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z S1: Bio Chem 2 > Final > Flashcards

Final Flashcards

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1
Q

Unlike fats and carbs there is no _______ _____ for amino acids

A

storage form

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2
Q

Nitrogen ________ is nitrogen ingested = nitrogen excreted

A

balance

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3
Q

What are the 3 ways to get amino acids

A

dietary proteins
de novo synthesis
degradation of cellular proteins (normal turnover)

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4
Q

What is the major stomach protease

A

pepsin

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5
Q

Protein degradation continues in the lumen of the intestine by _______ proteases

A

pancreatic

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6
Q

What are the two cellular protein degradation

A

Lysosomal degradation (no energy, extracellular proteins that are taken into cells by endocytosis)

Proteasomal degradation (requires ATP, mainly endogenous proteins)

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7
Q

Lysosomes contain about ___ hydrolytic enzymes

A

50

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8
Q

In lysosomal degradation-starving cells, there is a selective pathway that preferentially degrades cytosolic proteins containing the sequence ______

A

KFERQ

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9
Q

Proteins that are going to be degraded are “tagged” with protein called

A

ubiquitin (proteasome digests it, it is attached to lysine residues on target proteins)

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10
Q

____ or more ubiquitins have strong signals for degradation

A

4

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11
Q

What are the 4 fates of amino acids

A

-can be used for protein synthesis
-if not needed for protein synthesis must be degraded
-first step in amino acid degradation is the removal of the nitrogen
-removed amino group is converted urea in the liver

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12
Q

______ uses its own amino acids as fuel during prolonged exercise and during fasting

A

muscle

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13
Q

The amino group of the amino acid being degraded is first removed form the _____ ______ being degraded

A

amino acid

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14
Q

Once the amino acid is removed from the amino acid being degraded, its transferred to ____________ which then becomes __________

A

alpha-ketoglutarate
glutamate

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15
Q

alpha-ketoglutarate converted to glutamate is catalyzed by what enzyme

A

aminotransferases

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16
Q

All aminotransferases contain the cofactor

A

PLP (pyridoxal phosphate)

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17
Q

PLP is derived from what

A

pyridoxine (Vitamin B6)

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18
Q

The aminotransferase enzymes also have value clinically as _________ agents

A

diagnostic

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19
Q

What are the 4 clinical values of plasma aminotransferases

A

-normally intracellular enzymes
-plasma concentration are typically low
-elevated plasma levels = indicate damage to cells rich in these enzymes
-AST and ALT measurements are of particular diagnostic value

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20
Q

What do AST and ALTs test for

A

liver damage
heart damage
(high plasma levels of both indicate more severe damage)

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21
Q

What is amino acid catabolism

A

-transamination reaction occurs 1st
-then oxidative deamination to release ammonia which is combined with CO2 to make urea

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22
Q

What is glutamate dehydrogenase

A

occurs only in liver mitochondria
oxidative deamination and needs an electron acceptor of NAD+

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23
Q

In severely impaired hepatic function and cirrhosis _________ intoxication develop

A

ammonia

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24
Q

When ammonia concentration increases in blood and other bio fluids, it diffuses across the BBB causing ammonia _____________

A

encephalopathy

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25
Q

Why is ammonia toxic

A

lead to increased levels of glutamine
then causes an ATP decrease by TCA inhibition
can cause swelling of cells and coma

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26
Q

Carbon skeleton is converted to a _______ intermediate then used for energy or used to make ________ or fat

A

common
glucose

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27
Q

Degradation of the 20 amino acids funnel into ___ metabolic intermediates

A

7

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28
Q

What are the 5 glucogenic metabolic intermediates

A

Pyruvate
Oxaoloacetate
Fumarate
alpha-Ketoglutarate
Succinyl-CoA

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29
Q

What are the 2 Ketogenic metabolic intermediates

A

Acetyl-CoA
Acetoacetyl-CoA

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30
Q

What are the 5 glucogenic and ketogenic amino acids

A

Isoleucine
Phenylalanine
Threonine
Tryptophan
Tyrosine

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31
Q

What are the two Ketogenic amino acids

A

Leucine
Lysine

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32
Q

Amino Acids biosynthesis can not be used to make _______ or broken down for _______

A

proteins
energy

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33
Q

What are the three methods for obtaining amino acids for protein synthesis

A

Dietary Proteins
De novo synthesis
Degradation of cellular proteins

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34
Q

In order to make new amino acids from scratch we need what two things

A

nitrogen atom (amine)
carbon skeleton (alpha keto acid)

