Proteins and amino acids

Biochemistry 1 for Dental student

 Schedule of Biochemistry 1 for Dental student
1 Amino Acids

2 STRUCTURE OF PROTEINS

3 Structure-Function Relationship of protein

4 Classification of proteins

5 Carbohydrates

6 Carbohydrates

7 Lipids–I: Chemistry

8 Lipids–I: Chemistry

9 Water Soluble Vitamins

10 Fat Soluble Vitamins

11 Properties of Enzymes
Biochemistry
◼ Biochemistry is the language of biology
◼ The study of biochemistry is essential to understand
basic functions of the body. How the food that we
eat is digested, absorbed, and used to make
ingredients of the body? How does the body derive
energy for the normal day to day work? How are the
various metabolic processes interrelated? What is the
function of genes?
◼ • The study of biochemistry is necessary to give the
scientific basis for disease and is useful for treatment
of patients.
The relationship between structure and function is
a fundamental part of biochemistry
◼ More than 99% of the human body is
composed of 6 elements, i.e. oxygen,
carbon, hydrogen, nitrogen, calcium
and phosphorus.
◼ Human body is composed of about 60%
water, 15% proteins, 15% lipids, 2%
carbohydrates and 8% minerals
◼ The reader will be able to answer questions on the following
topics:
◼ 1. Classification of amino acids based on structure
◼ 2. Based on side chain character
◼ 3. Based on metabolic fate
◼ 4. Based on nutritional requirements
◼ 5. Isoelectric point
◼ 6. Reactions due to carboxyl and amino groups
◼ 7. Peptide bond formation
◼ 8. Primary, secondary, tertiary and quaternary structure of
proteins
◼ 9.. Classification of proteins
Functions of proteins
Proteins and amino acids
Proteins are polypeptides which are linear
polymers of amino acids linked together by
peptide bonds
Proteins and amino acids

Peptide Bond
Proteins are made by polymerization of amino
acids through peptide bonds
 Amino acids
◼ All organisms use the same 20 amino acids as
building blocks for the assembly of protein
molecules.
◼ These 20 amino acids are called the common, or
standard, amino acids.
◼ Despite the limited number of amino acids, an
enormous variety of different polypeptides can be
produced by connecting the 20 common amino acids
in various combinations
Amino acids
◼ Amino acids are called amino acids because they
are amino derivatives of carboxylic acids.
◼ In the 20 common amino acids the amino group
and the carboxyl group are bonded to the same
carbon atom: the a-carbon atom. Thus, all of the
standard amino acids found in proteins are α-amino
acids ( alpha amino acid )
in the physiological pH range of 6.8 to 7.4
,amino acids are zwitterions,or dipolar ions,
even though their net charge may be zero
 Ball-and-stick model of serine

Zwitterion

General structure
Solid wedges indicate
bonds above the plane
of the paper; dashed
wedges indicate bonds
below the plane of the
paper.

R group is —CH2OH
 Classification of amino acids
◼ 20 Amino acids are classified to 6 group Based on Structure
of different R group
◼

1. Aliphatic R
2. Aromatic R
3. Sulfur-containing R group
4. Alcohol-containing R group
Highly hydrophilic 5. Basic R
and charged
6. Acidic (& amides) R
 1. Aliphatic side chains
(Nonpolar)
NOTE: memorize the abbreviation of single and three words

proline

Less Highly hydrophobic

C
Little
 2. Aromatic side chains
(Nonpolar)

λ= 260 nm λ= 280 nm

Highly Less hydrophobic

 2. Aromatic R group
Phenylalanine contains benzene group
Tyrosine (phenol)
Tryptophan (Indole group);

◼ all aromatic amino acids absorb UV light .

◼ At neutral pH:
◼ Trp & Tyr absorbed light at wave length
280 while Phe at 260
3. Sulfur-containing R group

1- Methionine Met, M
contain nonpolar methyl thio-ether group in its side chain and this
makes it one of the more hydrophobic amino acids & it is always
the first amino acid in a polypeptide chain

2- Cysteine Cys, C ‫ستَئين‬

ْ ‫سي‬
ِ
( 2-Amino-3-mercaptopropanoic acid )
 3. Sulfur-containing side chains

•Less
•~acid
•bridge
Highly
4. Alcohol-containing side chains
(Polar)
 4. Alcohol-containing side chains

•Uncharged polar side chains – contain β hydroxyl

groups.

