R2
1. Lac operon vs Trp Operon:
Operon is a cluster of gene under the control of a single promoter.
There are 2 common types of operon in bacterial: Lac Operon and Tryptophan Operon
LAC OPERON | TRP OPERON |
Inducible operon | Repressible operon |
Transcription is normally OFF | Transcription is normally ON |
Turn on when the inducer (lactose) is present and binds to the repressor, preventing the repressor protein from binding to the operator, and promoting transcription initiation. | Transcription turns off when the co-repressor (tryptophan) binds to the repressor protein, activating the repressor protein to bind to the operator, blocking transcription |
Regulates the metabolism of allolactose | Regulates the synthesis of tryptophan |
Under negative and positive control | Primarily under negative control |
Not involving attenuation | When the level of tryptophan in the cell is high, termination sites cause early termination |
2. Mitosis / Meiosis:
2.1: Mitosis
- Prophase:
+ Chromosomes condense and become visible
+ Mitotic spindle forms
- Prometaphase:
+ Chromosomes continue condensing
+ Kinetochore are proteins found in the center of each chromatid, these proteins then attach with the microtubule of the spindle fiber, forming the kinetochore microtubules protein.
+ Nuclear envelop break down
- Metaphase: Chromosomes are aligned in a line at the equator of the cell (metaphase plate) by the kinetochore-microtubule proteins apparatus.
- Anaphase: 2 sister chromatids are pulled from each other toward the opposite end of the cells
- Telophase:
+ chromosomes reach the poles and become decondensing
+ 2 daughter nuclei are formed
+ nuclear envelop reforms around the separate sets of chromosome.
+ cytokinesis will follow to split the cytoplasm and the duplication of centrosomes.
+ Mitotic spindle disassemble.
2.2 Meiosis
Prophase 1:
+ Chromosome condenses
+ Homologous chromosomes pair up forming tetrads.
+ Crossing-over occurs between 2 non-sister chromatids (exchange their DNA segments)
Metaphase 1:
+ Homologous pairs are pulled to the middle of the cell by the spindle fiber apparatus.
+ Homologous pairs are aligned randomly, resulting in different recombinations of chromosome alignment each time meiosis occurs. (Independent assortment).
Anaphase 1:
+ 2 chromosomes in homologous pairs are pulled to the opposite pole of the cell by the spindle fiber apparatus.
+ Each of them is pulled to the opposite end of the cell.
Telophase 1:
+ Resulting in formation of 2 cells, each cell contains a pair of chromosomes
+ Chromosome stay relatively condense and nuclear envelop does not fully re-form.
+ Cytokinesis will follow to split the cytoplasm.
Prophase 2: The chromosomes stay condensed
Metaphase 2: The chromosomes are aligned at the equator of the cell by the spindle apparatus (metaphase plate)
Anaphase 2: 2 sister chromatids are pulled from each other …
Telophase 2: - 4 haploid daughter cells are formed. They are distinct from each other and distinct from their parents.
-Nuclear envelop re-forms
-Mitotic spindle disassemble
-Cytokinesis will follow to completely split the cytoplasm and the duplication of the centrosomes.
3. PCR: a technique for in vitro amplification for large number of specific pieces of DNA.
3 main steps:
3.1 Denaturation (94-98): 2 strands of DNA is separated by heat which break the hydrogen bonds of double-stranded DNA
3.2 Annealing (45-65): Short DNA primers are used to attach to the now single-stranded DNA. 2 primers are used (forward and backward) that are complementary to each end of the sequence to be amplified
3.3 Extension (68-72): The new strand of DNA is extended as tag polymerase incorporates new dNTPs to reform the doubl-stranded DNA
4. Restriction eznyme: Restriction enzyme or restriction endonuclease is a protein isolated from bacteria that cleaves DNA at specific sequences, producing DNA fragments with known sequences at each end.\
5. Repressible and Inducible Enzyme:
Repressible enzyme | Inducible Enzyme |
Regulates anabolic pathway | Regulate catabolic pathway |
Production decrease when the end product is abundant (negative feedback) | Production increases when the substrate is present |
Controlled by repressor protein | Controlled by the activator protein |
6. Adaptation vs Acclimation
Adaptation | Acclimation |
Involves genetic changes through natural selection or mutations | Involves morphological or physiological changes without altering genetic makeup |
Takes place in multiple generations | Occurs within an individual’s lifetime |
Result in permanent, heritable changes that increase an organism’s fitness | Result in reversible, non-heritable adjustment to immediate environmental conditions or changes. |
7. Cyclin-Cdk cycle:
Cyclin synthesis | Starts in late S phase and continue during G2 phase. Cyclin accumulates as it is protected from degradation |
MPF formation | Cyclin binds to Cdk forming MPF. MPF builup helps the cell pass G2 checkpoint, entering mitosis |
MPF activity | MPF phosphorylates various proteins, promoting mitosis. MPF’s activity peaks at metaphase |
MPF inactivity | Cyclin degrades during anaphase, ending M phase. The cell enters G1 |
Cyclin degradation and Cdk recycling | Cyclin degradation continues, Cdk from MPF is recycled |
8. Gene drive: Gene drive is a genetic technique that promotes the preferential inheritance of a specific allele among a population, causing it to be passed down to offspring with a higher rate expected than Mendelian law. One application of it is engineering mosquitoes that carry malaria-causing alleles. These edited mosquitoes might have resisted to malaria allele and their offspring experienced the same characteristics resulting in amplifying a large mosquito population that does not carry malaria allele => over time this type of genotype becomes advantageous and those individuals with the malaria allele will be natural selection removes.
