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171 Cards in this Set

  • Front
  • Back
What limits the chemistry of a enzyme?
The amino acid side chains
What stabilizes protein structure the most? How?
Hydrophobic interactions; Well b/c Hydrogen bonds are necessary to get the STRUCTURE of a protein but hydrophobic interactions stabilize the structure
What characterizes protein structure?
1. formation of regular secondary structure
2. H-bonds involving backbone and side-chain atoms
3. burial of non-polar side chains to form hydrophobic core
4. Stable structure that is in motion around a central core (like the crust of the earth moving around the Fe core)
What is Aspartame made of?
Aspartate and phenylalanine and a methyl ester
When does tyrosine become an essential amino acid?
When it is not able to be transported into the brain; normally phenylalanine and tyrosine are transported into the brain via the same transporter, but if you have PAH deficiency suddenly tyrosine will become an essential A.A.
What does tetramerization allow?
Tetramerization domain allows for dimers and trimers to form => quaternary structure
What happens in classic PKU?
The active site will not be available at all, H285 binds required iron atom in the active site but a mutation to H285 will cause the enzyme to not be able to bind Fe and so Classic (full-fledged) PKU will result
What is required as a cofactor for PAH?
BH4
What dz will result from BH4 deficiency?
The dz will present like PKU but it is easily solved if you give the pt BH4 because then they will be right back to normal
What does a mutation of valene to methionine cause?
Variant PKU b/c of the dec. affinity for phenylalanine and BH4, V388M is important for active site functionality
What is phenylalanine w/ respect to PAH?
Phenylalanine is an allosteric effect and substrate, phenylalanine is a competitive inhibitor for tyrosine on PAH
What effect will a mutation to the regulatory site of PAH have?
It will prevent activation or shift activity curve
What effect will a mutation to an enzymes phosphorylation site have?
It will remove the regulatory mechanism
What are most important for enzyme function?
Functional residues (A.A.)
What causes Marble Brain Syndrome?
A mutation in CA II; causes the brain to become calcified (turned to marble)
What influences the activity of an enzyme?
Temperature
What specific mutation causes cystic fibrosis?
A mutation to a single phenylalanine residue
What is the most common class of cystic fibrosis?
Class II: a defective maturation and premature degradation of the protein
What are kinetic traps?
Due to cell crowding, proteins can fold into local energitic minima that are not the right structure => a kinetic trap
How do chaperones work?
They recognize kinetic traps and exposed hydrophobic residues -> unfold proteins -> refold correctly or prevent trap from occurring
What will happen if the chaperone cannot bind to a protein?
It will bind to a proteasome and then degrade the protein
What do ribosome-associated chaperones do?
Trigger factors protect small proteins or single domains => creates a protective environment to help the protein fold
What do hydrolases do?
Use water to cleave a bond
What do lyases do?
Just cleave a bond w/o using H2O, this is what bacteria use
What is a mucopolysaccharidosis?
A deficiency of lysosomal enzymes that degrade GAGs
Where does cathepsin come from?
Lysosome
Where are lysosomal proteins synthesized? Where do they go then? and after that?
Proteins in the lysosome are synthesized in the ER, then go to the Golgi then to the LATE endosome
What is the difference b/e early endosomes and lysosomes?
Early endosomes come from the membrane and lysosomes have a drop in pH and presence of unique enzymes
How are hydrolases targeted to the lysosome?
N-linked => attached to asparagine residue => and mannose residue is phosphorylated which then attaches to a mannose-6-phosphate receptor

After binding to M6P receptor, clathrin will bind and coat the vesicle which will then break off and fuse w/ lysosome
What is type II pompe dz?
The only glycogen storage dz that is a lysosomal storage dz
How are GAGs degraded?
Must first be engulfed then fuse w/ a lysosome:
>oncloglycosidis produce oligosaccharides where degradation happens from the end so the parts added last will get degraded first
What causes mucopolysaccharidosis? what does this dz lead to?
A lysosomal hydrolase deficiency that is involved in heparin or dermatan sulfate degradation

