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| Question | Answer |
| Alanine , Valine , Leucine and Isoleucine interact in a special way within proteins | They tend to cluster together within proteins, stabilizing protein structure by means of Hydrophobic interactions |
| The secondary amino(imino) group of proline residues | Is held in a rigid conformation the reduces the structural flexibility of polypeptide regions containing proline |
| Having aromatic side chains helps you do what, Name amino acids with them | They are relatively non polar, thus hydrophobic which means they can all participate in hydrophobic interactions Phenylalanine, Tryptophan, Tyrosine |
| The importance of Tyrosine in enzymes | Its Hydroxyl group can form hydrogen bonds |
| What role do Disulfide Groups play in polypeptide structures ? | They form covalent links between parts of a polypeptide molecule or between two different polypeptides |
| Which amino have a significant positive charge at ph 7.0 | 1. Lysine : second primary group on its aliphatic chain 2. Arginine : Positively charged Guanidinium Group 3.Histidine : Aromatic Imidazole group, it may be positively charged or uncharged at pH7 |
| Which amino acids have a R group with a net negative charge | Aspartate and Glutamate, each of which has a second Carboxy Group |
| Name a derivative of proline and where they are found | 4-hydroxyproline found in plant cell wall and collagen |
| What is Collagen | is an important constituant of connective tissue |
| Name 4 examples of connective tissue | 1. Cornea of the eye 2. Cartilage 3. Bones 4. Tendons |
| Name an uncommon Amino Acid derived from lysine and where it is found | 5-Hydroxylysine found in collagen as well |
| Name a derivative of lysine found in myosin and say what myosin is | 6-N-Methyllysine and Myosin is a contractile protein of muscle |
| Name a derivative of Glutamate and its use | y-Carboxylglutamate found in the blood clotting protein Prothrombin and in other proteins that bind Ca+ |
| The derivative of Four lysine residues and its function | Desmosine which is found in the fibrous protein Elastin. |
| What is Circular Dichroism | The measure of the molar absorption difference of the right handed circularly polarized light |
| What are Chromophores and how do they act in the chiral Envronment | v |
| What did Anfisens experiment show | v |
| What conformation are favored by proteins | conformations that require less energie |
| How can proteins fold so fast | v |
| Two classes of molecular chaperons | Hsp70 and Chaperonins |
| What are Heat Shot Proteins and what do they do | With the help of ATP they help proteins to fold correctly |
| What catalyzes interchange or shuffling of s-s bonds | Protein disulfide isomerase |
| What catalyzes the interconversion of the cic and trans isomers of proline | Peptide prolyl cis-trans isomerase |
| What is the characteristic of proteins containing proline | v |
| What are Amyloidoses and what are they caused by | insoluble Amyloid Fibrils caused by the misfolding of proteins |
| Name Amyloid diseases | Diseases the trigger neurodegeneration Pancreatic diseases |
| Name some of these diseases | v |
| What is Parkinsons disease | v |
| What is Huntington's disease | Hereditary disease and is caused by the repetition of .. |
| What is Prion ? | Proteinaceous Infectious Only Protein |
| Name some Prions Disease | v |
| What is Proteostasis | Maintenace of cellular protein activity whic is accomplished by |
| What are the two major classes of proteins | Fibrous and Globular |
| What is Keratin and is it found | v |
| Name two anticoagulants | Lithium Heparinate and EDTA |
| What is the major difference between Plasma and Serum | Absence of Fibrinogen in serum |
| Name plasma proteins | Albumin , Transferrin, Ceruloplasmin and Immunoglobines |
| What are the two types of Immune systemes | Cellular immune system and Humoral Immune system |
| How does the Cellular immune system work | v |
| How does the Humoral Immune system work | v |
| What are Antigens and Antibodies and how do they relate | v |
| What is a epiotope and how does it relate to the immune system | v |
| How can Proteins High specifity be explained | It can be explained by ... |
| What are they complementary in | ... |
| How can we make Glycoproteins and proteoglycans | By covalently linking carbohydrates with proteins |
| What are carbohydrates | They are polyhydroxy Aldehydes and ketons |
| What are the three classes of carbohydrates | 1. Monosaccharides - single chains 2. oligosaccharides - short chains of single sugars covalently linked 3.Polysaccharides - Long chains of single sugar covalently linked eg. starch |
| What are Epimeres | They are two sugar molecules that differ only in the configuration around one carbon atom |
| What is the actual function of a buffer system such as acetate/acetic acid | To maintain the solution at a constant pH if the concentration of an acid or alkali increases |
| What two weak interactions are most important in the formation of a cluster of lipid molecules in an aqueous solution | Hydrogen and hydrophobic |
| How many of the 20 common amino acids have rings in their structures and which ones are they | 1.Tyrosine 2.Tryptophan 3.Phenyalanine 4.Histidine 5.Proline |
| What results from a condensation reaction between two amino acides, such as Glycine and Alanine | The formation of one molecule of water |
