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Orgo2 > Amino Acids > Flashcards

Amino Acids Flashcards

1
Q

What is a nucleophile?

A

a species that is electron-rich and seeks to donate electrons.

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2
Q

What is an electrophile?

A

a species that is electron-deficient and seeks to accept or “attack” electrons

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3
Q

When is the term peptide appropriate?

A

Short polymers

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4
Q

What direction are amino acids read?

A

N-term to c-term

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5
Q

What is the alpha carbon? In relation to amino acids?

A

The carbon beside the carboxylic acid. The alpha carbon in amino acids has the amino group.

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6
Q

What happens in an acid catalyzed hydrolysis?

A

Because the nuc is water in acid catylized reactions we must make the electrophile a better electrophile bc it isn’t very positive.

The H3O will give a proton and activate the electrophile so then H2O can come in and attack.

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7
Q

What happens in a hydrolysis under basic conditions?

A

Bc H2O is a bad nuc it will become OH- under basic conditions so it can better attack the electrophile.

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8
Q

What form are most natural and chiral amino acids?

A

L-amino acids

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9
Q

How do you identify L vs D amino acids?

A

In fisher you must put the COOH at the top and then identify where the amino group is:
-if it is on the left side it is an L amino acid
-if it is on the right side it is a D amino acid

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10
Q

Non-polar amino acids are:

A

hydrophobic
Gary and violet pushed timmy’s lunch into muddy puddles

aromatics are non-polar

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11
Q

Polar amino acids are:

A

hydrophilic

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12
Q

acidic amino acids are:

A

negatively charged
asp and glu

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13
Q

basic amino acids are:

A

positively charged
lys and arg

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14
Q

Why is tyrosine sometimes classified as non-polar?

A

The relatively hydrophobic ring

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15
Q

What does it mean to be a strong acid?

A

It means that you will be left with more products and less reactants-the Ka will be bigger therefore smaller pKa.

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16
Q

Ka eqn is:

A

products/reactants

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17
Q

pKa=

A

-logKa

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18
Q

pH=

A

pKa + log (conj base/acid)

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19
Q

what are the acidic groups on amino acids?

A

the ammonium and carboxyl groups

The most acidic will be the once closer to the electron withdrawing group.

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20
Q

What happens to molecules in acidic solutions?

A

Virtually all molecs are in protonated state

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21
Q

What happens when at neutral pH

A

Creates a zwitterion where the internal charges add to zero.

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22
Q

What happens to molecules in basic conditions?

A

Virtually all molec are deprotonated

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23
Q

What does amphoteric mean?

A

Amino acids that are bifunctional so they can act as an acid or a base like water.

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24
Q

Why are amino acids not soluble at neutral pH?

A

bc they form ion pairs.

(despite them being very polar they are not soluble)

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25
Q

Why are they soluble at acidic or basic conditions?

A

bc the amino acids have a net charge and ion pairs cannot form therefore extremely soluble

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26
Q

What is the primary structure of a protein?

A

The sequence of amino acids
residues are numbered n-c term

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27
Q

Why does the amide bond have a trans config?

A

to minimize steric hindrance

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28
Q

why can cis and trans be used to describe amide bonds (C-N)?

A

bc the C-N bond cannot rotate, it has double bond characteristics.

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29
Q

What is a secondary structure?

A

refers to the local folding of a protein into conformations stabilized by noncovalent forces such as h-bonds between non-adjacent AAs.

alpha helix and beta sheets

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30
Q

Characteristics of a alpha helix?

A

3.6 amino acid residues per turn
NH group hydrogen bonds to a carbonyl group four amino acids away
side chains stick out
right handed helix forms

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31
Q

Characteristics of a beta sheet?

A

adopt a sheet like folding pattern
hydrogen bonding between NH and carbonyl of neighbouring segments

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32
Q

What is the tertiary structure?

A

folding of secondary elements into the 3D shape of a whole molec
interactions are non-covalent
disulfide bond can form bc of the oxidation of thiols in cys
this can be reduced by excess thiols like beta mercaptoethanol

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33
Q

What is beta mercaptoethanol?

