Brainscape's Knowledge GenomeTM

Browse over 1 million classes created by top students, professors, publishers, and experts.


See full index

ESA 1 - Medical Cell Biology & Genetics > Session 4.1b - Pre-Reading [Book] > Flashcards

Session 4.1b - Pre-Reading [Book] Flashcards

You may prefer our related Brainscape-certified flashcards:
USMLE® Step 1 flashcards AP® Biology flashcards Biology 101 flashcards
1
Q

How are amino acids notated?

A

Each amino acid name has an associated three-letter abbreviation and a one-letter symbol (Figure 1.7).

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
2
Q

How are the one letter codes for amino acids determined?

A
  • Unique first letter
  • Most commonly occurring amino acids have priority
  • Similar sounding names
  • Letter close to initial letter
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
3
Q

What is the abbreviation for Cysteine?

A

Cys (first three letters)

C (unique first letter)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
4
Q

What is the abbreviation for Histidine?

A

His (first three letters)

H (unique first letter)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
5
Q

What is the abbreviation for Isoleucine?

A

Ile

I (unique first letter)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
6
Q

What is the abbreviation for Methionine?

A

Met (first three letters)

M (unique first letter)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
7
Q

What is the abbreviation for Serine?

A

Ser (first three letters)

S (unique first letter)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
8
Q

What is the abbreviation for Valine?

A

Val (first three letters)

V (unique first letter)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
9
Q

What is the abbreviation for Alanine?

A

Ala (first three letters)

A (most commonly occurring amino acids have priority)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
10
Q

What is the abbreviation for Glycine?

A

Gly (first three letters)

G (most commonly occurring amino acids have priority)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
11
Q

What is the abbreviation for Leucine?

A

Leu (first three letters)

L (most commonly occurring amino acids have priority)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
12
Q

What is the abbreviation for Proline?

A

Pro (first three letters)

P (most commonly occurring amino acids have priority)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
13
Q

What is the abbreviation for Threonine?

A

Thr (first three letters)

T (most commonly occurring amino acids have priority)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
14
Q

What is the abbreviation for Arginine?

A

Arg (first three letters)

R (similar sounding names
“aRginine”)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
15
Q

What is the abbreviation for Asparagine?

A

Asn

N (similar sounding names
contains N)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
16
Q

What is the abbreviation for Aspartate?

A

Asp (first three letters)

D (similar sounding names
“asparDic”)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
17
Q

What is the abbreviation for Glutamate?

A

Glu (first three letters)

E (similar sounding names
“glutEmate”)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
18
Q

What is the abbreviation for Glutamine?

A

Gln

Q (similar sounding names
“Q-tamine”)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
19
Q

What is the abbreviation for Phenylalanine?

A

Phe (first three letters)

F (similar sounding names
“Fenylalanine”)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
20
Q

What is the abbreviation for Tyrosine?

A

Tyr (first three letters)

Y (similar sounding names
“tYrosine”)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
21
Q

What is the abbreviation for Tryptophan?

A

Trp

W (similar sounding names
double ring in the molecule)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
22
Q

What is the abbreviation for Aspartate OR Asparagine?

A

Asx (see Asp or Asn)

B (letter close to initial letter
near A)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
23
Q

What is the abbreviation for Glutamate OR Glutamine?

A

Glx (see Glu or Gln)

Z (letter close to initial letter)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
24
Q

What is the abbreviation for Lysine?

A

Lys (first three letters)

K (letter close to initial letter
near L)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
25
Q

What is the abbreviation for an undetermined amino acid?

A

(no three letter)

X

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
26
Q

Fig. 1.7

Name the abbreviations and symbols for the commonly occurring amino acids.

A 
1) Unique first letter:
Cysteine = Cys = C
Histidine = His = H
Isoleucine = Ile = I
Methionine = Met = M
Serine = Ser = S
Valine = Val = V
2) Most commonly occurring amino acids have priority:
Alanine = Ala = A
Glycine = Gly = G
Leucine = Leu = L
Proline = Pro = P
Threonine = Thr = T
3) Similar sounding names:
Arginine = Arg = R ("aRginine")
Asparagine = Asn = N (contains N)
Aspartate = Asp = D ("asparDic")
Glutamate = Glu = E ("glutEmate")
Glutamine = Gln = Q ("Q-tamine")
Phenylalanine = Phe = F ("Fenylalanine")
Tyrosine = Tyr = Y ("tYrosine")
Tryptophan = Trp = W (double ring in the molecule)
4) Letter close to initial letter:
Aspartate or asparagine = Asx = B (near A)
Glutamate or glutamine = Glx = Z
Lysine = Lys = K (near L)
Undetermined amino acid = N/A = X
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
27
Q

What is the unique first letter rule in amino acid abbreviations?

