صفحه 1:
00
8
8 حؤك ity
5 4
ai
AMINO ACIDS
صفحه 2:
00 = Proteins are polymers of
amino acids, with each
+ — acid oe ۳
joined to its neighbor by a
H,N—C—H phecilic type of covalent
ond.
R " The additional carbons in
an R group are designated
B, y, 6, € etc.
€ 8 7 a
6 5
4 مس ™ Carbon atoms are
(CHa CHa CHa CHa CH COO numbered from one end,
+ + giving priority to carbons
NH3 NBs with substitutions.
containing atoms with the
highest atomic numbers.
Lysine
صفحه 3:
"= The a-carbon of AA is a chiral
center. Molecules with a chiral
center are optically active, they
rotate plane-polarized light.
= Enantiomers :
Nearly all biological compounds
with a chiral center occur naturally
in only one stereoisomeric form,
either D or L. The amino acid
residues in protein molecules are
exclusively L-stereoisomers.
D-Amino acid residues have been
found only ina few, generally small
Peptides, including some peptides
Of bacterial cell walls and certain
peptide antibiotics.
coo-
CH
D-Alanine
coo”
HEC =H
وب
o-Alanine
coo”
۳
ولاز
وب
p-Alanine
00
HAN
وب
L-Alanine (م
coo”
+ E
لاس ع -ااولا
و6
(b) تمقافت
coo-
| +
۳
وب
ای ۵0
صفحه 4:
CO Opwwos Owe Bride
Nonpolar, aliphatic R groups
fr
ماد
he
7
اه
Valine
cor
HCH
Methionine
coo" وم م
when sine 5
دب 1 I
سره
Glycine Alanine Proline
coo" coo"
بسع لوي بع ألو
۳ ۷-6-6
cH CH
as 1
CHs واه رقع
Leucine Isoleucine
صفحه 5:
ال
™ Glycine has the simplest structure, its very
small side chain makes no real contribution to
hydrophobic interactions
= Methionine, one of two sulfur containing
amino acids. has a nonpolar thioether
group. First AA residue in translation of
proteins
® Alanine, Valine, Leucine, and Isoleucine could
contribute to hydrophobic interaction.
™ The secondary amino (imino) group of Pro is
held in a rigid conformation that reduces the
structural flexibility of polypeptide regions
containing proline.
صفحه 6:
ال
Aromatic R groups
coo" coo" coo"
wc مارا ساره
cH, cH, Ge
لوت
۳
NH
56
on
Phenylalanine Tyrosine Tryptophan
صفحه 7:
= All are relatively
nonpolar (hydrophobic).
= -OH group of thyrosine
can form hydrogen
bonds and are important
functional group. Can be
phosphorylated as well.
= All can absorb UV light
(280 nm), Tyrosine and
Tryptophan are stronger
than phenylalanine. Use
for protein
quantification.
Tryptophan
9
2a 240 250 260 270 280 200 200 ato
Wavelength (nm)
Absorbance:
صفحه 8:
Sh
Polar, uncharged R groups
coo-
با لیب
é
be
Cysteine
گروه
هم
HSN cH
Gis
1?
c
Han’ 0
Glutamine
coo" coo"
لمع لیب بسع لیب
H—C—OH رميس
a
Serine Threonine
coo-
یه
9
HON AX
Asparagine
صفحه 9:
ا سس
= The R groups of these amino acids are more
soluble in water, or more hydrophilic, than
those of the nonpolar amino acids, because
they contain functional groups that form
hydrogen bonds with water.
™ Serine and Threonine has -OH(Such as Tyr),
which contribute to polarity, and could be
phosophorelated.
™ Asparagine and Glutamine are the amides of
Aspartate, and Glutamate, and are easily
hydrolyzed by acid or base.
صفحه 10:
ا
Disulfide Bond
per goo"
30 ae
Cystei
[Cysteine] با |
2H” + 2e
oe Cystine
ad ۱
2H* + Qe
CH, CH;
Cysteine| 5 1
۳ GAN
000 000
= Cysteine is readily oxidized to form a covalently linked dimeric
AA called cystine (disulfide bond).
