Experiment 8 and 9 PDF
Experiment 8 and 9 PDF
Nucleic Acid
- monomer: nucleotides
o an individual nucleotide consists of 3 parts
1. nitrogenous base
2. Sugar
3. phosphoric acid residue
o all of which are covalently bonded together
o bases are bonded to the sugars, forming nucleosides
- one of the essential biochemical molecules present in an
organism
- functions for encoding, transmitting, and expressing the
genetic information
- principal types are DNA and RNA
Nitrogenous Base
- Pyrimidines: single-ring aromatic compounds
- Purines: double-ring aromatic compounds
DNA
- It is an essential biochemical molecule of an organism
that contains genetic information
- It is responsible for the existence of our inherited
physical traits.
- is made up of molecules called nucleotides
- The Structure of DNA
- Double helical structure
- Proposed in 1953 by James Watson and Francis Crick
- It was based primarily on model building and X-Ray
diffraction patterns
Chargaff’s Rule
- A=T
- G=C
- The amount of Adenine was always the same
amount with Thymine, and Guanine always has the same amount as
Cytosine.
- The reason A goes with T, while C goes naturally with G, is because of
their bases connect through hydrogen bonding.
- The sugar-phosphate backbone is the outer part of the helix.
- And as you can see the chains run in antiparallel directions.
METHODOLOGY
A. Isolation of DNA from onion
Preliminaries:
1. Heat the tip of a dropper in a Bunsen flame until you can bend
the end back up towards the top forming a hook. This will be
used to spool and hook the DNA.
2. Cool 50mL of 95% ethanol in an ice bath
B. Determination of DNA Concentration and Purity
- *Chopping the onion allows its tissues to be broken up so that homogenizing solution can take effect and attack
the cell walls and membranes.
- *In this step, we will break up the onion tissues to separate and open cells.
- Cell walls, and cell and nuclear membranes get fragmented, and molecules contained within the cells (including
DNA) are liberated into the medium.
- We will briefly heat the tissue before homogenization, in order to inactivate DNAses (enzymes that degrade
DNA) that are present in our mixture.
- Once we degrade DNAses, we will maintain the homogenate at a cold temperature, in order to keep enzymes
deactivated and the DNA cold for the precipitation step.
- After we homogenize the onion tissue in the blender, we will strain it through cheesecloth to remove the bigger
debris, such as cell walls, membranes, etc.
2. Deproteinization
- hydrolysis of protein using Papain powder
- purify the homogenate by removing proteins that are associated with cells and DNA molecules
- *In this step, we will purify the homogenate by removing proteins and lipids that are associated with cells and
DNA molecules.
- We will take advantage of the differential solubility of DNA, proteins, lipids and other macromolecules, to
separate them using different solvents.
- DNA is soluble in water, but other macromolecules are more soluble in organic solvents.
- If we add chloroform (one such organic solvent) to our homogenate (which contains water), two layers will form
like in an oil/vinegar dressing.
- Those molecules that are soluble in water will remain in the top water layer, and those molecules that are
chloroform-soluble will drop to the bottom chloroform layer.
3. Precipitation
- Force DNA to come out of solution, or precipitate, by using cold alcohol
- Adding ethanol alcohol which causes every component in the filtrate to stay in solution except DNA
- In this step we will force DNA to come out of solution, or precipitate, by using very cold alcohol.
- When precipitation is completed, the liquid within the flask will become cloudy.
- This cloudiness is really the long nucleotide polymer (DNA).
- Once we are at this step, we will be able to spool the long DNA strands onto a very cold glass rod and out of the
beaker.