A

If only one amino acid begins with a particular letter, then that letter is used as its symbol. For example, I = isoleucine.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
28
Q

How are amino acids abbreviated if more than one amino acid begins with a particular letter?

A

Most commonly occurring amino acids have priority

= The most common of these amino acids receives this letter as its symbol.

E.g. glycine is more common than glutamate, so G = glycine

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
29
Q

How are amino acids such as phenylalanine or tryptophan abbreviated?

A

Some one-letter symbols sound like the amino acid they represent.

E.g. F = phenylalanine
W = tryptophan (“twyptophan” as Elmer Fudd would say)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
30
Q

How are the remaining amino acids named (ones not beginning with the first letter or similar sounding)?

A

For the remaining amino acids, a one-letter symbol is assigned that is as close in the alphabet as possible to the initial letter of the amino acid

e.g. K = lysine
B = aspartic acid or asparagine
Z = glutamic acid or glutamine
X = unidentified amino acid

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
31
Q

Which amino acids have a unique first letter?

A 
Cysteine
Histidine
Isoleucine
Methionine
Serine
Valine
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
32
Q

Which amino acids are the more commonly occurring amino acids have priority?

A 
Alanine
Glycine
Leucine
Proline
Threonine
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
33
Q

What are the optical properties of amino acids?

A

The a-carbon of an amino acid is attached to four different chemical groups and is, therefore, a chiral or optically active carbon atom.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
34
Q

What are chiral or optically active carbon atoms?

A

When an a-carbon is attached to four different chemical groups

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
35
Q

Which amino acid is NOT a chiral/optically active amino acid?

A

Glycine - its a-carbon has two hydrogen substituents and, therefore, is optically inactive

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
36
Q

What are the two forms of amino acids?

A

Amino acids with asymmetric centres at the a-carbon (i.e. not glycine) can exist in two forms: designated D and L, that are mirror images of each other (Figure 1.8).

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
37
Q

What are the two mirror image forms of amino acids termed?

A

D and L stereoisomers

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
38
Q

Stereoisomers can also be known as ___?

A

Optical isomers

Enantiomers

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
39
Q

All amino acids found in proteins are of which configuration?

A

L-configuration

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
40
Q

L-amino acids are found where?

A

All the amino acids found in proteins are L-isomers

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
41
Q

D-amino acids are found where?

A

In some antibiotics and in plant and bacterial cell walls (See D-Ammino acid oxidase for a discussion of D-amino acid metabolism)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
42
Q

Figure 1.8

Label and caption this iamge

A

D and L forms of alanine are mirror images

L-Alanine
D-Alanine

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
43
Q

Draw the L and D form of alanine

A

L: H3N-C-COOH-H-CH3

D: H-C-COOH-NH3-H3C

L-isomer (CoRN - clockwise)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
44
Q

What are the acidic and basic properties of amino acids?

A

Amino acids in aqueous solution contain weakly acidic a-carboxyl groups and weakly basic a-amino groups.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
45
Q

The carboxyl group in amino acids is weakly _____ in aqueous solution

A

acidic

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
46
Q

The amino group in amino acids is weakly _____ in aqueous solution

A

basic

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
47
Q

The _____ group in amino acids is weakly acidic in aqueous solution

A

carboxyl

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
48
Q

The _____ group in amino acids is weakly basic in aqueous solution

A

amino

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
49
Q

Which amino acids contain an ionisable group in its side chain?

A

Each of the acidic and basic amino acids

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
50
Q

Acidic and basic molecules can be _______

A

ionised

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
51
Q

Some amino acids can act as buffers. Where are they found and why?

