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Chemistry 501 Handout 3 Amino Acids, Peptides, and Proteins Chapter 3

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Dep. of Chemistry & Biochemistry Prof. Indig. Chemistry 501 Handout 3 Amino Acids, Peptides, and Proteins Chapter 3. Lehninger. Principles of Biochemistry. by Nelson and Cox, 5 th Edition; W.H. Freeman and Company. Amino Acids.

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slide1

Dep. of Chemistry & Biochemistry

Prof. Indig

Chemistry 501 Handout 3Amino Acids, Peptides, and ProteinsChapter 3

Lehninger. Principles of Biochemistry.

by Nelson and Cox, 5th Edition; W.H. Freeman and Company

slide2

Amino Acids

Steric relationship of the stereoisomers of Alanine to the absolute configuration of L- and D-glyceraldehyde

The amino acid residues in proteins are the L isomers

slide5

Reversible formation of disulfide bond by the oxidation of two molecules of cysteine

e.g. two polypeptide chains of insuline

slide7

Absorption of ultraviolet light

by aromatic amino acids

Lambert-Beer Law

log (Io/I) = e C L

slide8

imidazole

guanidino

slide10

prothrombim,

a # of Ca+ binding proteins

g

b

a

4

3

plant cell wall,

collagen

1

5

2

elastin

collagen

Lysine

residues

myosin

Uncommon amino acids also have important functions

Residues created by modification of common residues already incorporated into a polypeptide

~ 300 additional amino acids

have been found in cells

rare, introduced during protein

synthesis rather than created

through a postsynthetic modification

slide12

Amino acids can act as acids and bases

Nonionic and zwitterionic forms

of amino acids

Titration of glycine

Titration curves predict the

electric charge of amino acids

Isoelectric point (or isoelectric pH)

pI= ½ (pk1 + pk2) = ½ (2.34 + 9.60) = 5.97

amphoteric

(ampholytes - amphoteric electrolytes)

slide14

Amino acids differ in their acid-base properties

pka of the –COOH group: 1.8 – 2.4

pka of the –NH3+ group: 8.8 – 11.0

Amino acids with

R groups that do not ionize

Amino acids with ionizable R groups

e.g.

three stages (three ionization steps  three pka values)

slide17

Peptides are chains of amino acids

Pentapeptide

condensation

hydrolysis

Serylglyciltyrosylalanylleucine

or

Ser-Gly-Tyr-Ala-Leu

or

SGYAL

Two amino acid molecules can be covalently joined through a substituted amide linkage, termed a peptide bond, to yield a dipeptide

Peptides are named beginning with the amino-terminal

residue, which by convention is placed at the left.

just a few residues  oligopeptide

many residues  polypeptide

slide18

Biologically active peptides and polypeptides occur in a vast range of sizes

If at least two chains are identical → the protein

is said to be oligomeric, and the identical units

(consisting of one or more chains) are referred to

as protomers.

Multisubunit proteins: have two or more

polypeptide chains associated noncovalently

The vast majority of naturally occurring proteins contain fewer than 2,000 amino acid residues.

slide19

Polypeptides have characteristic

amino acid compositions

Some proteins contain chemical groups other

than amino acids (conjugated proteins).

The non-amino acid part of the conjugated protein is

usually called its prosthetic group.

slide20

Protein Separation and Purification

Column

Chromatography

Crude extract --> --> --> fractionation

slide21

Ion-Exchange

Chromatography

Example:

Cation-exchange chromatography

slide22

Exclusion

Chromatography

(gel filtration)

slide23

Affinity

Chromatography

slide24

Refers to the total number of units

of enzyme in a solution.

A measure of enzyme purity: it increases during purification

of an enzyme and becomes maximal and constant when the

enzyme is pure.

Number of enzyme units

per milligram of total protein.

1.0 unit of enzyme activity = amount of enzyme causing the transformation of 1.0 mmol

of substrate per minute at 25oC under optimal conditions of measurement.

slide25

Electrophoresis

gel stained with a protein-specific

dye (e.g. coomasie blue)

SDS-polyacrylamide gel

Purification of RNA

polymerize from E. coli

Cross-linked polymer

polyacrylamide

SDS

CH3(CH2)11SO4-Na+

acts as a molecular sieve, slowing the migration

of proteins approximately in proportion to their

charge-to-mass ratio.

slide26

Isoelectric focusing

Two-dimensional electrophoresis

slide27

There are several levels of protein structure

Multisubunit proteins

Arrangement is space of

polypeptide subunits

Particularly stable arrangements of

amino acid residues giving rise to

recurring structural paterns

All aspects of the 3-D folding

of a polypeptide

Includes disulfide bonds

slide28

Determination of amino acid sequence

Amino acid sequence of bovine insulin

(10 years of work by Sanger)

The amino acid sequences of millions of proteins have been determined

Identical in human, pig,

rabbit and sperm whale

Identical in cow, dog,

goat and horse

slide29

Short polypeptides are sequenced using automated procedures

Sanger’s method for identifying the amino-terminal residue

The Edman degradation procedure (carried out on a sequenator)

reveals the entire sequence

of a peptide

slide30

Large proteins must be sequenced in smaller fragments

Breaking disulfide bonds

Cleaving the polypeptide chain

Some proteases cleave only the peptide bond

adjacent to particular amino acid residues

slide32

Amino acid sequences can also be deduced by other methods

codon

Correspondence of DNA and amino acid sequences

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