General Biology

• Central Dogma of Molecular Biology

  • is a theory stating that genetic information flows only in one direction, from DNA, to RNA, to protein, or RNA directly to protein.
• 3 Processes of Central Dogma

  1. DNA Replication
  2. Transcription
  3. Translation
• G0 Phase - Resting phase; The cell is neither dividing nor preparing for division. The cell enters this phase after it is done dividing.
• G1 Phase - Growth/Gap Phase; The cell grows physically and increases the volume of both protein and organelles.

  Note: It is called Gap phase because from a microscopic aspect, little change is visible. However, the cell is quite active at the biochemical level.
• S Phase - DNA Synthesis Phase; The cell copies its DNA to produce two sister chromatids* and replicates its nucleosomes*.
• Chromatids -  One of the two identical halves of a chromosome that has been replicated. (The >)
• Sister Chromatids - (The > and the <)
• Chromosome - Contains single, linear double-stranded DNA molecule. (The X)
• Chromatin - The material that makes up the chromosome.
• Nucleosome - Basic structural unit of chromatin. Made up of a coil of DNA around a histone core.
• Histones - Protein associated with DNA in chromosomes. They guide the coiling of DNA.
• Before cell division, chromosomes are replicated. They are attached to each other in a region known as centromere.
• G2 Phase - Protein Synthesis Phase; The cell shows the second growth by making proteins and organelles and beginning to reorganize its contents in preparation for mitosis. Protein synthesis occurs in two stages: Transcription and Translation.
• Pentose - Deoxyribose sugar (Pentose is also present in RNA but it is called “ribose sugar”)
• Pyrimidines - Cytosine, Thymine, & Uracil

  Purines - Adenine & Guanine
• Nitrogenous Base - Able to undergo tautomerism*. (Ex: Adenine, Thymine, Guanine, Cytosine)
• Tautomerism - rapid conversion between the compound’s isomeric* form.
• Isomeric - one of two or more chemical compounds or groups that have the same numbers of atoms of the same elements but differ in structure.
• Phosphate Group - Backbone of the polynucleotide together with the pentose.
• DNA Replication

  • Occurs in the nucleus (for eukaryotes*).

  *DNA Replication occurs in the cytoplasm for prokaryotes.

  • Happens in interphase.
• Helicase - The unzipping enzyme

  • It breaks through the hydrogen bonds that hold the DNA bases together.
• DNA Polymerase - The builder

  • Replicates DNA molecules to actually build a new strand of DNA.
  • Has proofreading ability.
• Primase - The initializer

  • Makes the primer, that is made up of RNA, that helps the DNA polymerase where to go to start to work.
• Ligase - The gluer

  • It helps glue DNA fragments together.
• DNA Replication starts at a certain part called the origin. Replisome is responsible for starting the DNA replication. 
• Eukaryotes have multiple origins, while prokaryotes have only one.
• Helicase unzips the DNA and SSBP (Single-Stranded Binding Protein) binds to the unzipped DNA strands to keep them separated. Topoisomerase keeps the DNA from supercoiling, they unwind supercoils.
• Primase makes RNA primers on both strands.
• DNA polymerase builds the new strand in the 5’ to 3’ direction or the leading strand. However, the DNA polymerase in the 3’ to 5’ direction or the lagging strand is moving away from the helicase’s direction so it has to keep up to where the unwinding is happening. Primase needs to make primers for DNA polymerase to build. These fragments are known as okazaki fragments. Then, the primers have to get replaced with DNA bases since the primers are made up of RNA.
• Ligase glues the okazaki fragments sealing the strands together.
• At the end of replicating, you have two identical double helix DNA molecules. This is called semi-conservative because the two copies each contain one old original strand and one new original strand.
• Steps of RNA Transcription

  1. RNA Polymerase copies a DNA sequence into an RNA sequence.
  2. The RNA sequence is mRNA, mRNA goes out the nucleus, into the cytoplasm, and ends up in the ribosome. The ribosome is made up of rRNA (Ribosomal RNA).

  Non-coding RNA (Introns) are spliced out of the mRNA so that only the coding RNA (Exons) remain.
• Steps of Translation

  1. mRNA, since it has the complementary sequence of the DNA, is going to direct which tRNA comes in and therefore which amino acid should be transferred.
  2. When the tRNA finds the complementary bases of the mRNA, they transfer their amino acid by triplets—codon.
  3. At the end of mRNA, there is a stop codon. Stop codons do not code for an amino acid, it just indicates that the protein building is finished.
• Preformationism (Pythagoras and Aristotle) - until 17th Century

  The reproduction of organisms originate through formation of miniature versions of themselves known as homunculus. Each part/organ of the body can produce gemmules that contribute to the formation of an offspring.
• • The idea of preformationism originated from insects, amphibians, and reptiles, known as parthenogenesis, that allows them to reproduce without sexual interaction.

  1. Spermists - Sperm contains the miniature individual and only nourished by the ovum.
  2. Ovists - thought the same and the seminal fluid only stimulates it.

  • Since earlier civilizations are patriarchal, the widespread accepted idea is of the spermists.
• Epigenesis (William Harvey) - 1651

  William Harvey (popular ovist) criticized Aristotle’s work by asserting ex ovo omnia which states that all organisms come from eggs.
• Theory of Use and Misuse - The organs of an organism that is frequently and continuously used becomes more developed and prominent across the lifetime of an individual. On the other hand, organs that does not elicit frequent and continued use will be weak and deteriorated across the lifetime of an individual.
• Theory of Acquired Characteristics - The modifications that an organism underwent in its life due to the factors of use and misuse will be preserved and will be passed on to the next generation.
• Theory of Evolution of Natural Selection (Charles Darwin) - 1859

  • Contradictory to Lamarck’s theory, the inheritance of traits would neither depend on the use and misuse of an organ nor the prominence of development of organs in its own lifetime but would only depend on the adaptability on the environment, wherein only highly adapted individuals among same species would have higher chances of survival and reproduction.
• Germplasm Theory (August Weismann) - 1892

  • Weismann postulated that there are two types of cells in the body:

  1. Somatic Cells - Responsible for sustaining the body.
  2. Gametes - Contains hereditary information.

  • He also disproved the concept of preformation using twenty-two pairs of mice, that even the tails of parents are cut — all offspring have grown tails.