Proteins biochemistry

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Amino Acids and Proteins

Proteins and Amino Acids

(Amino Acids as Acids and Bases)

Copyright © 2007 by Pearson Education, Inc.Publishing as Benjamin Cummings

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Proteins are molecular toolsThey are a diverse and complex group of macromolecules

Protein Diversity

From McKee and McKee, Biochemistry, 5th Edition, © 2011 by Oxford University Press

Proteins

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Functions of Proteins

Proteins perform many different functions in the body.TABLE 19.1

Functions of Proteins

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Amino Acids

Amino acids Are the building blocks of proteins. There are 20 standard amino acids Contain a carboxylic acid group and an amino group

on the alpha (α) carbon. Are ionized in solution. Each contain a different side group (R).

R R │ + │

H2N—C —COOH H3N—C —COO− │ │

H H ionized form

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Examples of Amino Acids

H

+ │

H3N—C—COO−

│

H glycine

CH3

+ │

H3N—C—COO−

│

H alanine

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Types of Amino Acids

Amino acids are classified as

Nonpolar (hydrophobic) with hydrocarbon side chains.

Polar (hydrophilic) with polar or ionic side chains.

Acidic (hydrophilic) with acidic side chains.

Basic (hydrophilic) with

–NH2 side chains.

Nonpolar Polar

Acidic Basic

Copyright © 2007 by Pearson Education, Inc. Publishing as Benjamin Cummings

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Amino Acids Classification Table

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Nonpolar Amino Acids

A nonpolar amino acid has An R group that is H, an alkyl group, or aromatic.


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Polar Amino Acids

A polar amino acid has An R group that is an alcohol, thiol, or amide.


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Acidic and Basic Amino Acids

An amino acid is Acidic with a carboxyl R group (COO−).

Basic with an amino R group (NH3+).


Basic Amino Acids

D E

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Learning Check

Identify each as (P) polar or (NP) nonpolar.

+

A. H3N–CH2–COO− (Glycine)

CH3

|

CH–OH

+ │

B. H3N–CH–COO− (Threonine)

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Solution

Identify each as (P) polar or (NP) nonpolar.

+

A. H3N–CH2–COO− (Glycine) (NP) nonpolar

CH3

| CH–OH + │

B. H3N–CH–COO− (Threonine) (P) polar

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Optical Activity

Amino acids Are chiral except for glycine. Have Fischer projections that are stereoisomers. That are L are used in proteins.

L-alanine D-alanine L-cysteine D-cysteine

CH2SH

H2N H

COOH

CH2SH

H NH2

COOH

CH3

H NH2

COOH

CH3

H2N H

COOH

Fischer Projections of Amino Acids

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• Amino acids are amphoteric molecules have both basic and acidic group

• Zwitterions (dipolar molecules), have charged —NH3+

and COO- groups.

• Forms when both the —NH2 and the —COOH groups in an amino acid ionize in water.

• Has equal + and − charges at the isoelectric point (pI).

O O ║ + ║

NH2—CH2—C—OH H3N—CH2—C—O–

Glycine Zwitterion of glycine

Amphoteric PropertiesZwitterions and Isoelectric Points

At physiological pH (7.4), a zwitterion forms Both + and – charges

Overall neutral

Amphoteric Amino group is protonated

Carboxyl group is deprotonated

Soluble in polar solvents due to ionic character

Structure of R also influence solubility

Zwitterions

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In solutions more basic than the pI,

The —NH3+ in the amino acid donates a proton.

+ OH–

H3N—CH2—COO– H2N—CH2—COO– Zwitterion Negative ion at pI pH > pI

Charge: 0 Charge: 1−

Amino Acids as Acids

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In solutions more acidic than the pI, The COO− in the amino acid accepts a proton.

