II. Definitions

  1. Amino Acids
    1. Twenty common Amino Acids occur in humans, in which 9 are essential (must be ingested)
  2. Peptides
    1. Short chains of Amino Acids (two or more)
  3. Proteins (polypeptides)
    1. Long chains of peptides (which in turn are chains of Amino Acids)

III. Physiology: Structure

  1. Primary Protein Structure
    1. Specific Amino Acid sequence defining a Protein
  2. Secondary Protein Structure
    1. Regular local structure of the Protein
    2. Common secondary structures include alpha-helix (right-handed spiral) and beta strand (straight segment)
  3. Tertiary Protein Structure
    1. Overall spatial arrangement of a Protein (globular, membane, fibrous)
    2. Globular Proteins (spherical) include Hemoglobin, albumin and most enzymes
    3. Fibrous Proteins with straight chains include structural Proteins (e.g. Collagen, elastin, Fibrinogen)
  4. Quaternary Protein Structure
    1. Assembly of multiple Proteins combined (e.g. interwoven Collagen fibers)

IV. Physiology: Function

  1. Functioning Protein (Holoprotein) is composed of two components
    1. Apoprotein
      1. Active Protein without Cofactors (e.g. globin in Hemoglobin)
      2. Apoenzyme refers to the Apoproteins of enzymes
      3. Apolipoprotein refers to Apoproteins of Lipoproteins (e.g. HDL, LDL)
    2. Prosthetic Group
      1. Non-Protein Cofactor (e.g. heme in Hemoglobin)
      2. Coenzymes refers to the prosthetic groups of enzymes
  2. Zymogen
    1. Inactive precursor to an active enzyme
    2. Activated by a metabolic pathway that modifies the Zymogen (e.g. cleavage, phosphorylation)
    3. Examples
      1. Gastrointestinal Metabolism (e.g. Trypsinogen to trypsin, Pepsinogen to Pepsin)
      2. Clotting Pathway (e.g. Prothrombin to Thrombin, Fibrinogen to Fibrin)

V. Physiology: Essential and Non-Essential Amino Acids

  1. Essential Amino Acids are generated by complex biosynthetic pathways not available in humans
    1. Histidine
    2. Isoleucine
    3. Leucine
    4. Lysine
    5. Methionine
    6. Phenylalanine
    7. Threonine
    8. Tryptophan
    9. Valine
  2. Conditional Essential Amino Acids are deficient in early childhood and at times of physical stress
    1. Arginine
    2. Cysteine
    3. Glutamine
    4. Tyrosine
    5. Glycine
    6. Ornithine
    7. Proline
    8. Serine
  3. Nonessential Amino Acids
    1. Includes the 8 conditional essential acids (except at times of physical stress)
    2. Alanine
    3. Aspartate
    4. Glutamate

VI. Physiology: Amino Acid Polarity by R-Group

  1. aminoAcids.png
  2. Non-polar side chains (hydrophobic)
    1. Glycine
    2. Alanine
    3. Valine
    4. Leucine
    5. Isoleucine
    6. Cysteine
    7. Methionine
    8. Proline
    9. Phenylalanine
    10. Tryptophan
  3. Polar uncharged side chains
    1. Serine
    2. Threonine
    3. Asparagine
    4. Glutamine
    5. Tyrosine
  4. Positively charged side chains
    1. Lysine
    2. Arginine
    3. Histidine
  5. Negatively charged side chains
    1. Aspartic Acid
    2. Glutamic Acid

VII. Physiology: Amino Acid Structures by R-Group

  1. Background
    1. Amino Acids vary by their R group
    2. Amino Acids share 3 common bindings to a core carbon
      1. Amino group or NH3 (in Proteins, binds to the COOH on the prior Amino Acid on the left)
      2. Hydrogen
      3. COOH (in Proteins, binds to the NH3 on the next Amino Acid on the right)
  2. Aliphatic R Group (open carbon chains)
    1. Glycine
    2. Alanine
    3. Valine
    4. Leucine
    5. Isoleucine
  3. Aromatic R Group (benzene ring)
    1. Tyrosine (also contains a hydroxyl group)
    2. Phenylalanine
    3. Tryptophan
  4. Hydroxyl Containing R Group
    1. Serine
    2. Threonine
  5. Sulfur Containing R Group
    1. Cysteine
    2. Methionine
  6. Carbonyl Containing R Group (C=O)
    1. Aspartate
    2. Asparagine
    3. Glutamate
    4. Glutamine
  7. Alkaline R Group
    1. Arginine
    2. Lysine
    3. Histidine
  8. Imino Acid
    1. Proline

