Protein Biochem and Metabolism

Question 1

Proteins differ from Carbs and Fat

Answer 1

a. How Protein Differs than the other nutrients:
1. Pathways that handle nitrogen per se, in particular the urea cycle.
2. Issues that relate to specific important amino acids.

b. The daily intake of protein is roughly 15-22% of total energy, or 0.8-1 g/kg body weight.

c. Much of lean body mass is made of protein, but this protein is not in a storage pool like glycogen in liver or triglyceride in fat tissue.
i. Rather, proteins are structural constituents of most tissues, enzymes, immunoglobulins, receptors, ion channels and other molecules that play critical roles in the functioning of cells and tissues.

d. The daily turnover of proteins in the body is roughly 300-400 grams, demonstrating the highly dynamic processes of protein synthesis and breakdown.

Question 2

The Amino Acids:

Answer 2

a. The component building blocks of proteins are the 20 amino acids.
i. There are many more that are post-translational modifications of these basic 20 amino acids.
ii . This large number of chemically distinct components allows the flexibility to construct protein molecules with a wide range of functions.

b. Amino acids can be categorized a number of ways based on qualities that differentiate them. T

c. One way to distinguish amino acids is on the basis of chemical features of their side chains.
i. These chemical differences in the “R” groups or side chains allow particular amino acids play important functional roles in whole proteins.

Question 3

Chemical Properties of the R-Group on an mino acid

Answer 3

These chemical properties include:
1. Acidic or basic: These chemical qualities of the R groups make the amino acid more reactive with substrates or other molecules.

2. Polar or non-polar: These chemical qualities of the R groups make the protein associate with a lipid mono/bilayer or with the aqueous portion of a cell or plasma.

Question 4

Amino acids could also be categorized on the body’s ability to synthesize them or not

Answer 4

1. Essential: cannot be synthesized by the body, but must be obtained from the diet.
2. Non-essential: can be synthesized from other amino acids.
3. Conditionally essential: These amino acids can be made by the body, but the capacity for their synthesis is limited, and in states of high consumption like critical illness, deficiency may develop.

Question 5

Specific classes of amino acids can be based on specific chemical constituents or structures present on the side chain.

Answer 5

These classes include
1. Sulfur containing amino acids

2. Amino acids with nitrogen in the side chain which are involved in nitrogen transport.
3. Branched chain amino acids
4. Aromatic amino acids which are precursors for a number of neurotransmitters and hormones.

Question 6

Amino acids can be broken down and their carbon skeletons then used for energy needs

Answer 6

Following the removal of the amino group…

1. Glucogenic: these amino acids can be used as substrates for gluconeogenesis.
2. Ketogenic: when broken down, these amino acids generate acetyl CoA, and like fatty acids cannot participate in gluconeogenesis, but rather can produce ATP through the TCA cycle or (like acetyl CoA that results from beta oxidation) be used for ketone synthesis.

Question 7

Post-translationally Modified Amino Acids:

Answer 7

A number of examples of post-translationally modified amino acids will be discussed.
These include:
1. Hydroxy-Proline and Hydroxy Lysine which are structural components of collagen, Vitamin C is needed for their synthesis.
i. Vitamin C deficiency causes scurvy because of a failure to synthesize sufficient quantities of these amino acids.

2. Gamma carboxyglutamate: Prothrombin uses this to target membranes
3. Ornithine: part of the Urea cycle

Question 8

Protein breakdown:

Answer 8

a. Protein in the diet is broken down in the GI tract by a group of peptidases.

b. These enzymes need to be activated in the gut lumen to be functional.
i. Once activated, these different peptidases have different specificities for specific types of peptide bonds.

c. Peptidases are categorized by the type of enzyme they are and the type of bond that they cleave.
d. These peptidases work sequentially to break down long peptide chains into their component amino acids which are then absorbed and enter the circulation.

Question 9

Proteins within cells also need to be broken down.

