Term
| What is the angle between Hydrogens in water? |
|
Definition
|
|
Term
| What is the molarity of pure water? |
|
Definition
|
|
Term
| What is the equilibrium constant for water? |
|
Definition
|
|
Term
| What is the key function of a peroxisome? |
|
Definition
Lipid metabolism (oxidation/degredation and synthesis)
*Other roles include synthesis of glycerolipids, plasmogens, and isoprenoids) |
|
|
Term
| What enzyme catalyzes hydrogen peroxide to oxygen and water, as well as oxidation of various compounds by hydrogen peroxide (such as methyl groups)? |
|
Definition
|
|
Term
| What are the two most important buffers in the body? |
|
Definition
Carbonic acid and Phosphoric acid
H2CO3 and H3PO4 |
|
|
Term
| What is the pH of blood plasma? Interstitial fluid? Cytosol? |
|
Definition
|
|
Term
| What is the pH of lysosomal matrix? Gastric juice? Pancreatic juice? |
|
Definition
|
|
Term
| What is the pH of human milk? Saliva? Urine? |
|
Definition
|
|
Term
|
Definition
|
|
Term
| What physical property of CO2 makes it easily expelled at varying rates of respiration? |
|
Definition
|
|
Term
| What is the k3 value for the bicarbonate buffer system? |
|
Definition
|
|
Term
| What is the pK3 of the bicarbonate buffer system? |
|
Definition
|
|
Term
| T/F Prokaryotes have an inner and outer membrane? |
|
Definition
|
|
Term
| Name four features of an amino acid. |
|
Definition
1. Asymmetric carbon
2. Carboxyl group
3. Amino group
4. Side chain (which is hydrophobic, hydrophilic, charged, and/or neutral) |
|
|
Term
| What is the abbreviation and single letter code for the following amino acids: glycine, alanine, valine, leucine, isoleucine? |
|
Definition
glycine - Gly G
alanine - Ala A
valine - Val V
leucine - Leu L
isoleucine - Ile I |
|
|
Term
| What is the abbreviation and single letter code for the following amino acids: proline, phenylalanine, tyrosine, tryptophan, methionine? |
|
Definition
proline - Pro P
Phenylalanine - Phe F
Tyrosine - Tyr Y
Tryptophan - Trp W
Methionine - Met M |
|
|
Term
| What is the abbreviation and single letter code for the following amino acids: serine, threonine, cysteine, asparagine, glutaminme, aspartate, glutamate, lysine, arginine, and histadine? |
|
Definition
| serine - Ser S threonine - Thr T Cysteine - Cys C Asparagine - Asn N Glutamine - Gln Q Aspartate - Asp D Glutamate - Glu E Lysine - Lys K Arganine - Arg R Histadine - His H |
|
|
Term
| What chemical property of a peptide bond makes it fixed and unable to rotate? |
|
Definition
| Resonance (between the carbonyl carbon and the oxygen and nitrogen it is attached to) |
|
|
Term
| What is the torsion angle in the trans conformation of a peptide? |
|
Definition
|
|
Term
| What type of bond occurs between cysteine residues of adjacent AA's? |
|
Definition
|
|
Term
| Which peptide bond conformation is more energetically favorable cis or trans? |
|
Definition
|
|
Term
| Define the isoelectric point. |
|
Definition
| The average of the two pK values involved in the formation of the zwitterionic form. |
|
|
Term
| If the pH is greater than the isoelectric point than a molecule has what charge? |
|
Definition
|
|
Term
| Where is the site of the synthesis of proteins and enzyme metabolic pathways? |
|
Definition
| Cytoplasm (as per lecture slides) |
|
|
Term
| What is the most soluble amino acid? |
|
Definition
|
|
Term
| What are the two most prevalent anions in the extracellular fluid? |
|
Definition
|
|
Term
| T/F Most proteins have a negative charge at a pH of 7.4. |
|
Definition
|
|
Term
| Through what does the outer surface of a cell make adhesive interactions with the extracellular matrix? |
|
Definition
|
|
Term
| What are the enzymes present in the smooth ER that are involved in lipid synthesis? |
|
Definition
|
|
Term
| What organelle is responsible for the production of glycoproteins? |
|
Definition
|
|
Term
| What permits larger molecules into the outer membrane of the mitochondria? |
|
Definition
|
|
Term
| What are the main group of enzymes found in lysosomes? |
|
Definition
|
