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L2 Cyto
L2 Cyto
Lesson 2
Lecturer: Niña Betina Marie M. Igaña, MPH(c)
OBJECTIVES:
1. DNA STRUCTURE
1.1. Nucleotide
1.2. Chargaff’s Rule
1.3. Central Dogma of Biology
1.4. The Genetic Code
2. DNA EXTRACTION
2.1. Extracting DNA from living organisms
2.2. DNA Extraction Experiment (homework)
2.3. Know the Appearance of Extracted DNA
● DNA and RNA are polynucleotides, meaning they are made up of repeating units of nucleotide
● The sugar component of the genetic material is a five-carbon molecule or called a pentose
● For DNA: the sugar is deoxyribose
● For RNA: the sugar is a ribose
NUCLEOTIDES
● Nucleotides are the monomer units of building blocks of nucleic acids. It is a compound consisting of a
nucleoside linked to a phosphate group.
● They form a part of many coenzymes. Nucleotides form the basic structural unit of nucleic acids such
as Deoxyribonucleic Acid or DNA, and Ribonucleic acid or RNA.
● The universal currency of energy, namely ATP, is a nucleotide derivative.
○ Nucleotides are concerned with the storage and transfer of genetic information
● Serve as donors of phosphoryl groups (eg. ATP or GTP) of sugars (eg. UDP- or GDP sugars), or of
lipid (eg. CDP-acylglycerol)
○ There are coding and non-coding regions found on DNA.
○ For the coding regions, these code for genes such as proteins
○ For the non-coding regions, can be either for DNA junk or to help regulate protein synthesis.
NITROGENOUS BASES
● These are ring structures or aromatics that contain nitrogen as well as carbon in their rings thus
referred to as heterocyclic.
● The Nitrogen bases can either be:
○ PURINES: Adenine (A), Guanine (G)
○ PYRIMINDES: Cytosine (C ), Thymine (T), Uracil (U)
● Purines and Pyrimidines are cyclic compounds whose rings contain both carbon and other elements
(hetero atoms)
PURINES PYRIMIDINE
● Purines and Pyrimidines are the nitrogen bases that hold DNA strands together through hydrogen
bonds
○ The purines in DNA are adenine and Guanine, same as in RNA
○ The pyrimidines in DNA are cytosine and thymine, but in RNA they are cytosine and Uracil.
DNA STRUCTURE
● DNA stands for Deoxyribonucleic Acid
○ D from the name of the sugar
○ N and A from Nucleic Acid
● DNA contains the information that determines inherited characteristics
● It has the code for making proteins
● DNA is found in the nucleus of eukaryotic cells and in the cytosol of prokaryotes if we take a closer look
at the chromatin inside the nucleus
○ Cells require some form of instructions to be able to function properly. They need guidelines,
rules, and codes for making materials in the cell, and that code is the DNA
● Let’s talk further about the structure of the DNA. The DNA has repeating sub units and those units are
called monomers or nucleotides.
● The nucleotide has three main parts, a phosphate group, a sugar, and a nitrogen base.
● In the DNA, the name of the sugar is deoxyribose, which is part of the DNA’s name, and there are for
nitrogen bases, namely: Adenine, Guanine, Cytosine, and Thymine
● Two of the bases are purines, which have two ring structures: Adenine and Guanine
● Two of the bases are pyrimidines, which have one ring structure: Cytosine and Thymine. Pyrimidines
are the bases with a “y’ in their name, just like cytosine and thymine and pyrimidine itself.
● Appearing always in pairs with a pyrimidine and the slanted shape of DNA molecule causes it to form a
spiral or helix.
● Along the sides of the molecule, it is a backbone made up of alternating sugar and phosphate
molecules. While on the inside are nitrogen bases.
● Adenine and Thymine form hydrogen bonds together while Cytosine and Guanine form hydrogen
bonds together.
DNA RNA
Bases & DNA is a long polymer with a deoxyribose RNA is a polymer with a ribose & phosphate
Sugars: & phosphate backbone backbone
Job/Role: Medium of long-term storage and Transfer the genetic code needed for the
transmission of genetic information creation of proteins from the nucleus to the
ribosome
Description: A nucleic acid that contains the genetic Single-stranded chain of alternating
instructions used in the development & phosphate & ribose units with the bases A, G,
functioning of all known living organisms C, U bonded to the ribose.
Unique The helix geometry of the DNA is of The helix geometry of RNA is of A-form.
features: B-form.
DNA is completely protected by the body. RNA strands are continually made, broken
Because the body destroys enzymes that down and reused.
cleave DNA.
CHARGAFF’S RULE
This is the cell, the basic unit of all living tissue. So,
in most human cells there is a structure called the
nucleus. The nucleus contains the genome.
Once the last amino acid has been added, the chain
folds into a complex 3D shape to form a protein.
