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BICH 411 > EXAM 1 > Flashcards

EXAM 1 Flashcards

1
Q

what are the four functions of metabolism

A
  1. obtain free energy for the cell
  2. degrade macromolecules as required for biological function
  3. convert nutrients into macromolecules
  4. assemble macromolecules into cellular structures
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2
Q

T/F metabolism does not require tightly coordinated cellular activity

A

F, it does require

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3
Q

T/F living organisms need a continuous influx of energy to battle entropy

A

T

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4
Q

what is known as the sum of all of the chemical reactions occuring in the cell

A

Metabolism

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5
Q

define metabolism

A

the overall processes by which living things acquire and utilize free energy in the cell

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6
Q

what are the basic units of metabolism

A

enzymes

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7
Q

substrates of the enzymes of metabolism are called

A

metabolites

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8
Q

define metabolic pathway

A

a series of connected enzymatic reactions that produces a specific product

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9
Q

T/F metabolic pathways consist of sequential steps

A

T

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10
Q

two compartments of metabolism

A

catabolism and anabolism

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11
Q

define catabolism

A

degradative pathways the produce free energy

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12
Q

define anabolism

A

biosynthetic pathways that consume free energy

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13
Q

In a catabolic pathway the electrons energy-yielding nutrients lost are stored in…

A

NADH
FADH2
NADPH

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14
Q

List the energy-yielding nutrients that are used in catabolism

A

Cabrohydrates
Fats
Proteins

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15
Q

In an anabolic pathway, where do you get the energy you need to proceed the reaction

A

NADPH

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16
Q

List the cell macromolecules of anabolic pathways

A

Proteins
Polysaccharides
Lipids
Nucleic Acids

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16
Q

List the precursor molecules in anabolic pathway

A

Amino Acids
Sugars
Fatty Acids
Nitrogenous bases

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17
Q

ATP hydrolysis is important for

A

biosynthesis
osmotic work
cell motility/muscle contraction

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18
Q

Energy-requiring cellular activities are powered by ATP hydrolysis, liberating what as products

A

ADP and Pi

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19
Q

In energy requiring cellular activities are powered by

A

ATP hydrolysis

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20
Q

Why is ATP a high energy compound?

A

hydrolysis increased resonance stabilization which allows for shifting of bonds

hydrolysis decreased electrostatic interactions

hydrolysis increased energy of solvation/entropy

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21
Q

what is the reaction that occurs between NAD+ and NADH ?

A

dehydrogenase reaction

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22
Q

what is the most common e- carrier that always transfer two e- at a time

A

NADH

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23
Q

What is NADH used in? What about NADPH?

A

NADH used in fuel metabolism , mobile e- carrier for ETC/PMF/ATP synthesis, catabolism

NADPH used for biosynthesis, anabolism

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24
Q

Compartmentalization

A

Metabolic pathways are localized within different cellular compartments/locations

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25
Q

T/F anabolic and catabolic pathways involving same product are not the same

A

T

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26
Q

T/F some steps may be common to both anabolic and catabolic pathways

A

T

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27
Q

what ensures that each pathway is spontaneous/thermodynamically favorable

A

unique enzymes

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28
Q

define biosynthetic enzymes

A

operate as part of anabolic pathways

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29
Q

define degradative enzymes

A

operate as part of catabolic pathway

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30
Q

water-solube vitamins almost always ……

A

converted to coenzymes

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31
Q

T/F Fat soluble vitamins are stored for longer periods of time

A

T

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32
Q

how are metabolic pathways controlled?

A

Thermodynamics
compartmentalization
metabolic flux

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33
Q

how can metabolic flux be controled

A

allosteric
covalent modification
substrate cycles
genetic control

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34
Q

T/F ATP does not need to be biosynthesized

A

F, it must be biosynthesized

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35
Q

ATP/equivalent molecules are used to….

