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Chapter 2
The Same 20 Amino Acids Serve as
Amino acids
Building Blocks for All Proteins in Nature
生物化学精品课程
1. Proteins are extremely versatile (通用的) in function
and crucial in virtually all biological processes.
1.1 Almost all chemical reactions occurring in living
organisms are catalyzed by enzymes.
Amino acids
1.1.1 Many thousands of enzymes have been
discovered, each catalyzing a different kind of chemical
reaction.
1.1.2 Life would not occur without enzyme
catalysis.
1.1.3 Enzymes are the most varied and most
highly specialized proteins.
生物化学精品课程
1. Proteins are extremely versatile (通用的) in function
and crucial in virtually all biological processes.
1.2 Many small molecules and ions are transported by
specific proteins.
Amino acids
1.2.1 Some proteins transport molecules from one
organ to another, many exist in the blood plasma, e.g.,
hemoglobin (oxygen), serum albumin (fatty acids),
lipoproteins (lipids), and transferrin (iron).
1.2.2 Some proteins transport molecules across
plasma membrane or organelle membranes (glucose, amino
acids, nucleotides, chloride, potassium, sodium ions but not
water).
生物化学精品课程
1. Proteins are extremely versatile (通用的) in function
and crucial in virtually all biological processes.
1.3 Some proteins function as nutrient or storage proteins. For
example, many of such kind exist in plant seeds, animal eggs
(Ovalbumin of egg white, casein of milk). Ferritin （铁蛋白）
Amino acids
in animal tissue function to store ion (about 4500 ions are
stored in the cavity of each ferritin complex!).
1.4 Some proteins are responsible for the coordinated协调运动
motions (contraction, changing shape, moving about). For
example, actin and myosin in muscle and nonmuscle cells.
Tubulin and dynein in eukaryotic flagella and cilia.
生物化学精品课程
1. Proteins are extremely versatile (通用的) in function
and crucial in virtually all biological processes.
1.5 Some proteins are responsible for mechanical support
(strength and protection)
Amino acids
1.5.1 Collagen in tendons (筋腱), cartilage（软骨）,
and leather.
1.5.2 Elastin in ligaments (韧带).
1.5.3 Keratin角蛋白in hair, fingernails, feathers.
1.5.4 Fibroin in silk fibers and spider webs.
1.5.5 Resilin（节肢弹性蛋白） in wing hinges of
some insects.
生物化学精品课程
1. Proteins are extremely versatile (通用的) in function
and crucial in virtually all biological processes.
1.6 Some proteins function to defend the organisms
1.6.1 Immunoglobins in vertebrates
Amino acids
1.6.2 Fibrinogen纤维蛋白原and thrombin (凝血酶) in
blood-clotting
1.6.3 Snake venom, bacterial toxins, and toxic plant
proteins (ricin,篦麻毒素, 篦麻蛋白).
1.7 Some proteins help regulate cellular or physiological activity
1.7.1 Growth factors and transcription factors regulate cell
growth and differentiation.
1.7.2 Hormones (e.g., insulin, growth hormon) coordinate
activities of different cells in multi-cellular organisms.
生物化学精品课程
1. Proteins are extremely versatile (通用的) in function
and crucial in virtually all biological processes.
1.8 Some proteins are responsible for the generation and
transmission of nerve impulses.
Amino acids
1.8.1 Rhodopsin (视紫红质, 视网膜色素) responses to light
to generate vision.
1.8.2 Acetylcholine (乙酰胆碱) receptor are responsible for
transmitting nerve impulses at synapses (神经突触).
1.9 Many proteins have other functions. Antifreeze proteins protect
the blood of Antarctic fish from freezing. Special heat stable
proteins in thermophile（嗜热生物）bacteria.
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Chymotrypsin with its active site
Amino acids
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Fireflies emit light catalyzed by luciferase with ATP
Amino acids
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Erythrocytes contain a large amount of hemoglobins,
the oxygen-transporting protein.
Amino acids
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The protein keratin （角蛋白）is the chief structural
components of hair, scales, horn, wool, nails and feathers.
