Nelson & Cox (2000) Lehninger Principles of Biochemistry (3e) p.

129

(1)
A-T-C-G-G-C-T-A-

Gly-Ala-Lys-Glu-Asp-Val-

(2)
Double Helix

Helix, Sheet

(3)
5------------3'

N----------C
Juang RH (2007) BCbasics

 (Backbone)
Constant
Variable

O
H

NC
N C
C C N
C
C
O
C
N
C
R
C
C R
-O
R C
HH H
O
N H H
C
H
N
+ O
N
C
R
N
C
C
H
C
O
C
N C
O
O H
R
R

COO+
H3 N

N-C-C-N-C-C-N-C-C

R group
Juang RH (2007) BCbasics


F NH3

B-chain

V
N
Q
H
L
C

+NH

G
I
V
E
Q

F. Sanger
(1951, Cambridge U)
Insulin (A, B chains)

V L H
E
S G
A
S S
C
L
C
S
Y
T
-OOC
S
L
S
N
V
I C S
S S C
C
Y
L
COON
G
Y
E
T
E
L Q
K
R
P
G
A-chain
T
Y F F
Nelson & Cox (2004) Principles of Biochemistry (4e) p.97

 (Primary structure)

(1)
Edman degradation
F. Sanger (Cambridge U.)
Insulin (A, B chains)

(2) cDNA
DNA F. Sanger
DNA
Juang RH (2007) BCbasics

Alberts et al (2002) Molecular Biology of the Cell (4e) p.506

 (1994) , p61

destroy me

Cut me

Juang RH (2007) BCbasics

Signal Peptide

Signal Peptide:
ER signal ()
signals (, )
PEST site
Juang RH (2007) BCbasics


G Blobel (1999)

KDEL

Alberts et al (2002) Molecular Biology of the Cell (4e) p. 667

Juang RH (2007) BCbasics

Nelson & Cox (2000) Lehninger Principles of Biochemistry (3e) p.165

+
Garrett & Grisham (1999) Biochemistry (2e) p.161

Helix, Sheet
(1) Peptide bond Peptide bond
(2) R R
Peptide bond
(3) R
Helix, Sheet Ramachandron plot
(4)
Juang RH (2007) BCbaiscs

Nelson & Cox (2004) Lehninger Principles of Biochemistry (4e) p.125

Ramachandron
plot

Mathews et al (2000) Biochemistry (3e) p.164

helix
sheet

 (Secondary structure)

Hydrogen bond

(1)
(2) DNA A:T; G:C
(3)
(4) -
-
+
(5)

-N--H ... O-

Juang RH (2007) BCbaiscs

Mathews et al (2000) Biochemistry (3e) p.100

Alberts et al (2002) Molecular Biology of the Cell (4e) p.58

 helix

Garrett & Grisham (1999) Biochemistry (2e) p.165

Linus Pauline
& helix

Judson (1996) The Eighth Day of Creation

Campbell (1990) Biology (2e) p.65

3.6
3

11 12

13

10

26

3
N
H

5.4 A
C
N

O
C C
N

Alpha Helices by Geis

Linus Pauling (Caltech)

Helix:
(1) Right handed ()
(2) 3.6 5.4
(3) Carbonyl (C=O) H-N-
(4) 13 (13)
(5) helix
(Myoglobin):

helix turn
Juang RH (2007) BCbaiscs

Nelson & Cox (2000) Lehninger Principles of Biochemistry (3e) p.165-166

helix

 helix
Zubay (1988) Biochemistry (2e) p.64

myoglobin

 helices

Stryer (1995) Biochemistry (4e) p.436

Alberts et al (2002) Molecular Biology of the Cell (4e) p.679

helix

Garrett & Grisham (1999) Biochemistry (2e) p.1054


Sheet:
(1)
(2) (parallel)
(3) sheet

helix

Reverse Turns:
Turns turn, turn

Irregular: ( )
Random: ()
Juang RH (2007) BCbaiscs

 sheet

Garrett & Grisham (1999) Biochemistry (2e) p.174

 sheet
anti-parallel

turn

parallel
Alberts et al (2002) Molecular Biology of the Cell (4e) p.140

all helices

all sheets

helices + sheets

Kleinsmith & Kish (1995) Principles of Cell and Molecular Biology (2e) p.26


Sheet:
(1)
(2) (parallel)
(3) sheet

helix

Reverse Turns:
Turns turn, turn

Irregular: ( )
Random: ()
Juang RH (2007) BCbaiscs

turn

turn

Pro

Mathews et al (2000) Biochemistry (3e) p.181

Mathews et al (2000) Biochemistry (3e) p.179

 (Tertiary structure)

