Protein Synthesis: Transcription and Translation

Posted on February 27, 2020 by Randie

How is mRNA different than DNA?

Firstly the structure is quite different, DNA is huge and has Two strands (also double helix), while mRNA is small single stranded. mRNA also carries the code for DNA, DNA has all the genetic codes in its bases, mRNA gets the code from DNA during transcription and eventually carriers the code to produce amino acids and proteins. A bunch of other differences is DNA uses the sugar Deoxyribose and mRNA uses sugar ribose. DNA is formed in DNA replication, mRNA is from transcription. DNA is found in the nucleus while mRNA is mostly found in the cytoplasm.

Process of Transcription:

Unwinding and Unzipping

So the DNA Helicase breaks the H-bonds in the DNA allowing mRNA to complimentary base pair with the DNA.

Complimentary base pairing

The RNA polymerase H-bonds together with floating mRNA with the DNA. The mRNA builds up and produces a polypeptide of mRNA. The DNA Information is copied onto the mRNA.

Separation

The mRNA separates from the DNA. Since the DNA is too big and important to leave the Nucleus, the mRNA a smaller single stranded polypeptide leaves with the DNA’s Information in the Nucleus pores and enters the cytoplasm so it can be read by the ribosome to create proteins.

How did this model do a good job in modelling RNA transcription? What ways is it inaccurate?

like the pipe cleaner activity it shows the overall process, but it’s hard to show every small detail and process. An example is we cannot see RNA Polymerase really do its job as it attaches single nucleotides and then bonds them next to each other for the backbone, but in this activity instead it shows it attaching in one step.

Describe the process of translation: initiation, elongation, and termination:

Initiation

this starts the translation process, the P sight of the Ribosome reads the AUG start Codon on the mRNA strand. The tRNA will bring in the first amino acid then it will start elongation until a stop codon is reached.

Elongation

The amino acid chain starts to grow. A-site reads the next codon on the mRNA strand and then brings the matching tRNA. Then the tRNA on the P-site transfers over to the tRNA on the A-site.

Termination

A stop Codon is read on the mRNA strand, and this tells the ribosome to stop reading, and it produces no amino acid. Then the Ribosome releases the amino acid chain.

How does today’s activity do a good job of modelling the process of translation? In what ways was our model inaccurate?

It’s accurate showing the Ribosome holding on to the RNA. Also the tRNA building process. amino acid in the p-site and a-site match up with the codons. However what is inaccurate is the amino acid in the P-site and A-site match up with the codons.

DNA and Protein synthesis

Posted on February 20, 2020 by Randie

Explain the Structure of DNA:

DNA (Deoxyribonucleic acid) is a nucleic acid made of monomers of nucleotides. Nucleotides include a Phosphate group, a 5-carbon sugar, and a nitrogenous base. There are two types of these nitrogenous base’s, purines and pyrimidines. Purines are a double ringed structure (2 beads), while pyrimidines are single ringed (single bead). The purines in DNA are adenine and guanine and the pyrimidines are cytosine and thymine. DNA has two strands, which are antiparallel meaning they run in opposite directions. The head of one strand is always at the tail of the other strand (one strand is 5’ to 3’ the other is 3’ to 5’). The pink bead in the picture below symbolizes the phosphate. On the left strand the pink bead (phosphate) is the head (5’) but the strand on the right has the 5’ at the bottom.

The white pipe cleaners show bonding between the two strands, through Hydrogen bonding. This is also when the town nitrogenous bases are paired together with complimentary base pairing. This means that cytosine and guanine in DNA are bonded together with 3 hydrogen bonds and adenine and thymine are paired together with 2 hydrogen bonds in between. As shown above there are specific rules for complimentary base pairing. Yellow and blue (thymine and adenine) and purple and green (cytosine and guanine). After these two strands are bonded together through complimentary base pairing the monomer nucleotides. The final step of the structure occurs, the strands twist together through forces between the bonds, this is called double helix. It is visually displayed below.

How does this activity help model the structure of DNA? What changes could we make to improve the accuracy of this model?

It gives you a prime visual of what DNA looks like. For me personally having the white pipe cleaner showing the H-bond between the strands is great. Also the beads show purines with 2 and pyrimidines with 1. Then having the blue pipe cleaner resemble the 2 Strands of nucleotides backbones and pink beads as the phosphate. It gives me a great visual of all the pieces of DNA. However it would be cool to somehow have a glimpse of how long they are, for this model only shows about 20 nucleotides long, when DNA can be up to 85 million long. To improve accuracy maybe we could show the 5-carbon sugar more accurately by having another bead for it, and then putting the phosphate to the side of it somehow because technically they aren’t on top of each other as this model shows.

When does DNA Replication Occur?

DNA replication happens in all living organisms. This process happens before cell division, and passes down genetic information to be inherited. It’s called a semi-conservative process where the replicated strands keeps an original strand and a replicated strand to create a brand new DMA in a double helix.

Name and Describe the 3 Steps Involved in DNA Replication. Why Does the Process Occur Differently on the “Leading” and “Lagging” Strands?

Unwinding and unzipping, something called DNA Helicase unwinds the double helix so it’s like a straight ladder. Them it unzips by breaking through the H-bonds, as The green enzyme shows below.

Complimentary base pairing, so after the strands are unzipped DNA Polymerase uses the free-floating nucleotides in the nucleoplasm to pair them to the unzipped strands. DNA Polymerase can only build from 5′ to 3’, so it cannot go 3’ to 5’. This first strand can work without interruption and is know as the leading strand. Then the other strand has to work backwards because it has to go 5’ to 3’ resulting in Okazaki fragments. This strand is called the lagging strand.

Adjacent nucleotides joining, the individual nucleotides that we’re bonded in the process before are now bonded beside each other with a sugar phosphate backbone. The enzyme DNA Ligase is responsible for this. And then finally it’s capable of winding into a double helix strand, creating a complete DNA strand.

What Did You do to Model the Complimentary Base Pairing and Joining of Adjacent Nucleotide Steps of DNA Replication. In What Ways was This Activity Well Suited to Showing This Process? In What Ways Was it Inaccurate?

In this this activity we showed the phosphate bonds and the nucleotides joining at the same time, this is inaccurate. However, it was a good example of the unzipping and the creation of the template strands.