biochem > amino acids > Flashcards

amino acids Flashcards

(38 cards)

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1
Q

Common structural features of amino acids

A
  • alpha carbon attached to R group, amino group, and carboxyl group
  • R group differentiates them
  • alpha carbon is a chiral center
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2
Q

How can R groups vary

A
  • size
  • structure
  • polarity
  • solubility
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3
Q

stereoisomers vs constitutional isomers

A
  • stereoisomers differ in the spatial orientation of the bond (ie. enantiomers)
  • consitutional isomers are connected differently
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4
Q

why do amino acids tend to be the L conformer over the D conformer

A
  • Overtime, things have evolved to favor the L isomer
  • positive feedback - L-isomers interact better with L-isomers so more things will tend to evolve to be L
  • don’t know specifically why L over D
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5
Q

properties of amino acids that make them well suited to carry out a variety of biological functions

A
  • have useful acid-base properties
  • capacity to polymerize
  • diversity of amino acids –> many different proteins
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6
Q

Amino acids besides alpha

A
  • some amino acids have different groups
  • only alpha are used in making proteins
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7
Q

5 categories of amino acids

A

-nonpolar, aliphatic
- aromatic
- polar, uncharged (hydroxyl, sulfhydryl, and amido groups)
-positively charged
- negatively charged
- determined at biological pH

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8
Q

which amino acids can form disulfide bonds?

A

cystine
- disulfide bonds occur via the reversible oxidation of two cysteine molecules

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9
Q

How does the charge of the R group relate to acidity or basicity

A
  • negatively charged R groups are acidic
  • Positively charged R groups are basic
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10
Q

aromatic rings in amino acids

A
  • generally nonpolar except tyrosine
  • allow proteins to absorb light
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11
Q

cysteine

A
  • SH oxidized to form disulfide bridges
  • important in stabilizing tertiary and quaternary structures
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12
Q

glycine

A
  • R group is H
  • very small
  • fits in tight places
  • achiral
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13
Q

proline

A
  • R group bends around to form a ring wby covalently bonding to the amino group of the alpha carbon
  • introduces kink in folding of polypeptide chain
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14
Q

Proteinogenic amino acids

A
  • amino acids in final form as protein components
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15
Q

are all amino acids used to make proteins

A
  • no, but they can have other important functions
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16
Q

types of rare amino acids

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A
  • post-translational
    • created by modification of common amino acids after they are incorporated into a protein
  • proteinogenic
    • amino acids in final form as protein components
    • ex: methionine with formyl group attached to amino group
17
Q

transient modifications (three kinds and why are they useful)

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A

o Reversible post-translational modifications that are important in regulation and signaling
o three kinds
- phosphorylation of OH groups – adds negative charge and changes protein conformation
- Acetylation – removes positive charge of lysine by adding acetyl group
- Methylation – can mark recruiting other proteins
- Adds hydrophobicity

18
Q

amino acid role in acidity and basicity

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A
  • they can act as weak acids/bases
  • some R groups can ionize at certain pH levels
19
Q

weak acid equilibrium

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A

o Each reaction has Ke q as a fixed equilibrium constant
o If the chemical environment changes, [H+], [A-] and [HA] will adjust to return to equilibrium under the new conditions to satisfy Keq

20
Q

what is the formula to find Ka or Kb

21
Q

What is the formula for pKa

22
Q

what is the relationship between strength of acid, Ka, and pKa

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A

strong acid = higher Ka = lower pKa

23
Q

what does it mean when pH = pKa

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A
  • half of the molecules of weak acid have lost their protons
  • [HA]=[A-]
24
Q

what 3 pieces of information about a weak acid/conjugate base system does the Henderson-Hasselbalch equation link?

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A

pKa, pH, and concentrations

25
How is a titration curve done and what does it show
o A titration curve is done by adding a strong acid or base to a weak acid or base and tracking the pH o It shows changes in pH over the course of the titration o Reveals things like pH=pKa, and buffer regions
26
equation relating pH to concentrations
o pH=-log[H+]
27
equation to find Ka in terms of concentrations
o Ka = [H+][A-]/[HA]
28
How is pKa related to Ka?
o pKa = -logKa
29
buffer regions
o within a certain pH range, small amount of acid or base can be added without major changes in pH o exist 1 pH above and below pKa o surrounds area where pH=pKa
30
buffers
o Mixture of weak acids and conjugate bases o Prevent major changes in pH around a specific pH
31
Why do weak acid/conjugate base systems make good buffers
o Weak acids/conjugate bases exist in equilibrium (compared to strong acids that fully dissociate) and this equilibrium helps allow the system to neutralize the added acid or base without significantly changing the pH of the system
32
Why are buffers important physiologically and in a lab setting?
o Almost every biological process in pH dependent o Buffers are crucial in maintain a stable pH in the body o In lab – provides stable environment to run experiments in
33
Amino acids as weak acids
o Amino acids have at least 2 protons o Multiple buffer regions (pK1 and pK2) o Ex in pic: glycine o At 1 equiv, all carboxyl H+ will dissociate
34
isoelectric point (pI)
o pH where there is no net charge o will be the average of two pK values o occurs at one equivalence of OH o ex: glycine – pI is where all carboxy groups have been deprotonated but amino groups have their proton o pH higher that PI – aa has neg charge o pH lower than PI – aa has pos charge
35
Why is the carboxy group more acidic than the amino group
o It’s resonance stabilized so it holds the negative charge better
36
Does the same particular functional group (ex:COOH) always have the same pKa in any molecules?
o No o The aa can have different other functional groups, which can either donate or withdraw electrons, effecting the ionizability
37
Titrations for amino acids with ionizable R group
o PI Average the pK values surrounding the molecule with net charge = 0 o Ex: PI is the average of pK1 and pKr
38
Example of pH in biological system: mitochondria
o Mitochondrial matrix has higher pH than cytosol (H+ pump)  About 7.9-8.4 in matrix vs 7.2-7.4 in cytosol o High concentrations of Taurine in mitochondria relative to cytosol  Taurine pKa=8.6, so it can act as a buffer in the matrix
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