1

Proteins• Proteins have many

structures, resulting in a wide range of functions

• Proteins do most of the work in cells and act as enzymes

• Proteins are made of monomers called amino acids

2

• An overview of protein functions

Table 5.1

3

• Enzymes– Are a type of protein that acts as a

catalyst, speeding up chemical reactions

Substrate(sucrose)

Enzyme (sucrase)

Glucose

OH

H O

H2OFructose

3 Substrate is convertedto products.

1 Active site is available for a molecule of substrate, the

reactant on which the enzyme acts.

Substrate binds toenzyme.

22

4 Products are released.Figure 5.16

4

Polypeptides• Polypeptides

– Are polymers (chains) of amino acids

• A protein– Consists of one or more

polypeptides

5

• Amino acids– Are organic molecules possessing

both carboxyl and amino groups– Differ in their properties due to

differing side chains, called R groups

6

Twenty Amino Acids• 20 different amino acids make up proteins

O

O–

H

H3N+ C CO

O–H

CH3

H3N+ C

H

CO

O–

CH3 CH3

CH3

C CO

O–

H

H3N+

CHCH3

CH2

C

H

H3N+

CH3CH3

CH2

CH

C

H

H3N+ C

CH3

CH2

CH2

CH3N+

H

CO

O–

CH2

CH3N+

H

CO

O–

CH2

NH

H

CO

O–

H3N+ C

CH2

H2C

H2N C

CH2

H

C

NonpolarGlycine (Gly) Alanine (Ala) Valine (Val) Leucine (Leu) Isoleucine (Ile)

Methionine (Met) Phenylalanine (Phe)

CO

O–

Tryptophan (Trp) Proline (Pro)

H3C

Figure 5.17

S

O

O–

7

O–

OHCH2

C CH

H3N+

O

O–

H3N+

OH CH3

CHC CH O–

O

SHCH2

CH

H3N+ C

O

O–

H3N+ C C

CH2

OH

H H H

H3N+

NH2

CH2

OC

C CO

O–

NH2 OCCH2

CH2

C CH3N+

O

O–

OPolar

Electricallycharged

–O OCCH2

C CH3N+

H

O

O–

O– OCCH2

C CH3N+

H

O

O–

CH2

CH2

CH2

CH2

NH3+

CH2

C CH3N+

H

O

O–

NH2

C NH2+

CH2

CH2

CH2

C CH3N+

H

O

O–

CH2

NH+

NHCH2

C CH3N+

H

O

O–

Serine (Ser) Threonine (Thr) Cysteine (Cys)

Tyrosine(Tyr)

Asparagine(Asn)

Glutamine(Gln)

Acidic Basic

Aspartic acid (Asp)

Glutamic acid (Glu)

Lysine (Lys) Arginine (Arg) Histidine (His)

