Hydrogen Bonding Between Two Peptide Bonds, R Groups in Amino Acids | BIO 311C, Study notes of Biology

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BIO 311C Spring 2009

Lecture 16 – Friday 27 Feb.

Important characteristicsof amino acids -^ they all contain at least one carboxylic acid functionalgroup and at least one amine functional group. -^ Combinations of 20 different amino acids (each with adifferent “R”

group) occur in polypeptide chains.

-^ All but one of these 20 amino acids contain at least oneasymmetric carbon atom.

Review

Direction of polypeptide chain

Hydrogen Bonding Between Two Peptide Groups

Direction of polypeptide chain N-terminalend C-terminalend The structure imposed on portions of a polypeptide chain due tohydrogen bonding between different peptide bonds is called thesecondary

structure

of the polypeptide chain.

Categories of R Groups that Occur in Amino Acids

I.^ No R-group (glycine

contains only H)

II.^ With R-group^ A. Nonpolar

R-Group

B. Polar R-Group^ 1.

non-ionized 2. ionized^ a.^ cationic^ b.^ anionic

How many asymmetric carbon atoms does glycine

have?

generalized amino acid

Aspartic acid an amino acid withan anionic R-group

Lysine an amino acid with acationic R-group

The Amino Acid Sequence of a Polypeptide Chain

From textbook Fig. 5.21,

p. 82

Each living cell producesseveral thousands ofdifferent kinds ofpolypeptide chains. Each kind of polypeptide chain has an exact number of amino acids.The sequence of amino acids is exactlythe same for each copy of the samekind of polypeptide chain. The amino acids of a polypeptidechain are numbered sequentially,starting from the N-terminal (amino- terminal) end.

Some Features of ThisSpecific Polypeptide Chain It consists of 127 amino acids. Its N-terminal amino acid is Gly. Its C-terminal amino acid is Glu.^ Amino acid number 25 is Ala.

From Textbook Fig. 5.19, p. 81

Secondary Structures Contribute to the Overall Size and Shape of a Polypeptide Chain

Each alpha helix and beta (pleated) sheet secondary structure contributes toonly a portion of the overall three-dimensional shape of the molecule.

A beta-sheet secondary structure

An alpha-helix secondary structure

+^ HN 3

• COO

Ala^

Asp^

Gly^

Phe^

Leu^

Lys^

Ser^

Cys

• COO

• NH 3 OH^

SH

Examples of Specific R-groups Along a Region of a Polypeptide Chain

example^ The differing R-groups on different amino acids carry functional groups that conferspecific properties to each amino acid position along the polypeptide chain.^ Some positions along the polypeptide chain are nonpolar, some are polar anduncharged, some are positively charged, and some are negatively charged.

Representations of the Shape of a^ Functional Polypeptide Chain Ribbon model

Space-filling model

The three-dimensional shape of a polypeptide chain that is folded in some manneris called its tertiary

structure

From Fig. 5.19, p. 81, of textbook The secondary structure and tertiary structure of a polypeptide chain aredetermined by its primary structure. Thus, each different polypeptide chainwith its unique sequence of amino acids also has its own unique size and3-dimensional shape.

The ribbon structure of ribonuclease

is shown here folded into its

native conformation. It serves as an enzyme when in thisconformation.^ The 3-dimensional shape of a molecule is called its conformation

A polypeptide chain that is folded into its normal, functionalconformation is said to in its native

conformation

A polypeptide that is folded improperly so that it cannot functionis said to be to be denatured

Ribonuclease

Ribonuclease

is a functional protein

A protein that consists of only one polypeptide chain is called amonomeric

protein

A protein that consists of several (2 or more) polypeptide chains iscalled an oligomeric

protein

The three-dimensional shape of an oligomeric

protein is called its

quaternary structure. The individual polypeptide chains of an oligomeric

protein are

called subunits

Monomeric^ of the protein

and Oligomeric

Proteins tubulin

a dimeric

protein

lysozyme

a monomeric

protein

α -tubulin

β -tubulin

Hemoglobin is a conjugated protein.

prosthetic group }

apoprotein subunits

From Fig. 5.21, p. 83, of textbook

Proteins that include one or more additional kind of componentbesides polypeptide chain(s) are called conjugated

proteins

The polypeptide-chain portion of a conjugated protein is called anapoprotein The non-polypeptide-chain component of a conjugated protein iscalled a prosthetic

group

Some Ways of Classifying a Protein

I.^ According to the number of polypeptide chains it contains^ A. Monomeric

proteins contain only one polypeptide chain. B.^ Oligometric

proteins contains two or more polypeptide chains.

II.^ According to whether its structure contains components other than polypeptide chains^ A. Simple proteins contain nothing other than polypeptide chain(s). B. Conjugated proteins include a prosthetic group in the structure. III.^ According to how it folds^ A. Fibrous proteins remain extended such that they don't have a tertiary structure. B. Globular proteins fold into a rounded structure.

Domain of a Protein

Domain for binding to aspecific small molecule

Lysozyme A domain

of a protein is a specific region of the protein in its native conformation that has a defined function.

Phosphofructokinase