; ; 88 () Motif, Supersecondary

Juang RH (2007) BCbaiscs

sheet

helix
trypsin inhibitor

Garrett & Grisham (1999) Biochemistry (2e) p.181

Cys, His, Glu, Asp

(1)
(2)
Stryer (1995) Biochemistry (4e) p.1000


()
Alberts et al (2002) Molecular Biology of the Cell (4e) p.135


C
CH2
SH

C
CH2
SH

Interchain
Disulfide bond

SH
CH2
C

Oxidation
Reduction

SH
CH2
C

Intrachain
Disulfide bond

C
CH2
S S
CH2
C
C
CH2
S S
CH2
C

Adapted from Alberts et al (2002) Molecular Biology of the Cell (4e) p.152

()
Cys-S-S-Cys Cys-SH + HS-Cys
RNase A (RNA )
124

Chaperonin
Proteasome

Myoglobin:
Myoglobin 3D
Kendrew & Perutz (X-Ray crystallography)
Juang RH (2007) BCbaiscs

 RNase A
Anfinsen

- Urea, Mercaptoethanol

+ Urea, Mercaptoethanol

Stryer (1995) Biochemistry (4e) p.38

DNA

mRNA

Chaperone
Proteasome

Starr & Taggart (1987) Biology (4e) p.216

Protein


chaperone

Alberts et al (2002) Molecular Biology of the Cell (4e) p.357

Chaperone

Alberts et al (2002) Molecular Biology of the Cell (4e) p.705

UPS

Lowe et al (1995) Science 268: 533

Proteasome ()

Proteasome (20S)

Chaperonin (GroEL)
Weissman et al (1995) Science 268: 524

 X-Ray

()
Cys-S-S-Cys Cys-SH + HS-Cys
RNase A (RNA )
124

Chaperonin
Proteasome

Myoglobin:
Myoglobin 3D
Kendrew & Perutz (X-Ray crystallography)
Juang RH (2007) BCbaiscs

1962

Perutz
Nelson & Cox (2000) Lehninger Principles of Biochemistry (3e) p.189

Judson (1996) The Eighth Day of Creation

Kendrew


helix

sheet

turn

Glu
Met
Ala
Leu
Lys
Phe
Gln
Trp
Ile
Val
Asp
His
Arg
Thr
Ser
Cys
Tyr
Asn
Pro
Gly

Garrett & Grisham (1999) Biochemistry (2e) p.197

GP = Glycogen
phosphorylase

SP = Starch
phosphorylase

(L-SP)

L78

SP

L
H

GP
Mathews et al (2000) Biochemistry (3e) p.194

Computer modeling of L-SP

(base on the template of GP)

Starch binding site

PLP binding site

PEST site

A site
B site

Active site

L78
Helix a

Helix b

Phosphorylation site (Ser 71)


Alberts et al (2002) Molecular Biology of the Cell (4e) p.701, 630

Hydropathic plot



+ (glycoprotein)
+ (lipoprotein)
+ (metalloprotein)
+ (prosthetic group)
heme
(active protein)
myoglobin
+
insulin

chymotrypsinogen

+ (phosphorylation)
+ (coenzyme) (holoenzyme)
Juang RH (2007) BCbaiscs

Alberts et al (2002) Molecular Biology of the Cell (4e) p.703

 ()
Nelson & Cox (2000) Lehninger Principles of Biochemistry (3e) p.176

heme

A
B
X

Alberts et al (2002) Molecular Biology of the Cell (4e) p.156

Campbell (1999) Biochemistry (3d) p.179

Alberts et al (2002) Molecular Biology of the Cell (4e) p.178

NADH
Binding
domain
NADH
Gly-3-P

substrate
Binding
domain
Glyceraldehyde-3-phosphate
dehydrogenase

Kleinsmith & Kish (1995) Principles of Cell and Molecular Biology (2e) p.25

Alberts et al (2002) Molecular Biology of the Cell (4e) p.122


Domain
Domain
(1)
(2) Domain
(3) domain (myoglobin)
(4) domains (hexokinase)
(5) domains (Ab )

domain
Gly
-3-P
EtOH

Dehydrogenase
Juang RH (2007) BCbaiscs

Hexokinase

Domain 1
Domain 2
Alberts et al (1994) Molecular Biology of the Cell (3e) p.196


Edelman, Porter (1972)