Leads to inc. glycosaminoglycans -> which are found in pee
What dz'es are mucopolysaccharidosis dz'es?
1. Hurler
2. Hunter
3. SLY
4. San Filippo
What do phospholipids need in order to be degraded?
phospholipase or sphingomyelinase
What causes Neimann-Pick dz?
Degradation of sphingomyelin deficiency
What do lysosomal enzymes degrade primarily?
Degrade primary extracellular proteins and cell-surface membrane proteins that are used in receptor-mediated endocytosis
What is I cell dz? Where will stuff accumulate?
When you are deficient in the enzymes that are needed for M6P formation=> if you cannot traffic the hydrolase properly by M6P they will be secreted into cell cytosol
What steps are required for formation of M6P?
UDP-acetylglucosamine: lysosomal enzyme N-acetylglucosamine-1-phosphotransferase

N-acetylglucosamine 1-phosphodiester-N-acetylglucosaminidase
What does a deficiency in enzyme N-acetylglucosamine-1-phosphotransferase or N-acetylglucosamine 1-phosphodiester-N-acetylglucosaminidase result in?
An I-cell dz: b/c hydrolase will not be trafficted to lysosome, so hydrolases will float around in the cytosol w/ no target, but this is not fatal b/c they are not at their optimal pH for full functioning
What do extracellular hyaluronidases do? (Hyal-2)
Make smaller chains by hydrolysis
What do HARE receptors do?
They are hyaluronan receptors for endocytosis that recognize smaller chains and cause endocytosis

Endosomes w/ hyaluronan fuse w/ the lysosome
What do hyaluronidases do? where is it located?
1. Hydrolize hyaluronan into pieces by cleaving beta (1,4) bonds
2. excreted enzyme so it is extracellular and is linked to a lipid -> will be on the plasma membrane
Where are Hyal-2 and Hyal-1 found?
Hyal-2: found extracellular and GPI linked
Hyal-1: in the lysosome, also in serum
What is hyaluronan catabolism like?
Occurs in lysosome, the terminal sugar is removed from the non-reducing end of hyaluronan fragments by exoglycosidases

Hyaluronan fragments inside lysosome are broken down beta-glucoronidase and beta-N-acetylglycosaminidase who finish degradation to monosaccharides which leave the lysosome and are re-usable
What does beta-glucoronidase do?
Cleaves glucuronic acid
What does beta-N-acetylglucosaminidase do?
Cleaves N-acetylglucosamine
What enzyme breaks down the repeating disaccharides in hyaluronan?
Beta-glucuronidase and beta-N-acetylglucosaminidase
Where is antithrombin synthesized?
In the liver
What does antithrombin do?
It is a serine protease inhibitor that binds and inactivates thrombin, Factor Xa and Factor IXa which are required for homeostasis (coagulation)
What does the anti-coagulant heparin do?
Binds to antithrombin and accelerates the rate of antithrombin inactivation of serine proteases

*basically makes anti-coagulation happen faster
What is the function of heparanase?
>Degrades the basement membrane
>Procoagulant activity

So cancer cells that overexpress Heparanase are more metastatic
What happens during heparan sulfate catabolism?
Acetyl transferase in lysosomal membrane needs Acetyl CoA to do the reaction, then the sulfate is removed first
What does chondroitan sulfate have in it?
Glucoronate
What does dermatin sulfate have in it?
A iduronic acid
Where does glucosamine tend to be found?
IN chondroitan instead of keratin sulfate
Where does mitophagy happen? What is it?
Occurs in pre-RBC cells, it is the fusion of the mitochondria w/ the lysosome
What is the charge of the erythrocyte glycocalyx?
Negative or neutral
what limits the attraction btw RBCs and endothelial cells?
Carbohydrates on the RBC membrane as well as membrane proteins
When are spectrin and ankyrin added to the membrane?
They are minimally present on the membrane until Band-3 and protein 4.1 are synthesized
What mutation will be caused by a mutation to spectrin alpha or beta?
Spherocytosis
What will happen in decreased spectrin synthesis or dec. ankyrin synthesis?
Leads to poor binding of molecules which lack binding will decrease spectrin recruitment and weaken verticle interactions => this leads to microvesicles being popped off=> dec. RBC surface area => leads to dec. O2 and CO2 exchange
What are ABO Ags?
Mostly carbohydrates that are part of RBC membrane, they are basically a part of the glycoprotein coat

