Chem 150 unit 10 biological molecules iii peptides proteins and enzymes
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Chem 150 unit 10 biological molecules iii peptides proteins and enzymes

Chem 150Unit 10 - Biological Molecules IIIPeptides, Proteins and Enzymes

  • Proteins are the workhorses in living systems. Their many roles include providing structure, catalyzing nearly all the reactions that take place in a living cell, transporting and storing materials, and controlling and defending living systems. Like carbohydrates, proteins are polymers, but unlike the polysaccharides, proteins are able to assume a much wider range of 3-dimensional structures and a functions. In this unit we will focus on one the of the most important functions of proteins; that of biological catalysts (enzymes).


Amino acids

Amino Acids

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

    • Every amino acid contains,

      • A carboxylic acid group

      • An amino group

      • A side chain (R)


Amino acids1

Amino Acids

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


Question clickers unit 7

Question (Clickers) (Unit 7)

  • At pH 7, which will be the predominant species?

    • Carboxylic acid

    • Carboxylate ion

pKa ≈ 5

carboxylic acid

carboxylate ion


Carboxylic acids phenols as weak acids unit 7

Carboxylic Acids & Phenols as Weak Acids (Unit 7)

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

    • At pH = pKa

    • At pH < pKa

    • At pH > pKa

pH = 7

pKa ≈ 5


Amino acids2

Amino Acids

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


Amines as weak bases unit 7

Amines as Weak Bases (Unit 7)

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


Amines as weak bases unit 71

Amines as Weak Bases (Unit 7)

  • The conjugate acids are called ammonium ions

    • When placed in water, these ammonium ions will behave like acids.


Amino acids3

Amino Acids

Net charge

  • At pH 7, amino acids are in their zwitterionic form.

    • There is no pH value at which there are no charges on an amino acids.

    • However, there is a pH value at which the net charge is zero.

      • This pH value is called the isoelectric point.

+1

0

-1


Amino acids4

Amino Acids

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

    • These are classified according to their physical properties as

      • Non-polar

      • Polar acidic (negatively charged at pH 7)

      • Polar basic (positively charged at pH 7)

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


Amino acids5

Amino Acids

  • Non polar sidechains

    • Most of these sidechains are hydrocarbons


Amino acids6

Amino Acids

  • Polar acidic sidechains

    • Sidechains contain carboxylic acids

    • Negatively charged at pH 7


Amino acids7

Amino Acids

  • Polar basic sidechains

    • Sidechains contain amines

    • Positively charged at pH 7


Amino acids8

Amino Acids

  • Polar neutral sidechains

    • Sidechains contain polar groups that are capable of hydrogen bonding

      • alcohols

      • phenols

      • amides

    • Uncharged at pH 7


Amino acids9

Amino Acids

  • For all of the amino acids, except one (glycine), the α-carbon is chiral.

    • Fisher projection of the amino acids alanine:

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


Peptides proteins and ph

Peptides, Proteins, and pH

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

    • Collectively, oligopeptides and polypeptides are called peptides.

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

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


Amides unit 7

Amides (Unit 7)

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

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


Amides unit 71

Amides (Unit 7)

  • Amides are important in biochemistry.

    • For example, amino acids are connected together to form proteins using amide groups.

amino acid


Peptides proteins and ph1

Peptides, Proteins, and pH

  • Peptide bond formation

Peptide Bond

Dipeptide


Peptides proteins and ph2

Peptides, Proteins, and pH

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

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

The proteinubiquitin


Peptides proteins and ph3

Peptides, Proteins, and pH

  • Proteins are sensitive to the pH because they contain numberous acid and base groups

    • The pH affects the charge on a proteins, which in turn, can have a marked effect on a protein’s structure and function.


Peptides proteins and ph4

Peptides, Proteins, and pH

  • Example

    • The charges on the tripeptideLys-Ser-Asnas a function of pH.

