BB451 Unit 3

Which type of protien degration if most active under conditions of nutrient starvation

lysosomal degration (autophagy)

Lysosomal degration uses what to break down extra and intracellular components

acidic hydrolases

humans are

ureotelic

the fate of the maority of AAs generated from protien degration are used for and how are they broken down

protien synthesis or energy produdction.

they are broken down throigh the lysosoal pathway of protien degration, with 2 major lysosomal based pathways. lysosome are organelles with low pH, and cathepsins (proteases that break down protiens)

1) endosome-lysosome pathway: extracellular protiens broken down by lysosomes after entering the cell via endocyosis, stores in a phagosome.

2) autophagy: cytoplasmic protiens adn damadges organelles are degraded by lysosomes

how would you experimentaly determin if certain circumstances affects the half life of your protien of interest

western blot/ immuno blot of normal half life and then the half life of the circumstances and compare

explani the ubiquitin-protease pathway

goal: puts a long chain of individual ubiquitin molecules to form a longer chain or “flag” to mark a protien target for degration.

The stps are Uniquitation ( 1. activation, 2. conjugation, 3. litigation) and Deubiquitination (4. proteoalysis)

Ubiquination

1) Activation: ubquitin is activated by E1.

2) Conugation: the ubiquitin is then conugated to E2.

3) Litgation: E3 will ligate the ubiquiton from E2 onto the target protien. The protien (still attached to to the ubiquitin chain is chaperones to a proteosome by a chaperone protien .

Deubiquination- ubiquitin breaking off to fo their job elsewhere

4) The protien will be unfolded by going through the protease barrel, which turns the protien into peptides and AA. the ubiquitins leave.

Where do we get pools of amino acids from, and where do they go

Get from 1) Diet via protiens 2) breaking down existing cellupar protines into AAs to reuse 3) De Novo AA synthesis, can only make certain AAs

Where do we use them:

-Energy prod

-synth of glucose or FAs

-synth of non-protien molecules that contain nitrogen

If you have a high prptien and low carb/fat diet, how do you get your energy?

1) glucogenetic AA catabolism: converted to glucose via gluconeogenesis

2) Ketogenetic AA catabolism: converted into ketone bodies via ketogenesis

How are amino acids catabolized for energy and what happens to the excess AAs

protiens are broken down into pools of AAs. excess AAs cannot be stored, so instead they are pieced apaert into a) carbon skeletons and b) Ammonia NH4+

-carbon skeletons: the alpha-keto acid form of AAs (no amine groups, these groups go to option 2: ammonia) to be fed into CAA to make oxaloacetate (gluconeogenesis CO2, H2O and ATP products also made which can be sent to urea cycle.

-Ammonia : amine groups from AAs can go to synthesize anything (such as other AA, nucelotides or biomol) that the cells may need, or to make CARBAMOYL PHOSPHATE to enter the urea cycle to make urea for nitrogen to be extrcreted via urine

Unneeded amine groups generally are used, ,broken into carbon skeletons or into ammonia for elimination

Explain transanimation reactions and the ping pong or double displacement reaction, give example

the transfer of alpha-amine groups to alpha-ketoglutarate.

summary: the amino group from an AA is bound to PLP. The aa will leave the amine group and take up O, converting the aa to its alpha-keto acid form. The amine group attached to PLP is donated to the alpha-ketoglutarate to form glutamine. PL P is regenerated as before.

-Alpha-ketoglutarate: acts as primary amine grop acceptor and turns into glutamate

-Alpha keto acid: acts either as the initial donor left over carbon skeleton or as a specific alt acceptor molecule

1) remove alpha-amino group (contains nitrogen) via transferring it to the alpha ketoglutarate, which will become glutamate via AMINO TRANFERASE.