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35
Q

Where do we get the nitrogen when we need to make new amino acids

A

Glu or Gln
(transfer their amine group to other compounds)

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36
Q

The amine of glutamine (Gln) = source of the amino group for most ____ ______ while the amide of Gln = source of ________ for other N-containing compounds

A

amino acids
nitrogen

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37
Q

Essential amino acids defn

A

amino acids that can only be synthesized in plants and microorganisms

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38
Q

Nonessential amino acids defn

A

amino acids that can be synthesized in mammals from common intermediates

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39
Q

____ is synthesized in the urea cycle, but the rate is too slow to meet the needs of growth in children = essential in infants and children

A

Arg

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40
Q

____ is required to produce cysteine if the latter is not supplied adequately by the diet

A

Met

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41
Q

___ is needed in larger amounts to form Tyr (if there is not enough Met in the diet)

A

Phe

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42
Q

What are the 3 common intermediates that go through glycolysis

A

3-phosphoglycerate
PEP
Pyruvate

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43
Q

What is the one common intermediate that goes through PPP

A

Ribose 5 Phosphate

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44
Q

What are the 2 common intermediates that go through TCA

A

alpha-ketoglutarate
oxaloacetate

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45
Q

What common intermediate is arginine made from

A

alpha-ketoglutarate

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46
Q

What common intermediate is histidine made from

A

ribose-5-phosphate

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47
Q

What common intermediate is phenylalanine and tryptophan made from

A

phosphoenolpyruvate

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48
Q

What common intermediate is valine and leucine made from

A

pyruvate

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49
Q

What common intermediate is methionine, threonine, lysine, and isoleucine made from

A

oxaloacetate

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50
Q

During the transfer of electrons from NADH and FADH2 potential energy is produced in the form of what

A

a proton gradient

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51
Q

Why is oxidative phosphorylation termed the way it is

A

oxidative: electrons are transferred
phosphorylation: Pi is transferred to ADP to make ATP

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52
Q

Cellular respiration is also called what

A

aerobic respiration

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53
Q

the energy released be electron transport is used to transport protons _______ an electrochemical gradient

A

against

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54
Q

chemiosmotic energy coupling requires a _______ to establish a gradient

A

membrane

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55
Q

membrane must contain proteins that can couple the _______ flow of electrons with the ________ flow of protons across the membrane

A

uphill
downhill

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56
Q

Enzyme used when membrane contains another protein that couples the downhill flow of protons to the generation of new ATP

A

ATP synthase enzyme

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57
Q

The potential energy generated by the pumping of protons is called the

A

proton motive force

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58
Q

What are the two results in potential energy

A

concentration difference
molecule is a protone (charged and no counterion is transported with it causing charge repulsion)

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59
Q

FAD (FMN) can accept or donate ___ electrons at a time = hydride ion or it can accept or donate ___ electrons at a time = hydrogen radical

A

2
1

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60
Q

Coenzyme Q (ubiqinone) can accept or donate ___ electrons at a time but it can hold up to __ electrons

A

1
2

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61
Q

What other electron carriers in ETC can hold only 1 electron at a time

A

cytochrome
iron-sulfur clusters
copper ions

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62
Q

Electrons from _____ enter through complex I while electrons from _____ enter through complex II

A

NADH
FADH

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63
Q

What is another name for complex 1

A

NADH: coenzyme Q oxidoreductase

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64
Q

If you inhibit complex 1 ATP can still be made because electrons from _____ can still enter ETC through complex 2 but overall the energy level will drop

A

FADH2

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65
Q

Complex 2 is an _____ that is located in the inner membrane of the mitochondria

A

enzyme
(use FAD asa cofactor)

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66
Q

No protons are pumped at which complex

A

2

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67
Q

Complex 2 does not pump H+ thus less ATP is made when electrons come from _______ than when they come from ______

A

FADH2
NADH

68
Q

Coenzyme Q is a mobile electron carrier that has a long isoprene tail (very ___________) that allows it to move easily w/in the inner membrane

A

hydrophobic

69
Q

What is another name for complex 3

A

coenzyme Q-cytochrome C oxidoreductase

70
Q

The transfer of electrons through complex 3 also results in the transfer of __________ from the matrix to the intermembrane

