biochem - exam 1 Flashcards

Question

Racemic Mixture (Racemates)

Answer 1

is an equimolar solution of two enantiomers (50% R/ 50% S)

Answer 2

The two enantiomers in a racemic mixture are called racemates, rotate plane-polarized light in opposite directions, so there is no net rotation.

Answer 3

One stereoisomer is usually active, the other inactive (or opposite), or has a different activity than the first form. Why? Ideally… So what happens to the dose if you have a racemic mixture, compared to enantiopure?

Answer 4

Celexa (trade name) of Citalopram (racemate) Lexapro (trade name) of Escitalopram (S)-Citalopram

Answer 5

The (R)-(-) enantiomer is active The (S)-(+) enantiomer is inactive

Answer 6

mean equal! Reactions tend to go to completion, notto “equality”

Answer 7

on a specific set of concentrations, described by an Equilibrium Constant, Keq

Answer 8

concentration products/concentration reactants One can compare where the reaction is going when you used Q and compare it to Keq. Given the concentrations of all of the constituents and the Keq.

Answer 9

Q = Keq = [C]^c [D]d / [A]^a[B]^b

Answer 10

Products/reactants = Keq

Answer 11

net rxn towards reactants or the left Q>K

Answer 12

net rxn towards products or the right Q

Answer 13

no net rxn Q=K

Answer 14

Energetics/Thermodynamics

Answer 15

enthalpy: number & type of chemical bonds the net change in enthalpy, delta H, for a rxn depends on the relative strengths of the bonds broken and formed delta H < 0: exothermic: heat generated/released delta H > 0: heat energy transformed measured in kilojoules per mole (kJ/mol)

Answer 16

Sum Enthalpy (Products)minusSu m Enthalpy (Reactants)

Answer 17

As time moves forward, the net entropy (degree of disorder) of any isolated or closed system will increase. It takes *a lot* of effort (energy?) to decrease entropy.

Answer 18

randomness delta S > 0: system becomes more random, less ordered (favored) delta S < 0: system becomes more ordered, more ordered

Answer 19

Delta G < 0: exergonic, rxn releases energy Delta G > 0: endergonic, must put energy into system to make rxn happen It is the energy available to do work

Answer 20

products predominate at equilibrium (occurs spontaneously as written) reactants predominate at equilibrium (does not occur spontaneously as written [occurs spontaneously in reverse directional]) Rxn release energy

Answer 21

Delta G = delta H - T delta S

Answer 22

delta G * = -RT*ln(Keq)

Answer 23

-negative delta H (exothermic rxn) -postive delta S (increasing entropy [more random])

Answer 24

-positive delta H (endothermic rxn) -negative delta S (decreasing entropy [more ordered])

Answer 25

left alone (w/o any energy input), biosystems would fall apart (entropy maximization) to maintain order, and to grow, energy input is required to accomplish this, exergonic rxns are couples to endergonic rxns

Answer 26

The sum total of all chemical reactions in an organism. Metabolism = Anabolism + Catabolism

Answer 27

Synthetic reactions. Normally endergonic (+∆G) Usually involves reduction (Entropy, too

Answer 28

Degrative Reactions Normally exergonic (-∆G) Usually involves oxidation (Entropy?- +)

Answer 29

Some reactions are not energetically favorable. The first reaction of glycolysis, for example, wants to go in reverse. In living organisms, an energy-releasing reaction can be coupled to an energy-requiring reaction to drive the otherwise unfavorable reactions.

Answer 30

High-energy compounds are used by all organisms to provide a driving force for thermodynamically unfavorable reactions (entropy). Two reactions are “coupled” when one reaction is energetically favorable and can provide energy which allows the second reaction (unfavorable on its own) to occur. Energy released by the second reaction drives the first reaction! Thermodynamically unfavorable reactions (anabolic?; ∆G > 0) create order andrequire work and energy. We gotta get that energy from somewhere.

