Exam 3 AA Metabolism I (breakdown)

Question 1

what are the 2 sources for protein degradation?

Answer 1

1. cellular proteins

2. dietary proteins (ingest)

Question 2

once we “steal” the amino group from an aa, what is the fate of that amino group?

Answer 2

go on to the urea cycle of be converted into other aas, nucleotides, and biological amines

Question 3

what is the fate of the carbon skeleton left behind

Answer 3

carbohydrate and lipid pathways

Question 4

when we ingest proteins, the low pH of the stomach does what proteins

Answer 4

unfolds proteins and activates pepsin

Question 5

the small intestine has enteropeptidase that acts how

Answer 5

located in the duodenum and cleaves trypsinogen (zymogen) into active trypsin

Question 6

the small intestine has aminopeptidases that act how

Answer 6

exopeptidases that chew from N-terminus

Question 7

small intestine has dipeptidases that act how

Answer 7

break apart dipeptides into individual aas

Question 8

what can be transported into cells

Answer 8

aas, dipeptides, tripeptides (1-3 aas long)

Question 9

what are the two intracellular primary structures that degrade proteins

Answer 9

1. the proteosome (ubiquitin)

2. the lysosome (autophagy)

Question 10

what is the “N-end Rule”?

Answer 10

the N-terminal aa identity determines rate of ubiquitination

Question 11

highly stabilizing residues include

Answer 11

small and non-polar

Question 12

is ubiquitin reusable?

Answer 12

yes

Question 13

what happens to ubiquitinated tagged proteins

Answer 13

they are fragmented inside the proteosome

Question 14

what happens to the peptide fragments

Answer 14

cytosolic proteases (proteolysis) further degrade peptide fragments into individual aas

Question 15

what can we do with individual aas?

Answer 15

reduce, reuse, and recycle

Question 16

what is it meant to “reduce” aas?

Answer 16

we are reducing waste in our cell (urea)

Question 17

what is it meant to “reuse” aas?

Answer 17

once we get to the individual aas stage, these aas are still viable to make new proteins

Question 18

what is it meant to “recycle” aas?

Answer 18

repurpose the carbon skelelton

Question 19

what part of “reduce, reuse, recycle” slogan does deamination fall under?

Answer 19

reducing and reusing

Question 20

what is deamination?

Answer 20

separates (-NH3) from backbone (alpha carbon) and leaves behind carbon skeleton

Question 21

how can we perform deamination (2)

Answer 21

1. aas can be directly deaminated by their respective ammonia lyases (dehydratases)
2. 2-enzyme mechanism: an aminotransferase + glutamate dehydrogenase

Question 22

what is the coenzyme for deamination?

Answer 22

pyridoxal phosphate (PLP)

Question 23

how do we perform direct deamination?

Answer 23

need an ammonial lyase/dehydratase to remove and add back the H2O to remove (NH4+)

Question 24

_ is deaminated to pyruvate

Answer 24

serine

Question 25

threonine is deaminated by

Answer 25

threonine dehydratase (like serine)

Question 26

histidine is deaminated by

Answer 26

histidase

Question 27

what is step 1 of the 2-enzyme mechanism of deamination?

Answer 27

use an aminotransferase to make glutamate (Glu, E)(combines a primary/alpha aa with a-ketoglutarate).

Question 28

step 1: when you combine an a-aa with a-ketoglutarate, what are the products?

Answer 28

a-keto acid and glutamate

Question 29

step 1: what are the 2 names of the aminotransferases

Answer 29

1. Aspartate Aminotransferase (AST) - in cells or Serum Glutamate-Oxaloacetate Transaminase (SGOT) - in serum 2. Alanine Aminotransferase (ALT) - in cells or Serum Glutamate-Pyruvate Transamminase (SGPT) - in serum

Question 30

step 1: what is AST and SGOT function?