Amino acids
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2. All natural proteins were found to be built from a
repertoire （保留剧目）of 20 standard -amino acids
2.1 The earliest studies of proteins focused on the free
amino acids derived from these proteins.
Amino acids
2.1.1 The 1st amino acid (asparagine) was
discovered in 1806 from asparagus（芦笋，a green
vegetable).
2.1.2 The last (threonine) was not identified until
1938!
2.1.3 All the amino acids were given a trivial
(common) name. Glutamate from wheat gluten (sticky).
Tyrosine from cheese (“tyros” in Greek).
生物化学精品课程
2. All natural proteins were found to be built from a
repertoire （保留剧目）of 20 standard -amino acids
2.2 The 20 -amino acids share common structural
features.
Amino acids
2.2.1 Each has a carboxyl group and an amino
group (but one has an imino 亚氨基 group in proline)
bonded to the same carbon atom, designated as the carbon.
2.2.2 Each has a different side chain (or R group,
R=“Remainder of the molecule”).
2.2.3 The -carbons for 19 of them are asymmetric
(or chiral), thus being able to have two enantiomers（对
映体）. Glycine has no chirality.
生物化学精品课程
2. All natural proteins were found to be built from a
repertoire （保留剧目）of 20 standard -amino acids
Amino acids
In protein chemistry, we use Greek letter nomenclature.
生物化学精品课程
2. All natural proteins were found to be built from a
repertoire （保留剧目）of 20 standard -amino acids
2.3 The two enantiomers of each amino acid defined by the -carbon
are designated D- and L- forms (D for Dextrorotary, L for
Levorotary)
Amino acids
2.3.1 The D- and L-forms of amino acids are named in
reference to the absolute configuration of D- and L- glyceraldehydes
(whose structure was orignally assumed and confirmed by X-ray
crystallography later).
2.3.2 Only the L-amino acids have been found in proteins (Disomers have been found only in small peptides of bacteria cell walls
and in some peptide antibiotics).
2.3.3 The correlation of structure (or configuration) with
optical rotation is very complex and has not been successful to date!
(i.e., the D- and L-signs do not tell anything about their optical
rotation!)
生物化学精品课程
2. All natural proteins were found to be built from a
repertoire （保留剧目）of 20 standard -amino acids
2.4 The amino acids ionize in aqueous solutions.
Amino acids
2.4.1 Crystalline amino acids (in neutral aqueous
solutions) have melting points much higher than those of
other organic molecules of similar size.
2.4.2 The amino acids ionize to various states
depending on pH values.
2.4.3 The amino acids (of neutral side chains) exist
predominantly as dipolar ions, known as zwitterions
(German for “hybrid ions”).
生物化学精品课程
2. All natural proteins were found to be built from a
repertoire （保留剧目）of 20 standard -amino acids
2.5 Each amino acid is given a three-letter abbreviation and a oneletter symbol. They often the first three letter and the first letter.
When there is confusion, an alternative is used. They must be
remembered. (fig.)
Amino acids
2.6 All proteins in all species (from bacteria to human) are
constructed from the same set of 20 amino acids.
2.6.1 All proteins, no matter how different they are in
structure and function, are made from the 20 standard amino acids.
2.6.2 This fundamental alphabet of the protein language is at
least two billion years old.
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2. All natural proteins were found to be built from a
repertoire （保留剧目）of 20 standard -amino acids
Amino acids
Stryer’s method: walk from the amino group to the carboxyl
group, the hydrogen atom is on your left. L-Alanine
生物化学精品课程
2. All natural proteins were found to be built from a
repertoire （保留剧目）of 20 standard -amino acids
Amino acids
Align carbon atoms with L-glyceraldehyde, the amino group
is on the left.
生物化学精品课程
2. All natural proteins were found to be built from a
repertoire （保留剧目）of 20 standard -amino acids
Amino acids
The horizontal bonds project out of the plane of the paper,
the vertical behind.
