Download the chemistry of villin

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 Acid
Name
Aspartic acid,
Letter: D
Abbreviation:
Asp
Info
4
4
6
1
oxygen
carbon
hydrogen
nitrogen
Looks
E – Glutamic Acid
Name
Info
Glutamic acid
Letter: E
Abbreviation:
Glu
5
8
4
1
carbon
hydrogen
oxygen
nitrogen
Looks
F – Phenylalanine
Name
Info
Phenylalanine
Letter: F
Abbreviation:
Phe
9 carbon
11 hydrogen
1 nitrogen
2 oxygen
Looks
K – Lysine
Name
Info
Lysine
Letter: K
Abbreviation:
Lys
6 carbon
14 hydrogen
2 nitrogen
2 oxygen
Looks
A – Alanine
Name
Info
Alanine
Letter: A
Abbreviation:
Ala
3
7
1
2
carbon
hydrogen
nitrogen
oxygen
Looks
V – Valine
Name
Info
Valine
Letter: V
Abbreviation:
Val
5 carbon
11 hydrogen
1 nitrogen
2 oxygen
Looks
G – Glycine
Name
Info
Glycine
Letter: G
Abbreviation:
Gly
5 carbon
11 hydrogen
1 nitrogen
2 oxygen
Looks
M – Methionine
Name
Info
Methionine
Letter: M
Abbreviation:
Met
5 carbon
11 hydrogen
1 nitrogen
2 oxygen
1 suphur
Looks
T – Threonine
Name
Info
Threonine
Letter: T
Abbreviation:
Thr
4
9
1
3
carbon
hydrogen
nitrogen
oxygen
Looks
R – Arginine
Name
Info
Arginine
Letter: R
Abbreviation:
Arg
6 carbon
14 hydrogen
4 nitrogen
2 oxygen
Looks
S – Serine
Name
Info
Serine
Letter: S
Abbreviation:
Ser
3
7
1
3
carbon
hydrogen
nitrogen
oxygen
Looks
N – Asparagine
Name
Info
Asparagine
Letter: N
Abbreviation:
Asn
4
8
2
3
carbon
hydrogen
nitrogen
oxygen
Looks
L – Leucine
Name
Info
Leucine
Letter: L
Abbreviation:
Leu
6 carbon
13 hydrogen
1 nitrogen
2 oxygen
Looks
P – Proline
Name
Info
Proline
Letter: P
Abbreviation:
Pro
5
9
1
2
carbon
hydrogen
nitrogen
oxygen
Looks
W – Tryptophan
Name
Info
Tryptophan
Letter: W
Abbreviation:
Trp
11 carbon
12 hydrogen
2 nitrogen
2 oxygen
Looks
Q – Glutamine
Name
Info
Glutamine
Letter: Q
Abbreviation:
Gln
5 carbon
10 hydrogen
2 nitrogen
3 oxygen
Looks
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 yellowgreen 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