Net Charge

+2

0

-2


Peptides proteins and ph5

Peptides, Proteins, and pH

  • Example

    • The charges on the tripeptideLys-Lys-Alaas a function of pH.

Net Charge

+3

+2

-1


Peptides proteins and ph6

Peptides, Proteins, and pH

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

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

    • At pH’s below the isoionic point (pI) the charge is positive

    • At pH’s above the isoionic point (pI), the charge is negative

pI = 3.2


Peptides proteins and ph7

Peptides, Proteins, and pH

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

    • e.g. Lysine is a basic amino acid

    • At pH’s below the isoionic point (pI) the charge is positive

    • At pH’s above the isoionic point (pI), the charge is negative

pI = 9.7


Peptides proteins and ph8

Charges at different pH values

pH 1

pH 7

pH 14

Acids

A

Include:

α-COOH

Asp sidechain

Glu sidechain

0

-1

-1

Bases

B

Includes:

α-NH2

His sidechain

Lys sidechain

Arg sidechain

+1

+1

0

Peptides, Proteins, and pH

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


Question

Question

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

  • Lysine

  • Phenylalanine

  • Leucine


Question1

Charges at different pH values

pH 1

pH 7

pH 14

A

α-COOH

0

-1

-1

B

α-NH2

+1

+1

0

B

Lys sidechain

+1

+1

0

Net

+2

+1

-1

Question

  • Lysine

B

A

B


Question2

Question

  • Draw the structure of the following tripeptide Glu-Asp-Phe at pH 1 and high pH 14.


Question3

Question

  • Draw the structure of the following tripeptide Glu-Asp-Phe at pH 1 and high pH 14.

Draw the backbone


Question4

Question

  • Draw the structure of the following tripeptide Glu-Asp-Phe at pH 1 and high pH 14.

Add the sidechains and identify the acids (A) and bases (B)

A

B

A

A


Question5

A

B

A

A

Question

  • Draw the structure of the following tripeptide Glu-Asp-Phe at pH 1 and high pH 14.

At pH 1, Acids (A) are 0 and Bases (B) are +1

Net Charge = +1

at pH 1


Question6

A

B

A

A

Question

  • Draw the structure of the following tripeptide Glu-Asp-Phe at pH 1 and high pH 14.

At pH 14, Acids (A) are -1 and Bases (B) are 0

Net Charge = -3

at pH 14


Protein structure

Protein Structure

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

  • There two general classifications of proteins

    • Fibrous proteins exist as long fibers that are usually tough and insoluble in water; examples include

      • collagen (skin and bones)

      • Keratin (hair)

    • Globular proteins are spherical, highly folded, and usually soluble in water; examples include

      • enzymes

      • antibodies

      • transport proteins like hemoglobin and myoglobin


Protein structure1

Protein Structure

  • Fibrous versus globular


Protein structure2

Protein Structure

  • Proteins display up to four levels of structure

    • Primary structure

      • This is the amino acid sequence, which is unique for each protein

      • This defines the covalent structure of a protein

    • Secondary structure

      • Regular, periodic structures, that involve hydrogen bonding between the backbone amides


Protein structure3

Protein Structure

  • Proteins display up to four levels of structure

    • Tertiary structure

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

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

The proteinubiquitin


Protein structure4

Protein Structure

  • Primary Structure

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

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

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


Protein structure5

Protein Structure

  • Primary Structure

Glycine

Gly

Alanine

Ala

Serine

Ser

Aspartic Acid

Asp

C-Terminus

N-Terminus

Phenylalanine

Phe

Leucine

Leu

Lysine

Lys

Gluctamine

Gln


Protein structure6

Protein Structure

  • Primary Structure

C-Terminus

N-Terminus

Glycylphenylalanylalanylleucylseryllysylaspartylglutamine

H2H-Gly-Phe-Ala-Leu-Ser-Lys-Asp-Gln-COOH

Gly-Phe-Ala-Leu-Ser-Lys-Asp-Gln

GFALSKDQ


Protein structure7

Protein Structure

  • Primary structure

    • The Central Dogma

      • DNA → mRNA → Polypeptide

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

  • All living organisms use the same code


Protein structure8

Protein Structure

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

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

    • View the polypeptides as beads on a string, with one of 20 possible 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-o


Protein structure9

Protein Structure

  • The Earth weighs 6.0 x 1027 g, how many Earths would it take?


