Final Flashcards
Unlike fats and carbs there is no _______ _____ for amino acids
storage form
Nitrogen ________ is nitrogen ingested = nitrogen excreted
balance
What are the 3 ways to get amino acids
dietary proteins
de novo synthesis
degradation of cellular proteins (normal turnover)
What is the major stomach protease
pepsin
Protein degradation continues in the lumen of the intestine by _______ proteases
pancreatic
What are the two cellular protein degradation
Lysosomal degradation (no energy, extracellular proteins that are taken into cells by endocytosis)
Proteasomal degradation (requires ATP, mainly endogenous proteins)
Lysosomes contain about ___ hydrolytic enzymes
50
In lysosomal degradation-starving cells, there is a selective pathway that preferentially degrades cytosolic proteins containing the sequence ______
KFERQ
Proteins that are going to be degraded are “tagged” with protein called
ubiquitin (proteasome digests it, it is attached to lysine residues on target proteins)
____ or more ubiquitins have strong signals for degradation
4
What are the 4 fates of amino acids
-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
______ uses its own amino acids as fuel during prolonged exercise and during fasting
muscle
The amino group of the amino acid being degraded is first removed form the _____ ______ being degraded
amino acid
Once the amino acid is removed from the amino acid being degraded, its transferred to ____________ which then becomes __________
alpha-ketoglutarate
glutamate
alpha-ketoglutarate converted to glutamate is catalyzed by what enzyme
aminotransferases
All aminotransferases contain the cofactor
PLP (pyridoxal phosphate)
PLP is derived from what
pyridoxine (Vitamin B6)
The aminotransferase enzymes also have value clinically as _________ agents
diagnostic
What are the 4 clinical values of plasma aminotransferases
-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
What do AST and ALTs test for
liver damage
heart damage
(high plasma levels of both indicate more severe damage)
What is amino acid catabolism
-transamination reaction occurs 1st
-then oxidative deamination to release ammonia which is combined with CO2 to make urea
What is glutamate dehydrogenase
occurs only in liver mitochondria
oxidative deamination and needs an electron acceptor of NAD+
In severely impaired hepatic function and cirrhosis _________ intoxication develop
ammonia
When ammonia concentration increases in blood and other bio fluids, it diffuses across the BBB causing ammonia _____________
encephalopathy
Why is ammonia toxic
lead to increased levels of glutamine
then causes an ATP decrease by TCA inhibition
can cause swelling of cells and coma
Carbon skeleton is converted to a _______ intermediate then used for energy or used to make ________ or fat
common
glucose
Degradation of the 20 amino acids funnel into ___ metabolic intermediates
7
What are the 5 glucogenic metabolic intermediates
Pyruvate
Oxaoloacetate
Fumarate
alpha-Ketoglutarate
Succinyl-CoA
What are the 2 Ketogenic metabolic intermediates
Acetyl-CoA
Acetoacetyl-CoA
What are the 5 glucogenic and ketogenic amino acids
Isoleucine
Phenylalanine
Threonine
Tryptophan
Tyrosine
What are the two Ketogenic amino acids
Leucine
Lysine
Amino Acids biosynthesis can not be used to make _______ or broken down for _______
proteins
energy
What are the three methods for obtaining amino acids for protein synthesis
Dietary Proteins
De novo synthesis
Degradation of cellular proteins
In order to make new amino acids from scratch we need what two things
nitrogen atom (amine)
carbon skeleton (alpha keto acid)
Where do we get the nitrogen when we need to make new amino acids
Glu or Gln
(transfer their amine group to other compounds)
The amine of glutamine (Gln) = source of the amino group for most ____ ______ while the amide of Gln = source of ________ for other N-containing compounds
amino acids
nitrogen
Essential amino acids defn
amino acids that can only be synthesized in plants and microorganisms
Nonessential amino acids defn
amino acids that can be synthesized in mammals from common intermediates
____ 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
Arg
____ is required to produce cysteine if the latter is not supplied adequately by the diet
Met
___ is needed in larger amounts to form Tyr (if there is not enough Met in the diet)
Phe
What are the 3 common intermediates that go through glycolysis
3-phosphoglycerate
PEP
Pyruvate
What is the one common intermediate that goes through PPP
Ribose 5 Phosphate
