BIOCHEM II Exam 1

feedback inhibition

3-phosphoglycerate dehydrogenase exemplifies...

carnitine acyl carnitine translocase (CACT)

Acyl carnitine is then shuttled across the mitochondrial membrane by ___________

ketogenic amino acids

Amino acids that are degraded into acetyl CoA or acetoacetyl CoA are termed...

glucogenic amino acids

Amino acids that are degraded into pyruvate, oxaloacetate, fumarate, succinyl CoA or α-ketoglutarate are termed...

CO2

An additional ____ molecule is needed for RuBisCo to function

it increases the solubility of glycogen and increases the number of terminal ends that can be broken down by glycogen phosphorylase.

Branching is important because...

argininosuccinate synthetase

Citrulline is transported out of the mitochondria to the cytoplasm, where it condenses with aspartate (the donor of the second nitrogen of urea); this reaction is catalyzed by...

beta-carbon, beta-oxidation pathway

Degradation of acyl CoA: because the oxidation takes place at the _________ atom, this series of reactions is called the _________

delta symbol, superscript

Delta (Δ) nomenclature: here, the position of the double bond is represented by the _______ followed by a ______ that represents the first carbon in the double bond

transketolase, transaldolase

Enzymes known as ______ and _________ play a major role in the regeneration of ribulose 1,5-bisphosphate.

alpha-ketoacid

Every α-amino acid has a corresponding ______, which is essentially the deamidated form

DAGs, MAGs, fatty acid + glycerol

Fatty acid degradation: TAGs --> _____ --> ______ --> _____

beta-ketoacyl synthase

Fatty acid synthesis begins with the condensation of malonyl ACP and acetyl ACP to form acetoacetyl ACP; this reaction is catalyzed by _________ and releases CO2, which results in a four-carbon β-ketoacyl product.

fatty acid synthase

Fatty acids are synthesized by a complex of enzymes that are collectively referred to as ________

triaglycerols (TAGs)

Fatty acids are typically stored as _____

arginase

Finally, arginine is hydrolyzed to generate urea and regenerate ornithine; this reaction is catalyzed by...

enoyl reductase, NADPH

Finally, crotonyl ACP is reduced by ________, using _____ as a reductant.

beta-ketothiolase

Finally, the 3-ketoacyl CoA is cleaved by the thiol of a free CoA molecule, which yields acetyl CoA and an acyl CoA that has been shortened by two (2) carbon units; this reaction is catalyzed by _______

uridine diphosphate glucose (UDP-glucose)

Glycogen is synthesized by a pathway that utilizes _____

The phosphoglycolate is dephosphorylated and converted to glycine, and 2 glycines are converted into serine, which is converted to 3-phosphoglycerate

How is the RuBisCo oxygenase reaction salvaged?

cyclic AMP (cAMP) signal transduction cascade

In order to trigger the breakdown of glycogen (intracellular process), such hormone signals need to be transduced to the inside of the cell. This occurs through a...

the carbonyl group of the ketose substrate and the e-amino group of an active-site Lys

In transaldolase, a Schiff base is formed between...

lipases

Intestinal enzymes called ________ are secreted by the pancreas following a meal and degrade TAGs to free fatty acids and monoacylglycerol (MAG)

1,4; 12; 1,6

Most of the glucose residues in glycogen are linked through α-___ glycosidic bonds, with branch points approximately every ___ residues; the branch points are created by α-___ glycosidic bonds.

carboxyl carbon, first carbon in the double bond

Numbering from carboxyl carbon: here, the _________ is number 1 and the double bond is named for the _______

last carbon, number of carbons from that end

Numbering from the omega (ω) carbon: in this nomenclature, the _______ in the chain is named the ω carbon and the double bond is named for the ________

carnitine

Once activated, the fatty acids are trafficked into the mitochondrial matrix by a specialized transport mechanism; this mechanism requires that the fatty acids be decoupled from CoA and conjugated to _____

phosphoglucomutase

Once glucose 1-phosphate is released from glycogen, it is converted into glucose 6-phosphate by the fourth enzyme in this process:

glutamate dehydrogenase

Once transferred to Glu, the nitrogen atom is converted to free ammonium ion by oxidative deamination; this reaction is catalyzed by...

