Chem 150 Unit 10 - Biological Molecules III Peptides, Proteins and Enzymes Proteins are the workhorses in living systems. Their many roles include providing

Chem 150Chem 150Unit 10 - Unit 10 - BiologicalBiological Molecules III Molecules IIIPeptides, Proteins and EnzymesPeptides, Proteins and Enzymes

Proteins are the workhorses in living systems. Proteins are the workhorses in living systems. Their many roles include providing structure, Their many roles include providing structure, catalyzing nearly all the reactions that take catalyzing nearly all the reactions that take

place in a living cell, transporting and storing place in a living cell, transporting and storing materials, and controlling and defending living materials, and controlling and defending living

systems. Like carbohydrates, proteins are systems. Like carbohydrates, proteins are polymers, but unlike the polysaccharides, proteins polymers, but unlike the polysaccharides, proteins

are able to assume a much wider range of 3-are able to assume a much wider range of 3-dimensional structures and a functions. In this dimensional structures and a functions. In this

unit we will focus on one the of the most unit we will focus on one the of the most important functions of proteins; that of important functions of proteins; that of

biological catalysts (enzymes).biological catalysts (enzymes).

22

Amino AcidsAmino Acids

αα-Amino acids are the building blocks (monomers) for -Amino acids are the building blocks (monomers) for polypeptides and proteins.polypeptides and proteins.

• Every amino acid contains,Every amino acid contains,• A carboxylic acid groupA carboxylic acid group• An amino groupAn amino group• A side chain (R)A side chain (R)

33


Back in Unit 7 we saw that carboxylic acids behave as acids Back in Unit 7 we saw that carboxylic acids behave as acids when dissolved in water. when dissolved in water.

44

Question (Clickers) (Unit 7)Question (Clickers) (Unit 7)

At At pHpH 7, which will be the predominant species? 7, which will be the predominant species?

A)A) Carboxylic acidCarboxylic acid

B)B) Carboxylate ionCarboxylate ion

CH3 C

O

OH + H2O CH3 C

O

O + H3O+

acid acidbasebase

CH3 C

O

OH + H2O CH3 C

O

O + H3O+

acid acidbasebase

pKpKaa ≈ 5 ≈ 5pKpKaa ≈ 5 ≈ 5

carboxylic acidcarboxylic acidcarboxylic acidcarboxylic acid carboxylate ioncarboxylate ioncarboxylate ioncarboxylate ion

55

Carboxylic Acids & Phenols as Weak Acids Carboxylic Acids & Phenols as Weak Acids (Unit 7)(Unit 7)

• At At pHpH 7, the carboxylate ion of carboxylic acids predominate 7, the carboxylate ion of carboxylic acids predominate

• At At pH = pKpH = pKa a

• At At pH < pKpH < pKaa

• At At pH > pKpH > pKaa

CH3 C

O

OH + H2O CH3 C

O

O + H3O+

acid acidbasebase

CH3 C

O

OH + H2O CH3 C

O

O + H3O+

acid acidbasebase

pKpKaa ≈ 5 ≈ 5pKpKaa ≈ 5 ≈ 5pHpH = 7 = 7pHpH = 7 = 7

CH3 C

O

OH

acid

CH3 C

O

O

base

=CH3 C

O

OH

acid

CH3 C

O

O

base

=

CH3 C

O

OH

acid

CH3 C

O

O

base

>CH3 C

O

OH

acid

CH3 C

O

O

base

>

CH3 C

O

OH

acid

CH3 C

O

O

base

<CH3 C

O

OH

acid

CH3 C

O

O

base

<

66


Back in Unit 7 we also saw that amines behave as bases Back in Unit 7 we also saw that amines behave as bases when dissolved in water.when dissolved in water.

77

Amines as Weak Bases (Unit 7)Amines as Weak Bases (Unit 7)

Like ammonia, 1°, 2° and 3°, act as Brønsted-Lowry bases.Like ammonia, 1°, 2° and 3°, act as Brønsted-Lowry bases.

+ H2O (l) + OH- (aq)N H (aq)

H

CH3 N H (aq)

H

CH3

H

methanamine(base)

methylammonium ion(acid)

+ H2O (l) + OH- (aq)N H (aq)

H

CH3 N H (aq)

H

CH3

H

methanamine(base)


88

Amines as Weak Bases (Unit 7)Amines as Weak Bases (Unit 7)

The conjugate acids are called ammonium ionsThe conjugate acids are called ammonium ions• When placed in water, these ammonium ions will behave When placed in water, these ammonium ions will behave

like acids.like acids.

+ H3O+ (aq)+ H2O (l) N H (aq)

H

CH3N H (aq)

H

CH3

H

methanamine(base)


pKa ≈ 10+ H3O+ (aq)+ H2O (l) N H (aq)

H

CH3N H (aq)

H

CH3

H

methanamine(base)


pKa ≈ 10

99


At At pHpH 7, amino acids are in their 7, amino acids are in their zwitterionic zwitterionic form.form.• There is no There is no pHpH value at which value at which

there are no charges on an there are no charges on an amino acids.amino acids.

• However, there is a However, there is a pHpH value at value at which the which the net chargenet charge is zero. is zero.• This This pHpH value is called the value is called the

isoelectric pointisoelectric point..

Net chargeNet chargeNet chargeNet charge

+1+1+1+1

0000

-1-1-1-1

1010


There are 20 different sidechains for the amino acids that are There are 20 different sidechains for the amino acids that are used to build proteins.used to build proteins.

