Introductory to Molecullar Biology

Rizki Meizikri (1010311010) Wahyu Tri Novriansyah (1010312013) Muhammad Farid (1010312041) Shofi Faiza (1010312069) Deby Nelsya Eka Putri (1010312097) Muhammad Ihsan Fachruddin (1010313013) Akbara Pradana (1010313047) Ghucyka Jhonelta (1010313082) Afrilizia Putri (1010313095)

Group 10

Scenario
Riri, 18, read news on the mass media about a terrorist shot to death by the police. To check the validity of the terrorists identity, a DNA test should be done. Riri who is currently learning about molecullar biology is very excited with the news. She recalls her highschool lesson about DNAs function which can maintain its characteristic through replication process, and mutation may occur if DNA is exposed to radiation. Riri learns from several sources that DNA transcription produces RNA that will be translated in protein synthesis. DNA recombination, a genetical engineering technique, can also help producing stem cell, vaccines, medicines, and even cloning which becomes ethical dilemma. How do you describe these problems?

Scheme
Biomolekuler rRNA Cloning Stem Cell

Rekayasa Genetika Recombin ant DNA Vaccin e

Transkrip si

RNA

DNA

mRNA tRNA

Replikasi

Ekspresi

Mutasi

Translasi

Protein

1. Students Able to Explain About Structure and Function of DNA and RNA
Nitrogen Base

DNA

Phosphat e Group

Nucleotid e

RNA
Sugar

Thymine (T) Pyrimidines

Cytosine (C)

Adenine (A) Purines

Guanine (G)

Nitrogenous base (A, G, C, or U) Phosphate group

tRN A

Uracil (U)

Sugar (ribose)

Differences Between DNA and RNA

Differences Shape Sugar Pyrimidines Function(s) Stability Location DNA Double Helix Deoxyribose Cytosine, Thymine Protein synthesis, Inheritance Stabile Nucleus RNA Single Strand Ribose Cytosine, Uracil Protein synthesis Less stabile Nucleus and Cytoplasm

2. Students Able to Understand Factors That Affect DNA Stability

Hydrogen Bonding Thermal Melting Phosphate bonding

pH
Radiation, ex : UV, infra red, X-

Ray Virus DNA and RNA

3. Students Able to Explain DNA Replication Process

DNA polymerase molecule Parental DNA Daughter strand synthesized continuously Daughter strand synthesized in pieces

How Nucleotides Added in DNA Replication

Leading Strand
Primase enzyme put a primer RNA on the strand DNA polymerase III begin adding nucleotides

DNA polymerase I transforms the primer RNA to

DNA The replication continues until the end of the strand

Lagging Strand
Primase enzyme put a primer RNA on the strand DNA polymerase III begin adding nucleotides Primase enzyme put another primer RNA on the strand DNA polymerase III stop its activity and move to the new primer RNA DNA polymerase III stops when it meets the first primer RNA, leaving the strand unfilled. The blank space is called Okazaki Fragment Primer RNA will be transformed to DNA by DNA polymerase I, so that ligase can bind it with the DNA made by DNA polymerase III

4. Students Able to Explain Protein Synthesis Process

Transcribed strand DNA

Transcription

RNA

Start codon

Translation

Stop codon

Polypeptide

RNA polymerase DNA of gene DNA Promoter DNA Initiation Terminator DNA Cap Transcription Addition of cap and tail Exon Intron Exon Intron Exon

RNA transcript with cap and tail

Introns removed

Tail

Elongation mRNA

Exons spliced together

Coding sequence NUCLEUS Termination

Growing RNA
CYTOPLASM Completed RNA RNA polymerase

5. Students Able to Explain DNA Mutation

Types of DNA mutation: Missense Mutation Nitrogen base changed, amino acid changed (ex: Sickle Cell Anemia) Nonsense Mutation Nitrogen base changed, codon turned into stop codon Silent Mutation Nitrogen base changed, amino acid doesnt change
Frameshift Mutation

Abnormal number of nitrogen base Splice Site Mutation Failure in intron removal

6. Students Able to Explain Genetic engineering

Genetic engineering:

Direct manipulation on

organisms genetic material in a way that does not occur under natural conditions

Goals of genetic engineering: Improve understanding of how

genes work Advance biotechnologythe manipulation of organisms to create products or cure diseases

 Process of Genetic Engineering

Isolation of the Genes

Constructs

Selections

Transformations

Regenerations

Confirmations

What is cloning???
Cloning processes used to create copies of DNA

fragments (molecular cloning), cells (cell cloning), or organisms.