8

Amino Acid Polymers• Amino acids

– Are linked by peptide bonds

9

Protein Conformation and Function

• A protein’s specific conformation (shape) determines how it functions

10

Four Levels of Protein Structure

• Primary structure– Is the unique

sequence of amino acids in a polypeptide

Figure 5.20–

Amino acid

subunits

+H3NAmino

end

oCarboxyl end

oc

GlyProThrGlyThr

GlyGluSeuLysCysProLeu

MetVal

LysVal

LeuAspAlaValArgGlySerPro

Ala

GlylleSerProPheHisGluHis

AlaGlu

ValValPheThrAlaAsnAsp

SerGlyProArg

ArgTyrThr lleAla

AlaLeu

LeuSerProTyrSerTyrSerThr

ThrAlaVal

ValThrAsnProLysGlu

ThrLysSer

TyrTrpLysAlaLeu

GluLleAsp

11

O C helix

pleated sheetAmino acid

subunitsNCH

CO

C NH

CO H

RC N

H

CO H

CR

NHH

R CO

RCH

NH

CO H

NCO

RCH

NH

HCR

CO

CO

CNH

H

RC

CO

NH H

CR

CO

NH

RCH C

ONH H

CR

CO

NH

RCH C

ONH H

CR

CO

N H

H C RN H O

O C NC

RC

H O

CHR

N HO C

RC H

N H

O CH C R

N H

CC

NR

HO C

H C R

N HO C

RC H

HCR

NH

CO

C

NH

RCH C

ONH

C

• Secondary structure– Is the folding or coiling of the

polypeptide into a repeating configuration

– Includes the helix and the pleated sheet

H H

Figure 5.20

12

• Tertiary structure– Is the overall three-dimensional shape

of a polypeptide– Results from interactions between

amino acids and R groups

CH2CH

OHOCHOCH2

CH2 NH3+ C-O CH2

O

CH2SSCH2

CH

CH3CH3

H3CH3C

Hydrophobic interactions and van der Waalsinteractions Polypeptid

ebackbone

Hyrdogenbond

Ionic bond

CH2

Disulfide bridge

13

• Quaternary structure– Is the overall protein structure that

results from the aggregation of two or more polypeptide subunits

Polypeptidechain

Collagen

Chains

ChainsHemoglobin

IronHeme

14

Review of Protein Structure

+H3NAmino end

Amino acidsubunits

helix

15

Sickle-Cell Disease: A Simple Change in Primary Structure

• Sickle-cell disease– Results from a single amino

acid substitution in the protein hemoglobin

16

Fibers of abnormalhemoglobin deform cell into sickle shape.

Primary structure

Secondaryand tertiarystructures

Quaternary structure

Function

Red bloodcell shape

Hemoglobin A

Molecules donot associatewith oneanother, eachcarries oxygen.Normal cells arefull of individualhemoglobinmolecules, eachcarrying oxygen

10 m 10 m

Primary structure

Secondaryand tertiarystructures

Quaternary structureFunction

Red bloodcell shape

Hemoglobin SMolecules interact with one another tocrystallize into a fiber, capacity to carry oxygen is greatly reduced.

subunit subunit

1 2 3 4 5 6 7 3 4 5 6 721

Normal hemoglobin

Sickle-cell hemoglobin . . .. . .

Figure 5.21

Exposed hydrophobic

region

Val ThrHis Leu Pro Glul Glu Val His Leu Thr Pro Val Glu

17

What Determines Protein Conformation?

• Protein conformation Depends on the physical and chemical conditions of the protein’s environment

• Temperature, pH, etc. affect protein structure

18

•Denaturation is when a protein unravels and loses its native conformation(shape) Denaturation

Renaturation

Denatured proteinNormal protein

Figure 5.22

19

The Protein-Folding Problem• Most proteins

– Probably go through several intermediate states on their way to a stable conformation

– Denaturated proteins no longer work in their unfolded condition

– Proteins may be denaturated by extreme changes in pH or temperature

20

• Chaperonins– Are protein molecules that assist in the

proper folding of other proteins

Hollowcylinder

Cap

Chaperonin(fully assembled)

Steps of ChaperoninAction: An unfolded poly- peptide enters the cylinder from one end.

The cap attaches, causing the cylinder to change shape insuch a way that it creates a hydrophilic environment for the folding of the polypeptide.

The cap comesoff, and the properlyfolded protein is released.

CorrectlyfoldedproteinPolypeptide

2

1

3

Figure 5.23

21

• X-ray crystallography– Is used to determine a protein’s three-

dimensional structure X-raydiffraction pattern

Photographic filmDiffracted X-

raysX-raysource

X-ray

beam

CrystalNucleic acid Protein

(a) X-ray diffraction pattern(b) 3D computer modelFigure 5.24

22

Nucleic Acids• Nucleic acids store and

transmit hereditary information• There are two types of nucleic

acids– Deoxyribonucleic acid (DNA)– Ribonucleic acid (RNA)

23

• DNA– Stores information for the synthesis of specific proteins– Found in the nucleus of cells

• RNA– Reads information in DNA– Transports information to protein building structures

within cell

Function of DNA and RNA