A

power endergonic processes

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36
Q

glycolysis is divided into 2 phases what are they

A

investment phase
payoff phase

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37
Q

define glycogen

A

multi-branched polysaccharide of glucose

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38
Q

where does glycogen fit into metabolic picture

A

degraded when glucose is needed ( low energy status)

synthesized for energy storage ( high energy status)

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39
Q

define glycolysis

A

pathway for glucose breakdown that consists of 10 enzymes that make end product pyruvate

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40
Q

define PPP

A

alternative pathways that allows for NADPH production and provides biosynthetic precursors

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41
Q

define GNG

A

pathway in liver and kidneys that allows for the production of glucose from pyruvate, lactate and amino acids

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42
Q

where does glycolysis occur

A

in cytoplasm

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43
Q

T/F glycolysis is anaerobic

A

T

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44
Q

the first phase of glycolysis converts glucose to

A

2 glyceraldehyde-3-phosphate at the expense of 2 ATP

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45
Q

second phase of glycolysis produces

A

2 pyruvate
2 ATP YIELD
2 NADH

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46
Q

List all substrate and enzymes along with biproducts in glycolysis in order

A
  1. Glucose

ATP -> ADP || Hexokinase/glucokinase

                2. Glucose 6 Phosphate 

                  || Phosphoglucoisomerase
               3. Fructose 6 Phosphate

ATP –> ADP || Phosphofructokinase

               4. Fructose - 1,6 - bisphosphate 

                   || aldolase
  1. Dihydroxyacetone phosphate + Glyceraldehyde 3 phosphate
    ( Triose phosphate isomerase)

NAD+ –> NADH||Glyceraldehyde-3-Phosphate DH

  1. 1,3- Bisphosphoglycerate

ATP –> ADP || Phosphoglycerate kinase

  1. 3 phosphoglycerate
                   || Phosphoglycerate mutase
  2. 2-phosphoglycerate

release H2O || enolase

  1. phosphoenol pyruvate

ADP –> ATP || pyruvate kinase

  1. Pyruvate
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47
Q

lactate DH function

A

reduces pyruvate to lactate using NADH

reversible

cori cycle

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48
Q

TPP defecincy causes

A

beriberi disease

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49
Q

symptoms of TPP deficiency

A

Pain
Paralysis
wasting
heart failure

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50
Q

pyruvate decarboxylase requires

A

thiamine pyrophosphate (TPP)

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51
Q

the making of glucose from non-carbohydrate precursor is what pathways

A

GNG

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52
Q

GNG meets body’s glucose needs under

A

fasting conditions

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53
Q

GLUT 2

A

low affinity transporter in hepatocytes (liver) and pancreatic cells

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54
Q

GLUT 4

A

higher affinity transporter in adipose tissue and muscle cells

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55
Q

why is it important for GLUT 4 to have higher affinity for glucose than GLUT 2

A

liver is able to make its own glucose so we want to give other cells such as the muscle and adipose tissue to have first dibs to get the sugar they need

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56
Q

what glucose transporter serves as sensor for insulin release

A

GLUT 2

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57
Q

compare and contrast GLUT 2 and GLUT 4 in terms of Km and kinetics

A

GLUT 4 has a low Km and 0th order kinetics

GLUT 2 has high Km and 1st order kinetics

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58
Q

how does insulin promote glucose entry into cells

A

allows for increased production of GLUT4 through vesicle fusion

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59
Q

T/F glycolysis does not use oxidative phosphorylation it is a substrate level phosphorylation reaction

A

T

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60
Q

what is the enzyme used for the priming reaction in glycolysis

A

hexokinase/glucokinase

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61
Q

compare hexokinase and glucokinase

A

HK
- present in muscle and most tissues
- low Km

GK
- present in the liver and pancrea ( b-islet cells)

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62
Q

how is Hexokinase regulated

A

inhibited by high levels of glucose-6-phosphate

Insulin activates

glucagon inhibits

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63
Q

how is glucokinase hormonally regulated

A

induced by insulin in liver

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64
Q

why do we have two different enzymes (HK/GK) for the conversion of glucose to G6P?

