Exam 3 BCH4024 UF

4 purposes of endogenous protein turnover

1) removes misfolded proteins

2) removes old and damaged proteins

3) regulates cellular metabolism

4) plays critical role in cell cycle transitions

Ingested amino acids can be digested in what two manners?

Ketogenically and glucogenically

Essential amino acids?

HV MILK FTW (high value milk ftw)

What nonessential AA becomes super essential for children and pregnant women?

Arginine

What two pairs of amino acids have a "this AA becomes essential when this AA is low" relationship?

Tyr:Phe::Cys:Met

What enzyme catalyzes trypsinogen --> trypsin and where is located?

Enterokinase, mucosa of small intestine

What is the key step in digestion?

Trypsinogen --> trypsin cleavage

Name active form, location, and optimal pH of the following:

pepsinogen

trypsinogen

chymotrypsinogen

procarboxypeptidase

pepsin, stomach, low

trypsin, pancreatic secretion to intestine, neutral

chymotrypsin, pancreatic secretion to intestine, neutral

carboxypeptidase, pancreatic secretion to intestine (no pH listed but one -COOH is removed upon zymogen activation)

What enzyme is known as aspartic protease?

pepsin

What digestive enzyme is autocatalytic?

pepsin

Amino acids are transported into the intestinal brush border using what system?

Na+ symporter (powered by Na+ gradient/Na+K+ATPase)

Two major pathways of protein turnover?

Lyso/phagolysosomal proteases: acidic compartments where proteins go through isoelectric expansion which makes them more susceptible to proteolysis

Ubiquination pathway: ubiquinates proteins which are then sent to proteosomes

Negative nitrogen balance occurs during what

starvation, malnutrition, disease, burns, trauma, surgery, etc

Features of marasmus?

-edema

-Protein-Energy Malfunction resulting from inadequate consumption of both proteins and calories

-Point of No Return

-must treat both symptoms and resulting complications

features of Kwashiorkor?

-acute childhood protein malnutrition

-abdominal edema (defining feature)

-insufficient protein intake but adequate caloric intake

-linked to lack of micronutrients and antioxidants

What amino acids can transanimases not bind and why?

proline and hydroxyproline are cylical and thus the amine group can't be removed

the products of lysine and threonine deanimation are toxic and thus transanimase can't bind them

What cofactor is required for transanimation?

pyridoxal phosphate (PLP) (derived from vitamin B6)

What role does pyridoxal phosphate play in transanimation?

It is attached to transanimase and serves to accept the amine group from the donating amino acid. It is then turned into PMP, pyridoxamine phosphate, and donates the amine group to the receiving alpha-keto-acid, turning it into an amino acid and turning itself back into PLP

(T/F) transanimase reactions are fully reversible and their Keq is one

T

T/F you can obtain ammonia from transanimation reactions

F

What gets reduced in deanimation reactions?

NAD+

Where does glutamate get oxidized in deanimation?

the mitochondrial matrix

The availability of what determines the direction of glutamate dehydrogenase?

NAD+ in one direction, and NADPH/NH3 in other

NAD+ drives GDH in which direction?

Oxidative deamination of glutamate

GDH uses NADPH or NADH to make glutamate?

NADPH

You just ate a big meal. What is the status of GDH in your body?

Big meal = much ATP, much NADH, so GDH is inhibited

Why do we need D-amino acid oxidases?

Generates H2O2, which is used to fight bacteria

D-AA in old food/proteins

What coenzyme do D- and L-AA oxidases use?

FMN

Breakdown of Q by glutanimase yields what?

NH3 and glutamate

Glutanimase and asparginase are enzymes that catalyze what type of reaction?

hydrolytic deanimation

Histidinase is an enzyme that catalyzes hydrolytic deanimation T/F?

false, it catalyzes eliminative deanimation

What four processes catalyze ammonia assimilation?

