Biochemistry (Test 3)

Front 1

what is catabolism?

Back 1

degredation; nutrients and cell comstituents are broken down to salvage their compnoents and/or to generate energy

Front 2

what is anabolism?

Back 2

biosynthesis; biomolecules are synthesized from simpler components

Front 3

which type of reaction carries out the exergonic oxidation of nutrient molecules?

Back 3

catabolic = exergonic

breakdown = energy liberation

Front 4

the energy released by the exergonic reactions in catabolism is used to drive what...?

Back 4

endergonic processes (anabolic reactions & active transport of molecules against gradient)

Front 5

exergonic and endergonic processes are often coupled though the intermediate synthesis of what?

Back 5

high energy compounds such as ATP

Front 6

many metabolic reactions can be classified as what?

Back 6

redox reactions

Front 7

autotrophs synthesize all of their cellular components from what?

Back 7

simple molecules like h20, co2, NH3 & H2s

Front 8

chemolithotrophs and photoautotrophs are classified as what?

Back 8

autotrophs

Front 9

from where do chemolithotrophs obtain their energy?

Back 9

from the oxidation of inorganic compounds such as NH3, H2S of Fe+2

Front 10

from where do photoautotrophs obtain their energy?

Back 10

photosynthesis

Front 11

from where do heterotrophs obtain free energy?

Back 11

through the oxidation of organic compounds

Front 12

what is an obligate aerobe?

Back 12

requires oxygen

Front 13

what is an anaerobe?

Back 13

employs oxidizing agents such as sulfate or nitrate

Front 14

what is a facultative anaerobe?

Back 14

can grow in either the presence or absence of oxygen

Front 15

what is an obligate anaerobe?

Back 15

are poisoned in the presence of oxygen -can only survive and function in its absence.

Front 16

what are the major minerals needed for metabolism?

Back 16

SPCCSPM

sodium, potassium, calcium, chlorine, sulfur, phosphorus, magnesium

Front 17

what are the trace elements required for metabolism?

Back 17

iron, copper, zinc, selenium, iodine chromium and fluorine

Front 18

what role does magnesium play in metabolic processes?

Back 18

Mg is involved in nearly all reactions that that involve ATP and other nucleotides including the synthesis of DNA, RNA and proteins.

Front 19

what role does zinc play in metabolic processes?

Back 19

zinc is a cofactor in a variety of enzymatic reactions

Front 20

what role does calcium play in metabolic processes?

Back 20

calcium is vital in signal transduction

Front 21

most water-soluble vitamins are converted into what?

Back 21

coenzymes

Front 22

from is nicotinamide a component of ?

Back 22

NAD+

Front 23

what disease is associated with nicotinic acid/ nicotinamide malfunction?

Back 23

pellagra

Front 24

the water-soluble vitamins in the human diet are all precursors to what?

Back 24

coenzymes

Front 25

what are metabolic pathways?

Back 25

series of connected enzymatic reactions that produce specific products

Front 26

the reactants, intermediates, and products of metabolic pathways are known as what?

Back 26

metabolites

Front 27

In degradative pathways, the major nutrients (complex metabolites) are broken down into what? in what manner are they broken down?

Back 27

complex metabolites are broken down in a exergonic manner, into simpler products

Front 28

what happens to the free energy released in the degradative process ?

Back 28

it is conserved by the synthesis of ATP from ADP +Pi or by the reduction of the coenzyme NADP+ to NADPH.

Front 29

what are the two major free energy sources for biosynthetic reactions?

Back 29

ATP and NADPH

Front 30

a striking characteristic of degradative metabolism is that the pathways for the catabolism of a large number of diverse substances commonly converge on what common intermediate?

Back 30

Acetyl CoA

Front 31

the citric acid cycle produces what reduced coenzymes based on the principle that when acetyl carbons are oxidized in the TCA cycle, other substances must be reduced in counteraction? pg. 452

Back 31

NADH
FADH2

Front 32

what happens to the electrons carried by NADH and FADH?

Back 32

they are passed onto O2 to produce water in the processes of electron transport and oxidative phosphorylation

Front 33

the interconversion of metabolites in degradative and biosynethetic pathways are catalyzed by what?

