Flashcards
Biochemistry - Final 1
Cards in this deck (200)
- 1Give a definition of BiochemistryThe science concerned with the chemistry of biological processes and life at the molecular level. Includes structure, behaviour, and interaction of molecules.
- 2What are Bio-moleculesThey are the building blocks of the cell. Notes that C, H, N, O, P, S make up 99% of these molecules.
- 3What are the 3 small bio-moleculesAmino Acids, Sugars, Fatty Acids
- 4Discuss amino acids as small bio-moleculesBuilding blocks of proteins, have an amino group on the left and a carboxyl group on the right. Their R-groups determine their properties
- 5Discuss sugars as small bio-moleculesThe basic unit is the monosaccharide. They serve to store fuel as starch and glycogen
- 6Discuss Fatty Acids as small bio-moleculesThey are mono-carboxylic acids that make up lipids who store energy as fat and synthesize hormones. Can be saturated (all single bonds) or unsaturated (at least 1 double bond)
- 7What is metabolismIt is the sum of all chemical reactions in a living organism. Functions include waste removal, use of energy, synthesizing molecules
- 8What is anabolic metabolismMetabolic pathway that deals with building molecules
- 9What is catabolic metabolismMetabolic pathways that deal with breaking molecules for energy
- 10What are the 6 biochemical reactionsNucleophilic substitution, elimination reactions, Addition reactions, Isomerization, Redox reactions, Hydrolysis
- 11What is the nucleophilic substitutionWhen an atom from one molecule is substituted for another
- 12What is the elimination reactionWhen an atom from a molecule is removed and a double is formed in its place
- 13What is an addition reactionWhen 2 molecules come together and become one
- 14What is an Isomerization reactionIntramolecular shift of atoms or groups
- 15What are redox reactionsTransfer of electrons from a donor to an acceptor
- 16What is hydrolysisWhen a water molecule is added to a molecule in order to break a bond
- 17What are geometric isomersCis and Trans isomers
- 18What are the 2 kinds of stereoisomersenantiomers, diastereomers
- 19What are enantiomers2 Molecules that are mirror images of eachother but non-superimposable
- 20What are diastereomers2 Non-superimposable molecules that aren't mirror images of eachother
- 21What is free energy + its equationThe flow of energy in a reaction.
DeltaG=DeltaH - TDeltaS
If G is -'ve then rxn is spontaneous - 22What is cohesionIts attraction between molecules of the same kind
- 23What is adhesionIt is the attraction between different molecules as a result of H-bonds
- 24What is electronegativityIt is the tendency of an atom to attract an electron. Increases as we go top right in periodic table.
- 25What are the 3 kinds of solutes that may be in waterHydrophobic -> Water fearing, immiscible
Hydrophilic -> Water loving, will dissolve
Amphipathic -> Both hydrophobic and hydrophilic - 26What is pHA measure of hydronium concentration in a solution.
pH = -log[H+] - 27How do acids impact pHThey dissociate and release H+ ions which lower pH
- 28How do bases impact pHBases combine with the H+ and decrease its concentration which increases pH
- 29What are buffers and how do they workThey are a weak acids and its salt. They resist changes in pH by donating and removing H+ as needed.
