Proteins

Chapter 3

A. P. Biology

Mr. Knowles

Liberty Senior High School

Proteins are Most Common

Functions of Proteins1. Enzymes- Metabolism2. Structural- Collagen and Keratin3. Cell Recognition- proteins on

cellular surface.4. Regulation of Gene Expression-

Gene Repressors or Enhancers.5. Defense- Antibodies.

• An overview of protein functions

Table 5.1

Two Types of Proteins

1. Fibrous Proteins- rope-like, structural proteins; form shape of cells and tissues. Ex. Collagen-the most abundant protein of vertebrates.

2. Globular Proteins- have specific shapes for their functions. Ex. Enzymes and antibodies.

1. Proteins can be Structural

2. Proteins can be Globular

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

dimensional structure. X-raydiffraction pattern

Photographic film

Diffracted X-raysX-ray

sourceX-ray beam

Crystal Nucleic acid Protein

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

Figure 5.24

Papain

Proteins• Most diverse organic compound.

• Composed of amino acids- each with an amino group (NH2) and a carboxylic acid group (COOH).

• Different chemical group(s) attached to central C- R group .

Amino Acid Polymers• Amino acids

– Are linked by peptide bondsOH

DESMOSOMES

DESMOSOMESDESMOSOMES

OH

CH2

C

N

H

C

H O

H OH OH

Peptidebond

OH

OH

OH

H H

HH

H

H

H

H

H

H H

H

N

N N

N N

SH Side chains

SH

OO

O O O

H2O

CH2 CH2

CH2 CH2CH2

C C C C C C

C CC C

Peptidebond

Amino end(N-terminus)

Backbone

(a)

Figure 5.18 (b) Carboxyl end(C-terminus)

• 20 different amino acids make up proteins

O

O–

H

H3N+ C C

O

O–

H

CH3

H3N+ C

H

C

O

O–

CH3 CH3

CH3

C C

O

O–

H

H3N+

CH

CH3

CH2

C

H

H3N+

CH3

CH3

CH2

CH

C

H

H3N+ C

CH3

CH2

CH2

CH3N+

H

C

O

O–

CH2

CH3N+

H

C

O

O–

CH2

NH

H

C

O

O–

H3N+ C

CH2

H2C

H2N C

CH2

H

C

Nonpolar

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

Methionine (Met) Phenylalanine (Phe)

C

O

O–

Tryptophan (Trp) Proline (Pro)

H3C

Figure 5.17

S

O

O–

O–

OH

CH2

C C

H

H3N+

O

O–

H3N+

OH CH3

CH

C C

HO–

O

SH

CH2

C

H

H3N+ C

O

O–

H3N+ C C

CH2

OH

H H H

H3N+

NH2

CH2

O

C

C C

O

O–

NH2 O

C

CH2

CH2

C CH3N+

O

O–

O

Polar

Electricallycharged

–O O

C

CH2

C CH3N+

H

O

O–

O– O

C

CH2

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+

NH

CH2

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)

Amino Acids• Are the monomers of proteins.• Only 20 naturally occurring amino

acids.• The R group gives each of the amino

acids its unique property.• All 20 amino acids can be grouped into

5 basic groups.

5 Groups of Amino Acids (Fig. 3.15)

1. Nonpolar- have R groups that contain CH2 and CH3.

2. Polar Uncharged- R groups that have O or only H.

3. Ionizable- have R groups that are acids and bases.

4. Aromatic- R groups that have organic rings.

5 Groups of Amino Acids (Fig. 3.15)

5. Special-function- amino acids that are only used for very specific functions; methionine begins protein synthesis, proline causes kinks in the protein polymer, cysteine links chains together.

The 20 Common Amino Acids (Fig. 3.15) Click

below for another view!

Proteins

• Are polymers of amino acids.

• Joined by peptide bonds.

• Di- Tri- and Polypeptides.

Globular Proteins• Are long amino acids chains

folded into complex shapes.• All of the internal amino acids are

nonpolar.• Water excludes nonpolar amino

acids – hydrophobic interactions.

Globular Proteins Have Four Levels of Structure

1. Primary- the specific sequence of amino acids in the polypeptide chain.

• R groups have no role in the backbone, so any sequence of amino acids is possible.

• Therefore, 100 amino acids may be rearranged in 20100 different possible sequences.

Primary Structure:

Is the unique sequence of amino acids in a polypeptide.

