Shriya Dhar

&. Questions will be asked on the basis of identifying Amino Acids

1. Identify the R sequence (um) Leven codons

Essential Semi-Essential Non-essential

H- His-histadine A- Ala - Alanine G-Guy-Glycine

I-lle - Isoleucine N-Asn -

Asparagie X
-

Tur-Tyrosine
L-Len-leucine D-Asp -

Aspartic Acid C CyS-cysteine

-

K-lys -lysine E- Glr-Glutamic Acid P-Pro-Proline

M-Met - Methionine S-Ser-Sevive &-Glu-Glutamiene

F-Phe-Phenylalamine
+- Thr-Threonine 13 -> ASP/Asn

Tryptophan J / Ler
W-Trp -> 1e
-

U-Val-Value X +
Anything
GIr/GIU
R-Arg-Argineine z ->

U ->
Selenocysteine

0 Pyrolysine
Always
->
write pH 0
=

PUJpKa:deprotonated Ha = In+] AO +

PULpKa:Protonated ka
[n+] [A-]
=

pka=-log ka
[HAI

Stronger Acid => Ka4, PKat Weaker Acid=> Kah, PKa*

AA UN* - -coo 2
-

↓
ve
& ↳ Pka coon>pU

2.8
pKa = -

N
its ka is
very less
thus deprotonated form
PKa NULLPH
↳ thus protonated form
 G-Gly-Glycine
H H

u3n*- c-coo
I

⑰ -- n
=>
SimplestA. A H3N
I

=>
Achival A.A ⑪ COO

Spcarbon
=>

axis
with of
sym.
A. A
Sweet
=>

A- Ala-Alanine
H
I
⑰ -

43N- (x-200
-> R (43 =

Hydrophobic
-> A. A ins

V-vaL-Valine H

43hE 1-2008

cus/4-cns
neutral
-> Amino Aci

-da-coor
L- lew-leucine

-cus
n3w*
a
Alliphatic R-group
->

=) Hydrophobic CU3

-cus
Isoleusie -
11 -
I

(somes
Chain
->

inz
ins
 Hydrophobic
Valine, Alanine, Leucine, Isoleucine

↑
G ↓
X R (n3
=
I

Sulfur
containing AA

Buz ·

re
Cysteine
forms

in
=> the disulfide

bond that
stableze - cystine
the tertial structure

thiol

&. Differentiate
blu (w/structure) Cysteine & cystine

M Met
-
- Methionine

Pinz
seconday S-group ->
ArG
=>

Crz codon
start
sulphur but
AA
containing
ins
=>

↓
not a thiol for
codes Methionine
(Met >

Aromatic, Non Polar

I
I
/
-12 ->Tyrosine/
Phenylalanine I

(pue) ↳ (Tyn)
 change net)
Acidic AA (-ve

B-CH2-100--> Asp, D, Aspartic Acid

1 -
(12-12-2008 ->
Glu,E, Glutamic Acid

chohol
containing AA

Serine, Ser, s I
chzon
Threonine. The, I

H -
B-on
Cus

Basic AA (net +vel

change

lysine, lys, K (a,B, y, 5,5,w]

↳ ↳

2- amino acid Usn* -ca-coo-

Binz
crz
86nz
a cuz
I
TO
NN,
 Arginine, R.
Arg
usnit-coo- NU

cre
-
H2N =
c
y -
NHz
6
cnc
1

NA Guanidium
-> group
H2N 2
=

Ne

Histidine, His, 4

i
present
-> at active site of
cnz dazole
many enzymes

un*wnt ring
-> near the neutral pt
pka 6
=

↓
neutral pH thus receptor
bind to active
at site
enzyme can
near,
to

thus can exist in 2 diff config (protonated or deprotonated) ace to

micro enviornment

Imidazole Ring -> protein

ANA formation
complex

base
in
(Rich
Annte Ave Histone Proteins

Acid Anides

Minz z P
d0
*
c0 =
inc
c0
=

Nnz !O =

Line
Asparagine
hAn) [N] Glu (a)
 largestAA z
Sh (mostly not
Tryptophan (w) TrP in
can exist the

Indole
=>
Rig

Provine (Pro), (P)

-> forms
side chain
2- x42
-
u

rings with itsel H2C

cyclised
->

only
zw"coo-
H
-> 20 Amine (All others 10)

-> kinks in protein structure (destabilize structure)

--1008
4 0 U
I
43N -
- -
=
n H20 is
=> produced

↳ ↳ k How
->

does Attach happen?

