Download 3 Amino Acids/Proteins

Protein:
MONOMER –
AMINO ACID
What is protein?
Proteins are polymers of amino acids.
What is amino acid?
Amino acid: a compound that
contains both an amino group and a
carboxyl group attach to -carbon
• -carbon also bound to side
chain group, R
• R gives identity to amino acid
Terminology
• - carbon = the carbon that
attach next to the carboxyl group
• - amino group = amino group
that attach to -carbon
• Other type of amino group –
eg. in Lysine, has
-amino group
Lysine
Amino acid
1. All 20 are -amino acids
2. For 19 of the 20, the -amino group is primary;
for proline, it is secondary amino acid
-Amino acid has an amino group attached to the
carbon (-carbon) adjacent to the carboxyl group
Generic amino acid at physiological
pH amino acids exist as dipolar ionic
species (have positive and negative
charge on the same molecule) zwitterion form
Physiological
pH
Amino acids as
dipolar ions
Enantiomer
• The amino acids can exist in two enantiomeric forms
(nonsuperimposable mirror image) forms – exceptional for
glycine
• Two steroisomers of amino acids are designated L- or D-.
L – amino
acid:
abundant in
nature, found
in proteins,
amino group
on the left
O
C
+
H3N
 carbon
C
R1
O
O
H
H
Mirror plane
O
C
C
R1
+
NH3
Amino acid
• Only the L - form of amino acids is commonly
found in proteins. Vs monosaccharide : D - form
• Depending on the nature of the R group, amino
acids are classified into four groups.
1. nonpolar
2. polar – neutral/uncharged side
chain
3. acidic
Polar, charged
4. basic
Classification of amino acid
• Nonpolar (9 amino acids)
• Polar
neutral/uncharged (6 amino acids)
charged
basic (3 amino acids)
acidic (2 amino acids)
Classification of amino acids
Simplest amino acid due to the R group = H
No stereoisomer because the is achiral
Nonpolar
Aliphatic cyclic structure – N is bonded to C2 atoms
Amino group of become secondary amine – often called an imino acid
Amino acids with nonpolar side chains - hydrophobic
Polar uncharged
Amide bond – highly
polar
Phenol
Thiol / sulfhydryl group – polar
– under oxidizing condition, with other thiol groups to form disulfide
bridges (-S-S-) – important in 3o structure
Polar charged
Basic
Aspartate
Glutamate
Acidic
Essential Amino acid
• An essential amino acid or
indispensable amino acid is
an amino acid that cannot be
synthesized de novo by the
organism (usually referring
to humans), and therefore
must be supplied in the diet.
• vs non-essential amino acid
Ionization of Amino Acids
In acidic solution – as
base (protonation)
In basic solution – as
acid (deprotonation)
• Remember, amino acids without charged groups on side chain
exist in neutral solution as zwitterions with no net charge
Ionization of amino acids
• At physiological pH, the carboxyl group of the
amino acid is negatively charged and the amino
group is positively charged.
• Amino acids without charged side chains (Group 1
and 2) are zwitterions and have no net charge.
(H3+N-HCR-COO- ).
• A titration curve shows how the amine and carboxyl
groups react with hydrogen ion.
Titration of Alanine
• When an amino acid is titrated, the titration curve represents the
reaction of each functional group with the hydroxide ion
Anionic form
Cationic form
pI (isoelectric point)
= pH at which the
amino acid has no
net
charge/ all
amino acids are in
zwitterionic form
All amino acids
are in the
zwitterion form –
at isoelectric
point (pI)
Terminology
• peptide: the name given to a short polymer of
amino acids joined by peptide bonds; they are
classified by the number of amino acids in the chain
• dipeptide: a molecule containing two amino acids
joined by a peptide bond
• tripeptide: a molecule containing three amino acids
joined by peptide bonds
• polypeptide: a macromolecule containing many
amino acids joined by peptide bonds
• protein: a biological macromolecule of molecular
weight 5000 g/mol or greater, consisting of one or
Primary structure
more polypeptide
chains = one polypeptide
Protein:
o
o
o
1 , 2 and 3
structure
Peptide
*
*
*
*
*
Amino acid residue: a monomeric unit of amino acids
PROTEIN
STRUCTURE
:OVERVIEW
Primary structure
Primary (1o) Structure =
Peptide bond
• The amino acids are linked through peptide bond
Peptide bond: the
special name given
to the amide bond
between the carboxyl group of
one amino acid and
the -amino group
of another amino
acid
• peptide bond –
covalent bond
Peptide bond: Feature
1
2
3
4
5
Free
rotation
COO-
NH3+
Peptide bond – in trans configuration, acts as a rigid
and planar unit. Has limited rotation around the peptide
bond (C-N).
Secondary structure
• The planar peptide group and free rotating bonds
between C-N and C-C are important
N
O
• Two types: -helix and -pleated sheet
• 2o structure: involves the hydrogen-bonded arrangement
of the backbone of the protein
Secondary structure: -helix
Structural features:
1. One polypeptide chain
2. Hydrogen bonds between the -CO
and the –NH in the same polypeptide
chain (intrachain)