A

a disulfide reducing agent

34
Q

What are quaternary structures?

A

the assembly of protein subunits to create a larger molec.

35
Q

How do you determine amino acid composition?

A

Amino Acid Analysis (AAA)
This technique does not determine the primary structure (the sequence)

just determines the relative amts of an amino acid present in a peptide or protein

36
Q

What are the three steps to an Amino Acid Analysis

A
  1. The complete hydrolysis of a peptide into its constituent amino acids
  2. Separation of this amino acid mixture by ion-exchange HPLC
  3. Quantification of the separated amino acids by converting them into a chromophore and then measuring the amt of light absorbed by they sample using UV-vis spectroscopy
37
Q

What was the HPLC column we focused on in class like?

A

It was a negatively charged column with aromatic rings and therefore non-polar and hydrophobic

38
Q

What order do substances come out if filtered through a negatively charged hydrophobic column?

A

Negative
polar
non-polar (bc the hydrophobic bind hydrophobic)
positive

39
Q

What is ninhydrin?

A

A purple (ruhemann’s purple) that reacts with amino acids to convert them into chromophores so they can be detected by the UV-vis spectrophotometer

40
Q

How does the interaction between the amino acids and ninhydrin work?

A
  1. reacts w the amino acid to form an imine (double bond right at N)
  2. decarboxylation happens carboxyl group is lost as CO2
  3. hydrolysis will break off the newly formed imine
  4. there is a reaction with another ninhydrin molec

the more ninhydrin that is formed they more amino acid there is present

amino acids are destroyed as they react ninhydrin and the side chain is lost as an aldehyde.

41
Q

What molecule cannot accurately be detected by ninhydrin?

A

proline bc there is no primary amine

42
Q

Steps of protein seqeuncing?

A
  1. first the protein is partially hydrolyzed into many smaller, overlapping fragments
  2. the fragments are then separated and subjected to further studies
43
Q

Acid

A

not specific cleavage

44
Q

CNBr

A

will cut after a Met

45
Q

Edman

A

N-terminal amino acid

46
Q

Trypsin

A

will cut after Arg and Lys
(basic)

47
Q

Chymotrypsin

A

after the phe tyr and trp
non-polar aromatic

48
Q

carboxypeptidase A

A

c-terminal amino acid

49
Q

N-terminal sequencing (edman degradation)

A

N-terminal is chemically cleaved as a phenylthiohydantoin derivative

it is separated from the shorted peptide and identified and then the cycle is repeated

40-60 amino acids can be seq before the accumulation of side products interferes with the procedure

involves the nuc addition of peptide to PITC

50
Q

N-term seq process

A

SO we react the protein with PITC and then we need to cleave the peptide off so we can use the next bit for the next round

if we treat the PITC derivative with a relatively strong acid like HCl or CF3COOH it will cleave the peptide and form a thiazolinone derivative which can be extracted using an organic solvent

51
Q

What is a thiazolinone derivative?

A

The derivative right after the phenylthiocarbamoyl derivative to cleave of the extra peptide

52
Q

What is the PTH derivative?

A

the derivative that you get after excess acid interacts with the thiazolinone derivative

53
Q

Original N-terminal identification

A

It identifies the N-terminal does not do sequencing

use DNFB, (Sanger’s Reagent) reacts with an amino group to form a coloured product via a nucleophilic aromatic substitution reaction

tags the end with a colour basically

54
Q

What is special about lysine when it reactions with DNFB (sangers reagent)?

A

it will have 2 DNP groups attached bc of the extra amine group

55
Q

Difference between sanger’s reagent and edman degradation?

A

sanger can only identify the n-term
edman degradation can seq from the n-term

56
Q

C-terminal sequencing

A

identifies the amino acid and provides seq info

carboxypeptidase remove AA from the c term
this is done by sampling the mixture during a carboxypeptidase digestion and analyzing the sample by HPLC to identify and quantify the release amino acids

57
Q

What does lab synthesis of peptides need?

A

Protecting groups

bc we need the proper amino and cooh groups interacting with each other

58
Q

what are the two types of synthetic synthesises?