3, 2, 12

Oxidation by the respiratory chain can produce approximately ___ molecules of ATP for every NADH and ___ molecules of ATP for every FADH2; furthermore, approximately ___ molecules of ATP are generated for every acetyl CoA oxidized through the citric acid cycle.

cAMP, protein kinase A, phosphorylase kinase, phosphorylase b, phosphorylase a

Regulatory Cascade for Glycogen Breakdown: ATP activates _____, which activates ______, which activates _____, which converts ______ to ______

phosphopentose epimerase

Ribulose 5-phosphate is converted into the appropriate epimer for the transketolase reaction by _____

8 large (L, 55 kDa) subunits and 8 small (S, 15 kDa) subunits; each L chain contains a catalytic site and a regulatory site.

RuBisCo consists of...

carbonic anhydrase

RuBisCo mechanism is analogous to...

3-phosphoglycerate

Ser is synthesized from _________, an intermediate in glycolysis.

fatty acids and glycerol

TAGs are degraded into...

3-phosphoglycerate dehydrogenase

The The first step in Ser synthesis is catalyzed by ___________

19S, 20S

The ____ unit functions to bind Ub and feed the protein into the ____ unit

magnesium ion and a carbamate functionality.

The activity of the RuBisCo enzyme depends on the presence of...

reduces the Vmax

The binding of Ser to 3-phosphoglycerate...

ornithine transcarbamoylase

The carbamoyl group of carbamoyl phosphate has a high transfer potential due to its anhydride linkage; this allows the carbamoyl group to be transferred to ornithine, a non-proteogenic amino acid similar to Lys with one less methylene group in its sidechain. This reaction is catalyzed by...

glycogenin

The center protein of glycogen is called...

glycogen phosphorylase

The key enzyme in glycogen breakdown is...

argininosuccinase

The next reaction in the urea cycle is the cleavage of argininosuccinate into fumarate and arginine; here, the four-carbon skeleton of aspartate is conserved as fumarate (recall that fumarate is a citric acid cycle intermediate). The cleavage of argininosuccinate is catalyzed by...

Vitamin B12 (cobalamin)

The pathway to succinyl CoA from propionyl CoA is interesting because it entails a rearrangement that involves...

1. The release of glucose 1-phosphate from the ends of glycogen polymers. 2. The remodeling of the glycogen polymer to permit further degradation. 3. The conversion of glucose 1-phosphate to glucose 6-phosphate for further metabolism.

The process of glycogen breakdown occurs when the cell or organism needs energy and involves three steps:

succinyl CoA

The three-carbon propionyl unit is a metabolic dead end and can only enter the citric acid cycle after it has been converted to...

carbamoyl phosphate synthetase I

The urea cycle begins with the coupling of free NH3 (the ammonium atom is deprotonated by the enzyme) with HCO3- to yield carbamoyl phosphate; the enzyme that catalyzes this reaction is

nitrogenase complex

To meet the energetic demands of nitrogen fixation (the N≡N bond contains about 940 kJ mol-1 of energy), microorganisms employ an enzyme complex with multiple redox centers; this is called the ________

thiamine pyrophosphate (TPP)

Transketolase contains a tightly bound ________

tryptophan 2,3-dioxygenase

Trp breakdown: _________ cleaves the pyrrole ring to form N-formylkynurenine; this intermediate is then deformylated to form kynurenine.

palmitate, 16

Typically, mammalian fatty acid synthesis generates _______, a ___-carbon fatty acid that serves as a precursor for a wide variety of other fatty acids.

thioesterase

Upon reaching 16 carbons (palmitate) the synthesis is typically stopped, and the 16-carbon molecule is cleaved from the ACP protein by _______

propionyl CoA (a three-carbon molecule) and acetyl CoA (a two-carbon molecule)

What are the final products of uneven fatty acid breakdown?