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2. All natural proteins were found to be built from a
repertoire （保留剧目）of 20 standard -amino acids
Amino acids
Lined up by similarity: chiral to chiral, COO to CHO
生物化学精品课程
2. All natural proteins were found to be built from a
repertoire （保留剧目）of 20 standard -amino acids
Amino acids
生物化学精品课程
2. All natural proteins were found to be built from a
repertoire （保留剧目）of 20 standard -amino acids
Amino acids
生物化学精品课程
2. All natural proteins were found to be built from a
repertoire （保留剧目）of 20 standard -amino acids
Amino acids
Gly, G
Ala, A
Val, V
Leu, L
Met, M
Ile, I
生物化学精品课程
2. All natural proteins were found to be built from a
repertoire （保留剧目）of 20 standard -amino acids
Phe, F; Tyr, Y; Trp, W
Amino acids
生物化学精品课程
2. All natural proteins were found to be built from a
repertoire （保留剧目）of 20 standard -amino acids
Amino acids
Ser, S
Thr, T
Cys, C
Pro, P
Asn, N
Gln, Q
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2. All natural proteins were found to be built from a
repertoire （保留剧目）of 20 standard -amino acids
Lys, K; Arg, R; His, H
Amino acids
生物化学精品课程
2. All natural proteins were found to be built from a
repertoire （保留剧目）of 20 standard -amino acids
Asp, D; Glu, E
Amino acids
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3. The 20 amino acids are usually grouped according
to the properties (mainly polarity) of their R groups
3.1 Six amino acids have nonpolar, aliphatic（脂肪族的）
(hydrophobic) R groups.
3.1.1 They are Gly, Ala, Val, Leu, Ile, and Pro.
Amino acids
3.1.2 Gly has a hydrogen as its R group, having
minimal steric hindrance.
3.1.3 Pro has an imino group, instead of an amino
group, forming a five-membered ring structure, being
rigid in conformation.
生物化学精品课程
3. The 20 amino acids are usually grouped according
to the properties (mainly polarity) of their R groups
3.1.4 Pro is often found in the bends of folded protein
chains and often present on the surface of proteins.
Amino acids
3.1.5 In protein structure Gly offers the most flexibility,
while Pro the least!
3.1.6 Ala, Val, Leu, and Ile, have hydrocarbon R groups,
often involved in hydrophobic interactions.
生物化学精品课程
3. The 20 amino acids are usually grouped according
to the properties (mainly polarity) of their R groups
3.2 Phe, Tyr, and Trp have aromatic（芳香族的） R groups
3.2.1 Phe and Tyr both have benzene rings.
3.2.2 Tryptophan has an indole ring.
Amino acids
3.2.3 All three participate in hydrophobic interactions.
3.2.4 The -OH group in Tyr is an important functional group
in proteins. (phosphorylation, hydrogen bond, etc)
3.2.5 They are jointly responsible for the light absorption of
proteins at 280 nm
A=Log Io/I = ecl
Lambert-Beer’s law
e, extinction coefficient; c, concentration; l, optical length
生物化学精品课程
3. The 20 amino acids are usually grouped according
to the properties (mainly polarity) of their R groups
Amino acids
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3. The 20 amino acids are usually grouped according
to the properties (mainly polarity) of their R groups
3.3 Ser, Thr, Asn, Gln, Cys, and Met have polar,
uncharged R groups.
Amino acids
3.3.1 The R groups are more hydrophilic, due to
the presence of hydroxyl groups, sulfur atoms, or amide
groups.
3.3.2 -SH group of two Cys in proteins can be
oxidized to form a covalent disulfide bond.
3.3.3 Cys and Met often participate in
hydrophobic interactions.
生物化学精品课程
3. The 20 amino acids are usually grouped according
to the properties (mainly polarity) of their R groups
Amino acids
生物化学精品课程
3. The 20 amino acids are usually grouped according
to the properties (mainly polarity) of their R groups
3.4 Asp and Glu have carboxyl in their R groups. They have net
negative charge at pH 7.0, thus usually named as aspartate and
glutamate (conjugate base names, instead of aspartic acid and
glutamic acid, un-ionized form).