pH = pka + log [A-]/[HA] - 30What is the effectiveness of a buffer dependent onThe pH of the environment and the concentration of the buffer
- 31if pH > pKa of the buffer then what can be said about concentration of the entitiesMore A- than there is HA
- 32What are the 7 functional groupsHydrogen
Hydroxide
Carboxyl
Carbonyl
Amino
Sulfhydryl
Phosphate - 33What is an etherOxygen bonded to 2 carbon chains
- 34What is a thiolIt is a functional group with SH at the end of a carbon chain
- 35What is an anhydride linkageO=C-O-C=O
- 36What is an esterWhen there's a O=C-O and then the single bond Oxygen is bonded to something else as well
- 37What is an amideO=C-NH
- 38What is a nitrileA carbon and nitrogen triple bond
- 39What is an amine functional groupNH bonded at the end of a carbon chain
- 40What is a molecules2 or more atoms covalently bound together
- 41What is the biochemical importance of chiralitySome receptor sites are chiral and only favour 1 specific binding manner
- 42What form of amino acids do we get in acidic solutionsCOOH and NH3+
- 43What form of amino acids do we get in basic solutionsCOO- and NH2
- 44What is the zwitterion for an amino acidNH3+ and COO-
- 45What is the pKa of alpha carboxyl2.2
- 46What is the pKa of alpha amino (NH3+)9.3
- 47What is the pKa of Beta Carboxyl (Asp)3.9
- 48What is the pKa of Gamma-Carboxyl (Glu)4.1
- 49What is the pKa of sulfhydryl (Cys)8.3
- 50What is the pKa of phenolic (Tyr)10.1
- 51What is the pKa of Guadinium (Arg)12.5
- 52What is the pKa of Imidazolium6.0
- 53What is the pKa of epsilon amino10.8
- 54What are the titratable groups of the important pKa you have to knowAlpha Carboxyl
Alpha Amino
Sulfhydryl
Phenolic
Guadinium
Imidazole - 55How do you find isoelectric pointpI = pKa (alpha carboxyl) + pKa (Alpha amino) divided by 2
- 56What are the 20 amino acidsGlycine
Alanine
Valine
Proline
Tyrosine
Tryptophan
Leucine
Isoleucine
Histidine
Asparagine
Methionine
Threonine
Serine
Phenylalanine
Glutamine
Cysteine
Arginine
Lysine
Asaparatic Acid
Glutamic Acid - 57How do you draw Glycine2 hydrogens coming off the backbone (doesn't have the extra methyl)
- 58How do you draw AlanineBack bone plus the methyl group (is the backbone for all other amino acids)
- 59How do you draw ValineJust a "V" coming off the backbone
- 60How do you draw LeucineMake an L with the methyl and then cut long side in half
- 61How do you draw IsoleucineMake half of an "I" with the backbone
- 62How do you draw methioneSideways "M" off the backbone except there's a break for a Sulfide atom
- 63How do you draw ProlineBackbone but there's a 5 point ring that integrates the Nitrogen from the amino group
- 64How do you draw PhenylalanineIt's alanine except with a phenyl group attached to the methyl
- 65How do you try tyrosineSame as phenylalanine (phenyl coming off the methyl) but there's a hydroxy group at the top of the benzene ring
- 66How do you draw tryptophanDraw a "W", the right side is a benzene ring and the left side is a 5 point ring with nitrogen and a double bond at the bottom left
- 67How do you draw SerineJust an hydroxy group coming off the methyl
- 68How do you draw ThreonineMake a T with the backbone but slap a hydroxy group at one of the ends
- 69How do you draw AsparagineJust a carboxamide off the methyl
- 70How do you draw glutamineCarboxyamide coming off the methyl except 2 carbons before it
- 71How do you draw CysteineJust a sulfhydryl coming off the methyl
- 72How do you draw LysineDraw a K off the methyl but without the vertical component, slap an amino at the tip
- 73How do you draw ArginineHas a Guadinium group (CN3+) that is preceded by 2 carbons
- 74How do you draw HistidineHas the imidazole group (5 ring strucutre with 2 Nitrogens and double bonds)
- 75How do you draw Asparatic AcidCarboxyl group coming off the methyl
- 76How do you draw Glutamic AcidCarboxyl group preceded by 2 carbons
- 77What are Post Translational Protein Modifications that take placeAcetylation of N-terminal
Oxidation (Pro and Lys)
Carboxylation (Glu)
Post-synthesis cleavage
Glycation (diabetes) - 78What are the 2 outlined Amino Acid DerivativesHistamine, from histidine, is released and gives allergy-like symptoms
Serotonin, from tryptophan, is a neurotransmitter - 79What are essential amino acids and list themAmino acids that can't be naturally produced by our bodies so they must be consumed as part of our diets:
Arg, His, Ile, Leu, Lys, Met, Val, Phe, Thr, Trp - 80What is steric inheritanceEssentially the excluded volume of overlapping electron orbitals between two atoms
- 81Discuss peptide bondsPlanar structure with partial double bonds. Are polar and experience no rotation. Found in the trans form because of reduced steric hinderance. Adding water causes the split of the bond
- 82What enzyme is used to help metastable polypeptides synthesize proteinsaminoacyl tRNA synthaze
- 83What is amino acid residueThe original part of the amino acid in a peptide -> missing the OH and an H on the nitrogen
- 84Where does the amino acid go once ATP is brokengoes onto the 3' OH end of tRNA
- 85What is an oligopeptidePeptides with a few AA residues
- 86what is a PolypeptidePeptides with a big chain of AA residue
- 87What is the MALDI spectrometerA laser fires at a target plate measures the time it takes for the light to reach and time it takes for ion to get back and then it can find the relative mass
- 88What is peptide mass fingerprintingBacktracking process where mass spectrometry is done for protein digested y proteolytic enzyme
- 89Discuss Protein SynthesisAmino acids are added in a linear sequence and the C-terminus is added to a support and then goes through 3 chemical reactions:
- Deprotection (removal of protecting group)
- Activation
- Coupling -> Ester forms amide bond with deprotected amide - 90Discuss the Merrifield Solid Phase Synthesis TechniqueAnchor C-terminal to a support
Deblock and condense
Release peptide - 91List protein functions and examplesMotor Proteins (myosin)
Structural Support (collagen)
Enzymes (DNA polymerase)
Antibodies
Hormones
Transport proteins (hemoglobin)
Storage Molecules (Casein)
Signalling Molecules (Insulin)
Receptor Molecules (Rhodopsin)
Regulatory molecules (Lactose repressor)
Speciality Molecules (anti freeze) - 92What can protein failure lead toCystic Fibrosis -> Insufficient protein production and sus folding
Diabetes in Adults -> Protein misfolding leads to blood vessel damage
Alzheimers -> Clumps of wrongly folded proteins - 93Give a general overview of protein structurePrimary Structure -> linear amino acid sequence
Secondary Structure -> Spatial alignment of repeating conformations of peptide chains
Tertiary Structure -> Overall 3D shape of fully folded protein
Quaternary Structure -> 2 or more polypeptides together - 94Describe Primary structure of proteinsLinear sequence from N terminus to C terminus
Delta G is negatie - 95Discuss the Alpha HelixTelephone cord type structure that is stable bc of H bonds between H and O
Direction is determined by whichever hand curls in the direction of the spin and then thumb shows which way it goes
12 AA on average and 3.6 AA per turn
Fits perfectly into major groves of an binding proteins - 96What is Pitch in terms of alpha helixThe vertical distance between turns, 5.4 residues
- 97What is vertical distance in terms of alpha helixVertical distance between residues, 1.5 AA
- 98What is the helical wheelJust a tool to visualize the helix
- 99What is a triple helix3 polypeptides intertwined together like a braid
- 100Discuss the Beta SheetPretty much an accordion of a bunch of polypeptides with alternating R-groups.
A collection of accordions/sheets gives a barrel.
Fits in minor groves of DNA double helix.
H bonds can be parallel (evenly spaced), anti-parallel (not evenly spaced) - 101What kinds of bonds are in Tertiary and QuaternaryDisulfide bridges
Salt bridges
Hydrogen bonding
Hydrophobic interactions - 102What is protein denaturing and what makes it happenWhen one or all the bonds in the tertiary + quaternary structure get fucked. peptide bonds and primary structures are guwop.
Caused by extreme heat, mechanical agitation (drives oxygen), Detergents (fuck up hydrophobic side chains), pH change (disrupt salt bridges), Organic and inorganic compounds that compete for bonding sites - 103What is the tertiary structureOverall 3D shape from folding which is dependent on attraction between amino side chains on the same side
- 104What is the Quaternary structure2 or more polypeptides that come together to form a single 3D unit
- 105Discuss the Afinsen ExperimentFigured out that tertiary structure is most thermodynamically stable and all info for it is in the primary structure.
Found this by denaturing protein with urea then renatured it and it went straight to tertiary.