The AA is deaminated to its alpha-keto acid analogue. (ping pong method)

Ping-pong/double displacement is when two reactions do not happen at the same time. Reaction B cannot be complete until a certain part of reaction A is completed.

example of ping pong is converting trypophan to pyrvate

1) tryptophan is converetd to alaline

2) alpha-ketoglutarate will be brought in and will become glutamate via ALANINE AMINO TRANSFERASE (plp)

3) the alanin will become pyruvate (left over carbon skeleton from AA trptophan) to go into the CAC, be turned into acetyl-coa, etc.

COFACTOR USED IS PLP

STEPS:

1) AAs are ctbolized by removing amino groups by transferring ut to alpha keto-glutarate (this becomes glutarate eventally). The deaminated AA is now in its alpha-keto acid catalque.

2) Alpah ketoglutarate is changed to glutamine with the help of PLP

alpha-KG cannot bind to become glutamate until the alpha-keto acid leaves the active site of PLP. THIS IS EX OF PING PONG RXN

PLP=Amino transferase if not an enzyme but a cofactorm and helps convert ammonia to alpha keto caid.

Steps option b

1) PLP is covalently bound ot lysine residue at the actve site of the enzume, H2O is release from this reaction .

2) Amino groups from AA is bound to PLP to make PYRIDOAMINE PHOSPHATE. the aa wil leave the amine group and take up O instead, leaving it as its alpha keto acid form.

3) the amine group attached to the PLP is fonated to alpha-ketoglutarate to form glutamate. PLP is regenerated as before

What does tetrahydrofolate metabolism result in

folate derivatives carrying one carbon units of varying oxidataive states

How do humans get stable nitrogen N2→ NH3 (ammonia)

certain bacterias and organisms sich as cyanobacteria, other species of bacteria that exist in roots of legumes can fix N2 for us. crop rotaions as well.

How do humans get rid of excess ammonia

formation of urea in hepatocyes (liver cells). NH3 is moved from the perpheral tissues to liver for this dispoal bc high levels of ammonia in lood is toxic to CNS

What is PLP

A cofactor used in transamination reactions (not an enyme)

-recieves AAs in transamination reactions

-all aminotransferase use it as a prosthetic group

-coenzyme for Vit B6

What is the purpose of oxidative deamination of glutamate

glutamate ← glutamate DH → alpa-KG

release of nitrogen group in form of ammonia to regenerate alpha-KG

Ammonia will go to urea cycle

what is the purpose of making glutamine from glutamate

easy conversion that can go both ways. uses GLUTAMINE SYNTHASE anf GLUTAMINASE

Ecplain the glucoe alanine cycle

when a muscle runs out of glucose after using all of its glucose stores, the glucose amine cycle will provide more glucose.

Some pyrvate will be. taken up from alanin to convert glutamate ← ALANIN AMINOTRANSFERASE → Alpha-KG.

Alanine can enter the blood stream and go to the liver where it is converted back to pyruvare for gluconeogenesis. this creates glutamate which is used to donate NH4+ to the urea cycle for excretion..

This process is so unique bc you can take AAs anc make glucose from them and send unneeded trogen to the urea cycle for excreation via SPECIAL CONCERTED COOPERATION BETWEEN DIFF CELL TYPES.

The liver in involved

The job of alanine is to act as a safe carrier to transport tocix nitrogen waste and carbon skeletons from skeletal muscles and liver.

What can ALT and AST in blood tell you

ALT: alanine aminotransferase (uses PLP) [alanine + a-KG —ALT→ pyruvate + glutamate]

AST: asparatre amino transferase (uses PLP) [aspartate + alpha-KG —AST→ oxaloacetate + glutamate]

AST and ALT are great biomarkers for liver damagde. dead cells release ALT and AST into blood, so too much ALT/AST can mean there is liver necrosis or other liver issues

What are the iff nitrogenous waste products, which is most efficeint, and why do we get rid of excess nitrogen

urea: mammals (1N)

Uric acid: birds and repltiles (2N)

Ammonia: fish (3N)

