Biomolecules

The Raw Materials of Biotechnology

The Molecules of Cells

Sardar Hussain,

asst.prof.Biotechnology,

Gsc.cta

[email protected]

Molecular/atoms lowest level of organization

Entire organism

System

Tissue

Cells

Organelle

Molecules

Atoms

Organic chemistry

Chemistry of Carbon

CHNOPS◦ Carbon

◦ Hydrogen

◦ Nitrogen

◦ Oxygen

◦ Phosphorus

◦ Sulfur

◦ Several Trace Minerals

Forms a bond with

4 other atoms in which

electrons are shared forming

a covalent compound

C

H

H C H

H CH4

H\

H C OH

HCH3OH

H H

H C C OH

H H

CH3CH2OH

O

H C H

CH2O

All are polymers

All are organic (C) compounds

Carbohydrates

Proteins

Lipids

Nucleic Acids

Differ in terms of composition and function

Carbohydrates……. Energy, support and recognition

Proteins……………..Enzymes, structure, recognition, transport pigments, signals, mov’t

Lipids………………..Cell membrane structure energy storage, signals cellular metabolism (VitK..)

Nucleic Acids……….Hereditary and protein information, energy, signals

Carbohydrates……. Polysaccharide..of simple sugars

Proteins……………..Polypeptide..of amino acids

Lipids………………..Insoluble in water..although common polymer glycerol and fatty acid

Nucleic Acids……….Polynucleotide..of

nucleotides

-OH Several OH (alcohol) groups

This group LOVES water

Makes sugars solids and water soluble

C=O C with a double bond to an oxygen

Aldehyde or ketone

Joins w/an –OH to form a cyclic structure

The resulting C (C-1) has OH/H

Position of OH determines further bonding

Open Chain Cyclic

Loss of H and -OH Loss of Water !!!!!

Lactose = Milk Sugar

Lactose = Glucose and galactose

Lactase = Enzyme that digests lactose

Most mammals express lactase only as juveniles

Adults are lactose intolerant

Once weaned = NO MILK!!!!!

Starch...bonds between glucose can be digestedAmylose=plant Glycogen =animal

Cellulose…bonds between glucose cannot be digested by mammals

Starch stores glucose molecules for energy

Amylose MaltoseAmylase

Maltose 2 Glucose

Maltase

Good for providing energy

Cellulose is a rigid molecule of support

Cellulose Cellobiose Cellulase

Cellobiose 2Glucose Cellobiase

Good for making paper

Chitin

Benedict's …Chemical test for reducing sugars

To test for the presence of monosaccharides and reducing disaccharide sugars

in food, the food sample is dissolved in water, and a small amount of Benedict's

reagent is added.

During heating in a water bath, which is usually 4-10 minutes, the solution

should progress in the colors of blue (with no glucose present), green, yellow,

orange, red, and then brick red or brown (with high glucose present).

Lugol’s …Chemical test for starchAn indicator test for the presence of starches

Reacts by turning a dark-blue/black.

Stain starches due to iodine's interaction with the coil structure of the

polysaccharide

A Deeper Look

Billiard Balls, Exploding Teeth, and Dynamite—The Colorful History of Cellulose

Although humans cannot digest it and most people’s acquaintance with cellulose is limited to comfortable cotton clothing, cellulose has enjoyed a colorful and varied history of utilization. In 1838, ThéophilePelouze in France found that paper or cotton could be made explosive if dipped in concentrated nitric acid. Christian Schönbein, a professor of chemistry at the University of Basel, prepared “nitrocotton” in 1845 by dipping cotton in a mixture of nitric and sulfuric acids and then washing the material to remove excess acid. In 1860, Major E. Schultze of the Prussian army used the same material, now called guncotton, as a propellant replacement for gunpowder, and its preparation in brass cartridges soon made it popular for this purpose. The only problem was that it was too explosive and could detonate unpredictably in factories where it was produced. The entire town of Faversham , England, was destroyed in such an accident. In 1868, Alfred Nobel mixed guncotton with ether and alcohol, thus preparing nitrocellulose, and in turn mixed this with nitroglycerine and sawdust to produce dynamite. Nobel’s income from dynamite and

also from his profitable development of the Russian oil fields in Baku eventually formed the endowment for the Nobel Prizes.

