The Chemistry of Villin

Gary Benz and Claudia Winkler

The Chemistry of Villin• Villin is a protein• Proteins are macromolecules (polymers)

formed by a defined sequence of small similar molecules (monomers) of amino acids

• Amino acids are organic compounds containing at least one amino group (NH3) and one carboxyl group (-COOH).

• 20 different amino acids make up all proteins

The amino-acid alphabet

• Biologists represent each amino acid with a capital letter

• For instance:– D=Aspartic Acid, E=Glutamic Acid,

F=Phenylalanine, K=Lysine, A=Alanine, V=Valine, F=Phenylalanine

• All amino acids are made of 4 elements: Carbon, Hydrogen, Oxygen, Nitrogen. Two also contain Sulfur.

Villin’s Single Chain

• Biologists describe the sequence of amino acids that make villin as:– DEDFKAVFGMTRSAFANLPLWKQQNLKK

EKGLFMLS – Although villin is made of a chain of

36 letters, only 16 different letters are needed to describe villin

– In the next slides we shall look at the individual amino acids that make up villin

D – Aspartic AcidName Info Looks

Aspartic acid,Letter: DAbbreviation: Asp

4 oxygen4 carbon6 hydrogen1 nitrogen

E – Glutamic AcidName Info Looks

Glutamic acidLetter: EAbbreviation: Glu

5 carbon8 hydrogen4 oxygen1 nitrogen

F – PhenylalanineName Info Looks

PhenylalanineLetter: FAbbreviation: Phe

9 carbon11 hydrogen1 nitrogen2 oxygen

K – LysineName Info Looks

LysineLetter: KAbbreviation: Lys

6 carbon14 hydrogen2 nitrogen2 oxygen

A – AlanineName Info Looks

AlanineLetter: AAbbreviation: Ala

3 carbon7 hydrogen1 nitrogen2 oxygen

V – ValineName Info Looks

ValineLetter: VAbbreviation: Val

5 carbon11 hydrogen1 nitrogen2 oxygen

G – Glycine

Name Info Looks

GlycineLetter: GAbbreviation: Gly

5 carbon11 hydrogen1 nitrogen2 oxygen

M – MethionineName Info Looks

MethionineLetter: MAbbreviation: Met

5 carbon11 hydrogen1 nitrogen2 oxygen1 suphur

T – ThreonineName Info Looks

ThreonineLetter: TAbbreviation: Thr

4 carbon9 hydrogen1 nitrogen3 oxygen

R – ArginineName Info Looks

ArginineLetter: RAbbreviation: Arg

6 carbon14 hydrogen4 nitrogen2 oxygen

S – SerineName Info Looks

SerineLetter: SAbbreviation: Ser

3 carbon7 hydrogen1 nitrogen3 oxygen

N – AsparagineName Info Looks

AsparagineLetter: NAbbreviation: Asn

4 carbon8 hydrogen2 nitrogen3 oxygen

L – LeucineName Info Looks

LeucineLetter: LAbbreviation: Leu

6 carbon13 hydrogen1 nitrogen2 oxygen

P – ProlineName Info Looks

ProlineLetter: PAbbreviation: Pro

5 carbon9 hydrogen1 nitrogen2 oxygen

W – TryptophanName Info Looks

TryptophanLetter: WAbbreviation: Trp

11 carbon12 hydrogen2 nitrogen2 oxygen

Q – GlutamineName Info Looks

GlutamineLetter: QAbbreviation: Gln

5 carbon10 hydrogen2 nitrogen3 oxygen

Elements

• Carbon (C), Hydrogen (H), Oxygen (O), Nitrogen (N) and Sulfur (S) are the only chemical elements that make up all villin’s amino acids.

• We shall review some of their properties in the next pages.

Carbon• (Latin: carbo, charcoal)

Carbon, an element of prehistoric discovery, is very widely distributed in nature. It is found in abundance in the sun, stars, comets, and atmospheres of most planets.

• Carbon is the source of energy for life through carbohydrates, just like a burning log is a source of energy to a cold room.

Atomic number

6

Atomic Symbol

C

Atomic mass 12.011 u

Electron Configuration

[He]2s22p2

Hydrogen• (Greek: hydro, water,

and genes, forming) Hydrogen is the most abundant of all elements in the universe.

• The heavier elements were originally made from Hydrogen or from other elements that were originally made from Hydrogen.

• Used in rocket fuel.

Atomic number

1

Atomic symbol

H

Atomic mass 1.0070 u

Electron Configuration

1s1

Oxygen• Greek: oxys, sharp, acid,

and genes, forming; acid former) Oxygen is the third most abundant element found in the sun. Oxygen is vital to the respiration of living organisms.

• Oxygen is responsible for the bright red and yellow-green colors of the Aurora.

• Essential element for combustion (i.e. burning).

Atomic number

8

Atomic symbol

O

Atomic mass 15.9994 u

Electron Configuration

[He]2s22p4

Nitrogen• (Latin Nitrum, Greek.

Nitron, native soda; genes, forming).

• Nitrogen gas (N2) makes up 78.1% of the Earth’s air, by volume.

• Nitrogen is found in all living systems as part of the makeup of biological compounds.

• Ammonia (NH3) is the most important commercial compound of nitrogen, with a very pungent smell, used in cleaning supplies.

Atomic number

7

Atomic symbol

N

Atomic mass 14.00674

Electron Configuration

[He]2s22p3

Sulfur• (Sanskrit, sulvere; Latin

sulpur) Known to the ancients; referred to in Genesis as brimstone.

• Sulfur occurs native in the vicinity of volcanoes and hot springs.

• It is widely distributed in nature in various minerals (iron pyrites, galena, sphalerite, cinnabar, stibnite, gypsum, epsom salts, celestite, barite, etc.)

• Sulfur is found in meteorites.

Atomic number

16

Atomic symbol

S

Atomic mass 32.6

Electron Configuration

[Ne]3s23p4

Yellowstone hot springs

Molecules, Bonds

• Atoms are bonded together to form molecules and molecules are bonded together to form macromolecules.

• The next slides shows some characteristics of chemical bonds.

Chemical Bonds

Peptide Bond• Amino acids join together via a special

bond called “peptide bond”.

• In a peptide bond, two molecules (amino acid 1 and amino acid 2) are joined together with the accompanying removal of a molecule of water.

Activity• Knowing that villin is made of the following

sequence of amino acids– DEDFKAVFGMTRSAFANLPLWKQQNLKKEKGLFMLS

• Compute the molar mass of villin.• Compute the percentage by number of each

atom component.• Compute the percentage by mass of each

atom component.• (Remember that amino acids are joined

together through peptide bonds….)

• Lesson Plan