Answer 31

water, weak forces and acids/bases

Answer 32

≥ 70% of weight of most organisms Universal solvent  Chemical reactions occur in aqueous environment Drugs work in an aqueous environment (Pharmacy, right?) Drug targets are in an aqueous environment (Pharmacy, right? Right?) How drugs behave depends on their electrical charge, and this depends on how they interact with water Water forms hydrogen bonds with polar solutes Water and non-polar things have an interesting relationship Weak forces! Therefore, water is a critical determinant of the structure and function of proteins, nucleic acids, and membranes! (Basically biochemistry, right here) non polar elements will ball up in aqueous environment

Answer 33

Hydrogen Bonds- strong association bwtn FNO Ionic Interactions Hydrophobic Interactions- hide from water and keep to themselves Van der Waals Interactions These weak interactions allow for dynamic (rapidly changing/temporary)molecular processes.

Answer 34

unequal distribution of charge that results when a hydrogen is covalently bonded to an electronegative atom, such as oxygen or nitrogen interacts with a FNO somewhere else H-Bonding is for F, O, N Sulfhydryl (sulfur, below oxygen, behaves like oxygen ) groups too Directional Polarity!

Answer 35

N or O FNO test question amphipathic is a hydrophobic interaction

Answer 36

polar there's lots of oxygens pulling electro density to itself leaving the hydrogen more positive and so there is a net negative and net positive end

Answer 37

non polar no FON

Answer 38

decreases we order it and put it in something giving it order not letting it run around me be free

Answer 39

alcohol: hydroxyl group and water ketone: carbonyl and water polypeptides: peptide groups in polypeptides DNA: nitrogen and carbonyl

Answer 40

The salt crystal is ordered. It is thermodynamically favorable for water to break it apart and surround the individual components of Na-Cl with water molecules. Charge of the electron: negative. Add a negative charge: be negative. If you remove this then become positive Charge of proton: Positive Opposites attract Like charge repel This all may change the shape of something so it is needed to know when something might be negatively charged or positive Salt in water, Na and Cl dissociate and associate with water—entropy increases The positive part of water surrounds Cl, negative part of water surrounds Na—this is a hydration shell Broken up solid into bits and pieces—this is thermodynamically favorable because entropy increases. The universe tends towards disorder Ionization of water gives us acids and bases—het H+ and OH -

Answer 41

it broke and reformed even though it is weak the cumulative effect is great think of velcro

Answer 42

hydrophilic: yes hydrophobic (lipophilic): no mixed: partly soluble in water

Answer 43

polar gases--yes non-polar gases---less

Answer 44

highest: polar solids, lipids, and gases middle: non-polar solids, liquids lowest: non-polar gases

Answer 45

Any gas in the container: entropy decreases because set at a volume Any gas in the universe: entropy increases, more volume, more random eqn: deltaG = deltaH - Temp deltaS Solid or liquid solute: if polar, becomes more disordered; if non-polar becomes ordered Gas --entropy always decreases, because the gas is confined to a small volume --decrease is smaller if polar (molecules disperse), larger if nonpolar (molecules cluster)

Answer 46

contain regions that are polar (charged/hydrophilic) and regions that are non-polar (hydrophobic) Complex hydrophobic/hydrophilic interactions are thermodynamically favorable! 3. Lipids group together, increasing the amount of entropy in the system  water molecules are less ordered around individual lipids. Water near hydrophilic solute: water in oil, tends to itself and does not mix—less entropy Lipid organizes to itself-–water does not have to form hydration shell. Oil and water mixture is thermodynamically favorable—universe tends to thermo. The state, has to have entropy increasing, keep entropy high

Answer 47

Yes, I know all of them!!!!!! God is good!!! Nah I don't but I will go practice them!!!!!!!! God is STILL GOOD!!!!!!!!!

Answer 48

The association or folding of non-polar molecules in aqueous solution is one of the main factors behind: Formation of lipid micelles (and membranes) Protein folding Protein-protein association Binding of steroid hormones totheir receptors Drug/Ligand Receptor Binding!