VIII. Physiology: Protein Metabolism

  1. proteinMetabolism.png
  2. See Protein Metabolism
  3. Non-Essential Amino Acid Synthesis (via Kreb Cycle or from other Amino Acids)
    1. Aspartate is synthesized from oxaloacetate
      1. Asparagine is synthesized from Aspartate
    2. Glutamate is synthesized from alpha-ketoglutarate
      1. Glutamine and Proline are synthesized from Glutamate
    3. Glycine and cysteine are synthesized from serine
    4. Tyrosine is synthesized from phenylalanine
  4. Synthesis of other molecules from Amino Acids
    1. Nucleic Acids (DNA, RNA)
      1. Ribose 5-P backbone is synthesized from Glucose-6P or Glyceraldehyde
      2. Purines (ATP and GTP) are synthesized from Aspartate, Glutamine and Glycine
      3. Pyrimidines (TTP, CTP and UTP) are synthesized from Aspartate and Glutamine
    2. Sphingolipids (e.g. Sphingomyelin, Cerebroside, Ganglioside)
      1. Serine acts as a backbone for Fatty Acid attachment (similar to glycerol in Triglycerides)
    3. Hormonal synthesis
      1. Histidine is converted to Histamine
      2. Tyrosine is converted to Thyroxine,Triiodothyronine, Melanin, Norepinephrine, Dopamine and Epinephrine
      3. Tryptophan is converted to Serotonin and Melatonin
  5. Catabolism: Protein as Fuel
    1. Protein yields 4 kcals/g with catabolism
    2. Protein is the last to be catabolized in starvation (after Carbohydrate and fat)
    3. Proteins are broken down to Amino Acids and some small peptides before absorption
      1. See Gastrointestinal Metabolism
      2. Mediated by Stomach acid, pepsin, trypsin and peptidases
    4. Amino Acids are broken down into ammonia (NH3) and a carbon skeleton
      1. Ammonia is excreted as urea (via urea cycle)
        1. 2-Ketoglutarate mediated transamination removes NH3, and forms glutamate
        2. Glutamate mediated oxidative deamination releases NH3 and forms 2-Ketoglutarate
          1. Glutamate (and asparate) donate NH3 for various synthesis (e.g. Purines, Pyrimidines)
        3. Ammonia enters urea cycle as carbamoyl phosphate and is ultimately excreted as urea
          1. Urea cycle primarily occurs in the liver
      2. Carbon skeleton is further processed
        1. Kreb Cycle (glucogenic Amino Acids)
        2. Acetyl CoA and Acetoacetate (ketogenic Amino Acids)
    5. Most Amino Acids are glucogenic (may generate Glucose via Gluconeogenesis)
      1. Exceptions: Two Amino Acids are only ketogenic (metabolized to acetyl CoA and Acetoacetate)
        1. Lysine
        2. Leucine
      2. Some Amino Acids are both glucogenic and ketogenic
        1. Isoleucine
        2. Tyrosine
        3. Phenylalanine
        4. Tryptophan
        5. Threonine
    6. Amino Acids enter the Kreb Cycle at various points (for energy generation)
      1. Pyruvate
        1. Glycine
        2. Alanine
        3. Tryptophan
        4. Serine
        5. Threonine
        6. Cysteine
      2. Acetyl CoA (Ketogenic Amino Acids)
        1. Lysine
        2. Leucine
        3. Isoleucine
        4. Tyrosine
        5. Phenylalanine
        6. Tryptophan
        7. Threonine
      3. Alpha Ketoglutarate (2-Ketoglutarate)
        1. Proline
        2. Glutamate
        3. Glutamine
        4. Arginine
        5. Histidine
      4. Succinate
        1. Valine
        2. Isoleucine
        3. Threonine
        4. Methionine
      5. Fumarate
        1. Tyrosine
        2. Phenylalanine
        3. Aspartate
      6. Oxaloacetate
        1. Aspartate
        2. Asparagine

IX. Physiology: Protein Function

  1. Transport and storage Proteins
    1. Hemoglobin And Myoglobin (oxygen transport)
    2. Transferrin and Ferritin (iron transport and storage respectively)
    3. Thyroglobulin (Thyroxine)
    4. Albumin (binds many molecules in plasma)
  2. Structural Proteins
    1. Collagen (cartilage, bone, connective tissue)
    2. Elastin (connective tissue elasticity)
    3. Keratin (nails, hair)
  3. Motion
    1. Myosin and actin (Muscle)
    2. Tubulin (cilia, flagellae)
  4. Hormones
    1. Insulin
    2. Human Growth Hormone
    3. Adrenocorticotropic Hormone (ACTH)
    4. Prolactin
  5. Enzymes
    1. Nearly all cellular metabolic processes are catalyzed by enzymes
  6. Miscellaneous
    1. Transcription factors (regulate gene expression)
    2. Antibody
    3. Clotting Factors
    4. Growth Factors