1) formation of glutamate using NADPH, NH3 and alpha keto glutarate

2) glutamine synthetase

3) carbamoyl phosphate synthetase 1

4) carbamoyl phosphate synthetase 2

T/F Q is a major nitrogen source in many biosynthetic reactions

T

Glutamyl-P is an intermediate in what biosynthetic reaction?

Formation of glutamine through glutamine synthetase

What enzyme is highly abundant in E. coli?

Glutamine synthetase

What residue is right out GS's active site?

Tyrosyl

The hydrolysis of PII-UMP will raise or lower glutamine levels?

Lower - PII will bind to adenyl transferase and deactivate GS

High levels of ATP will raise or lower glutamine levels?

Raise - ATP activates uridylation of adenyl transferase, which results in deadenylation of GS, which results in more glutamine.

This also makes sense because GS uses ATP to synthesize glutamine, so high levels of ATP will drive the reaction forward

An ammonia transfer tunnel is used in the synthesis of carbamoyl-P using carbamoyl-P synthetase 1 T/F

F, the tunnel is used in carbamoyl-P synthetase II

T/F both carbamoyl synthetases use ammonia to synthesize carbamoyl-P

F, only carbamoyl synthetase I uses it

CPS-I is located in the ______ and CPS-II is located in the

mitochondria, cytosol

T/F CPS-II is part of the urea cycle

false, it is part of the pyrimidine nucleotide pathway. CPS-I is part of the urea cycle

CPS-I is activated by which two molecules?

N-acetyl-glutamate, ornithine

Why is high NH3 accumulation detrimental?

Large amount of NH3 affects proton gradients

It also depletes the amount of alpha keto glutarate (an essential TCA cycle intermediate) by means of GDH, GS

Describe the Urea Cycle

Carbamoyl-P is formed in the mitochondria through CPS-I. It reacts with ornithine to form citrulline using ornithine transcarbamoylase. Cirtulline then reacts with aspartate to form argininosuccinate using argininosuccinate synthetase. Then, the molecule is split into arginine and fumarate using argininosuccinate lyase. Arginase hydrolyzes arginine back into ornithine and urea, and the urea cycle can begin anew.

Does a high or low protein diet stimulate the urea cycle?

High

What hormone induces urea cycle intermediate formation?

Glucagon

The high presence of what two amino acids indicate high amino acid levels in a cell?

Arginine and glutamate

N-acetyl glutamate synthase is allosterically activated by what?

Arginine

What does N-carbamoylglutamate do?

Acts as an N-acetyl glutamate analog to restore urea cycle function

What two phenomenons in the acinar space of the liver serve to consume ammonia?

Urea cycle enzymes and glutamine synthetase

Do periportal hepatocytes have a low or high affinity for ammonia?

Low

Do perivenous scavenger cells have a high or low affinity for ammonia?

High

From what sources do we get arginine from?

1) as a urea cycle intermediate

2) diet

3) recycled cell proteins

What glutatmate-producing enzyme is found only in microorganisms?

Glutatmate synthase

What are the three ways humans can make glutatmate?

1) transanimation (gets amine from a different AA)

2) glutamine hydrolysis (uses H2O)

3) glutamine reductive animation (get amine from NH3, uses NADPH)

What TC cycle intermediate is used to form aspartate? What enzyme catalyzes this reaction?

oxaloacetate, transaminase

Asparaginase does what?

Catalyzes hydrolysis of asparagine to form aspartate

What are the functions of the two active sites in aspargine synthetase?

1) removal of amine from E

2) makes acyl-AMP intermediate and facilitates acyl-AMP attack using NH3

Interorgan transfer of ammonia as an amine group in what AA prevents NH3 toxicity?

Alanine

T/F alanine can be formed from pyruvate using reductive animation?

False, it can only be formed from transanimation of pyruvate

What is the key step in the synthesis of proline?

Reduction of glutamate to glutamate semi-aldehyde

What intermediate in the formation of proline can be converted to a urea cycle intermediate?

