PROTEINS

COLLEGE OF MEDICAL TECHNOLOGY

LECTURE

OBJECTIVES
The students would be able :
1. to describe and recognize amino acids structures and illustrate how they are connected in
proteins.

2. to describe how the properties of amino acids depend on their side chains and how their
ionic charges vary with pH.

3. to define protein primary structure, explain how primary structures are represented, and
draw a simple protein structure, given its amino acid sequence.

4. to explain what is responsible for handedness and recognize simple molecules that display
this property.

5. to describe and recognize disulfide bonds, hydrogen bonding along the protein
backbone, and noncovalent interactions between amino acid side chains in proteins.

6. to be able to define these structures and the attractive forces that determine their
nature , describe the lpha helix and -sheet, and distinguish between fibrous and
globular proteins.

7.to be able to define quarternary structures and give examples .

8. to describe protein hydrolysis and denaturation , and give some examples of
agents that cause denaturation.

 Biochemical reactions must continuously break down food molecules, generate

energy and store energy, build up new molecules, and eliminate waste.

Each biomolecule has a role to play in these processes.

All the principles of chemistry introduced thus far apply to biochemistry.
Functional Groups are of greatest importance in biomolecules.

PROTEINS
Large biological molecules made of many amino acids linked together
through amide (peptide) bonds.

Two or more amino acids can link together by forming amide bonds.
Dipeptide results from the formation of a peptide bond between the
NH2 group of one amino acid and the COOH group of a second
amino acid.

FUNCTIONAL GROUPS
Amino group -NH3 ; -NH2
Hydroxyl group -OH

Carbonyl group - C=O

Carboxyl group - COOH
Amide group

- CN=O

Carboxylic acid ester - C=OOR

Phosphates PO2 ;PO3;

Hemiacetal group

- C-OH

Acetal - C -OR
l

OR

OR

DEFINITIONS:
Amino acid molecule that contains both an amino group and a carboxylic
acid group

Alpha amino acid amino acid in which the amino group is bonded to the C
atom next to the COOH group.

Side chain group bonded to the C next to the carboxyl group in an amino
acid

Zwitterion a neutral dipolar ion that has one + charge and charge.

POLYMERS OF AMINO ACIDS

Every amino acid in a protein contains an amine group(NH2), a
carboxyl group, and an R group.

R groups may be hydrocarbons, or may contain a functional group.

Alpha amino acids the amine group is connected to a C atom
connected to the carboxylic acid group.

Peptide bond an amide bond that links two amino acids together.

 Intermolecular forces are of central importance in determining the

shape and functions of proteins.

Covalent act between organic compounds

Noncovalent act between different molecules or between
different parts of the same large molecule

 Hydrophobic water fearing; a hydrophobic substance does not

dissolve in water

Hydrophilic water loving; a hydrophilic

substance dissolves in

water

Isoelectric point the pH at which a sample of an amino acid has

equal numbers of + and - charges

AMINO ACIDS
Non polar side chain
Polar, neutral Side chains
Acidic Side chains
Basic Side chains

NONPOLAR SIDE CHAINS

Alanine
Glycine
Isoleucine
Leucine
Methionine
Phenylalanine
Proline
Tryptophan
Valine

POLAR, NEUTRAL SIDE CHAINS

Asparagine
Cysteine
Glutamine
Serine
Threonine
Tyrosine

ACIDIC SIDE CHAINS

Aspartic acid
Glutamic acid

BASIC SIDE CHAINS

Arginine
Lysine
Histidine

AMINO ACIDS: NATURE

Nature uses the 20 alpha amino acids to build the proteins in all
living organisms.

19 of them differ only in the identity of the R group

Classified according to their acidity and basicity.
Classified as nonpolar side chains and polar side chains.(15 )

PROPERTIES OF AMINO ACIDS

Amino acid contain both an acidic group, COOH, and a
basic group, -NH2.

These groups can undergo intramolecular

acid-base

reactions.

Dipolar ions are known as zwitterions, which allows many

physical properties (salts).