| What is the average weight of an amino acide | 110 Da |
| Which amino acid would most likely be found in the interior of a globular protein | v |
| Which functional group is used to form Disulfide bonds | Sulfhydril |
| Which type of weak interaction is more important for cohesiveness and strength between beta-strands in beta-sheets | Hydrogen bond |
| What is the highest level of protein structure in human insulin, | The highest level of protein structure in Human insulin which has two polypeptides of different mass linked by several disulfide bonds, |
| Which amino acid would most likely be found in the interior of a globular protein | Alanine |
| Protein folding to a native conformation is highly dependent upon what | 1. The relative size of amino acid R groups 2. The rotation about the alpha-carbon and carbon bond in the backbone 3.The polar character of sequences of amino acids 4.The rotation about the alpha-carbon and nitrogen bond |
| What are the four main steps of sequencing a protein | 1. Breaking DiSulfide bonds 2. Cleaving the polypeptide chain 3.Sequencing of the peptides 4. Ordering the peptide fragments |
| There are two main ways of breaking disulfide bonds name them and the resultant residues | 1. Oxidation with perfomic acid which resultes in cysteic acid residues 2. Reduction by Dithiothretiol DTT followed by carbomethylation by iodoacetate which results in Carbomethylated cysteine residues |
| Name the four Reagents for fragmenting polypeptide chains and where do they fragment | Trypisine (Bovine pancrease)--> Lysine and Arginine(C term) Chymotrypsine (Bovine pancreas)--> Tryptphan, Tyrosine(C) and Phenylalanine Pepsine --> Tyrosine(N), Tryptophan, Leucine and Phenylalanine (CNBr)Cyanogen Bromide --> Methionine (C) |
| Name two sequencing methods | 1. Edman Degradation (The succesive framentation thing) 2. Mass spectronometry |
| What is the difference between the Edman degradation method and the Sanger's method | The sangers method uses FNDB Edmans method uses Phenylisothiocyanate |
| Describe the Edmans degradation for peptide sequencing | Switch from low ph to high ph favors the reagent to join to one AA |
| Name the four favorable interactions within a protein | 1. Hydrogen bonding 2. Electrostatic interactions 3.London dispersion(Van der Waals) 4.Hydrophobic effect |
| Why is rotation around the C-N bond restricted for planar peptide groups in polypeptide chain | Because of the double bond nature of the peptide bond, thanks to the resonance in the peptide bond |
| Why are nearly all peptide groups in proteins in trans conformation | Minimizes steric interference between adjacent side chains |
| What are dihedral angles | Dihedral angles PHI and PSI define peptide conformations |
| Name four functions filled by Carbohydrates | 1. Energy source and storage 2. Structural component of cell walls and exoskeletons 3. cell to cell signaling |
| Is it true that L and D glucose have different solubility levels | False these enatiomeres have the same solubilty |
| Most Hexoses in living organisms are L steriomeres | False |
| What are Diastereoisomeres | Stereoisomeres that are not mirror images |
| Name the three D aldoses seen in class and say if they have the same level of solubility | And threose and erythrose dont have the same solubility |
| Draw the two glucose epimers seen in class | |
| What compound is found in self tanner lotion and how is it made | |
| Draw Ribose, glucose, galactose, Mannose and Fructose | |
| Between Aldehydes, Ketone carbons and Alcohol oxygens which are nucleophilic and which are electrophilic | Nucleophilic : Alcohol oxygen Electrophilic : Aldehyde and Ketone carbons |
| What are Hemiacetals and Hemiketals and how are they formed | Hemiacetals are formed when Aldehyde carbons are attacked by alcohols Hemiketals are formed when Ketone Carbons are attacked by alcohols |
| what are six membered oxygen containing rings called and draw three | |
| What are five membered oxygen containing rings called | They are called furanoses |
| What can carbohydrates be covalently bonded with ? | 1. Glycoproteins 2.Proteoglycans |
| Give an example of a dissacharide that is 1. A Ketone 2. A polyhydroxyl aldehyde | 1. Fructose 2. glucose |
| How can bonds between carbohydrates be 1. Broken 2. synthesized | 1. Hydrolysis 2.Condensation |
| Name three 3 common disaccharides | 1. Trehalose 2.Sucrose 3.Lactose |
| Name important Haxose Derivatives 6 in the course | |
| Glycosidic bonds in carbohydrates are between | The anomeric carbon and hydroxyl carbon |
| In gycosidic linkages which elements are reducing or non reducing | 1. The anomeric carbon is non reducing 2. The second hemiacetal monomere is reducing |
| Where in nature can trehalose be found in nature and what disease in humans could it be used to treat | Found in blood sugar of insects and might be used to treat amyloid diseases |
| Name two oligosaccharides that are components of antibiotics | |
| Natural carbohydrates can be found as polymers, these polysaccharides can be of different types. Which ones | 1. Homopolysaccharides 2.Heteropolysaccharides 3.Linear 4. Branched |
| Name three heteropolysaccharides | 1. Agarose 2. Peptidogylcans 3.Hyaluronan(glycosaminoglycan) |
| What type of polysaccharide is glycogen | Heteropolysaccharide multitype branched |
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