Download Amino acids

2013-10-16
Amino acids
1.
Amino acids of proteins:
•
classification of amino acids based on the polarity of the side
chain group, amino acids present in proteins
essential amino acids,
glycogenic and ketogenic amino acids,
non-standard (derived) amino acids,
the ionic state of amino acids (acid-base properties, dipolar
form, isoelectric point, the Henderson-Hasselbach equation),
reactions of α-amino and α-carboxyl groups: formation of
ester, acid chloride, Schiff’s base, decarboxylation,
N-methylation, N-acetylation.
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2. The peptide bond: consequences of resonance structure,
partial double bond, geometric isomerism.
Department of General Chemistry
Poznań University of Medical Sciences
2013/14
Protein Amino Acids
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While their name implies that
amino acids are compounds that
contain an —NH2 group and a —
COOH group, these groups are
actually present as —NH3+ and —
COO– respectively.
More than 700 amino acids occur
naturally, but 20 of them are
especially important.
These 20 amino acids are the
building blocks of proteins. All
are α-amino acids.
Only L-isomer can build proteins.
They differ in respect to the group
attached to the α carbon.
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Fundamentals
• The precise amino acid content, and the sequence of those
amino acids, of a specific protein, is determined by the
sequence of the bases in the gene that encodes that protein.
• The chemical properties of the amino acids of proteins
determine the biological activity of the protein.
• Proteins not only catalyze all (or most) of the reactions in
living cells, they control virtually all cellular process.
• Proteins contain within their amino acid sequences the
necessary information to determine how that protein will fold
into a three dimensional structure, and the stability of the
resulting structure
Amino Acids
H
O
C
C
+
H3N
–
O
R
• The amino acids obtained by hydrolysis
of proteins differ in respect to R (the
side chain).
• The properties of the amino acid vary as
the structure of R varies.
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Amino Acids - glycine
Glycine
+
H3N
H
O
C
C
–
O
(Gly or G)
H
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Glycine is the simplest, the smallerst, and the only one that is achiral amino
acid.
It is ambivalent, meaning that it can be inside or outside of the protein
molecule.
In aqueous solution at or near neutral pH, glycine will exist predominantly
as the zwitterion
The isoelectric point or isoelectric pH of glycine will be centered between
the pKas of the two ionizable groups, the amino group and the carboxylic
acid group.
Amino Acids - alanine
H
O
C
C
+
H3N
–
O
CH3
Alanine
(Ala or A)
•Alanine is a hydrophobic molecule.
• It is ambivalent, meaning that it can be inside or outside of the protein molecule.
•The α carbon of alanine is optically active; in proteins, only the L-isomer is found.
• Alanine is the α-amino acid analog of the α-keto acid pyruvate, an intermediate in sugar
metabolism. Alanine and pyruvate are interchangeable by a transamination reaction.
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Amino Acids - valine
H
O
C
C
+
H3N
–
O
CH(CH3)2
Valine
(Val or V)
•Valine, an essential amino acid, is hydrophobic, and as expected, is usually found in
the interior of proteins.
•Valine is often referred to as one of the amino acids with hydrocarbon side chains, or as
a branched chain amino acid.
Amino Acids - leucine
H
O
C
C
+
H3N
–
O
CH2CH(CH3)2
Leucine
(Leu or L)
•Leucine, an essential amino acid, is one of the three amino acid with a
branched hydrocarbon side chain.
•Like valine, leucine is hydrophobic and generally buried in folded
proteins.
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Amino Acids - isoleucine
H
O
C
C
+
H3N
–
O
Isoleucine
(Ile or I)
CH3CHCH2CH3
•Isoleucine, an essential amino acid, is one of the three amino acids having branched
hydrocarbon side chains.
•It is usually interchangeable with leucine and occasionally with valine in proteins.
The side chains of these amino acids are not reactive and therefore not involved in any
covalent chemistry in enzyme active centers. However, these residues are critically
important for ligand binding to proteins, and play central roles in protein stability.
•The β carbon of isoleucine is optically active, just as the β carbon of threonine.
Amino Acids - methionine
H
O
C
C
+
H3N
–
O
Methionine
(Met or M)
CH3SCH2CH2
•Methionine, an essential amino acid, is one of the two sulfur-containing amino
acids.
•The side chain is quite hydrophobic and methionine is usually found buried within
proteins.
•Unlike cysteine, the sulfur of methionine is not highly nucleophilic, although it will
react with some electrophilic centers.
•It is generally not a participant in the covalent chemistry that occurs in the
active centers of enzymes.
