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Proteins, Amino Acids, Peptides, and Polypeptides

Peptides and Proteins

Peptides consist of two or more amino acids. Polypeptides and proteins both contain ten or more amino acids, but peptides consisting of more than fifty amino acids are classified as proteins.

Human Growht Hormone  
Human Growth Hormone

Some Important Peptide Hormones
   Hormone Number of
amino acids
   Function
Insulin 51 Lowers blood glucose level, promotes glucose storage as glycogen and fat. Fasting decreases insulin production.
Glucagon 29 Increases blood glucose level. Fasting increases glucagon production.
Ghrelin 28 Stimulates release of Growth Hormone, increases feeling of hunger.
Leptin 167 Its presence suppresses the feeling of hunger. Fasting decreases leptin levels.
Growth Hormone 191 Human Growth Hormone (HGH), also called somatotropin, promotes amino acid uptake by cells and regulates development of the body. Growth hormone levels increase during fasting.
Prolactin 198 Initiates and maintains lactation in mammals
Human Placental Lactogen 191 Produced by the placenta late in gestation
Luteinizing Hormone 204 Induces the secretion of testosterone
Follicle Stimulating Hormone 204 Induces the secretion of testosterone and dihydrotestosterone
Chorionic Gonadotropin 237 Produced after implantation of an egg in the placenta
Thyroid Stimulating Hormone 201 Stimulates secretion of thyroxin and triiodothyronine
Adrenocorticotropic Hormone 39 Stimulates production of adrenal cortex steroids (cortisol and costicosterone)
Vasopressin 9 Increases the reabsorption rate of water in kidney tubule cells (antidiuretic hormone)
Cys-Tyr-Phe-Gln-Asn-Cys-Pro-Arg-Gly
Oxytocin 9 Causes contraction of mammary gland cells to produce milk and stimulation of uterine muscles during childbirth
Cys-Tyr-Ile-Gln-Asn-Cys-Pro-Leu-Gly
Angiotensin II 8 Regulates blood pressure through vasoconstriction
Asp-Arg-Val-Tyr-Ile-His-Pro-Phe
Parathyroid Hormone 84 Increases calcium ion levels in extracellular fluids
Gastrin 14 Regulates secretion of gastric acid and pepsin, a digestive enzyme consisting of 326 amino acids

Peptide hormones are produced by the endocrine glands (pituitary, thyroid, pineal, adrenal, pancreas) or by various organs such as the kidney, stomach, intestine, placenta, or liver. Peptide hormones can have complex, convoluted structures with hundreds of amino acids. The following graphics illustrate the chemical structure of human insulin and its three-dimensional shape. Insulin is made of two amino acid sequences. The A-Chain has 21-amino acids, and the B-Chain has 30-amino acids. The chains are linked together through the sulfur atoms of cysteine (Cys). Peptide hormones are generally different for every species, but they may have similarities. Human insulin is identical to pig insulin, except that the last amino acid of the B-Chain for the pig is alanine (Ala) instead of threonine (Thr).

Human Insulin
Chemical Structure of Human Insulin
Insulin (ribbon representation)
Ribbon representation
shows shape of peptide links
Insulin (stick diagram)
Stick representation
shows all the atoms

Insulin (space-filling representation)
Space-filling representation shows external shape

How are proteins created?

The genetic code in DNA (deoxyribonucleic acid) provides the instructions for building proteins. In the 1960s, Marshal Nirenberg at the National Institutes of Health (NIH) deduced how DNA is mapped into proteins. DNA consists of long molecular sequences containing four nucleotide bases: Adenine (A), Cytosine (C), Guanine (G), and Thymine (T). Each combination of three bases, a DNA codon, corresponds to one specific amino acid. Since there are 64 different 3-base combinations and only 20 amino acids, some combinations do not have unique mappings. The genetic code applies to the vast majority of genes in animals, plants, and microorganisms. The same codons correspond to the same amino acids and to the same START and STOP signals, but in some rare cases one or two of the three STOP codons are assigned to an amino acid instead.