• These are classified according to their physical properties These are classified according to their physical properties asas

• Non-polarNon-polar

• Polar acidic (negatively charged at Polar acidic (negatively charged at pHpH 7) 7)

• Polar basic (positively charged at Polar basic (positively charged at pHpH 7) 7)

• Polar neutral (polar, but not charged at Polar neutral (polar, but not charged at pHpH 7) 7)

1111

Non polar Non polar sidechainssidechains• Most of these Most of these

sidechains sidechains are are hydrocarbonshydrocarbons


1212

Polar acidic sidechainsPolar acidic sidechains• Sidechains contain Sidechains contain

carboxylic acidscarboxylic acids• Negatively charged Negatively charged

at at pH 7pH 7


1313

Polar basic sidechainsPolar basic sidechains• Sidechains contain Sidechains contain

aminesamines• Positively charged at Positively charged at pHpH 7 7


1414

Polar neutral sidechainsPolar neutral sidechains• Sidechains contain polar Sidechains contain polar

groups that are capable of groups that are capable of hydrogen bondinghydrogen bonding• alcoholsalcohols• phenolsphenols• amidesamides

• Uncharged at Uncharged at pHpH 7 7


1515

For all of the amino acids, except one (glycine), the For all of the amino acids, except one (glycine), the αα-carbon -carbon is chiral.is chiral.• Fisher projection of the amino acids alanine:Fisher projection of the amino acids alanine:

• With few exceptions, only the With few exceptions, only the LL-amino acids are used to -amino acids are used to make proteins.make proteins.


1616

Peptides, Proteins, and Peptides, Proteins, and pHpH

Amino acids are joined together to form polymers of amino Amino acids are joined together to form polymers of amino acids called acids called oligopeptidesoligopeptides (2-10 amino acids) and (2-10 amino acids) and polypeptides polypeptides (more than 10 amino acids).(more than 10 amino acids).

• Collectively, oligopeptides and polypeptides are called Collectively, oligopeptides and polypeptides are called peptidespeptides..

• The amino acids are joind together by an amide bond The amino acids are joind together by an amide bond called a called a peptide bondpeptide bond, which is analogous to the , which is analogous to the glycosidic bond found in oligosaccharides and glycosidic bond found in oligosaccharides and polysaccharides.polysaccharides.

• Back in Unit 7 we saw how carboxylic acids can react with Back in Unit 7 we saw how carboxylic acids can react with ammonia and amines to form amides.ammonia and amines to form amides.

1717

Amides (Unit 7)Amides (Unit 7)

• When a carboxylic acid reacts with an amine it also When a carboxylic acid reacts with an amine it also produces and ammonium saltproduces and ammonium salt

• If the ammonium salt is then heated, an If the ammonium salt is then heated, an amideamide is is produced.produced.

1818

Amides (Unit 7)Amides (Unit 7)

Amides are important in Amides are important in biochemistry.biochemistry.• For example, amino For example, amino

acids are connected acids are connected together to form together to form proteins using amide proteins using amide groups.groups.

amino acidamino acidamino acidamino acid

1919

Peptide bond formationPeptide bond formation

Peptides, Proteins, and Peptides, Proteins, and pHpH

H3NC

C

OH

H

O NC

C

H OH

CH2

OH H+ H3NC

CN

CC

O

H

O

O

H

HH

CH2

+ H O HH3NC

C

OH

H

O NC

C

H OH

CH2

OH H+ H3NC

CN

CC

O

H

O

O

H

HH

CH2

+ H O H

Peptide BondPeptide BondPeptide BondPeptide Bond

DipeptideDipeptideDipeptideDipeptide

2020

Peptides, Proteins, and pHPeptides, Proteins, and pH

• The amide bond that The amide bond that connects the amino connects the amino acids together in a acids together in a peptide is called a peptide is called a peptide bondpeptide bond..

• ProteinsProteins are long are long polypeptide chains, polypeptide chains, usually with 50 or usually with 50 or more amino acids, more amino acids, which fold into a well which fold into a well defined structure.defined structure. The proteinThe protein

ubiquitinubiquitinThe proteinThe protein

ubiquitinubiquitin

2121

Peptides, Proteins, and pHPeptides, Proteins, and pH

Proteins are sensitive to the Proteins are sensitive to the pHpH because they contain because they contain numberous acid and base groupsnumberous acid and base groups• The The pHpH affects the charge on a proteins, which in turn, can affects the charge on a proteins, which in turn, can

have a marked effect on a protein’s structure and function.have a marked effect on a protein’s structure and function.

2222

Peptides, Proteins, and pH


ExampleExample• The charges on The charges on

the tripeptidethe tripeptideLys-Ser-AsnLys-Ser-Asnas a function of as a function of pHpH..

Net ChargeNet ChargeNet ChargeNet Charge

+2+2+2+2

0000

-2-2-2-2

2323



ExampleExample• The charges on The charges on

the tripeptidethe tripeptideLys-Lys-AlaLys-Lys-Alaas a function of as a function of pHpH..

Net ChargeNet ChargeNet ChargeNet Charge

+3+3+3+3

+2+2+2+2

-1-1-1-1

2424

Amino acids with acid or base side chains have additional Amino acids with acid or base side chains have additional charge groups:charge groups:

• e.g. e.g. Glutamic acid Glutamic acid is an acid amino acidis an acid amino acid

• At At pHpH’s below the isoionic point (’s below the isoionic point (pIpI) the charge is positive) the charge is positive

• At At pHpH’s above the isoionic point (’s above the isoionic point (pIpI), the charge is negative), the charge is negative


pIpI = 3.2 = 3.2pIpI = 3.2 = 3.2

H3N C

H

C

O

OH

CH2

CH2

C

OH–

H+

pH < 2

+1

O

OH

H3N C

H

C

O

O

CH2

CH2

C

OH–

H+

2 < pH < 4.4

0

O

OH

H3N C

H

C

O

O

CH2

CH2

C

OH–

H+

4.4 < pH < 9

-1

O

O

H2N C

H

C

O

O

CH2

CH2

C

9 < pH

-2

O

O

2525


Amino acids with acid or base side chains have additional Amino acids with acid or base side chains have additional charge groups:charge groups:

• e.g. e.g. Lysine Lysine is a basic amino acidis a basic amino acid

• At At pHpH’s below the isoionic point (’s below the isoionic point (pIpI) the charge is positive) the charge is positive

• At At pHpH’s above the isoionic point (’s above the isoionic point (pIpI), the charge is negative), the charge is negative