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Amino Acids - proline
H
O
C
C
+
•Proline is formally NOT an amino acid,
but an imino acid. Nonetheless, it is
called an amino acid.
When proline is in a peptide bond, it does
not have a hydrogen on the α amino
group, so it cannot donate a hydrogen
bond to stabilize an α helix or a β sheet.
–
H2N
O
CH2
H2C
Proline
C
H2
(Pro or P)
It is often said, inaccurately, that proline
cannot exist in an α helix. When proline
is found in an α helix, the helix will
have a slight bend due to the lack of
the hydrogen bond.
Amino Acids- phenylalanine
•As the name suggests, phenylalanine,
an essential amino acid, is a derivative
of alanine with a phenyl substituent on
the β carbon.
•Phenylalanine is quite hydrophobic
and even the free amino acid is not very
soluble in water. Due to its
hydrophobicity, phenylalanine is
nearly always found buried within a
protein.
•The π electrons of the phenyl ring can
stack with other aromatic systems
and often do within folded proteins,
adding to the stability of the
structure.
H
O
C
C
+
H3N
–
O
CH2
Phenylalanine
(Phe or F)
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Amino Acids - tryptophan
H
O
C
C
+
•Tryptophan, an essential amino
acid, is the largest of the amino
acids.
• It is also a derivative of alanine,
having an indole substituent on the
β carbon.
•The indole nitrogen can
hydrogen bond donate, and as a
result, tryptophan, or at least the
nitrogen, is often in contact with
solvent in folded proteins.
–
H3N
O
CH2
Tryptophan
N
(Trp or W)
H
Amino Acids - asparagine
•Asparagine is the amide of aspartic acid.
The amide group does not carry a formal
charge under any biologically relevant pH
conditions.
•The amide is rather easily hydrolyzed,
converting asparagine to aspartic acid. This
process is thought to be one of the factors
related to the molecular basis of aging.
•Asparagine has a high propensity to
hydrogen bond, since the amide group can
accept two and donate two hydrogen bonds.
•It is found on the surface as well as buried
within proteins.
•Asparagine is a common site for
attachment of carbohydrates in
glycoproteins.
H
O
C
C
+
H3N
–
O
H2NCCH2
O
Asparagine
(Asn or N)
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Amino Acids - glutamine
•Glutamine is the amide of glutamic acid,
and is uncharged under all biological
conditions.
•The additional single methylene group in
the side chain allows glutamine in the free
form or as the N-terminus of proteins to
spontaneously cyclize and deamidate
yielding the six-membered ring structure
pyrrolidone carboxylic acid, which is found
at the N-terminus of many immunoglobulin
polypeptides. This causes obvious
difficulties with amino acid sequence
determination.
+
H3N
H
O
C
C
–
O
H2NCCH2CH2
O
Glutamine
(Gln or Q)
Amino Acids - serine
H
O
C
C
+
H3N
Serine
(Ser or S)
–
O
CH2OH
•Serine differs from alanine in that one of the methylenic hydrogens is replaced
by a hydroxyl group.
•Serine is one of two hydroxyl amino acids.
•Both are commonly considered to by hydrophilic due to the hydrogen bonding
capacity of the hydroxyl group.
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Amino Acids - threonine
H
O
C
C
+
H3N
Threonine
(Thr or T)
–
O
CH3CHOH
•Threonine, an essential amino acid, is a hydrophilic molecule.
•Threonine is an other hydroxyl-containing amino acid.
• Both the α and β carbons of threonine are optically active.
Amino Acids - aspartate
H
O
C
C
+
H3N
–
Aspartic Acid
(Asp or D)
O
•Aspartic acid is one of two acidic amino acids.
Aspartic acid and glutamic acid play important
roles as general acids in enzyme active centers,
as well as in maintaining the solubility and
ionic character of proteins.
•The pKa of the β carboxyl group of aspartic acid
in a polypeptide is about 4.0
•Aspartic acid has an α-keto homolog,
oxaloacetate, just as pyruvate is the α-keto
homolog of alanine.
• Aspartic acid and oxaloacetate are
interconvertable by a simple transamination
reaction, just as alanine and pyruvate are
interconvertible. Oxaloacetate is one of the
intermediates of the Krebs cycle.
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Amino Acids - glutamate
•Glutamic acid has one additional methylene
group in its side chain than does aspartic acid.
The side chain carboxyl of aspartic acid is
referred to as the β carboxyl group, while that of
glutamic acid is referred to as the γ carboxyl
group.