Protein structure10

Protein Structure

  • The Sun weighs 2.0 x 1033 g, how many Suns would it take?


Protein structure11

Protein Structure

  • The Milky Way galaxy weighs 1.2 x 1045 times the mass of the sun

    • (1.2 x 1045suns)(2.0 x 1033 g/sun) = 2.4 x 1078 g

    • How may galaxies would it take?


Protein structure12

Protein Structure

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


Protein structure13

Number of polypeptides (20100)

1.26 x 10130

Avg. Mass of each polypeptide

1.83 x 10-22g

Total mass needed

2.32 x 10108g

Number of Earths

3.9 x 1080

Number of Suns

1.2 x 1075

Number of Galaxies

9.7 x 1029

Protein Structure


Protein structure14

Protein Structure

  • Secondary structure

    • The polypeptide backbone can take on regular shapes that allow the backbone amides to hydrogen bond to one another.

    • The primary forms of secondary structure include

      • α-helix

      • β-sheet


Protein structure15

Protein Structure

  • Secondary structure

α-Helix


Protein structure16

Protein Structure

  • Secondary Structure

β-Sheet


Protein secondary structure

Protein Secondary Structure

  • Secondary Structure

Antiparallel β-Sheet


Protein structure17

Protein Structure

  • Secondary Structure

Parallel β-Sheet


Protein structure18

Protein Structure

  • Tertiary Structure

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

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

The proteinubiquitin


Protein structure19

Protein Structure

  • Tertiary Structure

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

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

The proteinubiquitin


Protein structure20

Protein Structure

  • Tertiary Structure

Explore thetertiary structureand thesecondary structure of the protein ubiquitin

The proteinubiquitin


Protein structure21

Protein Structure

  • Tertiary Structure

    • The tertiary structure is stabilized by the same non-covalent interactions that we looked at in determining boiling points and solubilites

      • Charge/Charge interactions (Salt bridges)

      • Ion/Dipole interactions

      • Dipole/Dipole interactions

      • Hydrogen bonding

      • Hydrophobic interactions (nonpolor/water)

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

      • Disufide bond


Protein structure22

Protein Structure

  • Tertiary Structure

    • The interactions that stabilize the tertiary structure.


Protein structure23

Protein Structure

  • Quaternary Structure

    • Some proteins contain multiple polypeptides

      • Each peptide is called a subunit

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

Explore thequaternary structure of the protein ubiquitin


Protein denaturation

Protein Denaturation

  • Because the secondary, tertiary and quaternary structures of proteins are stabilized by weak, non-covalent interactions, these structures are easily disrupted by agents that disrupt theses interactions, including:

    • Changes in temperature

    • Changes in pH

    • Mechanical stress (agitation)

    • Soaps and detergents

  • These agents typically cause the protein to unfold

    • Only the primary structure remains

    • The protein loses it function

  • The process is called protein denaturation.


Protein denaturation1

Protein Denaturation

  • Christain Anfinsen won a Nobel Prize for showing that protein denaturation can be reversed.

    • The experiment demonstrated that the information necessary to obtain the correctly folded protein structure is contained within the protein’s amino acid sequence (primary structure).

Active

Protein

Inactive

Protein


Enzymes

Enzymes

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

    • Enzymes are biological catalysts

    • Most enzymes are proteins

  • Many human diseases involve enzymes misbehaving

    • Many treatments for diseases involve drugs that target enzymes.


