BIOCHEMISTRY LEC 2 A - Amino Acids

AMINO ACIDS AND PROTEINS ● Building blocks of proteins

● Amine group (NH2) is attached
to the C atom next to the
Proteins
carboxyl group.
- To be broken down
- Proteios “first importance”

CELLULAR FUNCTIONS
Enzymes
- Speed up the metabolism/
chemical reaction
- Biological catalyst
- To digest carbohydrates/fats
Antibodies Groups of Amino Acids
- Are specific protein molecules ● According to the polarity
produced by specialized cells in of their side chains
the immune system(plasma Hydrophobic Amino Acids
cells) in response to foreign - Prefer Contact with one another
bodies(antigens). over contact with water.
- Also called as immunoglobulins - Generally found buried in the
Transport Proteins interior of proteins, where they
- Carry materials from one place can associate with one another
to another in the body. and remain isolated from water
- E.g. transferrin, hemoglobin, - 9 amino acids:
myoglobin ● Alanine
Regulatory Proteins ● Valine
- Control many aspects of cell ● Leucine
function, including metabolism ● Isoleucine
and reproduction. ● Tryptophan
- E.g. Protein Hormones ● Proline
Structural Proteins ● Glycine
- Provide mechanical support ● Methionine
large animals and provide them ● Phenylalanine
with their outer coverings
- E.g. Keratin
Movement Proteins
- Necessary for all movements
- E.g. Myosin and actin
Nutrient Proteins
- Serve as sources of amino
acids for embryos or infants
- E.g. Albumin (egg), casein
Hydrophilic Amino Acids
(milk)
- Attracted to polar water
 molecules acids have a net charge
- Often found on the surfaces of of -1 because the
proteins ionization of the
3 classes: carboxylic acid releases
1. Polar, Neutral Amino Acids a proton
- Have R groups that have ● Glutamate
a high affinity for water ● Aspartate
but that are not ionic at 3. Positively Charged Amino Acids
pH 7 - At ph 7, have a net
● Serine positive charge because
● Threonine of their side chains
● Tyrosine contain positive groups
● Cysteine - Are basic because the
● Asparagine side chain reacts with
● Glutamine water, picking up a
proton and releasing a
hydroxide anion
● Lysine
● Arginine
● Histidine

