Protein Structure and Functions - Biochemistry

In a globular protein, the amino acid chain can twist in a way that polar groups lie at the protein's surface. This allows the protein to interact with water and enhances the protein's solubility in water. This does not occur in fibrous proteins, so fibrous proteins are insoluble in water.

Actin chain growth occurs at the (+) end of the chain, and nucleotide hydrolysis promotes dissociation of actin chains. 2 microfilaments of G-actin monomers make 1 filament of F-actin. However, actin filament assembly is powered by ATP, not GTP.

An O-linked glycoprotein is a protein that has a sugar attached to it. It is called O-linked because the sugar is attached to an oxygen atom on either a threonine residue or a serine residue within the protein.

When a protein is damaged, it can be tagged with the molecule, ubiquitin. This signals to the cell that the protein is no longer functioning properly and needs to be degraded.

HMGCoA reductase is the rate-limiting enzyme in cholesterol synthesis. The reductase is present on the endoplasmic reticulum membrane. When levels of its product, cholesterol, are high, the enzyme gets ubiquitinated and degraded in smaller peptides and amino acids. It first binds to insulin-induced gene 1 protein before ubiquitination.

Phosphoglucomutase is responsible for altering the position of the phosphate on the glucose from the "1" position to the "6" position. However, notice how the molecular formula for the product and the substrate are the same. Enzymes that rearrange the structure of a molecule in this manner are referred to as isomerase enzymes.

Mammalian DNA ligase I has this function, and there are other DNA ligases which perform it in other animals and eukaryotes (prokaryotes also have their own DNA ligases). All the other functions mentioned are done by other classes of enzymes, not ligases (i.e. hydrolases, aminotransferases, oxidoreductases, etc.).

A high carbon dioxide concentration will decrease the pH and produce the Bohr effect. These conditions will cause a slight conformational change in hemoglobin that results in a lower oxygen binding affinity. However, since the partial pressure of oxygen in the lungs in so high, most of the available oxygen will be loaded on to the hemoglobin anyway. Since the oxygen affinity is lowered, the hemoglobin will release the oxygen more freely, resulting in a greater oxygen to load in tissue. Functioning hemoglobin always has four cooperative subunits.

The process of creating transport vesicles via clathrin coats proceeds in distinct steps. Before any budding occurs of the membrane, clathrin attaches to it, bound to adaptin which is attached to a transmembranal cargo receptor. (Cargo molecules are what trigger the creation of the vesicle in the first place.) The clathrin coating is believed to cause the membrane to bud. After the vesicle forms, dynamin uses GTP to pinch the vesicle off, and it is only then that the clathrin coat disassembles and we have a transport vesicle.

Charged molecules do not permeate the lipid bilayer easily at all. So despite its small size, among our choices, a sodium ion passes least easily through. Polar molecules also have a hard (but less difficult) time passing through, and the larger the molecule, the harder that becomes, so after the sodium ion comes glucose, followed by water, which is polar but much smaller. Small, hydrophobic molecules -- such as carbon dioxide -- diffuse through most easily, because they can pass through the longest (hydrophobic) part of the membrane.

There are two types of transport: passive transport and active transport. Active transport requires an expenditure of energy and a protein pump. Passive transport includes simple diffusion and facilitated diffusion. Diffusion is the movement of a substance from an area of high concentration to one of low concentration. Simple diffusion is the name for the diffusion process which does not require a protein; facilitated diffusion is the name for the diffusion process which requires a carrier protein for transport. Osmosis is the simple diffusion of water and thus does not require protein.

In hemoglobin, the nitrogen group on the amino acid Histidine coordinates the heme ring in hemoglobin by binding to an iron atom located in the middle of the heme ring.

A gap junction is a hexagonal protein that openly connects two adjacent cells. It is nonspecific, meaning it allows various different molecules and ions to travel through it. This type of transport is important for rapid communication between adjacent cells. For instance, gap junctions serve an important function in the heart - allowing the many cells present there to act as a functional syncytium. Integrins and tight junctions do not allow the passage of molecules between adjacent cells.

GLUT are integral membrane proteins.The proteins cross the membrane having the amino and carboxyl termini on the cytoplasmic side of the plasma membrane. Binding of glucose to the transporter leads to a conformational change, transport of glucose to the other side of the membrane. GLUT-1, GLUT -3 and GLUT-4 are present in most tissues; GLUT-2 is found in the liver, pancreas and kidney.

This problem requires knowledge of the endopeptidase properties. Trypsin cleaves after the amino acids lysine and arginine, and chymotrypsin cleaves after the amino acids phenylalanine, tyrosine, and tryptophan.

Using this information, the slashes below indicate where each enzyme cleaved the polypeptide.

(AM) (SAK)/ (YMPLWGIR)/ trypsin

(MPLW)/ (GIRAM) (SAKY)/ chymotrypsin

Because the (AM) and (GIRAM) fragments have no slash after M in both the first and second treatment, one can conclude that this piece is at the end of the polypeptide. The other two pieces are sequenced by realizing that S starts the (SAK) and (SAKY) fragments and is never found in the middle of a fragment.

There are 4 main steps in the unfolded protein response: (1) Translation of proteins is stopped, (2) Chaperones are recruited to the location of misfolded proteins, (3) Misfolded proteins are "tagged" with ubiquitin chains for degradation by the 26S proteasome, (4) if the above steps fail, the cell undergoes programmed cell death. Thus, all of the answers choices are affiliated with the unfolded protein response.

Trypsin will cleave the primary sequence after the lysine residue (on its carboxyl side). Thus, Lys will be the new carboxyl terminal and Glu will be the new amino terminal. Remember that a protein's primary sequence is written from N to C.

Trypsin will cleave lysine and arginine at the carbonyl side. Chymotrypsin will cleave phenylalanine, tyrosine, and tryptophan at the carbonyl side. Pepsin will cleave leucine, phenylalanine, tryptophan, and tyrosine at the amino side. Pepsinogen is the inactive form of pepsin, which gets activated via cleavage by hydrochloric acid in the stomach.

Chymotryspin cleaves Phe, Trp, and Tyr at the carbonyl side. This means that there will be a cleavage after any of these three amino acids appears. This results in Gly-Ala-Pro-Tyr, His-Cys-Gly-Phe, Gly-Gly-Asn.