The pKa of the γ carboxyl group for glutamic acid
in a polypeptide is about 4.3, significantly higher
than that of aspartic acid. This is due to the
inductive effect of the additional methylene
group.
•In some proteins, due to a vitamin K dependent
carboxylase, some glutamic acids will be
dicarboxylic acids, referred to as γ
carboxyglutamic acid, that form tight binding
sites for calcium ion.
+
H3N
H
O
C
C
–
O
–
OCCH2CH2
O
Glutamic Acid
(Glu or E)
Amino Acids - tyrosine
•Tyrosine, an essential amino acid, is also an
aromatic amino acid and is derived from
phenylalanine by hydroxylation in the para
position.
• Tyrosine is significantly more soluble that is
phenylalanine. The phenolic hydroxyl of tyrosine
is significantly more acidic than are the aliphatic
hydroxyls of either serine or threonine, having a
pKa of about 9.8 in polypeptides. As with all
ionizable groups, the precise pKa will depend to
a major degree upon the environment within the
protein.
•Tyrosines that are on the surface of a protein
will generally have a lower pKa than those that
are buried within a protein; ionization yielding
the phenolate anion would be exceedingly
unstable in the hydrophobic interior of a protein.
H
O
C
C
+
H3N
–
O
CH2
Tyrosine
OH
(Tyr or Y)
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Amino Acids - cysteine
H
O
C
C
+
H3N
Cysteine
–
O
(Cys or C)
CH2SH
•Cysteine is one of two sulfur-containing amino acids; the other is methionine.
•Cysteine also plays a key role in stabilizing extracellular proteins.
•Cysteine can react with itself to form an oxidized dimer by formation of a disulfide bond.
The environment within a cell is too strongly reducing for disulfides to form, but in the
extracellular environment, disulfides can form and play a key role in stabilizing many such
proteins, such as the digestive enzymes of the small intestine
Amino Acids - lysine
H
O
C
C
+
Lysine
(Lys or K)
H3N
–
O
+
CH2CH2CH2CH2NH3
•Lysine. an essential amino acid, has a positively charged ε-amino group (a primary
amine).
•The ε-amino group has a significantly higher pKa (about 10.5 in polypeptides) than does
the α-amino group.
•The amino group is highly reactive and often participates in a reactions at the active
centers of enzymes.
•Lysines are often found buried with only the ε amino group exposed to solvent.
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Amino Acids - arginine
H
O
C
C
+
H3N
–
O
Arginine
(Arg or R)
CH2CH2CH2NHCNH2
+
NH2
•Arginine, an essential amino acid, has a positively charged guanidino group.
•Arginine is well designed to bind the phosphate anion, and is often found in the active
centers of proteins that bind phosphorylated substrates.
•As a cation, arginine, as well as lysine, plays a role in maintaining the overall charge
balance of a protein.
•Arginine also plays an important role in nitrogen metabolism.
Amino Acids - histidine
H
O
C
C
+
H3N
–
O
Histidine
CH2
(His or H)
N
NH
•Histidine, an essential amino acid, has as a positively charged imidazole functional
group.
•The imidazole makes it a common participant in enzyme catalyzed reactions. The
unprotonated imidazole is nucleophilic and can serve as a general base, while the
protonated form can serve as a general acid.
•The residue can also serve a role in stabilizing the folded structures of proteins.
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Amino Acids: #21
(2001)
Selenocysteine
Selenocysteine is incorporated into some proteins at a
UGA codon, which is normally a stop codon.
Fischer Projections of Amino
Acids
• All amino acids except glycine are chiral.
• Amino acids have stereoisomers.
• In biological systems, only L amino acids are
used in proteins.
COOH
COOH
H2N
H
CH3
L-Alanine
Cysteine
H
NH2
CH3
D-Alanine
COOH
H2N
H
CH2SH
L-Cysteine
COOH
H
NH2
CH2SH
D-
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CLASSIFICATION
Nonpolar Amino Acids
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Amino acids are classified as nonpolar when the R groups
are H, alkyl, or aromatic.
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Polar Amino Acids
(not charged)
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Amino acids are classified as polar when the R groups are
alcohols, thiols, or amides.
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Acidic and Basic Amino Acids (charged)
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Amino acids are classified as acidic when the R group is a
carboxylic acid.
Amino acids are classified as basic when the R group is an
amine.
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Essential amino acids
• Humans can produce 10 of the 20 amino acids.
The others must be supplied in the food.
• Failure to obtain enough of even 1 of the 10 essential
amino acids, those that we cannot make, results
in degradation of the body's proteins and so forth —
to obtain the one amino acid that is needed.