H3N C

H

C

O

OH

CH2

CH2

CH2

CH2

NH3

OH–

H+H3N C

H

C

O

O

CH2

CH2

CH2

CH2

NH3

OH–

H+H2N C

H

C

O

O

CH2

CH2

CH2

CH2

NH3

OH–

H+H2N C

H

C

O

O

CH2

CH2

CH2

CH2

NH2

pH < 2 2 < pH < 9 9 < pH < 10.3 10.3 < pH

+2 +1 0 -1

pI = 9.7pI = 9.7pI = 9.7pI = 9.7

2626


We are going to simplify the determination of charge as a We are going to simplify the determination of charge as a function of function of pHpH by looking only at by looking only at pHpH 1, 1, pH pH 7, and 7, and pHpH 14: 14:

Charges at different pH Charges at different pH valuesvalues pHpH 1 1 pH pH 77 pH pH 1414

AcidsAcidsAA

Include:Include:αα-COOH-COOH

Asp sidechainAsp sidechainGlu sidechainGlu sidechain

00 -1-1 -1-1

BasesBasesBB

Includes:Includes:αα-NH-NH

22

His sidechainHis sidechainLys sidechainLys sidechainArg sidechainArg sidechain

+1+1 +1+1 00

2727

QuestionQuestion

At At pH 7pH 7, which of the following amino acids have a net , which of the following amino acids have a net positive charge, which have a net negative charge, and which positive charge, which have a net negative charge, and which are neutral?are neutral?

LysineLysine

PhenylalaninePhenylalanine

LeucineLeucine

2828

QuestionQuestion

LysineLysine

C C

H

H2N

O

OH

CH2

CH2

CH2

CH2

NH2

BBBB

BBBB

AAAA Charges at Charges at different pH valuesdifferent pH values pHpH 1 1 pH pH 77 pH pH 1414

AA αα-COOH-COOH 00 -1-1 -1-1

BB αα-NH-NH22 +1+1 +1+1 00

BB Lys sidechainLys sidechain +1+1 +1+1 00

NetNet +2+2 +1+1 -1-1

2929

QuestionQuestion

Draw the structure of the following tripeptide Draw the structure of the following tripeptide Glu-Asp-PheGlu-Asp-Phe at at pHpH 1 and high 1 and high pH pH 1414. .

3030

QuestionQuestion

Draw the structure of the following tripeptide Draw the structure of the following tripeptide Glu-Asp-PheGlu-Asp-Phe at at pHpH 1 and high 1 and high pH pH 1414. .

H2N C C N C C N C C

H H HO O O

OH

R R RH H

H2N C C N C C N C C

H H HO O O

OH

R R RH H

Draw the backboneDraw the backboneDraw the backboneDraw the backbone

3131

QuestionQuestion

Draw the structure of the following tripeptide Draw the structure of the following tripeptide Glu-Asp-PheGlu-Asp-Phe at at pHpH 1 and high 1 and high pH pH 1414..

H2N C C N C C N C C

H H HO O O

OH

CH2 CH2 CH2H H

CH2

C

O OH

C

O OH

Glutamic Acid(Glu)

Aspartic acid(Asp)

Phenylalanine(Phe)

BBBB AAAA

AAAAAAAA

Add the sidechains and identify the acids (Add the sidechains and identify the acids (AA) and bases () and bases (BB))Add the sidechains and identify the acids (Add the sidechains and identify the acids (AA) and bases () and bases (BB))

3232


QuestionQuestion

H3N C C N C C N C C

H H HO O O

OH

CH2 CH2 CH2H H

CH2

C

O OH

C

O OH

Glutamic Acid(Glu)

Aspartic acid(Asp)

Phenylalanine(Phe)

BBBB AAAA

AAAAAAAA

At At pH pH 11, Acids (, Acids (AA) are 0 and Bases () are 0 and Bases (BB) are +1) are +1At At pH pH 11, Acids (, Acids (AA) are 0 and Bases () are 0 and Bases (BB) are +1) are +1

Net Charge = +1Net Charge = +1at at pHpH 1 1

Net Charge = +1Net Charge = +1at at pHpH 1 1

3333


QuestionQuestion

BBBB AAAA

AAAAAAAA

H2N C C N C C N C C

H H HO O O

O

CH2 CH2 CH2H H

CH2

C

O O

C

O O

Glutamic Acid(Glu)

Aspartic acid(Asp)

Phenylalanine(Phe)

At At pH pH 1414, Acids (, Acids (AA) are -1 and Bases () are -1 and Bases (BB) are 0) are 0At At pH pH 1414, Acids (, Acids (AA) are -1 and Bases () are -1 and Bases (BB) are 0) are 0

Net Charge = -3Net Charge = -3at at pHpH 14 14

Net Charge = -3Net Charge = -3at at pHpH 14 14

3434

Protein StructureProtein Structure

Proteins are polypeptides that fold to adopt a well-defined, Proteins are polypeptides that fold to adopt a well-defined, three-dimensional structure.three-dimensional structure.

There two general classifications of proteinsThere two general classifications of proteins

• Fibrous proteinsFibrous proteins exist as long fibers that are usually exist as long fibers that are usually tough and insoluble in water; examples includetough and insoluble in water; examples include• collagen (skin and bones)collagen (skin and bones)• Keratin (hair)Keratin (hair)

• Globular proteinsGlobular proteins are spherical, highly folded, and usually are spherical, highly folded, and usually soluble in water; examples includesoluble in water; examples include• enzymesenzymes• antibodiesantibodies• transport proteins like hemoglobin and myoglobintransport proteins like hemoglobin and myoglobin

3535

Fibrous versus globularFibrous versus globular


3636


Proteins display up to four levels of structureProteins display up to four levels of structure

• Primary structurePrimary structure• This is the amino acid sequence, which is unique for each proteinThis is the amino acid sequence, which is unique for each protein• This defines the covalent structure of a proteinThis defines the covalent structure of a protein

• Secondary structureSecondary structure• Regular, periodic structures, that involve hydrogen bonding between Regular, periodic structures, that involve hydrogen bonding between

the backbone amidesthe backbone amides

N C

H

C

O

H R RH

N

O

C

H

CN

H

O

N C

H

C

O

H RRH

C

O

C

H

CN

hydrogen bondsbetween amides

3737


Proteins display up to four Proteins display up to four levels of structurelevels of structure

• Tertiary structureTertiary structure

• The 3-dimensional fold of the The 3-dimensional fold of the the polypeptide in which the the polypeptide in which the backbone twists and turns its backbone twists and turns its way through the folded structure way through the folded structure of the protein.of the protein.