1. The fixation of carbon dioxide to ribulose 1,5-bisphosphate; ultimately forming two (2) molecules of 3-phosphoglycerate. 2. The reduction of 3-phosphoglycerate to form hexose sugars. 3. The regeneration of ribulose 1,5-bisphosphate so that more carbon dioxide can be fixed.

What are the three stages of the Calvin cycle?

isomerase and reductase

What are the two additional enzymes needed for unsaturated fatty acid breakdown?

oxidative phase - NADPH is generated through the oxidation of glucose 6-phosphate to ribulose 5-phosphate and CO2; also generates metabolites for the non-oxidative phase. non-oxidative phase - three-, four-, five-, six-, and seven-carbon sugars are interconverted in a series of non-oxidative reactions; generates glycolytic intermediates.

What are the two phases of the pentose phosphate pathway?

reductase and nitrogenase

What are the two proteins in the nitrogenase complex?

20S catalytic unit and 19S regulatory unit

What are the two subunits of the 26 proteasome?

Ser

What binds to the regulatory domain of 3-phosphoglycerate dehydrogenase?

RuBisCo

What catalyzes carbon fixation to form two molecules of 3-phosphoglycerate?

oxygenases

What category of enzymes is used to break down aromatic amino acids?

ATP

What drives the 26S proteasome?

protein phosphatase I (PPI)

What enzyme turns phosphorylase off, thus shutting down glycogen breakdown?

recycled

What happens to Ub after proteins are digested?

Acetyl CoA and succinyl CoA

What is the fate of Isoleucine's carbon skeleton?

pyruvate

What is the fate of alanine's carbon skeleton?

alpha-ketoglutarate

What is the fate of arginine's carbon skeleton?

oxaloacetate

What is the fate of asparagine's carbon skeleton?

oxaloacetate and fumarate

What is the fate of aspartate's carbon skeleton?

pyruvate

What is the fate of cysteine's carbon skeleton?

alpha-ketoglutarate

What is the fate of glutamate's carbon skeleton?

alpha-ketoglutarate

What is the fate of glutamine's carbon skeleton?

pyruvate

What is the fate of glycine's carbon skeleton?

alpha-ketoglutarate

What is the fate of histidine's carbon skeleton?

acetyl CoA and Acetoacetyl CoA

What is the fate of leucine's carbon skeleton?

succinyl CoA

What is the fate of methionine's carbon skeleton?

acetoacetyl CoA and fumarate

What is the fate of phenylalanine's carbon skeleton?

alpha-ketoglutarate

What is the fate of proline's carbon skeleton?

pyruvate

What is the fate of serine's carbon skeleton?

pyruvate and succinyl CoA

What is the fate of threonine's carbon skeleton?

pyruvate, acetyl CoA, and acetoacetyl CoA

What is the fate of tryptophan's carbon skeleton?

acetoacetyl CoA and fumarate

What is the fate of tyrosine's carbon skeleton?

succinyl CoA

What is the fate of valine's carbon skeleton?

serine

What is the first step in the 3-phosphoglycerate family?

glutamate

What is the first step in the alpha-ketoglutarate family?

aspartate

What is the first step in the oxaloacetate family?

phenylalanine, tyrosine, and tryptophan

What is the first step in the phosphoenolpyruvate + erythrose 4-phosphate family?

alanine, valine, and leucine

What is the first step in the pyruvate family?

histidine

What is the first step in the ribose 5-phosphate family?

phosphopentose isomerase

What isomerizes rubulose 5-phosphate to ribose 5-phosphate?

