Tishk International University

Faculty of Science

Department of Medical Analysis

General and systemic Biochemistry

Protein

Dr. Rundk A. Hwaiz

Grade 2-Fall 2020-2021

Dr. Rundk A. Hwaiz

Lec2

Nutritional classification:

1- Essential amino acids: These amino acids can’t be formed

in the body and so, it is essential to be taken in diet. Their

deficiency affects growth, health and protein synthesis.

2- Semiessential amino acids: These are formed in the body

but not in sufficient amount for body requirements especially

in children.

Summary of essential and semiessential

amino acids: valine, isoleucine, lysine, leucine, arginine*,

histidine*, methionine, tryptophan, threonine, phenyl alanine

*= arginine and histidine are semiessential

3- Non essential amino acids: These are the rest of amino acids

that are formed in the body in amount enough for adults and

children. They are the remaining 10 amino acids.

Metabolic classification: according to metabolic or

degradation products of amino acids they may be:

1- Ketogenic amino acids: which give ketone bodies . Lysine

and Leucine are the only pure ketogenic amino acids.

2- Mixed ketogenic and glucogenic amino acids: which give

both ketonbodies and glucose.

These are: isoleucine, phenyl alanine, tyrosine and tryptophan.

3- Glucogenic amino acids: Which give glucose. They

include the rest of amino acids.

These amino acids by catabolism yields products that enter in

glycogen and glucose formation.

Amphoteric properties of amino acids: that is they have both

basic and acidic groups and so can act as base or acid. Neutral

amino acids (monobasic, monocarboxylic) exist in aqueous

solution as “ Zwitter ion” i.e. contain both positive and

negative charge.

Proteins and peptides are polymers made up of

amino acid units (residues) that are linked together through the

formation of amide bonds (peptide bonds) from the amino

group of one residue and the carboxylate of a second

residue.

A peptide or polypeptide has two different ends. The amino

terminal (N-terminal) is the amino group while the

carboxyl terminal (C-terminal) is the carboxyl group. The

order of amino acids from N-terminal to C-terminal is the

primary structure of the protein.

In a peptide, the amino acids are written from left to right

with the (NH3+) group on the left and (COO-) group on the

right.

The left hand amino acid is called the N-terminus and the

right hand amino acid is called the C-terminus.

▫ 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, consisting of

one or more polypeptide chains. Consist of

polypeptides with more than 50 A.A.

• Write three-letter abreviations and names of tripeptides that

could form from two glycine and one alanine.

Glycine glycine alanin Gly-Gly-Ala

Glycine alanine glycine Gly-Ala-Gly

Alanine glycine glycine Ala-Gly-Gly

What is the possible tripeptides formed from one each of

leucine, glycine and alanine?

Luc-Gly-Ala

Leu-Ala-Gly

Ala-Gly-Leu

Ala-Leu-Gly

Gly-Ala-Leu

Gly-Leu-Ala

Protein Structures

1. Primary structure

2. Secondary structure

3. Tertiary structure

4. Quarternary structure

Primary structure

1. Protein primary structure is the linear sequence of amino

acids in a peptide or protein.

2. The amino acids in the primary structure are held

together by covalent bonds, which are made during the

process of protein synthesis.

A peptide or polypeptide has two ends. The amino terminal

(N-terminal) is the amino group (on the first amino acid in the

chain) while the carboxyl terminal (C-terminal) is the carboxyl

group on the last amino acid in the peptide.

The order of amino acids from N-terminal to C-terminal is the

primary structure of the peptide or protein.

Secondary structure

1. α-helix is a right-twisted helical structure

2. The structure allows hydrogen bonds between the amide

proton and the carbonyl acid in the peptide bond to be

formed.

3. The hydrogen bond is formed between the amide proton

of an amino acid and the carbonyl acid of the other amino

acid.

1. A β-strand is an extended structure.

2. Two or more β-strands may be adjacent to each other,

thereby forming a β-sheet which is held together with

hydrogen bonds between the amide proton in one β-

strand and the carbonyl acid in another β-strand.

β-sheet

B-sheet

Tertiary structure

1. The final structure that a protein forms depends on which

amino acids are included in the primary structure. Through

the hydrophobic effect, the protein is folded so that unpolar

amino acids are placed inside the protein without contact

with the surrounding water. By folding, polar side chains

will be placed on the surface, making the protein water-

soluble.

2. The structure formed is stabilized by hydrogen bonds,

ionic bonds, van der Waals interactions and disulfide

bonds between the amino acid side chains.

Quarternary structure

Some proteins consist of several parts (subunits) and therefore

have an additional structural level. The quaternary structure

describes how these individual parts relate to each other in

space.

An example of a protein with quaternary structure is

hemoglobin.

1. The primary structure contains all the information needed

to properly fold a protein.

2. If you destroy the structure and denture the protein (with

heat, acid or otherwise) while reducing all the disulfides,

you get a completely unfolded protein chain. If you then

lower the temperature or remove the agent that caused

the denaturation, the protein will be folded back to its

normal structure.

Native Structure

Sometimes the use of special proteins, called chaperones

("aprons"), is necessary for the folding to occur properly and

for the protein to become functional.

CHAPERONES are special proteins which only helps

proteins to fold into correct conformation, The chaperones

need energy to carry out the process. ex. heat shock protein (hsp)

A real protein

The oxygen we breathe is transported with the blood bound to

the protein hemoglobin which brings it to the various tissues

that need the oxygen. On the way back to the lungs,

hemoglobin takes with it the carbon dioxide formed during

energy conversion. We have two proteins that take care of

oxygen: myoglobin that can store oxygen and hemoglobin

that transports it.

1. Hemoglobin consists of 4 polypeptides, or two pairs of

subunits. Each subunit contains a heme group that can bind

oxygen.

2. By putting together several subunits, you get a protein that

has a cooperative ability to bind oxygen. This property is

very valuable to us because it makes hemoglobin readily

bind to oxygen in the lungs and at the same time it binds

much worse when hemoglobin enters the tissue and

therefore easily loosens.

Hemoglobin

Summary

• Proteins are biological workhorses that carry out most

of the functions within the cell.

• Proteins are large biological molecules that serve

diverse functional and structural roles within cells.

• Proteins are synthesized during the translation

process.

• Proteins are composed of amino acids that are

covalently linked by peptide bonds.

• Proteins have four basic levels of structure. However,

proteins must fold correctly in order to function

properly.