October 2021 archive

17
Oct
2021

DNA and Protein Synthesis

categories: Bio 12
  • Explain the structure of DNA – Use the terms nucleotides, antiparallel strands, and complimentary base pairing?
    1. DNA looks like a ladder that has been twisted (Double Helix)
      1. The frame/backbones of the “ladder” is made up of alternating phosphate and (5-Carbon) sugar molecules.
      2. DNA is antiparallel strands meaning that they are opposite. Both backbones have a 5′ and a 3′ end. A backbone has the 3′, the other strand across will have the 5′ end. Go in opposite directions of one another. 
      3. Bonded to the sugars are Nitrogenous bases. There are 4 nitrogenous bases. These bases have complimentary base pairs that specifically match up like a puzzle piece.
        1. The bases consist of 2 groups called: Purines and Pyrimidines
        2. Purines – Adenine and Guanine
        3. Pyrimidines – Thymine and Cystosine.
      4. A set of a phosphate molecule, sugar molecule, and one base is called a nucleotide.

  • When does DNA replication occur?
    1. DNA replication occurs prior to cell division. It happens in the Synthesis-stage of interphase (S-Stage)
  • Name and Describe the 3 steps involved in DNA replication. Why does the process occur differently on the leading and lagging strands.
    1. The first step of replication is the unwinding and unzipping of the double-helix. The enzyme DNA Helicase is responsible for the unzipping of the bases. It breaks the double/triple bonds between the complimentary bases. It is being represented by the Scissors.
    2. The second step of replication is complementary base paring. It is being represented by the circle with triangles. Adjacent nitrogenous base pairs line up. DNA polymerase is responsible for hydrogen bonding new nucleotides to the template/parent strands. It reads DNA in one direction from the 3′ end to the 5′ end. This is why the DNA polymerase is pointed in different directions. 
    3. The third step of replication is the rejoining/complete separation/rewinding of the DNA strands of the 2 new strands. DNA ligase is responsible for attaching the nucleotides of the backbones to one another (Okazaki fragments). 4. It differs because since the DNA polymerase only can read in one direction (3′ to 5′ end), the leaded ing strand can read in one constant motion whereas, on the lagging strand, the DNA polymerase must jump back up in sections to catch up. DNA polymerase does this in sections.
  • Todays modelling activity was intended to show the steps involved in DNA replication. What did you do to model the complimentary base pairing and joining of Adjacent nucleotides steps? In what way was this activity well suited to showing this process? In what ways was it inaccurate?
    1. We began by building the backbones and then placing the complementary bases across form one another. We drew the hydrogen bonds between the nitrogenous bases, shown as the dotted lines (Red). Guanine and Cytosine have should have 3 lines in the hydrogen bonds but were not represented in the photo. The bonds between the Phosphate  and sugars are covalent, shown as the straight lines (Purple).
    2. The adjacent nucleotides come in after the DNA Helicase breaks the bonds.
    3. This activity was well suited because it allows students to understand the process of how each molecule of the DNA strand (Phosphate, Sugars, and Bases) bond and pair. You can visually see each molecule and whether they have covalent or hydrogen bonds and how many. You can also see the antiparallel strands and how the enzymes move.This model was inaccurate because you aren’t able to see the true visual of the double helix and how it resembles a twisted ladder.
  • How is mRNA different than DNA?
    1. DNA is the parent strand. It is made of  phosphate molecules, 5-carbon sugars called Deoxyribose, and 4 nitrogenous bases (Adenine, guanine, Cytosine, and Thymine)  and it is long and millions of nucleotides long. It is also a double-helix. mRNA is a branch of RNA, proving that is is a single backbone and short. It is made of phosphate molecules, 5 -carbon sugars called Ribose, and 4 nitrogenous bases (Adenine, Guanine, Cytosine and Uracil).  mRNA is used for the process of transcription and translation. While it collects data from a segment of DNA it is used for the process of building amino acids -> proteins. mRNA never enters the nucleus, it is present it cytoplasm after synthesis, while DNA is present in the nucleus.
  • Describe the process of transcription?
    1. In the first step of transcription, DNA unwinds and a section of it unzips. This is done by the enzyme RNA polymerase. It is represented by the star.
    2. The second step is when the mRNA single backbone comes in and collects a section of data of the DNA that codes for a specific protein used in protein synthesis. It collects data from one strand of DNA. You can clearly see the difference of mRNA vs DNA based on the different colour sugars (Red = Ribose, Green = Deoxyribose) and the difference in the bases Thymine vs Uracil (Thymine = yellow, Uracil = yellow with hashtag). The complimentary base pairs between mRNA and DNA align and form hydrogen bonds (Adenine and Uracil, and Guanine and Cytosine).
    3. The third step is the separation of DNA and mRNA. Once the mRNA has collected its data, it will separate from the DNA. The DNA will reform its ladder and rewind up into the double helix.
  • How did todays activity do a good job of modelling the process of RNA transcription? In what ways was our model accurate?
    1. This activity was well suited because it allows students to understand the process of how each molecule of the DNA strand and the mRNA strand bond and pair. You can visually identify each molecule due to the different colours [the sugars (Red vs Green) and the change in pyrimidines (Thymine vs Uracil)] and bonds. You can clearly see the enzyme that was used and how each complimentary base paired. Again It was inaccurate because we were able to see the winding and unwinding of the DNA double helix.
  • Describe the process of translation: Initiation, elongation, termination.
    1. The enzyme RNA polymerase (yellow transcription machine) begins the separation of DNA to allow mRNA to collect data from the DNA (template strand). That is known as transcription.
    2. After the process of transcription has been completed, the first step in Translation is Initiation. The ribosome (Red) slides along the mRNA strand until it it reads that codon that codes for the start (AUG). The ribosome will move to the right after that point.
    3. The next step is elongation. The tRNA, represented by the green shapes, is responsible for coding the anti-codons (opposite of the codon). the anti-codon codes for a specific amino acid. The ribosome has 2 spots for the tRNA, the P position must be full at all times (left side), whereas the A position doesn’t not (right side).The tRNA in the A position (right side) is responsible for going to the cytoplasm to retrieve a amino acid and bring it back to the ribosome. It places the amino acid at the bottom of the chain. From there the ribosome will move over to the right so it can read the next codon.
    4. After the process has been repeated numerous times, there will be a codon that codes for the ribosome to stop reading. When that code enters the A position, translation can no longer continue. That is called termination. You will have a polypeptide chain of amino acids. That polypeptide transcribed a very small portion of a protein.
  • How did todays activity do a good job of modelling translation? In what ways was it inaccurate?
    1. This activity did a good job because it allows students to understand the process of how each enzyme did its job in translation. While the process was long, we were able test our ability to making the anti-codons and use the charts to find the amino acid. We were able to each process step-by-step.This was inaccurate because we weren’t able to the entire process of each amino acid. We showed each step for the first two, then did the rest.