What are the 2 common intermediates that go through TCA
alpha-ketoglutarate
oxaloacetate
What common intermediate is arginine made from
alpha-ketoglutarate
What common intermediate is histidine made from
ribose-5-phosphate
What common intermediate is phenylalanine and tryptophan made from
phosphoenolpyruvate
What common intermediate is valine and leucine made from
pyruvate
What common intermediate is methionine, threonine, lysine, and isoleucine made from
oxaloacetate
During the transfer of electrons from NADH and FADH2 potential energy is produced in the form of what
a proton gradient
Why is oxidative phosphorylation termed the way it is
oxidative: electrons are transferred
phosphorylation: Pi is transferred to ADP to make ATP
Cellular respiration is also called what
aerobic respiration
the energy released be electron transport is used to transport protons _______ an electrochemical gradient
against
chemiosmotic energy coupling requires a _______ to establish a gradient
membrane
membrane must contain proteins that can couple the _______ flow of electrons with the ________ flow of protons across the membrane
uphill
downhill
Enzyme used when membrane contains another protein that couples the downhill flow of protons to the generation of new ATP
ATP synthase enzyme
The potential energy generated by the pumping of protons is called the
proton motive force
What are the two results in potential energy
concentration difference
molecule is a protone (charged and no counterion is transported with it causing charge repulsion)
FAD (FMN) can accept or donate ___ electrons at a time = hydride ion or it can accept or donate ___ electrons at a time = hydrogen radical
2
1
Coenzyme Q (ubiqinone) can accept or donate ___ electrons at a time but it can hold up to __ electrons
1
2
What other electron carriers in ETC can hold only 1 electron at a time
cytochrome
iron-sulfur clusters
copper ions
Electrons from _____ enter through complex I while electrons from _____ enter through complex II
NADH
FADH
What is another name for complex 1
NADH: coenzyme Q oxidoreductase
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
FADH2
Complex 2 is an _____ that is located in the inner membrane of the mitochondria
enzyme
(use FAD asa cofactor)
No protons are pumped at which complex
2
Complex 2 does not pump H+ thus less ATP is made when electrons come from _______ than when they come from ______
FADH2
NADH
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
hydrophobic
What is another name for complex 3
coenzyme Q-cytochrome C oxidoreductase
The transfer of electrons through complex 3 also results in the transfer of __________ from the matrix to the intermembrane
protons
What happens if you inhibit complex 3
electron transport is shut down and therefore so is ATP synthase
What are the 2 inhibitors of complex 3
Antimycin A
Myxothiazol
Heme iron can be either ferrous (FE3+ _________) or ferric (FE2+ __________)
oxidized
reduced
cytochrome C is highly conserved in nature and is the ________ mobile electron carrier
second
Cytochrome c carries a single electron from the complex ___ to complex ____
3 to 4
What is another name for complex 4
cytochrome oxidase
(should be called cytochrome c-oxygen oxidoreductase)
Mammalian cytochrome oxidase contains ___ heme groups and ___ copper ions
2, 2
Since mammalian cytochrome oxidase contains 2 heme groups and 2 copper ions it can only transfer ___ electrons at a time
1
(eventually transfers a total of 4 electrons to molecular oxygen)
What are the 3 inhibitors of complex 4 that bind in place of oxygen
cyanide (CN)
carbon monoxide (CO)
azide (N3-)
What happens to ETC and ATP syn if you inhibit complex 4
electron transport is shut down and therefore so is ATP syn
If there is no oxygen to accept electrons from complex 4, electron transport is shut down and so is ____________
ATP syn
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
NADH inhibits TCA cycle and no oxygen = no TCA
What are the three places where protons are pumped when electrons are donated by NADH
complex 1, 3, and 4
What are the two places where protons are pumped when electrons are donated by FADH2
complex 3 and 4
ETC results in transfer of electrons to ______ to form water
O2
complex 4 holds O2 very tightly to prevent escape of damaging oxygen _________
radicals
(could also be formed from reduced coenzyme QH2)
What are the 3 reactive oxygen species
superoxide
hydrogen peroxide
hydroxyl radical
What are the 2 reactive oxygen species enzymes
superoxide dismutase and catalase
