Organic Molecules: Proteins

Proteins • Most structurally & functionally diverse group

• Function: involved in almost everything – enzymes (pepsin, DNA polymerase)– structure (keratin, collagen)– carriers & transport (hemoglobin, aquaporin)– cell communication

• signals (insulin & other hormones) • receptors

– defense (antibodies) – movement (actin & myosin)– storage (bean seed proteins)

Proteins• Structure– monomer = amino acids

• 20 different amino acids

– polymer = polypeptide• protein can be one or more polypeptide chains folded

& bonded together

• large & complex molecules

• complex 3-D shape

Rubisco

hemoglobin

growthhormones

H2O

Amino acids

• Structure– central carbon

– amino group

– carboxyl group (acid)

– R group (side chain)• variable group

• different for each amino acid

• confers unique chemical properties to each amino acid- like 20 different letters of an alphabet

- can make many words (proteins)

Oh, I get it!amino = NH2 acid = COOH

Effect of different R groups:Polar amino acids

▪ polar or charged & hydrophilic

Why are these polar & hydrophillic?

H+ acceptorsH+ donors

Effect of different R groups:Nonpolar amino acids

Why are these nonpolar & hydrophobic?

▪ nonpolar & hydrophobic

Sulfur containing amino acids• Form disulfide bridges S-S

– covalent cross links betweens sulfhydryls – stabilizes 3-D structure

H-S – S-H

AP Biology

Building proteins• Peptide bonds– covalent bond between NH

2 (amine) of one

amino acid & COOH (carboxyl) of another

– C–N bond

peptidebond

dehydration synthesisH2O

Building proteins• Polypeptide chains have direction– N-terminus = NH

2 end

– C-terminus = COOH end– repeated sequence (N-C-C) is the

polypeptide backbone• can only grow in one direction

http://www2.nl.edu/jste/proteins.htm

Protein structure & function• Function depends on structure– 3-D structure

• twisted, folded, coiled into unique shape

hemoglobin

collagen

pepsin

Protein Structure• Protein types include globular proteins which

are usually enzymes and Fibrous proteins which usually serve for structure (eg. Hair)

• Proteins Exhibit 4 levels of structure.

Primary (1°) structure• Order of amino acids in chain

– amino acid sequence determined by gene (DNA)l; dictates all further levels of protein structure

– slight change in amino acid sequence can affect protein’s structure & its function

• even just one amino acid change can make all the difference!

Sickle cell anemia

I’mhydrophilic!

But I’mhydrophobic!

Just 1out of 146amino acids!

15

Fibers of abnormalhemoglobin deform cell into sickle shape.

Primary structure

Secondaryand tertiarystructures

Quaternary structure

Function

Red bloodcell shape

Hemoglobin A

Molecules donot associatewith oneanother, eachcarries oxygen.

Normal cells arefull of individualhemoglobinmolecules, eachcarrying oxygen

α

β

β

α

10 μm 10 μm

α

β

β

α

Primary structure

Secondaryand tertiarystructures

Quaternary structure

Function

Red bloodcell shape

Hemoglobin S

Molecules interact with one another tocrystallize into a fiber, capacity to carry oxygen is greatly reduced.

β subunit β subunit

1 2 3 4 5 6 7 3 4 5 6 721

Normal hemoglobin Sickle-cell hemoglobin. . .. . .

Figure 5.21

Exposed hydrophobic

region

Val ThrHis Leu Pro Glul Glu Val His Leu Thr Pro Val Glu

Secondary (2°) structure• “Local folding”– folding along short sections of polypeptide

– interactions between adjacent amino acids

– H bond: weak bonds between R groups

– forms sections of 3-D structure

•α-helix

•β-pleated sheet

Tertiary (3°) structure

• “Whole molecule folding”– interactions between distant amino acids

• hydrophobic interactions

– cytoplasm is water-based

– nonpolar amino acids cluster away from water

• Covalent, H bonds & ionic bonds

• disulfide bridges – covalent bonds between

sulfurs in sulfhydryls (S–H)

– anchors 3-D shape

Quaternary (4°) structure• More than one polypeptide chain bonded together

– only then does polypeptide become functional protein• pH, changes or heat can disrupth bonds perm. denaturing

the protein

collagen = skin & tendons hemoglobin

Protein structure (review)

amino acid sequencepeptide bonds

1°

determinedby DNA R groups

H bonds

R groupshydrophobic interactionsdisulfide bridges(H & ionic bonds)3°

multiple polypeptideshydrophobic interactions4

°2°

Protein denaturation• Unfolding a protein– conditions that disrupt H bonds, ionic bonds,

disulfide bridges• temperature

• pH

• salinity

– alter 2° & 3° structure• alter 3-D shape

– destroys functionality• some proteins can return to their functional shape after

denaturation, many cannot

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

• Chaperonins– Are protein molecules that assist in the proper

folding of other proteins

23

Hollowcylinder

Cap

Chaperonin(fully assembled)

Steps of ChaperoninAction: An unfolded poly- peptide enters the cylinder from one end.

The cap attaches, causing the cylinder to change shape insuch a way that it creates a hydrophilic environment for the folding of the polypeptide.

The cap comesoff, and the properlyfolded protein is released.

Correctlyfoldedprotein

Polypeptide

2

1

3

Figure 5.23

Review Questions

A. What happens when a protein denatures? *1. It loses its primary structure.

2. It loses its secondary and tertiary structure.

3. It becomes irreversibly insoluble and precipitates.

4. It hydrolyzes into component amino acids.

5. Its hydrogen bonds, ionic bonds, and peptide bonds are disrupted.

B. The R group or side chain of the amino acid serine is –CH

2 –OH. The R group or side chain of the amino

acid alanine is –CH3. Where would you expect to find

these amino acids in globular protein in aqueous solution?1. Serine would be in the interior, and alanine would be on

the exterior of the globular protein.2. Alanine would be in the interior, and serine would be on

the exterior of the globular protein.3. Both serine and alanine would be in the interior of the

globular protein.4. Both serine and alanine would be on the exterior of the

globular protein.5. Both serine and alanine would be in the interior and on

the exterior of the globular protein.