Introduction to Biochemistry

COURSE TITLE: INTRODUCTION TO BIOCHEMISTRY

COURSE CODE: BC 120
LECTURE 3- Amio acids & Proteins Chemistry
SPR-2024
Protein classification
 1. Classification Based on Functions
1. Structural Proteins: Provide support and shape to cells and tissues e.g. Collagen (bone , cartilage, tendons,
ligaments, and skin), Keratin (hair, nails, and the outer layer of the skin), and Elastin (found in connective
tissues, particularly in structures that require flexibility and resilience, such as skin, lungs, and blood vessels).
2. Contractile proteins: involved in muscle contraction and movement. e.g. Actin, and Myosin.
3. Catalytic Proteins (Enzymes): act as biological catalysts that accelerate chemical reactions. e.g. DNA
polymerase, amylase, Lipase, and Pepsin.
4. Regulatory and Signaling proteins: They include various Transcription factors: Proteins that help initiate
and regulate the transcription of DNA to RNA. Hormones: Regulate various physiological processes (insulin,
growth hormone, , thyroid hormones), Cytokines: Proteins that facilitate cell signaling in immune responses,
and Neurotransmitters: Transmit signals between nerve cells.
5. Transport Proteins: Involved in the bind & carry of substances. e.g. Serum albumin (calcium, fatty acids,
hormones, and many drugs), Transferrin (Fe), Ceruloplasmin (Cu), and Hemoglobin (O₂ and CO₂).
6. Nutrient and storage proteins: They act as the store of metal ions and amino acids in the cells. e.g. Ferritin
(iron store), Ovalbumin-egg (amino acids storage), and Casein-milk (amino acids storage).
7. Defensive or Immune or Protective proteins: These defend against pathogens. e.g. Immunoglobulins or
Antibodies, Complement proteins, Clotting factors, Cytokines, and snake venom.
 2. Classification based on the shape of protein molecule into 3 groups:
A. Fibrous or Scleroproteins: They are linear (long fibrous) in shape. These proteins typically
provide structural support and are generally insoluble in water; soluble in strong acids or
bases. Fibrous proteins have a secondary structure that is often predominantly helical or beta-
pleated sheet. Hydrolytic proteolytic enzymes are not able to digest fibrous proteins.
Examples of fibrous proteins: are collagen (The most abundant protein in mammals), keratin,
Elastin, myosin, actin, and fibrin.
B. Globular proteins: Spherical or globular; the polypeptide chain is tightly folded into a
compact shape. Tertiary structure is the most important functional structure in globular proteins.
They are generally soluble in water and play various roles, including enzymatic, transport, and
regulatory functions. Examples of globular proteins include hemoglobin, myoglobin,
immunoglobulins, amylase, pepsin, DNA Polymerase, and insulin.
C. Intermediate Proteins: Their structure is intermediate to linear and globular structures. They
are soluble in water. Function: blood clotting proteins Example: Fibrinogen.
 3. Classification based on composition and solubility
A. Simple proteins: are Composed of only amino acid residues, linked by peptide bonds. These
proteins yield only amino acids on their hydrolysis such as:
i. Albumins: These are soluble in water. They are coagulated by heat. They can be
precipitated by high salt concentrations. Examples: Serum albumin and ovalbumin (egg
white).
ii. Globulins: The globulins are a family of globular proteins that have higher molecular weights
than albumins and are insoluble in pure water but dissolve in dilute salt solutions. Globulins
can be coagulated by heat and precipitated using half-saturated salt solutions, allowing them
to be isolated from other proteins in the plasma. Examples are plasma globulin alpha, beta,
and gamma globulins.
iii. Histones. These are soluble in water. e.g. chromatin.
iv. Scleroproteins: Insoluble in water, such as collagen and keratin.
ii. Conjugated proteins (complex proteins): In these compounds the protein molecule remains
conjugated with another non-protein prosthetic group. This class includes the following:
i. Nucleoproteins: Prosthetic group is nucleic acid, Example- proteins in chromosomes e.g. nucleo-
histones, nucleo-protamines.
ii. Lipoproteins: Serum lipoproteins e.g. both low-density lipoprotein (LDL) cholesterol and high-
density lipoprotein (HDL) cholesterol.
iii. Glycoproteins: The prosthetic group is carbohydrate, which is less than 4% of protein, The term
mucoprotein is used if the carbohydrate content is more than 4%. Example- Most of the
membrane proteins, Mucin (component of saliva).
iv. Phosphoproteins: Phosphoric acid is the prosthetic group e.g. casein (milk).
v. Metalloprotein: proteins contain metal ions such as ceruloplasmin (Cu), carbonic anhydrase (Zn).
vi. Chromo protein: The prosthetic group is coloured in nature e.g. hemoglobin, cytochromes.
vii. Flavoproteins: Flavoprotein enzymes contain flavin mononucleotide (FMN) or flavin adenine
dinucleotide (FAD) as prosthetic groups. FMN and FAD are formed in the body from the vitamin
riboflavin.
C. Derived proteins:
• These are derivatives of proteins resulting from the action of heat, enzymes or chemical
reagents. This group also includes.
• Proteins derived from simple and conjugated proteins by physical or chemical treatment
(Hydrolyzed, degraded or denatured product of simple or conjugated protein). Examples:
Coagulated proteins, proteoses, peptones, peptides, etc..
Classification of Proteins Based on structure, Solubility and Composition
 Protein denaturation
• Protein denaturation results in the unfolding and disorganization of the protein’s secondary
and tertiary structures, especially the destruction of alpha-helix and beta sheets. However,
the primary structure of the protein remains even after the denaturation. The most common
observation when denaturing a protein is the precipitation or coagulation.
• Denaturing agents include heat, organic solvents, mechanical mixing, strong acids or bases,
detergents, and ions of heavy metals such as lead and mercury.
• Denaturation may, under ideal conditions, be reversible, in which case the protein refolds
into its original native structure when the denaturing agent is removed. However, most
proteins, once denatured, remain permanently disordered.
• Denatured proteins are often insoluble and, therefore, precipitate from solution.