A

Free amino acids (carboxyl and amino groups) and some amino acids combined in peptide linkages (acidic and basic side chains)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
52
Q

Free amino acids and the acidic/basic amino acids in peptide linkages can act as what?

A

Buffers

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
53
Q

Define acid and base.

A 
Acid = proton donor
Base = proton acceptor
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
54
Q

What is a “weak” acid or base?

A

These ionise to only a limited extent.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
55
Q

Which chemicals ionise to only a limited extent?

A

“Weak” acids and bases.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
56
Q

What does pH measure?

A

The concentration of protons in aqueous solution

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
57
Q

How is the concentration of protons in aqueous solution termed?

A

pH

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
58
Q

What is the definition (equation) of pH?

A

log 1/[H+]
or
- log [H+]

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
59
Q

What is the Henderson-Hasselbalch equation?

A

The quantitative relationship between the pH of the solution and concentration of a weak acid (HA) and its conjugate base (A-)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
60
Q

What is the relationship between pH and the concentration of a weak acid and its conjugate base known as?

A

Henderson-Hasselbalch equation

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
61
Q

How is a weak acid and its conjugate base notated as?

A 
Weak acid (HA)
Conjugate base (A-)
How well did you know this?
1
Not at all
2
3
4
5
Perfectly
62
Q

Denote the release of a proton by a weak acid represented by HA.

A

HA H+ + A-

weak acid proton + salt form or conjugate base

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
63
Q

What is the “salt” or conjugate base, A-?

A

It is the ionised form of a weak acid

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
64
Q

What is the ionised form of a weak acid?

A

The “salt” or conjugate base, A-

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
65
Q

What is the dissociation constant of the acid?

A

By definition, Ka, is

Ka = [H+][A-]/[HA]

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
66
Q

What is Ka?

A

The dissociation constant of the acid

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
67
Q

What does this equation represent?

[H+][A-]/[HA]

A

Ka: dissociation constant

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
68
Q

What does the Ka value tell you?

A

The larger the Ka, the stronger the acid - this is because most of the HA has dissociated into H+ and A-

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
69
Q

What does a small Ka value tell you?

A

The smaller the Ka, the less acid has dissociated and, therefore, the weaker the acid.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
70
Q

How can the Ka be used to derive Henderson-Hasselbalch equation?

A

By solving for the [H+] in the Ka equation, taking the logarithm of both sides of the equation, multiplying both sides of the equation by -1, and substituting pH = -log [H+] and pKa = -log Ka

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
71
Q

What is the Henderson-Hasselbalch equation?

A

pH = pKa + log [A-]/[HA]

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
72
Q

What is this equation called?

pH = pKa + log [A-]/[HA]

A

Henderson-Hasselbalch equation

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
73
Q

What is a buffer?

A

A solution that resists change in pH following the addition of an acid or base.

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
74
Q

How can a buffer be created?

A

By mixing a weak acid (HA) with its conjugate base (A-).

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
75
Q

Give an example of an acid,

A

HCl

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
76
Q

What happens when an acid, such as HCl, is added to a buffer?

A

If an acid such as HCl is then added, A- can neutralise it, in the process being converted to HA.

77
Q

What happens when a base is added to a buffer?

A

If a base is added, HA can neutralise it, in the process being converted to A-.

78
Q

What is the neutralising agent in buffers and what are they converted to, for both acids and bases?

A

Acid
Neutraliser: A-
Product: HA

Base
Neutraliser: HA
Product: A-

79
Q

When does maximum buffer capacity occur?

A

At a pH equal to the pKa

80
Q

What happens when the pH is equal to the pKa?

A

Maximum buffering capacity occurs

81
Q

When the pH of a solution is within approximately +/- 1 pH unit of the pKa, what happens?

A

A conjugate acid/base pair can still serve as an effective buffer

82
Q

When are the limits of a conjugate acid/base pair being still able to serve as an effective buffer?

A

When the pH of a solution is within approximately +/- 1 pH unit of the pKa.

83
Q

When is pH equal to pKa?

A

If the amounts of HA and A- are equal.

84
Q

Define an equation when the amounts of HA and A- are equal.

A

The pH is equal to the pKa.

85
Q

What is acetic acid?

A

A weak acid (HA)

CH3-COOH

86
Q

What is acetate?