Also removed protein to oxidize the S groups and got no activity, then he re-blessed it and say it go straight to tertiary - 106What are the different classes of proteinsFibrous Proteins
Globular Proteins
Membrane Proteins - 107Discuss Fibrous ProteinsElongated molecules in the secondary structure. Deals with structural support because it is difficult to dissolve.
Things that fall under the class: Alpha helix, Beta helix, triple helices, aloha and beta keratin - 108Discuss Globular proteinsCompact 3D folding that deals with catalytic processes and transportation
Hydrophobic interior and hydrophilic exterior - 109Discuss the motion of Globular proteinsAtomic -> Short distance and fast bc of kinetic energy and temp
Collective motion -> Group of atoms moving in synch. Slower and longer distances
Conformational Changes -> Movement of domains in response to a stimuli - 110What are membrane proteinsSame as globular proteins but they lay in fat
- 111Discuss Alpha Keratin311-314 residue segments capped with non helical termini.
In hair and fingernails
Primary structure is 7 residue repeats
In hair we have protofibril which is 2 pre twisted segments coming together to make 4 molecules.
8 protofibrils makes a microfibril with 32 molecules - 112What is Beta KeratinType of fibrous protein that is found in feather and scales
- 113How is hair curledS-S bonds are reduced
Hair is curled to to offset the disulfide bridges
Reoxidated and S-S bonds are formed again - 114Discuss Levinthal's ParadixPretty much found out that there are specific pathways for protein folding
Polypeptide -> secondary structure -> Domain -> folded protein
Hydrophobic collapse and molten globules hep make the tertiary shape - 115What are protein motifsCombinations of secondary structure elements with specific geometric arrangements -> allow us to see similarities (Beta-sheets becoming a barrel)
- 116What is the goal of protein purificationTo obtain a protein in a pure and active form using minimal steps and time
- 117Discuss the process of protein purification1) Remove non-protein components with a centrifuge
2) Get rid of salts through dialysis (note too much buffer and salt will croak it)
3) Use chromatography to purify the sample - 118Discuss Ion-exchange chromatographusing singly charged polymer beads to separate proteins by cahrge
- 119What is size exclusion chromatographyPorous polymer beads separate the proteins by MW -> bigger proteins leave first bc they dont fit in pore
- 120What is affinity chromatographyFinding out what desired protein will bond to and adding that substrate to a polymer and throwing it in there to catch that protein
- 121What is electrophoresis chromatographyA charged field moves proteins base on MW and an SDS detergent with negative charge causes proteins to go to cathode
- 122What is isoelectric focusing chromatographySeparation of proteins base on pI.
Makes use of Gel with ampholytes that creates pH gradient -> wherever protein stops, that's its pI - 123What is 2D electrophoresis chromatographyMakes use of electrophoresis and isoelectric focusing.
Is a graph of MW and pI. Isoelectric gel with ampholyte is poured sideways - 124What are reaction rates dependent onTemperature, environment, and concentration of reactants
- 125What is the law of mass actionKc = [reactants ^ their coefficient]/[products ^ their coefficient]
- 126What must occur for a reaction to happenA collision must occur with sufficient energy and orientation
- 127What happens if there's an imbalance in Keq vs mass action in vivo?There is a flux generation of enzymes
- 128Define thermodynamicsRelationship among different forms of energy and how the energy effects matter microscopically. Tells us whether or not a reaction will happen
- 129What is entropyMeasure of disorder. Is favoured by the universe. Increase in disorder leads to spontaneity.
- 130What are the laws of thermodynamicsEnergy of an isolated system is constant
Entropy of an isolated system never decreases - 131What is an isolated systemSystem that can't exchange matter or energy
- 132What is a closed systemSystem that can only exchange energy
- 133What is an open systemSystem that can exchange both energy and matter
- 134Discuss free energyEnergy available to do work.
G = H-TS
If delta G is negative then rxn is spontaneous
Delta Gnoght = -RTlnKeq
Delta G = Delta Gnoght + RTlnQ - 135What is an extensive propertyThermodynamic property directly related to the mass of a subject
- 136What is an intensive propertyThermodynamic property that is not directly related to mass of a subject
- 137What is Reaction couplingPretty much using 1 reaction to drive the other. Follows Hess' law typa thing when solving problems
- 138What is delta G noght primeDelta G noght at different conditions -> pH of 7
- 139How is ATP used in couplingIf reaction has Delta G noght lower than 30kJ/mol, then ATP to ADP can be used to drive it.