• Unlike fat and starch, the human body does not store
excess amino acids for later use—the amino acids must
be in the food every day.
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Essential and nonessential amino acids
“PVT TIM HALL”
• Proline, Valine, Threonine,Tryptophan,
Isoleucine, Methionine Histidine, Arginine,
Leucine, Lysine
• “PVT TIM HALL”
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Semiessential amino acids
• The essential amino acids are arginine (required for the
young, but not for adults)
• Histidine, and
• Tyrosine is produced from phenylalanine, so if the diet is
deficient in phenylalanine, tyrosine will be required as well.
Food source
• Eggs, milk, meat
• Wheat, rice, oats
• Corn
• Beans
• Peas
• Almonds, walnuts
• Soy
Amino acid missing
None
Lys
Lys, Trp
Met, Trp
Met
Lys, Trp
Low in Met
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Effects of Low Levels in Diet
• Deficiencies of tyrosine, tryptophan,
phenylalanine, and histidine can cause
neurological problems and depression
• Low tryptophan can also cause anxiety and
insomnia
• Low methionine causes allergy like symptoms and
autoimmune disorders
• leucine, isoleucine, and valine, provide recovery
and energy needs
Related disorders
PKU (PHENYLKETONURIA)
• Deficient in enzyme phenylalanine hydroxylase, therefore can
not metabolize phenylalanine to tyrosine and it accumulates
• If left untreated can lead to brain damage, mental retardation,
and seizures
• Tested in newborns with blood test
• Management is low PKU diet, no meat, dairy, eggs, starchy
foods, nuts, legumes, and aspartame
• Phenylalanine is precursor for tyrosine synthesis and without
it tyrosine can not be synthesized, therefore must be
supplemented
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Related disorders
Maple Syrup Urine Disease
• deficiency of branched- chain α-keto acid dehydrogenase
complex (BCKDH)
• Build up of leucine, isoleucine and valine
• Characterized in infant by sweet smelling urine similar to
maple syrup
• Vomiting, poor feeding , dehydration, seizures, ketoacidosis,
brain damage and eventually death
• Managment with supplements and special diet
Biologically important derivatives
of protein amino acids
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Anyone who has used an "anti-histamine" to alleviate the symptoms
of exposure to an allergen can appreciate the role that histamine
a decarboxylated derivative of histidine plays in mediating the
body's response to allergic reactions.
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L-DOPA, which is a derivative of tyrosine, has been used to treat
Parkinson's disease. This compound received notoriety a few years
ago in the film Awakening, which documented it's use as a treatment
for other neurological disorders.
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Thyroxine, which is an iodinated ether of tyrosine, is a hormone
that acts on the thyroid gland to stimulate the rate of metabolism.
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Tyroxine
L-DOPA
Histamine
Ketogenic and glucogenic amino acids
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Glucogenic amino acids are those that give rise to a net
production of pyruvate or Krebs cycle intermediates, such as
a-ketoglutarate or oxaloacetate, all of which are precursors to
glucose via gluconeogenesis.
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All amino acids except lysine and leucine are at least partly
glucogenic.
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Lysine and leucine are the only amino acids that are solely
ketogenic, giving rise only to acetylCoA or acetoacetylCoA,
neither of which can bring about net glucose production.
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Ketogenic and glucogenic amino acids
Ketogenic and glucogenic amino acids
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Non-standard (derived) amino acids
• Other non-standard amino acids found in proteins are formed
by post-translational modification, which is modification
after translation in protein synthesis.
• These modifications are often essential for the function or
regulation of a protein; for example, the carboxylation of
glutamate allows for better binding of calcium cations,
• and the hydroxylation of proline is critical for maintaining
connective tissues.
Non-standard (derived) Amino Acids
•
Hydroxylysine and hydroxyproline, are simply functionalized
derivatives of a previously described compound. These two amino
acids are found only in collagen, a common structural protein.
•
Homoserine and homocysteine are higher homologs of their
namesakes. Homocystein is related to a higher risk of coronary
heart disease, stroke and peripheral vascular disease.
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The amino group in beta-alanine has moved to the end of the
three-carbon chain. It is a component of pantothenic acid,
a member of the vitamin B complex and an essential nutrient.
Acetyl coenzyme A is a pyrophosphorylated derivative of a
pantothenic acid amide.
•
The gamma-amino homolog GABA is a neurotransmitter inhibitor
and antihypertensive agent.