2. Negatively Charged Amino

Acids
- Have ionized carboxyl
groups in their side
chains. The Peptide Bond
● Amide group that links amino
acids
Dipeptide
The molecule formed by
condensing two amino acids
N-Terminal Amino Acids
With a free N+H3
C-Terminal Amino Acids
With a free -COO- Group
Nomenclature
● PEPTIDES are named as
derivatives of the C-terminal
- At pH 7 these amino amino acids, which receives it
 entire name
● For all other amino acids, the
ending -ine is changed to -yl.
Primary Structure of Proteins
- Amino acid sequence of the
protein chain
- It results from the covalent
bonding between the amino
acids in the chain (peptide
bonds)
- Are translation of information
contained in genes
Secondary Structure of Proteins
- Where the peptide chains are
folded regularly
- In the result of hydrogen
bonding between the amide
hydrogens and carbonyl
oxygens of the peptide bonds
Tertiary Structure of proteins
- Three-dimensional structure
- Polypeptide chain with its
regions of secondary structure
further folds on itself.
Quaternary Structure of Protein
- Hemoglobin
- With four individual globular
peptide subunits
- 2 identical alpha-subunits
- 2 identical beta-subunits
Classes of Proteins
Fibrous Proteins
- Are tough, insoluble, and
composed of fibers and sheets
- E.g. collagen, Keratin, Elastins,
Myosin, Fibrin
Globular Proteins
- Are water-soluble and have
chains folded into compact
shapes
- E.g. hemoglobin, myoglobin,
insulin, immunoglobulins
Simple Protein
- A protein composed of only
amino acid residues
- E.g. Ribonuclease (124 amino
acids), albumin
Conjugate Protein
- A protein that incorporate one or
more non-amino acid units in
its structures
- E.g. Glycoproteins,
Lipoproteins, metalloproteins
Dietary Proteins
Nutritional Classes of Amino Acid-
● Essential Amino Acids
- Cannot be synthesized
by the body and are
required in the diet.
➢ Isoleucine
➢ Leucine
➢ Lysine
➢ Methionine
➢ Phenylalanine
➢ Threonine
➢ Tryptophan
➢ Valine
● Nonessential Amino Acids
- Are those amino acids
that can be synthesized
 by the body and need not
be included in the diet
➢ Alanine
➢ Arginine
➢ Asparagine
➢ Aspartate
➢ Cysteine
➢ Glutamate
➢ Glutamine
➢ Glycine
➢ Histidine
➢ Proline
➢ Serine
➢ Tyrosine
● Complete Protein
- Protein derived from
animals
- It provides all of the
essential and
nonessential amino acids
● Incomplete Protein
- Derived from vegetable
sources
- It lacks a sufficient
amount of one or more
essential amino acids
Physical and Chemical properties of
Proteins
- Generally tasteless
- Mostly are colorless, few are
colored and crystalline
- Insoluble in fat solvents and
present varied degrees of
solubility in water, salt solution,
dilute acids, and alkalis
- Mostly are with high molecular
weight
- Most of them form non-diffusible
colloid solutions of the emulsoid
type
- Are amphoteric
- Most of them are labile and
readily modified in solution
when subjected to alterations in
pH, UV, heat, and organic
solvents
- Very reactive and highly specific
Amphoterism
- Can act as an acid or base
(depending on the pH of the
medium)
- In acid solution, it acts like a
base
- In alkaline solution, it acts like
an acid
- Principle of electrophoresis
- If the acidity or alkalinity of the
solution is made lass and less,
a point will be reached when the
amino acid group tend to
migrate equally on both
directions - this pH is called the
ISOELECTRIC POINT
Zwitterions or Dipolar Forms
- Amino acids are completely
ionized (zwitterion or dipolar
view) but the positive and
negative charges neutralizes
each other.
Denaturation of Proteins
● Occurs when the organized
structures of a globular protein
become completely
disorganized
Temperature
- As the temperature increases,
increases the rate of molecular
movement within the solution
and the bonds within the
proteins begin to vibrate more
violently
- Lose their characteristics 3-
dimensional conformation and
 become completely
disorganized
- 56-60 degrees celsius
- Coagulation occur as the
protein molecules then unfold
and become entangled; they
have aggregated to become a
solid
pH
-When the pH of a protein
solution is above the pl, all the
protein molecules will have a
net negative surface charge
- Below the pl, they will have a
net positive charge
- In either case, these like-
charged molecules repel one
another, and this repulsion
helps keep these very large
molecules in solution.
- At the pl, the protein molecules
n longer have a net surface
charge. As a result, they no
longer strongly repel one
another and are at their least
soluble.
Organic Solvent
- Polar organic solvents denature
proteins by disrupting hydrogen
bonds within the protein, in
addition to forming hydrogen
bonds to solvent, water.
Detergents
- Have both a hydrophobic region
and a polar or hydrophilic region
- When interacts with proteins,
they disrupt the hydrophobic
interactions, causing the protein
chain to unfold.
Heavy Metals
- Mercury or lead
- May form bonds with negatively
charged side chain groups
- This interferes with the salt
bridges formed between amino
acid R group, resulting in loss of
conformation
Mechanical Stress
- Stirring, whipping or shaking
can disrupt the weak
interactions that maintain
conformation.
Hemoglobin Molecule
● Is a tetramer composed of four
polypeptides subunits:
- 2 alpha-subunits
- 2 beta-subunits
Heme group
- Iron portion
- Can bind four molecules for
oxygen
Immunoglobulins
- Antibodies
- Produced by plasma cells
- Highly specific
- Has a memory
- Can recognize “self” from
“nonself”
- Contain 4 peptide chains that
are connected by disulfide
bonds and arranged in a Y-
shaped quaternary structure
Enzymes
Enzymology
● Study of enzymes
- Activity of enzymes
- Chemical reactions it
catalyzes
- Clinical use
Biological Catalysts
● Hasten chemical reaction
- Not consumed during the
reactions
- Not undergoing a
 chemical change after - Lactate dehydrogenase
the reaction

Transferases
● Transfer of functional groups
other than hydrogen from one
substrate to another.
- E.C. 2.6.1.1 :
L-Aspartate: 2-Oxaloglutarate
Aminotransferase
Nomenclature of Enzymes - Aspartate Aminotransferase
1. Substrate + -ase
● Lipid = lipase
● Ester = esterase
● Protein = protease
HYDROLASES
2. Reaction it catalyzes
● Hydrolysis of various bonds
● Oxidation = oxidase
● Addition of water to a bond
● Reduction =reductase
resulting in bond breakage
● Hydrolysis = hydrolase
E.C. 3.2.1.1 : 1,4-D-Glucan
● Dehydrogenase =
Glucanohydrolase
remove hydrogen atoms,
- Alpha-Amylase
transferring them to a
coenzyme
● Decarboxylase =
remove carboxyl groups
3. Enzyme Commission
Nomenclature (E.C.)
E.C 1.1.1.21
- 1st digit = class LYASES
- 2nd digit = subclass ● Addition of a group to a double
- 3rd and 4th = serial number bond or the removal of a group
to form a double bond
Classification of Enzymes - Carbonic Anhydrase
- Citrate Lyase
Oxidoreductases
● Oxidation and reduction
- Oxidation - removal of H
ion
- Reduction - acceptance
of H ion ISOMERASES
● E.C 1.1.1.27 : L-lactate NAD= ● Rearrange the functional groups
Oxidoreductase within a molecule and catalyze
 the conversion of one isomer
into another
- Phosphoglycerate mutase
● Inactive form of enzyme
● It is then converted, usually by
proteolysis, to the active form
when it has reached the site of
its activity

LIGASES

● Catalyze a reaction in which C-

C, C-S, C-O, or C-N bond is
made or broken
- Accompanied by an ATP-ADP
interconversion

TERMS
Substrate
● Acted upon by the enzyme
● Specific
Isoenzyme
● Different form but with the same
action
Cofactor
● Non-protein molecule
Activator
● Inorganic cofactor
Coenzyme
● Organic cofactor
Apoenzyme
● Polypeptide portion
Holoenzyme
● Apoenzyme + Coenzyme
Proenzyme
● Also known as zymogen