A

The conjugate form (A-) of acetic acid

CH3-COO-

87
Q

What is the pKa of acetic acid/acetate?

A

4.8

88
Q

If the pKa for acetic acid is 4.8, for what pH can this solution resist a change from?

A

A change in pH from pH 3.8 to 5.8, with maximum (optimal) buffering at pH 4.8

89
Q

At pH values less than the pKa, what is the predominant species in solution?

A

The protonated acid form

E.g. acetic acid (CH3-COOH) over acetate

90
Q

For weak acids, when is the protonated acid form predominant?

A

At pH values < pKa

91
Q

At pH values greater than the pKa, what is the predominant species in solution?

A

The deprotonated base form

E.g. Acetate (CH3-COO-) over acetic acid

92
Q

For weak acids, when is the depronated base form more predominant?

A

At pH values greater than the pKa

93
Q

Draw the titration curve of acetic acid.

A 
CH3COOH FORM I (acetic acid, HA)
—OH- to H2O —>
 [II]
Buffer region = pH 3.8 - 5.8
PKa = 4.8 [I] = [II]
PH > 4.8 [II] > [I]
94
Q

Fig. 1.9

Label the chemicals in the solution

Draw on the axis of the graph and explain what it is showing

Caption the image

A 
FORM I (acetic acid, HA)
FORM II (acetate, A-)

PH 0..3-7 (x-axis)
Equivalents OH- added 0…..0.5…..1.0

<3.8 [I] > [II]
3.8-5.8 Buffer region
PKa = 4.8 [I] = [II]
>5.8 [II] > [I]

95
Q

What does the titration curve of an amino acid appear?

A

It can be analysed in the same way as described for acetic acid.

96
Q

What amino acid has a titration curve similar to that of acetic acid??

A

Consider alanine, for example, which contains both an a-carboxyl and an a-amino group (and a nonpolar side chain)

97
Q

At a low (acidic) pH, which groups are protonated in alanine?

A

At a low (acidic) pH, both of the a-carboxyl and a-amino groups are protonated (see Fig. 1.10).

98
Q

Alanine has a nonpolar side chain, and therefore only the a-carboxyl and a-amino groups can gain or lose a proton. At what pH are both of these groups protonated?

A

Low (acidic) pH

99
Q

What happens when the pH is raised from an acidic pH?

A

As the pH of the solution is raised, the -COOH group of Form I can dissociate by donating a proton to the medium.

100
Q

Which group donates a proton first as the pH is raised in amino acids?

A

The -COOH group

101
Q

When does a -COOH group donate a proton to the medium?

A

As the pH of a solution is raised

102
Q

What does the release of a proton from a -COOH group form?

A

A carboxylate group, - COO-

103
Q

What is a carboxylate group (- COO-) formed from?

A

A -COOH group releasing a proton

104
Q

What is the dipolar form of an amino acid?

A

When the carboxylate ion has released a proton (COO-) and the amino group has received a proton (NH3+)

105
Q

What is a deprotonated carboxyl group and a protonated amino group of an amino acid called?

A

Its dipolar form

106
Q

What is a zwitterion?

A

A chemical that has both separate positively and negatively charged groups

107
Q

The dipolar form of a molecule can also be known as what?

A

A zwitterion

108
Q

Describe the chemical properties of a zwitterion.

A

It is isoelectric; that is, it has an overall (net) charge of zero.

109
Q

When does an amino acid have an overall (net) charge of zero?

A

When the pH is sufficient enough for the carboxylate group to lose a proton and the amino group to gain a proton - a dipolar form, also called a zwitterion, the isoelectric form.

110
Q

Fig. 1.10

Label and caption the image.

A

FORM I - Alanine in acid solution (pH less than 2)
Net charge = +1

PK1 = 2.3

FORM II - Alanine in neutral solution (pH approximately 6)
Net charge = 0 (Isoelectric form)

PK2 = 9.1

FORM III - Alanine in basic solution (pH greater than 10)
Net charge = -1

Ionic forms of alanine in acidic, neutral, and basic solutions.

111
Q

Draw the ionic forms of alanine in acidic, neutral, and basic solutions. Explain when they would occur.

A

FORM I - Alanine with COOH and NH3+ (acid solution, pH < 2)
Net charge = +1

— OH- to H2O —>

10)
Net charge = -1

112
Q

What is the dissociation constant of the carboxyl group of an amino acid called?

