Protein: MONOMER

1
Protein MONOMER AMINO ACID
2
What is protein?
Proteins are polymers of amino acids.
Primary Structure
Secondary Structure
Tertiary Structure
Quaternary Structure
3
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

4
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
5
Amino acid

• 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
6
(No Transcript)
7
(No Transcript)
8


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 acid is an amphoteric molecule act either
as an acid or a base
Amino acids as dipolar ions
? - carboxyl group ? carboxylate ion
? - amino group ? protonated amino acid
9
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
a carbon
10
Amino acid

• Only the L - form of amino acids is commonly
  found in proteins.
• 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
• 4. basic

Vs monosaccharide D - form
Polar, charged
11
Classification of amino acid

• Nonpolar (9 amino acids)
• Polar neutral/uncharged (6 amino acids)
• charged basic (3 amino acids)
• 
  acidic (2 amino acids)

12

Classification of amino acids

Simplest amino acid due to the R group H No
stereoisomer because the is achiral
Nonpolar
13


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
14

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
15

Polar charged

Basic
Aspartate
Acidic
Glutamate
16
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

17
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

18
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.
  (H3N-HCR-COO- ).
• A titration curve shows how the amine and
  carboxyl groups react with hydrogen ion.

19
Titration of amino acid

• At low pH a nonacidic/nonbasic amino acid is
  protonated and has the structure H3NHCRCOOH
  (amino acid in cationic form)
• Increase of pH, dissociation of proton (H) from
  COOH group form H3NHCRCOO- (amino acid in
  zwitterionic form)
• At pK1, amount of cationic form amount of
  zwitterionic form
• Beyond pK1, additional base ions will results in
  all amino acids in cationic forms deprotonated to
  zwitterionic forms all amino acids have no net
  charge
• pI isoelectric point pH at which the amino
  acid has no net charge/all amino acids are in
  zwitterionic form
• Increase of pH beyond pI, will cause the
  dissociation of H / deprotonation
• from H3N resulting in formation of H2NHCRCOO-
  (anionic form)
• Increase of pH, more dissociation of proton (H)
  from H3Ngroup, more amino acids in anionic form
• At pK2, amount of zwitterionic form amount of
  anionic form

20
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
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)
Cationic form
21
Titration of amino acid

• pK1 and pK2 are proton dissociation constant from
  carboxyl group and amino group
• From titration of amino acid, the pI can be
  calculated
• The charge behavior of acidic and basic amino
  acids is more complex. Group Polar/charged
  amino acid

22
(No Transcript)
23
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 more polypeptide chains

Primary structure one polypeptide
24
(No Transcript)
25
Protein 1o , 2o and 3o structure
26
Peptide





Amino acid residue a monomeric unit of amino
acids
27

PROTEIN STRUCTURE OVERVIEW
28
Primary structure

Primary (1o) Structure sequence of a chain of
amino acids. Determines the final structure,
eventually the properties of proteins
29
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

30
Peptide bond Feature
5
1
2
3
4
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).
31
Secondary structure

• The planar peptide group and free rotating bonds
  between C?-N and C?-C are important
• Two types ?-helix and ?-pleated sheet
• 2o structure involves the hydrogen-bonded
  arrangement of the backbone of the protein

N O
32
Secondary structure ?-helix

• Structural features
• One polypeptide chain
• Hydrogen bonds between the -CO and the NH in the
  same polypeptide chain (intrachain)
• The hydrogen bonds are parallel to the helix axis
  
• Winding can be right- or left- handed (L- amino
  acid favor right-handed)

?
H bond
?
N O
33
Secondary structure ?-pleated sheet

• Structural features
• More than one polypeptide chain
• Two types antiparallel and parallel pleated
  sheet
• Hydrogen bonds between the -CO and the NH in the
  same polypeptide chain or with other polypeptide
  chain (interchain)
• The hydrogen bonds are perpendicular to the
  direction of chain

?
?
?
?
34
Secondary structure ?-pleated sheet

• antiparallel pleated sheet peptide chains are
  in the opposite directions
• parallel pleated sheet chains are in the same
  direction, the N- and C- terminal ends are
  aligned

35
Tertiary structure

• Results from folding and packing of secondary
  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
36
Tertiary structure

• Is the three-dimensional arrangement of all atoms
  in protein molecule
• Involves non-covalent interaction and covalent
  bonds
• Hydrogen bonds between the side chain
• Hydrophobic interaction
• Electrostatic interactions/attractions
• Disulfide bonds between the R group
• Complexation with metal ions

37
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

38

• Native conformation three-dimensional shape of a
  protein with biological activity
• Tertiary or quaternary structures

39
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
3
4
1
40
Quaternary Structure

• Oligomers are multisubunit proteins with all or
  some identical subunits.
• The subunits are called protomers.
• two subunits are called dimers
• four subunits are called tetramers

41
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

• Has four subunits tetramers

• Overall structure ?2?2
• Heme - Fe

Structure of Hemoglobin
42
Classification of protein

• Proteins are classified in two ways
• Shape
• Composition

43
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

44
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

45
Comparison of Shapes of Fibrous and Globular
Proteins
46
Proteins by Composition

• Simple protein (apoprotein)
• Contain only amino acids
• ex. serum albumin and keratin
• Conjugated protein
• simple protein (apoprotein)
• prostetic group (nonprotein)
• ex. Glycoproteins, lipoproteins,
  metaloproteins - hemoglobin

47
Denaturation

• Definition complete loss of organized structure
  in a protein, ?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

48

• Due to loss of 2o? 4o of protein structure, but
  not 1o , the amide bond (peptide bond) is intact

49
Denaturation

• Several ways to denature proteins
• Heat ? in temp, ? vibrations within the
  molecule, the energy of these vibrations
  can disrupt the 3o
• pH ? or ? pH, affect the charges of protein,
  the electrostatic interactions that normally
  stabilize the native conformation is reduced.
• Detergents (eg. SDS) - disrupt hydrophobic
  interactions, if the detergent is charged, this
  can also disrupt electrostatic interactions
• Reducing agents(eg. Urea) will form stronger
  H bonds, stronger than within the protein. Also
  disrupt the hydrophobic interaction
• Heavy metal ions
• Mechanical stress

50
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

51
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.

52
Protein Functions