EL's+Logbook+week+of+Oct+22


 * 10/22/07**
 * **Information** ||
 * *Important Proteins
 * http://www.ncbi.nlm.nih.gov/books/bv.fcgi?rid=stryer.appendix.4984** ||
 * ===What I did & Opinion=== ||
 * 1. Searched the structure of protein
 * ===What I did & Opinion=== ||
 * 1. Searched the structure of protein
 * 1. Searched the structure of protein

2. Searched the significant proteins in human body

3. Updated Tasklist and sent it to Dr. Loughran ||

10/23/07
 * ===Information=== ||
 * ===What I did & Opinion=== ||
 * 1. Reorganized my logbook.
 * ===What I did & Opinion=== ||
 * 1. Reorganized my logbook.
 * 1. Reorganized my logbook.

2. Sent an e-mail to Jill ||

10/24/07 The tertiary structure of a protein molecule, or of a subunit of a protein molecule, is the arrangement of all its atoms in space, without regard to its relationship with neighbouring molecules or subunits (IUPAC-IUB, 1970).
 * ===Information=== ||
 * **Tertiary Structure**
 * **Tertiary Structure**

The quaternary structure of a protein molecule is the arrangement of its subunits in space and the ensemble of its intersubunit contacts and interactions, without regard to the internal geometry of the subunits. The subunits in a quaternary structure must be in noncovalent association. Haemoglobin contains four polypeptide chains (alpha2b2) held together noncovalently in a specific conformation as required for its function.
 * Queternary Structure**

[|**http://guweb2.gonzaga.edu/faculty/cronk/biochem/**] The biotin-dependent carboxylases are enzymes that add carbon dioxide to substrates, making use of a covalently-linked biotin prosthetic group. Pyruvate carboxylase is a member of this group of enzymes, which also includes acetyl CoA carboxylase and propionyl CoA carboxylase. The latter two enzymes play important roles in fatty acid metabolism. All the biotin-dependent carboxylase reactions require ATP hydrolysis as well as participation of the biotin prosthetic group. A general form of the reaction catalyzed by biotin-dependent carboxylases is shown below. The substrates include an a-keto acid (pyruvate) and thioesters. The pyruvate carboxylase reaction, for example, is represented when X COO– and R **H.
 * biotin-dependent carboxylases**


 * [[image:http://guweb2.gonzaga.edu/faculty/cronk/biochem//images/carboxylase.gif width="700" height="137" caption="Generalized carboxylas reaction"]] ||
 * Generalized carboxylas reaction ||

Peptide** A short, linear chain of amino acids, linked by peptide bonds. A peptide is usually distinguished from a protein simply as a matter of size, or (somewhat equivalently) being routinely producible by common solid-phase synthetic methods. The roughly synonymous term polypeptide is often used to denote peptides or proteins. Many hormones, such as insulin and glucagon are peptides.

Peptide bond
A type of amide bond formed - typically - by the condensation of the a-carboxyl group of an amino acid with the a-amino group of a second amino acid. The peptide bond is planar and rigid by virtue of partial double-bond character. ===Ribonucleic acid (RNA)=== A linear polymer of nucleotide monomers (ribonucleotides) that plays a key roles in the expression of genetic information. A ribonucleotide consists of one of four bases (adenine, cytosine, guanine, or uracil) linked to C-1 of D-ribose, which in turn is linked to phosphate via the C-5 hydroxyl. The polymer chain is linked via phosphates bridging the C-5 and C-3 hydroxyl groups of ribose (these are denoted the 5' and 3' carbons; unprimed numbers refer to atoms on the bases). The bases thus project away from this sugar-phosphate backbone. The composition of deoxyribonucleic acid (DNA) is similar to that of RNA, except that DNA contains deoxyribose instead of ribose, and the base thymine replaces uracil.There are three main types of RNA. Ribosomal RNA (rRNA) is the major component of ribosomes, the cellular machinery responsible for protein synthesis. Messenger RNA (mRNA) is in essence a copy of the DNA of genes that encode proteins. mRNA serves as a template for ribosomal protein synthesis. Transfer RNAs (tRNA) are the smallest RNA molecules, and they serve as adaptors, bringing together activated amino acids for linkage in a polypeptide (protein) in a sequence dictated by the mRNA template. In a given organism, there are tRNAs specific for each of the 20 naturally-incorporated amino acids in proteins. ===Deoxyribonucleic acid (DNA)=== A long, polymeric molecule, made up of repeating units called nucleotides, DNA has a central role in biology as the carrier of genetic information. A strand of DNA is a single, covalently linked chain of nucleotides that form a sugar-phosphate backbone to which four types of bases are attached. The sugar component of DNA nucleotides is deoxyribose, thus the nucleotides that make up DNA are more precisely termed deoxyribonucleotides. The four types of bases incorporated into DNA are adenine, cytosine, guanine, and thymine. The information carried by DNA is encoded in the sequence of bases that occur along a single strand. In this context, the bases are usually represented by single-letter abbreviations: A, C, G, T. In a DNA strand, deoxyribonucleotides are linked through a phosphate diester bridge between the 3' hydroxyl of one and the 5' hydroxyl of the next. This forms the sugar-phosphate backbone of DNA, which has directionality or polarity. DNA sequences are read in the 5' -> 3' direction, meaning the direction established by tracing the sugar-phosphate backbone through a single deoxyribose from its 5' position to its 3' position. ||
 * ===What I did & Opinion=== ||
 * 1. Which structure the major proteins in the body have according to own Van diagrams?
 * 1. Which structure the major proteins in the body have according to own Van diagrams?
 * 1. Which structure the major proteins in the body have according to own Van diagrams?