|
Term
| What occurs during "I cell disease"? |
|
Definition
| Cellular mechanisms for storing lysosomal enzymes in lysosomes is disrupted and instead diffuses into the ECM damaging everything around it. |
|
|
Term
| What two types of mammalian insulin most closely resembles human insulin? |
|
Definition
| Dog and Porcine (pig), which both have only a 1 amino acid difference. |
|
|
Term
| T/F Quaternary structures do not have ANY covalent bonds. |
|
Definition
|
|
Term
| How many amino acids per 360 degree turn do alpha helices have? |
|
Definition
|
|
Term
| What are the two types of beta pleated sheets? |
|
Definition
| Parallel and anti-parallel |
|
|
Term
| In which beta sheet conformation are the hydrogen bonds planar? |
|
Definition
|
|
Term
| What was the first mitochondrial disease discovered? |
|
Definition
|
|
Term
| What kind of disease is Leber's Hereditary Optic Neuropathy? |
|
Definition
|
|
Term
| What is an abnormality in which uric acid is produced in excess and why do the symptoms occur? |
|
Definition
| Gout - Symptoms occur because uric acid crystals build up in joints and lysosomal enzymes burst with too much uric acid, causing cell lysis. |
|
|
Term
| What is the cause of Cholesteryl Ester Storage Disease (CESD) and Wolfman's Disease? What type of disease is it? |
|
Definition
Genetic deficiency of hLAL (human lysosomal acid lipase).
Autosomal recessive |
|
|
Term
| What is a rare autosomal recessive disease characterized by decreased levels of plasmalogens, increased levels of long chain fatty acids, and cholestanoic acid derivatives? Give the main type of disorder and the most severe. |
|
Definition
Peroxisome Biogenesis Disorders (PBD)
Zellweger's Disease |
|
|
Term
| When looking at electrophoretic analysis of plasma proteins, what does a delayed response indicate? |
|
Definition
|
|
Term
| What is the designation for the variant form of hemoglobin in which a nonconservative substitution occurs in the 6th position of the b-globin chains? |
|
Definition
|
|
Term
| In sick cell anemia what is the non-conservative substitution that takes place? |
|
Definition
| Valine replaces Glutamic acid |
|
|
Term
| What is the best analytical determination of sickle cell anemia and why? |
|
Definition
| Gel electrophoresis because the lack of glutamic acid makes HbS less acidic and therefore it does not migrate as quickly to the anode. |
|
|
Term
| Ehlers-Danlos syndrome, osteogenesis imperfecta, and scurvy are all examples of what type of disease? |
|
Definition
| Diseases of Collagen Synthesis |
|
|
Term
| What is the cause of type 1 hyperlipidemia? |
|
Definition
| Accumulation of chylomycrons. |
|
|
Term
| What is the cause of type 2 hyperlipidemia? |
|
Definition
| Elevated levels of LDL caused by genetic defects in the synthesis, processing, or function of the LDL receptor. |
|
|
Term
| What is the cause of type 3 hyperlipidemia? |
|
Definition
|
|
Term
| What is the cause of type 4 hyperlipidemia? |
|
Definition
| Increased VLDL levels due to obesity, alcohol abuse, or diabetes. |
|
|
Term
| What is the most common form of hyperlipidemia? |
|
Definition
|
|
Term
| What is a genetic disease that is characterized by absence of chylomicrons, VLDL, and LDL due to an inability to synthesize apolipoproteins apoB-100 and apoB-48? |
|
Definition
|
|
Term
| What rare autosomal recessive disease causes a deficiency of a-lipoprotein? |
|
Definition
|
|
Term
| The changes in concentration of what in diabetes patients can be used to follow the effectiveness of treatment for the diabetes? |
|
Definition
|
|
Term
| What are proteins that act as infectionus agents in the absence of DNA or RNA? |
|
Definition
|
|
Term
| What is the most common prion disease? |
|
Definition
| Creutzfeldt-Jakob disease |
|
|
Term
| What prion protein is conformationally changed in Creutzfeldt-Jakob disease? |
|
Definition
|
|
Term
| What is a typical molarity of [HCO3-]? |
|
Definition
|
|
Term
| What diseases are caused by enlarged lysosomes, full of undigested material? |
|
Definition