They are the most reactive Ag on the RBC membrane
What is the difference b/e Type A, B and O blood types?
A has an N-aceteal linkage

B does NOT have a N-aceteal linkage

and O has an enzyme but it does not work
What are stealth RBCs?
They are Ags that are modified to hide via carbohydrates, they shield their proteins w/ sugar so Abs cannot bind and attack the blood
What does 2,3DPG preferentially bind to?
deoxyHb or RBCs in the T state
What is synthesized by glycolysis per glucose molecule?
4 ATP (2 net ATP), 2 NADH and 2 pyruvate from 1 glucose and 2 NAD+ and 2 ATP
What would accumulate in triosephosphate isomerase deficiency?
dihydroxyacetone phosphate
What effect does oxidant stress have on RBCs?
High levels of oxidant stress lyses RBCs due to membrane damage (causing ion leakage) and proteins (loss of enzyme activity)
What effect does oxidizing a thiol residue in GSSG have?
Will deactivate the enzyme b/c thiol will participate in the chemical event
What does glutathione peroxidase use in its reaction?
Will take glutathione and oxidize H2O2 to water and GSSG using NADPH
What deficiency is protective against malaria?
G6P dehydrogenase deficiency b/c cells can't handle the stress of malaria invasion and lyse and trigger the immune system before the bacteria can invade
What does xanthine oxidase do?
makes superoxide which reacts w/ NO to form ONOO-; which will destroy anything around it
How can vitamin C act as a pro-oxidant?
By converting Fe(III) to Fe(II) which is good BUT then the Fe(II) can be reconverted to Fe(III) and produce another OH*
What reduces methemoglobin?
Cytochrome b5 (NADH) and methemoglobin reductase reduce methemoglobin
What will band 3 protein (CDB3) bind to in high oxygen situations? low oxygen situations?
High O2: CDB3 will bind to PFK and force glucose to go to the PPP and make NADPH for anti-oxidant purposes

Low O2: CDB3 will bind to deoxy Hb and release PFK, so glucose will now undergo glycolysis
How do neutrophils, monocytes/macrophages kill bacteria? How do Eosinophils kill bacteria?
Using HOCl and OH*, they have myeloperoxidase

Eosinophils generate HOBr
What does myeloperoxidase do?
Makes bleach HOCl which
How are cholesterol deposits broken down?
Removed by macrophages and packed w/ apolipoprotein A1, activation of macrophages produces ROS (HOCl)

HOCl damages apoprotein A1 preventing removal of cholesterol => so macrophages actually CANNOT remove cholesterol
What is ataxia?
A pyruvate dehydrogenase deficiency, so not enough ATP will be made
What are the three enzymes of the pyruvate dehydrogenase complex?
1. pyruvate decarboxylase
2. dihydrolipoyl transacetylase
3. dihydrolipoyl dehydrogenase
What is the E1 (pyruvate decarboxylase) enzyme? what does it do? what is a biproduct of its reaction? what cofactor does it require?
Composed of a tetramer w/ 2 alpha and 2 beta that requires thiamine (B1) as a cofactor that converts TPP to thiamine pyrophosphate which release CO2 as a biproduct
What is E2 (dihydrolipoyl transacetylase)? what does it do? what cofactor does it require?
A monomer w/ a long flexible chain that picks up actetylTPP and transfers it to CoA to make acetyl CoA; links to lipoic acid which is joined to a lysyl residue through amide links