A
nucleophile will attack (A site

cititw--won
Oxygen will take my protonations
H3N

I
- -

O has alp, leaves, attack

carbocation
↳
the over Nitrogen balanced by leaving

↓
has peptide bond (Resonance
-
20 shows)

it
H

4N*_ d- H
I
In iP

I
↳ 4gN* - - -
I
-
Ht
I
H

MnO_
430
↳
removed

dehydration c- de-
 0 H

U3N* -Y -
I
c N
=
-
I
c -
Nns* Leach in diff planes)
↳ ↓ ↳

-0 i)
R
- L
-
-X

XTE/"sainydral
2
C
-
x = -
3 -
angles

Ramachandran

↑ -;
W
W
1-120,120)

:8
right
left X helix
-
handed 260,60)

x (-60, - 50) I kinks in

polypeptide Sequence

D-B-D. confirmation -

=where there is minimum clash

Natural Structure of
proteinpp 15% clash allowed

:thats what he proved [clash allowed)

&. Whatis Paradox

Levinthall's 100% will come

Supercomputer - 100 AA polypeptide seq.

"scouk -> 3confirmation -> 2x102urs (impossible

does it miliseconds (-140)

body most-ve, its probable
most
 0. PYD+ Extra o's

1. in isolate
OS angles
4 AA
The no. of and an

None
->

A Imp
2. No. of Atoms held into geometric plane
a
by a peptide
bond.

6 (six)
=>

3. How bonded atoms are reg constitute

to a dinedral
many
angle such as &Y?
h (Fours
=>

h de
bondbond is blu 2 AA

=>> O
-N
its structure is
,
i

Y
5. ↓
4 · 4
0 ·
↓ ① 0
L L I
X-helix (Right) B-sheets Bx
B motif

E
6.
Why are
peptide grps planar?

Resonance
->
- i - c

in
 A
7. Flow of es from is to carbon & rice-versa fuels life. Explain
or Life is Redox (5)
Rxn

-> Resp-"c->0

Photosynthesis 0-> Glucose

8. PKa, pH usmin->30min-Carbonydrates
2 8m) -
1 -Antigens over RBC

2 ->
Design Exp. (Glycemic index

-> DDL isomers of Rice)

-> True or false o's

-> Match the following (Water 0's)

is high heat
capacity -> Temp
(ii) from ice
high density
hiis high
heat of fusion

(iv) H-bond
(3m Iv)
-> Diff blu
high heatof vaporisation
(i) Aldose a ketose

(ii) Epiner & Anomal

(iii) Furanoed & Pyranose

#
non-covalent Interactions
* Peptides
Charge on

RAY

Arginine W
Valine V
Alanine Isoleucine

MA - "H+ +
A-

(Acid)

ka:
[us4A] pKa=-logka

Take peptide or molecule and place it in solt of particular pH.

any a

s000 h
so
sai-Ionisable group
(ka)
--> ph)
gorgon
x
=

If phpka, the group exists in

sothe
deprotonated form.
NIc -> NU2

cool -> L00-

Sa -> s-

If PH<pka, the group exists

in protonated form.
NUz-> Nus*
coon->coon

Su -> SH
 RAVI

U2N-Arg-Ala-Val-le-coon
term
Arg
-> Term -x-x-x- cool
-

NUz

PH 0
=

Nus*
N uz

term ⑦ A ph0
+ +
2
NUz
=

9.04
Nus
NU2

- peptide
Arg NH2
cool cuo-
net
charge on

Term wor ⑧
2.36

Arg NU2 -> 12

His rnc ->

6

6
lys - (NV2 ->

Term NU2 -> 19.6 This depends which A.A

I
on

Terminal L004->42 is terminal upon

Asp coon -> 4.1

Glu Coon -> 4.1

sinziysosome
Term NH2 of
Net
charge on Peptide=+

Term ⑦
COOM
2.36
⑦
Arg Nuz
12

(ii) pu 7.2 (cytoplasm)

Term I Net charge

NHz
9.0h
on the peptide= + 1

Term COOH ⑦
2.36

Arg NHz
12
⑦
(iii) ph 8 (Mitochondrial
⑰
Term NH2 go
Not
Term COOM 2.36 ⑦
charge on the peptide= + 1
⑰
Aug NUz in

so electric Point

The at
point which/pH at which, not charge on the peptide
is 0.

Term ⑰ UIN-RAVI-COOH
NH2 9ou
Term COOH
2.36 ⑧ At pho, + 2 State
↓
⑰
Ang Nrz is
At any point where CPU (2.36, +2

charge peptide.
on Because only at

2.37pH, coon->2008 and net

charge
reduce
by 1 to +1

Term NUz
don At 2.36 <ph 29.04 peptide will

Term ⑦ in
exist
cool
2.36 +1 state

Arg whe ⑰
is

Term NU2 gon ⑧ At 9.04 <PUC12

peptide will

Term COOH 2.30 exist

in 0 state. (net
chrg
0)
=

Arg Nuz in

Tarm NU2 ·on 8 At 12 <phC14 Peptide will

⑧
Term coor 2.36 in-1
exist state.
(netchg=-1)
Aug NH2
12 ⑧
 Isoelectronic is
point where net
charge on peptide is 0.