Back 33

enzymes

Front 34

why are enzymes necessary in catabolic/anabolic reactions?

Back 34

-without them the processes would occur too slowly to support life

-their specificity ensures regulation & efficiency

-enzymes provide a mechanism for coupling endergonic reactions with energetically favorable ones***

Front 35

what feature of eukaryotic cells allows different metabolic pathways to operate simultaneously in different locations?

Back 35

compartmentalization of eukaryotic cytoplasm

Front 36

the electron transport chain & oxidative phosphorylation occur where?

Back 36

in the mitochondria

Front 37

glycolysis and fatty acid biosynthesis occur where?

Back 37

in the cytosol

Front 38

what are transport proteins used for in metabolism?

Back 38

transporting metabolites between compartments

Front 39

where does gluconeogenesis occur?

Back 39

the mammalian liver

Front 40

what are isoenzymes?

Back 40

enzymes that catalyze the same reaction but are encoded for by different genes and have different kinetic or regulatory properties.

Front 41

what metabolic processes occur in the mitochondria?

Back 41

Krebs cycle, ETC, Oxidative phosphorylation, fatty acid oxidation, AA breakdown

Front 42

what metabolic processes occur in the cytosol?

Back 42

glycolysis, pentose phosphate pathway, fatty acid biosynthesis, gluconeogenesis

Front 43

what metabolic function occurs in the lysosomes?

Back 43

enzymatic digestion of cell components and ingested matter

Front 44

what metabolic function occurs in the nucleus?

Back 44

DNA replication and transcription and RNA processing

Front 45

what metabolic function occurs in the golgi app?

Back 45

post-translational processing, formation of PM

Front 46

what metabolic function occurs in the RER?

Back 46

synthesis of membrane bound an secretory proteins

Front 47

what metabolic function occurs in the SER?

Back 47

lipid and steroid biosynthesis

Front 48

what metabolic function occurs in the peroxisome? (glyoxysome in plants)

Back 48

oxidative reactions catalyzed by amino acid oxidases and catalase; glyoxylate cycle reactions in plants**

Front 49

do enzymes in metabolic reactions usually operate far from or near equilibrium?

Back 49

near; therefore having net rates that vary with their substrate concentrations.

Front 50

enzymes that operate far from equilibrium are strategically located in metabolic pathways. What are the three implications of this?

Back 50

1. metabolic pathways are irreversible
2. every metabolic pathway has a first committed step
3. catabolic and anabolic pathways differ

Front 51

Living organisms are thermodynamically open systems that tend to maintain a steady state rather than reaching equilibrium, thus deltaG is what?

Back 51

deltaG < 0

(negative delta G)

Front 52

the flux of intermediates through a metabolic pathway in a steady state is more or less ... what?

Back 52

constant; the rates of synthesis and breakdown of each pathways intermediate maintain it at a constant concentration.

Front 53

thermodynamically, where does the rate-determining step function?

Back 53

far from equilibrium with a large negative free energy change (highly exergonic)

Front 54

what is true of the flux through steady-state systems?

Back 54

it is constant and set by the slowest, rate-determining step

Front 55

what are the 4 ways cells regulate metabolic flux?

Back 55

1. allosteric control
2. covalent modification
3. substrate cycles
4. genetic control

Front 56

negative feedback regulation is an example of what type of flux regulation?

Back 56

allosteric

Front 57

what makes ATP such an important high-energy intermediate?

Back 57

the large amount of free energy that is liberated accompanying the cleavage of its phosphoanhydride bonds.

Front 58

the conversion of ATP to ADP + pi is what type of reaction?

Back 58

hydrolysis (when water is the acceptor)

Front 59

what constitutes a high-energy compound?

Back 59

one with bonds whose hydrolysis proceeds with large negative deltaG values

Front 60

what makes the phophoryl group-transfers of ATP so exergonic?

(cleavage of phosphoanhydride bonds)

Back 60

1. resonance stabilization
2. the destabilizing effect of electrostatic repulsions between charged groups
3. the destabilizing influence of the smaller solvation energy of a phosphoanhydride bond

Front 61

because ATP and its hydrolysis products are ions, what else does deltaG depend on besides concentration of reactants and products?