In 1869, concerned over the precipitous decline (from hunting) of the elephant population in Africa, the billiard ball manufacturers Phelan and Collander offered a prize of $10,000 for production of a substitute for ivory. Brothers Isaiah and John Hyatt in Albany, New York, produced a substitute for ivory by mixing guncotton with camphor, then heating and squeezing it to produce celluloid. This product found immediate uses well beyond billiard balls. It was easy to shape, strong, and resilient, and it exhibited a high tensile strength. Celluloid was used eventually to make dolls, combs, musical instruments, fountain pens, piano keys, and a variety of other products. The Hyatt brothers eventually formed the Albany Dental Company to make false teeth from celluloid. Because camphor was used in their production, the company advertised that their teeth smelled “clean,” but, as reported in the New York Times in 1875, the teeth also occasionally exploded!

Portions adapted from Burke, J., 1996. The Pinball Effect: How Renaissance Water Gardens Made the Carburetor Possible and Other Journeys Through Knowledge. New York: Little, Brown, & Company.

Biomolecule Role in Cell Monomer DistinguishingFeatures

Carbohydrate Energy/Support Monosaccharide

•C=O, OH group

•Substitute -OH•The way they

are connected

Proteins (also known as polypeptides) are organic compounds made of amino acids.

Proteins are essential parts of organisms

Proteins participate in virtually every process

within cells.

Proteins make up half the dry weight of an Escherichia coli cell (other macromolecules such as DNA and RNA

make up only 3% and 20%, respectively).

Proteins have diverse functions due to their ability to bind other molecules specifically and tightly

Structural…. Bones,skin, nails, hooves, hair

Enzymatic… Digest sugar, makes DNA, makes fatty acids

Transport… Carries oxygen and fats in blood, Ca2+/Cl-

Contractile.. Muscles for movement, move chromosomes

Hormone…. regulate blood sugar, increase heart rate

Immunity... Antibodies fight foreign substance

Pigment….. Pigment in skin, eyes

Recognition. On cell surfaces—Other molecules (receptors)

Toxins…… Stops nerve transmission, effects movement of

ions, enzymes that destroy red blood cells

Polymer of many amino acids

Amino Acid

H O

H N C C OH

H R

Central Carbon

R group

Twenty different amino acid are found in proteins

Most microorganisms and plants can biosynthesize all 20

Animals (including humans) must obtain some of the amino acids from the diet.

The amino acids that an organism cannot synthesize on its own are referred to as essential amino acids.

Humans require 8 essential amino acids

Also called a condensation reaction

An octapeptide

The order in which

amino acids are bonded is called the sequence

The sequence of amino acids determines the primary structure of a protein

Determined by the genetic code (sequence of DNA)

Some amino acid groups are attracted to each others

Some amino acid groups are repelled by each other

http://www.biog1105-1106.org/demos/105/unit1/proteinstructure.html

http://www.biog1105-1106.org/demos/105/unit1/proteinstructure.html

Amino acid groups determine the overall shape of protein

Proteins are not long straight molecules, but are usually folded into a 3-D shape

Structural proteins confer stiffness and rigidity to otherwise-fluid biological components.

Most structural proteins are fibrous proteins.

Polymerize to form long, stiff fibers that comprise the cytoskeleton, which allows the cell to maintain its shape and size

http://en.wikipedia.org/wiki/Polymer

http://en.wikipedia.org/wiki/Cytoskeleton

Central Dogma of Molecular Biology

DNA

RNAmRNA to be exact

Protein

Angelman’s Syndrome Color Blindness Cystic Fibrosis Duchenne muscular dystrophy Hemophilia Sickle Cell Disease Tay Sacs Phenylketonuria Ataxia telangiectasia Gaucher disease Amyotrophic lateral sclerosis Parkinson Disease Huntington Disease Alzheimer Disease Cancer (Breast, Colon, etc.. And the list goes on and on and on

Gene Expression

DNATranscription

RNAmRNA to be exact

Translation

Protein

Regulation of transcription determines genes expressed (and proteins produced)

Shortly after or even during synthesis, the residues in a protein are often chemically modified by post-translational modification

Alters the physical and chemical properties, folding, stability, activity, and ultimately, the function of the proteins.