Fructose 6-phosphate, glucose 1-phosphate, glucose 6-phosphate

What three hexoses make up the hexose monophosphate pool?

stroma

Where does the Calvin Cycle take place?

stromal surface of the thylakoid membrane

Where is RuBisCo located?

carbons, double bonds

X:Y nomenclature: where X is the number of ________ in the fatty acid and Y is the number of _______ in the molecule

chylomicrons

_____ are stable nanoparticles (200 nm in diameter) that transport TAGs, fat-soluble vitamins and cholesterol throughout the bod

aldolase

_____ is a transaldolase specific for DHAP

alanine transaminase, pyruvate, glutamate

______ catalyzes the transfer of the amino group from alanine to α-ketoglutarate, this generates _______ (α-ketoacid of Ala) and _________

Ser, tetrahydrofolate

_______ is also the precursor of Gly; in the formation of Gly, the sidechain methylene group is transferred to a _______, a carrier of activated one-carbon units

Acetyl CoA

_______ is the precursor molecule for nearly all fatty acids during synthesis

degradation, acetyl CoA, citric acid cycle

________ is an oxidative process and converts fatty acids into ________ that are processed by the ________

aspartate transaminase, oxaloacetate, glutamate

_________ catalyzes the transfer of the amino group from aspartate to α-ketoglutarate, this generates _________ (α-ketoacid of Asp) and ________.

branching enzyme

_________ is required to add the α-1,6-glycosidic bonds of the final glycogen granule.

glutamine synthetase

a large multi-subunit enzyme that is involved in regulating the flow of nitrogen in bacterial metabolism.

HMG CoA cleavage enzyme

acetoacetate formation: A molecule of acetyl CoA is then removed from HMG-CoA by ___________, resulting in acetoacetate.

D-3-hydroxybutyrate dehydrogenase

acetoacetate formation: Acetoacetate is then reduced by ____________ to form ᴅ-3-hydroxybuterate; acetoacetate can also spontaneously decarboxylate to form acetone.

HMG CoA Synthase

acetoacetate formation: Acetoacetyl CoA then reacts with acetyl CoA and water to produce 3-hydroxy-3-methyl-glutaryl CoA (HMG-CoA); this reaction is catalyzed by _______

thiolase

acetoacetate formation: Two molecules of acetyl CoA condense to form acetoacetyl CoA; this reaction is catalyzed by _____ and is the reverse of the thiolysis step during fatty acid oxidation.

ketone bodies

acetoacetate, ᴅ-3-hydroxybutyrate and acetone are collectively known as...

threonine deaminase

an enzyme that catalyzes the formation of α-ketobutyrate

Acyl-CoA dehydrogenase

beta-oxidation: The first step is the oxidation of acyl CoA by __________ to yield trans-Δ2-enoyl CoA , which includes a trans double bond between carbons C-2 and C-3.

enoyl-CoA hydratase, L

beta-oxidation: The second step involves the hydration of the double bond between C-2 and C-3 by ________; this reaction is stereospecific and only the ___-isomer of 3-hydroxyacyl CoA is formed.

L-3-hydroxyacyl CoA dehydrogenase

beta-oxidation: The third step is a second oxidation reaction, which converts the C-3 hydroxyl group to a ketone and generates NADH; this reaction is catalyzed by _______

RuBisCo

by some accounts _____ is the most abundant protein in the entire biosphere.

zwitterionic alcohol

carnitine is a ____

alpha 1,6-glucosidase

cleaves the α-1,6-glycosidic bond through hydrolysis

MAG lipase

completes the mobilization process by releasing another free fatty acid, generating a free fatty acid and glycerol.

ketone bodies

contain ketones within their structures.

Adipose Triglyceride Lipase (ATGL)

converts TAG into diacylglycerol (DAG) and releases a fatty acid.

F, H, I, K, L, M, T, V, W and sometimes Y

essential amino acids in humans are...

protein kinase A, cAMP cascade

fatty acid breakdown: hormones activate _________ through the ___________

cytoplasm

fatty acid synthesis takes place in the...

β-ketoacyl reductase.

fatty acid synthesis: Acetoacetyl ACP is then reduced using NADPH, forming ᴅ-3-hydroxybutyryl ACP; this reaction is catalyzed by...

acyl carrier protein (ACP)

fatty acid synthesis: Intermediates for synthesis are linked to the sulfhydryl group of...

