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Biochemistry
Midterm 1
| Term | Definition |
|---|---|
| 2 carbon short chain saturated fatty acid | acetic |
| 3 carbon short chain saturated fatty acid | propionic |
| 4 carbon short chain saturated fatty acid | butyric |
| 6 carbon medium chain saturated fatty acid | caprioc |
| 8 carbon medium chain saturated fatty acid | caprylic |
| 10 carbon medium chain saturated fatty acid | capric |
| 14 carbon long chain saturated fatty acid | myristic |
| 16 carbon long chain saturated fatty acid | palmitic |
| 18 carbon long chain saturated fatty acid | stearic |
| 20 carbon long chain saturated fatty acid | arachidic |
| 16 carbon monounsaturated fatty acid | palmitoleic |
| 18 carbon monounsaturated fatty acid | oleic |
| 18 carbon polyunsaturated fatty acid with 2 double bonds | linoleic |
| 18 carbon polyunsaturated fatty acid with 3 double bonds | linolenic |
| 16:1(9) | palmitoleic |
| 18 :1(9) | oleic |
| 18:2(9,12) | linoleic |
| 18:3(9,12,15) | linolenic |
| w-3 | number of carbons-last number of double bond=3 |
| w-6 | number of carbons-last number of double bond=6 |
| 20 carbon polyunsaturated fatty acid with 4 double bonds | arachidonic |
| 20 carbon polyunsaturated fatty acid with 5 double bonds | EPA |
| 22 carbon polyunsaturated fatty acid with 6 double bonds | DHA |
| 20:4(5,8,11,14) | arachidonic |
| 20:5(5,8,11,14,17) | EPA |
| 22:6(4,7,10,13,16,19) | DHA |
| Which is not used in membrane lipids | triacylglycerol |
| What is triacylglycerol used for | storing fatty acids |
| Why is butter solid at room temperature | higher proportion of saturated fatty acids in triacylglycerol |
| Why is oil liquid at room temperature | higher proportion of polyunsaturated fatty acids in triacylglycerol |
| What is cardiolipin | diphosphatidylglycerol |
| What is sphingomyelin | ceramide plus phosphate plus choline |
| What is a cerebroside | ceramide plus sugar |
| What is a sulfatide | ceramide plus sugar |
| What is ganglioside | ceramide plus more than one sugar, where one sugar is oxidized |
| 5 carbon alkene | isoprene |
| 10 carbon alkene | monoterpene |
| 15 carbon alkene | sesquiterpene |
| 20 carbon alkene | diterpene |
| 30 carbon alkene | triterpene |
| Squalene | most common triterpene and is the precursor to cholesterol |
| 40 carbon alkene | tetraterpene |
| beta-carotene | precursor to retinoic acid |
| What are a pair of enantiomers | same name sugar one has L configuration the other has D |
| What are a pair of anomers | same name sugar, same configuration one is alpha other is beta |
| What is mannose | c-2 epimer of glucose |
| What is galactose | c-4 epimer of glucose |
| What is furanose | five membered ring with oxygenated sugar |
| What if pyranose | six membered ring with oxygenated sugar |
| What is maltose | two glucoses |
| What is lactose | galactose and glucose |
| What is sucrose | glucose and fructose |
| What is a reducing sugar | one greek letter |
| What is a non-reducing sugar | two greek letters |
| What is amylose | alpha 1-4 glucan |
| What is amylopectin | alpha 1-4 with alpha 1-6 branching |
| What is cellulose | beta 1-4 glucan |
| What is starch | mixture of amylose and amylopectin |
| What is a purine | adenine and guanine |
| What is a pyrimidine | cytosine, uracil, and thymine |
| What is adenine | purine with exocyclic amino |
| What guanine | purine with exocyclic amino and keto group |
| What is cytosine | pyrimidine with exocyclic amino and keto |
| What is uracil | pyrimidine with two exocyclic keto groups |
| What is thymine | methylated uracil |
| adenine plus sugar | adenosine |
| guanine plus sugar | guanosine |
| cytosine plus sugar | cytidine |
| uracil plus sugar | uradine |
| thymine plus sugar | thymidine |
| What comprises TTP | thymine plus deoxyribose plus triphosphate |
| Which of the 5 properties is in correct | parallel, left-handed, syn bases inside, a&t +c&g, bases don't stack are all wrong |
| What type of DNA do prokaryotes have | circular with no ends |
| What types of DNA do eukaryotes have | linear DNA with ends that must be protected |
| What is polycistronic | prokaryotic mRNA has the ability to read across more than one geen |
| What is monocistronic | eukaryotic mRNA has the ability to read one gene |
| Which of the 5 properties is in correct | four base sequence, all codons make amino acids, overlapping/random, one codon for one amino acid are all incorrect |
| Replication | DNA dependent DNA synthesis |
| Transcription | DNA dependent RNA synthesis |
| Translation | RNA dependent protein synthesis |
| Intact prokaryote ribosome | 70s |