Biuret test Other Tests

Chemical test used for detecting the presence of peptide bonds.

In a positive test, a copper(II) ion is reduced to copper(I)

Forms a complex with the nitrogen and carbon of the peptide bonds in an alkaline solution.

A violet color indicates the presence of proteins

Alternative protein assays include:◦ UV spectroscopy

◦ Lowry protein assay

◦ Bicinchoninic acid protein assay (BCA)

◦ Amido black protein assay

Venom released by the brown recluse spider contains a complex collection of enzymes. Primarily protein-based, the brown recluse spider's venom has antigenic and locally destructive properties. Among other subcomponents, esterases, hyaluronidases and proteases have been isolated from recluse spider venom through various purification techniques. Of these, Sphingomyelinase-D has been identified as the primary substance with a toxic effect on red blood cells.

Sphingomyelinase-D directly causes hemolysis, which damages red blood cell walls and leads to the leakage of the red, oxygen-bearing protein known as hemoglobin. Anemia may result. After red blood cell casts are discarded, they are filtered through the kidneys and can cause renal failure.

Brown recluse venom triggers the aggregation of platelets and endothelial swelling in order to combat harm caused to red blood cells. White blood cells are brought to the area of the injury. However, instead of forming blood clots where needed, these white blood cells form blood clots in capillaries, resulting in necrosis.

Biomolecule

Role in Cell Monomer DistinguishingFeatures

Test

Carbohydrate

Energy/Support

Mono-saccharide

•C=O, OH group


are connected

Benedict’sTest

Lugol’sTest

Protein Regulation/support

AminoAcid

Central C w/H-NH2

-COOHR groups

BiuretReagent

Sometimes used as a synonym for fats

Fats are a subgroup of lipids called triglycerides

Lipids are defined as molecules that are hydrophobic or amphiphilic◦ Hydrophobic..they don’t dissolve in water

◦ Amphiphilic nature = some lipids form structures such as vesicles, liposomes, or membranes in a water environment

Broad group of molecules that includes:

Fats Waxes

Sterols

Fat-soluble vitamin(such as vitamins A, D, E and K),

Monoglycerides,

Diglycerides,

Phospholipids,

and others.

The main biological functions of lipids include:

Energy storage

Structural components of cell membranes

Important signaling molecules.

They Don’t like water…They Don’t like water..They don’t like water

Made of mostly C-H

Some oxygen

Some phosphorus

Might see nitrogen

Made of mostly C-H

That’s why they are hydrophobic

Triglycerides

Phospholipids

Steroids

Remember …mostly carbon and hydrogen!

Animal fat and plant oils

Energy storage molecules

Composed of glycerol and fatty acids

Saturated fats..All C-C single bonds

Molecules pack together well—a solid –or fat--at room temperature

Unsaturated fats..A few to many C = C double bonds

Molecules don’t pack together—a liquid—or oil—at room temperature

Phosphate = polar head

Found primarily in cell membranes

Similar to triglycerides except…these have a phosphate group

Makes the molecule capable of interactions with water

Phosphate = A negative charge

Hydrophilic-phosphate (head)

Hydrophobic-fatty acid (tail)

Make membrane bilayer in water environment (like the cell)

Overlapping rings of C-H

Complex molecules with many functions◦ Horomone

◦ Pigments

◦ Vitamins

◦ Cholesterol one of most important

Testosterone

Grease-spot test for lipids has been used for centuries.

Produce a translucent stain on paper or fabric

Consists of sodium or potassium salts of fatty acids

Made by reacting common oils or fats with a strong alkaline solution (the base, NaOH) in a process known as saponification.

The fats are split from glycerol by the base, yielding alkali salts of fatty acids (crude soap) and glycerol

https://anitagrant.com/images/stories/ingredients/SiteUpdates/SAPprocess.gif

https://anitagrant.com/images/stories/ingredients/SiteUpdates/SAPprocess.gif

Biomolecule


Test

Carbohydrate

Energy/Support

Mono-saccharide

•C=O, OH group


are connected

Benedict’sTest

Lugol’sTest


AminoAcid

Central C w/H-NH2

-COOHR groups

BiuretReagent

Lipids EnergySupportSignaling

Glycerol and fatty acids?Cholesterol

Mostly C-H

Insoluble in waterGrease spot test

A nucleic acid is a polymer composed of chains of monomeric nucleotides.