NADH or NADPH

glutamate dehydrogenase uses either _____ or _____

molecules in which they received nitrogen from glutamine

glutamine synthetase can be cumulatively inhibited by...

cumulative feedback inhibition

glutamine synthetase exemplifies

adding orthophosphate (Pi) to yield glucose 1-phosphate.

glycogen phosphorylase cleaves the substrate by...

1. Phosphorylation of glucose to glucose 6-phosphate. 2. Conversion of glucose 6-phosphate to glucose 1-phosphate. 3. Activation of glucose 1-phosphate by addition of uridine triphosphate (UTP) 4. Addition of the UDP-glucose to the end of the glycogen polymer. 5. Remodeling of the glycogen polymer to permit further addition.

glycogen synthesis (glycogenesis) occurs when glucose is abundant and takes place in the following five (5) steps:

26S proteasome

large protein complex that digests ubiquitinated proteins

epinephrine, glucagon

muscle cells respond to ______ and liver cells are sensitive to _______

reductase

nitrogenase complex protein with Fe that provides electrons and reducing power.

nitrogenase

nitrogenase complex protein with MoFe protein that uses electrons supplied by the reductase to reduce N2 to NH3.

cumulative feedback inhibition

observed in cases where a common step of a biosynthetic reaction is inhibited by multiple (albeit independent) final products

enzyme multiplicity

observed when the committed step of a biosynthetic pathway can be catalyzed by two (2) or more isozymes; here, these enzymes have essentially identical catalytic mechanisms, but different regulatory properties.

feedback inhibition and activation

observed when two (2) pathways with a common initial step may be inhibited by the product of one pathway and activated by the product of the other pathway.

processivity

phosphorylase is an enzyme with relatively high _______

Hormone-sensitive lipase (HSL)

releases another fatty acid from DAG, generating a free fatty acid and monoacylglycerol (MAG)

acyl CoA molecule shortened by 2 carbons, an acetyl CoA, an FADH2, and an NADH

saturated acyl CoA molecules degradation produces:

transferase

shifts a block of three (3) glucosyl residues from one branch to another

cytoplasm

the PPP takes place in the _____

antiporter translocation

the carnitine translocation mechanism is known as a ______ mechanism

phosphorolysis

the cleavage of a chemical bond by the addition of orthophosphate is referred to as _____

corrin ring

the core of cobalamin (Vitamin B12) is a...

O2, oxygenase, phosphoglycolate

the enediolate of the RuBisCo reaction sometimes reacts with ______ instead of CO2; this results in a deleterious _____ reaction that generates one (1) molecule of 3-phosphoglycerate and one (1) molecule of _________

Monooxygenases

these enzymes add one (1) oxygen atom of O2 to the amino acid and the other to water

dioxygenases

these enzymes add two (2) oxygen atoms of O2 to the amino acid

feedback inhibition and activation

threonine deaminase exemplifies

Ile, Val

threonine deaminase is allosterically inhibited by _____ and activated by ___

glyceraldehyde 3-phosphate, fructose 6-phosphate

transketolase and transaldolase regenerate ribulose 1,5-bisphosphate from _________ and ________

2, 2

transketolase converts and ketose to an aldose (n - ___)and an aldose to a ketose (n + ___)

prosthetic group (TPP) , Schiff base

transketolase uses a _______ whereas transaldolase uses a ______

E1

ubiquitin activating enzyme

E2

ubiquitin conjugating enzyme

E3

ubiquitin ligating enzyme

cis, trans, acyl CoA dehydrogenase

unsaturated fatty acid breakdown: isomerase converts a ____ bond to a _____ bond, making it a substrate for _________, allowing beta-oxidation to continue

glycogen phosphorylase kinase

what enzyme phosphorylates glycogen phosphorylase, converting it from b to a form?

3-hydroxyacyl dehydratase

ᴅ-3-hydroxybutyryl ACP is then dehydrated by __________; this reaction releases water and generates crotonyl AC (trans-double bond between C-2 and C-3).