Download Glossary of Biochemistry Terms and Concepts and more Exams Biochemistry in PDF only on Docsity!
pKa (chapter 3) - ANSWER measure of the tendency of a group to give up a proton (acidity); tendency decreases tenfold as pKa increases by one unit thioester bond (1) - ANSWER compounds with functional group C-S-CoA-C (eg, in acetyl-CoA) zwitterion (3) - ANSWER dipolar ion with both positive and negative groups but overall neutral charge; can act as either an acid or base Isoelectric point - pI (chapter 3) - ANSWER the characteristic pH at which the net electric charge is zero SDS - Sodium Dodecyl Sulfate (chap 3) - ANSWER detergent used to unfold proteins and give them uniform negative charge SDS Page (3) - ANSWER chromatography used to separate proteins based on mass. light proteins travel fast than heavier ones PCR-Polymerase chain reaction (3)- ANSWER copies DNA multiple times to increase sample size
Isoelectric focusing (chapt 3)- ANSWER procedure used to determine the isoelectric pt (pI) of a protein. Protein migrates through gel until pH = pI (net charge = 0) Two-Dimensional Electrophoresis (3)- ANSWER combines isoelectric focusing and SDS electrophoresis; separates proteins by both molecular weight and pI specific activity (3) - ANSWER number of enzyme units per mg of total protein (a measure of enzyme purity) activity (3) - ANSWER total units of a certain enzyme in a solution Peptide bonds (chapter 4) - ANSWER C-N bond with double bond character due to resonance (C-N bond cannot rotate, and is planar) Edman degredation (3) - ANSWER used in the sequencing of polypeptides; labels and removes ONLY the amino-residue from a polypeptide. carried out in a machine called a sequenator φ in peptide bonding (chapter 4) - ANSWER angle around the α-carbon - amide nitrogen bond ψ in peptide bonding (chapter 4) - ANSWER angle around the α-carbon - carbonyl carbon bond Ramachandran Plot (4) - ANSWER shows favoreable φ-ψ angle combinations. 3 main "wells" for α-helices, β-sheets, and left handed α-helices
so take a short - and rapid - path through the column, around the beads. Small proteins enter the cavities, and migrate through the column more slowly as a result. Affinity chromatography (3) - ANSWER based on the binding affinity of a protein. The beads in the column have a covalently attached chemical group. A protein with affinity for this particular chemical group will bind to the beads in the column, and its migration will be retarded as a result HPLC, or high-performance liquid chromatography. - ANSWER pumps speed the movement of the protein molecules down the column, as well as higher- quality chromatographic materials that can withstand the crushing force of the pressurized flow. By reducing the transit time on the column, HPLC can limit diffusional spreading of protein bands and thus greatly improve resolution. cation-exchange chromatography (3) - ANSWER solid matrix (stationary phase) has negatively charged groups. In the mobile phase, proteins with a net positive charge migrate through the matrix more slowly than those with a net negative charge. The two types of protein can separate into two distinct bands. Induced fit - ANSWER conformational changes (in either ligand or protein) that can occur upon ligand binding in order for tighter binding of ligand. ex: HbA porphin - ANSWER organic compound that is aromatic and heterocyclic, consisting of 4 pyrole rings joined by 4 methine (=CH-) groups to form a larger macrocycle ring. Ex: hemoglobin hemoglobin, HbA (5) - ANSWER sigmoidal curve (positive cooperativity); four subunits bind four O2; binding one O2 increases affinity for binding the other three (heme-heme interaction)
ligand (5) - ANSWER any molecule that binds reversibly to a protein myoglobin, Mb (5) - ANSWER hyperbolic curve; one subunit binds one O2; higher affinity for oxygen than HbA, binds oxygen dropped by HbA in low oxygen environments (myo = muscle) Hill plot (5) - ANSWER turns sigmoid into straight lines. slope = n (# of binding sites). allows measurement of cooperative binding sites. Hill number, n/nH (chapter 5) - ANSWER provides a measure of the degree of cooperativity between states. nH < 1,0, negative cooperativity, binding of first ligand makes binding of second LESS likely; nH > 1.0, positive cooperativity, binding of first ligand makes binding of second MORE likely. nH = 1.0, not a cooperative system Hemoglobin "Tense-state" - ANSWER low pH, high CO2, high 2,3-BPG PO2 (5) - ANSWER about 13 kPa in lungs, 4 kPa in tissues Bohr effect (5) - ANSWER effect of H+ and CO2 on the binding and release of O2 from Hb. O2 binds well at higher pH and low CO2. 2,3-bisphosphoglycerate (5) - ANSWER decreases affinity of Hb for O2, stabilizing T-state antibodies or immunoglobulins, Ig (chapter 5) - ANSWER bind bacteria, viruses, or large molecules identified as foreign and target them for destruction
chymotrypsin (6) - ANSWER cleaves proteins on C-terminal end of Phe, Trp, and Tyr mutarotation (7) - ANSWER transformation between α and β forms of sugar at the anomeric carbon ionophore (11) - ANSWER hydrophobic molecule that binds to ions and carries them through cell membranes disrupting concentration gradients. ethanol fermentation (14) - ANSWER pyruvate --> acetylaldehyde --> ethanol. uses pyruvate decarboxylase and alcohol dehydrogenase. NADH --> CO2 (TPP)
- NAD+ what enzyme is utilized in the conversion of pyruvate to oxaloacetate? (14) - ANSWER pyruvate carboxylase (in mitochondria). cofactors include biotin (carries activated biocarbonate). ATP is utilized. pyruvate dehydrogenase complex enzymes (14) - ANSWER 1) Pyruvate dehydrogenase, 2) dihydrolipoyl transacetylase, 3) dihydrolipoyl dehydrogenase stimulates gluconeogenesis / inhibits glycolysis (14) - ANSWER acetyl-CoA, glucagon stimulates glycolysis / stimulates glycolysis (14) - ANSWER ADP, AMP, insulin sum for gluconeogenesis (14) - ANSWER 2 pyruvate + 4ATP + 2GTP + 2NADH + 2H+ + 4H2O --> glucose + 4ADP + 2GDP + 2NAD + 6Pi
ultimate electron acceptor of oxidative decarboxylation in the TCA cycle - ANSWER O Hexokinase IV (glucokinase) - ANSWER inhibited by fructose 6-phosphate and G6P. found in hepatocytes and βcells of pancreas; buffers blood glucose PFK - 1 - ANSWER activated by AMP, F26BP. pyruvate kinase - ANSWER allosterically inhibited by high ATP; activated by F1,6-BPase pyruvate carboxylase - ANSWER activated by acetyl-CoA carnitine shuttle (17, p. 634) - ANSWER transports free fatty acids across inner mitochondrial membrane. 3 enzymatic reactions:
- esterification to CoA (acyl CoA synthetases)
- transesterification to carnitine (folllowed by transport)
- transesterification back to CoA electron carriers for the electron transport chain (19) - ANSWER 1) coenzyme Q - ubiquinone
- cytochromes (heme prosthetic groups) plastocyanin (19) - ANSWER carries electrons from photosystem II to photosystem I