A

K1, rather than Ka, because the molecule contains a second (two) titratable group.

113
Q

What part of an amino acid has a dissociation constant called K1?

A

The carboxyl group of an amino acid, becuase the molecule contains a second titratable group (rather than Ka; there is K1 [carboxyl] and K2 [amino]).

114
Q

What is the Henderson-Hasselbalch equation for the dissociation of the carboxyl group of alanine?

A

It can be described in the same way as acetic acid:

K1 = [H+][II]/[I]

where
I is the fully protonated form of alanine
II is the isoelectric form of alanine (see Figure 1.10)

115
Q

What does this represent?

K1 = [H+][II]/[I]

A

The Henderson-Hasselbalch equation for the dissocation of the carboxyl group of alanine (described in the same way as acetic acid)

where
I is the fully protonated form of alanine
II is the isoelectric form of alanine (see Figure 1.10)

116
Q

What do [I] and [II] represent here in terms of amino acid carboxyl group dissociation?

K1 = [H+][II]/[I]

A

I is the fully protonated form of alanine

II is the isoelectric form of alanine (see Figure 1.10)

117
Q

Write an equation defining the amino acid carboxyl group dissociation constant, where I is the fully protonated form of alanine and II is the isoelectric form of alanine.

A

K1 = [H+][II]/[I]

118
Q

How can you work out the pH from

K1 = [H+][II]/[I] ?

A

This equation can be rearranged and converted to its logarithmic form to yield:

pH = pK1 + log [II]/[I]

119
Q

What can this equation be rearranged to tell you?

pH = pK1 + log [II]/[I]

A

K1 = [H+][II]/[I]

Henderson-Hasselbalch dissocation constant

120
Q

What is the second titratable group of an amino acid, e.g. alanine?

A

The amino (-NH3+) group (Figure 1.10).

121
Q

What is the dissociation constant called of the amino group in amino acids?

A

K2

carboxyl is K1

122
Q

Which is the stronger acid

-COOH group
or
-NH3+ group?

A

The -COOH group (hence K1)

123
Q

Which is the weaker acid

-COOH group
or
-NH3+ group?

A

-NH3+ is a much weaker acid, and therefore has a much smaller dissociation constant, K2.

124
Q

Which group has a bigger dissociation constant, and why?

-COOH group
or
-NH3+ group?

A

-COOH group because it is a much stronger acid and therefore has a much bigger dissociation constant (K1)

125
Q

Which group has a smaller dissociation constant, and why?

-COOH group
or
-NH3+ group?

A

-NH3+ group because it is a much weaker acid and therefore has a much smaller dissociation constant (K2)

126
Q

Which group has a bigger pKa?

-COOH group
or
-NH3+ group?

A

-NH3+ group

The larger the pKa, the weaker the acid

127
Q

Which group has a smaller pKa?

-COOH group
or
-NH3+ group?

A

-COOH group

The lower the pKa, the stronger the acid

128
Q

What is the relationship of pKa to Ka and therefore acids and bases?

A

pKa = -logKa

So pKa is inversely proportional to Ka
(Ka is the amount of dissociation - stronger acids dissociate more hence larger numerator/denominator)

The larger the pKa, the weaker the acid

129
Q

What does release of a proton from the protonated amino group of amino acids result in?

A

A fully deprotonated form of alanine (see Figure 1.10, Form II and Form III)

130
Q

How does a fully deprotonated form of alanine arise?

A

Release of a proton from the protonated amino group of amino acids (see Figure 1.10, Form II and Form III)

131
Q

What does Fig. 1.10 depict?

A

The sequential dissociation of protons from the carboxyl and amino groups of alanine.

132
Q

Draw the sequential dissociation of protons from the carboxyl and amino groups of alanine.

A

See Fig. 1.10

133
Q

What is the pKa of alanine?

A

Each titratable group has a pKa that is numerically equal to the pH at which exactly one half of the protons have been removed from that group (by definition)

134
Q

What does the pH that is exactly one half of the protons removed tell you?

A

The pKa

135
Q

What is the nomenclature of pKa of amino acids?

