Sessions 22-23: Amino Acid Metabolism

Question 1

what are essential amino acids

Answer 1

the 10 amino acids that we can’t synthesize. they’re obtained from 2 main sources: dietary sources and the breakdown of proteins in our bodies

Question 2

what does pepsin do

Answer 2

pepsin breaks down proteins in the stomach. it is activated by the low pH in the stomach

Question 3

what do the proteolytics in the small intestines do

Answer 3

cleave the pre-digested protein into oligopeptides and free amino acids

Question 4

what happens to oligopeptides from digestion

Answer 4

they’re broken down into di/tri peptides via enzymes on the brush border of the small intestine membrane

Question 5

name 3 ways that cellular proteins are used for amino acid digestion

Answer 5

enzymes can be inactivated and recycled, damaged and recycled, or misfolded and recycled

Question 6

what is ubiquitin

Answer 6

a 76 amino acid protein that is used as a marker for proteins designated for degradation

Question 7

what amino acid is used to attach ubiquitin to a target protein

Answer 7

glycine on the carboxyl end of ubiquitin. The lysine residues on the protein are what generate the bond with glycine

Question 8

what is the isopeptide bond

Answer 8

the bond between glycine and the lysine residue on target protein. ATP has to be hydrolyzed for this bond to be formed

Question 9

describe ubiquitin activating enzyme (E1)

Answer 9

harvests energy from hydrolyzing ATP and activates ubiquitin

Question 10

describe ubiquitin conjugating enzyme (E2)

Answer 10

it transfers ubiquitin from enzyme E1 onto E2 by attaching it to a cysteine residue of E2

Question 11

describe ubiquitin protein ligase (E3)

Answer 11

it transfers ubiquitin group onto the target protein.

Question 12

how many ubiquitin molecules are required for targeting a protein

Answer 12

at least 4 ubiquitin are required. the 48th residue in ubiquitin is lysine so it is used to attach ubiquitin onto ubiquitin.

Question 13

describe the proteasome complex

Answer 13

it consists of two 19s subunits and one 20s subunits. the 19s are regulatory while the 20s is what catalyzes the breakdown of the protein

Question 14

describe the subunits of 20s

Answer 14

the alpha and beta subunits. there are four layers of rings stacked on top of each other (the barrel core).

Question 15

what do the 19s subunits do

Answer 15

they locate and bind the ubiquitin bound protein and then unfold the protein (using ATP) so it can be fit into the barrel core. they also protect non ubiquitinated proteins from being broken down.

Question 16

what does the barrel core do once 19s subunits have fed protein into it

Answer 16

shreds protein into short peptide segments of 7-9 amino acids and removes the ubiquitin molecules. ubiquitin is recycled it is not degraded.

Question 17

what do cellulose proteases do

Answer 17

they digest the short peptides down into individual amino acids.

Question 18

where is the majority of amino acid breakdown

Answer 18

in the liver

Question 19

describe transamination

Answer 19

catalyzed by aminotransferase. this enzyme uses pyridoxal phosphate (it must be present for the enzyme to be effective). the alpha amino acid is transferred to form glutamate and the left over group is the alpha ketoacid (which can be used for energy purposes).

Question 20

what is a-ketoglutarate

Answer 20

the molecule used to transfer an amino group off of an unwanted amino ac id

Question 21

what do you get from reacting alanine with a-ketoglutarate

Answer 21

pyruvate + glutamate

Question 22

what do you get from reacting aspartate with a-ketoglutarate

Answer 22

oxaloacetate + glutamate

Question 23

is transamination in equilibrium

Answer 23

yes thus these enzymes can be used to form new amino acids

Question 24

what is oxidative deamination

Answer 24

two step process that removes an amino group from glutamate. it is catalyzed by glutamate dehydrogenase. it can use both NAD and NADP to perform the dehydrogenation. the second step is a hydrolysis reaction to form ammonium and a-ketoglutarate. this reaction can go backwards as well

Question 25

where is glutamate dehydrogenase found

Answer 25

in the mitochondria. ammonium is very toxic. keeping it in mitochondria keeps it from damaging the cell.

