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Bioc 221 > BIOC 221 - Lab Exam > Flashcards

BIOC 221 - Lab Exam Flashcards

1
Q

In the catalytic process, metal ions act as?

A

electrophiles

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2
Q

Metal ions help enzymes in what ways? (3)

A

1) aid in binding of S
2) accept/donate e’s
3) withdraw e’s to change partial charge distribution in S

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3
Q

The ability of certain metals to bind multiple ligands in their coordination sphere enables them to participate in? (2)

A

1) binding S and coenzymes to enzymes

2) polarizing reactive groups in active site

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4
Q

Example of a metal ion that contributes to the polarization of a functional group?

A

Zinc in Alcohol Dehydrogenase contributes to polarization of alcohol group

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5
Q

Role of Mg ions in many enzymatic reactions?

A

essential role in the binding of negatively charge phosphate group of ATP

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6
Q

Phosphatases - broadly classified into (3) groups depending on pH optima of the enzyme:

A

1) acid
2) neutral
3) alkaline Pases

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7
Q

What is Alkaline phosphatase? (what type of enzyme? uses?)

A
  • non-specific hydrolase
  • uses H2O as second substrate for a number of phosphate monoesters including PNPP (p-nitrophenyl-P) to produce yellow p-nitrophenyl & Pi
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8
Q

What is Alkaline phosphatase? (what type of protein?)

A
  • glycoprotein with dimer of 2 similar sub units, each containing different binding sites for Zn(2+) and Mg(2+) that are required for catalysis
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9
Q

cofactors

A

inorganic ions (Fe2+, Mg2+, Mn2+, Zn2+)

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10
Q

coenzymes

A

complex organic/metalloorganic molecules

ex. NAD+

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11
Q

Some enzymes require both of what (2) things for activity? give an example.

A

require both a coenzyme & 1+ metal ions

alcohol dehydrogenase

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12
Q

prosthetic group

A

coenzyme or metal ion that is bound to enzyme

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13
Q

holoenzyme

A

enzyme with bound coenzyme and/or metal ions

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14
Q

apoenzyme (apoprotein)

A

protein part of enzyme

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15
Q

Some enzymes are modified covalently by __, ___ and other processes. These modifications are required to ___ enzyme activity.

A

phosphorylation, glycosylation

regulate

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16
Q

Alkaline Pase is found where?

A

in all tissues

high [c] in liver, bile duct, kidney, bone, placenta

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17
Q

Regulation of metabolic pathways involves 1+ of these (7) mechanisms:

A

1) amount of E present
2) [S]
3) reversible inhibition (by products or other compounds)
4) covalent modification
5) modulator protein binding
6) proteolytic cleavage
7) allosteric activation/inhibition

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18
Q

The regulatory mechanism used depends what on (2) things?

A

1) the function of the metabolic pathway where enzyme resides
2) purpose of regulation

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19
Q

Energy production pathways must be regulated by a mechanism that can do what?

A

respond quickly to ATP requirement

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20
Q

Storage pathways can be controlled by a mechanism that?

A

responds slowly to changing conditions

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21
Q

Allosteric Enzymes

A

enzymes that are regulated by binding of activators or inhibitors (allosteric effectors) to regulatory sites

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22
Q

Allosteric Enzyme - plot of reaction velocity vs. [S]

A

sigmodal

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23
Q

Non-regulatory Enzymes - plot of reaction velocity vs. [S]

A

hyperbolic

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24
Q

Allosteric effector molecules bind where?

A

bind to enzyme at site distinct and physically separate from S binding site

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25
Q

Allosteric Effectors affect?

A

overall S binding and/or reaction velocity

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26
Q

Homotropic effect

A

when S is effector molecule

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27
Q

Homotropic effects are observed when?

A

reaction of one S with E affects reaction of 2nd S with diff active site on multimeric protein.

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28
Q

The interaction between sub unites makes the binding of S ____ and results in what type of curve in plot of v vs. [S]?

A

cooperative

sigmoidal

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29
Q

Negative cooperativity

A

reaction of substrate with 1 active site makes it harder for another S to react at another active site

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30
Q

Positive cooperativity

A

reaction of substrate with 1 active site makes it easier for another S to react at another active site

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31
Q

Why can’t allosteric enzymes (with homotropic effector) be described by simple Michaelis-Menton Kinetics.