+ H+ +

H3N—CH2—COO– H3N—CH2—COOH

Zwitterion Positive ionat pI pH< pI

Charge: 0 Charge: 1+

Amino Acids as Bases

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pH and Ionization

H+ OH−

+ +

H3N–CH2–COOH H3N–CH2–COO– H2N–CH2–COO–

positive ion zwitterion negative ion

(at low pH) (at pI) (at high pH)

Aas have multiple pKa’s due to multiple ionizable groups

Acid-base Properties

pK1 ~ 2.2

(protonated below 2.2)

pK2 ~ 9.4

(NH3+ below 9.4)

pKR

(when applicable)

Table 3-1

Note 3-letter and 1-letter

abbreviations

Amino acid organization chart

http://a-s.clayton.edu/cclower/CHEM4202/worksheets%20and%20assignments/Amino%20Acids.doc

Titration of Glycine

pK1

[cation] = [zwitterion]

pK2

[zwitterion] = [anion]

First equivalence point Zwitterion

Molecule has no net charge

pH = pI (Isoelectric point)

pI = average of pKa’s = ½ (pK1 + pK2)

pIglycine = ½ (2.34 + 9.60) = 5.97

Animation

http://www.wiley.com/college/fob/quiz/quiz04/4-8.html

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Electrophoresis: Separation of Amino Acids

In electrophoresis, an electric current is used to separatea mixture of amino acids, and The positively charged amino acids move toward the

negative electrode. The negatively charged amino acids move toward the

positive electrode. An amino acid at its pI does not migrate. The amino acids are identified as separate bands on

the filter paper or thinlayer plate.

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Electrophoresis

With an electric current, a mixture of lysine, aspartate,and valine are separated.


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CH3 CH3

+ | |H3N—CH—COOH H2N—CH—COO–

(1) (2)

Which structure represents:

A. Alanine at a pH above its pI?

B. Alanine at a pH below its pI?

Learning Check

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CH3 CH3

+ | |H3N—CH—COOH H2N—CH—COO–

(1) (2)

Which structure represents:

A. Alanine at a pH above its pI? (2)

B. Alanine at a pH below its pI? (1)

Solution

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Essential amino acids Must be obtained

from the diet. Are the ten amino

acids not synthesized by the body.

Are in meat and diary products. Are missing (one or

more) in grains and vegetables.

Essential Amino Acids

TABLE 19.3

Copyright © 2007 by Pearson Education, Inc Publishing as Benjamin Cummings

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Formation of Peptides


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The Peptide Bond

A peptide bond Is an amide bond. Forms between the carboxyl group of one amino acid

and the amino group of the next amino acid.

O CH3 O + || + | ||

H3N—CH2—C—O– + H3N—CH—C—O–

O H CH3 O + || | | ||

H3N—CH2—C—N—CH—C—O– + H2O peptide bond

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Formation of A Dipeptide


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Learning Check

Write the dipeptide SerThr. OH CH3

| | CH2 O HCOH O

+ | ║ + | ║ H3N─CH─C─O – + H3N─CH─C─O–

Ser Thr

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Solution

Write the dipeptide SerThr. OH CH3

| | CH2 O HCOH O + | ║ + | ║

H3N─CH─C─O – + H3N─CH─C─O– Ser peptide Thr

OH bond CH3

| | CH2 O H HCOH O + | ║ | | ║

NH3─CH─C─N ─CH─C─O– + H2O

SerThr

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Naming Dipeptides

A dipeptide is named with A yl ending for the Nterminal amino acid. The full amino acid name of the free carboxyl group

(COO) at the Cterminal end.


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Write the threeletter abbreviations and names of the tripeptides that could form from two glycine and one alanine.

Learning Check

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Write the names and threeletter abbreviations of the tripeptides that could form from two glycine and one alanine.

Glycylglycylalanine GlyGlyAla

Glycylalanylglycine GlyAlaGly

Alanylglycylglycine AlaGlyGly

Solution

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Learning Check

What are the possible tripeptides formed from one each of leucine, glycine, and alanine?