It oxidizies the active acetaldehyde to make acyl group which is transferred to CoA
How does arsenic affect the PDH complex?
Arsenic binds to reduced lipoic acid and makes it unavailable to work, so administer a chelating agent to get rid of it
What is E3? (dihydrolipoyl dehydrogenase) What does it do? what cofactor does it require?
A monomer that oxidizes lipoic acid by reducing FAD to FADH2, it then reduced NAD+ to NADH by using FADH2. It needs Riboflavin (B2) to reduce FADH2 to FAD+ and Niacin (B3) to reduce NAD+ to NADH
What effect does excess intake of riboflavin (B2) have? deficiency?
Excess: causes yellow urine and interferes w/ B1 and B6
Deficiency: leads to neurologic problems
What does Niacin (B3) do in the PDH complex? What does a deficiency of Niacin cause?
Niacin is needed to convert NAD+ to NADH; a deficiency causes pellagra, but tryptophan can serve as an alternative source
What is the function of panthothenic acid (B5)
Important for acetyl CoA; w/o pantothenic acid (B5) Acetyl CoA cannot be made
What does PDH kinase do? what triggers it?
Converts PDH to inactive form; which is triggered by inc. ATP, inc. NADH, dec. pH, inc. acetyl CoA and inc pyruvate
What does PDH phosphatase do? what triggers it?
Converts PDH complex to active form via Ca
What regulates PDH kinase/phosphatase?
phosphorylation; phosphorylation will inhibit the enzyme
What does biotin do? where is it synthesized? what does it do?
Active in bond making and forming in enzyme especially in TPP and B5, it is synthesized by intestinal bacteria inside you
How does large amounts of EtOH effect the cell?
Affects NADH/NAD+ ratio, by making a lot of NADH it turns PDH A (active) into PDH B (inactive) which backs the system up and results in lots of storage of sugars and a fatty liver
What is the glycerophosphate shuttle?
Source of H+, through FADH2 => which feeds directly into the ETC
Source of H+, through FADH2 => which feeds directly into the ETC
What does the malate-aspartate shuttle do?
Shuttles NADH to the matrix
Shuttles NADH to the matrix
How does the malate-aspartate shuttle work?
OAA to malate (which cross inner mitochondrial membrane) to OAA => generates one NADH, the H+ is carried across by malate/a-KG BUT you need to transfer OAA back across the membrane or the cycle will stop
OAA to malate (which cross inner mitochondrial membrane) to OAA => generates one NADH, the H+ is carried across by malate/a-KG BUT you need to transfer OAA back across the membrane or the cycle will stop
How does the malate-aspartate shuttle retransport OAA across the innermitochondrial membrane?
By converting aspartate back to OAA
What does malate dehydrogenase work?
In the cytosol: converts NADH -> NAD+