Answer 9

a. Receptors, enzymes, transcription factors and other protein molecules are made following gene transcription and translation.

b. Chromatin unwinds, transcription factors and RNA polymerase initiate the production of a molecule of RNA which then serves as a template for protein synthesis in the process of translation.
i. Proteins that are made in this manner then move about the cell to intracellular sites or sites associated with membranes where they perform their functions.

c. At some point, these proteins will be inactivated and broken down. The half-life and mechanisms by which a protein is broken down will vary depending on the protein.

d. However, there are two intracellular pathways for protein degradation that are particularly important:
1. Ubquination which targets proteins for degradation in proteasomes
2. Degradation in lysosomes

Question 10

There are two intracellular pathways for protein degradation that are particularly important:

Answer 10

1. Ubquination which targets proteins for degradation in proteasomes
2. Degradation in lysosomes

Question 11

Handling of Nitrogen during the Metabolism of Amino Acids Transamination:

Answer 11

Amino acids contain an NH2 group.

a. For an amino acid to be used as a precursor for gluconeogenesis, this NH2 group must be removed.
b. For an amino acid to be made from a carbon skeleton, an NH2 group must be added.

c. Actually these NH2 groups are transferred from another nitrogen containing molecule to the carbon skeleton, or from an amino acid to an acceptor molecule.
i. These so called “transamination reactions” are typically bidirectional depending on the availability of substrates and acceptors.
ii. These reactions typically take place in the liver (and to a lesser extent in kidney, intestine and muscle).

Question 12

Transamination reactions introduction

Answer 12

a. In the prototypical reaction, an amino acid donates an NH2 group to alpha-ketoglutarate to produce L glutamate and an alpha keto acid.
i. The enzyme that catalyzes this reaction is an aminotransferase.

b. Different aminotransferases have different specificities for different amino acids.
c. The nitrogen that has been accepted by alpha-ketoglutarate with the production of glutamate can then be released as NH3 with the regeneration of alpha-ketoglutarate.
d. This ammonia is toxic and needs to leave the body. It does so through the process of urea synthesis.

Question 13

Urea Cycle:

Answer 13

a. In the first step of the urea cycle, the ammonia that was produced from transamination reactions is converted to carbamoyl phosphate
i. The production of carbamoyl phosphate is catalyzed by carbamoyl phosphate synthase 1 which is the key regulated step in protein catabolism.

b. The nitrogen from the carbamoyl phosphate enters the urea cycle, and ultimately is combined with an NH3 from aspartate to form urea which contains 2 nitrogen atoms.

c. The nitrogen thus transferred from amino acids to urea can then leave the body in urine as urine urea nitrogen.
i. Urinary nitrogen in the form of urea then represents a marker of amino acid catabolism and oxidation.

Question 14

Carbamoyl phosphate synthase 1 and Carbamoyl phosphate

Answer 14

a. In the first step of the urea cycle, the ammonia that was produced from transamination reactions is converted to carbamoyl phosphate
b. The production of carbamoyl phosphate is catalyzed by carbamoyl phosphate synthase 1 which is the key regulated step in protein catabolism.

Question 15

How aspartate is part of the Urea cycle

Answer 15

a. The nitrogen from the carbamoyl phosphate enters the urea cycle, and ultimately is combined with an NH3 from aspartate to form urea which contains 2 nitrogen atoms.
b. The nitrogen thus transferred from amino acids to urea can then leave the body in urine as urine urea nitrogen.
c. Urinary nitrogen in the form of urea then represents a marker of amino acid catabolism and oxidation

Question 16

Glutamine and its carrying of Nitrogens

Answer 16

a. Glutamine is an important nitrogen containing amino acid (has 2 nitrogen atoms) because it accepts nitrogen from other amino acids in peripheral tissues, carries the nitrogen to the liver and kidney where it is donated to glutamate and from there to alpha-ketoglutarate.

b. The conversion of glutamate to alpha-ketoglutarate is catalyzed by glutamate dehydrogenase.
i. This is the second key regulated step in protein catabolism.

Question 17

Glutamate Dehydrogenase

Answer 17

a. The conversion of glutamate to alpha-ketoglutarate is catalyzed by glutamate dehydrogenase.
i. This is the second key regulated step in protein catabolism.

b. Glutamine is an important nitrogen containing amino acid (has 2 nitrogen atoms) because it accepts nitrogen from other amino acids in peripheral tissues, carries the nitrogen to the liver and kidney where it is donated to glutamate and from there to alpha-ketoglutarate.