Back 61

pH and Ionic strength

Front 62

the __________ reactions of high energy compounds can be coupled to _________ processes to drive them to completion.

Back 62

the exergonic reactions of high energy bonds can be coupled to endergonic processes to drive them to completion

Front 63

what is hexokinase?

Back 63

enzyme that catalyzes the formation of glucose-6-phosphate in the first step of glucose metabolism.

Front 64

what is substrate level phosphorylation?

Back 64

the synthesis of ATP from ADP by phosphoryl group transfer from another compound*

Front 65

in the absence of the appropriate enzyme, what is true of phosphoanhydride bonds?

Back 65

they are stable

Front 66

ATP hydrolysis (the direct transfer of phosphoryl group to water) is ______________ favored, but _______________ disfavored.

Back 66

ATP hydrolysis is thermodynamically favored, but kinetically disfavored

Front 67

why is ATP hydrolysis is thermodynamically favored, but kinetically disfavored ?

Back 67

because the reaction has an unusually high activation energy, despite the large amount of free energy it liberates.

Front 68

what type of reactions supply living organisms with the majority of their free energy?

Back 68

redox rxns

(oxidation-reduction reactions)

Front 69

what are two of the most widely occurring electron carries?

Back 69

NAD & FAD

Front 70

what is the final electron acceptor in aerobic organisms?

Back 70

oxygen

Front 71

the nernst equation describes what reaction type?

Back 71

oxidation-reduction

Front 72

what is the organic approach to studying metabolism?

Back 72

labeling using radioactive isotopes

Front 73

how does the use of metabolic inhibitors (drugs) help elucidate the intermediates and enzymes of metabolic pathways?

Back 73

metabolic inhibitors block the pathway at specific points and cause preceding intermediates to build up

also can block electron transport- as used to deduce the sequence of carriers in the mitochondrial ETC

Front 74

how does human genetics aide in studying metabolic pathways?

Back 74

some genetic diseases result in deficiency of specific enzymes

Front 75

besides observation of human genetic diseases, how else can genetic help in studying metabolism?

Back 75

because the basic metabolic pathways in most organisms are essentially identical, "knock out" experiments can be very useful in causing genetic mutations that affect enzymatic production, thus metabolism.

Front 76

what is systems biology?

Back 76

a new approach to studying metabolism that is discovery-based and involves enormous amounts of data in searchable databases.

** aims to assess the "big picture" of biol. networks through the integration of genomic, transcriptomic, proteomic and metabolomic information. **

Front 77

Are near-equilibrium reactions reversible?

Back 77

yes

Front 78

are far-from-equilibrium reactions reversible?

Back 78

no; thus they serve as regulatory points and render metabolic pathways irreversible.

Front 79

how is flux through a metabolic pathway controlled?

Back 79

by regulating the activities of the enzymes that catalyze rate-determining steps.

Front 80

how many enzymatic reactions are involved in glycolysis?

Back 80

10

Front 81

in glycolysis, one molecule of glucose is converted into what?

Back 81

2 pyruvate
2 ATP

Front 82

what is the significance of glucose?

Back 82

it prepares it for further oxidative degradation

Front 83

what is the pentose phosphate shunt?

Back 83

an alternative pathway for glucose catabolism that functions to provide biosynthetic precursors

Front 84

what is stage one of glycolysis?

Back 84

energy investment (2 ATP); glucose is phosphorlyated and split into two molecules of glyceraldehyde-3-phosphate.

Front 85

what is stage 2 of glycolysis?

Back 85

energy recovery; the two molecules of glyceraldehyde-3-phosphate are converted into pyruvate and 4 ATP are generated.

Front 86

what is the net gain of ATP via glycolysis?

Back 86

2 ATP (2 consumed, 4 produced)

Front 87

what is the primary oxidizing in glycolysis?

Back 87

NAD+

Front 88

what is the first reaction in glycolysis? what enzyme catalyzes this reaction?