Enzymes1

Enzymes

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

    • The names usually end with -ase.

    • Example: alcohol dehydrogenase


Question clicker

Question (Clicker)

  • What class of reaction is the alcohol dehydrogenase reaction?

    • Hydrolysis

    • Decarboxylation

    • Oxidation/reduction

    • Acid/base

    • Hydration


Reactions of alcohols and thiols unit 8

Reactions of Alcohols and Thiols (Unit 8)


Enzymes2

Enzymes

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

    • The names usually end with -ase.

    • Example: pyruvate decarboxylase


Question clicker1

Question (Clicker)

  • What class of reaction is the pyruvate decarboxylase reaction?

    • Hydrolysis

    • Decarboxylation

    • Oxidation/reduction

    • Acid/base

    • Hydration


Carboxylic acids phenols other reactions unit 7

Carboxylic Acids & Phenols, Other Reactions (Unit 7)

  • The decarboxylation of β-keto acids produces ketones

  • The decarboxylation of α-keto acids produces aldehydes


Enzymes3

Enzymes

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

    • The names usually end with -ase.

    • Example: succinate dehydrogenase


Question clicker2

Question (Clicker)

  • What class of reaction is the alchohol dehydrogenase reaction?

    • Hydrolysis

    • Decarboxylation

    • Oxidation/reduction

    • Acid/base

    • Hydration


Oxidation and reduction unit 4

Oxidation and Reduction (Unit 4)

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

    • The longhand form of this reaction equation is


Enzymes4

Enzymes

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

    • The names usually end with -ase.

    • Example: succinate dehydrogenase


Question clicker3

Question (Clicker)

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

    • Hydrolysis

    • Decarboxylation

    • Oxidation/reduction

    • Acid/base

    • Hydration


Reactions involving water unit 4

Reactions Involving Water (Unit 4)

  • Hydration

    • In the hydration reaction water is also split, but instead of being used to split another molecule, it is added to another molecule to produce a single product.

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

    • The hydration of an alkene produces an alcohol.


Enzymes5

Enzymes

  • Specificity

    • Absolute spectificity - enzyme only accepts one specific substrate.

    • Relative specificity - enzyme accepts a range of related substrates.


Enzymes6

Enzymes

  • Specificity

    • Stereospecific specificity - enzyme only reacts with or produces one specific stereoisomer


Enzymes7

Enzymes

  • Specificity

    • Absolute

    • Relative

    • Stereospecific


Enzymes8

Enzymes

  • Catalysis

    • As catalysis, enzyme have no effect on the change in free energy, ΔG, for a reaction

    • Ezymes speed up reactions by decreasing the activation energy, Eact.

      • Enzymes do this by binding the substrates and by directing the reaction


Free energy and reaction rates unit 4

Free

Energy

(G)

Progress ofreaction

Free Energy and Reaction Rates (Unit 4)

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

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

Α → B

Eact > 0

without catalyst

-

with catalyst

A

ΔG < 0

spontaneous

Β


Enzymes9

Enzymes

  • Catalysis

    • The location on the enzyme where the substrate binds and the reaction occurs is called the active site.

    • Back in Unit 4 we saw a specific example of this with the hexokinase reaction

Explore the enzyme hexokinase


Enzymes10

Enzymes

  • Cofactors and Coenzymes

    • Sometimes enzymes need some help with catalzying the reactions.

    • Cofactors are non-protein components of an enzyme

      • Metal ions

      • Organic molecules (Coenzymes)

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


Enzymes11

Enzymes


Enzymes12

Enzymes

  • pH and Temperature

    • Enyzme activity is often critically dependent on the pH and temperature.


Control of enzyme catalyzed reactions

Control of Enzyme-Catalyzed Reactions

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

    • E = enyzme

    • S = substrate

    • ES = enzyme-substrate complex

    • P = product


Control of enzyme catalyzed reactions1

Control of Enzyme-Catalyzed Reactions

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

    • The Michaelis-Menten model is characterized by two parameters.