X. References

  1. Goldberg (2001) Clinical Biochemistry, Medmaster, Miami, p. 24-9

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Related Studies

Ontology: Amino Acids (C0002520)

Definition (NCI_NCI-GLOSS) One of several molecules that join together to form proteins. There are 20 common amino acids found in proteins.
Definition (NCI) Any organic compounds containing amino (-NH2) and carboxyl (-COOH) groups. In biochemistry, used to refer to the twenty-plus L-alpha-amino acids found in proteins.
Definition (MSH) Organic compounds that generally contain an amino (-NH2) and a carboxyl (-COOH) group. Twenty alpha-amino acids are the subunits which are polymerized to form proteins.
Definition (CSP) organic acid containing one or more amino groups, especially any of a group that make up proteins and are important to living cells; those that are nonessential can be synthesized by the body while essential acids must be obtained through the diet; there are also several important amino acids, such as the neurotransmitter g-aminobutyric acid, that have no relation to proteins.
Concepts Amino Acid, Peptide, or Protein (T116) , Biologically Active Substance (T123) , Pharmacologic Substance (T121)
MSH D000596
SnomedCT 99825001, 52518006
CPT 1011269
LNC LP18033-8, MTHU003140
English Acids, Amino, aminoacid, aa, Amino Acids, amino acid preparations (medication), amino acid preparations, Amino Acids [Chemical/Ingredient], amino acid, aminoacids, AMINO ACIDS, amino acids, AMINO ACID PREPARATION (product), AMINO ACID PREPARATION, Amino acids, Amino acid, AA - Amino acid, Amino acid (substance), Amino acid, NOS, AMINO ACID PREPARATION (substance), Amino Acid
Swedish Aminosyror
Czech pyridinolin, aminokyseliny
Finnish Aminohapot
French Aminoacides, Acides aminés, Amino-acides
Polish Aminokwasy
Spanish AMINO ACID PREPARATION, AMINO ACID PREPARATION (producto), Ácidos Aminados, Ácidos Amino, AMINO ACID PREPARATION (sustancia), aminoácido (sustancia), aminoácido, Aminoácidos
Norwegian Aminosyrer
German Aminosäuren
Italian Aminoacidi
Portuguese Aminoácidos

Ontology: Amino Acids, Essential (C0002525)

Definition (NCI) Refer to those amino acids that can not be synthesized in the body and can only be obtained through food supply.
Definition (NCI_CRCH) Amino acid which is not efficiently synthesized by humans and must be included in the diet.
Definition (MSH) Amino acids that are not synthesized by the human body in amounts sufficient to carry out physiological functions. They are obtained from dietary foodstuffs.
Definition (CSP) nine alpha amino acids required for protein synthesis that are not synthesized by the human body in amounts sufficient to carry out physiological functions; must be obtained from the diet.
Concepts Biologically Active Substance (T123) , Amino Acid, Peptide, or Protein (T116) , Pharmacologic Substance (T121)
MSH D000601
SnomedCT 112000000
English Acids, Essential Amino, Amino Acids, Essential, Essential Amino Acids, essential aminoacid, Amino Acids, Essential [Chemical/Ingredient], essential amino acids, amino acids essential, essential amino acid, acids amino essential, aminoacids essential, Indispensable amino acid, Essential amino acid (substance), Essential amino acid, Essential amino acid, NOS, Essential Amino Acid, AMINO ACIDS,ESSENTIAL
Swedish Aminosyror, essentiella
Czech aminokyseliny esenciální
Finnish Välttämättömät aminohapot
Japanese アミノ酸-必須, 不可欠アミノ酸, 必要アミノ酸, 必須アミノ酸
French Amino-acides indispensables, Acides aminés essentiels, Acides aminés indispensables, Aminoacides indispensables, Amino-acides essentiels, Aminoacides essentiels
Polish Aminokwasy podstawowe, Aminokwasy egzogenne
Spanish aminoácido esencial (sustancia), aminoácido esencial, Aminoácidos Esenciales
German Aminosäuren, essentielle, Essentielle Aminosäuren
Italian Aminoacidi essenziali
Portuguese Aminoácidos Essenciais

Ontology: Apoenzymes (C0003589)