Back 88

the transfer of a phosphoryl group from ATP to glucose to form glucose-6-phosphate (G6P)

catalyzed by hexokinase

Front 89

what is a kinase?

Back 89

an enzyme that transfers prosphoryl groups between ATP and a metabolite.

Front 90

what cofactor is essential for kinase activity?

Back 90

Magnesium (Mg+2)

Front 91

what is glucokinase?

Back 91

an isoenzyme of hexokinase that is found in the liver and is responsible for maintaining blood glucose levels

Front 92

how does hexokinase influence glucose?

Back 92

it induces a conformational change *

Front 93

what is reaction 2 in glycolysis?

Back 93

G6P is converted to F6P by the enzyme PGI (phosphoglucose isomerase)

Front 94

what happens when phosphoglucose isomerase catalyzes the reaction of G6P to F6P?

Back 94

both rings must be opened, isomerization must occur, then the rings must close.

Front 95

what occurs in reaction 3 of glycolysis?

Back 95

F6P is converted to fructose-1,6-biphosphate by the enzyme phosphofructokinase (PFK)

Front 96

what is the significance of PFK's role in glycolysis?

Back 96

phosphofructokinase catalyzes one of the rate determining steps in glycolysis; the conversion of F6P to fructose-1,6,-biphosphate (Step 3)

Front 97

what is reaction 5 of glycolysis?
(After FBP is converted to GAP and DHAP)

Back 97

Dihydroxyacetone phosphate must be converted to Glyceraldehyde-3-phosphate by triose phophate isomerase

Front 98

what is unique about the products formed in the conversion of FBP by aldolase?

Back 98

only GAP (glyceraldehyde-3-phosphate) can continue on glycolytic pathway

-DHAP must be converted to GAP by Triose phosphate isomerase

Front 99

GAP and DHAP produced in glycolysis are example of what?

Back 99

ketose-aldose isomers that can be interchanged by triose phosphate isomerase

Front 100

alcoholic fermentation converts pyruvate to what?

Back 100

ethanol and co2

Front 101

what is the anaerobic fate of pyruvate?

Back 101

fermentation

Front 102

under aerobic conditions, pyruvate is completely oxidized to what by the citric acid cycle?

Back 102

co2 and H20

Front 103

how is NADPH generated?

Back 103

by the oxidation of glucose-6-phosphate via an alternative pathway to glycolysis called the hexose monophosphate shunt

Front 104

what is considered the starting point of the pentose phosphate pathway?

Back 104

glucose-6-phosphate

Front 105

formation of what completes the oxidative portion of the pentose phosphate pathway?

Back 105

Ru5P (ribulose-5-phosphate)

Front 106

where are all of the enzymes of the citric acid cycle located?

Back 106

in the mitochondria

Front 107

acetyl CoA is formed from pyruvate through oxidative decarboxylation by a multienzyme complex called what?

Back 107

pyruvate dehydrogenase

Front 108

what reaction of the citric acid cycle produces the first CO2 and NADH?

Back 108

isocitrate -> alpha ketoglutarate

Front 109

what enzyme catalyzes the final reaction of the citric acid cycle?

Back 109

malate dehydrogenase

Front 110

one turn of the TCA cycle generates approximately how many ATP molecules?

Back 110

10

Front 111

what are cataplerotic reactions?

Back 111

reactions that deplete citric acid cycle intermediates

Front 112

what is the glyoxylate cycle?

Back 112

a variation of the citric acid cycle that occurs only in plants and converts acetyl-CoA to oxaloacetate

Front 113

where does mannose enter glycolysis?

Back 113

f6p

Front 114

where does galactose enter glycolysis?

Back 114

g6p

Front 115

where does fructose (muscle) enter glycolysis

Back 115

f6p

Front 116

where does fructose (liver) enter glycolysis?

Back 116

GAP

Front 117

for each molecule of g6p that enters the hexose monophosphate shunt what is generated?

Back 117

-2 NADPH
-co2
-ribulose-5-phosphate

Front 118

where does TPP come into play?

Back 118

alcohol fermentation

Front 119

what enzymes catalyze regulatory steps in glycolysis?

Back 119

-hexokinase
-phosphofructokinase
-pyruvate kinase