(subunits) = 2H (heavy) + 2L (light)

L2

L2
L
domains

H4 H4

H
domains

domain
Gene duplication
Alberts et al (2002) Molecular Biology of the Cell (4e) p.1382

Mathews et al (2000) Biochemistry (3e) p.246

Alberts et al (2002) Molecular Biology of the Cell (4e) p.146

domain

Lysozyme
Backbone
Hydrophobic
Hydrophilic
Total
+ substrate

Watson et al. (1987) Mol Biol Gene, Plate 3

 (Quaternary structure)

Myoglobin

Hemoglobin
Mathews et al (2000) Biochemistry (3e) p.214

(R)
relaxed state

Lung

Hb

Hb

Muscle

(T)
Hemoglobin tense state

Myoglobin
Juang RH (2007) BCbasics

Hemoglobin

80
60
40
20
0

20

40

60

80

100

Partial pressure of oxygen (pO2, mmHg)

120

Adapted from Garrett & Grisham (1999) Biochemistry (2e) p.480

Percent O2 saturation

100

Myoglobin

 heme

Stryer (1995) Biochemistry (4e) p.151

Stryer (1995) Biochemistry (4e) p.163

Garrett & Grisham (1999) Biochemistry (2e) p.486

WIKIPEDIA

Cartoon by I. Geis

1
Juang RH (2007) BCbasics

4
Mathews et al (2000) Biochemistry (3e) p.195

()

( helix, sheet)
Domain ( )
(monomer)

(dimer)

Juang RH (2007) BCbasics

GluVal

EF pocket
Mathews et al (2000) Biochemistry (3e) p.236

Mathews et al (2000) Biochemistry (3e) p.239

Conformation

Juang RH (2007) BCbasics

hemoglobin

pyruvate dehydrogenase

actin, myosin, virus

Juang RH (2007) BCbasics

product

Garrett & Grisham (1999) Biochemistry (2e) p.573

substrate

Garrett & Grisham (1999) Biochemistry (2e) p.173

Alberts et al (2002) Molecular Biology of the Cell (4e) p.153

Native protein
denaturation

renaturation

Denatured protein
Juang RH (2007) BCbasics

Darnell et al (1999) Molecular Cell Biology (2e) p.55

Guanidine HCl

NH2+
ClNH2- C -NH2

Mercaptoethanol

HOCH2CH2SH

SDS

SO4- -(CH2)11CH3

Urea

O
NH2- C -NH2

Juang RH (2007) BCbasics

O
-N H 2
NH 2-C
=

Mathews et al (2000) Biochemistry (3e) p.164

O
H2
N
-C
2
NH
=

helix
sheet

SDS

sodium dodecyl sulfate

Stryer (1995) Biochemistry (4e) p.275

SDS

SDS

boiling

Juang RH (2007) BCbasics

Beta-mercaptoethanol

HOCH2CH2SH
HOCH2CH2SH
HOCH2CH2SH

S
S

1
2

+ o

HOCH2CH3
HOCH2CH2S

HOCH2CH2S

+ HO
2

Oxidized form

HOCH2CH2SH

SH
SH

Juang RH (2007) BCbasics

Hexokinase

(1987) p.112

Carboxypeptidase A

Stryer (1995) Biochemistry (4e) p.220

Stryer (1995) Biochemistry (4e) p.220

Nelson & Cox (2000) Lehninger Principles of Biochemistry (3e) p.181

()

Hemoglobin
Bovine trypsin inhibitor

Mathews et al (2000) Biochemistry (3e) p.208

Mathews et al (2000) Biochemistry (3e) p.199

Stryer (1995) Biochemistry (4e) p.252

CHOM

Trypsin

(1984) p.199

Stryer (1995) Biochemistry (4e) p.250


I. Conformational Match:
Van der Waals interaction

II. Interaction Forces:

(1) Hydrogen bond
(2) Hydrophobic interaction
(3) Electrostatic interaction
(4) Van der Waals interaction

Kd

=OH-N-

+ Juang RH (2007) BCbasics


Roitt et al (2001) Immunology (6e) p.71

Darnell et al (1999) Molecular Cell Biology (2e) p.25

vdw

vdw

B
between non-polar surfaces

Juang RH (2007) BCbasics

Van der Waal interactions

Scientific American (2002) cover page