Question 26

where does ammonium go after being formed by deamination

Answer 26

it goes into the urea cycle thus driving the reaction forward.

Question 27

how are serine and threonine deamination different

Answer 27

it is a single step process catalyzed by a-dehydratase. serine is dehydrated into pyruvate and ammonium. and threonine is dehydrated into a-ketoglutarate and ammonium

Question 28

what is aminoacrylate

Answer 28

an unstable intermediate in serine deamination

Question 29

how does skeletal muscle get rid of ammonium from breaking down amino acids

Answer 29

one pathway is the glucose-alanine cycle: branch chain amino acids are broken down into carbon intermediates and ammonium is produced. ammonium is combined with pyruvate (from glycogen/glucose) to form glutamate which is then transformed into alanine (reverse of alanine deamination). alanine is then transported into blood cell and into hepatocytes in the liver. then alanine is deaminated into pyruvate and ammonium. this ammonium is then fed into the urea cycle. the pyruvate can also be used to form glucose from gluconeogenesis.

Question 30

how can glutamate be used to get rid of ammonium from skeletal muscle

Answer 30

ammonium and glutamate are combined via glutamine synthetase (using ATP) to form glutamine which can be transported to the liver similar to the glucose-alanine cycle

Question 31

what is the main purpose of the urea cycle

Answer 31

converting toxis ammonium into urea to be excreted in urine.

Question 32

name the 5 steps of the urea cycle

Answer 32

co2 from bicarbone is combined with ammonium using 2 ATP to form carbamoyl phosphate. then ornithine is combined with carbamoyl to form citrulline. (these first 2 steps take place inside the mitochondrial matrix of a liver cell. citrulline moves into the cytoplasm of liver cell and is combined with aspartate to form argininosuccinate. argininosuccinate is then broken down; the carbon skeleton leaves as fumarate and the amino group goes on to be arginine. arginine is then hydrolyzed to form urea and ornithine which then goes back to the first step

Question 33

where do the 2 amino groups and the oxygen molecule come from in urea

Answer 33

one amino group comes from ammonium at the beginning and another amino group comes from aspartate (to form argininosuccinate) the oxygen comes from the water used to hydrolyze arginine into urea and ornithine

Question 34

describe carbamoyl phosphate synthetase

Answer 34

one ATP is used to turn bicarbonate into carboxyphosphate. this makes it high enough energy to react with ammonia (from ammonium) to form carbonic acid. then ATP is used to transform into carbamoyl phosphate. this enzyme will only become active in the presence of N-acetylglutamate (located in the matrix of mitochondria)

Question 35

describe ornithine transcarboxylase

Answer 35

it transfers carbamoyl group onto ornithine to form citrulline the citrulline then moves into cytoplasm of the cell

Question 36

describe argininosuccinate synthatase

Answer 36

the second amino group needs to be added from aspartate. so ATP is used to bind aspartate to citrulline to form argininosuccinate. (pyrophosphate is formed as a byproduct so technically 2 ATP are used in this step)

Question 37

describe argininosuccinase

Answer 37

it takes argininosuccinate catalyzes the removal of carbon skeleton as fumarate leaving an arginine residue

Question 38

describe arginase

Answer 38

the 2 amino groups are removed from arginine by hydrolyzing (oxygen is gained to make urea from the hydrolyzation). and the carbon skeleton left over is ornithine

Question 39

where does the central carbon come from in urea

Answer 39

the bicarbonate at the beginning of step one

Question 40

net reaction of urea cycle

Answer 40

CO2 + NH4 + 2 H2O + 3 ATP + aspartate —> urea + 2 ADP + AMP + Pi + PPi + fumarate

Question 41

which aminos are ketogenic only

Answer 41

leucine and lysine

Question 42

what aminos are both glucogenic and ketogenic

Answer 42

tryptophan isoleucine phenylalanine and tyrosine

Question 43

what is a glucogenic amino

Answer 43

they can form krebs intermediates to form oxaloacetate to form glucose via gluconeogenesis

Question 44

what are ketogenic aminos

Answer 44

form acetyl CoA or acetoacetyl CoA to form ketone bodies