Chapter TwentyChapter TwentyProteins

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Type Examples• Structural tendons, cartilage, hair, nails• Contractile muscles• Transport hemoglobin• Storage milk• Hormonal insulin, growth hormone• Enzyme catalyzes reactions in cells• Protection immune response

Roles of Proteins

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Roles of Proteins

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• Proteins are polymers of amino acids• Contain a carboxylic acid group and an amino group

on the alpha carbon• Side group R gives unique characteristics

R side chain I

H2N— C — COOH I

H

Amino Acids

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• Nonpolar – An amino acid that contains a nonpolar side chain

– R = H, CH3, alkyl groups, aromatic

• Polar – An amino acid with a side chain that is polar but neutral– O

ll

R = –CH2OH, –CH2SH, –CH2C–NH2,

(polar groups with –O-, -SH, -N-)

Classifying Amino Acids

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The 20 Standard Amino Acids, Grouped According to Side-Chain Polarity.

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The 20 Standard Amino Acids, Grouped According to Side-Chain Polarity. (cont’d)

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• Polar/Acidic – An amino acid that contains a second carboxyl group in its side

chain

– R = –CH2COOH, or -COOH

• Polar/ Basic– An amino acid that contains a second amino group in its side

chain

– R = –CH2CH2NH2

Classifying Amino Acids

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The 20 Standard Amino Acids, Grouped According to Side-Chain Polarity. (cont’d)

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• 10 amino acids not synthesized by the body• Arg, His, Ile, Leu, Lys, Met, Phe, Thr, Trp, Val• Must obtain from the diet• All in diary products • 1 or more missing in grains

and vegetables

Essential Amino Acids

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Fischer Projections of Amino Acids

• All amino acids except glycine are chiral.• Amino acids have stereoisomers• In biological systems, only L amino acids are used in

proteins

COOH

CH3

NH2H

COOH

CH3

HNH2

COOH

CH2SH

HNH2

COOH

CH2SH

NH2H

D-Alanine L-Alanine L-Cysteine D-Cysteine

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Designation of handedness in standard amino acid structures involves aligning the carbon chain vertically and looking at the position of the

horizontally aligned NH2 group.

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• Ionization of the –NH2 and the –COOH group– -COOH loses a proton (acid)

– -NH2 gains a proton (base)

• Zwitterion has both a + and – charge• Zwitterion is neutral overall

NH2–CH2–COOH H3N–CH2–COO–

glycine Zwitterion of glycine

Zwitterions

+

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H+ OH–

+ +

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

Positive ion zwitterion Negative ion

Low pH neutral pH High pH

pH and Ionization

In solution, at least three different forms of amino acids can exist: positive ion, zwitterion, and negative ion

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pH and Ionization

• Acidic amino acids such as aspartic acid have a second carboxyl group that can donate and accept protons– Amino acids with ionizable side chains have 4 forms in

solution• -Cys, Tyr, Lys, Arg, His, Asp, Glu

• Whether a group is ionized or not depends on its pKa– If pH > pKa, the group has been deprotonated– If pH < pKa, the group is protonated

16

Amino Acid -carboxylic acid -amino Side chain

Alanine 2.35 9.87

Arginine 2.01 9.04 12.48

Asparagine 2.02 8.80

Aspartic Acid 2.10 9.82 3.86

Cysteine 2.05 10.25 8.00

Glutamic Acid 2.10 9.47 4.07

Glutamine 2.17 9.13

Glycine 2.35 9.78

Histidine 1.77 9.18 6.10

Isoleucine 2.32 9.76

Leucine 2.33 9.74

Lysine 2.18 8.95 10.53

Methionine 2.28 9.21

Phenylalanine 2.58 9.24

Proline 2.00 10.60

Serine 2.21 9.15

Threonine 2.09 9.10

Tryptophan 2.38 9.39

Tyrosine 2.20 9.11 10.07

Valine 2.29 9.72

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Step-wise Ionization of Amino Acids

• 1. Draw the amino acid in the fully protonated form– Low pH– All acid groups are protonated (-COOH)– All amino groups are protonated (-NH3

+)

• 2. Identify the protons that will come off (and the order in which they will come off)

• 3. Take the protons off 1 by 1

• Example: Glutamic Acid

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Ionization of Glutamic Acid

• Draw the step-wise ionization of glutamic acid

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HomeWork Assignment

• What overall charge will the following amino acids have at pH 5.5?