Answer 49

Dynamic Interactions and Functionality! Weak forces maintain biological structure and determine biomolecular interactions! Molecular Complementarity! Mediated via noncovalent interactions – permits tight, highly specific binding of biomolecules!

Answer 50

solutes decrease the concentration of water properties depend only on the number of solute particles not their size colligative properties: vapor pressure, boiling point, melting& freezing point and osmotic pressure osmolarity: moles solute particles/L solution osmolality: moles solute particle/kg solution 140 mol NaCl/kg = 280 mOsmol NaCl/kg osmosis: diffusion of solvent across a membrane along a solute concentration gradient water follows salt Osmotic pressure: forcing water through a membrane in an attempt to equalize concentrations; isotonic, hypertonic and hypotonic solutions

Answer 51

isotonic" no net water movement, cell stays at normal size because there is equal amount of water inside that outside hypertonic: water moves out of cell and cell shrinks because there is more salt outside that inside and water follows the salt outside hypotonic: water moves in the cell creating outward pressure ; cell swells and may burst because there is more salt inside that outside so water follows salt inside

Answer 52

when a water molecule dislocates: results in a proton and hydroxide H + H30+ & OH- this is the ionization of water pH = -log[H+] pH + pOH = 14 In pure water (neutral), [H+] = [OH] so pH equals 7 when [H+] > [OH], pH < 7.0 (acidic) when [H+] < [OH], pH > 7.0 (basic)

Answer 53

Molecules that release hydrogen ions (protons) in solution: acids (H+ donor): H2CO3 Molecules that can accept hydrogen ions: bases (H+ acceptor): HCO3

Answer 54

hypotonic the cell is in a hypotonic solution! the solution has LESS salt than the cell

Answer 55

the water will go into the lysosomes and the cell may burst remember: water will move to the solute/salt water outside will move to solute inside

Answer 56

10 ^ -8 pOH = 14 - pH 8 = 14 - 6 pOH = -log[OH-] 8 = -log[OH-] 10^-8 = [OH-]

Answer 57

H+ to pH: pH = -log[H+] pH to H+: [H+] = 10^-pH pH to pOH: pOH = 14 - pH pOH to pH: pH = 14 - pOH pOH to OH: [OH-] = 10^-pOH OH to pOH: pOH = -log[OH-]

Answer 58

because dissociation for a strong acid is complete: what does the H+ of that acid equal: [H+] - [acid] and pH = -log[H+] because dissociation for a weak acid is incomplete, what is the extent of the dissociation determined by: Ka pKA = -logKa "p" = -log Ka equal [products]/[reactants] can we find the pH of soln if Ka is known - yes Ka = [H+][A-]/[HA] -log of Ka = pKa * Equilibrium Constant (Keq = [C][D]/[A][B]) * Ion Product for water: Kw = [H+][OH-] = 1.0 x 10-14 pH = -log [H+]

Answer 59

large Ka means dissociating more and releasing more protons small pKa means. strong acid because it is the inverse of Ka what does it mean that an acid's pKa is 2.5: the acid loses a proton at pH 2.5 and therefore a strong acid do strong acids dissociate more or less than weak acids: more! what does a low pH indicate about proton loss: donates lots of protons, large Ka, low pKa can we change properties of molecules based on environment - yes pKa is the pH at which a “ionizable” H is removedfrom the molecule Monoprotic: 1 proton diprotic: 2 proton (e.g., carbonic) triprotic (e.g., phosphoric) acids: 3 protons

Answer 60

what does pH effect in biomolecules: effects structure and function what happens if blood pH drops: CNS becomes depressed resulting in coma and death what happens is blood pH rises: CNS overexcited, muscles spasms leading to convulsions and respiratory arrest so how do we stay In narrow range of pH?- buffer

