Protein structure

Amino Acids, PolypeptideLevels of Structure

Protein Structure

Monomer

The single unit that makes up a protein is an amino acid

Question: Based on its name, which 2 functional groups would be found in an amino acid?

An amino acid is sometimes referred to as a residue

Amino acid structure

four components attached to a central carbon: amino group carboxylic acid (carboxyl) group hydrogen atom variable R group (or side chain)

Question: Determine which functional group is acidic and basic. Explain how you know.

H

|

H2N – C – COOH

|

R

Amino acid structure

Amphiprotic: containing both acidic and basic functional groups

The ionized form is observed in aqueous solutions because the acidic group can donate H+ ion to the basic group

H

|

H2N – C – COOH

|

R

H

|

+H3N – C – COO-

|

R

+H2O

Amino acid R groups (side chains)differences in R groups produce the

20 different amino acids8 are essential: body cannot

synthesize them

Amino acid R groups (side chains)

Physical and chemical characteristics of the R group determine the unique characteristics of an amino acid

Amino acids are classified into 4 groups based on their R groups: Nonpolar Polar Acidic basic

H

|

H2N – C – COOH

|

R

Activity

Given the 20 amino acids, group them into the 4 categories based on the properties of their R groups

The 4 categories are: Nonpolar Polar Acidic basic

Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings

Nonpolar amino acids has hydrophobic R groupsHydrophobic R groups

Fig. 5.15a

Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings Fig. 5.15b

Polar amino acids

Polar R groupshydrophilic

Acidic and Basic Amino Acids

Amino acids with charged (ionized) functional groups at cellular pH can be either: Acidic: carboxylic acid, negative charge Basic: amino, positive charge

Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings Fig. 5.15c

Forming a Polypeptide

Condensation reaction to join 2 amino acid

Requires: Carboxyl group Amine

Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings Fig. 5.16

Forming a Polypeptide

Question: What is name of the new functional group formed?

Peptide bond: links between amino acids


Protein shape determines function

Amino acid order determines the shape (conformation) of a protein

Conformation determines functionFunction depends on its ability to

recognize and bind a molecule

Amino acids conformation function binding

Protein binding examples

Antibodies bind to particular foreign substances that fit their binding sites.

Enzymes recognize and bind to specific substrates, facilitating a chemical reaction.

Neurotransmitters pass signals from one cell to another by binding to receptor sites on proteins in the receiving cell.

Levels of protein structure

Primary (1o)Secondary

(2o)Tertiary (3o)

Quaternary (4o)

organizes folding within a single polypeptideinteractions between two or more polypeptides that make a protein

Primary (1o) Structure

unique sequence of amino acid

sequence determined by DNA

a slight change in primary structure can affect a protein’s conformation and ability to function


Primary (1o) Structure

Fig. 5.19Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings

Example: Sickle Cell Anemia abnormal hemoglobin develop because of

a single amino acid substitution (change) causes hemoglobin to crystallize,

deforming the red blood cells and leading to clogs in blood vessels.

Secondary (2o) Structure

results from hydrogen bonds at regular intervals along the polypeptide backbone

typical shapes: alpha helix (coils) beta pleated sheets

(folds) not found in all

proteins



Tertiary (3o) Structure

Interactions between:

R groups and R groups

R groups and backbone

Fig. 5.22


Tertiary (3o) Structure

Types of interaction: Hydrogen bonds Ionic bonds Hydrophobic

interactions often in interior of protein

Covalent bonds Disulfide bridge: formed

between the sulfhydryl groups (SH) of cysteine amino acids

Fig. 5.22

Tertiary (3o) Structure: Proline kink

Proline is the only amino acid in which the R group is attached to the amino group

Forms a natural kink in the polypeptide

Helps to shape tertiary structure

Quaternary (4o) Structure

aggregation of two or more polypeptide subunits

forms 2 types of proteins: globular and fibrous

not found in all proteins


Water solubleCompact, sphericalExample: hemoglobin

Quaternary (4o) Structure: Globular

Water insolubleThreadlikeExample: collagen

3 polypeptides supercoiled like a rope

provides structural strength for role in connective tissue

Quaternary (4o) Structure: Fibrous


Levels of Protein Structure


Protein Folding

Occurs spontaneouslyAided by chaperone proteins

(chaperonin)Provide ideal environment for folding

Tutorial: Protein Folding

http://www.wiley.com/legacy/college/boyer/0470003790/animations/protein_folding/protein_folding.htm



Conformational Change

Changing the shape of a proteinReversibleDoes not disrupt a proteins function

but rather is what defines the protein’s function

Change occurs in response to the physical and chemical conditions.

Example of conformational change

Carrier protein

http://bio1151b.nicerweb.com/Locked/media/ch07/07_15FacilitatedDiffusionB.jpg

Fig. 8.14


Fig. 5.25

Denaturation

A change in the shape of the protein that disrupts protein function.

Alterations in the environment (pH, salt concentration, temperature etc.) disrupt bonds and forces of attraction.


Denaturation

Renaturation: some proteins can return to their functional shape after denaturation

But others cannot, especially in the crowded environment of the cell.

Protein Denaturation Video

http://highered.mcgraw-hill.com/sites/0072943696/student_view0/chapter2/animation__protein_denaturation.html




HW Question

Contrast secondary and tertiary levels of protein structure. [2 marks]

Compare conformational change and denaturation. Use an example. [3 mark]

Protein structure

Education

amino acid r groups

basic amino acids amino

pearson education

different amino acids

function amino acid

tertiary structure

quaternary4o structure

properties oftheir r