A

The pKa for the most acidic group (-COOH) is pK1, whereas the pKa for the next most acidic group (-NH3+) is pK2.

136
Q

Which is pK1 and pK2 of amino acids?

A

pK1 for the most acidic group (-COOH)

pK2 for the next most acidic group (-NH3+)

137
Q

How can you calculate the complete titration curve of a weak acid?

A

By applying the Henderson-Hasselbalch equation to each dissociable acidic group.

138
Q

What does applying the Henderson-Hasselbalch equation to each dissociable acidic group of amino acids give you?

A

The complete titration curve of a weak acid.

139
Q

What changes the fully protonated form of alanine to produce the completely deprotonated form?

A

The pH

140
Q

What does a change in pH (from acidic to alkaline) do to amino acids?

A

Addition of base to the fully protonated form of alanine to produce the completely deprotonated form.

141
Q

Fig. 1.11

Label and caption the diagram.

A

The titration curve of alanine.

x-axis: pH 0 2 4 6 8 10
y-axis: Equivalent OH- added 0..0.5..1.0..1.5..2.0

pH 0 = Form I (CH3, COOH and NH3+)

Region of buffering pH 1.3-3.3
pK1 = 2.3 [I] = [II]

Form II (CH3, COO- and NH3+) pI = 5.7

Region of buffer pH = 8.1-10.1
pK2 = 9.1 [II]=[III]

FORM III (CH3, COO- and NH2)

142
Q

Draw the titration curve of alanine.

A

pH along the x-axis
Equivalents OH- added on the y-axis
Buffer regions between 1.3-3.3 and 8.1-10.1
Plateau between 4.7-6.7

Forms denotated - fully protonated acidic pH, fully deprotonated alkaline, isoelectric point has COO- and NH3+

143
Q

What are the buffer pairs of an amino acid?

A

The -COOH/-COO- pair can serve as a buffer in the pH region around pK1, and the -NH3+/-NH2 pair can buffer in the region around pK2.

144
Q

Where does the -COOH/-COO- buffer pair serve as a buffer for in amino acids?

A

A buffer in the pH region around pK1

145
Q

Where does the -NH3+/-NH2 buffer pair serve as a buffer for in amino acids?

A

A buffer in the pH region around pK2

146
Q

What serves as a buffer in the pH region around pK1 in amino acids?

A

The -COOH/-COO- buffer pair

147
Q

What serves as a buffer in the pH region around pK2 in amino acids?

A

The -NH3+/-NH2 buffer pair

148
Q

What happens when the pH is equal to the pK in amino acids, e.g. alanine?

A

Depending on the pKa value, the two forms of alanine exist in equal amounts in solution (if acidic pH=pK then fully protonated and COO-/NH3+; if alkaline pH=pK then COO-/NH3+ and fully deprotonated)

149
Q

What happens when the pH is equal to pK1 (2.3) of alanine?

A

Equal amounts of Forms I (fully protonated) and II (COO-/NH3+) of alanine exist in solution.

150
Q

When do equal amounts of Forms I (fully protonated) and II (COO-/NH3+) of alanine exist in solution?

A

When the pH is equal to pK1 (2.3).

151
Q

What happens when the pH is equal to pK2 (9.1) of alanine?

A

Equal amounts of Forms II (COO-/NH3+) and III (fully deprotonated) of alanine exist in solution.

152
Q

When do equal amounts of Forms II (COO-/NH3+) and III (fully deprotonated) of alanine exist in solution?.

A

When the pH is equal to pK2 (9.1).

153
Q

How does alanine exist at neutral pH?

A

Predominantly as the dipolar form, in which the amino and carboxyl groups are ionised, but the net charge is zero.

154
Q

When does alanine predominant exist in the dipolar form?

A

At neutral pH

155
Q

What is the dipolar form of alanine?

A

When the amino and carboxyl groups are ionised, but the net charge is zero.

156
Q

How is the isoelectric point denotated?

A

pI

157
Q

What is pI?

A

The isoelectric point

158
Q

What is the isoelectric point (pI)?

A

The pH at which an amino acid is electrically neutral, that is, in which the sum of the positive charges equals the sum of the negative charges.

159
Q

When is an amino acid electrically neutral?