| Lysosomal storage diseases |
|
|
Term
| In HbS what occurs in the deoxy form that cases problems? |
|
Definition
|
|
Term
| The formation of covalent cross links in collagen requires what? |
|
Definition
| Conversion of some e-amino groups of lysine to aldehydes. |
|
|
Term
| Abetalipoproteinemia is a disease in which chylomicrons, VLDL, and LDL are absent from the blood because of an inability to synthesize what? |
|
Definition
|
|
Term
| What class of immunoglobins is found mainly in mucosal secretions? |
|
Definition
|
|
Term
| What immunoglobin class is the initial defense against invading viral and bacterial pathogens prior to their entry into plasma or other internal space? |
|
Definition
|
|
Term
| What is the first antibodies produced in significant quantity on exposure to a foreign antigen? |
|
Definition
|
|
Term
| What two immunoglobin classes promotes phagocytosis of microorganisms? |
|
Definition
|
|
Term
| What immunoglobin plays an important role in allergic responses? |
|
Definition
|
|
Term
| What are inactive precursor serine proteases? |
|
Definition
|
|
Term
| What serine protease acts directly on fibrin to degrade a clot? |
|
Definition
|
|
Term
| Administration of what shortly after an MI significantly enhances recover? |
|
Definition
|
|
Term
| Which serine protease is believed to be required for metastasis of cancer cells? |
|
Definition
|
|
Term
| T/F Mitochondria are associated with apoptosis? |
|
Definition
|
|
Term
| T/F Peroxisomes have a role in oxidation of D-amino acids. |
|
Definition
|
|
Term
| T/F Peroxisomes have a role in hydrolysis of cholesteryl ethers. |
|
Definition
|
|
Term
| What is the term for two sequences that are highly alignable? |
|
Definition
|
|
Term
| What is a substitution of one AA for another that is of similar polarity? |
|
Definition
|
|
Term
| What is a substitution of one AA for another that is of dissimilar polarity or geometric configuration? |
|
Definition
|
|
Term
| How is human insulin made available? |
|
Definition
| genetically engineered bacteria |
|
|
Term
| What is the only protein structures (group) that does not have covalent bonds? |
|
Definition
|
|
Term
| Around what bonds is there rotation in peptides? |
|
Definition
|
|
Term
| What bond is between the alpha carbon and the carbonyl carbon? What about the alpha carbon and nitrogen? |
|
Definition
alpha carbon to carbonyl carbon --> psi
alpha carbon to nitrogen --> phi |
|
|
Term
| What is the Hill coefficient and what is the formula? |
|
Definition
|
|
Term
| Peptide bond planes are ______ to the alpha-helix axis. |
|
Definition
|
|
Term
| In an alpha helix how many hydrogen bonds form between AA's and where do they occur in the helix? |
|
Definition
| Two hydrogen bonds, one to the 4th AA above and one to the 4th AA below. |
|
|
Term
| In an alpha helix side chains are found _______ of the spiral structure. |
|
Definition
|
|
Term
| Explain the protein classification: class. |
|
Definition
| Based on predominant type of secondary structure. (a-helices, b-sheets) |
|
|
Term
| What protein domain classification deals with arrangements of secondary structures within the domain? |
|
Definition
|
|
Term
| What protein domain classification deals with the sequence identity between proteins? |
|
Definition
|
|
Term
| What type of proteins have spheroidal shapes, high water solubility, and act as transporters and catalysts? |
|
Definition
|
|
Term
| What kind of proteins contain larger amount of secondary structure, long cylindrical shapes, and low water solubility? |
|
Definition
|
|
Term
| What are the 2 largest constituents of collagen? |
|
Definition
| Glycine (33%) and proline (13%) |
|
|
Term
| What sequences are repeated several hundred times in collagen? |
|
Definition
|
|
Term
| What is covalently attached to the hydroxyl group of hydroxylysine in collagen? |
|
Definition
|
|
Term
| What is responsible for the highly twisted extended helix of collagen? |
|
Definition
|
|
Term