• Protein hydrolysis refers to the conversion of proteins into their amino acids and peptides.
When protein is denatured it losses its function examples are:
• A denatured enzyme ceases/stops its function.
• A denatured antibody no longer binds to its antigen.
Unfolding of native proteins
• A denatured milk proteins losses its biological activity.

❖ In all cases there is breakage of hydrogen bonds, disulfide bonds, hydrophobic

interactions, Vander Walls forces but there is no breakage of peptide bonds during
denaturation.
 Native Conformation of Protein
• Central to understanding protein structure is the concept of the native
conformation, which is the functional, fully-folded protein structure (for
example, an active enzyme or structural protein).
• The unique three-dimensional structure of the native conformation is
determined by its primary structure, that is, its amino acid sequence.
Interactions between the amino acid side chains guide the folding of the
polypeptide chain to form secondary, tertiary, and (sometimes)
quaternary structures, which cooperate in stabilizing the native
conformation of the protein. In addition, a specialized group of proteins
named “chaperones” is required for the proper folding of many species
of proteins.
 CHAPERONES
Chaperones or Heat shock proteins (Hsps) are evolutionarily ancient and extremely conserved
proteins found in almost all living organisms. These proteins are present in several intracellular
locations, e.g., in the nucleus, mitochondria, endoplasmic reticulum (ER), and chloroplast and
cytosol of eukaryotes.
 Role of chaperones in protein folding
Chaperones or Hsps plays a key role in cellular processes that occur during and after exposure
to oxidative stress that is caused by hazardous environmental and/or microbial agents. Hsps can
intervene following oxidative stress at several levels:

• Firstly, some Hsps, play a crucial role in protein sorting and quality control via selecting and
directing abnormal proteins to the lysosomes for degradation; thus, Hsps aid the clearance of
damaged proteins.

• In some cases, where misfolded proteins need to be rescued, the same machinery facilitates the
correct folding of damaged proteins.

• Moreover, the Hsp families, can negatively regulate apoptosis via the binding and inhibiting of
members of the apoptotic cascade.

• Some Hsps have immuno-enhancing actions.

Protein misfolding refers to the process where proteins fail to assume their correct three-
dimensional (3D) structures after synthesis. This incorrect folding can lead to various structural
conformations that are typically non-functional and may aggregate into larger structures. These
aggregates are often insoluble and can manifest as amyloid fibrils, which are associated with
several neurodegenerative diseases
 Protein Misfolding
➢ Factors Contributing to Protein Misfolding
• Environmental stress: Factors like heat, oxidative stress, and exposure to toxic substances can disrupt
the delicate balance required for proper protein folding.
• Cellular imbalances: Changes in pH, ion concentration, or the presence of molecular chaperones can
influence protein folding.
• Genetic mutations: Changes in the DNA sequence can lead to the production of proteins with altered
amino acid sequences, affecting their ability to fold correctly.

➢ Protein misfolding and aggregation are implicated in a wide range of diseases, including:
Neurodegenerative diseases: Alzheimer's, Parkinson's, Huntington's disease
• Amyloidoses: A group of diseases characterized by the deposition of amyloid fibrils, including type 2
diabetes, and certain forms of arthritis
 Protein Misfolding
• Prion diseases: Prions are misfolded versions of a normal protein found in the brain. These abnormal
proteins have the ability to induce normal proteins to misfold as well, creating a chain reaction that leads
to the formation of protein aggregates. These aggregates damage brain cells, causing the characteristic
symptoms of prion diseases.