A

b/c affinity of E changes with [S]

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32
Q

How are allosteric enzymes with homotropic effectors characterized?

A

by [S] giving half-max rate [S]0.5 and Hill Coefficient, h

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33
Q

h values for:

1) (+) cooperativity
2) (-) negative cooperativity)

A

1) h>1

2) h<1

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34
Q

Feedback inhibition

A

a situation in which endpoint of pathway controls its rate of synthesis
usually takes place at 1st committed step, early step or branch point of pathway.

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35
Q

In feedback inhibition, __ usually inhibits or __ __ activates a regulatory enzyme in pathway.

A

endproduct

related metabolite

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36
Q

Feedback regulation often makes use of properties of? because?

A

allosteric enzymes b/c allosteric activators of inhibitors don’t need to resemble S or bind in active site
- also small changes in their [c] can have strong effect of velocity of rxn

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37
Q

In glycolysis, pyruvate kinase catalyzes which reaction?

A

last reaction between ADP & PEP

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38
Q

Pyruvate Kinase - regulation

A

allosterically regulated by ADP, ATP & alanine

feedforward activation by FBP

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39
Q

Glycolysis can function either ___ or ___ depending on (2)?

A

anaerobically & aerobically

availability of oxygen and ETC

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40
Q

Fate of pyruvate in cells with mitochondria and oxidative metabolism?

A

pyruvate converted completely to CO2 & H2O

- aerobic glycolysis

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41
Q

In RBCs that lack mitochondria & oxidative metabolism?

A

pyruvate reduced to lactate (3C hydroxyacid)
- anaerobic glycolysis

1 mol glucose –>—> 2 mols lactate

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42
Q

Ability of glycolysis to produce ATP under hypoxic conditions is especially important for?

A

skeletal muscles which can perform at high work output levels when O2 supply is limited

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43
Q

Other functions of glycolysis other than ATP production

A

in liver & adipose tissue - pyruvate is precursor for FA biosynthesis (regulated by glucagon & insulin)

  • amino acids
  • pentoses (5C sugars)
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44
Q

In yeast & other microorganisms, glycolysis represents..

A

1st stage in process of alcohol fermentation convert glucose to ethanol under anaerobic conditions

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45
Q

Alcohol Fermentation

A

pyruvate first decarboxylated to acetaldehyde by pyruvate decarboxylase
then acetaldehyde is reduced to ethanol by alcohol dehydrogenase

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46
Q

Pyruvate –> Acetaldehyde

A

2CH3COCOOH –> 2CH3CHO + 2CO2

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47
Q

acetaldehyde –> ethanol

A

2CH3CHO + 2NADH + 2H+ –> 2CH3CH2OH + 2NAD+

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48
Q

Overall run of Alcohol Fermentation

A

Glucose + 2Pi + 2ADP –> 2Ethanol + 2ATP + 2CO2

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49
Q

Iodoacetate inhibits?

A

G3P DH (converts G3P –> 1,3-diphosphoglycerate)

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50
Q

Fluoride inhibits?

A

enolase (converts 2-Phosphoglycerate to PEP)

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51
Q

Bisulfite (NaHSO4)

A

forms additional compound with acetaldehyde when it becomes unavailable for reaction with NADH in alcohol DH run

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52
Q

In most pathways of fuel oxidation, fats, carbs, proteins & ketone bodies are degraded to?

A

activated 2-C acetyl portion of acetyl-CoA

53
Q

In the CAC, acetyl CoA is?

A

further oxidized to CO2 (oxidation occurs in 4 rxns that transfer e’s to e-accepting coenzymes NAD+ & FAD

54
Q

4 reactions of the CAC involve oxidation (transferring e’s to NAD+ & FAD). The other reactions in CAC have what purpose?

A

rearrange electrons to facilitate e transfer to e-accepting coenzymes

55
Q

Initially, what happens to acetyl-CoA in CAC?

A

combines with 4C intermediate OAA to form citrate (6C)

56
Q

After formation of Citrate in CAC?

A

rearrangement of bonds in citrate followed by 2 oxidative decarboxylations (transfer e’s to NAD+ & release 2CO2)

57
Q

After 2 oxidative decarbox. in CAC?