| The plane of peptide bond, in collagen, is _____ to the helix correctly oriented to form strong _____ bonds with other polyproline helical polypeptides. |
|
Definition
|
|
Term
| How many polypeptide chains are wound in a superhelical structure in collagen? |
|
Definition
|
|
Term
| How are polypeptide chains in collagen held together? |
|
Definition
| Hydrophobic interaction with glycines on apolar edge and lysine linkages |
|
|
Term
| What are the two non-covalent forces leading to protein folding? |
|
Definition
| hydrophobic interaction and hydrogen bonding |
|
|
Term
| Collagen makes up what percentages of skin, cornea, liver, heart, cartilage, and lungs? |
|
Definition
Skin - 74%
Cornea - 64%
Cartilage - 50%
Heart - 12-24%
Lungs - 10%
Liver - 4% |
|
|
Term
| What provides organs and tissues with elastic support in terms of stretching without tearing? |
|
Definition
|
|
Term
| T/F Elastin does not contain Gly-Pro-Y or Gly-X-Hyp as does collagen. |
|
Definition
|
|
Term
| Elastin lacks _____ structure but contains unordered coiled structure. |
|
Definition
|
|
Term
| Elastin contains what kind of crosslinks between which residues? |
|
Definition
| Contains covalent crosslinks between Lysine residues. |
|
|
Term
| What is responsible for blood type? |
|
Definition
|
|
Term
| What are the three main types of covalent linkages of carbohydrates to proteins? |
|
Definition
N-glycosyl linkage to asparagine
O-glycosyl linkage to serine
O-glycosyl linkage to 5-hydroxylysine |
|
|
Term
| What is the main type of glycosyl linkage seen in mammals? |
|
Definition
| Type 3 - O-glycosyl linkage to 5-hydroxylysine |
|
|
Term
| What is the most used protein analysis? |
|
Definition
|
|
Term
| What analytical technique separates proteins based on charge? |
|
Definition
ion exchange chromatography and polyacrylamide gel electrophoresis (non-denatured technique) |
|
|
Term
| What analytical technique separates proteins based on molecular weight? |
|
Definition
| Gel permeation chromatography and polyacrylamide gel electrophoresis (denatured form) |
|
|
Term
| What analytical technique separates proteins based on binding affinity? |
|
Definition
|
|
Term
| In polyacrylamide gel electrophoresis you can separate proteins in two forms. What two forms and how are they separated in each? |
|
Definition
Denatured - Based on MW
Non-denatured - based on charge |
|
|
Term
| What separates proteins on the basis of charge to mass? |
|
Definition
| capillary electrophoresis |
|
|
Term
| What is the condition where there is elevated levels of AA's in the blood? |
|
Definition
|
|
Term
| What is the name of the disease that is characterized by a deficiency of tryptophan? |
|
Definition
|
|
Term
| Name three types of proteases used in protein analysis. |
|
Definition
| Trypsin, chymotrypsin, and cyanogen bromide |
|
|
Term
| What is the science of protein synthesis and analysis? |
|
Definition
|
|
Term
| What type of analytical technique can separate all of the proteins in a cell? |
|
Definition
|
|
Term
| What two ways does 2D electrophoresis separate proteins? |
|
Definition
1st dimension - isoelectric focusing
2nd dimension - mass |
|
|
Term
| What is the first step in Edman degredation? |
|
Definition
| Cleaving of the first amino acid at the N-terminus. |
|
|
Term
| What are three denaturing agents? |
|
Definition
| urea, sodium dodecyl sulfate, and guanidine HCl |
|
|
Term
| What is the most common disease of human transmissible spongiform encephalopathies? How many forms are there? What is the most common pathway to the disease? |
|
Definition
| Creutzfeldt-Jakob disease 4 Sporadic (85%) |
|
|
Term
| What causes human transimissible spongiform encephalopathies? (what prion protein) |
|
Definition
|
|
Term
| What is a coil of several fibrils called? |
|
Definition
|
|
Term
| Amyloid fibrils are made of helical ______ of strands ________ to a cylindrical axis. |
|
Definition
|
|
Term
| What is the only AA capable of a disulfide bond? |
|
Definition
|
|
Term
| Disulfide bonds fall into what categorical structure of proteins? |
|
Definition
|
|
Term
