Exam 2

needed for normal operation of metabolic pathways and main cellular functions, such as AA, DNA, RNA

not needed for life. Important for drugs and plants. not needed for cell growth, development or reproduction. Ward off pathogens and predators, protect against osmotic damage.

Phe, Val, Thr, Trp, Ile, Met, His, Leu, Lys

conditional AA during growth

condition AA if Phe is low

conditional AA if Met is low

have ways to make gultamate and other non essential amino acids. Can break down to make amino acids if too much metabolic stress. Each organ has a different metabolism

primarily hydrophobic AA because they get heated quickly

Liver makes a lot of AA, Brain makes lots of Q

Created after proteolysis in stomach due to low pH. Low pH protonates all proteins, have either positive or neutral charge which causes proteins to repel each other and open up. Now easy to cut.

Mainly contains proteases from bacteria and WBC, not much going on.

in stomach; cleaves after Phe, Leu, and Glu linkages. ACRONYM: ELF

in intestine; cleave on carboxy side of peptide bond of aromatic residues

in intestine; cleaves on carboxy side of lysine and arginine residues

in intestine; cleaves C-terminal AA

in intestine; cleaves elastin

Protein fragments all cut up from Pepsin, cannot refold

After the small intestine

No, proteins are seen as foreign bodies. You do not want the body to overreact, so proteins must be proteolyzed to AA, Di/Tri peptides. Larger structures are not important in circulation

inactive form of proteases. Stored and made in pancreas. Activated after secretion into small intestine to protect pancreas. Prevents autophagy and apoptosis

zymogen of trypsin. Made in pancreas and stored in vesicle with trypsin inhibitor

Prevents unwanted proteolysis of host cells

ectoprotease on intestinal mucosal wall that converts the zymogen to active form of trypsin

activated to form carboxypeptidase, which removes AAs one by one from C-terminus of food protein

Protease would bind to other protease thinking it is a protein substrate, causes health issues

Zymogen synthesis, processing and transport in ribosome of rough ER, go to golgi for vesicle targeting and release

autocalalytic, meaning once pepsin forms, it catalyzes cleavage of pepsinogen to make more pepsin. Slow activation by stomach

pepsin operates at low pH by using its aspartic acid carboxyl groups for catalysis

pepsinogen is formed and released in these cells within stomach

When nitrogen intake is low, protein degradation is high because cells need amino acids to make essential proteins. Two paths, either lysosomal or ubiquitin pathway

Lysosome is acidic, proteins undergo partial unfolding via isoelectric expansion. This makes proteins more susceptible to proteolysis. ATP-dependent pump H+ into this compartment to make this proton gradient.

After chaperonins have failed to help guide protein folding, ubiquitin is enzymatically joined to misfolded protein. Ubiquitin is ticket to get into proteasomes, which is a barrel-like protease complex. Gets stuck and degraded.

High Na+, and AA

growth, healing of wounds, convalescence intake>excretion

starvation, malnutrition, disease excretion>intake

Not enough protein of kcals causing extensive tissue and muscle wasting with no edema. hair stays for little warmth

Enough kcal but not enough protein in diet. Causes irritability, enlarged liver due to fatty infiltrates from high carb diet, and edema caused by hypoalbuminemia.

has an aldehyde group

has a primary amino group which preserves the energy from the peptide bond of amino acid 1 in the first half reaction

Form aldimine (aldehyde but instead carbonyl have N bonded to CH), which gets converted to ketimine and hydrolyzes to ketoacid

Ketimine goes to aldimine. Just the reverse of reaction 1 but using R2-KA to make R2-AA.

has the same bonding in products as in substrate, hence a Keq of 1. Transpose the ketone and the amino group to opposing molecules.

Proline, hydroxyproline because too many carbon bonds due to secondary amines Lysine and Threonine because they would form toxic metabolites

Regenerates a-Ketoglutarate as an amino acceptor and provides ammonia for either reutilization or disposal as urea

located in the mitochondria, master control Uses Glutamate, NAD+, and H2O to make a-Kg and NH3

oxidized form

reduced form

makes 3 ATP

allow cells to manage chemical energy, can help to reduce other molecule

Oxidized so efficiently that nothing is around, mainly NAD+ in the mitochondria for GDH to use.