| Intact eukaryote ribosome | 80s |
| Prokaryote large subunit | 50s |
| Eukaryote large subunit | 60s |
| Prokaryote small subunit | 30s |
| Eukaryote small subunit | 40s |
| Prokaryote rRNA small subunit | 16s |
| Eukaryote rRNA small subunit | 18s |
| Prokaryote rRNA large subunit | 23s and 5s |
| Eukaryote rRNA large subunit | 28s, 5.8s, and 5s |
| Characteristics of the amino acids specified by the genetic code | All alpha amino acids and L amino acids |
| Characteristics of a peptide bond | secondary amide |
| Properties of secondary amide | rigid, planar, trans |
| Which dihedral angle if the one that distinguishes and extended beta sheet from a coiled alpha helix | psi |
| What stabilizes a beta sheet | main chain hydrogen bonding between strands |
| What stabilizes a alpha helix | main chain hydrogen bonding (i+4) and side chains are facing outward |
| What destabilizes a alpha helix | branching side chains, hydrogen bonding side chains, and proline rings |
| What is a supersecondary structure | Helix-turn-helix, hairpin, meander, beta-alpha-beta, greek key, and jelly roll |
| What is a alpha/beta twist | Open beta sheet structure formed by 4-10 parallel beta strands, with interconnecting alpha helices packed on both side of the sheet |
| What is a alpha/beta barrel | Closed beta sheet structure formed by 8 parallel beta strands, with interconnect alpha helixes pack on the outside of the barrel |
| What is a helix bundle | alpha helices (3-4) tightly packed in coiled-coil fashion with average orientation angle of 20 |
| What is a homeodomain | C-terminal helix roughly perpendicular to N-terminal helix-turn-helix pair |
| What is a globin fold | alpha helices (4) tightly packed with average orientation angle of 50 |
| What is a alpha solenoid | alpha helices arranged in a curved pattern that resembles a jelly roll |
| What is a beta barrel | large beta sheet (antiparallel) that twists to a closed structure |
| What is a beta propeller | Blade-shaped beta sheets (4 antiparallel strands) arranged toroidally around a central aixs |
| What is a immunoglobulin fold | two-layer sandwich of anti-parallel beta strands (7-9) in two sheets with greek key topology |
| What is a quaternary structure | multiple subunits |
| What is hydrophobic effect | the tendency of nonpolar substances to aggregate in highly polar solvents |
| What is the van der waals contact | term used to describe the slightly energetically favorable association of individual atoms |
| What is london dispersion forces | term used to describe the primary attractive force that allows van der Waals contacts between nonpolar solutes in water due to the hydrophobic effect |
| What is a hydrogen bond | proton covalently bonded to one electronegative atom is electrostatically attracted to a lone pair of electrons on another electronegative atom |
| What is a salt bridge | combination of hydrogen bonding and electrostatic attraction between polar opposite charged groups being with 4 A of each other |
| What are oxidoreductases | catalyze oxidation-reduction reactions |
| What are transferases | catalyze transfer of C-, N-, and P-containing functional groups |
| What are hydrolases | catalyze cleavage bonds by addition of water |
| What are lyases | catalyze cleavage bonds by means other than hydrolysis or oxidation |
| What are isomerases | catalyze conversion between chemical isomers |
| What are ligases | catalyze formation of chemical bonds utilizing energetic coupling hydrolysis of high energy phosphates |
| What is general acid catalysis | activation of a reacting group by transfer of a proton to the group |
| What is general base catalysis | activation of a reacting group by transfer of a proton from the group |
| What is electrophilic catalysis | placement of a full or partial positive charge |
| What is anionic catalysis | placement of a full or partial negative charge |
| What is covalent catalysis | activation of a reacting group by forming a covalent bond to the reacting group |
| What is entropy | fixation of reacting groups in proper position necessary for the reaction to occur |
| What is the michaelis-menten equation | a formula that is hyperbolic in nature |
| What is the maximum initial velocity (Vmax) | maximum rate of product formation where Vmax is proportional to the total enzyme concentration, M/s |
| What is the turnover number (kcat) | maximum number of substrate molecules converted to product per unit time, 1/s |
| What is the michaelis constant (Km) | concentration of substrate that yields 1/2 Vmax, M |