A

it makes sure that all other cells like muscles can get what they need and THEN the liver will deal with the leftover glucose and store it

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65
Q

what are other fates of glucose-6-phosphate other than glycolysis ?

A
  1. PPP to make NADPH
  2. Glycogen
  3. carbohydrate synthesis
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66
Q

describe the mechanism of HK and GK

A

glucose does nucleophilic attack in P group of ATP causing an induced fit releasing ADP and leaving a P group attached

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67
Q

what enzyme forms glucose-6-phosphate from glucose

A

HK/GK

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68
Q

Phosphoglucose isomerase function

A

reconfigures bonds to form F6P

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69
Q

T/F Phosphoglucose isomerase has a small value of free energy change indicating that the reaction is near equilibrium and is therefore a regulated step

A

F, it is reversible enzyme due to the small value in free energy change

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70
Q

why does the reaction of phosphoglucosisomerase occur

A
  • b/c next step is a second phosphorylation and a hemiacetal is a tougher reaction compared to Primary -OH
  • puts carbonyl at C2 which activates C3 for an aldolytic cleavage
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71
Q

what enzymes of glycolysis has an enediol intermediate

A

Phosphoglucoisomerase
Triose Phosphate Isomerase

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72
Q

what kind of reaction is PGI

A

acid-base catalysis

73
Q

what are the irreversible enzymes of glycolysis

A

GK/HK
PFK1
Pyruvate Kinase

74
Q

what is the enzyme known as the first committed step of glycolysis

A

PFK1

75
Q

How is PFK1 regulated

A

High levels of AMP activate it

High levels of ATP and Citrate inhibit

76
Q

when will we see PFK activity increase and decrease

A

increase: lw energy status
decrease: high energy status

77
Q

how is PFK allosterically regulated

A

Fructose-2,6-bisphosphate and AMP : activates PFK1

citrate and atp inhibit

78
Q

How is PFK1 hormonally regulated

A

High levels of insulin = activate
High levels of glucagon = inhibit

79
Q

how does insulin activate PFK1

A

it activates PFK2 which converts F6P to F26BP , a potent allosteric activator, which in turn activates PFK1

80
Q

How does glucagon inhibit PFK1

A

glucagon inhibits PFK2, and stimulates F26BPase of GNG inhibiting PFK1

81
Q

function of aldolase in glycolysis

A

cleavage step, beaks F16BP into 2 3C units, DHAP and GA3P

82
Q

There are 2 classes of aldolase enzymes, compare the two types

A

Class I Aldolase:
- found in animal tissues
- formation of covalent Schiff-Base E-S intermediate

Class II Aldolase:
- contain. an active site metal (ZN2+) to help shield the oxyanion intermediate

83
Q

function of Triose Phosphate Isomerase

A

undergoes isomerization reaction that is reversible interconvert b/w DHAP and GA3P

84
Q

what type of chemistry is utilize in TPI

A

acid base

85
Q

in TPI mechanism what amino acids function as general bases and acids

A

Histidine
Glutamate

86
Q

function of glyceraldehyde 3 phosphate DH

A

catalyzes oxidation and addition of Pi group to GA3P forming 1,3BPG and producing NADH

87
Q

what enzyme of glycolysis uses NAD+ as a cosubstrate that involves exchange of electrons

A

glyceraldehyde 3 P DH

88
Q

characteristics of the mechanism of GA3PDH

A

covalent catalysis ( thioester bond formed)
nicotinamide enzyme
oxidative

89
Q

T/F GA3PDH usess cystein residue to form thioester bond

A

T

90
Q

function of phosphoglycerate kinase

A

transfers a P group from 1,3BPG to ADP to make ATP and form 3- Phosphoglycerate

91
Q

what enzymes of glycolysis are referred to as substrate level phosphorylation

A

Pyruvate Kinase
Phosphoglycerate Kinase

92
Q

define mutase

A

an enzyme that catalyzes the migration of a function group within the substrate molecules