• It involves interactions between It involves interactions between the sidechains of the the amino the sidechains of the the amino acids and is highly influenced by acids and is highly influenced by the amino acid sequence.the amino acid sequence. The proteinThe protein


ubiquitinubiquitin

3838

Primary StructurePrimary Structure

• A protein’s amino acid sequence is referred to as its A protein’s amino acid sequence is referred to as its primary structureprimary structure..

• Every protein has a unique primary structure that is Every protein has a unique primary structure that is determined by the gene for that protein.determined by the gene for that protein.

• The primary structure defines the covalent structure The primary structure defines the covalent structure of a protein.of a protein.


3939



N-TerminusN-TerminusN-TerminusN-Terminus

C-TerminusC-TerminusC-TerminusC-Terminus

H3NC

CN

CC

NC

CN

CC

NC

CN

CC

NC

CN

CC

O

H

H

H

H

H

H

H

O

O

O

O

O

O

O

O

H

H

H

H

H

H

H

HH

CH2

CH3

CH2

HC CH3

CH3

CH2

OH

CH2

CH2

CH2

CH2

NH3

CH2

CO O

CH2

CH2

CO NH2

H3NC

CN

CC

NC

CN

CC

NC

CN

CC

NC

CN

CC

O

H

H

H

H

H

H

H

O

O

O

O

O

O

O

O

H

H

H

H

H

H

H

HH

CH2

CH3

CH2

HC CH3

CH3

CH2

OH

CH2

CH2

CH2

CH2

NH3

CH2

CO O

CH2

CH2

CO NH2

GlycineGlycineGlyGly

GlycineGlycineGlyGly

PhenylalaninePhenylalaninePhePhe

PhenylalaninePhenylalaninePhePhe

AlanineAlanineAlaAla

AlanineAlanineAlaAla

LeucineLeucineLeuLeu

LeucineLeucineLeuLeu

SerineSerineSerSer

SerineSerineSerSer

LysineLysineLysLys

LysineLysineLysLys

Aspartic AcidAspartic AcidAspAsp

Aspartic AcidAspartic AcidAspAsp

GluctamineGluctamineGlnGln

GluctamineGluctamineGlnGln

4040



N-TerminusN-TerminusN-TerminusN-Terminus

C-TerminusC-TerminusC-TerminusC-Terminus

H3NC

CN

CC

NC

CN

CC

NC

CN

CC

NC

CN

CC

O

H

H

H

H

H

H

H

O

O

O

O

O

O

O

O

H

H

H

H

H

H

H

HH

CH2

CH3

CH2

HC CH3

CH3

CH2

OH

CH2

CH2

CH2

CH2

NH3

CH2

CO O

CH2

CH2

CO NH2

H3NC

CN

CC

NC

CN

CC

NC

CN

CC

NC

CN

CC

O

H

H

H

H

H

H

H

O

O

O

O

O

O

O

O

H

H

H

H

H

H

H

HH

CH2

CH3

CH2

HC CH3

CH3

CH2

OH

CH2

CH2

CH2

CH2

NH3

CH2

CO O

CH2

CH2

CO NH2

HH22H-Gly-Phe-Ala-Leu-Ser-Lys-Asp-Gln-COOHH-Gly-Phe-Ala-Leu-Ser-Lys-Asp-Gln-COOHHH

22H-Gly-Phe-Ala-Leu-Ser-Lys-Asp-Gln-COOHH-Gly-Phe-Ala-Leu-Ser-Lys-Asp-Gln-COOH

Gly-Phe-Ala-Leu-Ser-Lys-Asp-GlnGly-Phe-Ala-Leu-Ser-Lys-Asp-GlnGly-Phe-Ala-Leu-Ser-Lys-Asp-GlnGly-Phe-Ala-Leu-Ser-Lys-Asp-GlnGFALSKDQGFALSKDQGFALSKDQGFALSKDQ

GlycylphenylalanylalanylleucylseryllysylaspartylglutamGlycylphenylalanylalanylleucylseryllysylaspartylglutamineine

GlycylphenylalanylalanylleucylseryllysylaspartylglutamGlycylphenylalanylalanylleucylseryllysylaspartylglutamineine

4141

Primary structurePrimary structure• The Central DogmaThe Central Dogma• DNA → mRNA → PolypeptideDNA → mRNA → Polypeptide


•The genetic code is The genetic code is used to match up the used to match up the DNA/mRNA sequence DNA/mRNA sequence to the sequence of to the sequence of amino acids in a proteinamino acids in a protein

•All living organisms use All living organisms use the same codethe same code

•The genetic code is The genetic code is used to match up the used to match up the DNA/mRNA sequence DNA/mRNA sequence to the sequence of to the sequence of amino acids in a proteinamino acids in a protein

•All living organisms use All living organisms use the same codethe same code

4242

• The functional diversity of proteins results from the large The functional diversity of proteins results from the large number of possible proteins that can be built using the 20 number of possible proteins that can be built using the 20 different amino acidsdifferent amino acids

• QuestionQuestion: How much mass would it take to construct one : How much mass would it take to construct one molecule each of all of the possible polypeptides molecule each of all of the possible polypeptides containing 100 amino acids residues?containing 100 amino acids residues?

• View the polypeptides as beads on a string, with one of 20 possible View the polypeptides as beads on a string, with one of 20 possible types of beads at each position.types of beads at each position.


o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-oo-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-oo-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-oo-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o-o

4343

The Earth weighs 6.0 x 10The Earth weighs 6.0 x 102727

g, how many Earths would it g, how many Earths would it take?take?