Amino acids
3.5 Arg, Lys, and His have positively charged R groups at pH 7.0.
3.5.1 Their R groups contain guanidino, amino, imidazole
groups respectively.
3.5.2 The side chain of His can be positively or uncharged
depending on the local environment near pH 7.0.
生物化学精品课程
3. The 20 amino acids are usually grouped according
to the properties (mainly polarity) of their R groups
3.6 The extent of hydrophobicity and hydrophilicity of the side
chains is reflected by their hydropathy index values. “-” values
usually mean hydrophilic, “+” values hydrophobic.
Amino acids
3.7 Nonstandard amino acids are found in certain proteins,
generally as a result of post-translational modifications.
3.7.1 These modifications are made after the standard
amino acids have been incorporated into proteins.
3.7.2 4-Hydroxyglutamate and 5-hydroxylysine in collagen.
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3. The 20 amino acids are usually grouped according
to the properties (mainly polarity) of their R groups
3.7.3 g-carboxyglutamate is found in the bloodclotting prothrombin (凝血素，an enzyme).
Amino acids
3.7.4 Desmosine is a covalent linkage made from
four Lys side chains in elastin（弹性蛋白）.
3.7.5 Selenocysteine is found in many enzymes
(having been recognized as the 21st amino acid in
ribosome-mediated protein synthesis!).
3.7.6 Many additional nonstandard amino acids
are found in cells, but not in proteins (e.g., ornithine 鸟氨
酸and citrulline瓜氨酸, intermediates in amino acid
metabolism).
生物化学精品课程
3. The 20 amino acids are usually grouped according
to the properties (mainly polarity) of their R groups
Amino acids
Nonstandard amino acids not found in protein
生物化学精品课程
3. The 20 amino acids are usually grouped according
to the properties (mainly polarity) of their R groups
Amino acids
Nonstandard amino acids not found in protein
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4. Amino acids, being both weak acids and bases, have
characteristic titration curves and pKa values
Amino acids
4.1 Amino acids can act both as acids and bases. The zwitterion
form of amino acids are ampholytes两性电解质. Amino acids can
be diprotic（双质子） and triprotic（三质子） acids.
4.2 Monoamino monocarboxylic α-amino acids (e.g., Gly, Ser,
Phe with no ionizable groups) all have similar two-stage titration
curves.
4.2.1 The first stage reflects the deprotonation（去质子化）
of the α-COOH group (pK1).
4.2.2 The second stage reflects the deprotonation of the α NH 3 + group (pK2).
4.2.3 The pKα value of the a-COOH is more than 2.0 units
smaller than that of acetic acid (pK α of 4.76), that is, a stronger
(weak) acid.
4.2.4 These amino acids have two buffering power regions.
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4. Amino acids, being both weak acids and bases, have
characteristic titration curves and pKa values
4.3 Acidic and basic amino acids have three-stage titration curves.
The additional stage is for the ionizable group on the side chains
(pKR).
Amino acids
4.4 There is a specific pH (designated pI) at which an amino acid
has equal positive and negative charge.
4.4.1 An amino acid does not move in an electric field at its
pI, called isoelectric point.
4.4.2 The pI of monoamino monocarboxylic amino acids
reflects a status at which the -COOH group is fully deprotonated,
but the -NH3+ group has not yet started deprotonating
pI = (pK1+pK2)/2
生物化学精品课程
4. Amino acids, being both weak acids and bases, have
characteristic titration curves and pKa values
4.4.3 The pI point of an acidic amino acid reflects a status at which
the α-COOH is fully deprotonated, but the side chain -COOH and
the a-NH3+ group have not yet started deprotonating
Amino acids
pI = (pK1+pKR)/2
4.4.4 The pI point of a basic amino acid reflects a status at which the
α -COOH and the side chain -NH3+ or -NH+= group have fully
deprotonated, but the NH3+ group not yet deprotonated
pI = (pKR+pK2)/2
4.4.5 The amino acids are positively charged at pH smaller than their
pI values, negatively charged at pH larger than their pI values.