93
Q

What is a detour of 1,3BPG other than going straight to 3-PG that is seen in RBC

A

forms 2,3BPG via 1,3BPG mutase and then forms 3-PG via 2,3BPG phosphatase

94
Q

function of 2,3BPG

A

regulators of Hemoglobin decreasing affinity for O2 which aids in O2 release ( R–> T state) in RBC

95
Q

function of Phosphoglycerate mutase

A

catalyzes a phosphoryl group transfer from C3 to C2 forming 2-phosphoglycerate

96
Q

what enzymes requires Mg2+ for enzymatic activity

A

phosphoglycerate mutase
enolase

97
Q

what enzyme utilizes a phosphohistidyl residue

A

Phosphoglycerate mutase

98
Q

function of enolase

A

a dehydration reaction ( loss of H2O)
forms phosphoenolpyruvate

99
Q

function of pyruvate kinase

A

uses PEP as a phosphate group donor to release ATP forming pyruvate

100
Q

How is Pyruvate Kinase Regulate

A

activated by high levels of AMP & F16BP

inhibited by high levels of ATP and acetyl-CoA

101
Q

function of lactate dehydrogenase

A

reversible enzyme that can oxidize NADH to NAD+ ( reduce NAD+ to NADH)

Cori Cycle

102
Q

function of DHAP other than glycolysis

A

used in liver and adipose tissue for TAG synthesis

103
Q

what are the high energy intermediates of glycolysis used to generate ATP by substrate level phosphorylation

A

1,3BPG
PEP

104
Q

what are the three fates of pyruvate

A
  1. TCA cycle
  2. Fermentation (yeast)
  3. Lactate ( in animals)
105
Q

what are the steps from pyruvate to form ethanol in yeast fermentation

A
  1. pyruvate decarboxylase
  2. alcohol DH
106
Q

Pyruvate Decarboxylase characteristics

A

requires TPP

107
Q

T/F high levels of lactate in muscles cause pain

A

T

108
Q

where does galactose enter to glycolysis and how many enzymes are used

A

enters as G6P via 4 enzymes

109
Q

where does mannose come into the glycolysis and how many enzymes

A

F6P via 2 enzymes

110
Q

where does fructos (muscle) come into glycolysis and name the enzyme

A

F6P via HK

111
Q

where does fructose (liver) come into glycolysis and how many enzymes

A

GA3P via 7 enzymes

112
Q

what pathway uses glucose catabolism to produce NADPH

A

PPP

113
Q

where does glucose synthesis occur

A

liver and kidneys in animals

114
Q

list out all the steps in GNG include enzymes and biproducts and substrates

A
  1. Pyruvate
    CO2 + ATP –> ADP|| Pyruvate Carboxylase
  2. OAA

GTP–>CO2 + GDP||PEP carboxykinase

  1. PEP
    enolase
  2. 2PG
    PGM
  3. 3PG
    ATP –> ADP || PGK
  4. 1,3-BPG
    NADH –> NAD+ || GA3PDH
  5. GA3P <— TPI —> DHAP

aldolase

  1. F16BP

H2O || Fructose bisphosphatase

  1. F6P

PGI

  1. G6P

H2O || G6Pase

Glucose

115
Q

list the important substrates for GNG

A

Pyruvate

Glycerol 3 P

Lactate

Alanine/ Gluconeogenic AA

116
Q

what are the irreversible enzymes of GNG

A

Pyruvate Carboxylase

PEP Carboxy Kinase

Fructose 1,6 Bisphosphatase

Glucose 6 - Phosphatase

117
Q

What is the only enzyme of GNG found in the mitochondria

A

Pyruvate carboxylase

118
Q

what is cofactor required for the mechanism of pyruvate carboxylase and its function

A

biotin
serves as a mobile CO2 carrier

119
Q

how is pyruvate carboxylase regulated

A

high levels of acetyl CoA activate

high levels of AMP inhibit

glucagon and cortisol activate

120
Q

describe the mechanism of pyruvate carboxylase

A

uses ATP to load CO2 onto biotin and then delivers it to pyruvate

121
Q

T/F biotin contains a lys residue

A

T

122
Q

what is unique about PEP carboxykinase mechanism

A

uses GTP rather than ATP for energy

123
Q

why in GNG does cell add CO2 with pyruvate carboxylase and then take it back off with PEPCK?

