Proteins

Function and Structure

Proteins• more than 50% of dry mass of most cells

• functions include– structural support

– storage, transport

– cellular communications

– movement

– defense against foreign substances (immunity)

- enzymatic reactions

Structure of Proteins

• Monomer: amino acid• 20 different a.a. used in cells

• Polymer of amino acids-->polypeptide

Complex of >1 polypeptides-->protein

Amino Acid Structure

• Organic molecules with– Amino end ?

– Carboxyl end ?

– Central -carbon

– Distinct side chain (or R group) bonded to -carbon

LE 5-UN78

Aminogroup

Carboxylgroup

carbon

What happens to ends in a cellular environment?

LE 5-17a

Isoleucine (Ile)

Methionine (Met) Phenylalanine (Phe) Tryptophan (Trp) Proline (Pro)

Leucine (Leu)Valine (Val)Alanine (Ala)

Nonpolar

Glycine (Gly)

Memorize structure

Amino acids

LE 5-17b

Asparagine (Asn) Glutamine (Gln)Threonine (Thr)

Polar

Serine (Ser) Cysteine (Cys) Tyrosine (Tyr)

LE 5-17c

Electricallycharged

Aspartic acid (Asp)

Acidic Basic

Glutamic acid (Glu) Lysine (Lys) Arginine (Arg) Histidine (His)

• Amino acids– linked together through peptide bonds

• Draw dipeptide bond showing bond

• Polypeptides range in length – a few a.a. to > thousand

• Each polypeptide has unique linear sequence of amino acids

Protein Conformation

• Helices, coils, pleats

• Sequence of amino acids determines 3-D conformation--> function

• Depicted in ribbon and space-filling models

LE 5-19

A ribbon model

Groove

Groove

A space-filling model

Four Levels of Protein Structure

• Primary structure (1o)– unique sequence of amino acids, like letters in a word

• Secondary structure (2o) -helices and -pleated sheets – Stabilized by H-bonds

• Tertiary structure (3o)– determined by interactions among various side chains

(R groups)

• Quaternary structure (4o)– Multiple polypeptide chains forming a functional protein

LE 5-20a

Amino acidsubunits

Carboxyl end

Amino end

1o structure

Four Levels of Protein Structure

• Primary structure (1o)– unique sequence of amino acids, like letters in a word

• Secondary structure (2o) -helices and -pleated sheets – Stabilized by H-bonds between amino and carbonyl groups- Creates 3-D conformation

• Tertiary structure (3o)– determined by interactions among various side chains

(R groups)

• Quaternary structure (4o)– Multiple polypeptide chains forming a functional protein

LE 5-20b

Amino acidsubunits

pleated sheet

helix

2o structure

Four Levels of Protein Structure

• Primary structure (1o)– unique sequence of amino acids, like letters in a word

• Secondary structure (2o) -helices and -pleated sheets – Stabilized by H-bonds

• Tertiary structure (3o)- determined by bonds between side chains (R groups) often between linearly distant amino acids

-ionic bonds, disulfide bonds, van der Waals forces, H-bonds

- creates to 3-D conformation

• Quaternary structure (4o)– Multiple polypeptide chains forming a functional protein

LE 5-20d

Hydrophobicinteractions andvan der Waalsinteractions

Polypeptidebackbone

Disulfide bridge

Ionic bond

Hydrogenbond

Four Levels of Protein Structure• Primary structure (1o)

– unique sequence of amino acids, like letters in a word

• Secondary structure (2o) -helices and -pleated sheets – Stabilized by H-bonds

• Tertiary structure (3o)- determined by bonds between side chains (R groups) often between linearly distant amino acids

-ionic bonds, disulfide bonds, van der Waals forces, H-bonds

- contributes to 3-D conformation

• Quaternary structure (4o)– Multiple polypeptide chains forming a functional protein

LE 5-20e

Chains

ChainsHemoglobin

IronHeme

CollagenPolypeptide chain

Polypeptidechain

LE 5-20

Amino acidsubunits

pleated sheet+H3N

Amino end

helix

Significance of Protein Conformation

• Small change in 1o structure– can change protein’s conformation and function

• Example– Sickle-cell disease

• an inherited blood disorder-->anemiaCaused by single amino acid substitution in hemoglobin

LE 5-21a

Normal cells arefull of individualhemoglobinmolecules, eachcarrying oxygen.

10 µm 10 µm

Fibers of abnormalhemoglobin deformcell into sickleshape.

Normal RBC Sickled RBC

LE 5-21b

Primarystructure

Secondaryand tertiarystructures

1 2 3

Normal hemoglobin

Val His Leu

4Thr

5Pro

6Glu Glu

7Primarystructure

Secondaryand tertiarystructures

1 2 3

Sickle-cell hemoglobin

Val His Leu

4Thr

5Pro

6Val Glu

7

Quaternarystructure

Normalhemoglobin(top view)

Function Molecules donot associatewith oneanother; eachcarries oxygen.

Quaternarystructure

Sickle-cellhemoglobin

Function Molecules interact withone another tocrystallize intoa fiber; capacityto carry oxygenis greatly reduced.

Exposedhydrophobicregion subunit subunit

One Amino Acid Substitution: Huge Effect!

pH

salt concentration

temperature

other environmental factors

Environment Affects Protein Structure & Function

Extreme conditions cause unraveling of protein structure:denaturation

?

LE 5-22

Denaturation

Renaturation

Denatured proteinNormal protein

Caused by, for example, high temperature (100oC)

Lowered Temp (37oC)

Proper Protein-Folding

• Chaperonins

– protein complexes that assist in the proper folding of other proteins

LE 5-23a

Chaperonin(fully assembled)

Hollowcylinder

Cap

LE 5-23b

Polypeptide

Correctlyfoldedprotein

An unfolded poly-peptide enters thecylinder from oneend.

Steps of ChaperoninAction:

The cap comesoff, and theproperly foldedprotein is released.

The cap attaches, causingthe cylinder to changeshape in such a way that it creates a hydrophilicenvironment for thefolding of the polypeptide.

Model

• X-ray crystallography (need to make protein crystals)

• Nuclear magnetic resonance (NMR) spectroscopy (not dependent on making protein crystals)

Techniques to Determine Protein Structure

How is the sequence of proteins determined? -encoded in DNA- two step process to decode

1. DNA is transcribed into mRNA

2. mRNA is translated into polypetide

More later