9. The reason underlying using co-dominance traits in HWE=> HWE assumes that both alleles of a locus are equally visible to natural selection, making their frequencies be tracked for in a population. With co-dominance, both alleles are expressed => enabling empirically determine their allelic frequencies => enabling monitor and compare to HWE expectations.
If one allele is dominant and one allele is recessive, the recessive allele could be masked under the heterozygotes form, making tracking changes in allelic frequencies harder.
10. What is CRISPR/Cas 9 and its relationship with gene drive?
CRISPR/Cas9 is a powerful editing tool that allows specific genetic modifications in the DNA sequences. Gene drive is a genetic technique that increases/ promote the preferential inheritance of specific alleles which then be passed to offspring with higher expected rates than usual. CRISPR/Cas 9 can be harnessed to create gene drive by introducing specific genetic modifications into an organism’s genome.
CRISPR/Cas 9 have 2 parts:
+ Cas 9 protein => cut the DNA
+ Guide mRNA => recognized the sequence of DNA to be editted
11. Physical distance and recombination distance or recombination frequency
Physical distance => actual length of DNA base pair (bp)
Recombination distance => the frequency of crossing-over events (cM)
12. Consequences of SNPs in intro, exon, enhancer, distal enhancer, promoter:
+ Promoter: Can impact gene expression and transcription level
+ Intron: Altering gene splicing => affecting final proteins.
+ Exon: Can cause amino acid changes => affecting the protein function.
+ Enhancer: Influence gene expression level
+ Distal enhancer: May alter gene expression in a tissue.
13. p53 and proto-oncogenes
P53 | Proto-oncogenes |
A tumor suppressor gene | Encodes protein regulating cell growth and function |
Activated in response to cellular stress or DNA damage | When become mutated => become onco genes => promoting cancer |
Function: cell cycle arrest, DNA repair, apoptosis | Example: ras, myc,…. |
Prevents proliferation of damaged cell, reduces cancer risks |
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14. Polivirus and Retrovirus
Polivirus | Retrovirus |
Single stranded + RNA | Single stranded RNA |
RNA dependent RNA polymerase | Reverse transcriptase |
+ RNA -> - RNA | RNA -> ddsDNA (polivral DNA) |
-RNA is used as a template for more production of +RNA => more production for viral genome and viral specific proteins | -Poliviral DNA is incorporated into the host cell genome and is replicated along with the host cell’s DNA.
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15. Exon shuffling and Alternative Splicing
Exon shuffling | Alternative Splicing |
Recombines exons between multiple genes. | Combines exons within a gene |
Result in new genes | Produces multiple proteins from a gene |
Affect gene evolution | Regualte gene expression |
16. Later gene transfer involves 3 main mechanisms:
1. Conjugation: Direct cell-to-cell contact and transfer of genetic materials via a conjugative bridge (a pilus)
2. Transformation: Direct uptake and incorporation of DNA between cells
3. Transduction: Direct cell-to-cell contact and transfer chromosomal or plasmid DNA by a bacteria virus (bacteriophage)
17. Gibb free energy is the useful energy or potential work that can be extracted from a biochemical reaction.
18.
Catabolism | Anabolism |
The breakdown of complex organic molecules like … | The synthesis of complex organic molecules from small simpler molecules |
Release energy | Require energy |
Providing energy and building blocks of cellular processes | growth, maintenance, and tissue buildup |
19. Transposons and retrotransposons are mobile genetic elements that can move within a genome.
Transposons | Retrotransposons |
The DNA sequences can change position by a specific ‘copy-and-paste’ mechanism | The RNA sequences are transcribed from DNA and then reverse-transcribed into DNA |
| Utilize ‘copy-and-paste’ mechanism |
Encodes protein transposase to catalyze their movements | Can increase genome size, contribute to the genetic diverse |
Can cause mutations, gene distribution. |
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20. The synthesis of ribosome
Eukaryotes | Prokaryotes |
Synthesized in nucleolus | Synthesized in the cytoplasm |
Assembly in the nucleolus and exported | Assemble in the cytoplasm |
Can be free-floating in the cytoplasm or bound to the rough ER | The ribosomes are always free-floating |
21. Protein synthesis in Eukaryotes and prokaryotes
Eukaryotes:
Transcription occurs in the nucleus.
mRNA is processed and transported to the cytoplasm.
Translation occurs on ribosomes (free or bound to rough ER).
Proteins may undergo further modifications in the ER and Golgi apparatus.
Prokaryotes:
Transcription occurs in the cytoplasm.
No mRNA processing.
Translation occurs on ribosomes in the cytoplasm.
Proteins may undergo post-translational modifications, but there is no ER or Golgi apparatus involvemen