4444

The Sun weighs 2.0 x The Sun weighs 2.0 x 10103333

g g, how many Suns would it take?, how many Suns would it take?


4545

The Milky Way galaxy weighs 1.2 x 10The Milky Way galaxy weighs 1.2 x 104545

times the mass of times the mass of the sunthe sun

• (1.2 x 10(1.2 x 104545 sunssuns)(2.0 x 10)(2.0 x 103333 g/sun) = 2.4 x 10 g/sun) = 2.4 x 107878 g g

•HowHow may galaxies would it take? may galaxies would it take?


4646

The Coma galaxy cluster contains several thousand galaxies, The Coma galaxy cluster contains several thousand galaxies, how many ...?how many ...?


4747


Number of polypeptides Number of polypeptides (20(20100100)) 1.26 x 101.26 x 10130130

Avg. Mass of each Avg. Mass of each polypeptidepolypeptide 1.83 x 101.83 x 10-22-22

gg

Total mass neededTotal mass needed 2.322.32 x 10 x 10108108 gg

Number of EarthsNumber of Earths 3.9 x 103.9 x 108080

Number of SunsNumber of Suns 1.2 x 101.2 x 107575

Number of GalaxiesNumber of Galaxies 9.7 x 109.7 x 102929

4848


Secondary structureSecondary structure• The polypeptide backbone can take on regular shapes that The polypeptide backbone can take on regular shapes that

allow the backbone amides to hydrogen bond to one allow the backbone amides to hydrogen bond to one another.another.

• The primary forms of secondary structure includeThe primary forms of secondary structure include• αα-helix-helix• ββ-sheet-sheet

4949

Secondary structure Secondary structure


α-Helixα-Helixα-Helixα-Helix

5050

Secondary Structure Secondary Structure


β-Sheetβ-Sheetβ-Sheetβ-Sheet

5151

Secondary StructureSecondary Structure

Protein Secondary StructureProtein Secondary Structure

Antiparallel β-SheetAntiparallel β-SheetAntiparallel β-SheetAntiparallel β-Sheet

5252

Secondary Structure Secondary Structure


Parallel β-SheetParallel β-SheetParallel β-SheetParallel β-Sheet

5353


Tertiary StructureTertiary Structure

• The different elements of The different elements of secondary structure come secondary structure come together to create the together to create the overall 3-dimensional overall 3-dimensional structure of the the proteinstructure of the the protein

• The structure is stabilized The structure is stabilized primarily by sidechain primarily by sidechain interactions and is highly interactions and is highly influenced by the amino influenced by the amino acid sequence (primary acid sequence (primary structure).structure).

The proteinThe proteinubiquitinubiquitin


5454



• This is usually the This is usually the nativenative, , or biologically active, form or biologically active, form of the protein.of the protein.

• When placed in water, the When placed in water, the polypeptide folds to polypeptide folds to maximize the number of maximize the number of nonpolar (hydrophobic) nonpolar (hydrophobic) residues that are buried residues that are buried on the inside away from on the inside away from exposure to water.exposure to water. The proteinThe protein


ubiquitinubiquitin

5555





Explore thetertiary structureand thesecondary structure of the protein ubiqu

itin

Explore thetertiary structureand thesecondary structure of the protein ubiqu

itin

http://www.chem.uwec.edu/Chem150_S07/overheads/unit10/ubiquitin/ubiquitin.html








5656


Tertiary StructureTertiary Structure• The tertiary structure is stabilized by the same non-The tertiary structure is stabilized by the same non-

covalent interactions that we looked at in determining covalent interactions that we looked at in determining boiling points and solubilitesboiling points and solubilites• Charge/Charge interactions (Salt bridges)Charge/Charge interactions (Salt bridges)• Ion/Dipole interactionsIon/Dipole interactions• Dipole/Dipole interactionsDipole/Dipole interactions• Hydrogen bondingHydrogen bonding• Hydrophobic interactions (nonpolor/water)Hydrophobic interactions (nonpolor/water)

• There is one covalent interactions that stabilizes the There is one covalent interactions that stabilizes the tertiary structure of some proteins.tertiary structure of some proteins.• Disufide bondDisufide bond

5757


Tertiary StructureTertiary Structure• The interactions that The interactions that

stabilize the tertiary stabilize the tertiary structure.structure.

5858


Quaternary StructureQuaternary Structure• Some proteins contain multiple Some proteins contain multiple

polypeptidespolypeptides• Each peptide is called a subunitEach peptide is called a subunit

• The polypeptides are held The polypeptides are held together by the same types of together by the same types of interactions that stabilize the interactions that stabilize the tertiary structure.tertiary structure.Explore thequaternary structur

e of the protein ubiquitin

Explore thequaternary structure of the protein ubiquit

in





5959

Protein DenaturationProtein Denaturation

Because the secondary, tertiary and quaternary structures of Because the secondary, tertiary and quaternary structures of proteins are stabilized by weak, non-covalent interactions, proteins are stabilized by weak, non-covalent interactions, these structures are easily disrupted by agents that disrupt these structures are easily disrupted by agents that disrupt theses interactions, including:theses interactions, including:• Changes in temperatureChanges in temperature• Changes in Changes in pHpH• Mechanical stress (agitation)Mechanical stress (agitation)• Soaps and detergentsSoaps and detergentsThese agents typically cause the protein to unfoldThese agents typically cause the protein to unfold• Only the primary structure remainsOnly the primary structure remains• The protein loses it functionThe protein loses it functionThe process is called The process is called protein denaturationprotein denaturation..

6060

Protein DenaturationProtein Denaturation

Christain Anfinsen won a Nobel Prize for showing that protein Christain Anfinsen won a Nobel Prize for showing that protein denaturation can be reversed.denaturation can be reversed.• The experiment demonstrated that the information necessary The experiment demonstrated that the information necessary

to obtain the correctly folded protein structure is contained to obtain the correctly folded protein structure is contained within the protein’s amino acid sequence (primary structure).within the protein’s amino acid sequence (primary structure).

