Proteins and its function • Amino acids: building blocks ... - Nptel

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Dr. Sanjeeva Srivastava IIT Bombay

IIT Bombay Proteomics Course NPTEL

•  Proteins and its function

•  Amino acids: building blocks

•  Different levels of protein structure

•  Primary, Secondary, Tertiary, Quaternary

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IIT Bombay Proteomics Course NPTEL 3

•  Derived from Greek “Proteios”

•  Linear polymers built of monomers (amino acids)

•  Most versatile macromolecules in living systems

•  Play key structural and functional roles


Prom

oter T

A T A

C A G

T A C

C G T

Q

Y

R

Message

DNA Sequence

Protein Sequence & Regula5on

Protein Structure

Protein/ Enzyme Structure

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Protein Functions

SIGNALLING

TRANSPORT

CATALYSIS

MOVEMENT

STRUCTURE

REGULATION

Off

On

Α

Β


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Glycine

H N C H

H

COO

+

3

-‐ -‐

CH2

CH2

COO

C H

H N +

2

H2C

Proline Alanine

COO

H N C H

CH3

+

3

-‐ COO

H N C H

CH

+

3

-‐

CH 3 CH 3

Valine

COO

H N C H

CH2

+

3

-‐

CH 3 CH 3

CH

Leucine

-‐ COO

H N C H

C

CH3

+

3

H CH 3

CH2

Isoleucine

COO

H N C H

CH2

+

3

-‐

CH 3

CH2

S

Methionine IIT Bombay Proteomics Course NPTEL 7

H N C H

CH2OH

COO +

3

-‐

Serine

COO

+

3

-‐

CH3

H OH

Threonine

COO +

3

-‐

SH

Cysteine

COO

H N C H

CH2

+

3

-‐

H N 2 O

C

Asparagine

COO

H N C H

CH2

+

3

-‐

H N 2 O

CH2

C

Glutamine

H N C H

C

H N C H

CH2


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COO

H N C H

CH2

+

3

-‐

CH 2

CH2

CH2

NH3 +

COO

H N C H

CH2

+

3

-‐

NH

CH2

CH2

NH2

C

NH2 +

Lysine Arginine

COO

H N C H

CH2

+

3

-‐

C

C

NH

CH

N H

His5dine


COO

H N C H

CH2

+

3

-‐

COO -‐

Aspartate

COO

H N C H

CH2

+

3

-‐

CH 2

COO -‐

Glutamate


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COO

H N C H

CH2

+

3

-‐

Phenylalanine

COO

H N C H

CH2

+

3

-‐

OH

Tyrosine

COO

H N C H

CH2

+

3

-‐

C CH

NH

Tryptophan

Hydrophilic Hydrophobic

Hydrophobic character


Wavelength (nm)

Exti

ncti

on c

oeff

icie

nt

220 240 260 280 300 320

10,000

8,000

6,000

4,000

2,000

0


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COO־

Cα

R

NH3

H

COO־

Cα

R

NH3

H

L-‐Isomer D-‐Isomer



COO־

Cα

R

NH3

H

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C

H R

+ H3N C

HR

+ H3N C

R H

+ H3N

0 2 4 6 8 10 12 14

Zwitterionic Form

Both groups Protonated

Both groups Protonated

C C N

R2

+ C

N C

R1

+


R1

C

+H3N C

O

N

H

C

R2 H

+ H20

H

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N

C

H

O

C

R1

H

N

C

C

O H

R2 H

N

C

H

O

C

R3

H

N

C

C

O H

R4 H

Backbone


N

C Cα

Cα

H

O


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C

O

C

N

C

H

C

O¯ˉ

C

N +

C

H


N

C

Cα

H

O

Cα

Trans


NC

Cα

H

O

Cα

Cis

Trans

20

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N

C Cα

Cα

H

OTrans


NC

Cα

O

Cα

Cis

21


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4H2O

Condensa5on

Free amino acids

Glycine Alanine

Valine

Lysine Primary Structure


+H3N

C

H2C

O

C

N

C

C

O H

H

N

C

H

O

C

H

N

C

C

O H

H2C H

H H

N

C

H2C

C

H

H

_

HC

CH3

CH3

H

OH


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•  Essential for elucidation of its mechanism of action

•  Determines 3-D structure of proteins

•  Amino acid alteration can produce abnormality

•  Sequence tells us an evolutionary history of protein


Cα

C

Cα C

H

H

O

N

N

H

H H

R1 R3

R2

Cα

Ψ

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-‐180 -‐150 -‐120 -‐90 -‐60 -‐30 0 30 60 90 120 150 180 -‐180

-‐15

0 -‐1

20 -‐90 -‐6

0 -‐30 0 30 60

90 120

15

0 180

Psi

Phi Ψ

= 90°, Ψ = - 90° IIT Bombay Proteomics Course NPTEL 27


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Ribbon diagram Ball and stick model


N C

H

O

C

Ri

H

N C

C

O H

Ri+1 H

N C

O

C

H

N C

C

O H

Ri+3 H

H Ri+2

N C

O

C

H

N C

C

O H

Ri+5 H

H Ri+4

Residue i (CO) ____________i + 4 (NH)


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•  α-Keratin

•  Two α helices wrap to form a stable structure

•  Collagen

•  It contains 3 helical polypeptide chain


•  β sheets: another common, periodic structural motif

•  Fully extended structure •  Parallel •  Anti-parallel

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•  More elaborate structures loops or omega turns

•  Loops are rigid, no periodic structures

•  Turns and loops on surfaces

•  Participate in protein and other molecule interactions

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α helix β sheets

Rod like structure Sheet like structure

Axial distance 1.5 A Axial distance 3.5 A

Polypeptide chain tightly coiled

Polypeptide chain fully extended

H-bond between NH and CO groups in same polypeptide chains

H-bond between NH and CO groups in different polypeptide chains

Examples – Ferritin, keratin, collagen

Fatty acid binding protein


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•  Three dimensional compactly folded structure of proteins

•  Overall organization of secondary structural elements in 3-D space

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•  Final level of protein structure

•  Spatial arrangement of subunits and their interactions

•  Polypeptide chains assemble to form multisubunit structure

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Individual polypeptide chains

Quaternary structure (Hemoglobin)

α- subunits

β- subunits

α

α

β

β


DNA Genetic blueprint

RNA molecular photocopy

Proteins Building blocks

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•  Proteins and its function

•  Amino acids: building blocks •  Different levels of protein structure

•  Primary, Secondary, Tertiary, Quaternary

•  Myoglobin and Hemoglobin

•  Proteins and diseases

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•  Berg J., Tmyoczko J. & Stryer L., Biochemitry fifth ed., W. H. Freeman & company, 2002. ISBN: 0716746840. •  Nelson D. & Cox M.,Lehninger, Principles of Biochemistry fourth ed., W. H. Freeman and company, 2004. . ISBN: 023022699X. •  Voet D. & Voet J., Biochemistry fourth ed., Wiley, 2000. ISBN: 047158651X.

Proteins and its function • Amino acids: building blocks ... - Nptel

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Transcript of Proteins and its function • Amino acids: building blocks ... - Nptel