Urea is most efficient bc 1) a lot of energy is needed to produce uric acis, not a lot of H2O 2) a lot of H2O but not a lot of energy is needed for ammonia 3) medium energy and H2O is needed for urea.

you get rid of excess nitrogen when there is more AA then an organisms needs. they can pull amino groups off of the carbon skeletons, but there is not much to o with the nitrogen group.

excess AA is converted to

carbon skeleton and ammonia. ammonia is converted to urea for elimation/excretion

Explain the urea cycle

occurs in lievr mitochondria and liver cutoplasm

1) NH4+ + CO2 + ATP —>CARBOMOYL PHOSPHATE 2) carbomoyl phoshate + orithine —> citrulline 3) citrulline (goes to cytocol) + aspartate —> arginisuccinate . 4) arginisuccinate —> arginine and fumerate. (fumerate → malate→ oxaloacetet for gluconegenesis. 5) arginine→ new orthinine and urea 6) urea is elimated but otrhinine is treansported into liver mitochondria to restart cylcle

ORANGE COLORED CATS ALWAYS ASK FOR AWESOME UMBRELLAS

urea and ammonia can travel throgh blood stream.

What is phenylketonuria (PKU)

a rare inherited genetic disorder caused by no PAH enzyme due to mutation. It stops the body from breaking down an amino acid called phenylalanine, which is found in foods with protein and artificial sweeteners. Without treatment, this buildup becomes toxic to the brain and causes severe damage.

Phenylalanine —PHENYLALANINE HYDROXYLASE [PAH} → tryosine

When no PAH: Phenylalanine —PLP, AMINOTRANSFERASE → Phenyllacetate and phenylacetate. both of these products are not usedful for us, and buildup is bad

Resuls in high concentrayion of Phe and low concentration of Tyr , and a build up of phenoalanin.

What important molecules are derived from tyrosine and tyrpophan

tyrosine: L-Dopa => dopamine => norepenephrine => epinephrine

melanin

tyrpophan:

seratonin→melatonin

Explain maple syrup urine disease

There is an error of metabolism causing a high concentrayion of leucine in the brain. this high amunt of luecine wll compete with other AAs in the brain (such as phenylalanine, glutamine, his, met, trp) which will harm brain growth and its ability to produce neurtransmitters and myeline

What cannot be broken down:

-alpha-ketoosocaprior acid KIC

-alpha- ketoisovalerate KIV

-3-Methyl-2-oxopentonoate KMV

The enxyme BRANCHED CHAIN ALPHA-KETO ACID DH COMPLEX (bckdc) is faulty. normally bracnedh chain amino acid intermediates go to the BCKDC to make acetyl-coa and succinyl-coa (these make ketone bodies)

explain homocystinuria, and explan MS and CBS enzymes

a buiild up of homosyctein (which is toxic) caused by an issue in the conversion of homocyseine to cystine, the enzyme CYSTATHIONINE-B-SYNTHASE is mutated, this enzyme uses PLP and catalyzes homocystein to cystein

methonine → homocystein → cyetein

glutathone is derived from cyctiene, 3 AA, which is super important for redoc reactions which detoxifies the body)

MS: methionine synthase

homocystein—MS→ methionine

CBS: cystrathionine B-synthase

homocystein—CBS→ cystathionine—> cystein

Where do we get nitrogen that help build amino acids

glutmate and glutamine

What feedback regulations help cells figure out which AAs to make and help them stay balanced, and waht is synergistic regulation

concerted inhibitoin:

products derived from a bio mol negativly feeds back to the enzyme producing the biomol.this causes synergttic and more additice effects. this controls the rate of various products produces from a bio mol (like seratonin)

ynergistic regulation in biomolecules occurs when two or more molecules (such as proteins, transcription factors, or hormones) interact to produce a combined cellular effect that is greater than the sum of their individual effects

Explain the difference between a nucleotide and a nucleoside

nucleotde: ribose sugar with nitrogen base.

nucleotide: ribose sugar, nit base and phosphate

Adeneine + ribose sugar is adenosine

guanosine

thimidine

cytidine

uridine

purines vs pyrimidines

purines: the purine ring is built directly ontp the sugar.