生物化学精品课程
4. Amino acids, being both weak acids and bases, have
characteristic titration curves and pKa values
Amino acids
生物化学精品课程
4. Amino acids, being both weak acids and bases, have
characteristic titration curves and pKa values
Amino acids
生物化学精品课程
4. Amino acids, being both weak acids and bases, have
characteristic titration curves and pKa values
Amino acids
生物化学精品课程
4. Amino acids, being both weak acids and bases, have
characteristic titration curves and pKa values
Amino acids
An acidic amino acid pI=(pK1+pKR)/2
生物化学精品课程
4. Amino acids, being both weak acids and bases, have
characteristic titration curves and pKa values
A basic amino acid pI=(pKR+pK2)/2
Amino acids
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5. The 20 amino acids can be separated from each
other by ion-exchange chromatography
5.1 Each of the amino acids has a different pI value. Therefore,
each amino acid has a different net charge at a given pH.
5.2 The variously charged amino acids bind to charged synthetic
resins with various affinities.
Amino acids
5.2.1 When the resin is positively charged, negatively charged
amino acids (or other anions) will bind, and vice versa.
5.2.2 Amino acids having the same charge as the resin will not
bind.
5.2.3 The positively charged resin is called anion-exchange resin.
The negatively charged called cation-exchange resin (e.g., the
sulfonated polystyrene聚苯乙烯).
5.2.4 The resin (serving as the stationary phase) is usually
packed in a column (providing the mechanical support and stable
fluid flow).
生物化学精品课程
5. The 20 amino acids can be separated from each
other by ion-exchange chromatography
5.3 The bound amino acids can be eluted by running a pH or salt
gradient (serving as the mobile phase).
5.3.1 Amino acids will be eluted out in the order of their
binding affinity (strongly bound ones being eluted out later).
Amino acids
5.3.2 This way of separating amino acids (or other charged
biomolecules) is called ion-exchange chromatography.
5.3.3 Chromatography is a method of separating substances
by allowing them to partition between two phases, one mobile, one
stationary (differences in charge, size, hydrophobic interactions,
specific interactions can be exploited for substance separation with
chromatography).
A.J. Martin and R.L. Synge won the Nobel Prize in 1952
for inventing chromatography.
生物化学精品课程
5. The 20 amino acids can be separated from each
other by ion-exchange chromatography
5.4 The mobile phase can percolate（过滤）through the column at low
pressure or high pressure.
5.4.1 To operate under high pressure, specially designed resins
and apparatus (the pumps and the plumbing system) are needed.
Amino acids
5.4.2 Using high pressure allows better separation in a much
shorter period of time, thus named High Performance Liquid
Chromatography (HPLC).
5.5 Quantitative estimates of each amino acid in a mixture can be
efficiently carried out using a fully automated Amino Acid Analyzer.
5.5.1 Addition of sample mixture, elution of each amino acid,
collection and analysis of fractions, and data recording are all fully
automated!
5.5.2 HPLC (ion exchange) column is used in the machine.
生物化学精品课程
5. The 20 amino acids can be separated from each
other by ion-exchange chromatography
Amino acids
生物化学精品课程
5. The 20 amino acids can be separated from each
other by ion-exchange chromatography
Cation-exchange
column
Amino acids
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6. The amino acids can be detected using
various chemical reagents
6.1 The free α-amino group of any amino acids will react with
ninhydrin[化](水合)茚三酮 to form a purple product.
6.1.1 Detects amino acids nonspecifically.
Amino acids
6.1.2 The imino group of Pro gives a yellow color.
6.1.3 The concentration/amount (micro gram) of amino
acid can be determined by measuring optical absorbance (at 440
nm for purple or 550 nm for yellow).
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6. The amino acids can be detected using
various chemical reagents
6.2 Other reagents also react with the α-amino group, keeping the R
group part of the products
6.2.1 1-Fluoro-2,4-dinitrobenzene and dabsyl chloride react
Amino acids
to form colored derivatives that are stable under harsh conditions
(heating in 6N HCl at 110C for 24 hours!)
