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Department of Industrial Chemistry: Bahir Dar University

This document discusses the structure and function of proteins. It begins by introducing proteins and their composition of amino acids. It then covers the four levels of protein structure: primary, secondary, tertiary, and quaternary. Key points include that proteins are made of amino acid monomers connected by peptide bonds, and that their structure determines their function. The document also addresses amino acid properties, peptide bond formation, common secondary structures like alpha helices and beta sheets, and factors that stabilize tertiary structure.

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Fikere'ab Habtamu
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195 views

Department of Industrial Chemistry: Bahir Dar University

This document discusses the structure and function of proteins. It begins by introducing proteins and their composition of amino acids. It then covers the four levels of protein structure: primary, secondary, tertiary, and quaternary. Key points include that proteins are made of amino acid monomers connected by peptide bonds, and that their structure determines their function. The document also addresses amino acid properties, peptide bond formation, common secondary structures like alpha helices and beta sheets, and factors that stabilize tertiary structure.

Uploaded by

Fikere'ab Habtamu
Copyright
© © All Rights Reserved
Available Formats
Download as PDF, TXT or read online on Scribd
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Bahir Dar University

Department of Industrial Chemistry

Biochemistry (Ichem.3061)

Protein Structure and Function.

2022, Bahir Dar


1
Introduction
 Proteins are the most abundant biological macromolecules, occurring
in all cells.
 Proteins are linear polymers built of monomer units called amino acids.
 Proteins contain a wide range of functional groups ,of alcohols, thiols,
thioethers, carboxylic acids, carboxamides, and a variety of basic groups
 Proteins can interact with one another and with other biological
macromolecules to form complex assemblies.
Proteins can be broken down (hydrolyzed) to their constituent
amino acids by a variety of methods.
 Proteins function as catalysts, transport and store molecules
like oxygen, provide mechanical support and immune protection,
generate movement, transmit nerve impulses, and control growth .
2
Structure and Function of Amino Acids

Over 300 naturally occurring amino acids, 20 constitute the monomer


units of proteins.
All 20 of the common amino acids are α -amino acids.
They have a carboxyl group and an amino group bonded to
the same carbon atom (the α-carbon).
 They differ from each other in their side chains, or R groups

- The amino group carries a positive charge, and


negatively charged carboxylic acid group.
-They are termed zwitterions , i.e no net charge

3
Structure and Function of Amino Acids

Common amino acids & its


abbreviation found in proteins

4
Common amino acids grouping into five main classes based on the
properties of their R groups.

5
6
Essential and Non –essential Amino Acids

 Among 20 different amino acids – nine of which are called “essential”


and 11 are “non-essential.”
i) Essential Amino Acids

They cannot create in our body and obtain by eating various foods.
 Essential acids are Methionine, valine, tryptophan, isoleucine, leucine,
lysine, threonine , phenylalanine and Histidine.
Instead of storing up the essential acids, the body uses them to create
new proteins on a regular basis.

7
Essential and Non – essential Amino Acids
ii) Non-Essential Amino Acids
They are synthesized by the body and important part of building proteins.
they do not need to be included in an everyday diet.
 They are mainly synthesized from glucose (alanine, asparagine,
aspartate, cysteine, glutamate, glutamine, glycine, proline, serine and
arginine [from the urea cycle in hepatic cells]).Tyrosine is synthesized
from phenylalanine.

8
- Routes of synthesis of nonessential
amino acids in the human

9
Amino Acids as Buffers
-Amino acids in aqueous solution contain weakly acidic α-carboxyl groups
and weakly basic α-amino groups.
- Each of the acidic and basic amino acids contains an ionizable group
in its side chain.
-Thus, both free amino acids and some amino acids combined in
peptide linkages can act as buffers.
-Maximum buffering capacity occurs at a pH equal to the pKa, but
a conjugate acid/base pair can still serve as an effective buffer when
the pH of a solution is with in approximately ± 1 pH unit of the pKa

10
Example

Ionic forms of alanine in acidic ,neutral and basic solutions

 The pKa for the acidic group (-COOH) is pK1, whereas the pKa
for the next acidic group (-NH3+) is pK2

11
-Based on the Henderson-Hasselbalch equation
to dissociable acidic group, the change in pH
that occurs during the addition of base to the
fully protonated form of alanine (I) to produce
the completely deprotonated form (III).

