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Animo acids are the unit molecular building blocks of proteins. A protein is a chain of amino acids in a certain sequence. Twenty main types of amino acid are found in the proteins of living things, and the properties of a protein are determined by its particular amino acid sequence.
Amino acids are encoded in the DNA by triplets of bases called codons. The four different bases – adenosine, cytosine, thymine and guanine – can be arranged in 64 (4 x 4 x 4) triplets, and each one codes for an amino acid. The relationship between triplet and amino acid has been deciphered and is called the genetic code.
It is possible to estimate the phylogenetic relatedness of two species by inferring their molecular evolution from the differences in amino acids between them.
Figure: the genetic code. The code is here expressed for mRNA. Each triplet encodes one amino acid (notice three triplets are "stop" codons, which signal the end of a gene).
Animo Acids
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Definition: Organic compounds that combine to form proteins
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When proteins are digested, amino acids are left. They are classified as "essential" amino acids (which must be consumed in the diet) and "nonessential" amino acids (which can be made by the body from the essential amino acids). Proteins are described as essential and nonessential proteins or amino acids.
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The human body requires approximately 20 amino acids for the synthesis of its proteins. The body can make only 13 of the amino acids; these are known as the nonessential amino acids. They are, in fact, essential but people do not have to get them from food we eat. There are 9 essential amino acids that are obtained only from food, and not made in the body. If the protein in a food supplies enough of the essential amino acids, it is called a complete protein. If the protein of a food does not supply all the essential amino acids, it is called an incomplete protein.
Animo acids
posted by SuPeR_GuRl617 on 1/2/05 3:55 PM
When proteins are digested, amino acids are left. They are classified as "essential" amino acids (which must be consumed in the diet) and "nonessential" amino acids (which can be made by the body from the essential amino acids). Proteins are described as essential and nonessential proteins or amino acids.The human body requires approximately 20 amino acids for the synthesis of its proteins. The body can make only 13 of the amino acids; these are known as the nonessential amino acids. They are, in fact, essential but people do not have to get them from food we eat. There are 9 essential amino acids that are obtained only from food, and not made in the body. If the protein in a food supplies enough of the essential amino acids, it is called a complete protein. If the protein of a food does not supply all the essential amino acids, it is called an incomplete protein.
Each amino acid has one amino group (NH2-) and one carboxyl group (-COOH), both attached to a central carbon atom.
Each amino acid also has another group of atoms, called the R-group, attached to the central carbon.
The R-group can be very simple or quite complex.
The monomers that make up proteins are called amino acids.
Each amino acid has one amino group (NH2-) and one carboxyl group (-COOH), both attached to a central carbon atom.
Each amino acid also has another group of atoms, called the R-group, attached to the central carbon.
The R-group can be very simple or quite complex.The common R-groups – the “alphabet of life” (GAVLIPFWYMCSTHKRDENQ)
Polarity: Nonpolar (aliphatic, aromatic); Neutral – polar; Acidic; Basic
R = Hydrogen ( Gly* )
Aliphatic ( Ala*, Val, Leu*, Ile, Pro)
Aromatic ( Phe, Trp, Tyr*)
Sulfur Containing ( Met*, Cys* )
Alcohol Containing ( Ser*, Thr )
Basic R Groups ( His*, Lys*, Arg )
Acidic R Groups ( Asp, Glu* )
Amides ( Asn, Gln* )
(You should know all amino acids by there 1 and 3 letter codes, and will
be responsible for drawing the structures of those marked with an *)
Aliphatic or Alkane (Gly, Ala, Val, Leu, Ile, Pro)
Aromatic Amino Acids (Phe, Trp, Tyr)