Question 18

Sulfur Containing Amino Acids:

Answer 18

The sulfur containing amino acids Cysteine and Methionine are important for several reasons

1. Cysteine can form disulfide bridges that change protein conformation.
2. S-adenosylmethionine (SAM) is an energy source for a number of important biochemical reactions.
   i. In addition, it is a methyl donor for a number of important reactions. (Tetrahydrofolate is another molecule that is important in one carbon or methyl transfer reactions. It will also be discussed.)
3. SAM is a precursor for homocysteine which is important in vascular disease, wound healing, and is involved in B12 and folate metabolism.
4. Glutathione is a tri-peptide that contains cysteine, and serves as an important redox buffer, and protects against free radical injury.

Question 19

The sulfur containing amino acids Cysteine and Methionine are important for several reasons

Answer 19

1. Cysteine can form disulfide bridges that change protein conformation.
2. S-adenosylmethionine (SAM) is an energy source for a number of important biochemical reactions.
   i. In addition, it is a methyl donor for a number of important reactions.
3. SAM is a precursor for homocysteine which is important in vascular disease, wound healing, and is involved in B12 and folate metabolism.
4. Glutathione is a tri-peptide that contains cysteine, and serves as an important redox buffer, and protects against free radical injury.

Question 20

Gluconeogenic, ketogenic and branched chain amino acids

Answer 20

a. As mentioned above, some amino acids can enter pathways involved in gluconeogenesis
i. While others generate acetyl CoA and as a result can produce energy via the TCA cycle or be converted to ketone bodies but do not result in a net production of glucose.

b. The catabolism of branched chain amino acids requires specific enzymes and the products enter the TCA cycle.
i. This is important because there are defects in these enzymes in affected children give rise to a specific disorder that is sometimes on boards: Maple Syrup Urine Disease.

Question 21

Tryptophan, phenylalanine and tyrosine:

Answer 21

a. These amino acids contain ring structures on their side chains.
b. These structural elements are used as precursors for a number of important products including serotonin, niacin, dopamine, norepinephrine, epinephrine, tetrahydrobiopterin and thyroid hormone.

Question 22

Amino acid Introduction

Answer 22

a. 20 amino acids initially produced for incorporation into proteins

b, these 20 have their own tRNAs that allow them to be “read” into proteins (i.e., translated).

c. Many amino acids are “post-translationally modified” after their incorporation into proteins (~300 additional amino acids on top of the 20).

Question 23

Many amino acids are “post-translationally modified” after their incorporation into proteins
(~300 additional amino acids on top of the 20)

Answer 23

Many examples of post-translationally modified amino acids exist that include the following:

1. Collagen is the most abundant protein in human body that forms a triple-stranded helix, which is comprised of both hydroxyproline (Hyp) and hydroxylysine (Hyl):
2. Hyp—>used in collagen for H-bonding that increases collagen strength. Prolyl hydroxylase converts Pro to Hyp.
3. Hyl –>use in collagen for interchain cross-links. Lysyl hydroxylase converts Lys to Hyl.
4. Prolyl hydroxylase, Lysyl hydroxylase rely on Vit-C (ascorbate) as coenzyme, thus, lack of Vit-C leads to Scurvy (i.e. reduced collagen strength).
5. g-Carboxyglutamate (Gla)–>used to target proteins to membranes via Ca chelation. G-glytamyl carboxylase converts Glu to Gla, which is Vit-K dependent

Question 24

Collagen is the most abundant protein in human body that forms a triple-stranded helix, which is comprised of both hydroxyproline (Hyp) and hydroxylysine (Hyl):

Answer 24

a. Hyp—>used in collagen for H-bonding that increases collagen strength.
i. Prolyl hydroxylase converts Pro to Hyp.

b. Hyl –>use in collagen for interchain cross-links. Lysyl hydroxylase converts Lys to Hyl.
c. Prolyl hydroxylase, Lysyl hydroxylase rely on Vit-C (ascorbate) as coenzyme, thus, lack of Vit-C leads to Scurvy (i.e. reduced collagen strength).

