PROTEINS

(Polymers of Amino Acids)

Properties of Amino Acids

capacity to polymerize
novel acid-base properties
varied structure and chemical functionality
chirality

20 Amino Acids
Grouped by properties of their side
chains
Non-polar (hydrophobic)
Polar (hydrophilic)
Acidic
Basic

Polypeptide
Many amino acids
linked together

Dehydration Synthesis
Cells link amino acids together by
dehydration synthesis

PEPTIDE
BOND

Carboxyl Amino
group
group
Dehydration
synthesis

Amino acid

Amino acid

Dipeptide

Peptide chemistry
the amino acid polymer forms
when the carboxyl group of
one amino acid condenses with
the amino group of the next

H20

H
H

N
H

N
C

H
O
peptide bond

O
C

OH

Amino acid structure

central carbon atom surrounded by

amino group
carboxyl group
single hydrogen
variable R group

Amino
group

Carboxyl (acid)
group

Amino acids are essentially -amino

acids:

When R is not H, the alpha carbon is

asymetric, giving rise to isomers.
-carbon is chiral (except for glycine)

Chirality of Amino Acids

Glycine, 2-amino-acetic acid, is achiral
In all the others, the carbons of the
amino acids are centers of chirality
Proteins are derived exclusively from Lamino acids

Glycine
H

+
H3N
Glycine
(Gly or G)

C
H

Fischer Projections of Amino

Acids
are chiral

have Fischer projections that are stereoisomers

with the :
- carboxylate group at the top,
- R group at the bottom, and
- amino group on the left are the L isomers

in proteins are all L isomers; no D isomers are found in proteins

Ionization of Amino
Acids

Because amino acids contain both an

acidic and a basic functional group, an
internal acid-base reaction occurs,
forming an ion with both a positive and
a negative charge called a zwitterion:

H3N CH2 COO

12

amino acids dissociate in aqueous solution to form a

zwitterion

H
H
H

N+
H

O-

N+

H
O

O
C

O-

Glycine
H

+
H3N
Glycine
(Gly or G)

C
H

+
H3N

CH(CH3)2

Valine
(Val or V)

+
H3N

CH2CH(CH3)2

Leucine
(Leu or L)

+
H3N

CH3CHCH2CH3

Isoleucine
(Ile or I)

+
H3N

CH3SCH2CH2

Methionine
(Met or M)

H
+
H2N

C
CH2

H2 C
C
H2

Proline
(Pro or P)

+
H3N

C
CH3

Alanine
(Ala or A)

+
H3N

CH2

Phenylalanine
(Phe or F)

+
H3N

CH2

Tryptophan
N
H

(Trp or W)

+
H3N

H2NCCH2
O

Asparagine
(Asn or N)

+
H3N

H2NCCH2CH2
O

Glutamine
(Gln or Q)

+
H3N

C
CH2OH

Serine
(Ser or S)

+
H3N

C
CH3CHOH

Threonine
(Thr or T)

+
H3N

C
OCCH2
O

Aspartic Acid
(Asp or D)

+
H3N

OCCH2CH2
O

Glutamic Acid
(Glu or E)

+
H3N

CH2

Tyrosine
(Tyr or Y)
OH

+
H3N

C
CH2SH

Cysteine
(Cys or C)

+
H3N

CH2CH2CH2CH2NH3

Lysine
(Lys or K)

+
H3N

+
NH2
Arginine
(Arg or R)

+
H3N

Histidine
(His or H)

MOLECULAR STRUCTURE
PRIMARY
Sequence of amino acids

MOLECULAR STRUCTURE
Single mutations can cause problems
Normal hemoglobin:
VAL HIS LEU THR PRO
GLU GLU

Sickle Cell Hemo.:

VAL HIS LEU THR PRO
VAL GLU

MOLECULAR STRUCTURE
SECONDARY

Alpha Helix:

Pleated Sheets

-Helix

44

-Pleated Sheet

45

MOLECULAR STRUCTURE
TERTIARY
3-D shape
Globular (round clusters hemoglobin)
Fibrous (long threads collegen)

Hydrophobic interaction nonpolar sections

of molecule clump to middle of protein away
from any possible sources of water

MOLECULAR STRUCTURE
QUATERNARY
Interaction of multiple polypeptide
chains

Levels of Protein
Structure

catalase

keratin

collagen

Fibrous proteins:
static molecules; provide mechanical support
typically water insoluble
usually built on single repetitive structure assembled into
cables or threads e.g. keratin, collagen, silk.

Globular proteins:
water soluble; compact, spherical; hydrophobic interior and
hydrophilic surface.
Most proteins are globular.
most enzymes are globular

DENATURATION
Protein loses its shape & no longer
function
More shape changes, greater impact on its
ability to function

Causes:
Temperature
pH (toxic chemicals)
Radiation

Example: Sickle Cell Anemia

Denaturation of Proteins

55

Denaturing Proteins
Heat

Ultraviolet
Radiation

Strong Acids
or Bases
Urea

Some Organic
Solvents

hydrogen bonds are broken by increased translational

and vibrational energy
Similar to heat
(sunburn)
salt formation; disruption of hydrogen bonds.
(skin blisters and burns, protein precipitation.)
competition for hydrogen bonds.
(precipitation of soluble proteins.)
(e.g. ethanol & acetone) change in dielectric constant
and hydration of ionic groups.
(disinfectant action and precipitation of protein.)
shearing of hydrogen bonds.

Agitation