| What is the specificity constant (kcat/Km) | refers to the properties and reaction of free enzyme leading to first irreversible step, 1/M*s |
| In a double reciprocal plot analysis of an enzyme reaction with a slope of __ M/s and a y-intercept of __ s, what is the specificity constant and the turnover number | specificity constant=reciprocal of slope turnover number= reciprocal of y-intercept |
| What is the enzyme activity versus substrate plot of an enzyme with michaelis-menten kinetics | hyperbolic |
| What is the shape of a curve for an enzyme that experiences positive cooperativity | s-shape curve |
| If you have a hyperbolic dependence on substrate concentration the enzyme follows what | michaelis-menten kinetics, exponent=1 |
| If you have a sigmoidal or s-shape dependence on substrate concentration the enzyme follows what | positive cooperativity, exponent>1 |
| What is the mechanism for competitive inhibition | an inhibitor that resembles the normal substrate binds to the enzyme and prevents the substrate from binding |
| What is the mechanism for non-competitive inhibition | the inhibitor binds at an allosteric site separate from the active site of substrate binding |
| What is the mechanism for uncompetitive inhibition | takes place when an enzyme inhibitor binds only to the complex formed between the enzyme and the substrate |
| What is the impact on kcat and Km on competitive inhibition | kcat is independent while Km increases |
| What is the impact on kcat and Km on non-competitive inhibition | kcat decrease Km is independent |
| What is the impact on kcat and Km on uncompetitive inhibition | kcat and Km both decrease |
| What is the double reciprocal plot/family of line for competitive inhibition | lines intersect on y-axis |
| What is the double reciprocal plot/family of line for non-competitive inhibition | lines intersect on x-axis |
| What is the double reciprocal plot/family of line for uncompetitive inhibition | lines are parallel |
| What is the equation for competitive inhibition | Km(app)=Ka(1+I/KI) |
| What is the equation for non-competitive inhibition | kcat(app)=kcat/(1+I/KI) |
| What is the equation for uncompetitive inhibition | kcat(app)=kcat/(1+I/KI) or Km(app)=Km/(1+I/KI) |
| What is phosphorylated | abbreviation has P also riboflavin |
| What has ADP | abbreviation has A |
| B1 | thiamin, thiamin pyrophosphate (TPP), thiazolium ring, aldehyde |
| B2 | riboflavin, flavin mononucleotide (FMN), isoalloxazine ring, electrons |
| B2 | riboflavin, flavin adenine dinucleotide (FAD), isoalloxazine ring, electrons |
| B3 | niacin, nicotinamide adenine dinucleotide (NAD+), nicotinamide ring, electrons |
| B3 | niacin, NAD phosphate (NADP+), nicotinamide ring, electrons |
| B5 | pantothenate, coenzyme a (CoA), thiol, acyl groups |
| B6 | pyridoxine, pyridoxal phosphate (PLP), Schiff base, amino acids |
| B7 | biotin, biotinylated enzyme, ureido ring, CO2 prosthetic group |
| B9 | folate, tetrahydrofolate (THF), pteridine ring, 1 carbon unites |
| B12 | cobalamine, methylcobalamine (MetB12) with 5'-deoxyadenosylcobalamine (AdoB12), CO- ,corrin ring with cobalt, MetB12=methyl, AdoB12=hydrogen |
| Lipoamide | lipoic acid, lipoamide, disulfide, acetyl groups and electrons prosthetic group |
| C | ascorbic acid, reductone, reducing agent/electron donor, collagen biosynthesis |
| K | phyllo/menaquinone, electrons, gamma-glutamyl, blood coagulation |
| A | beta-carotene, cleavage and oxidation, retinol=storage, retinal=eyes, retinoic acid=binds to transcription factors |
| D | Vitamin D, calcitriol, binds to transcription factors |
| E | Tocopherol, electron donor/reducing agent |
| Lipid/Fat soluble | B1,B2,B3,B5,B6,B7,B9,B12, and C |
| Water soluble | A,D2,D3,E,K1,K2 |
| alpha alpha (a2) | homodimer |
| a2B2 | heterotetramer |
| a2B2ysS2 | heterooctamer |
| Glycine | Gly G |
| Alanine | Ala A |
| Valine | Val V |
| Proline | Pro P |
| Leucine | Leu L |
| Isoleucine | Ile I |
| Methionine | Met M |
| Nonpolar | GAVPLIM |
| Aspartate | Asp D |
| Glutamate | Glu E |
| Negative charge | DE |
| Lysine | Lys K |
| Arginine | Arg R |
| Positive charge | KR |
| Cysteine | Cys C |
| Serine | Ser S |
| Threonine | Thr T |
| Asparagine | Asn N |
| Glutamine | Gln Q |
| Polar | CSTNQ |
| Phenylalanine | Phe F |
| Tryptophan | Trp W |
| Aromatic nonpolar | FW |
| Tyrosine | Tyr Y |
| Histidine | His H |
| Aromatic Polar | TH |
| Phosphatidate | diacylglycerol 3-phosphate |
| Phosphatidylethanolamine | cephalin |
| Phosphatidylcholine | lectihin |
| Fructose | Ketoisomer of glucose |
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Hopethisworks
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