d. g-Carboxyglutamate (Gla)–>used to target proteins to membranes via Ca chelation.
i. G-glytamyl carboxylase converts Glu to Gla, which is Vit-K dependent

Question 25

Protein degradation (cellular aspects)

Answer 25

Two primary methods (see Fig 2)

1) Ubiquitin-proteasome system: ATP dependent that is used to cross-link protein to ubiquitin. Ubiquitinated proteins are then sequestered to the proteasome (i.e. a giant cellular trashcan that has proteolytic activity to break down proteins).
2) Lysosomal path: ATP independent that is used primarily to “engulf” extracellular proteins (or even live pathogens). Proteins are broken down by acid hydrolysis and other lysosomal proteins (i.e. cathepsins).

Question 26

Ubiquitin-proteasome system of protein degradation

Answer 26

a. ATP dependent that is used to cross-link protein to ubiquitin.
b. Ubiquitinated proteins are then sequestered to the proteasome (i.e. a giant cellular trashcan that has proteolytic activity to break down proteins).

Question 27

Lysosomal path of protein degradation

Answer 27

a. Lysosomal path: ATP independent that is used primarily to “engulf” extracellular proteins (or even live pathogens).
b. Proteins are broken down by acid hydrolysis and other lysosomal proteins (i.e. cathepsins).

Question 28

Protein degradation (Proteases)

(Outside of Cell

Answer 28

a. To break down proteins to their respective amino acids, multiple proteases are used
b. These proteases are initially “proenzymes” (i.e. zymogens) and are cleaved in order to be activated.
c. Pepsin (stomach) : Pepsinogen is cleaved by HCl to produce pepsin that cleaves proteins to pieces (pepsin is an endopeptidase).

d. Enteropeptidase (intestine) : cleaves trypsin.
i. Activated by several proteases including trypsin.

e. Trypsin (produced in pancreas, goes to small intestine) : trypsinogen is cleaved by enteropeptidase to produce trypsin.
i. Trypsin cleaves all other zymogens in small intestine, which include chymotrypsinogen to chymotrypsin, procarboxypeptidases to carboxypeptidases

Question 29

Intestine involvement with amino acid metabolism

Answer 29

a. Enteropeptidase (intestine) : cleaves trypsin.
i. Activated by several proteases including trypsin.

b. Trypsin (produced in pancreas, goes to small intestine) : trypsinogen is cleaved by enteropeptidase to produce trypsin.
i. Trypsin cleaves all other zymogens in small intestine, which include chymotrypsinogen to chymotrypsin, procarboxypeptidases to carboxypeptidases

Question 30

Transamination- Large Summary

Answer 30

a. Aminotransferases: enzymes that transfer amino groups
i. These enzymes “Move Nitrogen”.

b. Aminotransferase–>Convert one a-keto acid to its corresponding amino acid and in the process converts another amino acid to its corresponding a-keto acid.
i. Reversible reaction and Keq~1.
ii. There are 100s of aminotransferases each selective for a few amino acids.

c. For protein degradation, aminotransferases move nitrogen to Asp & ammonia for Urea Cycle.

d. Two specific aminotransferases are:
i. Alanine aminotransferase (Alt)
ii. Aspartate aminotransferase (Ast)

e. Pyridoxal phosphate (PLP) is a derivative of Vit-B6 and is used by aminotransferases to “hold”/transfer the amino groups.

Question 31

Aminotransferases summary points

Answer 31

a. Aminotransferases: enzymes that transfer amino groups
i. These enzymes “Move Nitrogen”.

b. Aminotransferase:
1) Convert alpha-ketoglutarate acid + corresponding amino acid into another amino acid and a-keto acid.
2) Can do this in reverse.

Example: L-Glutumate + alpha-Keto Acid L-amino Acid + alpha-ketoglutarate

c. Reversible reaction and Keq~1.
i. There are 100s of aminotransferases each selective for a few amino acids.

d. For protein degradation, aminotransferases move nitrogen to Asp & ammonia for Urea Cycle.