A

high E phosphate bond in GTP is generated from substrate-level phosphorylation

58
Q

After substrate level phosphorylation in CAC?

A

2 e transfer reactions occur & OAA is regenerated

59
Q

Overall process of CAC occurs with conservation of most of the E in chemical bonds of acetyl-CoA as..

A

3 NADH, 1FADH2, 1 GTP

60
Q

Lactate is formed from..

A

degradation of carbohydrates via glycolysis

61
Q

During hypoxic conditions (oxygen limited), cells turn towards?

A

anaerobic metabolism

62
Q

In anaerobic metabolism, lactate DH…

A

converts pyruvate to lactate with concomitant NADH to NAD+. this increases [lactate] in blood

63
Q

Since lactate is metabolized by ___ to produce __ via ____ , high blood [lactate] is usually found in people with?

A

liver
glucose
gluconeogenesis
poor liver function

64
Q

One of the major products of amino acid metabolism is?

A

ammonia (NH3) which is highly toxic to higher organisms

65
Q

In the liver, ammonia and CO2 are used to produce?

A

water-soluble form of nitrogen: urea via urea cycle

66
Q

after urea is formed in urea cycle…

A

liver passes urea to blood which carries it to the kidney to be filtered out & excreted in urine

67
Q

Why is increased [urea] in kidney an indicator of poor kidney?

A

one function of the kidney is to collect & excrete urea

68
Q

Since urea is formed in the liver, low blood urea nitrogen is often the consequence of?

A

impaired liver function due to disease or infection (hepatitis)

69
Q

(3) exothermic reactions that need to be bypassed for gluconeogenesis

A

1) hexokinase: glucose –> G6P (G6Pase)
2) PFK-1: F6P –>F16BP (F1,6-BPase-1)
3) pyruvate kinase: PEP –> pyruvate (pyruvate carboxylase, PEP carboxylase)

70
Q

Gout

A

caused by excessive uric acid (ionized to urate in body) in the blood (final product of purine degradation) which causes inflammation of joints by precipitation of sodium urate crystals & can cause kidney stones (not very soluble)

71
Q

Purpose of Allopurinol

A

prescribed for patients suffering from gout
Xanthase Oxidase inhibitor - (similar structure to xanthine)
- decreases [uric acid] - hypoxanthine & xanthine are soluble and can be excreted

72
Q

energy from oxidation of fuels is converted to…. by process of..

A

high E phosphate bonds of ATP

oxidative phosphorylation

73
Q

Most of the E from oxidation of fuels in TCA cycle & other oxidative pathways is conserved in the form of?

A

reduced e-accepting coenzymes, NADH & FADH2

74
Q

The ETC does what?

A

oxidizes NADH & FADH2 & donates e’s to O2 which is reduced to H2O
E from reduction of O2 is utilized for the phosphorylation of ADP to ATP by ATP synthase

75
Q

The entire ETC consists of several large __ ___ & 2 small independent components: __ & ___

A

protein complexes

ubiquinone (coenzyme Q) & cytochrome C

76
Q

Electrons are conducted in a defined sequence from __ ___ through this system to __ and __ __ __ drives transport of __ from __ to ___

A 
reduced coenzymes 
oxygen
free energy change
protons 
matrix to IMS
77
Q

What provides a regulatory mechanism by which rate of ATP synthesis can control rate of e flow?

A

coupling of ATP synthesis to ETC through transmembrane proton gradient

78
Q

As a consequence of ATP synthesis coupled to ETC…

A

rate of O2 consumption is coordinated with rate of ATP utilization

79
Q

When ATP synthesis & e transport becomes ‘‘uncoupled” in brown adipose tissue, or in presence of chemical compounds…

A

E from ETC is converted to heat

80
Q

Genetic diseases & other problems with ETC result in..

A

increased level of NADH which inhibited TCA & entry of pyruvate & FAs into cycle. Consequently, pyruvate is converted to lactate which appears in blood and FAs accumulate in tissues as TAGs.

81
Q

Antimycin A inhibits?

A

Complex II

82
Q

Malonate inhibits?

A

Complex II

83
Q

Cyanide (CN-) & Carbon Monoxide (CO) inhibit?

