCED in Oxidation-Reduction?

A

The coenzyme “carrier/helper” starts oxidized and becomes REDUCED;
GAINS electrons

157
Q

What are the main Oxidation-Reduction Coenzymes?

A
  • NAD+ (Nicotinamide adenine dinucleotide);

- FAD (Flavin adenine dinucleotide)

158
Q

How is NAD+ produced?

A

Nicotinic acid (Niacin) > Nicotinamide > NAD+

159
Q

What is NAD+ converted to durring CATABOLISM (Breakdown)?

A

NADH;

-REDUCED, so gains a pair of electrons and an H atom (with the remain H+ leftover)

160
Q

Why does the leftover H+ not really matter?

A

The body’s buffers regulate them so they don’t have an affect on physiological pH

161
Q

What is the chemical equation for Catabolism/Oxidation of a substrate?

A

AH2 (sub) + NAD+ (coenzyme) A + NADH + H+

162
Q

What must be in EXCESS to push Catabolism/Oxidation to the LEFT (forward)?

A

NAD+;

Must have excess reactant to force the reaction mechanism to continue to oxidize the substrate and cause breakdown

163
Q

What is the DIFFERENCE between the structures of NAD+ and NADH?

A
  • Everything but the Nicotinamide portion is the SAME;
  • NAD+ is AROMATIC, NADH is NOT;
  • ADD 2 electrons and 1 proton (H) to NADH
164
Q

What are the problems associated with Catabolism/Oxidation (breakdown)?

A
  • Recycling;

- Reverse direction or Synthesis (Anabolism)

165
Q

Why the reverse Synthesis/Anabolism with NAD+ and NADH a problem?

A

To force equilibrium to the RIGHT (backwards) and cause the reaction, NADH would bee to be in EXCESS;
Can’t have both NAD+ and NADH is excess of one another;
The reaction would never move either way

166
Q

What is the solution for the problem with Synthesis from Oxidation-Reduction?

A

“Sister” coenzyme for the SYNTHESIS reaction;

NADP+ (Nicotinamide adenine dinucleotide phosphate) and NADPH

167
Q

How does using NADP+ fix the problem?

A

This coenzyme is ONLY recognized in Anabolic pathways and NOT by catabolic;
Having specific enzymes for each direction allows for excesses because they are not exactly “reverse” reactions

168
Q

What must be in EXCESS in an Anabolic/Reduction to push equilibrium to the RIGHT (backwards)?

A

NADPH;

Excess product causes reduction of the Substrates (reverse reaction)

169
Q

Why is the Anabolic (reverse) Oxidation-Reduction needed?

A

There is needs to be a reserve of Substrates available for use for reactions at all time;
Synthesizing them is essential to keep metabolic processes going

170
Q

What is FAD?

A

Flavin adenine dinucleotide

171
Q

What are the 2 differences between NAD+ and FAD?

A
  • Binds BOTH (H+), none left over, FADH2;

- FADH2 (reduced state) is unstable and is rapidly reoxidized back to FAD in the presence of O2

172
Q

Why is FADH2 not good for storage?

A

When it is reoxidezed in the presence of O2 it quickly loses its electrons;
Can easily pick them up but will almost immediately lose them as well;
NOT used for synthesis

173
Q

What is the chemical equation for Oxidation/Reduction with FAD?

A

AH2 + FAD A + FADH2

174
Q

What is an Activation Reaction?

A

Kickstart almost all pathway;
An initia reaction occurs to activate the substrate through the formation of high energy bonds with a PO4 or coenzyme;
The pathway can then proceed with the release of this energy

175
Q

What other coenzyme is commonly used besides PO4 for activation?

A

Coenzyme A (CoA);

176
Q

What is CoA made of?

A 
Adenine;
Ribose;
2 phosphates;
Pantothenic acid (vitamin);
Sulfhydryl group (-SH, important part)

Fall 2013 (6 decks)

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