Absorb light at 280 nm, UV absorption used as a measure of protein concentration–Warburg-Christian
Tyr side chain has pKa = 10.1
The OH of Tyr can also be phosphorylated–regulation of enzyme activitySulfur containing amino acids (Met, Cys)
Met is (almost always) first amino acid translated (AUG codon=Met)
Cys side chain, pKa= 8.3, carries a net negative charge at basic pH
Cys can form covalent disulfide bond by oxidation ( -C-S-S-C- )Hydroxyl containing amino acids (Ser, Thr)
OH group can be phosphorylated, mechanism for regulation of activity
OH group (Ser, Thr) site for attachment of carbohydratesBasic Amino Acids (Lys, Arg, His)
Lys: pKa= ~10; Arg: pKa= ~12; positive charge at physiological pH
His is the least basic, pKa= ~6-7; catalysis involving proton transfer
Acidic Amino Acids and Their Amides (Asp, Glu, Asn, Gln)Glu, Asp: pKa= ~4 for acidic side chains–negative charge at neutral pH
Asn, Gln; amides forms of Asp, Glu; uncharged but polar and hydrophilic
Modified amino acids
occurs after incorporated into protein
phosphorylation of Ser, Thr, Tyr
addition of carbohydrate (Ser, Thr, Asn) or lipid moieties
g-carboxyglutamic acid in prothrombin–binds Ca++4-hydroxyproline and 5-hydroxylysine in collagen
Uncommon amino acids and their derivatives
D-alaine (bacterial cell walls)
L-ornithine (urea cycle, polyamine synthesis)
Homoserine
GABA (g-amino butyric acid)
serotonin and melatonin (5-methoxy-N-acetyl tryptamine is an important hormone that plays a role in the regulation of the circadian sleep-wake cycle.)
adrenalin (phenylalanine precursor)– neurotransmitters
L-thyroxine is a thyroid hormone
histamine, allergy symptoms
Ionization / Titration properties of amino acids ; pKa ‘sTitration curves of amino acids involve two (or three) functional groups
+H3N – CHR – COOH : R acidic (Glu, Asp ) ~ 4
~9-10 ~2 R basic (His ~ 6; Lys ~ 10.5; Arg ~ 12.5)
R other (Cys ~ 8.3 ; Tyr) ~ 10.1)
Isoelectric point (pI)
pH at which there is no net charge, electrically neutral
amino acids with ionizable carboxyl side chains (+1 0 -1 -2)
pI= average of pKa’s of the two carboxyl groups ( pI = (pK1 + pK2) / 2 )
amino acids with N containing ionizable groups (+2 +1 0 -1)
pI = average of pKa’s of the N groups ( pI = (pK2 + pK3) / 2 )
(Another site for viewing AMINO ACIDS at OMM (Online Macromolecular Museum)
(Ready for an amino acid quiz – go to CMU or Curtin!!)Peptide Bonds – Proteins are linear polymers of a.a. residues linked by “peptide bonds.”
Reaction: a.a.R1 + a.a.R2 = dipeptide (R1-R2) + water
DG of this reaction is +10 kJ/mol ; proteins are metastable
(acid hydrolysis (6N HCl) / proteases
Resonance structures result in planar amide group – trans form is favored (Peptide bond, MIT site)
Peptides (dipeptide, tripeptide, etc. ….. polypeptide – proteins)
Primary Structure : +H3N – GVLAADEMLLKFYEE – COO-
N-terminus C-terminus
Animo acids –> amino acid residues (Glycyl-valyl-leucyl-alanyl-alanyl-aspartyl- etc.)
Blocking groups: N-terminus (formyl- , acetyl- ); C-terminus (amide)
Conformation of polypeptides – rotational freedom limited to bonds on a-carbon
f is the rotation with N1 bond
j is the rotation with the C2 bond
Properties of polypeptides
polyampholytes, amino acid side chains determines pI
charge on polypeptide varies with pH
charge characteristics used for separation of peptides by electrophoresis
isoelectric focusing in a pH gradient used to determine pI for a protein experimentally
Small Peptides of Physiological InterestGlutathione (GSH or gGlu-Cys-Gly) – antioxidant
scavenger for oxidizing agents (2 GSH = GS-SG + 2 H)
Enkephalins (pain relief–found in brain)- Tyr-Gly-Gly-Phe-Leu (or Met)
natural brain analgesics – have structural similarity to opiates
Oxytocin (induction of labor) and Vasopressin (antidiuretic) – Nonapeptides
Other hormones (insulin, Human growth hormone)
Aspartame (Asp-Phe-methyl ester)
"NutraSweet" – ~200x sweeter than sugar
Concern about Phe and oxidation of methanol
Phenylketonuria (PKU) – accumulation of phenylpyruvate
Gramicidin S – cyclic decapeptide – Peptides can be antibioticsGramicidin A (Arizona site)
15 alternating D- and L-amino acid residues blocked at both ends, containing mostly hydrophobic amino acids.