The disulfide bond must be ________ to reactivate GSH
reduced
The ratio of reduced glutathione to oxidized glutathione within cells is often used as a measure of cellular _________
toxicity
_____________ (white blood cells) will produce reactive oxidative species in order to kill bacteria during an infection
phagocytes
The potential energy generated by the pumping of protons is called the
proton motive force
Major component of the mitochondrial ATP synthase complex: F1
Catalytic unit
-projects into the matrix
-catalyzes the reaction to make ATP
-rotates as protons flow through
-made up of 5 subunits
Major component of the mitochondrial ATP synthase complex: F0
Proton channel
-embedded in the membrane
-forms a pore that H+ can pass through
-transports protons from intermembrane space back to matrix
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
ATP
What are the two enzymes that are ATP synthase inhibitors
oligomycin
dicyclohexylcarbodiimide (DCCD)
What is the importance of the ATP synthase inhibitors enzymes
they bind to F0 part of enzyme and block ATP synthesis and therefore e- transport
What are the subunits that regulate ETC
NADH2
FADH2
O2
What are the subunits that regulate ox/phos
ADP
Pi
The interdependence of ATP synthesis and electron transport is called
respiratory control
What are the three uncouplers of ATP synthesis and electron transport
2,4-dinitrophenol (DNP)
FCCP
Dicumarol
(all have acidic proton on ring)
Uncouplers pick up ___ from inner membrane space and bring it back to matrix. When gradient is dissipated by uncouplers, energy is released as _____
H+
heat
Naturally occurring uncouplers are found where in the body
brown fat
(called uncoupler protein, UCP, thermogenin)
UCP: produces heat as adaption to cold
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
H+ gradient
ATP, ADP, and Pi are highly ________ and can not diffuse through the membrane
diffuse
(ADP and Pi need to enter and ATP needs to leave)
When H+ are being pumped, ATP ____ is moving form a negative charged matrix to a positively charged inner membrane space
-4
(but this brings a negatively charged counter ion into the area where the H+ gradient is set up)
ADP and ATP is a coupled reaction therefore ADP can only enter if ____ leaves
ATP
What are the two shuttles that transport the electrons from cytosolic NADH into the mitochondria
Glycerol-Phosphate Shuttle
Malate-Aspartate Shuttle
(they transport the electrons from cytosolic NADH, not the NADH itself)
Electrons in the glycerol-3-phosphate shuttle start on NADH but end up on _______
FADH2
(then enter ETC via door 2 and less ATP made this way)
The glycerol-3-phosphate shuttle is used primarily in what two things in the body
skeletal muscle
brain
The malate-aspartate shuttle transfers electrons from cytosolic NADH to mitochondria NADH. What occurs with the ATP
no loss in amount of ATP made
The malate-aspartate shuttle is used in what three organs
liver, kidney, and heart
Where does beta oxidation occur
in the mito matrix
Where does fatty acid synthesis occur
cytosol
In beta-oxidation what is the carbon acceptor/donor
acetyl-coA
In fatty acid synthesis what is the carbon acceptor/donor
malonyl-coA
In beta-oxidation what is the electron acceptor/donor
NAD+ or FAD
In fatty acid synthesis what is the electron acceptor/donor
NADPH
FAS has __ different enzyme activities
7
In each cycle of FAS how many carbons are added
2
Through the addition of ____________ and loss of ____ in FAS 2 carbons can be added
malonyl-coA
CO2
What is reaction 1 of FAS
formation of malonyl-coA
uses CO2
produces ATP
needs biotin cofactor
enzyme: acetyl-coA carboxylase
Is rxn 1 of FAS (formation of malonyl-coA) reversible or irreversible and why
Irreversible because it is the committed step of FA synthesis since it makes ATP
How is rxn 1 of FAS (formation of malonyl-coA) locally and globally regulated
local: Allosteric
global: Hormonal
What is the reaction 2 in FAS
formation of acetyl-ACP
enzyme: acetyltransferase
What is reaction 3 in FAS
formation of malonyl-ACP
enzyme: malonyl transferase
What is reaction 4 of FAS
condensation of the growing chain with activated malonyl-acp
forms acetoacetyl-ACP
loss of CO2
enzyme: beta ketoacyl synthase
What is reaction 5 of FAS
reduction of carbonyl to hydrox
enzyme: beta ketoacyl reductase
need NADPH
donated hydride ion
beta keto group is reduced to an alcohol
What is reaction 6 of FAS
hydration of alcohol to trans-alkene
enzyme: beta hydroxyacyl dehydratase
loss water
form C=C
What is reaction 7 of FAS