ActiveActiveProteinProteinActiveActiveProteinProtein

InactiveInactiveProteinProteinInactiveInactiveProteinProtein

6161

EnzymesEnzymes

Nearly every reaction that takes place in a living cell has an Nearly every reaction that takes place in a living cell has an enzyme associated with it.enzyme associated with it.

• Enzymes are biological catalystsEnzymes are biological catalysts

• Most enzymes are proteinsMost enzymes are proteins

Many human diseases involve enzymes misbehavingMany human diseases involve enzymes misbehaving

• Many treatments for diseases involve drugs that target Many treatments for diseases involve drugs that target enzymes.enzymes.

6262

EnzymesEnzymes

The common names for enzymes often describe the The common names for enzymes often describe the substratesubstrate (reactant) for the reaction and a description of the (reactant) for the reaction and a description of the reaction that is being carried out on that substrate.reaction that is being carried out on that substrate.

• The names usually end with The names usually end with -ase-ase..

• Example: Example: alcohol dehydrogenasealcohol dehydrogenase

CH3 CH2 OH

NAD+ NADH + H+

CH3 C H

O

ethanol ethanal(acetaldehyde)

alcohol aldehyde

alcohol dehydrogenaseenzyme

CH3 CH2 OH

NAD+ NADH + H+

CH3 C H

O


alcohol aldehyde


6363

Question (Clicker)Question (Clicker)

What class of reaction is the alcohol dehydrogenase What class of reaction is the alcohol dehydrogenase reaction?reaction?

A)A) HydrolysisHydrolysis

B)B) DecarboxylationDecarboxylation

C)C) Oxidation/reductionOxidation/reduction

D)D) Acid/baseAcid/base

E)E) HydrationHydration

CH3 CH2 OH

NAD+ NADH + H+

CH3 C H

O


alcohol aldehyde


CH3 CH2 OH

NAD+ NADH + H+

CH3 C H

O


alcohol aldehyde


6464

Reactions of Alcohols and Thiols (Unit 8)Reactions of Alcohols and Thiols (Unit 8)

6565

EnzymesEnzymes



• Example: Example: pyruvate decarboxylasepyruvate decarboxylase

CH3 C

O

C

O

OH

α-keto acid

CH3 C H

O

ethanal(acetaldehyde)

aldehyde

+ CO2

pyruvic acidpyruvate

decarboxylase

CH3 C

O

C

O

OH

α-keto acid

CH3 C H

O


aldehyde

+ CO2


decarboxylase

6666


What class of reaction is the pyruvate decarboxylase What class of reaction is the pyruvate decarboxylase reaction?reaction?






CH3 C

O

C

O

OH

α-keto acid

CH3 C H

O


aldehyde

+ CO2


decarboxylase

CH3 C

O

C

O

OH

α-keto acid

CH3 C H

O


aldehyde

+ CO2


decarboxylase

6767

Carboxylic Acids & Phenols, Other Reactions Carboxylic Acids & Phenols, Other Reactions (Unit 7)(Unit 7)

The decarboxylation of The decarboxylation of ββ-keto acids produces -keto acids produces ketonesketones

The decarboxylation of The decarboxylation of αα-keto acids produces -keto acids produces aldehydesaldehydes

6868

EnzymesEnzymes



• Example: Example: succinate dehydrogenasesuccinate dehydrogenase

CH2CH2C

O

HO C

O

OH

FAD

succinatedehydrogenase

FADH2

succinic acid

CCC

O

HO

C

O

OH

fumaric acid

H

H

CH2CH2C

O

HO C

O

OH

FAD


FADH2

succinic acid

CCC

O

HO

C

O

OH

fumaric acid

H

H

6969


What class of reaction is the alchohol dehydrogenase What class of reaction is the alchohol dehydrogenase reaction?reaction?






CH2CH2C

O

HO C

O

OH

FAD


FADH2

succinic acid

CCC

O

HO

C

O

OH

fumaric acid

H

H

CH2CH2C

O

HO C

O

OH

FAD


FADH2

succinic acid

CCC

O

HO

C

O

OH

fumaric acid

H

H

7070

Oxidation and Reduction (Unit 4)Oxidation and Reduction (Unit 4)

The reaction equation on the previous slide also illustrates The reaction equation on the previous slide also illustrates another shorthand method of writing equations, which used another shorthand method of writing equations, which used multiple reaction arrows.multiple reaction arrows.

• The longhand form of this reaction equation isThe longhand form of this reaction equation is

HO C

O

C C

H H

C

OH H

OH

succinic acid(saturated)

HO C

O

C C

H

C

O

OH

fumaric acid(unsaturated)

FAD FADH2 H

H

HO C

O

C C

H H

C

OH H

OH

succinic acid(saturated)

FAD HO C

O

C C

H

C

O

OH

fumaric acid(unsaturated)

FADH2+ +

7171

EnzymesEnzymes



• Example: Example: succinate dehydrogenasesuccinate dehydrogenase

CCC

O

HO

C

O

OH

fumaric acid

H

H

CCH2C

O

HO C

O

OH

L-malic acid

fumarase

+ H2O

OH

H

CCC

O

HO

C

O

OH

fumaric acid

H

H

CCH2C

O

HO C

O

OH

L-malic acid

fumarase

+ H2O

OH

H

7272


What class of reaction is the fumarase reaction? (Unit 8)What class of reaction is the fumarase reaction? (Unit 8)






CCC

O

HO

C

O

OH

fumaric acid

H

H

CCH2C

O

HO C

O

OH

L-malic acid

fumarase

+ H2O

OH

H

CCC

O

HO

C

O

OH

fumaric acid

H

H

CCH2C

O

HO C

O

OH

L-malic acid

fumarase

+ H2O

OH

H

7373

Reactions Involving Water (Unit 4)Reactions Involving Water (Unit 4)

HydrationHydration• In the In the hydration hydration reaction water is also split, but instead of reaction water is also split, but instead of

being used to split another molecule, it is added to another being used to split another molecule, it is added to another molecule to produce a single product.molecule to produce a single product.