If lower than 60 kJ/mol, then ATP -> AMP - 140How are reaction rates measuredBy looking at how much product is formed or how much reactant is lost over a period of time
- 141What are rate lawsEquations that show the rate of reactions.
Deal with Reactants
Rate = k[A]^a[B]^b - 142What 4 factors affect reaction rateConcentration of reactant
Temperature
Catalyst
Surface area of reactant molecules - 143What is the rule of thumb with respects to temperature and reaction ratereaction rate doubles per 10 degree increase in temp
- 144What is the arrhenius equationk=Ae^(Ea/RT)
- 145What are reaction mechanismsPath of reactions, which bonds are broken/formed
- 146What are elementary steps in reactionsElementary step = rxn that happens bc of molecules colliding
- 147What is the rate determining stepThe slowest step in a reaction mechanism
- 148What is molecularityThe number of molecules involved in an elementary step
- 149What is a catalystA substance that speeds up reactions by lowering activation energy. These guys are not fully consumed by the reaction. They also do no change the amount of energy released
- 150Differentiate between the 2 types of catalystsHomogenous = catalyst and reactant are in the same phase
Heterogeneous = catalyst and reactant are in different phase - 151What are Enzymes and what do they doProteins that are catalysts in living cells (all proteins except for ribosome and spliceosome which are ribozymes).
They couple reactions, control rates.
"Homogenous catalysts for metabolic functions" - 152What are enzyme kineticsLooking at biological roles of enzymatic catalysts along with rates of enzyme reactions
- 153What is the active site in an enzymeIt is where the substrate binds onto and catalysis actually occurs. The enzyme induces the shape of the substrate. NOT lock and key.
- 154What are cofactorsComponent that works with an enzyme in doing catalysis
- 155What are coenzymesCofactors that are derivatives of vitamin B
- 156What are the 6 classes of enzymesOxidoreductase
Transferase
Hyrolase
Lyase
Isomerase
Ligase - 157Discuss Oxidoreductase enzymesThey do redo reactions.
Lactate dehydrogenase
Where substrate is lactate and product is pyruvate - 158Discuss Transferase enzymesEnzymes that transfer chemical groups.
Alanine Transaminase.
Substrate = alanine + alpha ketoglutarate
Product = pyruvate - 159Discuss Hydrolase enzymesEnzymes that cleave molecules, hydrolysis
Diphosphate phosphohydrolase
Substrate = pyrophosphate and H2O
Product = phosphate - 160Discuss Lyase enzymesRemove chemical groups (make bonds)
Pyruvate decarboxylase
Substrate = pyruvate
Product = acetaldehyde and CO2 - 161Discuss Isomerase enzymesChanges stereochemistry
Alanine racemase
Substrate = L-alanine
Product = D-alanine - 162Discuss Ligase enzymesLinks 2 groups together so essentially synthetase
L-glutamine synthesis
Substrate = L-glutamate and NH4+
Product = ATP - 163What 3 conditions must be met for a reaction to occur with respects to the moleculesMolecules must collide
Molecules must be oriented correctly
Molecules must have sufficient energy - 164How do Enzymes Work?E+S <-> ES <-> EP <-> E+P
Make use of transition state instead of intermediate.
Do not change anything other than lowering activation energy. Does not waste energy or build up toxins either - 165What is Gibbs free energy (G)The instability of a molecule / its tendency to react
If dG > 0 then more product than substrate so rxn won't be spontaneous - 166What 5 factors impact enzyme activityTemperature
pH
Substrate Concentration
Product Concentration
Presence on inhibitor/activator - 167In what 3 ways can Enzyme activity be measuredMeasure rate of product production
Measure change in cofactor absorption
If hard to measure then enzyme is coupled - 168What is the Michaelis-Menten EquationVo=(Vm[S])/Km+[S]
Note that Km is half Vmax
Lower Km means less S needed to achieve 1/2 Vmax - 169What are Turnover numbers (Kcat)Catalytic constant
The hardest that the enzyme can work
Max substrate converted to product per second per active site.