2. Need to clarify the difference between DNA and RNA

3. Reviewed the contents that I gathered before

4. Learned some biochemistry vocabularies

5. Can I imply any the exception of the protein structure ( There are countless number of protein structure that is not defined. ) ||

10/25/07
 * ===Information=== ||
 * http://www.jcb.org/cgi/content/abstract/123/6/1333[|]
 * Nuclear pore1 complexes** (NPCs) are anchoring sites of intranuclear filaments of 3-6 nm diameter that are coaxially arranged on the perimeter of a cylinder and project into the nuclear interior for lengths varying in different kinds of cells. Using a specific monoclonal antibody we have found that a polypeptide of approximately 190 kD on SDS-PAGE, which appears to be identical to the recently described NPC protein "nup 153," is a general constituent of these intranuclear NPC-attached filaments in different types of cells from diverse species, including amphibian oocytes where these filaments are abundant and can be relatively long. We have further observed that during mitosis this filament protein transiently disassembles, resulting in a distinct soluble molecular entity of approximately 12.5 S, and then disperses over most of the cytoplasm. Similarly, the amphibian oocyte protein appears in a soluble form of approximately 16 S during meiotic metaphase and can be immunoprecipitated from egg cytoplasmic supernatants. We conclude that this NPC protein can assemble into a filamentous form at considerable distance from the nuclear envelope and discuss possible functions of these NPC-attached filaments, from a role as guidance structure involved in nucleocytoplasmic transport to a form of excess storage of NPC proteins in oocytes.
 * Nuclear pore1 complexes** (NPCs) are anchoring sites of intranuclear filaments of 3-6 nm diameter that are coaxially arranged on the perimeter of a cylinder and project into the nuclear interior for lengths varying in different kinds of cells. Using a specific monoclonal antibody we have found that a polypeptide of approximately 190 kD on SDS-PAGE, which appears to be identical to the recently described NPC protein "nup 153," is a general constituent of these intranuclear NPC-attached filaments in different types of cells from diverse species, including amphibian oocytes where these filaments are abundant and can be relatively long. We have further observed that during mitosis this filament protein transiently disassembles, resulting in a distinct soluble molecular entity of approximately 12.5 S, and then disperses over most of the cytoplasm. Similarly, the amphibian oocyte protein appears in a soluble form of approximately 16 S during meiotic metaphase and can be immunoprecipitated from egg cytoplasmic supernatants. We conclude that this NPC protein can assemble into a filamentous form at considerable distance from the nuclear envelope and discuss possible functions of these NPC-attached filaments, from a role as guidance structure involved in nucleocytoplasmic transport to a form of excess storage of NPC proteins in oocytes.