In inner mito membrane: converts NAD+ -> NADH
Where does the glycerophosphate shuttle feed into the ETC?
In complex II where FADH2 is used
What is the final electron acceptor in the ETC?
O2
What is coenzyme Q?
Similar to ascorbic acid so it has antioxidant capabilities, it can transport one or two electrons at a time; it is a hydrophobic molecule that floats in the membrane
What complexes in the ETC are most likely to generate ROS?
complexes 1 and 3 b/c they are the most leaky
Why are mitochondria the most likely organelle to be mutated?
B/c they do not have the PPP (which is the in the cytosol); the mito balances this by having multiple copies of genome and lots of mitos in the cell
What inhibits ATP synthase?
Oligomycin
How can ATP synthase make a proton gradient?
By hydrolyzing ATP if there is loss of H+ gradient; this occurs in hypoxia or cyanide poisoning
What effect does salicylate toxicity have? (Aspirin)
Salicylate can cross membranes even though it is charged b/c it can make H-bonds b/e adjacent groups; but it is still acidic so at high concentrations it will disrupt the ability to make ATP by destroying the H+ gradient
What enzymes in the TCA release CO2?
Isocitrate dehydrogenase and alpha-ketoglutarate dehydrogenase
What is the rate-limiting step in the TCA?
citrate synthase
What enzymes have a neg. delta G?
citrate synthase, isocitrate dehydrogenase and a-KG dehydrogenase
What inhibits the enzymes of the TCA?
high [NADH] and high [ATP]
What does lipoprotein lipase do?
Hydrolyzes chylomicrons to free fatty acids and glycerol
What do lipolytic hormones do?
Signal tissue to release more fatty acid
What signaling mechanism do lipolytic hormones use?
AC => cAMP => PKA cascade
What activates hormone sensitive lipase?
PKA phosphorylation
What are fatty acids bound to in blood?
Albumin
What does PKA do when activated by lipolytic hormones?
phosphorylates porillipin protein whcih provides a docking place for adipose tissue triglyceride lipases which take fat and start to hydrolyze the fat
What are the steps to hydrolyze stored fat starting from the hormone binding?
Lipolytic hormones bind to G-protein receptor => AC->CAMP->PKA => PKA activates hormone sensitive lipase and porillipin => porillipin provides a docking place for adipose tissue triglyceride lipase to start hydrolyzing fat => hormone lipase hydrolyzes fat even more => then monoglyceride hydrolase will finish the job and release to surrounding tissue
What are the products of stored fat hydrolation?
A glycerol (which is a good gluconeogenic substrate) and fatty acids
What are the products of beta-oxidation? where does it occur?
products are acetyl CoA, FADH2 and NADH (acetyl CoA is oxidized to CO2 and H2O in the TCA cycle