6.2.2 Fluorescent derivatives, permitting the detection of
nanogram amount of amino acids.
6.2.3 Identity of amino acids can be revealed by comparing
with a standard.
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7. Amino acids covalently join one another to
form peptides
7.1 The a-carboxyl group of one amino acid joins with the α-amino
group of another amino acid by a peptide bond (actually an amide
bond)
Amino acids
7.1.1 This is a condensation reaction where a water
molecule is liberated or eliminated.
7.1.2 G of the condensation reaction is about 5 kcal/mol,
not being able to occur spontaneously (an endergonic吸能 reaction).
7.1.3 The condensation reaction can occur repeatedly to
form oligopeptides (with less than 50 aa), polypeptides (bwt 50-100
aa), and proteins (longer).
生物化学精品课程
7. Amino acids covalently join one another to
form peptides
7.2 The peptide chain is directional.
7.2.1 An amino acid unit in a peptide chain is called a
residue.
Amino acids
7.2.2 The end having a free α-amino group is called aminoterminal or N-terminal.
7.2.3 The end having a free a-carboxyl group is called
carboxyl-terminal or C-terminal.
7.2.4 By convention, the N-terminal is taken as the
beginning of the peptide chain, and put at the left (C-terminal at the
right). Biosynthesis starts from the N-terminal.
生物化学精品课程
7. Amino acids covalently join one another to
form peptides
7.2.5 The peptide chain consist of a regularly
repeating main chain (or backbone) and the variable side
chains of the residues.
Amino acids
7.2.6 Amino acid residues have an order or
sequence on a peptide.
7.2.7 The 20 amino acids are analogous to the 26
letters in English；the number of different peptides
made of them is unlimited.
生物化学精品课程
7. Amino acids covalently join one another to
form peptides
7.3 The size of a peptide can be described by its total number of
residues (e.g., a pentapeptide, a octapeptide八肽) or relative
molecular mass (molecular weight).
Amino acids
7.3.1 The mean molecular weight of an amino acid
residue in a peptide is ~110 dalton.
7.3.2 Most natural polypeptide chains contain between
50 and 2000 amino acid residues, thus having relative molecular
mass between 5500 daltons and 220,000 daltons, or 5.5 kDa and
220 kDa, respectively.
生物化学精品课程
7. Amino acids covalently join one another to
form peptides
7.4 Each peptide has a characteristic titration curve and a
isoelectric point (pI).
Amino acids
7.4.1 The titration curve of a peptide reflect the collective
behavior of all the acid-base groups.
7.4.2 The peptide would not move in an electric field at its
pI. (determined by IEF, isoelectric focusing gel).
7.4.3 2D gel in proteomics: one dimension is IEF
separation by pI; the other SDS-PAGE separation by molecular
weight.
生物化学精品课程
7. Amino acids covalently join one another to
form peptides
Amino acids
生物化学精品课程
7. Amino acids covalently join one another to
form peptides
Amino acids
生物化学精品课程
7. Amino acids covalently join one another to
form peptides
Amino acids
生物化学精品课程
7. Amino acids covalently join one another to
form peptides
Amino acids
生物化学精品课程
8. Many short peptides have important
biological activities
8.1 Some short peptides (neuropeptides神经肽) act as
neurotransmitters, neurohormones, and neuromodulators.
8.1.1 These peptides are secreted by the neurons.
Amino acids
8.1.2 The LHRH-like decapeptide (10-residue) act as a
neurotransmitter for the frog sympathetic ganglia神经中枢.
8.1.3 Thyrotropin-releasing factor (3-residue) is formed
in the hypothalamus视丘下部and stimulates the release of
thyrotropin 促甲状腺素 from the anterior 前面的 pituitary 垂体
gland.
生物化学精品课程
8. Many short peptides have important
biological activities
8.1.4 Oxytocin ([化]脑下垂体后叶荷尔蒙之一种 9residue) is secreted by the posterior pituitary and stimulates
uterine contraction.