Answer 61

what are acids: release hydrogen ions (protons) in soln what are bases: accept protons in soln what do buffers have: equal amounts of weak acid and its conjugate (weak) base what do buffers do: keep pH relatively constant at equilibrium, what can conj acid and conj bases do: able to neutralize small amounts of other acids and bases when they are added to the soln what does the base do: gobbles up free H+ when acid is added what does the acid do: releases H+ when a base is added to the soln what happens when pH = pKa: 50:50 mixture of acid and anion forms of the compound what can we say about buffering capacity at pH = pKa: greatest at pH = pKa when donating or accepting proton are biological processes pH sensitive: yes, very when is buffering capacity lost: when the pH differs from the pKa by more than 1 pH unit buffers consist of pairs of weak acids and their conjugate bases (salts) best at pH = pKa ± 1

Answer 62

8.6 and 10.6 GOOD JOB! Watch YouTube video to memorize amino acids -- (structure, 3 letter code, 1 letter code)

Answer 63

Glycine (Gly, G) = no stearichinderance, least non-polar Proline (Pro, P) = The ring decreases the flexibility of the structure (bonds can’t “wiggle” as much), this affectspolypeptide backbone flexibility MeTHIOnine (Met, M) = containssulfur. These amino acids as a group: -hydrophobic core of soluble proteins -membrane-spanning region of transmembrane proteins

Answer 64

Phenylalanine (Phe, F) Precursor to Tyrosine, and therefore catecholamines Tyrosine (Tyr, Y) Has an acidic proton in the Rgroup (pKR – 10.07) Tryptophan (Trp, W) Precursor to serotonin, melatonin, vitamin B3

Answer 65

Electrically neutral at neutral pH R-groups have hydroxyl (often modified), thiol, amide functionalgroups. R-groups can form hydrogen bonds! Cysteine (Cys, C) can form disulfide bonds! (Stay tuned!) pKR = 8.18 AsparagiNe (Asn, N) and Glutamine (Gln, Q) are have Amide functional groups!

Answer 66

Lysine (Lys, K) pKR = 10.53 Arginine (Arg, R – pirate!) pKR = 12.48Has a guanidium group. Histidine (His, H) pKR = 6.00 Remove the carboxyl group,what do you think we get? At physiological pH, are these groups protonated or deprotonated?

Answer 67

Aspartate (Asp, D) pKR = 3.65 Glutamate (Glu, E) pKR = 4.25Primary excitatory neurotransmitter of thecentral nervous system. Generally, “-ate” refers to a base. A base is a proton acceptor . Can theR group accept a proton?--YES! MAYBE EVEN 2!

Answer 68

Let’s say you have an unknownsolution and you want to know whether it is a protein. Spectrophotometer time! Tryptophan and Tyrosine absorb light at 280 nm. Beer’s Law: The concentration of a solution is directly proportional to absorbance. Absorbance is the inverse of transmittance. beer's law: [ ] = k x A280

Answer 69

Amino acids are weak polyprotic acids. Each amino acid has at least two titratable groups. At acidic pH, the carboxyl group is protonated and the amino acid is in the cationic form. At neutral pH, the carboxyl group is deprotonated but the amino group is protonated. The net charge is zero; suchions are called Zwitterions. At alkaline (basic) pH, the amino group is neutral –NH2 and, the amino acid is in the anionic form. Amphoteric” Acts as an acid AND a base Also, acts as a buffer all of them do except for glycine and proline

Answer 70

Remember, amino acids have different forms at different pH. can act of both acids and bases What is a pKa? What does it tell you?- pH where it is deprotanated pI = Isoelectric point pH at which a molecule has no net charge Every amino acid/protein has one Average of the two pKas COOH gets deprotanated first ON EXAM: Have a titration curve, ask what form of the A.A exist at what pKa For glycine, After pKa1- we have a zwitterion –this is the PI take average of pKa of both (2.34 + 9.60)/2 = PI PI = 0.5(pKa1 + pKaR) Find electrically neutral molecule nad take the pKa of both to find PI

Answer 71

Histidine has an ionizable Rgroup! (pKR = 6.0). No other AAside chain has a pKa near neutral pH. The only AA that can be an effective buffer at physiological pH pI = Isoelectric point Average of the two pKas This time, find the two pKs thatstraddle the neutral species andaverage those.