Definition (CSP) protein components of the enzyme minus any cofactors or prosthetic groups that might be required for the enzyme to be catalytically functional.
Definition (MSH) The protein components of enzyme complexes (HOLOENZYMES). An apoenzyme is the holoenzyme minus any cofactors (ENZYME COFACTORS) or prosthetic groups required for the enzymatic function.
Concepts Amino Acid, Peptide, or Protein (T116) , Enzyme (T126)
MSH D001051
English Apoenzymes, apoenzyme, Apoenzyme, Apoenzymes [Chemical/Ingredient]
Swedish Apoenzymer
Czech apoenzymy
Finnish Apoentsyymit
Japanese アポ酵素
French Apoenzyme, Apoenzymes
Polish Apoenzymy
Norwegian Apoenzym, Apoenzymer
German Apoenzyme, Enzyme, Apo-
Italian Apoenzimi
Portuguese Apoenzimas
Spanish Apoenzimas

Ontology: Apoproteins (C0003601)

Definition (MSH) The protein components of a number of complexes, such as enzymes (APOENZYMES), ferritin (APOFERRITINS), or lipoproteins (APOLIPOPROTEINS).
Concepts Amino Acid, Peptide, or Protein (T116) , Biologically Active Substance (T123)
MSH D001059
SnomedCT 259599001
English Apoproteins, Apoprotein, Apoproteins [Chemical/Ingredient], apoproteins, apoprotein
Swedish Apoproteiner
Czech apoproteiny
Finnish Apoproteiinit
Italian Apoproteina, Apoproteine
French Apoprotéine, Apoprotéines
Croatian Not Translated[Apoproteins]
Polish Apoproteidy, Apoproteiny
Japanese アポ蛋白, アポ蛋白質, アポタンパク質
Norwegian Not Translated[Apoproteins]
German Apoproteine, Proteine, Apo-
Portuguese Apoproteínas
Spanish Apoproteínas

Ontology: Proteins (C0033684)

Definition (NCI) A group of complex organic macromolecules composed of one or more chains (linear polymers) of alpha-L-amino acids linked by peptide bonds and ranging in size from a few thousand to over 1 million Daltons. Proteins are fundamental genetically encoded components of living cells with specific structures and functions dictated by amino acid sequence.
Definition (NCI_NCI-GLOSS) A molecule made up of amino acids that are needed for the body to function properly. Proteins are the basis of body structures such as skin and hair and of substances such as enzymes, cytokines, and antibodies.
Definition (MSH) Linear POLYPEPTIDES that are synthesized on RIBOSOMES and may be further modified, crosslinked, cleaved, or assembled into complex proteins with several subunits. The specific sequence of AMINO ACIDS determines the shape the polypeptide will take, during PROTEIN FOLDING, and the function of the protein.
Definition (CSP) linear polymers of alpha-L-aminoacids ranging in size from a few thousand to over 1 million daltons, capable of oligomerization, with specific functions dictated by aminoacid sequence and encoded genetically.
Concepts Biologically Active Substance (T123) , Amino Acid, Peptide, or Protein (T116)
MSH D011506
SnomedCT 88878007
LNC LP21236-2, LP15838-3, LP32142-9, MTHU001951
English Proteins, Protein (Obsolete), gene product, protein preparations, protein preparations (medication), Proteins [Chemical/Ingredient], protein, proteins, Protein (NOS), Protein, Protein (substance), Protein, NOS, PROTEIN
Swedish Proteiner
Czech proteiny, bílkoviny
Finnish Valkuaisaineet
Japanese プロテイン, タンパク質, 遺伝子産物, 遺伝子蛋白質, 蛋白質, 遺伝子産生物
Latvian Not Translated[Proteins]
Polish Białka, Proteiny
Norwegian Not Translated[Proteins]
Spanish proteína (sustancia), proteína, Proteínas
French Protéines
German Proteine, Eiweiße
Italian Proteine
Portuguese Proteínas

Ontology: Nonessential amino acid (C0311461)

Definition (NCI_CRCH) Amino acid which can be readily made by the human body in sufficient amounts.
Definition (NCI) Refers to those amino acids that your body can create out of other chemicals found in your body.
Concepts Biologically Active Substance (T123) , Amino Acid, Peptide, or Protein (T116) , Pharmacologic Substance (T121)
SnomedCT 63330006
English nonessential amino acid, acids amino nonessential, Nonessential Amino Acid, Nonessential amino acid (substance), Nonessential amino acid, Nonessential amino acid, NOS, Non-Essential Amino Acid
Spanish aminoácido no esencial (sustancia), aminoácido no esencial