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20 Amino Acids

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20 Amino Acids

Postby bearhug » Fri Jan 20, 2006 4:17 pm

I have a test coming up in my BCMB (Biochemistry) lecture. I have to memorize all 20 amino acids, 3 letter codes, 1 letter codes, pka values, and the structures for each amino acid at pH 1, 7, and 14. While structures will probably be pretty easy since they're all stereoisomers, I'm just curious other than Biochemists, how much of this will I have to remember for my future studies in biology? I'm assuming the naming will be useful but what about the rest?
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Postby Poison » Fri Jan 20, 2006 5:10 pm

I think it is completely USELESS. Just improves your memorizing skills nothing more. :) The names are useful, but I don't think the others are.
We are memorizing the names of animals and plants. They won't be useful for me either. But, unfortunately, that's it.
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Postby MrMistery » Fri Jan 20, 2006 6:16 pm

i had to learn the genetic code by heart last year to. Forgot everything by now :( Agreed with Ozge, it will probably be useless...
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Postby victor » Sat Jan 21, 2006 11:25 am

MrMistery wrote:i had to learn the genetic code by heart last year to. Forgot everything by now :( Agreed with Ozge, it will probably be useless...


What about the hint that I gave you? I even still remember all of them by now...and it really helps me in translating codon in this forum because I never bring bio-books while posting here.. :lol:
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Re: 20 Amino Acids

Postby Enzyme » Sat Jan 21, 2006 12:45 pm

bearhug wrote:I have a test coming up in my BCMB (Biochemistry) lecture. I have to memorize all 20 amino acids, 3 letter codes, 1 letter codes, pka values, and the structures for each amino acid at pH 1, 7, and 14. While structures will probably be pretty easy since they're all stereoisomers, I'm just curious other than Biochemists, how much of this will I have to remember for my future studies in biology? I'm assuming the naming will be useful but what about the rest?


You should only know the names and the structure of each amino acid. To memorize the values of pka of each amino acid is totally useless because numbers are very easily to be forgotten and to memorize the characteristics of each amino acid at different pH is useless too.

This information is useless because the most sure thing is that you'll forget it in a little time. If you work in Biochemistry field, don't worry, sure that the most of the people who work in it look for that information in books :).
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Postby MrMistery » Sat Jan 21, 2006 2:02 pm

@victor
I haven't opened that file since. :) I just don't need to know the genetic code now, i have a lot of other stuff to memorize. When i'll need it, i know where to go ;)
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Memorizing a whole load of stuff in bio

Postby nh » Thu Feb 09, 2006 5:03 pm

Hi guys, any method that is good on memorizing huge load of info for bio and medicine?
I m currently using acronyms but I do not know how to remember
bits and pieces of info thats very hard, if not impossible to link. Eg. the 20 amino acids properties. I know some things are not necessary to remember but I would like to know how if I ever have to.
Anybody knows how? Thanks!
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Postby CoolJay221 » Thu Feb 09, 2006 7:02 pm

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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 activity

Sulfur 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 carbohydrates

Basic 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 ‘s

Titration 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 Interest

Glutathione (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 antibiotics

Gramicidin 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
ANY GIRLS WANT TO TALK?
PM me to find out my personal!

Also My site!!!!!
http://napoleon.forumup.org/index.php?mforum=napoleon
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Postby victor » Fri Feb 10, 2006 10:18 am

I have one question....do anyone know an amino acid smbolized with Sec (three letter symbol) or U (one letter symbol)??
I think it's called Selenocysteine....have a profile about that??
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Postby 2810712 » Fri Feb 10, 2006 1:05 pm

i have heard about it vic.
but don't remember exactly...
2 AAs [ S containing] ...they ... :oops:
Last edited by 2810712 on Thu Feb 16, 2006 1:48 pm, edited 2 times in total.
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Postby Dr.Stein » Mon Feb 13, 2006 9:40 am

A Valentine's Gift from Dr.Stein for Victor :lol:

Selenocysteine (Sec, U)

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the curly thing reminds me of...alpha helix...aww :roll: :lol: :evil:

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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Postby victor » Mon Feb 13, 2006 10:22 am

Ahh :D thanks or the gift..:lol:
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