Glutatmate semialdehyde

T/F NAD+ is used as a cofactor in the synthesis of proline from glutamate

False, NADH is used

T/F there are more than two routes for serine synthesis

F, there are only 2

T/F serine can be made directly from pyruvate

F, it's made from 3-phosphoglycerate

T/F there only three ways to make glycine

false, there are much more

Phenylketonuria results from a lack of what enzyme?

Phenylalanine hydroxylase

T/F phenylalanine hydroxylase uses NADPH as a cofactor

False, it uses THB and diatomic oxygen

What is the rate of phenylketonuria in the population?

1/11,000 births

T/F S-adenosyl homocysteine has a methyl group attached to its sulfur atom?

False, methyl transferase removed it from S-adenosyl methionine

What reacts with homocysteine to form cystathionine during the synthesis of cysteine?

serine

T/F alpha keto glutarate is seen in the synthesis of cysteine

false, alpha keto butarate is seen

Thyroxin biosynthesis uses phenylalanine or tyrosine?

Tyrosine

Can biosynthesis of thyroxine occur on free AA?

No

What is the name of the enzyme that thyroxine synthesis occurs on, and how big is it?

Thyroglobulin, 660 kDa

T/F tri-iodothyronine stimulates and inhibits gene transcription

T

T/F tri-iodothyronine enters our cells via facilitated transport

F, it uses active transport

T3 is more likely to stimulate glucose breakdown or synthesis?

Synthesis (it stimulates metabolism to produce more glucose from glycogenolysis, gluconeogenesis; causes cell to increase uptake of glucose. It also stimulates increased O2 uptake and ATP hydrolysis)

What are the three neurotransmitters derived from AA and what AA are they derived from?

GABA, from glutamate

dihydroxyphenylalanine, from phenylalanine

Serotonin, from tryptophan

The first step of heme biosynthesis occurs where?

Mitochondrion

Heme biosynthesis requires the use of what TCA intermediate?

succinyl-CoA

The two reactants in the first step of heme biosynthesis combine to make what?

ALA (gamma-aminolevulinic acid)

What amino acid is a reactant in the first step of heme biosynthesis?

Glycine

What enzyme catalyzes the first reaction of heme biosynthesis?

ALA synthase

Without an iron atom, what is heme?

Protopophyrin IX

What enzyme inserts what oxidation state of iron to form heme in the final step of heme biosynthesis?

Ferrochelatase, Fe(II)

In addition to inhibiting heme synthesis, the lead ion also does what to damage cells?

Catalyzes DNA strand cleavage

What enzymes breakdown DNA/RNA upon ingestion?

Endonucleases, phosphodiesterases, nucleoside phosphorylases

On what carbons are the phosphates of PRPP located?

5 and 1

What enzyme catalyzes the formation of PRPP

PRPP synthetase

T/F nucleotide biosynthesis occurs at the same rate throughout all cells in our body, on average

False, major organ for producing nucleotides is liver

T/F the first nucleotide constructed in purine biosynthesis is xanthanine

False, it is inosine 5'-monophosphate

Tetrahydrofolate provides what in purine synthesis?

one carbon moieties

Where does the NH3 that reacts with PRPP in the first step of purine synthesis come from?

Glutamine, uses ammonia transfer tunnel

What reacts with PRbNH2 in the second step of purine biosynthesis?

Glycine, uses ATP

T/F FGAR is seen towards the end of purine synthesis?

False, it is the product of the third step

T/F By the time a second NH3 transfer tunnel is used in purine synthesis, a ring structure can be seen in the forming purine

F, this occurs just before the closure of the first ring

Just before the first ring is closed in purine synthesis, an NH3 replaces one of two carbonyls. Does it replace the carbonyl closed or farthest from the ribose sugar?

Closest, the farthest carbonyl is lost during the first ring closure

The first structure in purine synthesis in which is ring is evident is called what?

amnioimidazole ribonucleotide