Exam 3 - Biochemistry Honors

No regrets

What is the name of the catabolic process that breaks down amino acids?

oxidative deamination (oxidative degradation of amino acids)

The three circumstances under which amino acids undergo oxidative degradation

1. During the normal synthesis and degradation of cellular proteins

2. When the diet is rich in protein and there is an excess of amino acids

3. During starvation or uncontrolled diabetes mellitus

Under the metabolic conditions that allow amino acids to undergo oxidative degradation, amino acids…

lose their amino groups to form α-keto acids

The two key features of amino acid degradation

1. Separation of α-amino group from carbon skeleton

2. Separate pathways for amino group and skeleton

Following the separation of the α-amino group from the carbon skeleton, the amino group ends up in the

urea cycle

Following the separation of the α-amino group from the carbon skeleton, the carbon group ends up in the

citric acid cycle

Dietary amines are always associated with carriers. What are the primary carriers to the liver?

glutamine and alanine

Dietary amines are always associated with carriers. What is the primary pathway in muscle?

Ammonia is coupled to pyruvate, forming alanine

Dietary amines are always associated with carriers. What is the primary carrier from the liver to the renal system?

urea

Most amino acids are metabolized in the

liver

The urea cycle primarily occurs in hepatocytes, beginning in their mitochondria. Excess ammonia generated in extrahepatic tissues travels to the _ for conversion to the excretory form.

liver

Draw the structure of ammonia.

Draw the structure of urea.

Draw the structure of uric acid.

Hormones control digestion. Dietary protein in the stomach stimulates the _ to secrete _

gastric mucosa, gastrin

Gastrin stimulares the secretion of (1) (2)

1. HCl by the parietal cells

2. Pepsinogen by the chief cells of the gastric glands

_ triggers secretion of the hormone secretin into the blood.

Acidic stomach contents lower the pH which

Secretin stimulates the _ to secrete _

pancreas, bicarbonate

The pancreas secretes bicarbonate to

neutralize gastric HCl

How does the secretion of bicarbonate by the pancreas affect the pH?

it increases it to about 7

The presence of protein in the small intestines signal the release of

cholecystokinin

Cholecystokinin stimulates secretion of

several pancreatic digestive enzymes

At a very low pH (~1), pepsinogen is converted to _ by an _

active pepsin, autocatalytic cleavage

Pepsin is active at a very low pH (~1), and its function is

to cleave denatured proteins into peptides

What are the zymogens that are inactive precursors to proteases, secreted by the pancreas?

Trypsinogen, chymotrypsinogen, procarboxypeptidases A and B

Which enzyme is secreted by the small intestines to cleave trypsinogen into trypsin?

Enteropeptidase

Following the cleavage of trypsinogen,

the other two proteases are activated

What tissue absorbs amino acids?

intestinal mucosa

Free amino acids (generated by digestion) are transported into the epithelial cells lining the (organ), enter the blood capillaries in the (?), and travel to the (organ)

small intestine, villi, liver

The suffix “-ogen” indicates that the enzyme is

a precursor

The suffix “-ase” indicates that the enzyme is

active

Pepsin cleaves proteins

N-terminal to L, F, Y, and W

Trypsin cleaves peptides

C-terminal to K and R

Chymotrypsin cleaves peptides

C-terminal to F, Y, and W

Carboxypeptidase cleave

C-terminal residues

Aminopeptidases cleave

N-terminal residues

In the liver, aminotransferases (transaminases) complete a _ reaction

transamination reaction

Transamination Reaction

The α-amino group is transferred from the L-amino acid to the α-carbon of α-ketoglutarate.

The effect of transamination reactions is

to collect the amino groups from many different amino acids in the form of L-glutamate

This product of transamination reactions functions as an amino group donor for biosynthetic pathways or for excretion pathways that lead to the elimination of nitrogenous waste products

L-glutamate

The prosthetic group of all aminotransferases

Pyridoxal phosphate (PLP)

Coenzyme form of Vitamin B6

Pyridoxal phosphate (PLP)

PLP is covalently bound to an enzyme’s active site by

an aldimine linkage to the α-amino group of a Lys residue

The coupled form (PLP–Lys) is called (?) and helps to (?)

internal aldimine, resist oxidation of the aldehyde in the inactive form

Intermediate of transaminase reactions

external aldimine, formed when an amino substrate replaces the Lys’ bond to PLP

In the transaminase reaction, an active site (?) deprotonates the the external aldimine to form (?)

nucleophile, quinonoid intermediate

The acceptor that can reverse the transamination reaction

α-ketoglutarate, an acceptor keto acid

The keto acid formed during transamination reactions is formed by the reaction type

hydrolysis

Three main reactions facilitated by PLP

1. Transamination

2. Racemization (loss of stereochemistry)

3. Decarboxylation

In hepatocytes, glutamate is transported from

the cytosol into mitochondria

In the mitochondria, glutamate undergoes (reaction?) catalyzed by (enzyme?)

oxidative deamination, L-glutamate dehydrogenase

Where can you find L-glutamate dehydrogenase?

mitochondrial matrix

The only enzyme that can use either NAD or NADP as the acceptor of reducing equivalents

L-glutamate dehydrogenase

aminotransferase + glutamate dehydrogenase =

trans-deamination

Free ammonia produced in extrahepatic tissues is… + enzyme?

combined with glutamate to yield glutamine, catalyzed by glutamine synthetase

synthetases (do/do not) use ATP

DO USE ATP

Conversion of ammonia into a nontoxic compound.

Glutamate + ATP → (?) → (?)