Can form crystals . ( pure form)

Have high melting points.
Soluble in water

ESSENTIAL /NONESSENTIAL AMINO ACIDS

ESSENTIAL AMINO ACIDS - Cannot be synthesized by the

body and must be obtained from the diet

NON ESSENTIAL AMINO ACIDS can be synthesized by

the body

TWO NEW AMINO ACIDS

Selenocysteine (Sec) ;21st

amino acid; it is not coded directly in the genetic

code
Sec encoded by a UGA codon, stop codon; has a specialized tRNA;
present in formate dehydrogenase, glycine reductase

Pyrrolysine (Pyl) ; 22nd amino acid; genetically encoded used by archaea in

enzymes that are part of their methane-producing metabolism

AMINOACIDOPATHIES
Class of inherited errors of metabolism in which there is an enzyme defect that inhibits the bodys ability to
metabolize certain amino acids

Exist : 1. in the activity of specific enzyme in the metabolic pathway

2. in the membrane transport system for amino acids

Phenylketonuria

Tyrosinemia
Alkaptonuria
MSUD Maple Syrup Urine Disease

Other Examples of Aminoacidurias:

Isovaleric Acidemia
Homocystinuria
Citrullinemia
Arginosuccinic Aciduria
Cystinuria

HANDEDNESS
Chiral having right or left handedness; able to have two
different mirror image forms

Mirror image If you hold your left hand up to a mirror, the

image you see looks like your right hand.

Superimposable It is easy to mentally place the chair on

top of its mirror image.

Achiral having no right or left handedness and no non

superimposable mirror image

CHIRALITY
Alanine chiral molecule
Its mirror images cannot be superimposed on each other.
Result: it exist in two different forms that are mirror images
of each other.

D- alanine & L-alanine ( enantiomers or optical isomers )

Propane achiral molecules
Stereoisomers compounds with same formula and atoms
with same connections but different spatial arrangements

LEVELS OF STRUCTURE

Primary
Secondary
Tertiary
Quarternary

LEVELS OF STRUCTURE: PROTEINS

Primary structure -Sequence of amino acids in a protein chain
Secondary structure Regular and repeating spatial organization of
neighboring segments of protein chains

Tertiary structure Overall shape of

a protein molecule produced by regions

of secondary structure combined with the overall bending and folding of the
protein chain

Quarternary structure Overall structure of proteins composed of more than

one polypeptide chain

PRIMARY STRUCTURE
Sequence in which its amino acids are lined up and connected by
peptide bonds.

Backbone of protein is a chain of alternating peptide bonds.

Amino terminal amino acid free NH3 group at the end of a protein
Carboxyl- terminal amino acid free carboxyl group at the end of a
protein

 Zwitterions give amino acids many physical properties.

Pure amino acids :
A. can form crystals.
B. high melting points
C. Soluble in water
D. Insoluble in non polar solvents

CHARGE OF AMINO ACIDS

Depends on the following:
1. Structure of amino acids
2. pH of medium
Isoelectric point pH at which the net positive and negative charges
are evenly balanced (pI)
* At this point , the overall charge of all the amino acids in

INTERACTION: DETERMINE THE SHAPE

Structure function relationship , depends on the polypeptide chain
being held

1.
2.
3.
4.
5.

Hydrogen bonds along the backbone

Hydrogen bonds of R groups with each other or with Backbone atoms

Ionic attractions between R groups

Hydrophobic interactions between R groups
Covalent Sulfur-Sulfur bonds

SECONDARY STRUCTURE
Includes two repeating patterns:
a. alpha helix
b. Beta sheets
Hydrogen bonding between backbone atoms holds the polypeptide chain in place
Connects the carbonyl oxygen atom of one peptide unit with the amide hydrogen of
another peptide unit

The repeating patterns arranged in loops and coils in random

ALPHA - HELIX
Single protein chain coiled in a spiral with a right handed (clockwise)
twist

Resembles a phone cord, stabilize by hydrogen bonds between peptide

groups along its backbone

Secondary structure

BETA SHEET
Protein chains in the same or different molecules
Secondary structure
Held in place by hydrogen bonds along the backbones
Stack pleated sheets allow R groups above and below the sheets

SECONDARY : FIBROUS AND GLOBULAR

Fibrous proteins tough, insoluble; wool, hair, fingernails alpha
keratins

Hardness, flexibility, and stretchiness varies with the number of

disulfide bonds

Composed of alpha helices

Examples: Keratins, Elastin , Myosin, Fibrin

 Keratins found in skin, wool, feathers, hooves, silk, fingernails

Collagen found in animal hide, tendons, bone, eye cores, and
connective tissues

Myosins found in muscle tissues

Fibrin found in blood clots

 Globular proteins water soluble protein whose chain is

folded in a compact shape with hydrophilic groups on the
outside

Water loving outside accounts for their side chains

Tertiary structure
Examples: Insulin, Ribonuclease, Immunoglobulins,
Hemoglobin, Albumins

