Protein Synthesis

Protein synthesis had three process: 1) Transcription from DNA to mRNA. 2) RNA processing happens where introns are cut off. Protective cap/ G-cap and poly-A-tail are added. 3) Translation of RNA to protein. Translation happens in the ribosome.   

DNA Replication

DNA replication is the process of producing two identical copies from one original DNA molecule. This biological process occurs in all living organisms, and is the basis for biological inheritance. DNA is composed of two strands and each strand of the original DNA molecule serves as template for the production of the complementary strand, a process referred to as semiconservative replication. Cellular proofreading and error-checking mechanisms ensure near perfect fidelity for DNA replication.

First of all, helicase unzips the strand and breaks hydrogen bonds. Secondly, RNA primase lays down RNA at the 3’ end. Thirdly, DNA poly III lays down DNA nucleotides on the leading and lagging strands. Last but not least, DNA poly I replaces the RNA with DNA, and ligase glues the lagging strand (Okazaki fragments) together.

The DNA structure

DNA has a double helix shape, which is like a ladder twisted into a spiral. Each step of the ladder is a pair of nucleotides. Speaking of nucleotides, it is a molecule made of deoxyribose, a kind of sugar with 5 carbon atoms, and a phosphate group made of phosphorus and oxygen, and nitrogenous base. There are four types of nucleotide: Adenine (A)/ Thymine (T)/ Cytosine (C)/ Guanine (G). The DNA ladder is made of two bases, one base coming from each leg. The bases connect in the middle: 'A' only pairs with 'T', and 'C' only pairs with 'G'. The bases are held together by hydrogen bonds. Adenine (A) and thymine (T) can pair up because they make two hydrogen bonds, and cytosine (C) and guanine (G) pair up to make three hydrogen bonds.

What makes who we are --- Explanations of two pictures

I. Morning Glory

   As we known, DNA is copied from the “parent” cell to the “daughter” cell. Despite this process usually produces accurate copies, errors do occur. When an error does occur, the new combination of DNA sequences is a mutation.

   DNA can be modified in more ways that only by random mutations. By doing so, “jumping genes” are formed --- the whole sequence of DNA that moves from one place to another over times of environmental stress. Normal morning glory favors the color of blue over the color of white. Yet, due to the different growing environment, helpful mutation occurs that causes DNA retro-transposon happens; therefore, in the picture, the morning glory contains more of the color of white than the color of blue.

Normal Morning Glory

!! Mutation occurs!

II. Handy Genes

   As mentioned in Chapter 3 of Your Inner Fish, “Our limbs exist in three dimensions: They have a top and bottom, a pinkie side and a thumb side, a base and a tip. The bones at the tips, in our fingers, are different from the bones at the shoulder. Like wise, our hands are different from our thumbs.” What DNA actually makes a pinky different from a thumb? How does our body know to develop in this way? In order to find out these answers, Randy Dahn, a researcher in Dr. Shubin’s laboratory did experiments on the embryos of sharks and skates by injecting a form of Vitamin A.

Nevertheless, in the 1950’s and 1960’s a number of biologists did amazingly creative experiments on chicken eggs to understand how the pattern of the skeleton forms. By cutting up embryos and moving around tissues, biologists were able to discover that two little patches of tissue essentially control the development of the pattern of the bones inside limbs.

   On the other hand, Mary Gasseling did another experiment that could explain why the infant’s hand in the picture looks differently. In the picture, the infant has two more extra fingers growing out from the index finger. How so? This is because of ZPA (the zone of polarizing activity, also known as the patch of tissue that control the development of the pattern of the bones inside limbs.) Although ZPA causes fingers to look differently, something else inside ZPA controls how fingers form and what they look like, which is Sonic Hedgehog.

    Sonic Hedgehog is active in the ZPA tissue. If Sonic Hedgehog hasn’t turn on properly during the eighth week of one’s own development, then one either would have extra fingers or one’s fingers would look alike. Furthermore, moving a little patch of the ZPA tissue would cause the fingers to duplicate and supplying Vitamin A at the right concentration and at the right stage, fingers would form mirror-image duplication. This is why the infant’s hand looks differently in the picture.

Normal hand

Mirror - image

DNA Replication Enzymes - What do the following enzymes do in DNA replication?

Helicase:

Helicase is a class of enzymes vital to all living organisms. Their main function is to unzip an organism's genes. Helicases are often used to separate strands of a DNA double helix or a self-annealed RNA molecule using the energy from ATP hydrolysis, a process characterized by the breaking of hydrogen bonds between annealed nucleotide bases. 

They also function to remove nucleic acid-associated proteins and catalyse homologous DNA recombination. Metabolic processes of RNA such as translation, transcription, ribosome biogenesis, RNA splicing, RNA transport, RNA editing, and RNA degradation are all facilitated by helicases. Helicases move incrementally along one nucleic acid strand of the duplex with a directionality and processivity specific to each particular enzyme.

DNA Polymerase III:

Being the primary holoenzyme involved in replication activity, the DNA Polymerase III has proofreading capabilities that correct replication mistakes by means of exonuclease activity working 3'→5'(read in this direction). DNA Polymerase III is a component of the replisome, which is located at the replication fork.

DNA Polymerase I:

In the replication process, DNA Polymerase I removes the RNA primer (created by Primase) from the lagging strand and fills in the necessary nucleotides between the Okazaki fragments in 5' -> 3' direction, proofreading for mistakes as it goes.

It is a template-dependent enzyme - it only adds nucleotides that correctly base pair with an existing DNA strand acting as a template.

RNA Primase:

RNA Primase is a type of RNA polymerase, which creates an RNA primer. DNA polymerase uses the RNA primer to replicate ssDNA.

Primase catalyses the synthesis of a short RNA segment called a primer complementary to a ssDNA template. Primase is of key importance in DNA replication because no known DNA polymerases can initiate the synthesis of a DNA strand without an initial RNA primer.  

The RNA segments are first elongated by DNA polymerase and then synthesized by primase.

Ligase:

Ligase is an enzyme that can catalyse the joining of two large molecules by forming a new chemical bond, usually with accompanying hydrolysis of a small chemical group dependent to one of the larger molecules or the enzyme catalysing the linking together of two compounds, such as enzymes.