Why heat in a water bath until the solution reaches 60 Why use an ice-col 95% ethanol?
degrees Celsius? - This is added to cause the DNA to precipitate out
- Heating at 60C softens the phospholipid in the cell of the solution
membrane and denatures DNAse - 95% ethanol is recommended since DNA is not
- Why should the temperature be kept at 60 soluble in alcohol and the colder the alcohol, the
degrees Celsius? less soluble it is
o To prevent the denaturation of DNA that
involves the breaking of hydrogen bonds - The DNA precipitated out of this solution using salt
between the bases in the duplex and ethanol
Papain o Salt neutralizes the charges on the
- Proteolytic enzyme phosphate groups in the DNA backbone
- Degrades DNAses, RNAses, and proteins o The alcohol, having a lower dielectric
- Denatures the proteins clinging to the DNA making constant than water, then allows the
the molecule flexible and easy to spool sodium ions from the salt to interact with
the negatively charged phosphate groups
Why use 95% ethanol? closely enough to neutralize them and let
- When the DNA is liberated from the nucleus and the DNA fall out of the solution
the cell, alcohol must be added to recover it. 95% - Since DNA strands are negative, ethanol being an
alcohol is less dense than water and so floats on alcohol, which is non-charged, acts to repel the
the surface. The lipids and proteins will fall to the negative DNA
bottom of the test tube while the DNA, which is
less dense than the proteins and lipids, will rise Purpose of the following in the isolation of DNA
into the alcohol layer. • SDS (sodium dodecyl sulfate)
• Detergent used to break down nuclear
Why transfer the flask immediately into an ice bath? membrane
- Slows down the DNA breakdown • Anionic detergent which emulsify lipid and
- At room temperature, DNA begins to denature by protein components of the cell by
the action of DNAse (present in cell extracts) disrupting the noncovalent interactions
that hold the cell membrane together
Why is the onion tissue mixed in a blender? • Detergent form complexes with these
- To allow the release of DNA with homogenization lipids and proteins causing them to
media which breaks down the cell wall, cell precipitate out of the solution
membrane, and nuclear membrane • Chelating detergent
- Why 45 seconds only?
o Exceeding would expose the DNA to…
forces that rapidly break the DNA into
shorter and shorter length • Sodium citrate
• Provide sodium
Homogenizing solution ions that
- Separate the DNA from chromosomal protein neutralize the
through its chemical components which will cause negative charge of the DNA backbone
the proteins to precipitate out of solution (phosphates)
- • *to further dissociate the complexes and
Filtering of the homogenate through a cheesecloth denature the
- To remove bigger debris, such as cell walls, enzymes
membranes, or to remove any solid material,
resulting to a clear cell homogenate • EDTA
- More efficient compared to filtrate (Ethylenediaminetetraacetic
acid)
• Inactivates DNAse (breaks down DNA)
B. DETERMINATION OF DNA CONCENTRATION AND
PURITY
Method used: Spectrophotomeric quantification of - Absorbance ratio (A260/A280)
DNA - gives the relative measurement of DNA and
Principle: Ultraviolet absorption protein content in isolated DNA
Major absorption band for purified DNA - A260/A280 = 1.8-1.9 pure DNA, free of protein
peaks at 260nm contamination
Protein material has a peak absorption - A260/A280 < 1.8-1.9 protein contamination
at 280nm - A260/A280 >1.8-1.9 presence of RNA
Typical A260/A280 is 1.8 -
*Factors that affect UV absorption
UV/Vis Spectroscopy Presence of aromatic bases adenine,
- determined the purity of the isolated DNA guanine, cytosine, and thymine
- absorbance at 260nm is due to the DNA species Denaturating agents (Saline Sodium
- absorbance at 280nm is due to the protein Citrate)
species
Why not used alkaline hydrolysis?
C. ACID HYDROLYSIS OF DNA - Pentose of DNA doesn’t have an –OH group
• Hydrolysis of glycosidic bonds to the purine at the 2nd carbon
bases at pH4 - No formation of monophosphate
• Protonation of purine bases intermediate
• Isomerization of depurinated sugar into its open - DNA is stable in alkaline hydrolysis
chain form
Why is the DNA-HCl mixture heated at 100C?