H bond

3. The hydrogen bonds are parallel to
the helix axis
4. Winding can be right- or left- handed
(L- amino acid favor right-handed)
N
O
Secondary structure:
-pleated sheet
Structural features:
1. More than one polypeptide chain
2. Two types: antiparallel and parallel pleated sheet
3. Hydrogen bonds between the -CO and the –NH in the same
polypeptide chain or with other polypeptide chain (interchain)
4. The hydrogen bonds are perpendicular to the direction of chain




Secondary structure:
-pleated sheet
• antiparallel pleated sheet =
peptide chains are in the
opposite directions
• parallel pleated sheet = chains
are in the same direction, the Nand C- terminal ends are aligned
Tertiary structure
• Results from folding and packing of
secondary structure
Tertiary structure
• Bring together amino acid residues
far apart, permitting interactions
among their side chains
Tertiary structure
• Is the three-dimensional arrangement of all atoms in
protein molecule
• Involves non-covalent interaction and covalent bonds
1. Hydrogen bonds between the side chain
2. Hydrophobic interaction
3. Electrostatic interactions/attractions
4. Disulfide bonds – between the R group
5. Complexation with metal ions
Forces in 3˚ Structure
• Noncovalent interactions, including
– hydrogen bonding between polar side chains, e.g., Ser
and Thr
– hydrophobic interaction between nonpolar side
chains, e.g., Val and Ile
– electrostatic attraction between side chains of
opposite charge, e.g., Lys and Glu
– electrostatic repulsion between side chains of like
charge, e.g., Lys and Arg, Glu and Asp
• Covalent interactions: Disulfide (-S-S-) bonds
between side chains of cysteines
• Native conformation: three-dimensional shape
of a protein with biological activity
• Tertiary or quaternary structures
Quaternary structure
•
Final level of protein structure
•
Association of more than one
polypeptide chain to form a
complex
•
Subunit = individual parts of a large
protein molecule = polypeptide
chain
•
Quaternary structure is the result of
noncovalent interactions between
two or more protein chains.
•
Noncovalent interactions
 electrostatics,
 hydrogen bonds,
 hydrophobic
2
1
3
4
Quaternary Structure
• Oligomers are multisubunit proteins with all or
some identical subunits.
• The subunits are called protomers.
1. two subunits are called dimers
2. four subunits are called tetramers
Quaternary structure
• If a change in structure on one chain causes changes
in structure at another site, the protein is said to be
allosteric.
• Many enzymes exhibit allosteric control features.
• Hemoglobin is a classic example of an allosteric
protein. – oxygen = positive cooperativity
Structure of
Hemoglobin
• Has four subunits = tetramers
• Overall structure 22
• Heme - Fe
Classification of protein
• Proteins are classified in two ways:
1. Shape
2. Composition
Fibrous Proteins
• Fibrous proteins: contain polypeptide chains
organized approximately parallel along a single axis.
They
– consist of long fibers or large sheets
– tend to be mechanically strong
– are insoluble in water and dilute salt solutions
– play important structural roles in nature
Globular Proteins
• Globular proteins: proteins which are folded to a
more or less spherical shape
– they tend to be soluble in water and salt solutions
– most of their polar side chains are on the outside and
interact with the aqueous environment by hydrogen
bonding and ion-dipole interactions
– most of their nonpolar side chains are buried inside
– nearly all have substantial sections of -helix and sheet
Comparison of Shapes of Fibrous and
Globular Proteins
Proteins by Composition
• Simple protein (apoprotein)
Contain only amino acids
ex. serum albumin and keratin
• Conjugated protein
1. simple protein (apoprotein)
2. prostetic group (nonprotein)
Holoprotein
ex. Glycoproteins, lipoproteins, metaloproteins hemoglobin
Denaturation
 Definition - ….. , destroys the physiological
function of the protein.
 Definition – The unfolding of protein
 Eg. During cooking of egg
– Albumin (white egg) – denatured by heat and
changes from a clear, colorless solution to a white
coagulum
– Often irreversible – denatured protein cannot
returned to its native biological form – lost of
biological function – why microbes die when boiling
 Due to loss of 2o 4o of
protein structure, but not 1o ,
the amide bond (peptide bond)
is intact
Denaturation
Several ways to denature proteins
• Heat –
• pH –
• Detergents (eg. SDS) • Reducing agents(eg. Urea) –
• Heavy metal ions
• Mechanical stress
Denaturation
 Reversible denaturation – organic solvents (ethyl
alcohol or acetone), urea, detergents and acid or
base
 Denaturants disrupt only noncovalent
interactions not the covalent linkages of the
primary structure
– If removed, possible protein to unwound to native
structure
– eg. pH – addition of picric acid, protein (casein)
precipitate
addition of NaOH, the solution clear
Denaturation
• -mercaptoethanol example of reversible
denaturation.
- -mercaptoethanol reduced the disulfide
bridges of protein  the unfolding of
3o structure,
- the removal of -mercaptoethanol
will cause the oxidation of SH group
to form disulfide bridges again
and the 3o structure is recovered.
P
r
o
t
e
i
n
F
u
n
c
t
i
o
n
s