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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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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


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



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

e.g. two polypeptide chains of insuline


indole two molecules of cysteine

ring


Absorption of ultraviolet light two molecules of cysteine

by aromatic amino acids

Lambert-Beer Law

log (Io/I) = e C L


imidazole two molecules of cysteine

guanidino


prothrombim, two molecules of cysteine

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



Amino acids can act as acids and bases of protein activity

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)



Amino acids differ in their acid-base properties of protein activity

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)


Peptides are chains of amino acids of protein activity

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


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.


Polypeptides have characteristic vast range of sizes

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.


Protein Separation and Purification vast range of sizes

Column

Chromatography

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


Ion-Exchange vast range of sizes

Chromatography

Example:

Cation-exchange chromatography


Exclusion vast range of sizes

Chromatography

(gel filtration)


Affinity vast range of sizes

Chromatography


Refers to the total number of units vast range of sizes

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.


Electrophoresis vast range of sizes

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.


Isoelectric focusing vast range of sizes

Two-dimensional electrophoresis


There are several levels of protein structure vast range of sizes

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


Determination of amino acid sequence vast range of sizes

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


Short polypeptides are sequenced using automated procedures vast range of sizes

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


Large proteins must be sequenced in smaller fragments vast range of sizes

Breaking disulfide bonds

Cleaving the polypeptide chain

Some proteases cleave only the peptide bond

adjacent to particular amino acid residues


Ordering the peptide fragments vast range of sizes

Met (C)


Amino acid sequences can also be deduced by other methods vast range of sizes

codon

Correspondence of DNA and amino acid sequences




(9-fuorenylmethoxycarbonyl) vast range of sizes


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