• The water it is added to either an alkene or alkyne:The water it is added to either an alkene or alkyne:

• The hydration of an alkene produces an alcohol.The hydration of an alkene produces an alcohol.

C CH

H H

H + H OHacid

catalyst

C CH

H H

H

H OH

ethene(an alkene)

ethanol(an alcohol)

7474

EnzymesEnzymes

SpecificitySpecificity• Absolute spectificityAbsolute spectificity - enzyme only accepts one specific - enzyme only accepts one specific

substrate.substrate.• Relative specificityRelative specificity - enzyme accepts a range of related - enzyme accepts a range of related

substrates.substrates.

R CH2 OH

NAD+ NADH + H+

CH3 C H

O



alcohol aldehyde

R CH2 OH

NAD+ NADH + H+

CH3 C H

O



alcohol aldehyde

7575

EnzymesEnzymes

SpecificitySpecificity• Stereospecific specificityStereospecific specificity - enzyme only reacts with or - enzyme only reacts with or

produces one specific stereoisomerproduces one specific stereoisomer

CH2CH2C

O

HO C

O

OH

FAD


FADH2

succinic acid

CCC

O

HO

C

O

OH

fumaric acid

H

HCC

C

O

HO C

O

OH

maleic acid

HH

+

trans cis

CH2CH2C

O

HO C

O

OH

FAD


FADH2

succinic acid

CCC

O

HO

C

O

OH

fumaric acid

H

HCC

C

O

HO C

O

OH

maleic acid

HH

+

trans cis

CCC

O

HO

C

O

OH

fumaric acid

H

H

CCH2C

O

HO C

O

OH

L-malic acid

fumarase

+ H2O

OH

H

CCH2C

O

HO C

O

OH

D-malic acid

H

OH

+CCC

O

HO

C

O

OH

fumaric acid

H

H

CCH2C

O

HO C

O

OH

L-malic acid

fumarase

+ H2O

OH

H

CCH2C

O

HO C

O

OH

D-malic acid

H

OH

+

7676

EnzymesEnzymes

SpecificitySpecificity• AbsoluteAbsolute• RelativeRelative• StereospecificStereospecific

7777

EnzymesEnzymes

CatalysisCatalysis• As catalysis, enzyme have no effect on the change in free As catalysis, enzyme have no effect on the change in free

energy, energy, ΔΔG,G, for a reaction for a reaction• Ezymes speed up reactions by decreasing the activation Ezymes speed up reactions by decreasing the activation

energy, energy, EEactact..• Enzymes do this by binding the substrates and by directing the Enzymes do this by binding the substrates and by directing the

reaction reaction

7878

Free Energy and Reaction Rates (Unit 4)Free Energy and Reaction Rates (Unit 4)

There is a third way to speed up the reaction rate and that is There is a third way to speed up the reaction rate and that is to lower the height of the hill.to lower the height of the hill.

• This is done using This is done using catalystscatalysts, which provide an alternative , which provide an alternative pathway over the hill for the reactants.pathway over the hill for the reactants.

FreeFreeEnergyEnergy

(G)(G)

FreeFreeEnergyEnergy

(G)(G)

Progress ofProgress ofreactionreaction

Progress ofProgress ofreactionreaction

Α Α → → BBΑ Α → → BB

AAAA

ΒΒΒΒ

ΔΔGG < 0 < 0spontaneousspontaneous

ΔΔGG < 0 < 0spontaneousspontaneous

EEactact > 0 > 0without catalystwithout catalyst

--with catalystwith catalyst

EEactact > 0 > 0without catalystwithout catalyst

--with catalystwith catalyst

7979

EnzymesEnzymes

CatalysisCatalysis• The location on the enzyme where the substrate binds and The location on the enzyme where the substrate binds and

the reaction occurs is called the the reaction occurs is called the active siteactive site..• Back in Unit 4 we saw a specific example of this with the Back in Unit 4 we saw a specific example of this with the

hexokinase reaction hexokinase reaction

Explore the enzyme hexokinaseExplore the enzyme hexokinase





8080

EnzymesEnzymes

Cofactors and CoenzymesCofactors and Coenzymes• Sometimes enzymes need some help with catalzying the Sometimes enzymes need some help with catalzying the

reactions.reactions.• Cofactors are non-protein components of an enzymeCofactors are non-protein components of an enzyme• Metal ionsMetal ions• Organic molecules (Coenzymes)Organic molecules (Coenzymes)

• Many of the coenzymes are derived from the vitamins that Many of the coenzymes are derived from the vitamins that we take in in our diet.we take in in our diet.

8181

EnzymesEnzymes

8282

EnzymesEnzymes

pHpH and Temperature and Temperature• Enyzme activity is often critically dependent on the Enyzme activity is often critically dependent on the pHpH and and

temperature.temperature.

8383

Control of Enzyme-Catalyzed ReactionsControl of Enzyme-Catalyzed Reactions

Michaelis-Meten enzymes behave according to a model Michaelis-Meten enzymes behave according to a model proposed in the early 1900’s by Michaelis and Menten.proposed in the early 1900’s by Michaelis and Menten.

• E = enyzmeE = enyzme• S = substrateS = substrate• ES = enzyme-substrate complexES = enzyme-substrate complex• P = productP = product

8484


Raymond describes an analogy of reaching into a box for an Raymond describes an analogy of reaching into a box for an orgrange, pulling one out, and peeling it.orgrange, pulling one out, and peeling it.

• The Michaelis-Menten model is characterized by two The Michaelis-Menten model is characterized by two parameters.parameters.• KKMM (The Michaelis-Menten constant), which is related to the strength (The Michaelis-Menten constant), which is related to the strength

of the substrate binding.of the substrate binding.• VVmaxmax (The maximum velocity), which corresponds to the maximum (The maximum velocity), which corresponds to the maximum

rate that the enzyme-substrate complex forms product.rate that the enzyme-substrate complex forms product.

KKMMKKMM VVmaxmaxVVmaxmax

8585


Enzyme InhibitionEnzyme Inhibition• Can be a normal Can be a normal

event used by the cell event used by the cell to control enzyme to control enzyme activity.activity.