| What are immunoglobins produced by? |
|
Definition
|
|
Term
| How many peptides are typically in light and heavy chains? |
|
Definition
|
|
Term
| How are immunoglobin's polypeptide chains held together and how many are there? |
|
Definition
Disulfide bonds
2 holding the constant regions together and 1 on each of the light chains linking it to the heavy chain (total of 4) |
|
|
Term
| What is a small molecule to which an antibody can bind but can only elicit an antibody production if bound to a larger molecule? |
|
Definition
|
|
Term
| Haptens bind to macromolcules through what type of bonds? |
|
Definition
|
|
Term
| What is the minimal number of amino acids in sequence that allows binding to antibodies? |
|
Definition
|
|
Term
| What is a typical antibody production? |
|
Definition
|
|
Term
| The constant domains of immunoglobins are divided into what 3 groups? |
|
Definition
|
|
Term
| How does an immunoglobin go about crossing the placental membrane? |
|
Definition
| Constant regions bind complement |
|
|
Term
| Heavy and light polypeptide chains have _____ AA repeats that are not completely ______. |
|
Definition
|
|
Term
| How many repeats in the light and heavy chains of immunoglobins are there? |
|
Definition
| 2 in light chains and 4 in heavy |
|
|
Term
| Each fold of an immunoglobins structure contains ___ beta pleated sheets that are aligned ______. |
|
Definition
|
|
Term
| What is the most common immunoglobin? |
|
Definition
|
|
Term
| Which immunoglobin is present in the highest concentration (mg/mL)? |
|
Definition
|
|
Term
| What is the name of the chain that is linked by two disulfide bonds and links immunoglobins together? |
|
Definition
|
|
Term
| What analytical technique is used to identify immunoglobins? |
|
Definition
ELISA
enzyme linked immunoglobin substrate assay |
|
|
Term
| What type of binding associates antigens to the antigens binding site? |
|
Definition
| hydrophobic interactions, van der waals, and hydrogen bonds |
|
|
Term
| What is a class of enzyme that cleaves peptide bonds? |
|
Definition
|
|
Term
| What do serine proteases contain in the active site? |
|
Definition
|
|
Term
| What are the two different pathways to coagulation? |
|
Definition
Intrinsic - contact factors 7 and 9
Extrinsic- tissue formation
Both use contact factor 10 |
|
|
Term
| What are the 2 zymogens and 2 active proteins used in clot formation (not the factors, just the main proteins) |
|
Definition
Prothrombin --> Thrombin
Fibrinogen --> Fibrin
Thrombin catalyses the formation of fibrinogen to fibrin |
|
|
Term
| What is the protein responsible for dissolving a clot? |
|
Definition
| Plasmin (the zymogen form is plasminogen) |
|
|
Term
|
Definition
| t-PA (tissue plasminogen activator) |
|
|
Term
| What are the two AA's present in a serine protease responsible for cleavage? |
|
Definition
| Histadine and aspartic acid |
|
|
Term
| What is an aspartic protease composed of two identical monomers? |
|
Definition
|
|
Term
| Hemoglobin is composed of how many and which polypeptide chains? |
|
Definition
alpha and beta
2 alpha and 2 beta make up a hemoglobin |
|
|
Term
| What is the 5th bond to in the iron of hemoglobin? |
|
Definition
|
|
Term
| How is the heme bound to each protein subunit? |
|
Definition
| via 18 apolar AA's via hydrophobic association |
|
|
Term
| How many alpha helices make up the alpha and beta subunits of hemoglobin? |
|
Definition
|
|
Term
| What is the effect called when as the pH of the blood drops O2 becomes less willing to bind to hemoglobin? |
|
Definition
|
|
Term
| What happens to the structure of hemoglobin as more O2 binds and what is this called?? |
|
Definition
Tertiary and Quaternary structures change
cooperative binding |
|
|
Term
| By what angle does the oxy form change in relation to the deoxy form? |
|
Definition
|
|
Term
| What is the designation for hemoglobin when oxygen is bound? When it is not bound? |
|
Definition
|
|
Term
| What molecule modulates Hb-O2 binding affinity? It also has an affinity for the deoxy form. |
|
Definition
|
|