Source of atoms in purines:

-aspartate

-CO2

-Glycine

-Formate

-amide of glutamine

PYRIMIDINE: C, T, U and orotate

Source of atoms of pyrimidines:

-aspartate

-gultamine

-CO2

The first pyrimidne that is made in the pyrimidine pathway is uTP (we made RNA first bc of the RNA world hypothesis). After that, CTP is made.

Pyrimidines are not build onto the PRPP sugar, instead the orotate ring that us already made is attached to the riose-5-p from PRPPP, then converted to comm. pyrimidine.

What is IMP and how does it relate to AMP nad GMP and explain balacning purines

IMP is a precurosors of ATP and GTP. It stands for inosine monophosphate.

IMP —adenylsuccinate synthase + adenyl succinade lyase —> AMP (USES GTP AS SOURCE OF ENERGY)

IMP—IMP HD and XMP-Glutamine amido transferasde → GTP (USES ATP AS SOURCE OF ENERGY)

This helps balance the synthesis of the two A and G protiens by signaling that is there is enough ATP, ATP production stocks and GMP/GTP will be produced, and vice versae.

Feedback in balancing purines:

Inhibition of PRPP synthesis via allosteric regulation of the enzyme ribose PRPP kinase via ADP/AGP . When there is ecess ATP, this inhibits the production of AMP w/out impacting GMP synthesis.

When there is excess GMP, this inhibits the prodyction of IMP withoyt impacting AMD synthesis.

AMP and GMP will act synergestically in this concerted inhibiton

Explain purine catabolism

This is accomplished throigh AMP and GMP regulating themselves

1) 5’-nucleoide removed the phosphate group from the purine (GMP→ guanosine and AMP→ adenosine) . Guanosine is then cleaved and frees releasing ribose via nucleosidase.

Guanine and adenosine eventually becomes xanthine, and end up as uric acid via Xanthine oxidase to be excreted via urine

Explain the drug alopurinol

allopurinol is an inhibitor for xanthine oxidase. it is used to treat gout (uric acid build up in toas).

Alloprinual — Xanthine oxidase —> oxypurinal, which is a ocmp inhibitor that prevents uric acid producti

rivose -5-phsphate is a 5C sugar from that is developde via PRPP synthetase (PPP→ PRPP)

HOW IS SUGAR RELEASED FROM GUANOCINE TO GUANINE

NUCLEOSIDASE

explain pyrimidine cataolism

when pyrimidines are catabolized, this results in uracil, cytosine and thymine (carbons of cytosine and thymine go to create acetyl-coa to make ketone bodies, whule uracil is converted to succinul-coa which their carbons go to CAC)

this pathway also creates NH4+ which will go for urea synthesis to be excreted

DNA vs RNA

DNA has an H on C2 od the ribose sugar, which means it is deoxygenated

RNA has an OH on the C2 of the ribose sugar.

DNA is more stable and longer lived, while RNA is shorter lives.

RNA nucleotides are made before DNA nuceleotides.

RNA Iis deoxyngenated via Ribonucleotide reductase, which has 2 R1 subuiys and 2 R2 subunits.

R1 subunits have a substrate specificity site (which accepts ATP, dATP, dGTP, and dTTP,) and prumary regulation sites (which accepts aTP and dATP) . thuis tells you which rubstrates are going to be deoxygenized, and certain binding of diff molecules withh ravor the reduction of specific nucletc acids/

R2 has active sites and SH groups, this is where the substrates ADP, CDP, UDP AND GDP will go. here ATP activates the enzymes with dATP inactives it.

ATP.dATP favors reduction of UDP AND CDP

dTTP favors reduction of GDP

dGTP favors reduction of ADP.