Question 32

Urea Cycle Intro

Answer 32

a. Urea Cycle Purpose: to get rid of ammonia by forming less toxic compounds (i.e. urea).
b. Why: we do NOT store ammonia (i.e. nitrogen) and it’s toxic.

c. Overall Reaction:
3ATP + HCO3- + NH4+ + aspartate–> 2ADP + AMP + 2Pi + PPi + fumarate + urea

d. Part of urea cycle occurs in mitochondria and part in cytosol.
e. Ornithine is recycled in urea cycle.

f. There are two entry points for Nitrogen in urea cycle:
1) Apartate.
2) Free ammonia (incorporated into carbamoyl phosphate, see next).

Question 33

There are two entry points for Nitrogen in urea cycle:

Answer 33

1) Apartate.

2) Free ammonia
(incorporated into carbamoyl phosphate, see next).

Question 34

The amino acids & 3 letter abbreviations

Answer 34

1) Glucogenic
Alanine (Ala)
Arginine (Arg)
Asparagine (Asn)
Aspartate (Asp)
Cysteine (Cys)
Glutamate (Glu)
Glutamine (Gln)
Glycine (Gly)
Histidine (His)
Proline (Pro)
Serine (Ser)
Methionine (Met)
Threonine (Thr)
Valine (Val) 

2) Ketogenic
Leucine (Leu)
Lysine (Lys)

3) Both
Tyrosine (Tyr)
Isoleucine (Iso)
Phenylalanine (Phe)
Tryptophan (Trp)

Question 35

Post-translational modifications of aminco acids

Answer 35

a. ~300 additional amino acids are known.
b. Several are found within proteins (e.g. Hyp, Hyl, Gla)
c. But most serve alternative functions (e.g. Orn).

Question 36

Post Modified amino acids and collagen

Answer 36

Collagen is the most abundant protein in human body that forms a triple-stranded helix, which is comprised of both hydroxyproline (Hyp) and hydroxylysine (Hyl):

1) hydroxyproline (Hyp)–>used in collagen for H-bonding that increases collagen strength. Prolyl hydroxylase converts Pro to Hyp.
2) hydroxylysine (Hyl)–> use in collagen for interchain cross-links. Lysyl hydroxylase converts Lys to Hyl.

Question 37

Collagen incorporates Hyp & Hyl

Answer 37

a. Collagen is the most abundant protein in body.
b. Collagen fibrils strengthened by modified Pro (Hyp) and Lys (Hyl) residues.

Hydroxyproline (Hyp)–>used in collagen for H-bonding that increases collagen strength. Prolyl hydroxylase converts Pro to Hyp.

Hydroxylysine (Hyl)–> use in collagen for interchain cross-links. Lysyl hydroxylase converts Lys to Hyl.

Question 38

Collagen incorporates Hyp & Hyl

Wiki

Answer 38

a. The collagen protein is composed of a triple helix, which generally consists of two identical chains (α1) and an additional chain that differs slightly in its chemical composition (α2).[
b. The amino acid composition of collagen is atypical for proteins, particularly with respect to its high hydroxyproline content.
c. The most common motifs in the amino acid sequence of collagen are glycine-proline-X and glycine-X-hydroxyproline, where X is any amino acid other than glycine, proline or hydroxyproline.

Question 39

Pre-pro-peptide to pro-collagen:

Great Wiki summary *Look at step 2

Answer 39

Pre-pro-peptide to pro-collagen: Three modifications of the pre-pro-peptide occur leading to the formation of the alpha peptide:

1) The signal peptide on the N-terminal is dissolved, and the molecule is now known as propeptide (not procollagen).

2) * Hydroxylation of lysines and prolines on propeptide by the enzymes ‘prolyl hydroxylase’ and ‘lysyl hydroxylase’ (to produce hydroxyproline and hydroxylysine) occurs to aid cross-linking of the alpha peptides.
i. This enzymatic step requires vitamin C as a cofactor. In scurvy, the lack of hydroxylation of prolines and lysines causes a looser triple helix (which is formed by three alpha peptides).