Genetic information travels from the DNA to the RNA and all species contain DNA that contains our genetic
information.
REPLICATION TRANSCRIPTION TRANSLATION
DNA is capable of replication In transcription, RNA polymerase In translation, the mRNA is read
using DNA polymerase. So, this uses DNA as a template to make as a template by the rRNA and
shows when our hair is growing, RNA. proteins and ribosomes which also
nails are growing, bacteria is uses tRNA to make protein out of
spreading within our bodies. This mRNA ● Messenger RNA. amino acids. Proteins go on to
happens because our cell is ● Contains all the perform their cellular functions,
replicating. DNA contains genetic DNA information. such as replicating,
information, then it is transferred phosphorylating, signaling aspect
to the RNA through transcription. rRNA ● Ribosomal RNA. of the cell.
● Complexes with
proteins that make
up the cellular
organelle called
the ribosome.
SPECIAL TRANSFERS
The Extensions of the Central Dogma
GENETIC CODE
● Genetic code is a dictionary that corresponds with sequence of nucleotides and sequence of amino
acids.
● Genetic code is a set of rules by which information encoded in genetic material (DNA or RNA
sequences) is translated into proteins by living cells.
● Term given by “Goerge Gamow” – when i searched the name up it was spelled “George”.
● The letters A,G,T and C correspond to the nucleotides found in DNA. They are organized into
Codons.
● The collection of codons is called Genetic code.
● For 20 amino acids there should be 20 codons.
● Each codon should have 3 nucleotides to impart specificity to each of the amino acid for a specific
codon.
● 1 nucleotide – 4 combinations
● 2 nucleotide – 16 combinations
● 3 nucleotide – 64 combinations ( most suited for 20 amino acids )
GENETIC CODE
● Codon could be present in both DNA & RNA, but anticodon is always present in RNA & never in DNA
● Codons are written in 5 to 3 direction whereas anticodons are usually written in 3 to 5 direction.
● Anticodon of some tRNA molecules have to pair with more than one codon.
● Codons are sequentially arranged in nucleic acid strand while anticodons are discreetly present in
cells with amino acids attached or not.
● Codon defines which anticodon should come next with an amino acid to create the protein strand.
● Anticodon helps in bringing a particular amino acid at its proper position during translation.
CLINICAL SIGNIFICANCE
SILENT MUTATIONS
MISSENCE MUTATIONS
DNA EXTRACTION
MATERIALS:
● Blender ● Strainer
● Split peas (or any food you wish to extract the ● Meat tenderizer
DNA) ● Alcohol
● Salt ● Test tube
● Detergent ● Glass stirring rod
● Water ○ But you can improvise anything you
● Measuring cup and spoons can find in you home
PROCEDURE: (Disclaimer!! You may use other methods/sources for your final project)
1. The blender separated the pea cells from each other, so you now have a really thin peacell soup.
○ Assuming that we are using pea cells for our experiment.
2. Measure about 100 ml or ½ cup of split peas and place them in a blender.
3. Add a large pinch of salt (less than 1 ml or about ⅛ teaspoon) to the blender.
4. Add about twice as much cold water as the DNA source (about 200 ml or 1 cup) to the peas in the
blender.
5. Blend on high (lid on) for about 15 seconds.
(continuation of procedure)
6. The detergent captures the proteins and lipids of the cell membrane.
7. Pour the mixture into test tubes or other small glass containers, each about 1/3 full.
8. Add a pinch of enzymes to each test tube and stir gently.
● If you stir too hard, you’ll break up the DNA and you don’t want to do that. Its harder to see if
aggressive ra kayka.
● The DNA and nucleus of the cell is moulded, folded, and protected by proteins. The meat tenderizer
cuts the proteins away from the DNA.
(Use meat tenderizer for enzymes. If you can’t find tenderizer, try using pineapple juice or contact
lens cleaning solutions)
9. Tilt your test tube and slowly pour rubbing alcohol (70-95%
isopropyl or ethyl alcohol) into the tube down the side so that it
forms a layer on top of the pea mixture. Pour until you have
about the same amount of alcohol in the tube as pea mixture.
10. All of the grease and the protein that we broke up in the first two steps move to the bottom, watery
layer
11. DNA will rise into the alcohol layer from the pea layer. You can use a glass stirring rod or a wooden
stick to draw the DNA into the alcohol.
12. Slowly turning the stirring rod will spoon (wrap) the DNA around the rod so it can be removed from the
liquid.
● The DNA released from the cell nucleus is dissolved in the water/detergent/wheat germ solution and
cannot be seen.
● DNA precipitates (separates) out of solution in alcohol, where it can be seen.
○ Besides allowing us to see the DNA, the alcohol also separates the DNA from other cells
components which are left behind in the water solution.
RECAP: