Amino Acids

  1. Where are amino acids stored?  Where are amino acids obtained from? (3)
    Amino acids are not stored anywhere in the body.

    Amino acids are obtained from diet, de novo synthesis, or produced from normal protein degradation. 
  2. Define protein turnover.

    What is the rate of protein turnover in healthy adults? aka?
    Protein turnover: the simultaneous synthesis & degradation of protein molecules. 

    Its constant: rate of syn = rate of degradation.

    AKA nitrogen balance!
  3. What is a knockout mouse? What is the purpose?
    KO mouse: genetically engineered mouse in which researchers have inactivated an existing gene and replaced/disrupted it with artificial DNA.

    Purpose: Important for studying functions of genes that have been sequenced.
  4. What are the half lives for and general names for:
    1. Regulatory proteins/misfolded proteins?
    2. Majority of proteins in cell?
    3. Structural proteins? No general name.
    • 1. Short-lived proteins; minutes/hours
    • 2. Long-lived proteins; days to weeks 
    • 3. Structural proteins; months to years. 
  5. How do you make a knockout mouse? (6 steps)
    • 1. Target specific gene to eliminate exons & insert Neo gene for selection
    • 2. Without exons, gene codes for defective protein.
    • 3. Select embryonic stem cells that contain the targeted defective gene by growing with antibiotic. Cells WITH Neo (neomycin) will grow. Cells w/o will die. 
    • 4. Inject ES cell into blastocyst
    • 5. Implant blastocyst into pseudo-pregnant mouse
    • 6. Mouse will have some tissues derived from targed ES cells. Need targeted gonads to mouse will give birth to KO pup.
  6. What can amino acids from dietary proteins metabolize to? (4)
    • 1. Proteins
    • 2. Urea (excreted in urine)
    • 3. Ammonia - used in synthesis of AA, nucleotides, biological amines, or excreted in urine.
    • 4. A-keto acids - intermediates in metabolism. 
  7. Where do amino acids come from? Where do they go? (3 each)
    From: dietary protein, de novo synthesis of nonessential protein, and protein breakdown from body.

    Goes to: synthesis of body protein, amino acids consumed as precursors of essential N-containing molecules and conversion of AA to ketogenic, gluconeogenic (glucose, glycogen, FAs, ketone bodies, or CO2+H2O). 
  8. Where can free amino acids be found? 3
    In cells, blood and EC fluids
  9. What compounds for energy can be made from AAs? 5.
    • 1. Glucose
    • 2. Glycogen
    • 3. FAs
    • 4. Ketone bodies
    • 5. Doesn't really count, but CO2 + H2O.
  10. What is ALT? What does it do? What does it stand for?
    ALT = alanine amino transferase

    Converts pyruvate into alanine (amino acid) or vice versa (gluconeogenic), while converting glutamate to a-ketoglutarate.
  11. What kinds of processes can amino acids undergo  (4)
    • 1. Pyruvate
    • 2. Ketogenesis (lysine & leucine only). Produce acetyl CoA or acetoacetyl CoA CANNOT TURN INTO GLUCOSE. 
    • 3. Gluconeogenesis
    • 4. Oxidation - during starvation, the reduced C skeleton is oxidized to CO2 and H2O thereby producing ATP.
  12. What happens when amino acids undergo oxidation?
    During starvation, the reduced C skeleton is oxidized to CO2 and H2O thereby producing ATP.
  13. Which are the glucogenic and ketogenic AAs? (5)
    Isoleucine, phenylalanine, threonine, tryptophan, and tyrosine. 

  14. What are the two ketogenic amino acids? What can they turn into? Can they turn into glucose?
    Lysine & leucine

    Produces acetyl CoA or acetoacetyl CoA

    NO, they are solely ketogenic. 
  15. What makes an amino acid essential? (2)

    What are the 3 essential amino acids?
    • 1. Cannot be synthesized by humans at all
    • 2. Cannot be synthesized in sufficient amounts by humans. 

    Arginine (urea synthesis), methionine (cysteine), and phenylalanine (tyrosine). 
  16. Under what dietary condition would tyrosine become essential?

    How about cysteine?
    Tyrosine: If not enough phenylalanine is consumed

    Cysteine: if not enough methionine is consumed. 
  17. What disease would make tyrosine essential?
    PKU --> cannot process phenylalanine, so put on a phenylalanine restricted diet, so tyrosine becomes essential. 
  18. How many g of protein are turned over daily? 

    How many g of protein are secreted as digestive enzymes or lost daily from sloughing of the gut epithelial cells?
    400 g turned over daily

    20 g of protein --> digestive enzymes or lost from sloughing of gut epithelial cells. 
  19. Define:
    Steady state
    Positive N balance 3 ex
    Negative N balance 2 ex
    Steady state: rate of protein syn = rate of protein degradation

    Positive N balance: rate of protein syn>rate of protein degrad (growth, pregnancy, and recovery from illness). 

    Negative N balance: rate of protein syn < degradation (illness, starvation). 
  20. How are amino acids digested and absorbed? Where do they go after absorption?
    Proteins are hydrolyzed to AA by pepsin (stomach protease) & pancreatic enzymes (chymotrypsin & trypsin), 

    Absorption: AA are absorbed into hepatic portal blood, taken up by liver, and either used or shuffled elsewhere.
  21. How are proteins degraded? 3 main ways
    1. Lysosomes (ATP indep degradative enzyme systen of the lysosomes)  - general housekeeping, routine degradation of proteins from EC cells via phagocytosis & cell receptors

    2. Autophagy - last resort (prevents cell death by recycling noncritical proteins & uses AA to synthesize more important proteins).

    3. Ubiquitination - tags proteins for degradation (ATP-dep) in cytosol. Ubiquitin-proteasome system. 
  22. Explain how ATP-dep ubiquitination degrades proteins (4 steps). 

    What happens to ubiquitin? What is the last enzyme used?
    • 1. Ubiquitination: Proteins to be degraded are first covalently attached to ubiquitin.
    • 2. Ubiquitinated protiens are recognized by cytosolic proteasome
    • 3. Proteasome unfolds, deubiquitinates and transports protein to its proteolytic core (ATP dep). 
    • 4. Peptide fragments produced by proteasome are degraded to AA in the cytosol. 

    Ubiquitin is recycled. The last enzyme: non-specific proteases that split peptide fragments into amino acids. 
  23. Which enzyme degrades endogenous proteins? Which enzymes degrade primarily extracellular proteins? Another name for the enzyme?(2 ex for 2nd one). 
    Proteasomes degrade endogenous proteins

    Lysosomal enzymes (acid hydrolases) degrade EC proteins

    ex. plasma proteins taken into cell by endocytosis & cell-surface membrane proteins that are used in receptor-mediated endocytosis. 
  24. How selective are lysosomes in healthy cells?

    What do lysosomes do during prolonged fasting?
    In healthy cells, lysosomes are non-selective.

    During prolonged fasting, a special pathway is activated that selectively degrades cytosolic proteins containing a Lys-Phe-Glu-Arg-Gln pentapeptide sequence. 

  25. What is the function of autophagy? 3

    What is the mechanism?
    Function: (1) degradation of cellular proteins/organelles (2) to recycle nutrients (3) or break down damaged/toxic materials. 

    Vacuole forms around cytoplasmic constituents and fuses with lysosomes where contents are degraded by vacuolar hydrolases and proteases. 
  26. What is half-life influenced by for an amino acid?
    The N-terminal amino acid. 
  27. Does autophagy use lysosomes?
  28. What happens to autophagy during nutrient starvation? What does it prevent?
    Autophagy increases.

    Increases breakdown of nonvital proteins, releasing nutrients, ensuring vital processes can continue.
  29. What does rapamycin do? On which protein? Where was it found? What does rapamycin activate? What does it inhibit?
    Rapamycin suppresses immune system and is valuable for transplant surgeries by acting on mTOR (mammal target of rapamycin). 

    Found on Easter Island

    Rapamycin activates autophagy and inhibits mTOR.
  30. What is mTOR? What is it activated by? What is blocked by?
    mTOR (mammalian target of rapamycin) cell growth regulator that integrates growth factor & nutrient signals. 