= The disulfide-linked residues are strongly hydrophobic
(nonpolar). Disulfide bonds play a special role in the structures
of many proteins by forming covalent links between parts of a
protein molecule or between two different polypeptide chains. |
صفحه 11:
coo- coo coo"
رب بر H,N—C—H
cH, cH, ۳۹
oH, oh a
CH, CH, | oH سل
cH, Aa a
* و۱۱ on quarter
NH,
Lysine Arginine Histidine
صفحه 12:
اا ئس
Bp
™ Lysine has a second primary amino group at ¢ position.
Its R group has significant positive at pH=7.
= Arginine has a positively charged guanidino group
™ Histidine a imidazole group, and is the only standard
amino acid having an ionizable side chain with a pKa
near neutrality. It serves as a proton donor/ acceptor
in a enzyme-catalyzed reaction
صفحه 13:
0 اال"
pees
1 ™ Two amino acids
ia {0 having R groups
ابا —-HjN—C—H with a net negative
| charge at pH=7
ib ie are asparate and
coo" CH, glutamate, each of
iS <=@2Which has a second
Aspartate Glutamate carboxyl group
صفحه 14:
TABLE 3-1 Properties and Conventions Associated with the Common Amino Acids Found in Proteins
Occurrence in
proteins (%)1
ود
32
14
6
59
19
43
42
Hydropatty
Indox*
وم
0.7-
25
35
و
وف
2
2
-3.5
-3.5
Phe
ee
ser
bor
bas
ber
5.98
50
Bra
sas
0
ره
ses
#7
ae 5.07
bat
Ses
oes 9.74
se eS
gee) ee
ee
pK, values
وام
(ONS)
9.60
9.63
10.96
9.62
9.60
9.68
9.21
9.13
911
9.38
9.45
9.62
10.28
مود
9.13
8.95
9.17
9.04
9.60
9.67
كم
009
2.34
2:34
199
2:32
2.36
2.38
2.28
1.83
2.20
2.38
2.21
21
195
2.02
2.17
218
Tao
217
1.88
2.19
75
83
115,
117
131
131
149)
165
151
204
105
119
12
132
145,
146
155
174
133
127
cy ۵
Ala A
Fro P
Val ¥
Leu ا
ie 1
Met M
0
3
Amino acid
‘Nonpotat, aliphatic
R groups
Glycine
Alanine
Prone
Valine
Leucine
Isoleucine
Mothionine
Aromatic R groups
Phenyialenine
Tyrosine
‘Typtophan
Polar, uncharged
R groups
‘Serine
Threonine
cysteine
Asparagine
Glutamine
Positively charged
R groups
lysine
Histidine
Arginine
Negatively changed
R groups
Aspartate
Glutamate
صفحه 15:
Neutral Basic
Asn Ser Arg
Acidic
Asp
بت ده رو
Gln___ Thr
Glu
صفحه 16:
a
سس و
phat cell url coo"
2 “BOGEN لم لح
۱۷0-۰ CH,
| I y-Carboxyglutamate
3 و
H بر فو
4-Hydroxyproline
CH, —CH COO” ولا cH ایلوا
oH * NHS
5-Hydroxylysine
C—O C—O" (tom اس
“NH, Hal
Methyllysine Desmosine
16
صفحه 17:
ال
™ Selenocysteine is introduced during protein
synthesis, and contains Selenium rather than
sulfur of cysteine, derived from serine.
HSe —CH,—CH—COO-
* و۱۲
Selenocysteine
صفحه 18:
:انال"
mae
= Ornithine and citrulline are not constituents of proteins.
= They are key intermediates (metabolites) in the
biosynthesis of arginine and in the urea cycle.
H3N—CH—CH,—CH,—CH — Coo
*NH3
Ornithine
HaN—€—N—CH,—CHs—CHs— CH —COO™
+ ول
Citrulline 20
صفحه 19:
ال
ی
as either an acid (proton donor).
11
بعص وو اه
|
داز نز
Zwitterion
or a base (proton acceptor):
i
CO0- +H! == x COOH
ولا +NH,
19
Zwitterion or Amphoteric
1 ll
80-6 70-8
سنن 3م الوق =
R R
Nonionic Zwitterionie
form form
صفحه 20:
™ The pKa is a measure
of the tendency of a
group to give upa
proton, with the
tendency decreasing
tenfold as the pKa
increases by on unit.