1 **In cell & molecular biology** ([|**http://en.wikipedia.org/wiki/Pore)**]* Nuclear pore, a large protein complex that penetrates the nuclear envelope in eukaryotic cells
 * The ion-selective opening in the membrane of a eukaryotic cell formed by members of the ion channel family of proteins
 * A water-selective opening (water channel) in the membrane of a eukaryotic cell formed by assemblies of the protein aquaporin[|**http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1257468**] //<- **VERY HELPFUL SITE**!//===The two tempos of nuclear pore complex evolution: highly adapting proteins in an ancient frozen structure=== **By Eric Bapteste, Robert L Charlebois, Dave MacLeod, and Céline Brochier**In 1938, Copeland proposed to gather in a large but unnamed natural group all the organisms (both multicellular and unicellular) harboring a nucleus [[|1],[|2]]. He considered that the nucleus was too complex a structure to have appeared independently several times [[|1],[|2]]. The possession of a nucleus is still commonly considered as a good synapomorphy for eukaryotes. However, very little broad comparative analyses of eukaryotic nuclei have been conducted in order to test the homology of this structure. Very recently, Mans //et al.// [[|3]] investigated by BLAST searches the distribution of homologous proteins of the nucleus and of a few associated systems in the three domains of life. Yet, apart from this stimulating work, the nucleus is only well studied in vertebrates [[|4],[|5]] and in fungi [[|6]-[|8]], whereas little is known in protists or plants. For this reason, the origin and evolution of this structure are difficult to address and largely remain to be described.The nuclear pore complex (NPC) is one of the most important components of the nucleus. It is a gate between the nucleoplasm and the cytoplasm, mediating the nucleocytoplasmic transport of small molecules by either diffusion or active transport of large substrates [[|9]-[|15]]. Recent works have suggested that some components of the NPC may play a role in the structural and functional organization of perinuclear chromatin [[|16]], in chromatin boundary activities [[|17]] and in interactions with kinetochores [[|18],[|19]]. A role in numerous pathways has also been observed, such as the control of gene expression, oncogenesis and the progression of the cell cycle [[|20]-[|23]]. The NPC is thus a fully integrated structure and its evolution is likely very constrained.The NPC is also one of the largest macromolecular complexes in the eukaryotic cell (approximately 60 MDa and 125 MDa in yeast [[|6]] and vertebrates [[|24]], respectively), composed of more than 30 different interacting proteins generally referred to as nucleoporins [[|5],[|6],[|15],[|25]]. The nuclear pore exhibits an octagonal symmetry around its cylindrical axis. It consists of a cylindrical core, composed of eight interconnected spokes (each spoke being composed of the Nup93, Nup205, Nup188 nucleoporins; Figure [|1a]), that surrounds the central channel. Each spoke is connected on the nucleoplasm and cytoplasm sides to a Nup160 subcomplex (Nup133, Nup96, Nup107, Nup37, Nup43, Nup160, Nup75) that binds to the Sec13R and Seh1 proteins (Figure [|1a]; Table [|1]). The Nup160 complexes form a plane pseudo-mirror symmetry running parallel to the nuclear envelope. From the central ring, 50 to 100 nm fibrils extend into the nucleoplasm, where they conjoin distally to form a basket-like structure (Nup153, Nup98/Rae1, Nup50, Tpr; Figure [|1a]; Table [|1]), spreading outwards into the cytoplasm (Nup214, Nup88, Nup358, Ubc9, RanGap1, Nup35; Figure [|1a]; Table [|1]). The Nup62 subcomplex, also called the central transporter, may be involved in transport across the NPC (Figure [|1a]; Table [|1]). In vertebrates, the NPC is anchored to the nuclear envelope by the Gp210 and the Pomp121 proteins (Figure [|1a]) and is connected with the nuclear lamina, a meshwork of lamins and lamin-associated proteins that form a 15 nm thick fibrous structure between the inner nuclear membrane and peripheral chromatin (Figure [|2]).

||
 * ===What I did & Opinion=== ||
 * 1. What NPC stands for? Nuclear pore complexes
 * 1. What NPC stands for? Nuclear pore complexes

2. Details about NPC protein ||

10/26/07

or monomers, connected by covalent chemical bonds. http://en.wikipedia.org/wiki/Polymer
 * ===Information=== ||
 * * These contents are derived from Lehinger PRINCIPLES OF BIOCHEMISTRY fourth edition by David L. Nelson and Michael M. Cox- The basic unite of DNA is a linear __polymer__ of four different monomeric subunits, deoxyribonucleotides, arranged in a precise linear sequence.: A polymer is a substance composed of molecules with large molecular mass composed of repeating structural units,
 * * These contents are derived from Lehinger PRINCIPLES OF BIOCHEMISTRY fourth edition by David L. Nelson and Michael M. Cox- The basic unite of DNA is a linear __polymer__ of four different monomeric subunits, deoxyribonucleotides, arranged in a precise linear sequence.: A polymer is a substance composed of molecules with large molecular mass composed of repeating structural units,

- Despite the near-perfect fidelity of genetic replication, infrequent, unrepaired mistakes in the DNA replication process lead to changes in the nucleotide sequence of DNA, producing a genetic mutation and changing the instructions for some cellular component. Occasionally, a whole gene is duplicated. The secnod copy is superflous, and mutations in this gene will not be deleterious; it becomes a means by which the cell may evolve: by producing a new gene with a new funtion while retaining the original gene and gene funtion.

- Water is a polar solvent. It readily dissolves most biomolecules, which are generally charged or polar compounds; compounds that dissolve easily water are **hydrophilic**. In contrast, nonpolar solvents such as chloroform and benzene are poor solvents for polar biomolecules but easily dissolve those that are **hydrophobic**--nonpolar molecules such as lipids and waxes.

Hydrophobic interaction
The nonpolar regions of the molucules cluster together to present the smalles hydrophobic area to the aqueous solvent, and the polar regions are arranges to maximize their interaction with the solvent. These stable structures of amphipathic compounds in water, calles micelles, may contain hundreds or thousands of molecules. The forces that hold the nonpolar regions of the molecules together are called hydrophobic interactions. ||
 * ===What I did & Opinion=== ||
 * 1. Reviewed Lehinger PRINCIPLES OF BIOCHEMISTRY.
 * 1. Reviewed Lehinger PRINCIPLES OF BIOCHEMISTRY.

2. Canceled the appointment at Notre Dame ||