    • Activated by insulin & AA --> promotes growth
    • Inhibited by rapamycin and nutritiond deficit.
  31. Describe the mechanism of autophagy (4)
    • 1. Induction - external stimuli (starvation, nutrient depletion, ischemia, rapamycin) inhibits mTOR.
    • 2. Autophagosome formation - cytosolic proteins/organelles are sequestered by a 2xmembrane vesicle (maybe from ER?)
    • 3. Docking and fusion with the lysosome
    • 4. Breakdown  of autophagic vesicle and relase of contents (AA, nutrinets, etc) for recycling in cell.
  32. What activates autophagy? (2) Deactivates it? (3)
    Autophagy is activated by rapamycin and starvation/nutrient depletion

    Inhibited by mTOR (which is activated by insulin/AA). 
  33. Where are proteasomes found? What do they do? (2) -2 examples of second function.
    Found in nucleus & cytoplasm

    Degrade unneeded/damaged proteins and respond to cellular stresses (infection or oxidative damage). 
  34. What is responsible for controlled/programmed protein degradation?
    Ubiquitin-proteasome degradation process
  35. What elevates rate of protein degradation?
    • 1. Attachment of additional ubiquitin molecules
    • 2. N-terminal residue (met/pro = slow; arg/leu = fast)
    • 3. Presence of PEST sequences (Pro-Glu-Ser-Thr) speed up process. 
  36. Which protien degradation pathway requires energy?
    ubiquitin-proteasome degradation.

    lysosomal does NOT require ATP. 
  37. What are the 3 functions of lysosomes? 2 examples for 2nd and 3rd function. 
    • 1. Digestion of autophagic vesicles
    • 2. Phagocytosis (ingestion of other dying cells/EC material)
    • 3. Endocytosis (recycling of cell-surface receptors, LDL)
  38. What are the 6 outputs of amino acid pool?
    • 1. Body protein (400 g/day)
    • 2. Glucose
    • 3. CO2+ATP
    • 4. Ketone bodies/FAs/steroids
    • 5. Synthesis of purines, pyrimidines, NTs, porphyrins, creatinine
    • 6. Urea cycle
  39. What amino acids can carry ammonia? From where to where?
    Glutamine & alanine are carriers of NH3.

    From muscle/tissues to liver. 
  40. Where are amino acids metabolized?
    TRICK QUESTION. Mostly liver, but branched amino acids (isoleucine, leucine, valine) are preferentially metabolized in MUSCLE.
  41. When will AA undergo degradation? When will AA undergo GNG? What is the goal of AA degradation and what happens to the products (1, 3)
    AA undergoes degradation when AA intake exceeds biosynthetic needs. AA undergoes GNG when protein is needed as a fuel source.

    Goal: to separate a-amino group from C skeleton and shunt each into specialized pathways. 

    Amino group --> liver --> urea; C skeleton --> pyruvate, acetyl CoA or TCA intermediates. 
  42. What does transamination require? (2)
    B6 (pyridoxal phosphate) as intermediate & transaminase
  43. What is the predominant acceptor of a-amino groups from almost all AAs? Except? (2)
    A-ketoglutarate, except lysine & threonine. 
  44. Do B vitamins increase your energy?
    They help facilitate creation of energy, but they play an indirect role, so in themselves, do not create energy.
  45. What does AST stand for? What is its corresponding a-keto acid?

    What does it transfer amino group from - to? What does this form? For what cycle?

    Is it reversible?
    AST: Aspartate aminotransferase; OAA; transfers amino group from glutamate to OAA forming aspartate for urea cycle. 

    Yes, this is reversible. 
  46. What do high levels of aminotransferases in blood tell you? What is difference bt ALT and AST?

    What could they indicate?
    High levels signify damage to cells rich in these enzymes (liver, muscle, etc). 

    Could indicate liver disease, myocardial infarction, hepatitis, toxic injury, etc. 

    ALT is more specific than AST for liver disease, but AST is more sensitive bc liver has high levels of AST. 
  47. What are the two main functions of transamination in proteins?
    • 1. Help maintain adequate levels of non-essential AA required for protein synthesis
    • 2. Funnel AA groups from catabolized AA to glutamate & aspartate for eventual excretion as urea. 
  48. In body, what processes require ALT and AST? (3)

    For positive N balance will more or less transamination occur? What about for negative N balance?
    Needed for transamination for syn of nonessential AAs, production of glucose, and loss of amino group to urea. 

    + N Balance and - N balance both increase transamination because these reaction are all reversible. 
  49. Why does high BCAA precede metabolic disease?
    Bc BCAA are broken down in muscle and high BCAA in blood may directly promote insulin resistance. 
Card Set
Amino Acids
Amino acid lecture flashcards