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BIOC 311 > Amino Acids > Flashcards

Amino Acids Flashcards

1
Q

Amino acids are a source of ____ for which compounds?

A

They are a source of N for: metabolites, purines, heme, and hormones

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2
Q

_______ expresses ______ that fixes atmospheric nitrogen.

A

Diazotroph bacteria expresses nitrogenase that fixes atmospheric nitrogen.

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3
Q

How do higher organisms (e.g. humans) obtain nitrogen?

A
  • atmospheric nitrogen is fixated by bacteria
  • that fixated nitrogen serves as a substrate for the glutamine synthase reaction in plants
  • higher organisms then eat those plants and get nitrogen as glutamine
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4
Q

What is nitrogen assimilation?

A

The incorporation of ammonia to amino acids

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5
Q

What are different nitrogen assimilation reactions?

A
  1. Alpha-KG to glutamate by glutamate dehydrogenase
  2. Glutamate to glutamine by glutamine synthase
  3. Aspartate to asparagine by asparagine synthase
  4. CO2 and ATP to carbamoyl phosphate by carbamoyl phosphate synthase
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6
Q

What are the dietary sources of amino acids?

A

Anything composed of cells contains proteins

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7
Q

how are dietary proteins digested (enzyme, tissue type, claves at which AA, process)

A
  1. Pepsin: in stomach, cleaves after Phe/Leu/Trp/Tyr, protein to polypeptides
  2. trypsin (pancreas): in duodenum, claves after Arg/Lys, polypeptide to peptides
  3. Chymotrypsin (pancreas activated by trypsin): in duodenum, cleaves after Phe/Trp/Tyr, polypeptide to peptide
  4. Aminopeptidase (cleaves at N-term) and Carboxypeptidase A (cleaves at C-term): in small intestine, non-specific cleavage, peptides to amino acids
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8
Q

What is the path of dietary amino acids from the mouth to the blood?

A
  1. in mouth, mechanical breakdown
  2. in stomach, chemical digestion
  3. small intestine, broken down into AAs and peptides
  4. transported into mucosal cell
  5. inside cell, broken down into AAs, which are transported into the blood
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9
Q

Digested proteins are imported into enterocyte via ________.

A

Na+ or H+ symport

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10
Q

what is the exception for uptake of dietary AAs in neonatal mammals?

A

whole milk proteins can be either endocytosed and degraded in lysosome, or they pass as a whole through enterocyte and into circulation

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11
Q

What are the nonessential amino acids?

A
  • alanine
  • asparagine
  • aspartate
  • glutamate
  • serine
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12
Q

what are the conditionally essential amino acids?

A
  • arginine
  • cysteine
  • glutamine
  • glycine
  • proline
  • tyrosine
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13
Q

what are the essential amino acids?

A
  • histidine
  • isoleucine
  • leucine
  • lysine
  • methionine
  • phenylalanine
  • threonine
  • tryptophan
  • valine
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14
Q

Characteristics of the amino acid pool

A
  • homogenous
  • dynamic
  • same size
  • all AAs are available at the same time for protein synthesis
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15
Q

What is the AA intake and outflow when there is an equilibrium, positive balance, negative balance? When do these occur?

A
  • equilibrium: intake = outflow
  • positive (growth, pregnancy, weight lifting): intake > outflow
  • negative (illness, trauma): intake < outflow
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16
Q

Normally there is high plasma concentration of ____ and ____

A

Alanine and glutamine

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17
Q

Degradation of amino acids generates _____

A

Ammonia

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18
Q

How do we detoxify ammonia/ammonium?

A

By incorporating them into amino acids (glutamate, glutamine, alanine) which carry them to the liver, where it is just incorporated in the urea cycle, in a non toxic way

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19
Q

What is the fate of extra amino acids?

A

Go to liver to get degraded

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20
Q

What is the role of glutamine synthase?

A

To animate glutamate in order to carry ammonia in a non-toxic way

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21
Q

What is the role of glutaminase, where does this occur, what drives the reaction?

A
  • to deaminate glutamine to yield glutamate
  • in liver
  • consumption of NH4 by urea cycle drives it forward
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22
Q

What is the role of glutamate dehydrogenase (GDH), what is its cofactor, where does it occur, what drives the reaction, what regulates it?

A
  • to deaminate glutamate into alpha-KG
  • cofactor is NADH or NADPH depending on availability
  • in mitochondria of kidney, liver, and nervous tissue
  • consumption of NH4 by urea cycle and alpha-KG by CAC drives reaction forward
  • regulation: low [ADP] and is allosteric activator and high [GTP] is allosteric inhibitor
23
Q

Where does transamination occur?

A

In most tissue

24
Q

What is the general principle of amination, deamination, and transamination?

A
  • amination: a-keto-acid to amino acids
  • deamination: amino acid to a-keto acid
  • transamination: AA + keto acid to a-keto acid + AA (transfer Amine from one amino acid to another)
25
Q

What is the coenzyme of transaminases?

A

PLP (pyridoxal phosphate)

26
Q

PLP is derived from ____

A

Vitamin B6

27
Q

most transaminases prefer ______ as keto acid #2

A

a-ketoglutarate

28
Q

explain the “ping-pong” mechanism of transaminases

A
  1. PLP forms an “internal” Schiff base with the enzyme
  2. amino acid #1 forms an “external” Schiff base using PLP
  3. hydrolysis and release of keto acid #1 (transient transfer of NH2 to PLP/PMP
  4. keto acid #2 forms a Schiff base using PMP
  5. regeneration of PLP-enzyme and release of amino acid #2
29
Q

what is the corresponding amino acid for the following keto acids: pyruvate, oxaloacetate, a-KG

A
  • pyruvate: alanine
  • oxaloacetate: aspartate
  • a-KG: glutamate
30
Q

what is the glucose-alanine cycle?