• Normal and abnormal form of prion protein:

Normal prion protein has amino acids in α- helix
with less than 5% of β- sheets. Abnormal prion
protein is a misfolded protein, where majority of
alpha helices are converted into β- sheets resulting
in more than 50% of β- sheets.

• Prion diseases are transmissible neurodegenerative conditions that include Creutzfeldt-Jakob disease
(CJD) in humans and bovine spongiform encephalopathy (BSE) and scrapie in animals.
 Digestion and Absorption of Proteins
• Most of the dietary N₂ is consumed in the form of protein.
• Proteins are generally too large to be absorbed. They must, therefore, be hydrolyzed to yield
their constituent amino acids, which can be absorbed.
• Proteases (hydrolysis enzymes) are synthesized by 3 different organs of Gastrointestinal tract
lumen (GIT lumen), : the stomach, pancreas, and small intestine.
• Protease enzymes are synthesized as inactive precursors called a zymogen (or proenzyme),
that are subsequently activated.
• Note: Proteases and phospholipases (but not lipases and glycosidases) are dangerous
digestive enzymes. Must be kept chained and muzzled until they reach the Gastrointestinal
tract lumen (GIT lumen), Otherwise, they attack proteins and membrane lipids in the cells of
their birth and cause auto-digestion.
acts on the C- terminal peptide bond connected to Hydrophobic aa

and leu

and ser
 Digestion of Proteins
• In the Stomach, Gastrin (hormone) stimulates parietal cells to secrete HCI &
chief cells secrete pepsinogen.
• Gastric HCI denatures proteins & active (convert of Pepsinogen to pepsin).
• Pepsin acts as an endopeptidase active and is able to hydrolyze the peptide
bond in protein and convert it to peptide chains.
• In the Small intestine, HCO3‾ neutralizes HCl, and the pancreas secretes
several pancreatic proteases of inactive (proenzymes or zymogens), which, when
activated, collectively digest peptides to single amino acids, di- & tri-peptidase.
• Brush Border Proteases (Enterokinase & Aminopeptidase):
• Enteropeptidase, also known as enterokinase, is a crucial brush border enzyme
secreted by the enterocytes located in the intestinal mucosa of the duodenum. ,
This enzyme plays an essential role in protein digestion by activating
trypsinogen, which is secreted from the pancreas. Upon its conversion into the
active enzyme trypsin, it initiates a cascade of proteolytic enzyme activation,
aiding in the breakdown of dietary proteins into smaller peptides and AAs.
• Aminopeptidases, located on the brush border, cleave one amino acid at a time
from the amino end of peptides. Intracellular peptidases act on small peptides
that are absorbed by the cells.
The relationship between pepsin and pepsinogen:
Pepsinogen is a protein secreted by the chief cells of the stomach. It's the precursor of
the enzyme pepsin. Gastric HCl removes some of the amino acids from the pepsinogen,
converting it to pepsin. Once some pepsin is formed, it acts not only to digest dietary protein
but also acts on pepsinogen to create more pepsin—an autocatalytic effect.

Pepsin works best at a pH of 2.

And as the stomach has a very
acidic condition, pepsin works
well. But in the small intestine, the
pH is about 8, which is too high
for pepsin to function. Therefore,
pepsin gets denatured in the
small intestine.
• Free amino acids:
• Most AAs are absorbed into the bloodstream, but some remain in the enterocytes and are used to support the cells.
• Di- and tripeptides are absorbed more rapidly than AAs, due to Active transporter & Coupled to a sodium-hydrogen
exchanger.
• They are transported into the intestinal cells (enterocytes) via a specific carrier protein called PepT1. This process is
coupled with the transport of H+, making it an active transport mechanism.
• PepT1 (proton-coupled transporter)-Transported into enterocyte, then hydrolyzed to AAs.
Summary of protein digestion and absorption
 Major epithelial amino acid transporters
• Amino acid transporters and associated disorders:
Absorbed as amino acids across the gut lumen with a
specific transporter for difference classes of amino acids.
Four different amino-acid-urias can be discriminated:
(i) Cystinuria, a Decreased intestinal absorption &
transport of cationic or dibasic AA (lysine, arginine), and
cystine- defect in SLC3AI transporter;
(ii) Hartnup disorder, a defect of apical transport of
neutral amino acids (i.e. tryptophan)- Mutation in
SCL6A19 transporter);
(iii) iminoglycinuria, a defect affecting uptake of
proline and glycine; and
(iv) dicarboxylic aminoaciduria, a defect of anionic
amino acid transport.

It can be concluded from these defects that there are at least four major transport systems for proteinogenic AAs in the
intestine and kidney.