• Can also be exploited Can also be exploited in the design of drugs.in the design of drugs.• ExampleExample, the , the

irreversible irreversible inhibitioninhibition of COX of COX enzymes by aspirinenzymes by aspirin

8686


Enzyme Inhibition can also be ReversibleEnzyme Inhibition can also be Reversible• Competitive inhibitionCompetitive inhibition• The inhibitor competes with the substrate for the active siteThe inhibitor competes with the substrate for the active site


Competitive inhibitionCompetitive inhibitionaffect affect

KKMM but not V but not Vmaxmax

Competitive inhibitionCompetitive inhibitionaffect affect

KKMM but not V but not Vmaxmax

8787


Some drugs are competitive inhibitors of enzymesSome drugs are competitive inhibitors of enzymes• Example: the anti-HIV drug AZTExample: the anti-HIV drug AZT

• The AZT inhibits the enzyme The AZT inhibits the enzyme reverse trascriptase enzymereverse trascriptase enzyme, , which the HIV virus uses to converts it RNA to DNA. The which the HIV virus uses to converts it RNA to DNA. The drug mimics the normal substrate for this enzyme, dTTP.drug mimics the normal substrate for this enzyme, dTTP.

• This drug targets the activity of the HIV virus because This drug targets the activity of the HIV virus because humans do not use a reverse transcriptase enzyme.humans do not use a reverse transcriptase enzyme.

8888


Some drugs are competitive inhibitors of enzymesSome drugs are competitive inhibitors of enzymes• Example: the bacterial drug sufanilamide (a sulfa drug).Example: the bacterial drug sufanilamide (a sulfa drug).

• The sufanilamide inhibits the an enzyme that bacteria use The sufanilamide inhibits the an enzyme that bacteria use to synthesize the coenzyme folate. The drug mimics the to synthesize the coenzyme folate. The drug mimics the normal substrate for this enzyme, normal substrate for this enzyme, pp-aminobenoate.-aminobenoate.

8989


• This drug targets the activity of bacteria because humans This drug targets the activity of bacteria because humans do not synthesize their own folate, getting it instead from do not synthesize their own folate, getting it instead from their diet.their diet.

FolateFolateFolateFolate

9090


Enzyme Inhibition can also be ReversibleEnzyme Inhibition can also be Reversible• Noncompetitive inhibitionNoncompetitive inhibition• The inhibitor binds at a different site thatn the substrate.The inhibitor binds at a different site thatn the substrate.


Noncompetitive inhibitionNoncompetitive inhibitionaffects affects

VVmax max but not Kbut not KMM

Noncompetitive inhibitionNoncompetitive inhibitionaffects affects

VVmax max but not Kbut not KMM

9191


Noncompetitive inhibition is often used to regulate Noncompetitive inhibition is often used to regulate biosynthetic pathways by a mechanism called biosynthetic pathways by a mechanism called feedback feedback inhibitioninhibition..• The end product of the pathway binds to a site on an The end product of the pathway binds to a site on an

enzyme used earlier in the pathway, and turns it off.enzyme used earlier in the pathway, and turns it off.

9292


Enzymes that are inhibited by a substance binding to a site Enzymes that are inhibited by a substance binding to a site other than the active site are called other than the active site are called allosteric enzymesallosteric enzymes..• The enzymes that are regulated by noncompetive inhibition The enzymes that are regulated by noncompetive inhibition

in feedback inhibition are examples of allosteric enzyme. in feedback inhibition are examples of allosteric enzyme.• The substance that inhibits the enzyme in this way is called The substance that inhibits the enzyme in this way is called

a a negative effectornegative effector..

Some allosteric enzymes are activated instead of inhibited by Some allosteric enzymes are activated instead of inhibited by as substance binding at their allosteric site.as substance binding at their allosteric site.• These substances are called These substances are called positive effectorspositive effectors..

9393


Some enzymes are controlled by covalent modifications to Some enzymes are controlled by covalent modifications to their structure.their structure.• In some cases the modifications are reversible, such as In some cases the modifications are reversible, such as

placing a phosphate on an enzyme to turn it on, and then placing a phosphate on an enzyme to turn it on, and then taking the phosphate off to turn it off again.taking the phosphate off to turn it off again.

9494


Some enzymes are controlled by covalent modifications to Some enzymes are controlled by covalent modifications to their structure.their structure.• Example: Glycogen phosphorylase, which is the enzyme Example: Glycogen phosphorylase, which is the enzyme

that breaks down the polysaccharide glycogen.that breaks down the polysaccharide glycogen.• The phosphorylation/dephosphorylation of this enzyme is The phosphorylation/dephosphorylation of this enzyme is

under hormonal control.under hormonal control.

9595


Some enzymes are controlled by covalent modifications to Some enzymes are controlled by covalent modifications to their structuretheir structure• In other cases the covalent modification is irreversible.In other cases the covalent modification is irreversible.

9696


Some enzymes are controlled by covalent modifications to Some enzymes are controlled by covalent modifications to their structuretheir structure• Example: the digestive enzymes trypsin and chymotrypsin, Example: the digestive enzymes trypsin and chymotrypsin,

which are used to break down proteins in the small which are used to break down proteins in the small intestine are synthesized in the pancreas in an inactive intestine are synthesized in the pancreas in an inactive form called trypsinogen and chymotrypsinogen, form called trypsinogen and chymotrypsinogen, respectively.respectively.

• They are transported in this inactive form to the small They are transported in this inactive form to the small intestine, there are activated by removing parts of their intestine, there are activated by removing parts of their amino acids sequence.amino acids sequence.

9797


In a clinical setting, the presence of enzymes in blood is often In a clinical setting, the presence of enzymes in blood is often used to diagnose tissue damage that is related to various used to diagnose tissue damage that is related to various diseases.diseases.

The EndThe End

Documents

Chem 150 Unit 10 - Biological Molecules III Peptides, Proteins and Enzymes Proteins are the workhorses in living systems. Their many roles include providing