- The titration curve of alanine


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 The -COOH/-COO- pair can serve as a buffer in the pH region around
pK1 and the -NH3/ -NH2 pair can buffer in the region around pK2

 When pH = pK; when the pH is equal to pK1 (2.3), equal amounts of


forms I and II of alanine exist in solution. When the pH is equal to
pK2 (9.1), equal amounts of forms II and III are present in solution.

13
Peptide bond formation (Peptide bond linkage)

Two amino acid molecules can be covalently joined through a substituted


amide linkage, termed a peptide bond, to yield a dipeptide.
 Such a linkage is formed by removal of the elements of water from
The α-carboxyl group of one amino acid and the α-amino group of another.

Three amino acids can be joined by two peptide bonds to form a tripeptide
similarly, amino acids can be linked to form tetrapeptides, pentapeptides,
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and so forth.
The pentapeptide serylglycyltyrosylalanylleucine,/ Ser–Gly–Tyr–Ala–Leu.
 Peptides are named beginning with the amino terminal residue, which is
placed at the left and the free carboxyl end (C- terminal ) to the right
by convention.

15
Structure of Proteins
The complexity of protein structure is best analyzed by considering the
molecule in terms of four organizational levels, namely, primary,
secondary, tertiary, and quaternary.
I ) Primary (1O) structure of proteins

 It is the sequence of amino acids in a protein (polypeptide chain)


The 1O structure is held together by peptide bonds.

Example,

1O structure of proteins is important because many genetic diseases


result in proteins with abnormal amino acid sequences,
16
 1o structure of a polypeptide is analyzed via hydrolyzed by strong acid
at 110 o C for 24 hours.
 Treatment cleaves the peptide bonds, and releases the individual
amino acids, Thus, can be separated by Ion-exchange chromatography.
II) Secondary structure of proteins
 Polypeptide backbone three-dimensional structure, and regular
arrangements of amino acids that are located near to each other in the
linear sequence.
Examples of 2o structures; α-helix, β-sheet, and β-bend

17
 α-helix is consisting of a tightly packed,
coiled polypeptide backbone core, with the side
chains of the component amino acids.

 An α-helix is stabilized by extensive hydrogen


bonding between peptide-bond carbonyl
oxygens and amide hydrogens that are part of
the polypeptide backbone

 Each turn of an α-helix contains 3.6 amino acids.

18
 β-sheet is another form of 2o structure in which all of the peptide
bond components are involved in hydrogen bonding.
 β-sheet exist when a protein's backbone forms
an extended zig-zag structure that passes back
and forth.
 Unlike the α-helix, β-sheets are composed of two
or more peptide chains.
Hydrogen bonds help support secondary
structures
 In β-sheets the hydrogen bonds are perpendicular
to the polypeptide backbone 19
Tertiary structure of proteins

 The three dimensional shape of a protein.


 3o structures have a single polypeptide chain "backbone" with one
or more protein secondary structures.
Interactions stabilizing 3o structure
i) Disulfide bonds
ii) Hydrophobic interactions
iii) Hydrogen bonds
iv) Ionic-interactions
How Protein folding ?
- Interactions b/n the side chains of amino acids determine how
a long polypeptide chain folds into the intricate three-
20
dimensionals shape of the functional protein.
Quaternary structure of proteins

 Many proteins consist of a single polypeptide chain, and are


defined as monomeric proteins.
 Others consist of two or more polypeptide chains that may be
structurally identical or totally unrelated. The arrangement of these
polypeptide subunits is called the quaternary structure of the
protein.
 Subunits held together by
non- covalent interaction .
Example: Hemoglobin has
subunit composition
21
Summary

22
Denaturation of proteins

 Protein denaturation results in the unfolding and disorganization of the


protein's secondary and tertiary structures, which are not accompanied by
hydrolysis of peptide bonds.
Denaturing agents include heat, organic solvents, mechanical mixing,
strong acids or bases, detergents, and ions of heavy metals such as lead
and mercury.
Denaturation under ideal conditions, be reversible, in which the protein
refolds into its original structure, when the denaturing agent is removed.
However, most proteins, once denatured, remain permanently disordered.
Denatured proteins are often insoluble and be precipitate from solution.
23
Use of proteins

protein used to make


Enzymes,
Hormones,
Antibodies
Fibers
and other body chemicals.
It is an important building block of bones, muscles, cartilage, skin, and
blood.

24
THANK YOU FOR YOUR ATTeNTiON!

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