Figure 5.20

–

Amino acid subunits+H3N

Amino end

o

Carboxyl end

oc

Gly Pro Thr Gly

Thr

Gly

GluSeuLysCysProLeu

Met

Val

Lys

Val

LeuAsp

Ala Val ArgGly

SerPro

Ala

Gly

lle

SerPro Phe His Glu His

Ala

Glu

ValValPheThrAla

Asn

Asp

SerGly Pro

ArgArg

TyrThr

lleAla

Ala

Leu

Leu

SerProTyrSer

TyrSerThr

Thr

Ala

ValVal

ThrAsn Pro

Lys Glu

Thr

Lys

SerTyrTrpLysAlaLeu

Glu Lle Asp

Globular Protein Structure

2. Secondary- folding or coiling of the chain into a pattern due to weak H bonds between amino acids.

• H bonds form between the main chain of amino acids.

• Two Kinds of Secondary Structure

Secondary Structures• Alpha Helix- H bonds between one

amino acid and another further down the chain. Pulls the chain into a coil.

• Beta Sheet- H bonds occur across two separate chains. If chains are parallel, they may form a sheet-like structure.

O C helix

pleated sheet

Amino acidsubunits N

C

H

C

O

C N

H

C

OH

R

C N

H

C

O H

C

R

N

HH

RC

O

R

C

H

N

H

C

OH

N

C

O

R

C

H

N

H

H

C

R

C

O

C

O

C

N

HH

R

C

C

O

N

HH

C

R

C

O

N

H

R

C

H C

O

N

HH

C

R

C

O

N

H

R

C

H C

O

N

HH

C

R

C

O

N H

H C R

N HO

O C N

C

RC

H O

CHR

N H

O C

R

CH

N H

O C

H C R

N H

C

CN

R

H

O C

H C R

N H

O C

R

CH

H

C

R

N

H

C

O

C

N

H

R

C

H C

O

N

H

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

Alpha Helix- The First Type of Secondary Protein Structure

Beta Sheet- Another Type of Protein

Secondary Structure

Show me the levels of protein structure.

Secondary Structures• Some patterns of alpha helices

and/or beta sheets are very common in protein structures.

• When secondary structures are organized into specific structures within proteins-motifs. Ex. Β-Barrel or α-turn-α motifs

Β-barrel Motif in a Cell Membrane Protein

Globular Protein Structure3. Tertiary Structure- folding and

positioning of nonpolar R groups into the interior of the protein (hydrophobic interactions).

• Held together by weak van der Waal’s forces.

• Precise fitting of R groups within the interior. A change may destabilize a protein’s shape.

Tertiary Structure:– Is the overall three-dimensional shape of a

polypeptide.

– Results from interactions between amino acids and R groups.

CH2

CH

OH

O

CHO

CH2

CH2 NH3+ C-O CH2

O

CH2SSCH2

CH

CH3

CH3

H3C

H3C

Hydrophobic interactions and van der Waalsinteractions

Polypeptidebackbone

Hydrogenbond

Ionic bond

CH2

Disulfide bridge

Globular Protein Structure4. Quaternary Structure- two or more

polypepetide chains associate to form a protein.

• Each chain is called a subunit.• Subunits are not necessarily the same.• Ex. Hemoglobin = 2 α-chain subunits +

2 β-chain subunits.

Quaternary Structure:– Is the overall protein structure that results from

the aggregation of two or more polypeptide subunits.

Polypeptidechain

Collagen

Chains

ChainsHemoglobin

Iron

Heme

The four levels of protein structure

+H3NAmino end

Amino acid

subunits

helix

Quaternary Structure of Hemoglobin

Hemoglobin structure and sickle-cell disease

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 structure

Function

Red bloodcell shape

Hemoglobin S

Molecules 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

Is Protein Folding Important?

Normal Prion Scrapie Prion

Reverse Transcriptase of HIV

Cobra Toxin

Shape of the Protein

• Tertiary and Quaternary structures provide shape.

• These structures are maintained by H bonds and other weak forces between R groups of amino acids.

Protein Folding

Conditions that Affect Protein Shape

Can disrupt H bonds by:• High Temperature• pH Changes (Acidic or Basic)• Ion Concentration (Salt)Disrupting the 2°, 3°, 4° structure is

called denaturation.

Denaturation:

Is when a protein unravels and loses its native conformation.

Denaturation

Renaturation

Denatured proteinNormal protein

Figure 5.22

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

catalyst, speeding up chemical reactions.

Substrate(sucrose)

Enzyme (sucrase)

Glucose

OH

H O

H2O

Fructose

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

Enzymes are Proteins• Organic catalysts - increase the rate of

chemical reactions in cells.

• Hold reactant molecules close together for reaction to occur- uses an active site.

• The active site is used to bind the reactant molecules-substrate.

Lock-and-Key Model

Show me the model, Luke!

Write your predictions!

Gelatin = Substrate

Pineapple = Papain (Enzyme)