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Solution

Tripeptides possible from one each of leucine, glycine, and alanine

LeuGlyAla

LeuAlaGly

AlaLeuGly

AlaGlyLeu

GlyAlaLeu

GlyLeuAla

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Learning Check

Write the three-letter abbreviation and name for the

following tetrapeptide: CH3

│ CH3 S

│ │ CH–CH3 SH CH2

│ │ │ CH3 O H CH2 O H CH2O H CH2 O + │ ║ │ │ ║ │ │ ║ │ │ ║H3N–CH–C–N–CH–C–N–CH–C–N–CH–CO–

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Solution

Ala-Leu-Cys-Met Alanylleucylcysteylmethionine

CH3

│ CH3 S

│ │ CH–CH3 SH CH2

│ │ │ CH3 O H CH O H CH2O H CH2 O

+ │ ║ │ │ ║ │ │ ║ │ │ ║H3N–CH–C–N–CH–C–N–CH–C–N–CH–CO–

Ala Leu Cys Met

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Protein Structure: Primary and Secondary Levels

Copyright © 2007 by Pearson Education, IncPublishing as Benjamin Cummings

Protein Diversity

From McKee and McKee, Biochemistry, 5th Edition, © 2011 by Oxford University Press

Proteins

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Primary Structure of Proteins

The primary structure of a protein is The particular sequence of amino acids. The backbone of a peptide chain or protein.

Ala─Leu─Cys─Met

CH3

SH

CH2

CH3

S

CH2

CH2CH O

O-CCH

H

N

O

CCH

H

N

O

CCH

H

N

O

CCHH3N

CH3

CH3CH


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Primary Structures

The nanopeptides oxytocin and vasopressin Have similar primary structures. Differ only in the amino acids at positions 3 and 8.


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Primary Structureof Insulin

Insulin Was the first protein to

have its primary structure determined.

Has a primary structure of two polypeptide chains linked by disulfide bonds.

Has a chain A with 21 amino acids and a chain B with 30 amino acids.


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Secondary Structure – Alpha Helix

The secondary structures of proteins indicate thethree-dimensional spatial arrangements of thepolypeptide chains.

An alpha helix has A coiled shape held in place by hydrogen bonds

between the amide groups and the carbonyl groups of the amino acids along the chain.

Hydrogen bonds between the H of a –N-H group and the O of C=O of the fourth amino acid down the chain.

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Secondary Structure – Alpha Helix


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Secondary Structure – Beta Pleated Sheet

A beta-pleated sheet is a secondary structure that Consists of polypeptide chains arranged side by

side. Has hydrogen bonds between chains. Has R groups above and below the sheet. Is typical of fibrous proteins such as silk.

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Secondary Structure: β-Pleated Sheet


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Secondary Structure: Triple Helix

A triple helix Consists of three alpha

helix chains woven together.

Contains large amounts glycine, proline, hydroxy proline, and hydroxylysine that contain –OH groups for hydrogen bonding.

Is found in collagen, connective tissue, skin, tendons, and cartilage.


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Indicate the type of protein structure as1) primary 2) alpha helix3) beta-pleated sheet 4) triple helix

A. Polypeptide chains held side by side by H bonds.B. Sequence of amino acids in a polypeptide chain.C. Corkscrew shape with H bonds between amino acids.D. Three peptide chains woven like a rope.

Learning Check

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Indicate the type of protein structure as:

1) primary 2) alpha helix

3) beta-pleated sheet 4) triple helix

A. 3 Polypeptide chains held side by side by H bonds.

B. 1 Sequence of amino acids in a polypeptide chain.C. 2 Corkscrew shape with H bonds between amino acids.D. 4 Three peptide chains woven like a rope.

Solution

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Protein Structure: Tertiary and Quaternary Levels


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The tertiary structure of a protein Gives a specific three dimensional shape to the

polypeptide chain. Involves interactions and cross links between

different parts of the peptide chain. Is stabilized by

Hydrophobic and hydrophilic interactions. Salt bridges.

Hydrogen bonds.Disulfide bonds.

Tertiary Structure

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Tertiary Structure

The interactions of the R groups give a protein its specific three-dimensional tertiary structure.


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Tertiary Structure

TABLE 19.5

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Globular Proteins

Globular proteins Have compact,

spherical shapes. Carry out synthesis,

transport, and metabolism in the cells.

Such as myoglobin store and transport oxygen in muscle.