      • KM (The Michaelis-Menten constant), which is related to the strength of the substrate binding.

      • Vmax (The maximum velocity), which corresponds to the maximum rate that the enzyme-substrate complex forms product.

KM

Vmax


Control of enzyme catalyzed reactions2

Control of Enzyme-Catalyzed Reactions

  • Enzyme Inhibition

    • Can be a normal event used by the cell to control enzyme activity.

    • Can also be exploited in the design of drugs.

      • Example, the irreversible inhibition of COX enzymes by aspirin


Control of enzyme catalyzed reactions3

Control of Enzyme-Catalyzed Reactions

  • Enzyme Inhibition can also be Reversible

    • Competitive inhibition

      • The inhibitor competes with the substrate for the active site

KM

Vmax

Competitive inhibitionaffect KM but not Vmax


Control of enzyme catalyzed reactions4

Control of Enzyme-Catalyzed Reactions

  • Some drugs are competitive inhibitors of enzymes

    • Example: the anti-HIV drug AZT

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

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


Control of enzyme catalyzed reactions5

Control of Enzyme-Catalyzed Reactions

  • Some drugs are competitive inhibitors of enzymes

    • Example: the bacterial drug sufanilamide (a sulfa drug).

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


Control of enzyme catalyzed reactions6

Control of Enzyme-Catalyzed Reactions

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

Folate


Control of enzyme catalyzed reactions7

Control of Enzyme-Catalyzed Reactions

  • Enzyme Inhibition can also be Reversible

    • Noncompetitive inhibition

      • The inhibitor binds at a different site thatn the substrate.

KM

Vmax

Noncompetitive inhibitionaffects Vmax but not KM


Control of enzyme catalyzed reactions8

Control of Enzyme-Catalyzed Reactions

  • Noncompetitive inhibition is often used to regulate biosynthetic pathways by a mechanism called feedback inhibition.

    • The end product of the pathway binds to a site on an enzyme used earlier in the pathway, and turns it off.


Control of enzyme catalyzed reactions9

Control of Enzyme-Catalyzed Reactions

  • Enzymes that are inhibited by a substance binding to a site other than the active site are called allosteric enzymes.

    • The enzymes that are regulated by noncompetive inhibition in feedback inhibition are examples of allosteric enzyme.

    • The substance that inhibits the enzyme in this way is called a negative effector.

  • Some allosteric enzymes are activated instead of inhibited by as substance binding at their allosteric site.

    • These substances are called positive effectors.


Control of enzyme catalyzed reactions10

Control of Enzyme-Catalyzed Reactions

  • Some enzymes are controlled by covalent modifications to their structure.

    • In some cases the modifications are reversible, such as placing a phosphate on an enzyme to turn it on, and then taking the phosphate off to turn it off again.


Control of enzyme catalyzed reactions11

Control of Enzyme-Catalyzed Reactions

  • Some enzymes are controlled by covalent modifications to their structure.

    • Example: Glycogen phosphorylase, which is the enzyme that breaks down the polysaccharide glycogen.

    • The phosphorylation/dephosphorylation of this enzyme is under hormonal control.


Control of enzyme catalyzed reactions12

Control of Enzyme-Catalyzed Reactions

  • Some enzymes are controlled by covalent modifications to their structure

    • In other cases the covalent modification is irreversible.


Control of enzyme catalyzed reactions13

Control of Enzyme-Catalyzed Reactions

  • Some enzymes are controlled by covalent modifications to their structure

    • Example: the digestive enzymes trypsin and chymotrypsin, which are used to break down proteins in the small intestine are synthesized in the pancreas in an inactive form called trypsinogen and chymotrypsinogen, respectively.

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


Control of enzyme catalyzed reactions14

Control of Enzyme-Catalyzed Reactions

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


The end

The End


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