Buthere we
get a
range
of values where pl = 0

for this case, the

range is 9.04-12.

So
geta point, take
are of +12
to

2 10. 2
=
=

Why only average?

ionisable
Every ionisable
group has an x. All
gaps are weakacids or

weak base. So,

PH 12

I
=

Pk 9.04
=

------- distributed
↳ normally
Jo.
-

S in
S trying
acheive
to

100 Y
n

JUBIN

NUz -Lew
Selcys-AsP-ILe-Asn-coon
-

0 5.5 7.2 ⑧

Term ④ ⑰
Nuz 9.46 ·ano anc 9.46
⑧
Term COON zin 2.
⑦
!' ... *

Asp WOH ↳ ⑧ ⑦ ⑦ !O
↳ ↳
Net I I
Charge
+ I -
-
I -

pI 4
+
3.2
=

2 =
 RAVI U2N-Arg-Ala-Val-le-coon

PH 0
=

Nus*
N uz

term ⑦ A ph0
+ +
2
NU2
=

9.04
Nus
Naz

- peptide
Arg NH2
cool
net
charge on

Term coon 1000

2.36

0 < 2.36 coon-wool, 100

At pu 0,
=
net charge: + 2 on the protein

pr > 2.36 Nu
↳
Term NUS on +1

2.3629

Nur 2
charge:1
net
Arg. NU
iz 1
+

2.36 C12

coo
↳
Term 1
zoon
2.36
-

pu> 2.36, prypka (deprotonated (

9.04 <PUC 12

Term NUz
!ounazo
⑰ NU ->
+
iz
1
Arg Nn
=

I
coo--
1
Term COOH 2.36
Pu > 2.36
P1>12

NUz
Term NH2 0
9.04 ph> 9.04

Ang NH 0
12 Pu> 12
COO-
I
Term coor
2.36

Not
charge: -1

Iso electric pointor P.11

charge
not 6
=

phpU-1 pI
=

PI n+12 2104
=
=
10.52
=

-
what's the net
charge of the
pr
protein pu
at = c2

⑮ wn
* term coon

1) X -Helix

pitch 5.4A
=

no. of aa = 3.6 aa

handed
Right
Pp x,
-> 5.4A" -> 3.6aa

190
y, 1000A=
5
->
1000
x

laa 110
=
daltons

weight es move towards

2500 daltons electronegative atom

find of ac i 4
No-OF H-bonds
no. -

Total nos of an i-4

↳ total no-of AA 53

no-of r-bonds 49.(53-4 49)

=
=

Engineer Proteins,
How do determine linkes
they sequence?
bond
Depending on the macrodipole more -
ve ends can with thely charged
& vice versa.

it aa -> (itnith aa

total no. of H-bonds would be (n-n) total

n= no. of aa.

Motifs & Domains

when isolated can

function
Independent function
independently.
-

Supersecondary structure Units of 30 structure

Built from combinations of built

from combition of

helices a loops 20 & Super 20 structures.

-
Dependent
on entire structure

ofthe protein.
Non Covalent Interaction
1
17 Hydrogen bond

2) Hydrophobic & Hydrophilic

3) Salt Bridges
45 Vanderwaal's force

3] Charge Charges Interactions

CovalentInteraction -> Disulphid Linkage -> 3" structure

*
Anfinsen's Dogma
Native structure of a
protein is determined by its amino

acid
sequence (genetic code) The
subsequent folds are

not determined by the

sequence of amino acids or neucleotide
but determined by of
they
are microenviorment the

protein & the non-covalentInteractions.

* Levinthal's Paradox
100 Amino Acids (In a
polypeptide sey)

(0,4) -> 2 -> confirmations

A (d, Y.) A2 (PP2) ... A 100 (1100 410oS

A supercomputer 10-3 seconds for I confirmation

2100 x 10-3

20 1000

12110 x 10-13 210003" x 10-3

= = (103)1 x10-13
1030 X10B
=
10sec.
=

24 billion Yus
 And inside our cells reach
protein their state
most in

fraction of seconds

motif
* Rossman fold
(
look though
W

& How atoms in a plane

many

·
a
① Fructose synthase
Transference
-5,
② Glycemic index of rice &
Amylose Anglopection &