A

Complex IV

84
Q

(2) mechanism in humands for detox of xenobiotic materials & toxic metabolic waste

A

1) inactivation by reversibly binding to protein

2) chemical modification so it can be excreted (like ammonia –> urea)

85
Q

Detox of Xenobiotic compounds is usually accomplished by.. or?

A

hydroxylation mediated by cyt P-450 enzymes or conjugation with sulcate or carbohyrate

86
Q

Hydroxylation reaction consists of ?

A

NADPH, cyt reductase, cyt P-450 complex

87
Q

cytochrome P-450 represents a class of..

A

heme containing monooxygenase induced by drugs such as coumarin

88
Q

majority of cytochromes P450 are located in?

A

ER of liver

89
Q

What determines the duration of drug action?

A

Rate of degradation of drugs

90
Q

In Hydroxylation of drugs…

A

both NADH & NADPH donate reducing equivalents for reduction of cytochromes which in turn are oxidized by drugs in a series of hydrogenase reactions

91
Q

Hydroxylation purpose

A

modifies functional groups which increases drugs solubility & loss of physiological activity

92
Q

Conjugation of steroid hormones & phenolic drugs with sulfate & carbohydrate represents another …

A

significant mechanism for detox & removal of compounds

93
Q

fate of Sulfate conjugated compounds

A

excreted directly in urine since they are more H2O soluble

94
Q

fate of Carbohydrate conjugates

A

excreted into intestine lumen where hydrolysis of conjugates occurs & may result in some reabsorption of drug

95
Q

Phase 1 - Hydroxylation: needs?

A

NADH & cyt P450 (microsomes)

96
Q

Phase 2 - Conjugation of hydroxylated compounds with…

A

glucuronic acid, sulcate, acetate…

97
Q

Phase 1 - Hydroxylation cycle

A

drug binds to P-450-Fe(3+), NADPH donates e’s through NADPH cyt450 reductase to ferric ion (becomes ferrous, Fe2+), oxygen enters & binds to drug, 1 oxygen of O2 goes to H2O, the other becomes the hydroxyl group (OH) attached to drug, Fe2+ becomes Ferric ion (Fe3+) again. Drug is then released.

98
Q

Phase 2 - Conjugation pathway

A

UDP-glucose -(UDPG DH)-> UDP-glucuronate (reduction of 2NAD+ to 2NADH)

UDP-glucuronate donates glucuronate group to Drug-OH 
carboxylate group (- charge added) of glucuronate group on drug further increases solubility of hydroxylated compound
99
Q

Cofactor function of B1 vitamin

A

aldehyde transfer

100
Q

Cofactor function of B7 vitamin

A

carboxylation - helps aid transfer of CO2 groups

101
Q

PDH is regulated by covalent mod & product inhibition. Identify products involved in inhibition & give name of covalent modification

A

Product Inhibition: acetyl-CoA, ATP, NADH

Covalent modification: phosphorylation/dephosphorylation

102
Q

Monosaccharides other than glucose that can yield energy via glycolysis & identify reactions that are different from glucose involved in glycolysis

A

fructose/galactose/mannose
F6P cleaved by F1P aldolase forming glyceraldehyde & DHAP
glyceraldehyde is phosphorylated by ATP to form G3P

103
Q

PDH plays significant role in regulation of glycolysis & oxidation of pyruvate. which mechanisms are responsible for this regulation?

A

product inhibition (ATP, NADH, acetyl CoA) & covalent modification (phos/dephos)

104
Q

Glycolysis is connected to PPP through intermediates. Identify & show how intermediates are interconnected in these 2 pathways.

A

G6P, F6P, G3P are common to both pathways

105
Q

Why is cells ability to regenerate NAD+ critical to glycolysis

A

coenzyme NAD+ is needed for G3P DH rxn where G3P becomes 1,3-BPG so without it, glycolysis can’t proceed

106
Q

How many mols of ATP are generated in aerobic (1) and anaerobic (2) glycolysis

A

1) 32 mols of ATP

2) 2 mols of ATP

107
Q

Which tissues/cells function under hypoxic conditions to produce lactate?