Amino acids
8.1.5 The opioid peptides (including mainly enkaphalins,
endorphins, and dynorphins) have been implicated in the control
of pain, responses to stress, and other functions.
8.1.6 Some drugs, like morphine and heroin, generate
their addictive effect by binding to opioid peptide receptors!
生物化学精品课程
8. Many short peptides have important
biological activities
8.2 Some short peptides act as antibiotics
8.2.1 Gramicidin A (15-residue) is a well studied peptide
antibiotic (from Bacillus brevis). Its structure has been determined.
Amino acids
8.2.2 It contains alternating L- and D-amino acid residues.
8.2.3 It is not synthesized on ribosomes!
8.2.4 Gramicidin S ([生化]短杆菌肽10-residue, circular)
is another antibiotic also from Bacillus杆状菌brevis.
8.2.5 Peptide antibiotics have also been found in frog skins,
neutrophile 嗜中性cells, and insects.
生物化学精品课程
8. Many short peptides have important
biological activities
8.3 Many short peptides are used as defensive poisons.
Amino acids
8.3.1 α-Amantin (8-residue, circular) in mushroom
is an extremely toxic peptide (inhibiting RNA
polymerases II and III at picomolar levels!)
8.3.2 Very toxic short peptides are also found in
snake venom, spider.
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8. Many short peptides have important
biological activities
8.4 Many vertebrate hormones are small polypeptides.
8.4.1 Insulin (51-residue) is produced by the pancreas and acts to
lower blood glucose level, after food intake.
Amino acids
8.4.2 Glucagon (胰高血糖素，胰增血糖素，29-residue) is also
produced by the pancreas and acts to increase the blood glucose
level.
8.4.3 Corticotropin (促肾上腺皮质激素，or adrenocorticotropin,
39-residue) is produced by the anterior pituitary gland and stimulates
the growth of adrenal cortex and secretion of corticosteroid.
8.4.4 Vasopressin (后叶加压素，抗利尿激素，9-residue)
stimulates the reabsorption of water in the distal tubules of the
kidney (diabetes insipidus patients have deficient vasopression)
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8. Many short peptides have important
biological activities
8.5 Many such bioactive peptides are present in exceedingly small
amounts (thus difficult to discover!) and acts at very low
concentrations.
Amino acids
Bioactive short peptides can be selected by making random
peptide libraries (through chemical synthesis, combinatory 可组合
的，chemistry, or phage display). Very little is known about the
receptors of these bioactive peptides. They should be good
potential drug targets.
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9. Peptides can be synthesized chemically
9.1 Peptides of up to 150 residues can be synthesized by automated
solid-phase methods mainly invented by R. Bruce Merrifield (who
won the 1984 Nobel Prize in Chemistry for this).
Amino acids
9.1.1 Amino acids are added stepwise to a growing peptide
chain that is linked to an insoluble matrix, such as polystyrene聚苯
乙烯beads.
9.1.2 A major advantage is that the desired product at each
stage is bound the insoluble beads with other chemicals easily
filtered and washed away.
生物化学精品课程
9. Peptides can be synthesized chemically
9.1 Peptides of up to 150 residues can be synthesized by automated
solid-phase methods mainly invented by R. Bruce Merrifield (who
won the 1984 Nobel Prize in Chemistry for this).
Amino acids
9.1.1 Amino acids are added stepwise to a growing peptide
chain that is linked to an insoluble matrix, such as polystyrene聚苯
乙烯beads.
9.1.2 A major advantage is that the desired product at each
stage is bound the insoluble beads with other chemicals easily
filtered and washed away.
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9. Peptides can be synthesized chemically
9.1.3 The synthesis starts with fixing the C-terminal amino
acid on the insoluble beads through its a-carboxyl group. This is in
the reverse direction of biosynthesis.
Amino acids
9.1.4 The a-amino group of the next amino acid to be added
is protected and its carboxyl group activated. The amino group is
protected by the t-butyloxycarbonyl group (t-boc) and deprotected
by CF3COOH. The carboxyl group is activated by
dicyclohexylcarbodiimide (DCC).