Pro, Hyp, Thr, Lys, His

Oxidative phosphorylation in the mitochondria

Urea cycle

All enzymes would have to be like GDH. A mutation would cause death due to nitrogen accumulation being toxic

NAD+ levels are really high due to NADH oxidation making ATP in mitochondria. ONLY FORWARD Therefore, there is... Excess NAD+ + Glu -> a-Kg+NH4 + low NADH

Other pathways generate tons of NADPH to make fatty acids, sterols, and more. ONLY REVERSE. Therefore, there is... low NADP+ + Glu <- a-kg+NH4+excess NADPH

Inhibits GDH since this favors protein synthesis (use ATP to make peptide bonds), reduces AA degradation. Not oxidizing AA

Activate GDH. These conditions indicate there is little energy in the body. a-kg stimulates Krebs Cycle, which fuels ETS and Oxidative Phosphorylation.

A low pH

High pH. Think basic bonditions, want to be ammonia and not a ketone

Enzyme is not regulated and produces H2O2, which is highly toxic to body.

Don't want to waste energy bonds in D-AA. Protein ages, forms D isomer. Also has a antibacterial affect since D isomers are found in bacterial wall.

AA+O2-> a-ketoacid +NH4++H2O2, uses FMN

hydrolysis of glutamine to deaminate. Occurs in mitochondira to not interfere with glutamine synthetase. Makes ammonia that is sent to urea cycle Q+H2O-> E+NH3

catalyzes hydrolysis of Asn, deamination Asn+H2O->Asp+NH3

metabolically incorporate ammonia to keep concentration low since high concentrations are toxic

NH3 can easily pass membrane because it is neutral and steal protons that are there to maintain proton gradients. They can also deplete a-Kg because NH3 can drive the GDH reaction, which is needed for the Krebs Cycle which can interfere with ATP production.

GDH (reverse rxn with NADPH), Glutamine Synthetase, and CPS-1

In the cytosol to prevent a futile cycle with GDH

ATP+NH3+Glutamate->Glutamine+Pi+ADP+H+

Glutamine synthetase

Shuttle it around as Gln, never want to have ammonia in the circulation to prevent inducing a coma, protect the brain

Glutamine

phosphorylates negative O in E to make a better leaving group and drive ammonium ion deprotonation at neutral pH

1 to add a phosphate to make a better leaving group and 1 to use NH3 as a nuc to attack carbonyl

Use ∆G from ATP hydrolysis to deprotonate, and use arginine, with a pKa of 12, to manipulate the pH near NH4 to deprotonate right before the reaction

∂-glutamyl-P, which is just a phosphorylated glutamate

Mitochondria, need it to be there to make it for the urea cycle (for ornithine)

2 ATP+NH3+HCO3--> 2HN(C=O)-O-P+ Pi+2ADP+H+

Phosphorylate bicarb in step one to form carboxyl P as the intermediate which immediately gets attaked by NH3 to kick P off. Carbamate gets phosphoryalted again into final product

Allows glutamine dependent biosynthetic enzymes to generate ammonia in active site. That ammonia is then used as a nuclephile, without ever touching water so it cannot get protonated.Transfer ammonia to another nuc, will never touch water and won't go back to ammonia

Cytoplasm, site of pyrimidine nucleotide synthesis

Hydrolyzing glutamine to deprotonate NH3 exactly where and when it is needed, and avoids toxicity of ammonia elsewhere in our cells

Molecular weight of ammonia is lower than that of water. Also, water always bundles up to other water molecules unless at 100C, and a single one can't get into skinny tunnel. Tunnel is also hydrophobic.

Hydrolyzes Gln to Glu+NH3. The essential -SH group generates a y-glutamyl thiolester that occupies the active site, permitting NH3 to transfer quicker.

Unique to particular biosynthetic enzyme

Covalently bound E

N-Acetyl-Glutamate

NH3

NH3-excreting, fish just swim away

Uric acid secreting, like birds. Highly oxidized

Urea excreting

Too much uric acid

Liver

Urea, Glu, Gln, Ala