Answer 72

equal amounts of forms I & II pKa1 = 2.19

Answer 73

3.00 the zwitterionic form!

Answer 74

charged molecules are soluble so whichever solution will make it charged is where it is more soluble basic solutions take away protons acidic solutions give protons will this make the solution more or less charged and thus make it more soluble

Answer 75

net charge

Answer 76

Glycine- Gly, G alanine- Ala, A proline- Pro, P Methionine- Met, M Isoleucine- Ile, I Leucine- Leu, L Valine- Val, V

Answer 77

Phenylalanine- Phe, F Tyrosine- Tyr, Y Tryptophan- Trp, W

Answer 78

Glutamine- Gln, Q Asparagine- Asn, N Serine- Ser, S Threonine- Thr, T Cysteine- Cys, C

Answer 79

Histidine- His, H Arginine- Arg, R Lysine- Lys, K

Answer 80

Aspartate, Asp, D Glutamate- Glu, E

Answer 81

To determine the concentration on an (unknown) acid or base by exactly neutralizing it with an acid or base with a known concentration Can be used to determine the concentration of the unknown and/or pKa

Answer 82

When pH < pKa: still protonated when pH > pKA: deprotanated equivalence point: [acid] = [base] (50/50) AND pH = pkA in the buffering region, the pH does not change that much because the buffer has a base to gobble up hydrogens if it needs to and an acid to donate hydrogens if need to

Answer 83

Multiple ionizable H's pH determine the amount of each "species"

Answer 84

relates the [acid], [conj base], pH and pKa together pH = pKa + log [A-]/[HA] pKa equals the acid dissociation constant (pH at which H falls off)

Answer 85

an optimal acid-base balance is maintained in body fluids and cells despite large fluxes of metablites. a buffer system protects the body from fluctuations in pH by sacking up excess H+ or OH-

Answer 86

dihydrogenBiological Buffers Control the pH-phosphate buffering system carbon acid buffering system (blood) proteins

Answer 87

base: HCO3- acid: co2 pKa = 6.1

Answer 88

Proteins are the main agents of biological change Amino acids are the building blocks “monomers” of proteins Structure (Chemistry)  Function. Remember the last lecture about chemical interactions and weak forces…

Answer 89

Catalysts – Enzymes (as proteins). Change the rate of chemical reactions Enolase, Amylase, Kinase, Phosphatase, DNA Polymerase, etc Transport – Ion Channels, Membrane Transporters, etc. Hemoglobin (transports O2 in the blood), Lactose permease (transports lactose across the cell membrane) Structure – Need form. Collagen (connective tissue), Keratin (hair, nails, etc) Motion – Things gotta move around. Myosin (muscle tissue), Actin (muscle tissue, cell motility), Dynein/Kinesin (move components around the cell)

Answer 90

Proteins are linear heteropolymers of α-amino acids (functional groups attached to the CENTRAL carbon Amino acids have properties that are well-suited to carry out a variety of biological functions: Capacity to polymerize (dehydration synthesis forms bond between carboxy and amino groups) Useful acid-base properties (pay attention to where we can deprotonate – pKa!) Varied physical properties Various chemical functionality

Answer 91

For all amino acids (except proline [ring] and glycine [H]) the alpha carbon is bonded to 4 different groups. The α always has four substituents and is tetrahedral. Therefore, there are two possible configurations for each amino acid (except for when R = H [glycine]).  All amino acids (except glycine) are chiral! Non-superimposable mirror images One chiral center, so L/D instead of R/S COO- to the top -R group to the bottom IF: Amino is to the LEFT = L Amino is to the RIGHT = D

Answer 92

When synthesizing AA in the lab, racemic mixtures occur enzyme however are extraordinary precise the amino acids that occur in natural proteins are the L configurations D- amino acids do occur in nature -small peptides in peotodiglycan of bacteria cell walls -peptide anitbiotics -neurotranmsitters (D-glutamate) -platypus venom. but are not found in protein