3. Glycosylation occurs by adding either glucose or galactose monomers onto the hydroxyl groups that were placed onto lysines, but not on prolines.
4. Once these modifications have taken place, three of the hydroxylated and glycosylated propeptides twist into a triple helix forming procollagen. At this point, the procollagen is packaged into a transfer vesicle destined for the Golgi apparatus.

Question 40

Collagen incorporates Hyp & Hyl

Answer 40

a. Hyp forms (electrostatic) interstrand H-bonds formed.
b. Hyl forms covalent interstrand X-links.
c. Prolyl hydroxylase converts Pro to Hyp.
d. Lysyl hydroxylase converts Lys to Hyl.

•Both require ascorbate (i.e. Vitamin-C).

Question 41

γ-carboxyglutamate (Gla)

Answer 41

γ -Carboxyglutamate (Gla)–>used to target proteins to membranes via Ca chelation. G-glytamyl carboxylase converts Glu to Gla, which is Vit-K dependent.

1) Gamma-glutamyl carboxylase is a transmembrane protein
2) Vitamin-K dependent

Question 42

Scurvy Pathogenisis

Answer 42

a. Ascorbic acid (vitamin C) is needed for a variety of biosynthetic pathways, by accelerating hydroxylation and amidation reactions.

b. In the synthesis of collagen, ascorbic acid is required as a cofactor for prolyl hydroxylase and lysyl hydroxylase.
i. These two enzymes are responsible for the hydroxylation of the proline and lysine amino acids in collagen.

c. Hydroxyproline and hydroxylysine are important for stabilizing collagen by cross-linking the propeptides in collagen.
* Prolyl hydroxylase, Lysyl hydroxylase rely on Vit-C (ascorbate) as coenzyme, thus, lack of Vit-C leads to Scurvy (i.e. reduced collagen strength).*

Question 43

Protein degredation

*Good Summary Slide

Answer 43

1. ATP-dependent ubiquination targets enzyme to proteasome.
   i. Ubiquitin-proteasome mechanism utilizes several enzymes (E1-E3)
   and ubiquitin (Ub) to target proteins (S) for degradation.
2. The lysosome engulfs extracellular proteins to mix with digestive enzymes
   i. The lysosome engulfs extracellular proteins to mix with digestive enzymes.
   ii. Can engulf larger material such as bacteria as well.
   iii. Contains hydrolytic enzymes that include Aspartic proteases.

Question 44

Ubiquitin activation

Answer 44

a. E1 enzymes are responsible for activating UB, the first step in ubiquitinylation.
b. The E1 enzyme hydrolyses ATP and adenylates the C-terminus of UB, and then forms a thioester bond between the C-terminus of UB and the active site cysteine of E1.
c. To be fully active, E1 must non-covalently bind to and adenylate a second UB molecule.
d. The E1 enzyme can then transfer the thioester-linked UB to the UB-conjugating enzyme, E2, in an ATP-dependent reaction.

Question 45

Ubiquitination and targeting

Wiki

Answer 45

a. Proteins are targeted for degradation by the proteasome with covalent modification of a lysine residue that requires the coordinated reactions of three enzymes. In the first step, a ubiquitin-activating enzyme (known as E1) hydrolyzes ATP and adenylylates a ubiquitin molecule.
b. This is then transferred to E1’s active-site cysteine residue in concert with the adenylylation of a second ubiquitin.
c. This adenylylated ubiquitin is then transferred to a cysteine of a second enzyme, ubiquitin-conjugating enzyme (E2).
d. In the last step, a member of a highly diverse class of enzymes known as ubiquitin ligases (E3) recognizes the specific protein to be ubiquitinated and catalyzes the transfer of ubiquitin from E2 to this target protein.

e. A target protein must be labeled with at least four ubiquitin monomers (in the form of a polyubiquitin chain) before it is recognized by the proteasome lid
i. It is therefore the E3 that confers substrate specificity to this system.

Question 46

Enzymatic degradation of proteins in the body (outside cell)

Answer 46

In the stomach…
Pepsin

In the Intestine...
Trypsin
Chymotrypsin
Carboxypeptidase-A
Carboxypeptidase-B

Question 47

Enzymatic degradation in stomach & small intestine.