Formyl-L-Val-Gly-L-Ala-D-Leu-L-Ala-D-Val-L-Val-D-Val-L-Trp-
-D-Leu-L-Trp-D-Leu-L-Trp-D-Leu-L-Trp-ethanolamine
2 molecules form a helix with oily exterior, hydrophilic interior
form a pore in membrane transports ions into bacterial cells, disrupts the ion concentrations, and kill cells -
A Valentine’s Gift from Dr.Stein for Victor 😆
Selenocysteine (Sec, U)
the curly thing reminds me of…alpha helix…aww 🙄 😆 👿Selenocysteine is an amino acid that is present in several enzymes (for example glutathione peroxidases, tetraiodothyronine 5′ deiodinases, thioredoxin reductases, formate dehydrogenases, glycine reductases and some hydrogenases). Selenocysteine has a structure similar to cysteine, but with an atom of selenium taking the place of the usual sulfur. Proteins that include a selenocysteine residue are called selenoproteins.
Unlike other amino acids present in biological proteins, however, it is not coded for directly in the genetic code. Selenocysteine is encoded in a special way by a UGA codon, which is normally a stop codon. The UGA codon is made to encode selenocysteine by the presence of a SECIS element (SElenoCysteine Insertion Sequence) in the mRNA. The SECIS element is defined by characteristic nucleotide sequences and secondary structure base-pairing patterns. In eubacteria, the SECIS element is located immediately following the UGA codon within the reading frame for the selenoprotein. In archaea and in eukaryotes, the SECIS element is in the 3′ untranslated region (3′ UTR) of the mRNA, and can direct multiple UGA codons to encode selenocysteine residues. When cells are grown in the absence of selenium, translation of selenoproteins terminates at the UGA codon, resulting in a truncated, nonfunctional enzyme.
Like the other amino acids used by cells, selenocysteine has a specialized tRNA. The primary and secondary structure of selenocysteine tRNA, tRNA(Sec), differ from those of standard tRNAs in several respects, most notably in having an 8-base (bacteria) or 9-base (eukaryotes) pair acceptor stem, a long variable region arm, and substitutions at several well-conserved base positions. The selenocysteine tRNAs are initially charged with serine by seryl-tRNA ligase, but the resulting Ser-tRNA(Sec) is not used for translation because it is not recognised by the normal translation factor (EF-Tu in bacteria, EF1alpha in eukaryotes). Rather, the tRNA-bound seryl residue is converted to a selenocysteyl-residue by the pyridoxal phosphate-containing enzyme selenocysteine synthase. Finally, the resulting Sec-tRNA(Sec) is specifically bound to an alternative translational elongation factor (SelB or mSelB) which delivers it in a targeted manner to the ribosomes translating mRNAs for selenoproteins. The specificity of this delivery mechanism is brought about by the presence of an extra protein domain (in bacterial SelB) or an extra subunit (SBP-2 for eukaryotic mSelB) which bind to the corresponding RNA secondary structures formed by the SecIS elements in selenoprotein mRNAs. The SecIS elements of bacterial selenoproteins (as far as analysed) are located within the coding sequences immediately following the UGA codons for selenocysteine, those of Eukarya and Archaea are located in the 3′ UTR of the respective mRNAs. In addition, at least one case has been described for an archaeal selenoprotein mRNA containing its SecIS in the 5′ UTR.
An extra gift: Selenocysteine: The 21st Amino Acid
Enjoy 😉
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