9.1.5 The peptide bond is formed by the free a-amino group
(deprotected) of the fixed C-terminal residue attacking the DCC
activated α-carboxyl group of the free amino acid in solution.
9.1.6 After washing away unreacted free amino acids and
other reagents, step 9.1.4 and 9.1.5 are repeated. The synthesized
peptide is eventually cleaved off from the resin by adding HF.
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9. Peptides can be synthesized chemically
9.2 The efficiency of this solid phase synthesis is much lower than
biosynthesis in living organisms.
Amino acids
9.2.1 Synthesizing a 100 amino acid peptide will take about 4
days to finish with a fully automated machine with reasonable合理
的yield.
9.2.2 The same peptide would be synthesized with exquisite
fidelity in about 5 seconds in a bacterial cell!
9.3 Peptides having natural activity have been synthesized
chemically.
9.3.1 The complete bovine insulin was first synthesized and show
to be the same as the natural insulin in China in 1965!
9.3.2 Merrifield also synthesized the interferon干扰素(155 aa)
and ribonuclease (124 aa).
生物化学精品课程
9. Peptides can be synthesized chemically
Amino acids
生物化学精品课程
9. Peptides can be synthesized chemically
Amino acids
生物化学精品课程
9. Peptides can be synthesized chemically
Amino acids
生物化学精品课程
Homework
1. The four families of amino acid R groups can be classified as being either
hydrophobic or hydrophilic. What properties of the R group determine this?
Classify each family as hydrophobic or hydrophilic.
2. Compare the structures at physiological pH of the R groups of the following
pairs of amino acids. Determine which member of the pair is hydrophobic and
Amino acids
which is hydrophilic. Justify your choice.
(a) alanine/serine；
(b) phenyalanine/tyrosine；
(c) isolecuine/glutamate；
(d) praline/histidine.
3. Consider neutral (pH 7) solutions of the amino acids alanine., arginine,
asparagine, aspartate, glutamate, lysine, phenylalanine, and serine. Classify each
amino acids as one of the following: nonpolar, polar uncharged, negatively
charged, or positively charged.
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Homework
4. Why does the neutral amino acid phenyalanine exist as a dipolar molecule?
Determine whether the following statements are true or false. If false, explain why.
Amino acids
(a) All 20 standard amino acids found in proteins have at least one asymmetric
carbon atom.
(b) An epuimolar mixture of D- and L-alanine does not rotate the plane of
polarized light.
(c) The observed optical rotation of an amino solution is directly proportional to
the length of the light path through the polarimeter tube and the concentration of
the amino acid solution.
(d) Alanine obtained from a protein hydrolysate has the same absolute
configuration as D-glyceraldehyde.
5. (a) Which amino acid has good buffering capacity against added acid in the pH
region of intracellular fluids and bloods?
(b) Which amino acid is always positively charged at all pH values below 12?
(c) Which amino acid are negatively charged at all pH values above 4?
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Homework
6. Amino acids are frequently separated by either paper electrophoresis or ion
exchange chromatography.
(a) What is the basis for these separation techniques?
(b) Do both techniques use the acid-base properties of the amino acids to effect a
Amino acids
separation? How?
(c) How are the locations of the amino acids on the chromatogram detected?
(d) Can these techniques be used to separate peptides? Explain.
7. Glycine at Physiological pH: Distribution Between Zwitterion, Anion, and Cation.
At physiological pH, glycine exists predominantly as the zwitterion. Calculate the
percentage distribution of zwitterion, anion, and cation of a solution of glycine at
pH 7.4:
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Homework
8. A mixture of serine, glutamic acid, and lysine is separated by paper
electrophoresis in two experiments, one at pH 1 and one at pH 12. After the
separation, the papers are treated with ninhydrin to reveal the location of the
amino acids (purple spots). The results are shown in Figure. Match the
Amino acids
electrophoresis strips with the appropriate pH and identify all the spots. Draw the
strip corresponding to a separation at pH 7.
Origin
Cathode
Anode
Cathode
Anode
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