A

protons

71
Q

What happens if you inhibit complex 3

A

electron transport is shut down and therefore so is ATP synthase

72
Q

What are the 2 inhibitors of complex 3

A

Antimycin A
Myxothiazol

73
Q

Heme iron can be either ferrous (FE3+ _________) or ferric (FE2+ __________)

A

oxidized
reduced

74
Q

cytochrome C is highly conserved in nature and is the ________ mobile electron carrier

A

second

75
Q

Cytochrome c carries a single electron from the complex ___ to complex ____

A

3 to 4

76
Q

What is another name for complex 4

A

cytochrome oxidase
(should be called cytochrome c-oxygen oxidoreductase)

77
Q

Mammalian cytochrome oxidase contains ___ heme groups and ___ copper ions

A

2, 2

78
Q

Since mammalian cytochrome oxidase contains 2 heme groups and 2 copper ions it can only transfer ___ electrons at a time

A

1
(eventually transfers a total of 4 electrons to molecular oxygen)

79
Q

What are the 3 inhibitors of complex 4 that bind in place of oxygen

A

cyanide (CN)
carbon monoxide (CO)
azide (N3-)

80
Q

What happens to ETC and ATP syn if you inhibit complex 4

A

electron transport is shut down and therefore so is ATP syn

81
Q

If there is no oxygen to accept electrons from complex 4, electron transport is shut down and so is ____________

A

ATP syn

82
Q

If oxygen is low NADH can’t be able to donate its electrons into ETC and levels of NADH will stay high why is this bad

A

NADH inhibits TCA cycle and no oxygen = no TCA

83
Q

What are the three places where protons are pumped when electrons are donated by NADH

A

complex 1, 3, and 4

84
Q

What are the two places where protons are pumped when electrons are donated by FADH2

A

complex 3 and 4

85
Q

ETC results in transfer of electrons to ______ to form water

A

O2

86
Q

complex 4 holds O2 very tightly to prevent escape of damaging oxygen _________

A

radicals
(could also be formed from reduced coenzyme QH2)

87
Q

What are the 3 reactive oxygen species

A

superoxide
hydrogen peroxide
hydroxyl radical

88
Q

What are the 2 reactive oxygen species enzymes

A

superoxide dismutase and catalase

89
Q

The disulfide bond must be ________ to reactivate GSH

A

reduced

90
Q

The ratio of reduced glutathione to oxidized glutathione within cells is often used as a measure of cellular _________

A

toxicity

91
Q

_____________ (white blood cells) will produce reactive oxidative species in order to kill bacteria during an infection

A

phagocytes

92
Q

The potential energy generated by the pumping of protons is called the

A

proton motive force

93
Q

Major component of the mitochondrial ATP synthase complex: F1

A

Catalytic unit
-projects into the matrix
-catalyzes the reaction to make ATP
-rotates as protons flow through
-made up of 5 subunits

94
Q

Major component of the mitochondrial ATP synthase complex: F0

A

Proton channel
-embedded in the membrane
-forms a pore that H+ can pass through
-transports protons from intermembrane space back to matrix

95
Q

The H+ flow causes F1 site to rotate causing conformational change in the F1 site which allows for the synthesis and release of _____ from the active site of the enzyme into the mitochondrial matrix

A

ATP

96
Q

What are the two enzymes that are ATP synthase inhibitors

A

oligomycin
dicyclohexylcarbodiimide (DCCD)

97
Q

What is the importance of the ATP synthase inhibitors enzymes

A

they bind to F0 part of enzyme and block ATP synthesis and therefore e- transport

98
Q

What are the subunits that regulate ETC

A

NADH2
FADH2
O2

99
Q

What are the subunits that regulate ox/phos

A

ADP
Pi

100
Q

The interdependence of ATP synthesis and electron transport is called

A

respiratory control

101
Q

What are the three uncouplers of ATP synthesis and electron transport

A

2,4-dinitrophenol (DNP)
FCCP
Dicumarol
(all have acidic proton on ring)

102
Q

Uncouplers pick up ___ from inner membrane space and bring it back to matrix. When gradient is dissipated by uncouplers, energy is released as _____

A

H+
heat

103
Q

Naturally occurring uncouplers are found where in the body

A

brown fat
(called uncoupler protein, UCP, thermogenin)
UCP: produces heat as adaption to cold

104
Q

The inner membrane of the mitochondria is not permeable which is necessary for the generation of the ____ ___________ but bad for getting things in/out of the matrix