Answer 47

1) Aspartic protease:
i. Pepsin: hydrolyzes N-terminal side of aromatic residues (Phe,Trp,Tyr).

2) Serine proteases:
i.Trypsin: hydrolyzes C-terminal side of basic aminod acids (Arg,Lys).
ii. Chymotrypsin: hydrolyzes C-terminal side of aromatic & some hydrophobic
residues (Phe,Trp,Tyr & Leu,Met).

3) Metallocarboxypeptidases:
i. Carboxypeptidase-A: hydrolyzes C-terminal of hydrophobic amino acids.
(Ala, Ile, Leu, Val).
ii. Carboxypeptidase-B: hydrolyzes C-terminal of basic residues amino acids
(Arg, Lys).

Question 48

Aspartic protease:

Answer 48

Pepsin: hydrolyzes N-terminal side of aromatic residues (Phe,Trp,Tyr).

Question 49

Serine proteases:

Answer 49

a. Trypsin: hydrolyzes C-terminal side of basic aminod acids (Arg,Lys).

b. Chymotrypsin: hydrolyzes C-terminal side of aromatic & some hydrophobic
residues (Phe,Trp,Tyr & Leu,Met).

Question 50

Metallocarboxypeptidases:

Answer 50

a. Carboxypeptidase-A: hydrolyzes C-terminal of hydrophobic amino acids.
(Ala, Ile, Leu, Val).

b. Carboxypeptidase-B: hydrolyzes C-terminal of basic residues amino acids
(Arg, Lys).

Question 51

Transamination

Answer 51

a. Aminotransferases (transaminases) catalyze the reaction of an α-Keto acid
and an amino acid to another α -Keto acid and amino acid.
i. Reversible reaction & Keq~1.

•Major goal in regard to protein degradation: produce Asp,NH3 for Urea Cycle.

•We have 100s of aminotransferases within our genome, each selective for
at most a few amino acids.

• Mostly in cytosol of cells & especially abundant in liver,kidney,intestine,muscle.
• Increased levels in blood indicate liver damage/disease.

Question 52

Transamination

*Way Better Summary

Answer 52

a. Most amino acids are deaminated by transamination, a chemical reaction that transfers an amino group to a ketoacid to form new amino acids.
i. This is one of the major degradation pathways which convert essential amino acids to nonessential amino acids (amino acids that can be synthesized de novo by the organism).

b. Transamination in biochemistry is accomplished by enzymes called transaminases or aminotransferases.
c. α-ketoglutarate acts as the predominant aminogroup acceptor and produces glutamate as the new amino acid.

Aminoacid + α-ketoglutarate ↔ α-keto acid + Glutamate
i. The α-ketoglutarate will accept the NH3 and become the L-Glutamate

d. Glutamate’s amino group, in turn, is transferred to oxaloacetate in a second transamination reaction yielding aspartate.
i. Glutamate + oxaloacetate ↔ α-ketoglutarate + aspartate

Question 53

Transamination in biochemistry is accomplished by enzymes called transaminases or aminotransferases.

*Critical slide

Answer 53

a. α-ketoglutarate acts as the predominant aminogroup acceptor and produces glutamate as the new amino acid.
Amino acid + α-ketoglutarate ↔ α-keto acid + Glutamate

i. The α-ketoglutarate will accept the NH3 and become the L-Glutamate

b. Glutamate’s amino group, in turn, is transferred to oxaloacetate in a second transamination reaction yielding aspartate.
i. Glutamate + oxaloacetate ↔ α-ketoglutarate + aspartate

Question 54

Two most important aminotransferases:

Answer 54

Measure both of these in Liver Function Tests

Alanine aminotransferase
(ALT)

Aspartate aminotransferase
(AST)

Question 55

Transamination (PLP)

Answer 55

a. Aminotransferases require the coenzyme pyridoxal phosphate (PLP).
b. PLP is a derivative of vitamin B6.
c. PLP “holds” the amino group during its transfer.

Question 56

Control points for protein catabolism

Answer 56

The directionality of transamination (by ALT & AST) is regulated by the relative concentrations of “substrates” and “products”.

(In other words, regulating Nitrogen entry into the Urea Cycle)