Answer 93

Common amino acids can be placed in five groups depending on their R substituents Nonpolar, aliphatic (non-aromatic) – 7: G, A, P, V, L, I, M (all the first letters of the AA) Aromatic – 3: F, Y, W (kinda weird lettering here) Polar, uncharged – 5: S, T, C, N, Q (3/5 are the first letters of the AA) Positively charged – 3: K, H, R (K is random, but H and R (think pirate) make sense Negatively charged – 2: D, E (I got nothing)

Answer 94

Glycine (Gly, G) = no stearichinderance, least non-polar Proline (Pro, P) = The ring decreases the flexibility of the structure (bonds can’t “wiggle” as much), this affectspolypeptide backbone flexibility MeTHIOnine (Met, M) = containssulfur. These amino acids as a group: -hydrophobic core of soluble proteins -membrane-spanning region of transmembrane proteins glycine, proline, alanine, valine, leucine, isoleucine, methionine

Answer 95

Phenylalanine (Phe, F) Precursor to Tyrosine, and therefore catecholamines Tyrosine (Tyr, Y) Has an acidic proton in the Rgroup (pKR – 10.07) Tryptophan (Trp, W) Precursor to serotonin, melatonin, vitamin B3

Answer 96

Electrically neutral at neutral pH R-groups have hydroxyl (often modified), thiol, amide functionalgroups. R-groups can form hydrogen bonds! Cysteine (Cys, C) can form disulfide bonds! (Stay tuned!) pKR = 8.18 AsparagiNe (Asn, N) and Glutamine (Gln, Q) are have Amide functional groups! serine, threonine, cysteine, asparagine, glutamine

Answer 97

Disulfide bonds can form under oxidizing conditions (extracellular) Play an important role in folding and stability of proteins, esp. those secreted to the extracellular medium Holds two portions of the protein together  increasing the concentration of protein residues and decreasing the concentration of water. Stabilizes structure by preventing water from breaking H-bonds Can be a “seed” for hydrophobic interactions  increase folding Two cysteines that are connected via a disulfide bond become a cysteine

Answer 98

Lysine (Lys, K) pKR = 10.53 Arginine (Arg, R – pirate!) pKR = 12.48Has a guanidium group. Histidine (His, H) pKR = 6.00 Remove the carboxyl group,what do you think we get? At physiological pH, are these groups protonated or deprotonated? lysine, arginine, histidine

Answer 99

Aspartate (Asp, D) pKR = 3.65 Glutamate (Glu, E) pKR = 4.25The primary excitatory neurotransmitter of thecentral nervous system. Generally, “-ate” refers to a base. A base is a proton acceptor. Can theR group accept a proton? aspartate and glutamate

Answer 100

Let’s say you have an unknownsolution and you want to know whether it is a protein. Spectrophotometer time! Tryptophan and Tyrosine absorb light at 280 nm. Beer’s Law: The concentration of a solution is directly proportional to absorbance. Absorbance is the inverse of transmittance.-- concentration = k x A280

Answer 101

hydroxyproline in collagen carboxyglutamate in prothrombin

Answer 102

Amino acids are weak polyprotic acids. Each amino acid has at least two titratable groups. At acidic pH, the carboxyl group is protonated and the amino acid is in the cationic form. At neutral pH, the carboxyl group is deprotonated but the amino group is protonated. The net charge is zero; suchions are called Zwitterions. At alkaline (basic) pH, the amino group is neutral –NH2 and the amino acid is in the anionic form.

Answer 103

Carboxy group pKa ~ 2.3 Amino group pKa ~ 9.6 pI = Isoelectric point pH at which a molecule has no net charge Every amino acid/protein has one Average of the two pKas

Answer 104

Glutamate has an ionizable Rgroup! pI = Isoelectric point pH at which a molecule has no net charge Every amino acid/protein has one Average of the two pKas This time, find the two pKs thatstraddle the neutral species andaverage those.