0 05 1 15 2
OH (equivalents) 20
صفحه 21:
™ Isoelectric point (isoelectric pH): pl, The characteristic
pH at which the net electric charge is zero (eg. glycine).
+ +
وق ولاز "0
by 2 ty Se by
boo boo- )00-
pl = 5 (pK; + pKa) = 3 (2.34 + 9.60) = 5.97
صفحه 22:
PI=PK1+PKR
22
صفحه 23:
23
OH™ (equivalents)
صفحه 24:
Oxoid uvids diPPer io thei ovicd-base properties
pk, oP the -COOW oop: 1.0 - OF
wehbe wits مه
Rises bed sso isto pk, oP te OL, wow 8.0 — (0.0
(rote wotde wk rouble R yous
=
۳" ek 5 حجن ی که
ملف htt ed 0 wa 3
1: he | }
bis i
° i 2030 ° 10 20 30
‘OH (equivalents) OFF (equivalents)
three snes (rer iraizaioa steps > tree ph, valves)
صفحه 25:
ال ۲
PEPTIDES and
PROTEINS
صفحه 26:
1 rf
Hj3N—CH—C—OH + H—N—CH—COO7
ll
0
8 R
۰ [| |
H3N—CH Cc
Formation of a Peptide Bond by Condensation
26
صفحه 27:
serylglycyltyrosylalanylleucine
(Ser-Gly-Tyr-Ala-Leu) ۳
‘As Cis.
5
aoe 4 qi gts gis
“PF ۳
H H H H H
Amino- Carboxyl-
terminal end terminal end
0 لدت 0 امس
A few amino acids are joined - an oligopeptide.
Many amino acids are joined, - a polypeptide.
“Protein” and “polypeptide” are sometimes used.
interchangeably, molecules referred to as polypeptides
generally have molecular weights below 10,000 (D), and
those called proteins have higher molecular weights.
صفحه 28:
۰۳33۳۳7۳77۳93۳35 515 5 ود 0مطاونن Their
Ionization Behavior (Alanyl-glutamyl-
™ The acid-base behavior of
a peptide can be
predicted from its free -
amino and -carboxyl
groups as well as the
nature and number of its
ionizable R groups.
™ Peptides have
characteristic titration
curves anda
characteristic isoelectric
pH (pl) at which they do
not move in an electric
field.
glycyl-lysine)
NH,
Ala CH—CH,
و
۳
Glu سم 0
o=¢
۳
Gly Hy
8
wa
Lys GH, ch, cH cH fi
coo"
صفحه 29:
Biologically Active Peptides and Polypeptides
Occur in a Vast Range, gf, SiZPSituent of vertebrate
muscle, which has 27,000 AAs, and
M.W.=3,000,000.
Single peptide chain Vs. multisubunit
protein: two or more polypeptide
associated noncovalently.
The individual polypeptide chains in a
multisubunit
protein may be identical or different. If
at least two
are identical the protein is said to be
oligomeric, and the identical units
(consisting of one or more polypeptide
chains) are referred to as protomers.
Ex, Hemoglobin- has four polypeptide
subunits: two identical « chains and two
identical 6 chains, all four held together
by noncovalent interactions. Each
subunit is paired in an identical way
with « subunit within the structure of
this multisubunit protein, so that
hemoglobin can be considered either a
tetramer of four polypeptide subunits or
a dimer of af protomers.
The average M.W. of AA= 110 (128-48)
oo
bo dio
ممه واه
1-Aspartyl-Lphenylalan ine methyl ester
(aspartame)
Our Guveet - onPictal suweetecer
صفحه 30:
Levels of Structure in Protein
Primary Secondary Tertiary Quaternary
structure structure Structure structure
4”
Polypeptide chain Assembled subunits
Amino acid a Helix
residues
= Primary: A description of all covalent bonds. The sequence of
AA residues
= Secondary: particularly stable arrangements of AA giving rise
to recurring structural patterns.
= Tertiary: All aspects of the 3D folding of a polypeptide.
= Quaternary: The spatial arrangement of multisubunits protein
30