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Other Natural Amino Acids
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Amino acid naturally occuring but not
in proteins
Amino acids as acids and bases
• Amino acids contain ionizable groups which are
weak acids (proton donors) or weak base (proton
acceptors)
• The carboxyl group is a weak acid
• The ammonia group is a weak base
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Titration curve for glycine
Zwitterions
• Both the –NH2 and the –COOH groups in an amino acid
undergo ionization in water.
• A zwitterion forms that has + and – charge.
• At the isoelectric point (pI), the + and – charges in the
zwitterion are equal.
+
NH2—CH2—COOH
Glycine
H3N—CH2—COO
Zwitterion of glycine
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Amino Acids as Acids
•
In solutions more basic than the pI, the NH3+ in the amino acid
donates a proton.
OH–
+
H3N—CH2—COO–
H2N—CH2—COO–
Zwitterion
at pI
Negative ion
Higher pH
Amino Acids as Bases
•
In solution more acidic than the pI, the COO- in the amino acid
accepts a proton.
H+
+
H3N—CH2
—COO–
Zwitterion
at pI
+
H3N—CH2—COOH
Positive ion
Low pH
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pH and Ionization
•
Acidic amino acids such as aspartic acid have a second
carboxyl group that can donate and accept protons.
•
The pI for aspartic acid occurs at a pH of 2.8.
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Henderson-Hasselbalch equation
Ka = [H+][A]/[HA]
or
[H+] = Ka[HA]/[A]
- log [H+] = -log Ka + log [A]/[HA]
or
pH = pKa + log [A]/[HA]
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HH equation idea
The properties of a amino acid will be determined partly by whether the side
chain functional groups, the NH2 , and the COOH are charged or not. The HH
equation tells us that this will depend on the pH and the pKa of the functional
group.
•
•
•
•
If the pH is 2 units below the pKa of an amino acid, the HH equation becomes,
-2 = log A/HA, or .01 = A/HA.
This means that the functional group will be about 99% protonated ( with either
0 or +1 charge, depending of the functional group).
If the pH is 2 units above the pKa, the HH equation becomes
2 = log A/HA, or 100 = A/HA.
Therefore the functional group will be 99% deprotonated.
If the pH = pka, the HH equation becomes
0 = log A/HA, or 1 = A/HA.
Therefore the functional group will be 50% deprotonated
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Reactions of amino acids
• -NH2 group reactions
• -COOH group reactions
• -R group reactions
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Transamination
N-acetylation
Acetylation of the N-terminal alpha-aminoacids of proteins is a widespread
modification in eukaryotes. 80-90% of human proteins are modified in this
manner, and the pattern of modification is found to be conserved throughout
evolution. The modification is performed by N-alpha acetyltransferases
(NATs), a sub-family of the GNAT superfamily of acetyltransferases, which
also include histone acetyl transferases. In histone acetylation and
deacetylation, the histones are acetylated and deacetylated on lysine
residues in the N-terminal tail as part of gene regulation.
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S-adenosyl-L-metionine
S-Adenosyl methionine (SAM) is a common cosubstrate involved in methyl group
transfers. It is made from adenosine triphosphate (ATP) and methionine by methionine
adenosyltransferase (EC 2.5.1.6.). The methyl group (CH3) attached to the methionine
sulfur atom in SAM is chemically reactive. This allows donation of this group to an
acceptor substrate in transmethylation reactions. More than 40 metabolic reactions
involve the transfer of a methyl group from SAM to various substrates, such as nucleic
acids, proteins, lipids and secondary metabolites
N-methylation
Protein methylation is one type of post-translational modification. Typically takes
place on arginine or lysine amino acid residues in the protein sequence. Protein
methylation has been most-studied in the histones. The transfer of methyl groups
from S-adenosyl methionine to histones is catalyzed by enzymes known as
histone methyltransferases. Histones that are methylated on certain residues can
act epigenetically to repress or activate gene expression
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Reactions of α-Amino Acids
4. Specific Oxidation
Cysteine-Cystine Interconversion
L-cystine
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The Peptide Bond
• A peptide bond is an amide bond between the carboxyl
group of one amino acid and the amino group of the next
amino acid.
O
CH3 O
||
|
||
+
+
H3N—CH2—C—OH + H3N—CH—C—O–
O H CH3 O
|| | |
||
+
H3N—CH2—C—N—CH—C—O–
the peptide bond
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The peptide bond
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A Dipeptide
• A peptide is named from the free amine
(NH3+) using -yl endings for the names of the
amino acids.
• The last amino acid with the free carboxyl
group (COO-) uses its amino acid name.
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Peptides
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