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The Macromolecules of Life - Carbon

The dissociative chemisorption of methane on a metal catalyst is the rate limiting step in the steam reforming of natural gas, our primary source for the molecular hydrogen used in the Haber-Bosch process. In collaboration with the experimental group of Rainer Beck at the École Polytechnic Fédéral de Lausanne, we examined this reaction on a Pt surface containing step defects. We were able to differentiate between reactions at the step edges and the terrace sites, using both UHV molecular beam experiments and high-dimensional quantum scattering theory. Both approaches were also able to resolve the reaction probability with respect to the velocity and vibrational state of the methane molecule and the surface temperature, providing additional details about the reaction mechanism.

Lila M. Gierasch was awarded the Ralph F. Hirschmann Award in Peptide Chemistry for her seminal contributions to peptide structure and function, peptide models for protein folding and function, and roles of peptide and protein aggregation in disease.

  Proteins and Proteomics Animations (Rediscovering Biology)

(Interactive Concepts in Biochemistry)

RNA polymerase
RNA polymerase searches DNA for initial site. It unwinds a short stretch double helical DNA to produce a single stranded DNA template from which it takes instructions. Also selects the correct ribonucleotide and catalyzes the formation of phosphodiester bond and detects the termination signals which specify where a transcript ends. RNA polymerase interacts with activated and repressor proteins that modulate the rate of transcription initiation over a wide dynamic range. In prokaryotes, only one type of RNA polymerase is present. It transcribes mRNA, tRNA and rRNA. Eukaryotes possess three RNA polymerases: RNA polymerase I, II and III.

Post transcriptional controls/ RNA splicing
mRNA undergoes significant processing within the nucleus prior to transport to cytoplasm: by removal of non coding into internal sequences called introns. It undergoes modification of the 5’ base and an addition of adenine to 3’ end (poly A tail) takes place. RNA splicing is a process that removes introns and joins exons in a primary transcript.

(Northland Community & Technical College)

Information flow in the cell: DNA is transcribed to mRNA which is translated (decoded as) into Protein. Protein biosynthesis takes place in the ribosomes. tRNA brings specific amino acid to ribosome and mRNA provides the sequence information for protein. Protein biosynthesis has three processes: Initiation involved with initiation factors, elongation involved with growing of peptide chain and termination. Hydrolytic editing also takes place if a wrong amino acid is added.

Ribonucleic acids are made up of nitrogenous bases such as adenine, Uracil, guanine and cytosine, ribose sugar and phosphate group. RNA is normally single stranded which can have a diverse form of secondary structures other than duplex. tRNA shows secondary and tertiary structure. RNA synthesis is the process of transcribing DNA nucleotide sequence information into RNA sequence information. RNA synthesis is catalyzed by a large enzyme called RNA polymerase. RNA synthesis involves three steps: Initiation, elongation and termination. RNA splicing is a process that removes introns and joins exons in a primary transcript. Post transcriptional changes take place and mRNA, tRNA and rRNA are processed.

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RNAs involved in protein biosynthesis

$6.8 million in external research funding

Quality control and chaperones
If at all, a wrong amino acid is added, tRNA synthetase removes the incorrectly attached amino acid through hydrolytic editing. There are protein molecules called chaperones that catalyze the correct folding of other proteins within the cell. They also help in preventing aggregation. The hsp70 family of molecular chaperones helps in correct folding after synthesis.

Post transcriptional controls/ RNA splicing

RNA synthesis
RNA synthesis occurs in both prokaryotes and eukaryotes. There are three steps to RNA synthesis: Initiation, elongation and termination. In the initiation step, RNA polymerase binds to gene regulatory elements. In the elongation step, RNA polymerase unwinds DNA duplex next to a gene. RNA is transcribed 5’ to 3’ from the template of 3’ to 5’. Termination in eukaryotes is by cleavage and polyadenylation.

Interdisciplinary training programs and courses

Process of protein biosynthesis
There are signal sequences before the real coding sequence at the translation initiation sites. Amino acid activation is catalyzed by amino acyl-tRNA synthetase and couples it to its corresponding tRNA. Anti codon in tRNA molecule forms base pairs with the appropriate codon on the mRNA. In the initiation step, initiation factors are involved. Initiation factor is the protein that promotes the proper association of ribosomes with messenger RNA. In the elongation step, incorporation of an amino acid into a protein takes place. As a result, polypeptide chain is grown. Termination is the last stage in protein biosynthesis.

“Multiple exciton generation in isolated organic molecules”

For the most part, fundamental surface science studies have focused on model systems where the surface of the metal is smooth and regular. On the other hand, it has long been suspected that the activity of “real” heterogeneous catalysts is dominated by reactions at step edges and other defect sites.

Protein Synthesis - Biochemistry - NCBI Bookshelf

Types of RNA
mRNA represents about 5-10% of cellular RNA. It contains the sequence of bases coding for a particular amino acid sequence in a polypeptide chain. tRNA represents about 15-20% of cellular RNA. Each tRNA molecule is specific for one amino acid. There is an enzyme for each amino acid which recognizes the amino acid and its specific tRNA and joins the two together. The specific joining of tRNA to amino acid is the only place where the genetic code is realized. rRNA represents about 70-80% of cellular RNA. It is associated with specific set of ribosomal proteins. It functions as non-specific ‘workbench’ for the assembly of polypeptides. Many copies of genes coding for rRNA are located in nucleolar organizer regions of certain chromosomes.

Protein Synthesis - The Medical Biochemistry Page

Gierasch stated, “The environment in a cell is extremely complex and challenging for the process of protein folding, leading to a need for a network of species that protect protein states that are susceptible to aggregation—the protein homeostasis network. We are working with colleagues and collaborators to understand the underlying mechanisms of protein homeostasis from the level of the molecular chaperone machines that act on protein clients to the coordinated action of the network in all of its complexity. We would love to witness and contribute to new discoveries related to these questions, both because of the fascinating basic science involved and because failures in these systems are implicated in a wide array of diseases, including neurodegenerative diseases.”

Interactive Concepts in Biochemistry - Interactive …

RNAs involved in protein biosynthesis
Information flow in the cell: DNA is transcribed to mRNA which is translated (decoded as) into Protein. Protein biosynthesis takes place in the ribosomes. A series of ribosomes (poly ribosome) can simultaneously translate the same eukaryotic mRNA molecule. tRNA brings specific amino acid to ribosome and mRNA carries the genetic information to protein. Codons that encode the same amino acid often differ only by their third base. The binding of the third base is less stringent than the other two. Because of this wobble, one tRNA can pair with multiple mRNA codons.

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