A

brain, erythrocytes (RBCs), skeletal muscle, renal medulla, retina

108
Q

anapletoric reaction

A

enzyme catalyzed reaction that can replenish supply of metabolic intermediates of a metabolic pathway

109
Q

example of anapletoric reaction

A

pyruvate carboxylase reaction

pyruvate –> OAA

110
Q

(3) oxidative reactions along with enzymes in CAC in which NADH is produced

A

1) isocitrate –> α-KG + CO2 (isocitrate DH)
2) α-KG + CoA-SH –> Succinyl-CoA + CO2 (α-KG DH complex)
3) L-malate –> OAA (L-malate DH)

all with concomitant reduction of NAD+ to NADH

111
Q

Cofactors of PDH reaction

A

1) TPP
2) FAD
3) Coenzyme A
4) NAD+
5) lipoate

112
Q

Which cofactor of PDH is not classified as a vitamin?

A

lipase because it is a naturally occurring compound that is endogenously synthesized

113
Q

Cataplerotic reaction

example?

A

reactions that remove intermediates from a pathway to
be used in other pathways
ex. α-KG + glutamine + NADPH + H+ –> 2 glutamate + NADP+

114
Q

How is the energy of TCA cycle oxidations efficiently conserved?

A

conserved through reduction of 3 NAD+, 1 FAD, and 1 GDP (or ATP)

production 3 NADH, 1FADH2, 1 GTP

115
Q

Explain why humans cannot convert fats to carbohydrates.

A

pyruvate kinase & pyruvate DH reactions are irreversible & exergonic. Acetate can’t serve as a starting material.

116
Q

Substrates for gluconeogenesis in mammals? what role do fatty acids play in gluconeogenesis?

A

lactate, pyruvate, CAC intermediates, carbon skeletons of most aa’s.
FA breakdown provide ATP for gluconeogenesis

117
Q

potential control points for gluconeogenesis & glycolysis

A

use different enzymes for 3 exergonic rxns.

hexokinase - g6pase

PFK- FBPase

Pyruvate Kinase- pyruvate carboxylase, PEP carboxylase

118
Q

Outcome if individual has dietary thiamine deficiency?

A

pyruvate & α-KG DH are affected - impairment of pyruvate metabolism & lead to lactic acidosis causing neurologic disturbance

119
Q

Why does alcohol consumption after strenuous exercise cause low blood glucose?

A

alcohol becomes oxidized by NAD+ and produces NADH. the lactate produced must be converted back to pyruvate but this rxn also produces NADH.
so lack of NAD+ inhibits gluconeogenesis

120
Q

In amino acid metabolism in mammals, what are was finally broken down to?

A

amino group removed and formed urea. remaining carbon skeleton is broken down to CO2, h2o, glucose,acetyl-CoA or ketone body

121
Q

the presence of transaminases in muscle & liver cells make them useful markers of tissue damage. Which transaminases are used for monitoring liver damage?

A

SGOT & SGPT

122
Q

FEATURES shared by uncouplers?

A

hydrophobic & have dissociable H+

123
Q

If a student takes a tablet and she starts to hyperventilate & become very hot, what is the most likely action of the tablet she has taken?

A

uncoupling ox. phos & ETC produces heat. Since there is no ATP synthesis, ADP accumulates, glycolysis & CAC increase to produce ATP & increase rate of ETC which increases rate of O2 consumption

124
Q

In the inhibitor method for determining sequence of electron carriers, what is/are oxidized & what is/are reduced? Explain.

A

e carriers before step are reduced and e carriers after are oxidized

125
Q

Why does iron deficiency result in fatigue?

A

decreased level of iron-containing cytochromes & Fe-S centres
- many E’s including cytochromes need iron as cofactor for catalysis

126
Q

Although molecular oxygen doesn’t participate directly in any of the rxns of the CAC, why does the cycle operates only when O2 is present?

A

reduction of O2 reoxidizes NADH to NAD+ needed for glycolysis. If no O2 then NAD+ can’t be regenerated

127
Q

What compounds are necessary for hydroxylation of coumarin to 7-hydroxycoumarin? functions of each.

A

NADPH - e donor
NADPH cyt450 reductase - facilitates e transfer to:
cytochrome P450 enzyme - makes drug more water soluble- binds it, chemically modifies it

128
Q

Function of

1) UDGPA
2) microsomes

A

1) glucuronate donor
2) contain enzyme UDP-glucuronate transferase which catalyzes transfer of glucuronate to 7-hydroxycoumarin to form 7-OH coumaringlucuronide

Bioc 221 (4 decks)

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