A

Solution phase and solid phase

59
Q

How do you protect a COOH group?

A

with a benzyl (Bn) ester

deprotected with HBr/HOAc

60
Q

How do you protect a NH2?

A

with a BOC group
removed with a TFA or CF3COOH
its too weak to removed the Bn but can remove BOC

61
Q

How is DCC used to form new peptides?

A

By acting as a coupling reagent which activates the COOH to allow coupling. DCU is formed as a byproduct and acts as a good leaving group

62
Q

Solid phase synthesis

A

Discovered by Bruce Merrifield

use the same protecting groups but protect the cooh as an ester connected to an insoluble polymer

63
Q

In lab synthesis the peptide grows in what direction?

A

C->N

64
Q

What are the steps in solid phase synthesis?

A

link the polymer
tfa to deproctect then rinse to remove excess tfa
et3n to neutralize r-NH3+ then rinse
add the peptide with DCC
then rinse
then repeat until done where then u can use HBr to remove both protecting groups

65
Q

The math for efficiency?

A

A 95% efficeny

each step you do 0.95^(of which round your on)

example round 3 you would do 0.95^(3)

66
Q

What are the three main interactions that contribute to the initial binding of a substrate?

A

Hydrogen bonding
Hydrophobic forces
Ionic/electrostatic interactions

67
Q

Hydrogen bonding

A

when correct orientation delta g = 0
incorrect delta g = +

bond strength is about 5-10kcal/mol
BUT
H-bonding usually does not contribute to the substrate-protein binding energy bc any group that can H-bond will alr be bonded to water.

68
Q

hydrophobic forces

A

hydrophobic forces do not result from the attraction of hydrophobic regions rather the hydrophobic regions come together bc they are entropically driven bc water is highly ordered

  • delta g
69
Q

ionic interaction

A

arise from the attraction of opposite charges, but in water we do not find these two paired together due to the polar water that can stablize the individual ions

but in active sites this can be much lower in polarity and the ions wont be as stabilized and therefore more likely to form ion pairs. it only follows that the larger the charge on the ion the greater the attraction

70
Q

chiral environments of enzymes

A

enzymes are made from chiral amino acids so they are also chiral

bc chiral molec can interact diff wi other chiral molec they enzymes can recognize one stereoisomer over another

enzymes can also bind achiral products and make then achiral which will be termed as prochiral

71
Q

What is the purpose of enzymes?

A

To bring important substrates closer to each other

72
Q

How do enzymes help with proximity?

A

they tie the functional groups together to being closer to proper orientations so they can’t move

73
Q

Enzyme kinetics

A

help a rxn take a diff path to the same end point it alters the mechanism

74
Q

How do enzymes lower the activation barrier?

A

orient the reacting functional groups
provide a solvent enviroment that favours the chemical rxn
preform a complex reaction in a series of smaller steps ex the mechanism by which the catalyzed rxn proceeds is diff from the uncat
bind/stabilizes the transition state very well
act as an acid or base cat
form covalent bonds with the substrate after initial binding

75
Q

Chymotrypsin mechanism

A

will cut after trp, tyr, phe

hydrophobic amino acids

c-term side

trypsin will hydrolyse after basic residues lys and arg

chymotrypsin divides the rxn into 2 smaller rxns each with a smaller Ea

1) nuc in Ser will attack the amide causing the c-term to be removed, remaining n-term is covalently bonded to the enzyme as an ester

2) the enzyme uses water to hydrolyze the enzyme bound n-term will regenerate the original state of the enzyme

76
Q

why does the hydrolysis of an amide need to be enzyme catalyzed?

A

bc amide bonds are very stable
involves the formation of a tetrahedral intermediate and then a collapse causing the loss of a LG

77
Q

What amino acids are a part of the chymotrypsin enzyme?

A

Asp, His, Ser

78
Q

what are cofactors?

A

additional non-protein component required by some enzymes

79
Q

what are coenzymes?

A

small organic molec relative to the enzyme

they are usually derived from vitamins

80
Q

tRNA and amino acids

A

attached by ester linkage makes the carboxylic acid more reactive

Mg+ is a common cofactor

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