Myoglobin


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Fibrous Proteins

Fibrous proteins Consist of long, fiber-like shapes. Such as alpha keratins make up hair, wool, skin,

and nails. Such as feathers contain beta keratins with large

amounts of beta-pleated sheet structures.


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Select the type of tertiary interaction

1) disulfide 2) ionic

3) H bonds 4) hydrophobic

A. Leucine and valine

B. Two cysteines

C. Aspartic acid and lysine

D. Serine and threonine

Learning Check

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Select the type of tertiary interaction as:

1) disulfide 2) ionic

3) H bonds 4) hydrophobic

A. 4 Leucine and valine

B. 1 Two cysteines

C. 2 Aspartic acid and lysine

D. 3 Serine and threonine

Solution

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Quaternary Structure

The quaternary structure Is the combination of two or

more tertiary units. Is stabilized by the same

interactions found in tertiary structures.

Of hemoglobin consists of two alpha chains and two beta chains. The heme group in each subunit picks up oxygen for transport in the blood to the tissues.


hemoglobin

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Summary of Protein Structure

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Summary of Protein Structures


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Identify the level of protein structure as:1) Primary 2) Secondary3) Tertiary 4) Quaternary

A. Beta-pleated sheetB. Order of amino acids in a proteinC. A protein with two or more peptide chainsD. The shape of a globular proteinE. Disulfide bonds between R groups

Learning Check

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Identify the level of protein structure

1. Primary 2. Secondary

3. Tertiary 4. Quaternary

A. 2 Beta-pleated sheet.

B. 1 Order of amino acids in a protein.

C. 4 A protein with two or more peptide chains.

D. 3 The shape of a globular protein.

E. 3 Disulfide bonds between R groups.

Solution

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Protein Hydrolysis and Denaturation


Copyright © 2007 by Pearson Education, Inc. Publishing as Benjamin Cummings

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Protein hydrolysis Splits the peptide bonds to give smaller peptides

and amino acids. Occurs in the digestion of proteins. Occurs in cells when amino acids are needed to

synthesize new proteins and repair tissues.

Protein Hydrolysis

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Hydrolysis of a Dipeptide

In the lab, the hydrolysis of a peptide requires acid or base, water and heat.

In the body, enzymes catalyze the hydrolysis of proteins.

+

H3N CH COH

OCH3

+

H2O, H+

++

heat,

CH2

OH

H3N CH C

O

N

H

CH C

O

OH

CH3

CH2

OH

CH C

O

OHH3N

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Denaturation involves The disruption of bonds in the secondary, tertiary

and quaternary protein structures. Heat and organic compounds that break apart H

bonds and disrupt hydrophobic interactions. Acids and bases that break H bonds between polar

R groups and disrupt ionic bonds. Heavy metal ions that react with S-S bonds to form

solids. Agitation such as whipping that stretches peptide

chains until bonds break.

Denaturation

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Denaturation of protein occurswhen An egg is cooked. The skin is wiped with

alcohol. Heat is used to cauterize

blood vessels. Instruments are sterilized in

autoclaves.

Applications of Denaturation


• Ribonuclease is a small protein that

contains 8 cysteins linked via four

disulfide bonds

• Urea in the presence of 2-

mercaptoethanol fully denatures

ribonuclease

• When urea and 2-mercaptoethanol

are removed, the protein

spontaneously refolds, and the

correct disulfide bonds are reformed

• The sequence alone determines the

native conformation

• Quite “simple” experiment, but so

important it earned Chris Anfinsen

the 1972 Chemistry Nobel Prize

Ribonuclease Refolding Experiment

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What are the products of the complete hydrolysis of the peptide Ala-Ser-Val?

Learning Check

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The products of the complete hydrolysis of the peptide Ala-Ser-Val are

alanine

serine

valine

Solution

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Tannic acid is used to form a scab on a burn. An egg is hard boiled by placing it in boiling water. What is similar about these two events?

Learning Check

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Acid and heat cause the denaturation of protein. They both break bonds in the secondary and tertiary structures of proteins.

Solution

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Proteins biochemistry

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