 Ribonuclease enzyme that catalyzes RNA hydrolysis

Insulin regulatory hormone for controlling glucose
metabolism

Immunoglobulins proteins involved in immune response

Hemoglobin protein involved in oxygen transport
Albumins proteins that perform many transport functions in
blood; protein in egg white

TERTIARY STRUCTURE
over-all three dimensional shape that results from the
folding of a protein chain

Depends mainly on interactions

of amino acid side chains

that are far apart along the same backbone.

Noncovalent interactions and disulfide covalent bonds

Native protein with the shape (secondary, tertiary,
quarternary) in which it exists naturally in living organisms

CONJUGATED PROTEINS
Glycoproteins CHO; found in cell membranes
Lipoproteins Lipid; HDL,LDL,VLDL, chylomicrons
Metalloproteins Metal ions; cytochrome oxidase
Phosphoproteins Phosphate groups; milk casein
Hemoproteins Heme ; Hemoglobin, myoglobin
Nucleoproteins RNA; found in cell ribosomes

QUARTERNARY STRUCTURE
Final level of protein structure; most complex
Two or more polypeptide subunits form a single-three
dimensional protein unit

Held together by noncovalent forces and covalent forces

Hemoglobin composed of four polypeptide chains( 2
alpha chain and 2 beta chain)

Collagen most abundant of all proteins in mammals;

fibrous ; major constituent of skin, tendons, bones, blood
vessels, and other connective tissues

METHODS: ANALYSIS
1. Fractionation
2. Identification
3. Quantitation
Salt Fractionation
Electrophoresis
Immunochemical

SALT FRACTIONATION
Done by using precipitation reactions
Globulins are separated from albumins by salting out
Sodium salts are used to precipitate globulins.
Not used since direct methods are available.

IMMUNOCHEMICAL METHODS
Specific proteins are identified with antigen antibody reactions
Modified radial immunodiffusion (RID)
Immunoelectrophoresis (IEP)
Immunofixation (IFE)
Immunoturbidimetry
Immunonephelometry

PROTEIN ANALYSIS: ELECTROPHORESIS

Protein molecules an be separated by their positive and negative
charges.

Between electrodes, a positively charged particle

will moves toward

the negative electrode and the negatively charged particle will move
towards the positive electrode.

The overall positive and negative

charge of a protein is determined

by how many of the acidic or basic side chain functional groups in the
protein is ionized.

By changing the medium, proteins can be separated by their

molecular weight.

CHEMICAL PROPERTIES OF PROTEINS

1. Protein Hydrolysis

2. Protein Denaturation
a. Heat
b. Mechanical agitation
c. Detergents
d. Organic compounds
e. pH change

f. Inorganic salts

CLASSIFICATION OF PROTEINS :FUNCTIONS

Catalyze reactions -Enzymes
Regulatory - Hormones
Storage proteins - Ferritin
Transport proteins - Hemoglobin
Structural proteins - Cytoskeleton
Protective proteins - Antibodies
Contractile proteins Myosin ,Actin

SIGNIFICANCE OF PROTEINS
All biochemical reactions are catalyzed by enzymes, which contain protein.
The structure of cells and the extracellular matrix that surrounds all cells is
largely made of the protein group collagens. Collagens are the most
abundant protein in the human body.

The transport of materials in body fluids depends on proteins such as

transferrin , receptors for hormones .

FUNCTIONS OF PROTEINS
Energy tissue nutrition
Osmotic force maintenance of water distribution between cells and tissues, interstitial compartments, and the
vascular system of the body

Acid base balance participation as buffers to maintain pH

Transport metabolic substances
Antibodies part of immune defense system

Structure connective tissue

Enzymes catalysts
Hemostasis participation in coagulation of blood

ENZYMES
Catalysts for biochemical reactions
Reactions begin with the migration of the substrate or
substrates into the active site to form ESC.

Formation of new bonds , second substrate with atoms in the

enzyme.