-These alcohol give hydrophilic character to the

aliphatic side chain

-OH group of serine and threonine have weak

ionization properties
 5. Basic side chains
Positively Charged R Groups

•imidazole ring

Diamino acid
guanidinium ion
 5. Basic side chains
Positively Charged R Groups
◼ With hydrophilic side chain that are nitrogenous bases
The side chains can be positively charged at
physiological pH.
◼ Side chain of His contain imidazole ring
◼ Lys is di-amino acid
◼ Arginine contains guanidinium group (-NH-CNH— NH2)
and , Arginine is the most basic of the 20 amino acids
because its side-chain guanidinium ion is protonated
under all conditions normally found within a cell.
Arginine side chains also contribute positive charges in
proteins.
 6. Acidic side chains and Their
Amide Derivatives
Negatively Charged R
Amide Derivatives
Groups
Amide Derivatives
Amide Formation:
◼ The -COOH group of dicarboxylic amino acids
(other than alpha carboxyl) can combine with
ammonia to form the corresponding amide
◼ Aspartic acid +NH3 Asparagine
◼ Glutamic acid+NH3 Glutamine
◼ These amides are also components of
protein structure. The amide group of
glutamine serves as the source of nitrogen
for nucleic acid synthesis.
Formation of glutamine
 6. Acidic side chains and Their
Amide Derivatives

◼ Aspartate (Asp,D) and glutamate (Glu,E)

are dicarboxylic amino acids and have
negatively charged hydrophilic side
chains at pH 7
◼ asparagine and glutamine are uncharged these
amino acids are highly polar and are often
found on the surfaces of proteins where they
can interact with water molecules.
 Other classifications of side chains of A.A

➢ Polarity & charge 1. Non polar

2. Polar neutral
3. Positively charged
4. Negatively charged

➢ Hydrophobicity 1. Highly hydrophobic

2. Less hydrophobic
3. Highly hydrophilic

* Various side chain of aa range highly hydrophobic → weakly polar to → highly hydropilic.
* Hydropathy: is the relative hydrophobicity or hydrophilicity of each A A
* Is an important determinant of protein-chain folding
 Classifications of AA based on Polarity & charge of
side chains

◼ 1. Amino Acids having Nonpolar Side Chains These include

Alanine, Valine, Leucine, Isoleucine, Methionine, Proline,
Phenylalanine and Tryptophan. These groups are hydrophobic
(water repellant) and lipophilic.
◼ 2. Amino Acids having Uncharged or Nonionic Polar Side
Chains :Glycine, Serine, Threonine, Cysteine, Tyrosine,
Glutamine and Asparagine belong to this group. These amino
acids are hydrophilic in nature
◼ 3. Amino Acids having Charged or Ionic Polar Side Chains They
are hydrophilic in nature. (1) Acidic amino acids: They have a
negative charge on the R group: Aspartic acid and Glutamic acid
(2) Basic amino acids: They have a positive charge on the R
group: Lysine, Arginine and Histidine.
 Classification Based on Nutritional Requirement

◼ 1. Essential :Their carbon skeleton cannot be synthesized by human beings

and so preformed amino acids are to be taken in food for normal. Thus,
Valine, Isoleucine, Leucine, Threonine, Lysine, Methionine, Phenylalanine,
and Tryptophan, are essential amino acids.
◼ 2. Partially Essential or Semi-essential: Histidine and Arginine are semi-
indispensable amino acids. Growing children require them in food. But they
are not essential for the adult individual. Adult humans can synthesize
arginine and histidine in sufficient quantities, via the urea cycle. However,
infants are unable to effectively synthesize arginine, making it nutritionally
essential for infants.
◼ 3. Nonessential or Dispensable The remaining 10 amino acids are
nonessential. However, they are also required for the normal protein
synthesis. All body proteins do contain all the nonessential amino acids. But
their carbon skeleton can be synthesized by metabolic pathways and
therefore their absence in the food will not adversely affect the growth
 Essential Nonessential
Obtained from Synthesized by the
nutrition body
Isoleucine Alanine
Leucine Asparagine
Lysine Aspartate
Methionine Cysteine*
Phenylalanine Glutamate
Threonine Glutamine*
Tryptophan Glycine*
Valine Proline*
Arginine* Serine*
Histidine* Tyrosine*
 Formation of cystine
oxidation links the sulfhydryl groups of two cysteine molecules, the resulting
compound is a disulfide called cystine.

‫ِسي ْستين‬
 Derivatives of amino acids
◼ Several common amino acids are chemically modified to produce
biologically important amines.
◼ These are synthesized by enzyme-catalyzed reactions that include
decarboxylation and deamination, for example:
1) glutamate is converted to the neurotransmitter g-aminobutyrate (GABA)
2) . Histidine is converted to histamine , Histamine controls the constriction
of certain blood vessels and also the secretion of hydrochloric acid by the
stomach.
3) tyrosine is metabolized to epinephrine,also known as adrenaline. Is
hormones that help regulate metabolism in mammals.
4) Tyrosine is also the precursor of the thyroid hormones thyroxine and
triiodothyronine Biosynthesis of the thyroid hormones requires