A

decarboxylation drives the formation of enol that GTP phosphorylates

124
Q

function of PEP carboxykinase

A

converts OAA to PEP
via GTP and decarboxylation

125
Q

how is PEPCK regulated

A

activated by high levels of glucagon and cortisol

126
Q

how is fructose 1,6 bisphosphatase regulated include hormonal

A

high levels of citrate and ATP activate
high levels of AMP and F26BP inhibit

cortisol , glucagon, Epi and NE activate

127
Q

function of F16BPase

A

removes phosphate group from F16BP producing F6P

128
Q

hormonal regulation of Pyruvate carboxylase

A

High levels of glucagon and cortisol stimulate

129
Q

what is unique about glucose-6-phosphatase

A

found in the smooth ER lumen

130
Q

function of Glucose-6-phosphatase

A

converts G6P to glucose by removing a P group

131
Q

T/F all cells do GNG not just the liver and kidneys

A

F, it is only the liver and kidney

NOTE: Muscle and brain do not do GNG

132
Q

if Glucose 6Pase is in the ER lumen how is it able to release glucose into blood stream

A
  1. transporter that is concentration driven
  2. uses vesicles, that are filled with glucose, and fuses with plasma membrane allowing it to open and release into bloodstream
133
Q

what enzyme mechanism in GNG involves nucleophilic attack by a Histidine nitrogen

A

Glucose 6 Phosphatase

134
Q

what enzyme contains a phosphohistidine intermediate

A

Glucose 6 Phosphatase

135
Q

draw a simple sketch of cori cycle

A

slide 28 of GNG

136
Q

T/F PPP can occur in all cells

A

T

137
Q

what are the two functions of PPP

A

make NADPH and ribose-5-phosphate (imp nor nucleotide synthesis)

138
Q

name the rate limiting enzyme of PPP

A

Glucose-6-phosphate DH

139
Q

location of PPP

A

cytoplasm

140
Q

define oxidative phase of PPP

A

use glucose metabolism to help supply NADPH for reductive reactions

141
Q

define nonoxidative phase of PPP

A

use glucose metabolism to help supply ribose-5-phosphate (essential for nucleotide synthesis )

142
Q

list the steps of the oxidative phase of PPP

A
  1. G6P

NADP > NADPH || glucose-6-phosphate DH

  1. 6phosphogluconolactone

H2O || 6Phosphogluconolactonase

  1. 6 phosphogluconate

NADP > NADPH + CO2 || 6Phosphogluconate DH

  1. Ribulose 5 Phosphate
143
Q

what phase of PPP is irreversible and when is it operating

A

oxidative phase

on when cells need to make NADPH

144
Q

when will PPP be turned on

A

highhhh ATP levels

145
Q

functions of NADPH

A

biosynthetic metabolite for FA and cholesterol (electron donor )

protects against ROS ( acting as body natural antioxidant)

146
Q

Glucose - 6- Phosphate DH regulation

A

High levels of NADPH inhibits

High levels of NADP+ activates

147
Q

what metabolite is hydrolytically unstable and readily undergoes spontaneous ring opening hydrolysis

A

6-phosphogluconolactone

148
Q

what enzyme of PPP serves to to accelerate the spontaneous ring opening via hydrolysis

A

6-phosphogluconolactonase

149
Q

why is it important for the spontaneous ring opening in PPP to be accelerated by phosphogluconolactonase