Answer 105

Histidine has an ionizable Rgroup! (pKR = 6.0). No other AAside chain has a pKa near neutral pH. The only AA that can be an effective buffer at physiological pH pI = Isoelectric point Average of the two pKas This time, find the two pKs thatstraddle the neutral species andaverage those.

Answer 106

Remember your organic chemistry. How do electron-withdrawing groups affect the ease at which groups can be extracted?

Answer 107

primary secondary tertiary quaternary

Answer 108

The primary structure of a protein is the sequence of linked amino acids. These amino acids are linked together through the formation of peptide bonds via a condensation (dehydration synthesis) reaction (endergonic). Peptide bonds are covalent bonds formed between the α-COOH and α-NH2 groups of two amino acids Peptides and proteins are broken down by hydrolysis reactions (exergonic but high Ea). The primary structure of a protein is the sequence of linked amino acids. AND cross-links These amino acids are linked together through the formation of peptide bonds via a condensation (dehydration synthesis) reaction (endergonic).

Answer 109

Peptide – two or more amino acids (2-17) joined covalently by a peptide bond. Polypeptide – many amino acids joined (17-50) together by peptide bonds (M.W. < 10,000) Protein – macromolecule with one or more polypeptide chains Numbering and naming starts from the amino (N-) terminus which is usually on the left. The peptide is then read from left toright.

Answer 110

Identify the ionizable groups (look at your N-terminal, C-terminal, and side chains) Determine the charge of each at the given pH Is the pH < or > the pKa?, Is the charge +2, +1, 0, or -1 – add all charges together Add all of the charges together!

Answer 111

Which pKa’s do you need?

Answer 112

Proteins containing permanently-associated components other than amino acids. The non-amino acid part is called a prosthetic group.

Answer 113

oxytocin: stimulate uterine contractions bradykinin: inhibits tissue inflammation insulin: pancreatic hormones, need for sugar metabolism glucagon: pancreatic hormone, opposes action of insulin

Answer 114

It is essential that we know the sequence of the protein we are studying in order for further biochemical analysis Many drug targets are proteins. We should study the mechanism or pathway the target is involved in. We should determine its structure  function. It’s not easy. Proteins exist in extremely complex mixtures in cells, and to understand the function, gotta isolate. But that isolation cannot affect the structure or function of the protein. Gotta be careful. You might have to do this one day. Brownie points for sounding like you know what you’re talking about 

Answer 115

1- choose protein to purify 2- choose source 3- extract protein from cells 4- separate protein from cellular components 5- purify specific protein or Peoria complex 6- study (activity, structure, mechanism of action, work)

Answer 116

3. Extract proteins from cells Lyse cells by destroying membranes and releasing cytosolic protein mix  crude extract Might have to get physical… 4.. Separate Proteins from other cellular components Centrifugation!

Answer 117

separates large from small particles separate sub cellular fractions, isolate specific organelles or isolate all soluble porcine in a cll after cell lysis once protein-containing solution (supernate) Is separated from the rest of the cellular debris the protein of interest can be purified

Answer 118

4. Separate Proteins from other cellular components Dialysis: separating small solutes from proteins Can be put anywhere in the isolation/purification scheme

Answer 119

Purify specific protein or protein complex Separating one protein from the rest using fractionation based on physical and/or chemical properties Chromatography

Answer 120

stationary phase (resin/beads) and a mobile phase clomp Chromatography allows separate of a mixture of protein over a solid phase (porous matrix) using a liquid phase to mobilize the proteins protein with lower affinity for the solid phase will wash off first, proteins with higher affinity will retain on th exodus longer and wash off later ] fractions are collect and keep those with protein of interest

Answer 121

Sometimes the first round of chromatography. Column packed with porous beads Separates molecules by size (and shape) Small proteins pass through the porous beads. Longer net distance to travel. Elute later. Large proteins move around the porous beads. Smaller net distance to travel. Elute first.

