Soto Biochemistry 9/22
Soto Biochemistry 9/22 CHEM 351
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This 5 page Class Notes was uploaded by Kayli Antos on Friday September 25, 2015. The Class Notes belongs to CHEM 351 at Towson University taught by Ana Soto in Summer 2015. Since its upload, it has received 15 views. For similar materials see Biochemistry in Chemistry at Towson University.
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Date Created: 09/25/15
Biochem Soto FaJl 2015 0 me 77111343 Dimensional Structure Of Proteins 9 0 Tertiary And Quaternary Structure gt Tertiary structure is the 3D arrangement of all the atoms in a protein due to folding Amino acids that are far apart on the peptide chain may interact because of this folding The folded structure is held together by weak internal interactions gt Some proteins are made up of more than one polypeptide chain The arrangement of these subunits is the quaternary structure gt Proteins can be fibrous or globular n Fibrous have their polypeptides arranged in sheets or long strands Typically exist to provide support shape and protection 31 Globular have their polypeptides in a spherical shape These proteins are typically enzymes and regulatory proteins 0 0 Fibrous Proteins gt The fundamental structural unit is a repeating element of it s secondary structure gt They re insoluble in water due to containing hydrophobic amino acids gt X keratin is made up of X helices twisted around each other This twisting increases strength These coiled coils can be assembled into larger complexes 0 90 Collagen gt Three separate polypeptide chains twisted around each other These triple helical collagen molecules are also called tropocollagen This twisting is right handed gt Each of the X chains is lefthanded and has three amino acids per turn with the sequence Gly X Y X is usually Pro and Y is usually 4 Hyp 4 hydroxy proline gt Gly can fit at very tight turns and Pro and 4 Hyp can twist sharply gt Tropocollagen can withstand being pulled gt The next level of collagens structure is called fibrils which is made up of tropocollagen staggered and cross linked The alignment and crosslinking depends on the specific tissue gt The crosslinking is due to covalent bonds between Lys and His gt The fibrils are then arranged into fibers 9 0 Globular Proteins gt Have a compact shape due to different segments of the polypeptide chain folding back on itself gt This folding enables the diversity of structure for globular proteins to carry out a variety of functions gt Usually have a hydrophobic center and hydrophilic outer surface The structure is stabilized by hydrogen bonds and ionic interactions 39339 Protein Folds gt The 3D structure of a globular protein can be thought of as a combination of connected X helices and B sheets gt Two or more recognizable secondary structures will commonly be found together and these are called motifs or supersecondary structures gt Proteins may also fold into distinct parts called domains which are sections that would form the same shape regardless on if they were attached to the other domains or not 0 0 Oligomeric Proteins gt Proteins may have more than one polypeptide subunit and they are called multimers A multimer with only a few subunits is an oligomer The structural subunit that repeats is the protomer o 0 Protein Folding And Denaturation gt Denaturation is any loss of 3D structure that is enough for the protein to lose function gt As soon as a structure starts unfolding the rest of the protein will subsequently lose its structure as well gt Some things that can cause a protein to denature are heat extreme pH organic solvents and chaotropic agents like urea and guanidine hydrochloride gt Denaturing agents work by disrupting hydrophobic interactions hydrogen bonds or the charges in the protein causing it to be unable to hold itself together in its native state 9 0 Amino Ac1d Sequence Determines Structure gt Christian Anfinsen showed that the tertiary structure of a protein is based on its amino acid sequence by showing that denaturation is reversible and the protein loses its catalytic function when it is denatured gt Denatured ribonuclease A urea and a reducing agent 39339 Folding Is A Biased Process gt Proteins fold too fast to be going through random conformations until they reach their native state gt Levinthal s paradox is that if a small protein of 100 amino acids had 10 possible conformations for each amino acid that would be 10100 possible conformations It would take the protein 1077 years to form all conformations even if each conformation happened as fast as possible gt This proves that there is a method to the folding It begins with local secondary structures forming and then those structured arranging themselves into the tertiary structure gt Ionic and hydrophobic interactions help guide this folding process gt The folding of a protein can be looked at as a hydrophobic collapse where the non polar parts of the protein will be at the center of the protein 3 Stability Of The Folded State gt Native proteins are only slightly more stable than the unfolded state The AG is only about 20 to 65 kJmol gt The unfolded protein has more entropy and can make more interactions with water gt The folded state has disulfide bonds and weak non covalent bonds to stabilize it Since the folded state has the most weak interactions it has the lowest free energy gt The hydrogen bond between water and the polypeptide is not ideal The hydrogen bonds between water and the intramolecular bonds are stronger which is why the folded version persists over the unfolded gt Not all proteins have disulfide bonds Extracellular proteins are more likely to have disulfide bonds because the environment outside the cell is oxidizing while inside the cell it is reducing n 0 Protein Func on gt Protein Binding 1 The function of proteins is often dependent on their interactions with other molecules Molecules can bind reversibly to a ligand which binds with a high specificity to the proteins biding site The binding site is complementary to the ligand in respect to size shape charge and affinity for water Proteins are exible and any change in their conformation no matter how small will greatly affect their function When a protein binds to a ligand its conformation is often changed If a protein has multiple subunits a conformational change in one unit will affect the conformation of the others gt 92 Transport 1 Oxygen is not easily dissolved in an aqueous solution so proteins are used to carry it to tissues No amino acids are favorable for reverse binding of oxygen but certain transition metals are Iron is often used for this purpose and when incorporated into a prosthetic group it s called a heme A heme group is a protoporphyrin ring with iron bound in the center The iron has six bonds total four to the nitrogens of the ring one to a histidine in myoglobin and one to an oxygen molecule The ring is planar and the His and 02 are perpendicular to the ring gt Heme n The coordinated nitrogen atoms of the protoporhyrin ring are used to make sure that Fe2 stays at that oxidation state instead of converting to Fe3 The latter does not bind reversibly to oxygen and will then be useless In a free heme molecule one oxygen molecule can interact with two Fe2 and cause them to convert to Fe3 This is why the heme is deep within a protein so a single oxygen molecule can only interact with a single iron gt Myoglobin 1 1 The globin family of proteins contains myoglobin and hemoglobin Myoglobin stores oxygen and facilitates oxygen diffusion into muscle tissues Hemoglobin transports oxygen in the bloodstream Myoglobin is a single strand of 153 amino acids with one heme molecule and therefore can bind to one oxygen molecule The heme groups accessibility is highly restricted due to its placements in the proteins structure
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