Nucleotide Bases
adenine
Adenine (A)
cytosine
Citosine (C)
guanine
Guanine (G)
thymine
Thymine (T)

Chemical Structure of DNA

DNA forms a double helix in which the nucleotide bases are attached to deoxyribose units linked through phosphate groups. The bases in the center of the DNA helix always occur in complementary matched pairs, with cytosine linking to guanine and thymine linking to adenine through hydrogen bonding (shown as dotted lines). James Watson and Francis Crick described the structure of DNA in 1953, and received the Nobel Prize in 1962 for this work.

Chemical Structure of DNA
DNA double helix
Place cursor on image
to animate it.

The nucleotide bases in the center of the DNA helix are flanked by deoxyribose units linked by phosphate groups. The figure on the right represents oxygen as red, nitrogen as blue, and phosphorus as orange.


Transcription of DNA to mRNA, and of mRNA to proteins

The mechanism for producing proteins is analogous to offset printing where the image on a printing plate is covered with ink and transferred as a mirror image to a rubber blanket which is then pressed against a sheet of paper to produce the final image. The nucleotide sequence of DNA is not used directly in protein synthesis. Instead, the DNA molecule is transcribed into a complementary sequence of bases, called messenger ribonucleic acid (mRNA), which is then used for protein synthesis. How are peptides formed? Transcription begins when the DNA double helix hydrogen bonds break and each DNA nucleotide base links with a complementary matching base to build the mRNA molecule. Guanine links with cytosine and cytosine with guanine. Thymine links with adenine, but adenine, which would normally link to thymine, links with Uracil (U) during transcription. As an example, the DNA sequence GATACC is transcribed into the complementary mRNA sequence CUAUGG which builds the amino acid sequence Leu-Trp. Ribosomes, which are large and complex molecular machines found within all living cells, build the proteins by linking amino acids in the order specified by messenger RNA. The table below shows the correspondence of the amino acids and the mRNA codons.

uracil    
Uracil (U)
DNA transcription
The transcription process

The Genetic Code
Amino Acid Abb. SLC mRNA codons
Alanine Ala A GCA GCC GCG GCU
Arginine Arg R AGA AGG CGA CGC CGG CGU
Asparagine Asn N AAC AAU
Aspartic acid Asp D GAC GAU
Cysteine Cys C UGC UGU
Glutamic acid Glu E GAA GAG
Glutamine Gln Q CAA CAG
Glycine Gly G GGA GGC GGG GGU
Histidine His H CAC CAU
Isoleucine Ile I AUA AUC AUU
Leucine Leu L CUA CUC CUG CUU UUA UUG
Lysine Lys K AAA AAG
Methionine* Met M AUG
Phenylalanine Phe F UUC UUU
Proline Pro P CCA CCC CCG CCU
Serine Ser S AGC AGU UCA UCC UCG UCU
Threonine Thr T ACA ACC ACG ACU
Tryptophan Trp W UGG
Tyrosine Tyr Y UAC UAU
Valine Val V GUA GUC GUG GUU
Stop codons     UAA UAG UGA

SLC is the single-letter code used to represent the amino acids in protein data bases.
Example: The single-letter code for human glucagon is:
     HSQGTFTSDYSKYLDSRRAQDFVQWLMNT
Codon letters: A = Adenine, C = Cytosine, G = Guanine, U = Uracil
* AUG signals "start" of translation when it occurs at the beginning of a gene.


Amino acid profiles of food proteins

The following table shows representative amino acid profiles of some common foods and dietary protein supplements. The percentages are averages of several commercial products. Casein and whey are milk proteins. Casein is the protein that precipitates from milk when curdled with rennet; it is the basis for making cheese. Whey is the watery part of milk that remains after the casein is separated.