reduction of alkene to alkane
reduce C=C to CH2
enzyme: 2,3 trans enoyl reductase
use NADPH
Enoyl reductase is inhibited by antibiotic _______
Tricolsan (antibacterial)
The reactions of FAS are repeated until the fatty acid is ____ carbons long
16 (palmitate)
this is max length
How do we make unsaturated fatty acids
electrons from NADH are used to reduce O2 to H2O
enzyme uses cytochrome b5 and cytochrome b5 reductase
CH2 becomes oxidized to CH=CH
What enzyme is used in animals to make unsaturated fatty acids
fatty acyl-coA desaturases
Humans can not desaturate bonds beyond how many carbons
9
Arachidonic Acid is important because it is the precursor to what
eicosanoids
NSAIDs block what enzyme that creases prostaglandins
prostaglandin synthase
Since synthesis of Fatty acids occur in the cytosol acetyl coA must be transported out of the ________________
mitochondria
What are the local (allosteric) regulations of acetyl-coA carboxylase
citrate activates
palmitoyl-coA inhibits
AMP inhibits
What are the global (hormonal) regulations of acetyl-coA carboxylase
insulin activates
glucagon / epi inhibits
What acetyl-coA carboxylase is phosphorylated is it active or inactive
inactive
What are the 5 roles of nucleotides
Precursors of RNA/DNA
activated intermediates in some biosynthetic pathways
ATP
Adenine
Metabolic Regulators
What are the 2 possibilities of nucleosides biosynthesis
de novo synthesis: anew (from scratch)
salvage: bases scavenged from diet or from nucleic acid turnover
Breakdown of nitrogenous bases of nucleosides is not an energy source meaning no ____ is formed
ATP
What is reaction 1 of purine de novo synthesis
activate ribose sugar so you can start building base on it
enzyme: ribose phosphate pyrophosphokinase
creates: PRPP
What is reaction 2 of purine de novo synthesis
committed step
enzyme: glutamine-PRPP amidotransferase
In reaction 2 of purine de novo synthesis what three things inhibit the a site and what three things inhibit the g site
A: AMP, ADP, ATP
G: GMP, GDP, GTP
(only binding at both sites will inhibit activity)
In do novo synthesis of purines where do the carbons come from and where do the nitrogens come from
carbons: Gly, Asp, Gln, THF (folic acid, vit B9)
nitrogens: Asn and Gln
Folic acid is converted to DHF and then THF by what enzyme
dihydrofloate reductase
IMP can be converted into what two things
AMP
GMP
Many parasites lack de novo biosynthesis pathways and rely exclusively on salvage thus compounds that inhibit salvage pathways are promising ____________ drugs
anti-parasite
What two enzymes are needed for salvage pathway
adenine phosphoribosyltransferase (APRT) -> condenses A and PRPP
hypoxanthine-guanine phosphoribosyltransferase (HGPRT) -> condenses either H or G and PRPP
(this creates two inorganic phosphate molecules)
The complete lack of HGPRT causes severe clinical disorder called what syndrome
lesch-nyhan syndrome
(x linked genes that only effect males which causes increased anger)
What is the common intermediate and final result of primary urine degradation scheme
intermediate: xanthine
result: uric acid
production via xanthine oxidase
The buildup of uric acid causes what and what factors cause it to increase
gout
increase purine intake -> increase purine degradtion -> increase production
(occurs mainly in cancer therapy)
What is reaction 1 in pyrimidines de novo synthesis
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
How is reaction 1 in pyrimidine de novo synthesis inhibited and activated
inhibited: UDP and UTP
activated: PRPP, ATP
Thymidylate synthase requires N5, N10, CH2 tetrahydrofolate which is derived from what
folic acid
(vit B9)
ATP is generated by oxidation of fuel molecules such as what
glucose
FAs
AAs
_______ ___________ at irreversible step especially the committed step of rxn to allow early detection of changing cellular conditions
allosteric regulation
_________ __________ typically part of an amplifying hormonal cascade that allows pathways to be rapidly switched on or off
Covalent Modification
_______ ________ hormones can also affect gene transcription, translation, and/or degradation of enzyme, which changes amount of enzyme in cells
Gene Regulation
__________ the fate of certain molecules depends on where it is and transport into mito is controlled
compartmentalization
______ ________ higher eukaryotes have organs with different metabolic roles made possible by differential gene expression
organ-specialization
Excess G6P can be converted to ________ and made into fatty acids
acetyl-coA