ADP + γ-glutamyl phosphate + NH₄⁺ (glutamine synthetase) → glutamine + P_i

Together, (AA?) + (AA?) contribute to the regulation of blood pH

Hint: conjugate acid and base

glutamine + glutamate

What amino acid transports ammonia to the heptocytes from most extrahepatic tissues

glutamine

What enzyme converts glutamine to glutamate and NH₄⁺

glutaminase

During exercise, skeletal mmuslce tissue accumulates

pyruvate

In parallel to exporting lactic acid, ammonia from (AA?) is transferred to (?) to create (?)

glutamate, pyruvate, alanine

The aminotransferase that transfers ammonia from glutamate to pyruvate

alanine aminotransferase

The two precursors of pyruvate,

1. lactic acid

2. alanine

Lactic acid and pyruvate can be used by hepatocytes for

gluconeogenesis

Glutamine from extrahepatic tissue is the product of which enzyme

Glutamine synthetase

The three major processes of nitrogen excretion

1. Ammonotelic

2. Ureotelic

3. Uricotelic

Ammonotelic organisms excrete amino nitrogen as

ammonia

Ureotelic organisms extrete amino nitrogen in the form of

urea

Uricotelic organisms excrete amino nitrogen as

uric acid

Urea production (the fate of most ammonia) occurs mostly in the

mitochondria of liver cells

One amino group enters the urea cycle as (?), which is formed in the mitochondrial matrix

carbamoyl phosphate

One amino group enters the urea cycle as (?), formed in the matrix by transamination of oxaloacetate and glutamate, then is moved to the cytosol

Bonus: what enzyme catalyzes the transamination?

aspartate

aspartate aminotransferase

The four main steps of the urea cycle

1. First amino group: Ornithine + carbamoyl phosphate → citrulline → cytosol

2. Second amino group: Argininosuccinate formed via citrullyl-AMP intermediate

3. Argininosuccinate → arginine (+ fumarate → TCA)

4. Urea + ornithine

(#?) amines are required for the synthesis of urea by hepatocyte, which come from (AA?)

2, glutamine or glutamate

Urea Cycle: Activation Step

Enzyme:

Product:

Starting Material:

Cofactors:

Matrix or Cytosol?

carbamoyl phosphate synthetase I

carbamoyl phosphate (an amide)

NH₄⁺ (ammonia) + HCO₃^- (bicarbonate)

2 ATP

Matrix

The Carbamoyl Phosphate Synthetase I Reaction (3 steps)

ATP + Bicarbonate → carbonic-phosphoric acid anhydride + NH₃ → carbamate + ATP → carbamoyl phosphate

1. Phosphorylation of bicarbonate

2. Ammonia substitutes P_i

3. Phosphorylation of carbamate

What is the first committed step of the urea cycle?

Mitochondrial synthesis of carbamoyl phosphate, catalyzed by carbamoyl phosphate synthetase I

Urea Cycle: Step 1

Enzyme:

Product:

Starting Material:

Cofactors:

Matrix or Cytosol?

ornithine transcarbamoylase

citrulline + P_i

ornithine + carbamoyl phosphate

X

Matrix → Cytosol (citrulline is transported OUT)

mitochondrial antiport

citrulline/ornithine

Urea Cycle: Step 2

Enzyme:

Product:

Intermediate?

Starting Material:

Cofactors:

Matrix or Cytosol?

arginosuccinate synthetase

arginosuccinate

citrullyl-AMP intermediate

citrulline + aspartate

ATP

cytosol

One molecule of urea requires hydrolysis of (?) ATP molecules

3 ATP

The Argininosuccinate Synthetase Reaction (Two Activation Steps)

ATP + citrulline → citrullyl-AMP + aspartate → argininosuccinate + AMP

1. ATP + citrulline → Citruyll-AMP intermediate

2. Aspartate substitutes AMP

Urea Cycle: Step 3 - Connected to TCA

Enzyme:

Product:

Starting Material:

Cofactors:

Matrix or Cytosol?

argininosuccinase

arginine + (fumarate → malate → TCA)

argininosuccinate

X

cytosol

Urea Cycle: Step 4 - The Big One!

Enzyme:

Product:

Starting Material:

Cofactors:

Matrix or Cytosol?

arginase

urea + (ornithine → matrix for urea cycle)

arginine

X

cytosol → matrix

Where is carbamoyl phosphate synthetase I located?

hepatocyte mitochondria

4 mitochondrial enzymes of the urea cycle

1. glutamate dehydrogenase

2. aspartate aminotransferase

3. carbamoyl phosphate synthetase I

4. ornithine transcarbamoylase

3 cytosolic enzymes of the urea cycle

1. argininosuccinate synthetase

2. argininosuccinase

3. arginase

glutaminase releases

NH₄⁺ from Q (glutamine)

aspartate aminotransferase transfers the amine group from

glutamine to oxaloacetate to create aspartate

carbamoyl phosphate synthetase creates

carbamoyl phosphate from bicarbonate, ammonia, and ATP

ornithine transcarbamoylase couples

carbamoyl phosphate and ornithin to make citrilline

argininosuccinate synthetase couples

citrilline and aspartate to form argininosuccinatea

rgininosuccinase cleaves

arginionsuccinate into arginine and fumaratear

arginase cleaves

arginine into ornithine and urea

(?) concentration needs to remain low to drive the TCA forward

oxaloacetate

aspartate-argininosuccinate shunt

links TCA and urea cycle

the three main one-carbon transfer cofactors

1. biotin

2. tetrahydrofolate

3. S-adnosylmethionine

biotin carries carbon as

CO₂ or carbonic acid

tetrahydrofolate (THF or H₄ folate) carries carbon in

intermediate oxidation states