The most common nucleic acids are deoxyribonucleic acid(DNA) and ribonucleic acid (RNA).

Nucleic acids are universal in living things, as they are found in all cells and viruses

Named for their role in the cell nucleus

DNA is responsible for the long-term storage of information

DNA is often compared to a set of blueprints

DNA contains the instructions needed to construct other components of cells, such as proteins and RNA molecules.

All used in protein synthesis All encoded in the DNA

RNA includes:

mRNA (messenger)

tRNA (transfer)

rRNA (ribosomal)

mRNA roles is the transcribed genetic information from deoxyribonucleic acid (DNA)

rRNA acts as assembly site for protein synthesis in complexes or protein and RNA known as ribosomes,

tRNA serves as an essential carrier molecule for amino acids to be used in protein

synthesis.

The monomers from which nucleic acids are constructed are called nucleotides.

A sequence of nucleotides forms a polymeric chain that has the ability to interact with another chain or other parts of the chain

A double-stranded nucleic acid consists of two single-stranded nucleic acid chains held together by hydrogen bonds, such as in the DNA double helix.

RNA is usually single-stranded, but any given strand may fold back upon itself to form secondary structure as in tRNA and rRNA.

Each nucleotide consists of three components:

A carbon to carbon ringed structure with nitrogen◦ Called a nitrogenous base

◦ Either a purine or a pyrimidine

A 5-carbon sugar and

A phosphate group.

That OH makes RNA less stable---easily degraded

RNA is a transient molecule..

DNA contains

2-deoxyribose

RNA contains ribose

The only difference is the presence or absence of a a OH (hydroxyl group) on the second carbon

DNA = A T C G RNA = A U C G

Adenine, cytosine, and guanine are found in both RNA and DNA

Thymine only occurs in DNA and uracil only occurs in RNA.

Phosphate – as found in phospholipids

HPO4

Found between two adjacent nucleotides in a polypeptide

Sugar – phosphate backbone

The addition of a nucleotide requires a nucleotide tri-phosphate………the energy necessary to create the bond between adjacent nucleotide is found in the phosphates that leave

Adenine pairs with Thymine (or Uracil in RNA)

Cytosine pairs with Guanine

Making a new DNA or RNA polynucleotide requires a DNA molecule to be copied.

DNA is copied by matching complementary bases

Resulting DNA molecule:

Two chains of twisted nucleotides (two strands-a double helix)

Arranged anti-parallel

Just enough room for a purine (double ring) and a pyrimidine (single ring)…….This determines the match

Two chains are held together by a weak interaction between the bases

C= G A=T

The bond holding the nucleotides together within the strand is very strong

Order of bases on the polynucleotide chain is called the DNA sequence

This determines the message encoded by the molecule

ATTCGCTTGAACT…..

Although DNA is represented by a sequence of letters, it is important to remember that each nucleotide has a sugar and a phosphate

Uses uracil instead of thymine

-OH group on the second carbon of the sugar (its ribose—not deoxyribose)

Single stranded

How is RNA Translated?

DNATranscription

RNAmRNA to be exact

Translation

Protein

TACCGTCTCGAA

AUGGCAGAGCUUmRNA to be exact

Amino Acids….

AUGGCAGAGCUU

AUG GCA GAG CUU

1st 2nd 3rd 4th amino acid amino acid amino acid aacid

Met Ala Glu Leu

Electrophoresis with dyes that bind DNA

Best is Ethidium Bromide

Sybersafe with comparable sensitivity

Biomolecule


Test

Carbohydrate

Energy/Support

Mono-saccharide

•C=O, OH group


are connected

Benedict’sTest

Lugol’sTest


AminoAcid

Central C w/H-NH2

-COOHR groups

BiuretReagent

Lipids EnergySupportSignaling

Glycerol and fatty acids?Cholesterol

Mostly C-H

Insoluble in waterGrease spot test

Nucleic Acids

InformationEnergy, Signaling

Nucleotide SugarPhosphateCyclic N-Base

EthidiumbromideSybersafeMethyleneBlue

Biomolecules

Education

Transcript of Biomolecules