1/Kcat is the time needed to make 1 substrate into product
Vmax = Kcat [Enzyme] - 170What is the lineweaver-Burk equation1/Vo = Km/V[S] + 1/V
slope = Km/V - 171What is reversible enzyme inhibition and what are the 3 kindsEnzyme activity can be recovered by simply removing the inhibitor
Competitive Inhibition
Uncompetitive Inhibition
Noncompetitive Inhibition - 172What are competitive inhibitorsInhibitor and substrate compete for the same active site.
Increase Km bc more substrate needed - 173What are uncompetitive inhibitorsInhibitor binds onto the Enzyme-Substrate Complex
Lowers Vmax and Km - 174What are non-competitive inhibitorsInhibitor binds elsewhere than active site.
Km doesn't change but Vmax decreases bc less product being formed - 175What is irreversible enzyme inhibition and what are the 3 kindsInhibitor binds covalently to the enzyme and inactivates it.
Group specific
Affinity Labels
Suicide Inhibitors - 176What are group specific inhibitorsReactions with amino acid side groups to fuck with catalysis
- 177What are affinity label inhibitorsInhibitor and substrate covalently bond to active site and stay there 4ever
- 178What are Suicide InhibitorsModified substrates that trick enzymes into binding but then the EI complex is evil and goes on to croak other enzymes
- 179What are the 3 kinds of enzyme catlaysisGeneral Acid/Base Catalysis
Metal Ion Catalysis
Covalent Catalysis - 180What is metal ion enzyme catalysisMetal ions stabilize the transition state and help orientate the substrate
- 181What is general acid/base enzyme catalyssiTransfer of protons between enzyme side chains
- 182What is covalent enzyme catalysisCovalent bond between enzyme and substrate
- 183What are the 5 strategies in which enzyme activity can be controlledAllostery
Covalent Modifications
Binding of Regulatory Subunits
Limited Proteolysis
Regulation of stability - 184Discuss Allostery Enzyme RegulationThe end product of a pathway inhibits the original pathway or activation from a product generated early in pathways
- 185Discuss Binding of Regulatory Subunits Enzyme RegulationcAMP produced from ATP and goes on to bind onto regulatory subunits of PKA and frees the catalytic subunits which are then free
- 186Discuss Covalent Modifications Enzyme RegulationAmino Acids on enzymes are modified
Eg. Phosphorylation by PKA - 187Discuss Regulation of stability Enzyme RegulationProteins are continuously made and destroyed to regulate
Eg. Ubiquitin tags proteins for degradation and they go to proteosomes to croak - 188Discuss Limited Proteolysis Enzyme RegulationDigestive enzymes have 2-3 peptide bonds cleaved just to change them a bit
- 189What is the suffix for carbohydrates"ose"
- 190Discuss MonosaccharidesSimplest carbs, 3-7 carbons, and chiral
- 191What do carbs doEnergy storage and distribution
Precursor to amino acids
Tell proteins where to go in glycoproteins
Structural and mechanical roles
Antigenics - 192What is the chemical formula for carbrs(CH2O)n
- 193What are disaccharides2 monosaccharides covalently linked together
- 194What are oligosaccharidesA few monosaccharides covalently linked together
- 195What are polysaccharidesChains of monosaccharides and disaccharides
- 196What are aldoses and ketosesAldose = sugar with aldehyde
Ketose = sugar with ketone - 197Differentiate between L and D sugarsIf OH on bottom chiral carbon points to the right then it's D.
Inverse is true for L - 198What is D-Glyceraldehyde3 Carbon D-Aldose
- 199What is D-Erythrose4 Carbon D-Aldose.
All H on one side, all OH on the other (right) - 200What is D-Threose4 Carbon D-Aldose where an H and OH switch sides
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- Flashcards on Biochemistry - Final 1, created by Ramtin Habibi on 16/10/2017.
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