Three types of cloning: 1. Gene cloning a process where fragments of DNA

are transferred from one organism to another, usually carried on a DNA vector. Microbes like bacteria are convenient carriers and hosts for cloning DNA. 2. Reproductive cloning 3. Therapeutic cloning
Basic of gene cloning technologies recombinant

DNA

Reproductive and theraputic Cloning

 Recombinant DNA (rDNA) technologies is a genetic

engineering method on biomolecular level.

Recombinant DNA artificial DNA that is created by

combining two or more sequences on DNA that would normally occur together through the process of gene splicing.
Recombinant DNA technologies use enzymes that

cleave or copy DNA in living cells. The purified enzymes can perform DNA manipulations in vitro in recombinant DNA experiments.

 General Steps in rDNA procedures: 1. The DNA of interest that is to be transferred (also

called foreign DNA, insert DNA, cloned DNA, or transgene) is obtained by first extracting the DNA from the organism and then cutting out the specific DNA sequence using special enzymes. 2. The transgene is inserted into a special DNA molecule called a cloning vector and joined (by ligation) to produce a new recombinant DNA molecule (also called cloning vector-insert DNA construct, or simply DNA construct). 3. The DNA construct is transferred into, and maintained in, a host cell (bacterium) by the process of transformation. The vector replicates, producing identical copies (called clones) of the insert DNA.

4. The host cells that have incorporated the foreign

DNA are identified and isolated from untransformed cells. 5. The cloned DNA can be manipulated such that the protein product it encodes can be expressed by the host cell.

vectors
Vectors are entities for carrying the target DNA o o

into a host cell for multiplication or cloning. Cloning vectors: Plasmid vectors Viral vector Vectors for very large DNA fragments:
o o o o

Cosmids (hybrid of plasmid and bacteriophages) Bacterial artificial chromosomes Yeast artificial chromosomes Shuttle vectors a vector (usually a plasmid) constructed so that it can propagate in two different host species

Viral vectors (Phage)

Plasmid from E.coli

Cosmid vector

Stem cells
Stem cells special cells that have the ability to

divide for an indefinite period and can give rise to a wide variety of specialized cell types.
Types of stem cells based on its ability to differentiate: Totipotent stem cells differentiate to all kind of cells

and able to form new organism Pluripotent stem cells differentiate to derivates of three embryonal layer (ectoderm, mesoderm, endoderm) Multipotent stem cells differentiate to one specific organ or tissue Unipotent stem cells cant differentiate to specific tissues, but have fast regeneration and proliferation abilities

 In human, there are two types of stem cells:

1. Embryonic stem cells 2. Adult stem cells

7. Students Able to Explain Ethical Aspects of Genetic Engineering

Pros
Producing organisms

Cons
Fertile organism (ex:

with desired phenotypes and genotypes Supporting health and medical world (ex: producing insulin) Reducing pollution Producing efficient foods

watermelon) May be used for negative purposes (ex: forming a battalion of army with cloned human) Crisis of Identity Against the religion

8. Students Able to Explain DNA Test

What make we look different one another? Junk DNA loci of STRs (Short Tandem

Repeats)
STRs are sections of DNA arranged in back-to-back

repetition (a simple sequence is repeated several times in a row). Example of STRs: TCAT TCAT TCAT TCAT TCAT TCAT
The number of repeats found in pairs of STRs varies

from one person to another. STR DNA fingerprint of a person is completely different one another. The probability of anyone else having identical alleles with a person at each and every one of his or her loci is outrageously small.

General Process of DNA TEST

Collecting Biological Samples Extracting DNA Genetic Analysis

Collecting BIOlogical samples

Common samples for DNA tests:

Saliva
Buccal swabs Semen Blood Hair

DNA Extractions
General methods:

1. Break open the sample cells to free the DNA

from the nucleus (cell lysis). 2. Remove the proteins (which make up most of the biological sample) by digesting them with an enzyme. 3. Remove the DNA from the solution by adding alcohol.

ANALYSIS
Using PCR (Polynucleotide Chain Reactions)

copies of specific fragments of DNA molecules

Why we need copies of DNA? Current technology used in DNA fingerprinting

cant detect the DNA unless large amounts are present. Matches must be exact when it comes to DNA fingerprinting and forensic genetics. To avoid misidentifications, many STR loci from each sample must be examined.

PCR Methods

 Next step: Read DNA fingerprint using electrophoresis

DNA molecules is negatively charged. So, electrophoresis separate the DNA fragments based on its lengths and sizes.