A

H+ gradient

105
Q

ATP, ADP, and Pi are highly ________ and can not diffuse through the membrane

A

diffuse
(ADP and Pi need to enter and ATP needs to leave)

106
Q

When H+ are being pumped, ATP ____ is moving form a negative charged matrix to a positively charged inner membrane space

A

-4
(but this brings a negatively charged counter ion into the area where the H+ gradient is set up)

107
Q

ADP and ATP is a coupled reaction therefore ADP can only enter if ____ leaves

A

ATP

108
Q

What are the two shuttles that transport the electrons from cytosolic NADH into the mitochondria

A

Glycerol-Phosphate Shuttle
Malate-Aspartate Shuttle
(they transport the electrons from cytosolic NADH, not the NADH itself)

109
Q

Electrons in the glycerol-3-phosphate shuttle start on NADH but end up on _______

A

FADH2
(then enter ETC via door 2 and less ATP made this way)

110
Q

The glycerol-3-phosphate shuttle is used primarily in what two things in the body

A

skeletal muscle
brain

111
Q

The malate-aspartate shuttle transfers electrons from cytosolic NADH to mitochondria NADH. What occurs with the ATP

A

no loss in amount of ATP made

112
Q

The malate-aspartate shuttle is used in what three organs

A

liver, kidney, and heart

113
Q

Where does beta oxidation occur

A

in the mito matrix

114
Q

Where does fatty acid synthesis occur

A

cytosol

115
Q

In beta-oxidation what is the carbon acceptor/donor

A

acetyl-coA

116
Q

In fatty acid synthesis what is the carbon acceptor/donor

A

malonyl-coA

117
Q

In beta-oxidation what is the electron acceptor/donor

A

NAD+ or FAD

118
Q

In fatty acid synthesis what is the electron acceptor/donor

A

NADPH

119
Q

FAS has __ different enzyme activities

A

7

120
Q

In each cycle of FAS how many carbons are added

A

2

121
Q

Through the addition of ____________ and loss of ____ in FAS 2 carbons can be added

A

malonyl-coA
CO2

122
Q

What is reaction 1 of FAS

A

formation of malonyl-coA
uses CO2
produces ATP
needs biotin cofactor
enzyme: acetyl-coA carboxylase

123
Q

Is rxn 1 of FAS (formation of malonyl-coA) reversible or irreversible and why

A

Irreversible because it is the committed step of FA synthesis since it makes ATP

124
Q

How is rxn 1 of FAS (formation of malonyl-coA) locally and globally regulated

A

local: Allosteric
global: Hormonal

125
Q

What is the reaction 2 in FAS

A

formation of acetyl-ACP
enzyme: acetyltransferase

126
Q

What is reaction 3 in FAS

A

formation of malonyl-ACP
enzyme: malonyl transferase

127
Q

What is reaction 4 of FAS

A

condensation of the growing chain with activated malonyl-acp
forms acetoacetyl-ACP
loss of CO2
enzyme: beta ketoacyl synthase

128
Q

What is reaction 5 of FAS

A

reduction of carbonyl to hydrox
enzyme: beta ketoacyl reductase
need NADPH
donated hydride ion
beta keto group is reduced to an alcohol

129
Q

What is reaction 6 of FAS

A

hydration of alcohol to trans-alkene
enzyme: beta hydroxyacyl dehydratase
loss water
form C=C

130
Q

What is reaction 7 of FAS

A

reduction of alkene to alkane
reduce C=C to CH2
enzyme: 2,3 trans enoyl reductase
use NADPH

131
Q

Enoyl reductase is inhibited by antibiotic _______

A

Tricolsan (antibacterial)

132
Q

The reactions of FAS are repeated until the fatty acid is ____ carbons long

A

16 (palmitate)
this is max length

133
Q

How do we make unsaturated fatty acids

A

electrons from NADH are used to reduce O2 to H2O
enzyme uses cytochrome b5 and cytochrome b5 reductase
CH2 becomes oxidized to CH=CH

134
Q

What enzyme is used in animals to make unsaturated fatty acids

A

fatty acyl-coA desaturases

135
Q

Humans can not desaturate bonds beyond how many carbons

A

9

136
Q

Arachidonic Acid is important because it is the precursor to what

A

eicosanoids

137
Q

NSAIDs block what enzyme that creases prostaglandins

A

prostaglandin synthase

138
Q

Since synthesis of Fatty acids occur in the cytosol acetyl coA must be transported out of the ________________

