Chapter 3

Proteins

You Must Know• How the sequence and subcomponents of proteins

determine their properties.• The cellular functions of proteins. (Brief – we will come

back to this in other chapters.)• The four structural levels of proteins and how changes

at any level can affect the activity of the protein.• How proteins reach their final shape (conformation),

the denaturing impact that heat and pH can have on protein structure, and how these may affect the organism.

• The directionality of proteins (the amino and carboxyl ends).

Concept 3.5: Proteins include a diversity of structures, resulting in a wide range of functions

• Proteins account for more than 50% of the dry mass of most cells.

• Protein functions include defense, storage, transport, cellular communication, movement, and structural support.

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• Life would not be possible without enzymes.

• Enzymatic proteins act as catalysts, to speed up chemical reactions without being consumed by the reaction

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Enzyme

• Polypeptides are unbranched polymers built from the same set of 20 amino acids

• A protein is a biologically functional molecule that consists of one or more polypeptides

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Figure 3.UN04

Side chain (R group)

Carboxylgroup

Aminogroup

carbon

Amino Acids: the monomers of proteins

Figure 3.17a

What do the side chains of these amino acids have in common?

Side chain (R group)

Glycine (Gly or G)

Alanine (Ala or A)

Methionine (Met or M)

Phenylalanine (Phe or F)

Leucine (Leu or L)

Isoleucine (le or )

Tryptophan (Trp or W)

Proline (Pro or P)

Valine (Val or V)

Figure 3.17b

Serine (Ser or S)

Threonine (Thr or T)

Tyrosine (Tyr or Y)

Asparagine (Asn or N)

Cysteine (Cys or C)

Glutamine (Gln or Q)

What do the side chains of these amino acids have in common?

Figure 3.17c

Aspartic acid (Asp or D)

Glutamic acid (Glu or E)

What do the side chains of these amino acids have in common?

Figure 3.17c

Arginine (Arg or R)

Lysine (Lys or K)

Histidine (His or H)

What do the side chains of these amino acids have in common?

You don’t need to memorize all the different side chains of the amino acids, but when shown a side chain you should be able to identify its properties (e.g. polar, ionized, etc.)

C-terminusN-terminus peptide bond

Protein Structure and Function

• A functional protein consists of one or more polypeptides precisely twisted, folded, and coiled into a unique shape.

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Hemoglobin protein

A protein’s structure determines its function!

How does an organism “know” what proteins to make?

• DNA dictates the sequence of amino acids.

• The sequence of amino acids leads to the protein’s three-dimensional structure.

Four Levels of Protein Structure

• Proteins are very diverse, but share three superimposed levels of structure called primary, secondary, and tertiary structure.

• A fourth level, quaternary structure, arises when a protein consists of more than one polypeptide chain

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Figure 3.21aPrimary structure

Amino end

Carboxyl end

Primary structure of transthyretin

125

95

90

100105110

120

115

80

70 60

85

75

6555

504540

2530

35

20 15

1051

Amino acids

Figure 3.21ba

Secondary structure

Hydrogenbond

pleated sheet

helix

Hydrogen bond

strand

Figure 3.21d

Polypeptidebackbone

Hydrogenbond

Disulfidebridge

Ionic bond

Hydrophobicinteractions andvan der Waalsinteractions

Tertiary structure

Figure 3.21f

HemeIron

subunit

subunit

subunit

subunitHemoglobin

Quaternary Structure

“mad cow disease”

Figure 3.23-1

Normal protein

Figure 3.23-2

Normal protein Denatured protein

Figure 3.23-3

Denatured proteinNormal protein