Answer 122

Separates by charge: all proteins have a net charge(or neutral) at any given pH (depends also on pI) Column packed with a charge resin of a synthetic polymercontaining bound (+) or (-) groups. Lets say the resin is (-) charged… (-) charged proteins will move through faster and elutefirst. Why? because the resin is (-) charged and thus will repel the (-) charged protein (+) will move through slower and elute later. Why? because the resin is (-) charged and thus will attract the (+) charged protein To elute, just change the pH. Why?- Change pH, change charge and makes it remove from resin

Answer 123

Separates by specific binding. Beads in the column are complementary to the protein of interest. The protein will bind to the ligand on the beads. Other proteins flow right through. The most specific/efficient form of chromatography. How to elute? Add chemical that breaks the bonds. Add a high concentration of the ligand  competes for binding of the protein with the column (stay tuned)

Answer 124

Separates based on size! Smaller proteins get through the tangles of the gel easier than larger proteins  move farther Migration rate depends only on molecular weight SDS – Sodium dodecyl sulfate PAGE - Polyacrylamide Gel Electrophoresis

Answer 125

Separates based on charge (pI – isoelectric point) and pH! pI – isoelectric point. pH at which amino acid has no charge. Separates proteins by allowing them to reach the pH that matches their pI (net charge is zero).

Answer 126

Isoelectric Focusing (IEF) (charge based) SDS PAGE (size-based)

Answer 127

A280 - mass (mg) some activity - the protein's ability to carry out some concrete activity BCA: color, absorbance and amount

Answer 128

Total activity: the total units of enzyme in a solution Specific activity: the number of enzyme units per mg of total protein This is really just showing that Specific activity is an extension of signal:noise ratio. The other proteins in the impure sampleare noise (total activity). The protein of interest is the signal (specific activity). As we purify, noise decreases, signal increases. x

Answer 129

factors that contribute to making delta G more negative (less positive) - negative delta H (exothermic rxn) - positive delta S (increasing entropy [more random]) factors the contribute to making delta G more positive (less negative) - positive delta H (endothermic rxn) - negative delta S (decreasing entropy [more ordered])

Answer 130

- at all T: spontaneous at all T - at low T: spontaneous at low T + at high T: non-spontaneous at high T + at low T: non-spontaneous at low T - at high T: spontaneous at high T + at all T: non-spontaneous at all T

Answer 131

IF: Keq >> 1, ∆G° is large and negative  meaning? - spontaneous IF: Keq << 1, ∆G° is large and positive  meaning?- non-spontaneous

Answer 132

* Tyr and Trp absorb UV light at 280nm – a way of determining protein concentration

Answer 133

B. Cannot Configuration differs from conformation by a fact that conformations are only due to the orientation of the atoms in molecule around the covalent bond considering the bond as an axis. And changing the configuration causes the cleavage and formation of new chemical bonds

Answer 134

A. Configurational Configurational - mirror images that cannot be placed on top of each and be the same Conformational - rotated differently

Answer 135

B. Diastereomers

Answer 136

A. They are mirror images of each other B. They rotate the plane of plane-polarized light in opposite directions C. They require a chiral center

Answer 137

B. Racemic Mixture

Answer 138

D. Exothermic

Answer 139

A. Increases

Answer 140

B. Exergonic

Answer 141

C. We need more information to answer this question.

Answer 142

C. Exergonic

Answer 143

B. Non-polar

Answer 144

B. Decreases

Answer 145

C. Hypotonic

Answer 146

B. The lysosomes will expand and may burst.

Answer 147

D. pH 8.6-10.6

Answer 148

B. Equal amounts of Forms I & II. you have to know (for example) at Pka1, the molecule is in limbo which means that half is still the first form of the molecule and half is the second form of the molecule Pka is also the pH at which a proton is removed

Answer 149

B. pH 3.00 it is like you are finding the pI :)

Answer 150

B. Net charge.

Answer 151

C. SDS Polyacrylamide Gel Electrophoresis

Answer 152

B. Size-exclusion chromatography

biochem - exam 1 Flashcards

(190 cards)