• Lysine

• Phenylalanine

• Glutamic Acid

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Electrophoresis

• Electrophoresis separates amino acids according to their charges– Positively charged amino acids move towards the

negative electrode– Negatively charged amino acids move toward the

positive electrode– Neutral amino acids will not move in either direction

• Amino acids are visualized as separate bands on filter paper or thin layer plate

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Electrophoresis

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Amide bond formed by the carboxylate group of an amino acid and the –amino group of the next amino acid

O CH3

+ | | + |

NH3–CH2–COH + H3N–CH–COO–

O CH3

+ | | |

NH3–CH2–C – N–CH–COO–

| peptide bond H

Peptide Bonds

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Peptides

• Peptide– A sequence of amino acids in which the amino acids are

joined together through amide (peptide) bonds

• Dipeptide– A peptide consisting of 2 amino acids

• Tripeptide– A peptide consisting of 3 amino acids

• Polypeptide– A peptide consisting of many amino acids

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• Amino acids linked by amide (peptide) bonds

Gly Lys Phe Arg Ser

H2N- -COOH

end Peptide bonds end

Name: Glycyllysylphenylarginylserine

Peptides

N-terminus

C-terminus

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Protein Structure

• A polypeptide containing 50 or more amino acids is called a protein

• There are different ways to describe the structure of a protein:– Primary Structure– Secondary Structure– Tertiary Structure– Quaternary Structure

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• Three-dimensional arrangement of amino acids with the polypeptide chain in a corkscrew shape

• Held by H bonds between the H of –N-H group and the –O of C=O of the fourth amino acid along the chain

• Looks like a coiled “telephone cord”

Secondary Structure: Alpha Helices

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• Specific overall shape of a protein• Results from cross-links between R groups of amino acids

in chain

disulfide –S–S– +

ionic –COO– H3N–

H bonds C=O HO–

hydrophobic –CH3 H3C–

Tertiary Structure

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Levels of Protein Structure

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A telephone cord has three levels of structure.

Levels of Protein Structure

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Primary Structure

Human Myoglobin

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Secondary Structure

• Geometrical orientation of polypeptide chains• Two main kinds of secondary structure:

– Alpha helices– Beta pleated sheets

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The hydrogen bonding between the carbonyl oxygen atom of one peptide linkage and the amide hydrogen atom of another peptide linkage.

Secondary Structure

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Two pleated sheet protein structure.

Secondary Structure

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Four representations of the helix secondary structure.

Secondary Structure

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The secondary structure of a single protein.

Secondary Structure

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Four types of interactions between amino acid R groups produce the tertiary structure of a protein.

Tertiary Structure

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The tertiary structure of the single-chain protein myoglobin.

Tertiary Structure

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Disulfide bonds involving cysteine residues can form in two different ways.

Disulfide Bonding

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Human insulin, a small two-chain protein, has both intrachain and interchain disulfide linkages as part of its tertiary structure.

Human Insulin

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Substitutions in Insulin

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Disulfides and Hair

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A schematic diagram showing the tertiary structure of the single-chain protein myoglobin.

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• Proteins with two or more chains– Quaternary structure is the relative organization of multiple chains

to each other

• Example is hemoglobin

Carries oxygen in blood

Four polypeptide chains

Each chain has a heme group to bind oxygen

A conjugated protein (has a prosthetic group)

Quaternary Structure

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Tertiary and quaternary structure of the oxygen-carrying protein hemoglobin.

Quaternary Structure

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Globular proteins Fibrous proteins “spherical” shape long, thin fibersWater soluble Not water solubleMultiple Types of 2o structure 1 Type of 2o StructureTransport, Metabolism, etc. Strength, ProtectionMore numerous Few in the body

Insulin HairHemoglobin WoolEnzymes SkinAntibodies Nails

Globular and Fibrous Proteins

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The tail feathers of a peacock. Fibrous Protein is α-keratin

Fibrous Proteins

PhotoDisc

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The coiled-coil structure of the fibrous protein alpha keratin.

Fibrous Proteins

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Fibrous Proteins

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Three helical peptide chains.

Collagen

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→Electron Micrograph

Collagen fibers

Collagen

Prof. P.M. Motta & E. Vizza / Photo Researchers

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Protein denaturation process.

Protein Denaturation

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Heat denatures the protein in egg white.

Heat Denaturation

E.R. Degginger

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• Hard boiling an egg• Wiping the skin with alcohol swab for injection• Cooking food to destroy E. coli.• Heat used to cauterize blood vessels• Autoclave sterilizes instruments• Milk is heated to make yogurt

Applications of Denaturation

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Denaturation

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Disulfides and Hair

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Structure of immunoglobulin.

Immunoglobulins

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Immunoglobulin-antigen complex

Immunoglobulins

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• Break down of peptide bonds • Requires acid or base, water and heat• Gives smaller peptides and amino acids • Similar to digestion of proteins using

enzymes• Occurs in cells to provide amino acids to

synthesize other proteins and tissues

Protein Hydrolysis

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Hydrolysis of a Dipeptide