Answer 30

catalyzes the interconversion of asparatate and oxaloacetate

Question 31

step 1: what combination gets you products: glutamate (Glu, E) and oxaloacetate (OAA)

Answer 31

a-ketoglutarate and aspartate (Asp, D)

Question 32

step 1: what combination gets you products: glutamate (Glu, E) and pyrvuvate

Answer 32

a-ketoglutarate and alanine (Ala, A)

Question 33

step 1: what is ALT and SGPT function?

Answer 33

catalyze the interconversion of alanine and pyruvate

Question 34

step 1: ALT and AST tell us in the name

Answer 34

what aa

Question 35

step 1: SGOT and SGPT tell us in the name

Answer 35

what metabolite

Question 36

what is step 2 of the 2-enzyme mechanism of deamination?

Answer 36

use glutamate dehydrogenase to release an ammonium ion (hydrolase)

Question 37

a-aa -> glutamate -> _

Answer 37

NADH + (NH4+)

Question 38

NAD+ + H20 -> glutamate -> _

Answer 38

a-aa

Question 39

where is NH4+ converted to urea

Answer 39

liver

Question 40

what excretes urea

Answer 40

kidneys

Question 41

t/f: (NH4+) is a toxic byproduct of aa catabolism

Answer 41

true

Question 42

how do muscle cells get (NH4+) to the liver

Answer 42

via alanine and the action of ALT

Question 43

how does all other cells, except muscle, get (NH4+) to the liver

Answer 43

via glutamine (Gln, Q)

Question 44

mechanism behind (NH4+) transport from cells, except muscle, to the liver

Answer 44

Gln-synthetase adds an amine to Glu to make Gln and Glnase in the liver removes an amine from Gln to make Glu

Question 45

chemical formula of urea?

Answer 45

CO(NH2)2

Question 46

urea cycle: what is the purpose of carbamoyl phosphate synthetase I (CSPI)

Answer 46

the commited step where CPSI combines CO2 and NH3 to make carbamoyl phosphate using 2 ATP

Question 47

urea cycle: what is the allosteric activator of CPSI?

Answer 47

NAG (N-acetylglutamate) non-proteinogenic

Question 48

what are the non-proteinogenic aas of the urea cycle

Answer 48

ornithine and citrulline

Question 49

urea cycle: ornithine must move into the _ to combine with carbamoyl phosphate

Answer 49

mitochondria to make citrulline

Question 50

urea cycle: citrulline is exported from the _ to the _

Answer 50

from the mitochondria into the cytoplasm

Question 51

urea cycle: what aa donates an NH3 at the cost of 2 ATP-equivalents to citrulline

Answer 51

aspartate (Asp, D)

Question 52

urea cycle: what is created after Asp dontates NH3 to citrulline

Answer 52

the aa acid arginine (Arg, R) is created and the rest of Asp is fumarate that enters the mito to make OAA which uses TCA cycle

Question 53

urea cycle: OAA to Asp conversion is performed by

Answer 53

AST (regeneration loop)

Question 54

urea cycle: _ is created when urea is removed from Arg

Answer 54

ornithine via H2O which adds the final O to urea

Question 55

urea cycle: ornithine enters into the _ and continues the urea cycle...

Answer 55

mitochondria

Question 56

aas are glucogenic if they:

Answer 56

are degraded into intermediate molecules that can feed through gluconeogenesis to reform glucose ex pyruvate

Question 57

aas are ketogenic if they:

Answer 57

are degraded into intermediate molecules that can be used to create ketone bodies i.e. acetyl-coA and acetoacetate

Question 58

aas are both ketogenic and glucogenic if they:

Answer 58

can be degraded to more than one possible molecule

Question 59

what are the ketogenic only aas?

Answer 59

leucine (Leu, L) and lysine (Lys, K)

Question 60

what are the both ketogenic and glucogenic aas?

Answer 60

- isoleucine (Ile, I) - phenylalanine (Phe, F) - threonine (Thr, T) - tryptophan (Trp, W) - tyrosine (Try, Y)