A

to prevent accumulation of toxic molecule 6-phosphogluconolactone

150
Q

what makes the mechanism of 6-phosphogluconate DH unique

A

has 2 phase

  1. NADP+ dehydrogenation
  2. decarboxylation event
151
Q

function of phosphopentose isomerase

A

converts ketose to aldose

152
Q

function of phosphopentose epimerase

A

changes orientation of OH group at C3 changing stereochemistry

153
Q

Transketolase function

A

transfer of 2 carbon units

TPP dependent

154
Q

transaldolase function

A

transfers a 3-C unit

Schiffs base mechanism

155
Q

describe the function of Mode 1 of PPP

A

undergo oxidative phase because Ribose5P and NADPH is needed

156
Q

describe function of Mode 2 of PPP

A

nonoxidative phase from glycolytic intermediates to produce only Ribose 5 P because it is need and No NADPH is needed

157
Q

describe function of MODE 3 of PPP

A

NADPH is needed but no R5P
undergoes oxidative phase to produce NADPH and R5P

but since R5P is not needed it will feed into GNG so that it can continued to make NADPH

158
Q

describe function of MODE 4 of PPP

A

ATP is needed and NADPH is needed

will undergo oxidative phase and R5P produced feeds into glycolysis at F6P , GA3P, and DHAP

159
Q

define glycogen

A

multi-branch polysaccharide of glucose

stores glucose

160
Q

where does glycogenolysis and glycogenesis occr

A

skeletal muscle and liver

161
Q

what organ/tissue has a higher concentration of glycogen reservoir

A

Liver

162
Q

why does the liver have higher concentration of glycogen stored

A

it has a role to maintain blood glucose levels at 5mM

163
Q

what are the pros of having branch points in Glycogen

A

more efficient storage

allows for activity to move

164
Q

define starch

A

a-linked chains of glucose in plants

165
Q

amylase function and location

A

found in saliva

hydrolyzes a1–>4 glycosidic bonds of starch

166
Q

STARCH debranching enzyme a(1–>6) glucosidase function

A

hydrolyzes 1 glucose residuce at a time

targets a(1–>6) bonds

167
Q

STARCH debranching enzyme oligo (a1,4 –> a1,4)glucanotransferase function

A

takes a1->4 and moves it to another branch point

168
Q

a-glucosidase function

A

hydrolyzes 1 glucose at a time
SOLE enzyme capable of a(1>6) glycosidic bonds

169
Q

what enzyme leaves glycogen with one less branch point

A

a-glucosidase

170
Q

function of glycogen phosphorylase

A

allows for breakdown of a(1.4) glycosidic bonds forming glucose-1-phosphate

171
Q

regulation of glycogen phosphorylase in muscles

A

activated by high levels of AMP and Epi

inhibited by High levels of ATP & G6P

172
Q

regulation of glycogen phosphorylase in liver

A

activated by glucagon

173
Q

function of phosphoglucomutase

A

converts G1P to G6P

174
Q

what enzyme is shared between glycogenolysis and Galactose metabolism

A

Phosphoglucomutase

175
Q

function of glycogen synthase

A

forms a1,4 glycosidic bonds on linear glucose

176
Q

how is glycogen synthase regulated

A

activated by insulin and high levels of G6P & ATP

inhibited by glucagon and Epi via protein kinase cascade (PKA)

177
Q

function of UDP-glucose pyrophosphate

A

forms ester linkage b/w C1-OH and B-Phosphate of UDP activating glucose moiety of UDP glucose

178
Q

what enzyme of glycogenesis occurs via an oxonium ion intermediate

A

glycogen synthase

179
Q

amylo-(1,4 -> 1,6) transglycosylase function

A

cuts at a1,4 bond and moves it to C6 of glucose molecule forming an a1,6 glycosidic bond

180
Q

why is glycogen metabolism linked to G1P and not G6P

A

G1P cant escape the cell and gives cells time to determine what is needed conversion

separates point of flux for controlling whether glycogen is synthesized or broken down

181
Q

glucagon and Epi activate a cascade of reactions that stimulate what and inhibit what ( terms of glycogen)

A

glycogen breakdown

inhibit glycogen synthesis

BICH 411 (4 decks)

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