Active sites can provide acidic or basic groups without

change in the pH of the environment.

Enzyme and product molecules separate

from each other.

 Enzymes are mostly

water soluble.

Many enzymes incorporate co factors.( Can either be a metal ion

or a non protein organic molecules Zn, Mn, Cu, Cr, etc.)

Enzymes are globular proteins.

FACTORS : AFFECT ENZYME ACTIVITY

1. Substrate concentration
2. Enzyme concentration
3. Temperature
4. pH of the medium pH 5-9
5. Feedback

TERMS:
Feedback Control regulation of an enzyme s activity by the product
of a reaction later in a pathway

Allosteric control an interaction in which the binding of a regulator at

one site on a protein affects the proteins ability to bind another
molecule at a different site

Allosteric enzyme enzyme whose activity is controlled by the binding

of an activator or inhibitor at a location other than the active site

HYPOPROTEINEMIA
Occurs in condition where a negative nitrogen balance exist.
Total protein level less than the reference interval.
Can be cause by excessive loss by excretion in the urine in renal disease , or
leakage in the GI due to inflammation , excessive bleeding (internal or open
wound)

HYPERPROTEINEMIA
Occurs when there is an underlying cause e.g. dehydration
When excess water is lost from the vascular system, the proteins, remain within the
blood vessels.

Dehydration can be cause:

1. Vomiting
2. Excessive sweating
3. Diabetic acidosis
4. hypoaldosteronism

TOTAL PROTEIN METHODS: PRINCIPLES

Kjeldahl Digestion of protein; measurement of nitrogen content
Refractometry Measurement of the relative index due to solutes in serum
Biuret Formation of violet-colored complex chelate between Cu ions and
peptide bonds

Dye Binding Protein binds to dye and causes a spectral shift in the
absorbance maximum of the dye

ENZYME REGULATION
Reversible Noncompetitive Inhibition an inhibitor binds to an
enzyme elsewhere than at the active site ( reduce activity)

Reversible Competitive Inhibition- an inhibitor competes with a

substrate for binding to the enzyme active site

Irreversible Inhibition enzyme deactivation in which an inhibitor

forms covalent bonds to the active site , permanently blocking it.

CLASSIFICATION:FUNCTIONS
1.Hydrolases
2.Oxidoreductases
3. Lyases
4. Ligases
5. Isomerases
6. Transferases

CHEMICAL MESSENGERS
HORMONES controls our vital function; chemical messengers
secreted by cells of the endocrine system

Via bloodstream
Via neurotransmitters released by nerve cells
Chemical receptors molecule or portion of a molecule

which connects

to initiate a response in a target cell.

Neurotransmitter a chemical messenger that travels between a

neuron and a neighboring neuron or other target cells to transmit a
nerve impulse

AMINO ACID DERIVATIVES

Epinephrine
Norepinephrine
Thyroxine
Epinephrine
SOURCE: adrenal medulla , thyroid gland
TARGET: Most cells

MECHANISMS OF ENZYME CONTROL

1. Feedback - reactions with reactants, by allosteric control ( bonding

alter shape- efficiency)

2. Inhibition REVERSIBLE occur away from the active site(Non

Competitive); COMPETITIVE (at the active site)

iRREVERSIBLE covalent bonding is involved

3. Production of inactive enzymes must be activated by cleaving the
portion of the molecule

4. Covalent modification of the enzyme by addition or removal of a

phosphoryl group

5. Genetic control regulation of enzyme activity by control of the synthesis

of enzymes

ENZYME INHIBITORS AS DRUGS

Chemical structures of substrates and the active sites are
known, drug designers can create a molecule that is similar
to the substrate.

ACE Inhibitors Angiotensin Converting Enzyme

Angiotensin II - potent pressor
- elevates blood pressure; contracts
blood vessels
Angiotensin I inactive precursor of Angiotensin II; 2
amino acids must be cut off to be active ( His and Leu)

ENZYME INHIBITORS: AIDS

AZT azidothymidine; Zidovudine

AIDS fighting drugs
AZT is accepted by HIV enzyme, it prevents the virus
from producing duplicate copies of itself.

 Ritonovir
Protease inhibitor
Dramatic decrease in the virus population
Success includes a cocktail of drugs with AZT
Expensive Cocktail of drugs (20 pills/day)