A
  • ALT-1 is a transaminase in the liver which converts alanine to pyruvate (uses a-KG as keto acid), which can then be used to make glucose by gluconeogenesis
  • ALT-2 is a transaminase in skeletal muscle that converts pyruvate, which is made from glucose, to alanine (pyruvate is keto acid)
  • alanine can then travel between tissues and possibly to liver where ALT-1 is
31
Q

where does the Urea cycle occur?

A

in the liver

32
Q

what is the source of NH4 from for the urea cycle?

A
  • release from glutamine (glutaminase)
  • deamination of glutamate
33
Q

What is the rate-limiting step of the urea cycle?

A

CPS1

34
Q

how is CPS1 regulated?

A
  • is allosterically activated by NAG, which is produced byNAGS, which is stimulated by arginine
  • this means that NAG production, and therefore CPS1 activation, is proportional to amino acid concentration
35
Q

what is the difference between CPS1 and CPS2, how is it possible for both end products to be made?

A
  • CPS1: urea synthesis, in mitochondria, needs NAG, uses NH4
  • CPS2: pyrimidine synthesis, in cytoplasm, don’t need NAG, uses NH3 from glutamate
  • both are made since they are in different compartments
36
Q

what mutations or deficiencies can cause hyperammonia in humans?

A
  • CPS1 deficiency
  • NAGS deficiency
  • GDH gain-of-function
  • ornithine/citrulline transporters (ORC1)
  • OTC
  • arginosuccinate synthase (ASS)
37
Q

what is the energy cost and gain of the urea cycle?

A
  • cost: requires hydrolysis of 4 high-energy phosphate groups
  • generates 1 a-KG (10 ATP from CAC), 1 fumarate (converted to malate then oxaloacetate – 1 NADH) so total gain of 12.5 ATP
  • Net: 8.5 ATP gain
38
Q

Amino acids are broken down into ____ and _____

A

NH3 and carbon skeleton

39
Q

What are different ways amino acids are broken down?

A
  1. Require 1 step degradation (e.g. glutamate, aspartate)
  2. Require a conversion into another AA (e.g. glutamine, asparagine)
  3. From urea cycle (aspartate, arginine)
40
Q

What are three different fates of amino acid catabolism (breakdown)?

A
  1. Glucogenic (net extra CAC intermediates or pyruvate, make glucose - gluconeogenesis, and glucose exported to tissue)
  2. Ketogenic (makes ketone bodies and exported to blood to serve as energy source for brain and heart)
  3. Both
41
Q

How are branched amino acids broken down? Where does this occur?

A
  • in muscle, adipose, kidney, brain
  • by branched-chain aminotransferase which makes keto acids
  • then branched-chain a-keto acid dehydrogenase complex breaks them down into acyl-CoA derivatives
42
Q

How is the branched chain ketoacid dehydrogenase complex regulated?

A

The abundance of leucine’s keto acid shuts down BCKD’s kinase, which usually inhibits it, so it is now activated and can process branched ketoacids and the kinase also shuts down BCKA, so no more keto acids are made

43
Q

Which amino acids are glucogenic?

A
  • glycine
  • serine
    -valine
  • histidine
  • arginine
  • cysteine
  • proline
  • alanine
  • glutamate
  • glutamine
  • aspartate
  • asparagine
  • methionine
44
Q

Which amino acids are ketogenic?

A
  • leucine
  • lysine
45
Q

Which amino acids are glucogenic and ketogenic?

A
  • threonine
  • isoleucine
  • phenylalanine
  • tryptophan
  • tyrosine
46
Q

How are the following amino acids synthesized: alanine, aspartate, asparagine, glutamate, glutamine.

A
  • alanine: from pyruvate with aminotransferase
  • aspartate: from oxaloacetate with aminotransferase
  • asparagine: from aspartate and glutamine using asparagine synthase
  • glutamate: from a-KG using aminotransferase
  • glutamine: from glutamate using glutamine synthase
47
Q

Why is methionine so important? Where is it used?

A
  • protein synthesis (start codon)
  • synthesis of cysteine
  • one-carbon metabolism
  • methylation
48
Q

How is methionine used in the one-carbon cycle?

A

It is used to makes SAM which contains a sulfonium group which can easily give a methyl group

49
Q

Where does homocysteine come from and what is it used for?

A
  • In methyl cycle: methionine converted to SAM which converted to homocysteine
  • homocysteine can be used to make succinyl-CoA which can be used to makes glucose
50
Q

Which cofactors are required for homocysteine/methionine metabolism?

A
  • vitamine B12
  • folic acid (B9)
  • biotin (B8)
  • vitamine B6
51
Q

What can cause hyper-homocysteinenia?

A
  • B12 or folic acid deficiency
  • mutation in the enzyme converting homocysteine to cysteine
52
Q

Hyper-homocysteinenia is associated with which human diseases?

A
  • cardiovascular disease (interferes with formation of connective tissue-blood vessel defects)
  • cognitive impairment/dementia
  • neural tube defects and anencephaly (failure to develop brain)
53
Q

How is cysteine synthesized?

A

Transulfuration of homocysteine using PLP

54
Q

how often does vitamin B12 deficiency occur? where do we get out B12 from?

A
  • relatively rare since very little of needed and we get it from our diet (animal products and vegan food sources)

BIOC 311 (7 decks)

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