Percentage (%) by weight of amino acid
Amino Acid protein
 egg white   tuna   beef   chicken   whey   casein   soy   yeast 
 alanine 6.6 6.0 6.1 5.5 5.2 2.9 4.2 8.3
 arginine 5.6 6.0 6.5 6.0 2.5 3.7 7.5 6.5
 aspartic acid 8.9 10.2 9.1 8.9 10.9 6.6 11.5 9.8
 cystine 2.5 1.1 1.3 1.3 2.2 0.3 1.3 1.4
 glutamic acid 13.5 14.9 15.0 15.0 16.8 21.5 19.0 13.5
 glycine 3.6 4.8 6.1 4.9 2.2 2.1 4.1 4.8
 histidine * 2.2 2.9 3.2 3.1 2.0 3.0 2.6 2.6
 isoleucine * 6.0 4.6 4.5 5.3 6.0 5.1 4.8 5.0
 leucine * 8.5 8.1 8.0 7.5 9.5 9.0 8.1 7.1
 lysine * 6.2 9.2 8.4 8.5 8.8 3.8 6.2 6.9
 methionine * 3.6 3.0 2.6 2.8 1.9 2.7 1.3 1.5
 phenylalanine *  6.0 3.9 3.9 4.0 2.3 5.1 5.2 4.7
 proline 3.8 3.5 4.8 4.1 6.6 10.7 5.1 4.0
 serine 7.3 4.0 3.9 3.4 5.4 5.6 5.2 5.1
 threonine * 4.4 4.4 4.0 4.2 6.9 4.3 3.8 5.8
 tryptophan * 1.4 1.1 0.7 1.2 2.2 1.3 1.3 1.6
 tyrosine 2.7 3.4 3.2 3.4 2.7 5.6 3.8 5.0
 valine * 7.0 5.2 5.0 5.0 6.0 6.6 5.0 6.2
* Essential amino acids

Amino acid analysis of food products report cystine instead of cysteine. Cystine is an amino acid that is formed from the oxidation of two molecules of cysteine.


HOOC-CH(NH2)CH2-S-S-CH2CH(NH2)COOH
Cystine

Egg white protein is considered to have one of the best amino acids profiles for human nutrition. Plant proteins generally have lower content of some essential amino acids such as lysine and methionine. Soy protein is one of the best plant proteins, but nevertheless, the most prominent difference in this chart is the proportion of the essential sulfur-containing amino acid methionine. Egg white protein has approximately three times more methionine than is found in soy protein. The yeast information is for "brewer's yeast" (Saccharomyces Cervisiae).

Dietary Protein Requirements

The Institute of Medicine recommends a minimum dietary consumption of 0.8 grams of good quality protein per kilogram of body weight.[4] There are several factors that influence the nutritional value of a protein source including the metabolic availability of the essential amino acids. If the content of a single indispensable amino acid in the food is less than an individual's requirement, other amino acids cannot be used for normal protein synthesis even when the total nitrogen intake level is adequate. Thus, the "limiting amino acid" will determine the nutritional value of the total nitrogen or protein in the diet.

Studies have shown that more soy protein might be needed to maintain nitrogen balance when compared to egg-white protein, and that the difference may be eliminated by the addition of methionine to the soy diet. This indicates that sulfur amino acids can be limiting in soy. Similarly, the limiting amino acid in wheat protein is lysine. The Recommended Daily Allowance (RDA) for protein is estimated for people consuming complete proteins that prevent negative nitrogen balance due to the inadequate intake of limiting indispensable amino acids. The RDA recommendations also assume that the diet has enough nonprotein energy, such as carbohydrates and fats, to prevent the carbon skeletons of amino acids from being used to meet energy needs.


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References

  1. J.D. Watson and F.H.C. Crick., Molecular structure of nucleic acids: a structure for deoxyribose nucleic acid, Nature, No. 4356, April 25, 1953.
  2. Nirenberg MW, Matthaei JH, Jones OW, Martin RG, Barondes SH, Approximation of genetic code via cell-free protein synthesis directed by template RNA, Fed Proc., 1963 Jan-Feb; 22:55-61.
  3. USDA National Nutrient Database for Standard Reference
  4. Dietary Reference Intakes for Energy, Carbohydrate, Fiber, Fat, Fatty Acids, Cholesterol, Protein, and Amino Acids (Macronutrients) (2005) Food and Nutrition Board (FNB) Institute Of Medicine Of The National Academies [Full]


© Copyright  - Antonio Zamora

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