- To be able to destroy the hydrogen,
phosphodiester, and glycosidic bonds
- Results to the dissociation of DNA into its
components:
o Phosphate group
o Purine and pyrimidine
o Deoxyribose
- * A color test that is positive for all purines capable of oxidation to an alloxan derivative
- DNA reacted with nitric acid since purines is known to be readily soluble in diluted acid. Nitric acid oxidized it
leaving a yellow precipitate. The sample produced a yellow precipitate which indicates a positive result.
Discussion: D. 4 Test for Pyrimidines
• “Wheeler-Johnson”
• Standard: Cytosine solution
• Reagents:
• Bromine water
• Ba(OH) 2
• Positive Result: purple precipitate
• Positive in: Cytosine solution
Principle:
1. Bromination of pyrimidine to form dialuric acid
2. Neutralization of dialuric acid by Ba(OH)2 Bromination = converts pyrimidines into
dibromohydrouracil
to form Barium salt of Dialuric Acid
- *Bromine water reacted with the sample to form 5- bromo-6- hydroxyhydroxo derivative which provides a green
coloration.
- Upon addition of Ba(OH)2 will give a result of purple precipitate.
- The sample produced a white cloudy solution which is a negative result
- Composition of Urine
o 0.05% Ammonia o 0.1% Magnesium o 0.1% Creatinine
o 0.18% Sulfate o 0.015% Calcium o 0.03% Uric Acid
o 0.12% Phosphate o 0.6% Potassium o 2% Urea
o 0.6% Chloride o 0.1% Sodium o 95% Water
2. Odor
- Ordinarily, odor has little diagnostic significance and is not included in the routine laboratory result
- Reflection of what has been consumed or specific diseases
3. Turbidity
- Refers to the degree of cloudiness in a urine
- Otherwise known as clarity or transparency
- Normal: clear and transparent
- Turbid/cloudy urine indicates:
- Symptom of a bacterial infection
- Caused by crystallization of salt such as calcium phosphate
4. Volume Polyuria Excessive urine excertion; seen in increased
- Indicates balance between fluid ingestion and water water ingestion, diabetes; >2.5L /a day
lost from lungs, sweat, and intestines
Oliguria Scanty urine excertion; seen in dehydration,
- 1-2 L/a day is the normal adult volume
renal failure; <400 mL/day
Objectives
- The experiment aims to subject the urine samples acquired to several tests and to qualitatively examine the
presence of some normal organic constituents and pathological organic constituents.
METHODOLOGY
A. Initial Examination of the Urine Sample
STEP 2:
- Carbamoyl phosphate donates it carbamoyl group
to ornithine to form citrulline
- Citrulline is passed to cytosol
STEP 3:
- 2nd amino group enters: Aspartate
- Condensation reaction: amino group (Asp) +
carbonyl group (Citrulline) argininosuccinate
STEP 4:
- The only reversible step in the cycle
- Fumarate enters mitochondria to participate in Kreb’s cycle
2. Benedict’s Test
- Benedict’s Test is a test for glucose.
- The reagents used are the Benedict’s reagent,which is composed of sodium citrate, sodium carbonate and
copper sulfate.
- The principle behind this is that there is a reduction of copper sulfate to cuprous oxide when exposed to alkali
and heat. The positive result for this is the formation of yellow to red precipitate, which indicates a possibility of
having diabetes.
3. Exton’s Test
- Exton’s Test is a test for the presence of Albumin, which is a protein.
- The Exton’s reagent is composed of anhydrous sodium sulfate, which is a drying reagent and sulfosalicylic acid.
The sulfosalicylic acid is a precipitating reagent that can precipitate the Albumin to form a white precipitate with
cloudiness.
- When positive in this test, the kidney has a serious abnormality because proteins do not usually appear in urine.
4. Smith’s Test
- Bile pigments are being tested in the Smith’s Test.
- Iodine alcoholic tincture, which is composed of iodine crystals and sodium iodide in ethanol reacts with the bile
pigments that bring emerald green colored interphase. This may indicate an abnormality in the liver.
- Addition of a solution of alcoholic iodine to urine produces a green color. The green color indicates the presence
of bile.