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aa characters 3
- s config (except cysteine which is R)
- alpha C is chiral except glycine
- optically active
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in eukaryotic cells, AA are L and left of fischer projection
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nonpolar and non aromatic 7 (single bonds all around even 1 ring)
- glycine
- alanine
- valine
- isoleucine
- leucine
- methionine
- proline
- *get all violet incense,lets make perfume*
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aromatic side chains 3 (aromatic rings)
- tryptophan
- phenylalanine
- tyrosine
- *turkey produces tiredness*
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polar side chains 5 (have nh2, oh, or sh)
- serine
- threonine
- aspragine
- glutamine
- cysteine
- *screw the artic, get coats*
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negative side chains 2
- aspartate
- glutamate
- *all girls*
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positive side chains
- arginine
- lysine
- histidine
- *all hearts love*
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2 facts of behaviors for AA
- ionizable groups gain protons under acidic conditions and lose protons under basic
- if PHis ph>pka species will be deprotonated
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AA have 2 groups that can be deprotonated, COOH and NH2, the SC id ionizable. If it is already protonated then nothing will happen
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at neutral pH, you will only have depro version AA
- NH2 will b the same while COOH becomes COO-
- below pka of AA, NH2 will be protonated as its conjugate acid
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example of titration curve
- middle points of the curve are when ph is close to Pka and it creates a buffer
- at a low ph the AA was fine, and as more basic was added, cooh becomes deprotonated, when the equivalent is reached, the solution will be neutral
- as more basic is added,NH3 becomes depro
- cooh is first to change because its ph is 2 and NH3 is 9-10
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AA with ASC will have pi values below 6
AA with BSC will have pi values above 6
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extra step in AA side chains of glutamic acid and lysine
they are in a positive state, depro in main carboxyl group, then it becomes neutral before being deprotonated again to becomes negative
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structures of proteins
- primary - formation of pep bonds to AA
- secondary - alpha and beta pleated sheets occur due to intramolecular H bonding between nearby AA
- tertiary - creation of hydrophobic or philic side chains though a 3d structure
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alpha helices 3
- pep chain coils around central axis
- intramolecular H bondingbetween carbonyl oxy atom and amide H
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beta helices
- II or T lie along each to form rows
- IMHB between carbonyl oxy on one chain and amide H in an adjacent chain
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In teriary structure, phobic SC move inside of pro while philic get pulled by phobic to stabilize pro from inside
surface of AA have polar or chargd (philic) r groups
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structure of 3d of tert is determined by H bonds and AB rxns between AA and charged SC to create disulfide bonds(salt bridges)
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Hemoglobin and immunoglobins have 4 subunits in which can bind one molecule of oxygen
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a hydrophob SC is placed in an aqe solution w/ solvation layer
- the h2o molecules in the solvation layer cannot form h bonds so they can arrange into specifics to maximize h bond
- the hydophil residues in the aqe solutions gives h2o positioning
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amphoteric species
either accept or donate a pro
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zitterions
molecules with a - & + charge that is electrically neutral
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polyprotic acid
an acid that can donate more than one proton
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the conc of enzyme and substrate effct how quickly a reaction will occur, the higher the amount of enzyme and sub the reaction is saturated, meaning enzyme is working at max velocity **michaelis-menten equation**
- e+s=ES=E+p
- km is a constant to mean affinity of the enz for its sub
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example of km
- increae km has decrease affin for its sub b/c it needs increase sub
- when KM = conc of sub, 1/2 of the AE sites are full
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cooperative enzymes have multiple subunits
- low affinity tense state T have decreased affin
- high affinity relaxed state R have increased affin
- binding of a sub causes T to R
- loss of binding causes R to T and causes more substrate to disassociate from the subunit
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4 type of inhibition
- competitive
- noncompetitive
- mixed
- uncompetitive
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reversal inhibition
add more sub to increase sub to inhibit ratio, enzyme will want to bind to sub instead of inhibit
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competitive inhibition and reversal
- inhibitor binds to the site and sub can not bind to it
- **km will increase do to inhibit b/c it decreases affin
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noncompetitive inhibitors and reversal
- causes enzyme config change so no sub can bind
- it decreases Vma b/c less enzymes
- increases km b/c affin is still increased
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Vmax meaning
velocity at which the rate of the rxn is occurring
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mixed inhibition
- inhibitors can bind to enzyme of enzyme-sub complez
- can increase km inhibit binding to enzyme
- decrease km inhibiting binding to e-s complex
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uncompetitive inhibitors
- only bind to E/s complex and locks them in place
- cannot be removed from each other
- lowers km and increases affinity
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