Happens in the mitochondria
Where are fatty acids activated? by what?
Fatty acids must be activated before they are metabolized which occurs in the cytosol by fatty acyl-CoA synthetase (which uses ATP)
What does carnitine-acylcarnitine translocase do?
Transfers FA into the matrix and also transfers carnitine to the inner mito space
What does each turn of beta-oxidation yield?
14 ATP and each turn makes the fatty acid 2 carbons shorter
What is the basic structure of the beta-oxidation pathway?
What inhibits carnitine acyltransferase I?
Malonyl CoA by blocking the substrate getting into mito.
What inhibits beta-hydroxyacyl CoA Dehydrogenase?
High [NADH]
High [NADH]
What inhibits thiolase?
High [Acetyl CoA]
High [Acetyl CoA]
What cofactors are required for oxidative phosphorylation to occur?
ADP and Pi
What effect would diminishing the substrate for the anaplerotic reactions have?
It would slow the TCA cycle => Inc. [Acetyl CoA] => ketogenesis
What is the function of MPF? (Cyclin b-cdc2/cdc)
Reversible breakdown of the nuclear envelope and role of nuclear lamin proteins via DNA transfaction experiments
What do SMS (structural maintenance proteins) do?
Required for normal chromosome segregation, they are called condensins
What effect does phosphorylation of condensins have?
Necessary for maintaining the condensed state of the chromosomes via DNA binding
What does phosphorylation of APC result in?
initiation of anaphase
How is anaphase induced?
By degradation of the anaphase inhibitor (securin) via the APC pathway activated by MPF
What does securin do?
Stabilizes the cohesins to prevent them from separating; cohesins act as linchpins to tie sister chromatids together
What is the effect of degradation of mitotic cyclin B? when does this happen?
Degradation occurs via APC pathway late in anaphase, the cyclin must be degraded in order for anaphase to take place
What does M cyclin-CDK do?
Initially responsible to keep securin-separase complex stable and inactive so it needs to be degraded by APC for separase to cleave cohesin
When does regulated degradation of mitotic cyclins occur? how does it occur?
Occurs late in anaphase via the APC-ubiquitin pathway which makes use of a destruction box common to the N-T of mitotic cyclins
What does cyclin activation require?
2 STEPS: cyclin binding and then phosphorylation by CAK
Whose activity is reduced in G0 (quiescent) cells? whose activity is elevated in tumor cells?
CAK activity is decreased in quiescent cells and elevated in tumor cells
What is the sequene of cyclin-cdk activation in mitosis?
cyclin B => CDK1 => APC
What do INK4 proteins do?
Bind to CDK4/6 to block cyclin D binding
What do Cip/Kip do?
block CDK2-cyclin E but they also bind to and block active site of multiple CDKs
What do CKIs do?
Regulate entry into S phase => G1-S transition
What is the action of mitogens?
They activate the Cyclin D-CDK 4/6 complexes, inhibit CKIs
What does Rb inhibit?
E2F
What does E2F do?
a transcription factor of Cyclin A and D
What will happen if Rb is phosphorylated (inhibited)?
It will not block E2F, so E2F will keep influencing the cell cycle to continue
When is Rb normally activated?
Not until mid/late G1 phase when the buildup of CDK2-cyclin E and CDK 4/6 -Cyclin D leads to phosphorylation of Rb and release of E2F from suppression
What arrises due to DNA damage?
p53 protein which stabilizes DNA damage => chk2 will phosphorylate it and make it less susceptible to degradation
What happens when p53 is activated?
It will activate transcription of the CDK inhibitor CKJ which binds to all CDKs and inhibits their actions, which prevents the cell from moving through the cycle until the DNA damage has been repaired
What does p53 due if the DNA damage is too severe to be fixed?
p53 activates genes that lead to apoptosis via BCL-2
What is folate used for?
Used to make THF
What does thymidylate synthase do?
Catalyzes the conversion of dUMP to dTMP
What does catabolism of Purines create?
Uric acid which will make crystals and cause Gout
What effect does excess PRPP have?
Leads to increased purine synthesis and subsequent degradation of the extra purines which results in inc. uric acid and thus gout
What does a deficiency of HGPRT cause?
Lesch-Nyhan syndrome (which is characterized by pt desires to self-mutilate)
What does Adenosine deaminase deficiency cause (ADA)?
Severe combined immunodeficiency dz (SCID) which causes a build-up of dATP which inhibits ribonucleotide reductase and prevents the synthesis of the other dNTPs
What does Glycosylase do?
Flips base into active site to recognize a mismatch => glycosylase has some specificity b/c when you have incorrect base pairing you tend to have weak connections that could cause the damaged bp to be easily taken up by glycosylase
What does DNA polymerase beta do?
used for repair => not same as replication pool
What does AP endonuclease do?
Removes sugar and phosphate
What does oxidation of guanine cause?
Leads to purine-purine base pairing, 8-hydroxyguanine acts like thymine so bps w/ adenosine
What does Mut Y do?
Recognizes purine-purine base pairing and takes away "A" from daughter cells
What does Mut T do?
Takes away 8-hydroxyguanine => makes T-A bp
What inhibits thymidylate synthase?
fDUMP
What effect does inc. dUTP concentration and dec. dTTP concentration have?
results in putting uricil in DNA, polymerase will take uricil out of DNA so now you have an a-basic site
What is the effect of O6-methylguanine cause?
Causes methylation of guanine and base pairing w/ thymine instead of cytosine which results in G-C -> A-T transitions
What is the only DNA repair enzyme capable of direct repair?
O6-MGMT b/c it will go and remove the methyl group from O6-Mg
What effect does UV damage have on DNA?
Will cause crosslinks btw itself and will cause DNA damage => pyrmidine-pyrimidine linkage
How are thymine cross-links repaired?
By nucleotide excision repair
What effect does ionization damage have on DNA?
Causes a double-strand break that occurs when DNA damage or gaps are on both strands
How are double-strand breaks in DNA fixed?
By homologous recombination
Why is mismatch repair more error prone that nucleotide excision repair?
B/c unlike excision repair you do not need a specific glycosylase to recognize which of the two bases is wrong