Project Objective
Understand protein synthesis and how mutations in the DNA affect amino acids in the polypeptide chain
Key Concepts and Terms
Protein Synthesis: the process by which biological cells generate new proteins. The three steps of protein synthesis are transcription (DNA to mRNA), translation (mRNA to Polypeptide), and folding (Polypeptide to Protein).
Transcription: the genetic information in the DNA is copied to an mRNA molecule, as one strand of the DNA double helix is used as a template opened by an enzyme called RNA polymerase, taking place in the nucleus. There are three phases in transcription: initiation, elongation, and termination. Initiation is the RNA polymerase “finding” the promoter regions’ codon in the gene (3 nucleotides). Next is elongation, when the RNA polymerase uses the free floating RNA nucleotides in the nucleus and forms a messenger RNA or "mRNA" molecule out of them. Then comes termination, where the RNA polymerase finishes “copying”, indicated by the terminator region of the gene with 3 codons. After this, the mRNA has introns (non-coding regions), and exons (coding regions). To make sure that the mRNA is ready for future copying, spliceosomes remove the introns (splicing), to leave the mRNA with exons.
Protein Folding: Begins immediately after translation and even happens during it. It takes place in the endoplasmic reticulum and the golgi apparatus. The formation of the secondary structure (α "alpha" helices and β "beta"sheets) begins very rapidly after translation because they are stabilized by intramolecular hydrogen bonds. Alpha helices are formed when hydrogen bonds to the backbone to form a helix. Beta sheets are formed when the backbone bends back on itself to form the bonds. Their location on the polypeptide is determined by the amino acid sequence. The different secondary structures have hydrophobic and hydrophilic ends, which is crucial to the formation of the tertiary structure. The hydrophobic part of the structure will orient itself to the center of the protein away from the aqueous environment surrounding the protein in the cytoplasm while the hydrophilic ends will form the outside of the structure. Disulfide bridge covalent bonds may also form between cysteine residues and further stabilize the tertiary structure. The tertiary structure often has separate domains, which are areas of the polypeptide chain that fold independently and don’t interact with one another but are still part of the same polypeptide chain. Interactions between multiple tertiary structures can lead to the formation of quaternary structures. Each structure level have domains, which are just smaller parts of a structure. The secondary structure of α helices and β sheets, are comprised of primary structures as its domains. The tertiary structure uses α helices and β sheets from the secondary structure as domains, as the quaternary structure uses the teriary structure as the domains.
Transcription: the genetic information in the DNA is copied to an mRNA molecule, as one strand of the DNA double helix is used as a template opened by an enzyme called RNA polymerase, taking place in the nucleus. There are three phases in transcription: initiation, elongation, and termination. Initiation is the RNA polymerase “finding” the promoter regions’ codon in the gene (3 nucleotides). Next is elongation, when the RNA polymerase uses the free floating RNA nucleotides in the nucleus and forms a messenger RNA or "mRNA" molecule out of them. Then comes termination, where the RNA polymerase finishes “copying”, indicated by the terminator region of the gene with 3 codons. After this, the mRNA has introns (non-coding regions), and exons (coding regions). To make sure that the mRNA is ready for future copying, spliceosomes remove the introns (splicing), to leave the mRNA with exons.
- Nucleus: An organelle containing chromosomes, and other genetic material. It is the control center that tasks everything in a cell.
- Template: A molecule that acts as the pattern for the sequence of assembly, used for copying.
- DNA: Deoxyribonucleic acid, which has a double helix, anti-parallel sugar-phosphate backbones, where deoxyribose and phosphates are alternated, and nucleotides. The nucleotides are complementarily bonded though Hydrogen bonds, as Phosphodiester bonds bind the deoxyribose and the phosphate group from the 3' to 5' direction.
- Nucleotides: The Nitrogenous bases that create DNA and RNA.
- There are two classes of nucleotides: Purines, which bind to Pyrimidines.
- For DNA the nucleotides are Adenine (A), and Guanine (G), which are Purines, and Cytosine (C), and Thymine (T), which are Primidines. They bind as follows: A-T; G-C in a H=H double bond.
- For RNA the nucleotides are Adenine (A), and Guanine (G), which are Purines, and Cytosine (C), and Uracil (U), which are Primidines. They bind as follows: A-U; G-C, in a H=H double bond.