A

mitochondria

139
Q

What are the local (allosteric) regulations of acetyl-coA carboxylase

A

citrate activates
palmitoyl-coA inhibits
AMP inhibits

140
Q

What are the global (hormonal) regulations of acetyl-coA carboxylase

A

insulin activates
glucagon / epi inhibits

141
Q

What acetyl-coA carboxylase is phosphorylated is it active or inactive

A

inactive

142
Q

What are the 5 roles of nucleotides

A

Precursors of RNA/DNA
activated intermediates in some biosynthetic pathways
ATP
Adenine
Metabolic Regulators

143
Q

What are the 2 possibilities of nucleosides biosynthesis

A

de novo synthesis: anew (from scratch)
salvage: bases scavenged from diet or from nucleic acid turnover

144
Q

Breakdown of nitrogenous bases of nucleosides is not an energy source meaning no ____ is formed

A

ATP

145
Q

What is reaction 1 of purine de novo synthesis

A

activate ribose sugar so you can start building base on it
enzyme: ribose phosphate pyrophosphokinase
creates: PRPP

146
Q

What is reaction 2 of purine de novo synthesis

A

committed step
enzyme: glutamine-PRPP amidotransferase

147
Q

In reaction 2 of purine de novo synthesis what three things inhibit the a site and what three things inhibit the g site

A

A: AMP, ADP, ATP
G: GMP, GDP, GTP
(only binding at both sites will inhibit activity)

148
Q

In do novo synthesis of purines where do the carbons come from and where do the nitrogens come from

A

carbons: Gly, Asp, Gln, THF (folic acid, vit B9)
nitrogens: Asn and Gln

149
Q

Folic acid is converted to DHF and then THF by what enzyme

A

dihydrofloate reductase

150
Q

IMP can be converted into what two things

A

AMP
GMP

151
Q

Many parasites lack de novo biosynthesis pathways and rely exclusively on salvage thus compounds that inhibit salvage pathways are promising ____________ drugs

A

anti-parasite

152
Q

What two enzymes are needed for salvage pathway

A

adenine phosphoribosyltransferase (APRT) -> condenses A and PRPP
hypoxanthine-guanine phosphoribosyltransferase (HGPRT) -> condenses either H or G and PRPP
(this creates two inorganic phosphate molecules)

153
Q

The complete lack of HGPRT causes severe clinical disorder called what syndrome

A

lesch-nyhan syndrome
(x linked genes that only effect males which causes increased anger)

154
Q

What is the common intermediate and final result of primary urine degradation scheme

A

intermediate: xanthine
result: uric acid
production via xanthine oxidase

155
Q

The buildup of uric acid causes what and what factors cause it to increase

A

gout
increase purine intake -> increase purine degradtion -> increase production
(occurs mainly in cancer therapy)

156
Q

What is reaction 1 in pyrimidines de novo synthesis

A

committed step
CPS 1: functions in urea cycle, N source is NH3
CPS 2: functions only in pyrimidine synthesis, N source is glutamine
enzyme: carbamoyl phosphate synthetase II

157
Q

How is reaction 1 in pyrimidine de novo synthesis inhibited and activated

A

inhibited: UDP and UTP
activated: PRPP, ATP

158
Q

Thymidylate synthase requires N5, N10, CH2 tetrahydrofolate which is derived from what

A

folic acid
(vit B9)

159
Q

ATP is generated by oxidation of fuel molecules such as what

A

glucose
FAs
AAs

160
Q

_______ ___________ at irreversible step especially the committed step of rxn to allow early detection of changing cellular conditions

A

allosteric regulation

161
Q

_________ __________ typically part of an amplifying hormonal cascade that allows pathways to be rapidly switched on or off

A

Covalent Modification

162
Q

_______ ________ hormones can also affect gene transcription, translation, and/or degradation of enzyme, which changes amount of enzyme in cells

A

Gene Regulation

163
Q

__________ the fate of certain molecules depends on where it is and transport into mito is controlled

A

compartmentalization

164
Q

______ ________ higher eukaryotes have organs with different metabolic roles made possible by differential gene expression

A

organ-specialization

165
Q

Excess G6P can be converted to ________ and made into fatty acids

A

acetyl-coA

z S1: Bio Chem 2 (3 decks)

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