- There are two classes of nucleotides: Purines, which bind to Pyrimidines.
- Messenger RNA or "mRNA": The copy of the DNA template that contain codons.
- Transfer RNA or "tRNA": the molecule that carries one amino acid and one anticodon to match the mRNA codons.
- Ribosome: An organelle located in the cytoplasm, and on the rough endoplasmic reticulum, which is the processing site for translation.
- Amino Acids: Protein monomers, made of an Amino Group (NH3 ) a Carboxyl Group (COO-), A Hydrogen atom, and a variant group (R-group), that determines the role of a protein.
- Polypeptide Chain: The string of bound amino acids that creates a protein, and determines it's function. Also known as the Primary Protein Structure.
Protein Folding: Begins immediately after translation and even happens during it. It takes place in the endoplasmic reticulum and the golgi apparatus. The formation of the secondary structure (α "alpha" helices and β "beta"sheets) begins very rapidly after translation because they are stabilized by intramolecular hydrogen bonds. Alpha helices are formed when hydrogen bonds to the backbone to form a helix. Beta sheets are formed when the backbone bends back on itself to form the bonds. Their location on the polypeptide is determined by the amino acid sequence. The different secondary structures have hydrophobic and hydrophilic ends, which is crucial to the formation of the tertiary structure. The hydrophobic part of the structure will orient itself to the center of the protein away from the aqueous environment surrounding the protein in the cytoplasm while the hydrophilic ends will form the outside of the structure. Disulfide bridge covalent bonds may also form between cysteine residues and further stabilize the tertiary structure. The tertiary structure often has separate domains, which are areas of the polypeptide chain that fold independently and don’t interact with one another but are still part of the same polypeptide chain. Interactions between multiple tertiary structures can lead to the formation of quaternary structures. Each structure level have domains, which are just smaller parts of a structure. The secondary structure of α helices and β sheets, are comprised of primary structures as its domains. The tertiary structure uses α helices and β sheets from the secondary structure as domains, as the quaternary structure uses the teriary structure as the domains.
- Protein: A macromolecule that execute most of the functions of the cells. They are often used as catalysts and enzymes.
- Misfolding: A mutation in the primary structure affecting the higher level structures, and their function.
Application to Biology
In the second and third portions of our pamphlet, transcription, translation, and folding are discussed both as a process, and under the example of Familial Creutzfeldt-Jakob Disease (fCJD). The second portion incorporates the ideas above to provide a general understanding of these processes as the third portion includes the sequencing for the codons, anticodons, and polypeptides; examination of how these mutations lead to a structural change in the tertiary structure, in the scope of α helices and β sheets of the secondary structure domain; and how protein synthesis relates to this disease.
Pamphlet
Reflection
To be frank, I was concerned at the beginning of the project with time management, and group productivity, but as the project went on, this became less of an issue. The group dynamic was great; where people would joke and play around, add humor, while still being aware of and task-minded on the project. During our research phase, we had created organized notes, and had finished it almost ahead of schedule. But within this, groupmates would have fun replacing letters, and changing fonts, but were able to control themselves and make a separate document for their creativity, while those who were working weren't interrupted. There also was strong communication, and work responsibility among the members, having their tasks completed in or near time. Although a time management chart, Gantt Chart, was used in this project, I felt that it only detracted us from time spent on work rather than fixing and updating the chart. Another aspect that we could have improved on would be presentation. Although the pamphlet is good, other presentation media, a poster, or discussion would have made more sense. Another improvement could be made in presentation delivery and rehearsal. I felt that most of our presentation was non-projective and was reliant on reading, rather than presenting the highlights to the audience. But overall I had fun with this project,
( especially in the research phase where we ran into struggles that kept us stuck for days, such as tracking the amino acid sequence in relation to the genetic sequence, and overcame them was fun), and am proud of the way the group was able to work and the work that went into the product.
- Nihal Nazeem.
( especially in the research phase where we ran into struggles that kept us stuck for days, such as tracking the amino acid sequence in relation to the genetic sequence, and overcame them was fun), and am proud of the way the group was able to work and the work that went into the product.
- Nihal Nazeem.