A

At its isoelectric point (pH where the net charge is zero)

160
Q

What is the net charge of an amino acid at its isoelectric point?

A

Zero (the sum of the positive charges equals the sum of the negative charges - it is said to be electrically neutral)

161
Q

When is the net charge of an amino acid zero?

A

At its pI (isoelectric point)

  • The sum of the positive charges equals the sum of the negative charges, and the dipolar form of the amino acid predominates - which is electrically neutral.
162
Q

What is the pI of an amino acid, e.g. alanine?

A

For an amino acid, such as alanine, that has only two dissociable hydrogens (one from the a-carboxyl and one from the a-amino group), the pI is the average of pK1 and pK2 (pI = [2.3 + 9.1]/2 = 5.7, see Figure 1.11).

163
Q

How can the pI be calculated for alanine?

A

Alanine has only two dissociable hydrogens, therefore pI can be taken as the average of pK1 and pK2.

164
Q

When can the pI be calculated as the average of pK1 and pK2?

A

When these are the only two dissociable hydrogens in a molecule, e.g. alanine (amino acid)

165
Q

What does taking the average of pK1 and pK2 give you?

A

The pI, but only in an amino acid that only has two dissociable hydrogens (from the a-carboxyl and the a-amino group).

166
Q

When can you use the average of pK1 and pK2 to give you pI?

A

In an amino acid that only has two dissociable hydrogens (from the a-carboxyl and the a-amino group), e.g. alanine

167
Q

What is the pI of alanine?

A

Midway between pK1 (2.3) and pK2 (9.1)

168
Q

What is the pI of alanine?

pK1 = 2.3
pK2 = 9.1
A

5.7

pK1+pK2 / 2

169
Q

What molecules are present at pI?

A

Form II predominates (with a net charge of zero)

but there are also equal amounts of Forms I (net charge +1) and III (net charge -1).

170
Q

What does pI demonstrate, in regards to molecules?

A

The pH at which

Form II predominates (with a net charge of zero)

but there are also equal amounts of Forms I (net charge +1) and III (net charge -1).

171
Q

What are the charges of all the forms of an amino acid?

Form I (fully protonated)
Form II (dipolar)
Form III (fully deprotonated)
A

Net charges

Form 1 = +1
Form 2 = 0
Form 3 = -1

172
Q

If these are the net charges of the forms of an amino acid, what do their forms represent?

Form 1 = +1
Form 2 = 0
Form 3 = -1

A 
Form I (fully protonated)
Form II (dipolar)
Form III (fully deprotonated)
173
Q

Why is the charge on proteins negative when separating plasma proteins in the lab?

A

Separation of plasma proteins by charge typically is done at a pH above the pI of the major proteins, thus, the charge on the proteins is negative.

174
Q

Separation of plasma proteins by charge typically is done at a pH above the pI of the major proteins. What does this mean in regards to the proteins?

A

The charge on the proteins is negative

175
Q

During separation of plasma proteins, proteins move toward a positive or negative electrode?

A

Positive, because the charge on them is negative (pH > pI)

176
Q

How are plasma proteins separated in the lab?

A
  • Proteins are separated in a medium where pH > pI
  • This means proteins are NEGATIVE
  • Proteins will move toward the positive electrode in an electric field
  • The rate is determined by their net negative charge (thus separation)
177
Q

When plasma proteins are separated in the lab, what separates them?

A

The RATE of movement is determined by their net negative charge (thus separation)

178
Q

Why is a protein’s net negative charge significant in plasma protein separation?

A

The rate at which it moves is determined by the net negative charge, and therefore separates the proteins.

179
Q

How can you separation of a plasma protein be used clinically?

A

Plasma proteins are separated by rate depending on their net negative charge.

Variations in the mobility pattern are suggestive of certain disease.

180
Q

How are variations in the mobility pattern of plasma protein separation suggestive of certain diseases?

A

Plasma proteins are separated by rate depending on their net negative charge

If the protein is altered in some way, by disease, e.g. protein misfolding or base substitution, their overall charge will be different (due to different amino acids) and therefore they will move at a different rate - suggesting disease.

181
Q

How do amino acids appear at physiologic pH?

A

Amino acids have a negatively charged group (-COO-) and a positively charged group (-NH3+), both attached to the a-carbon.

182
Q

When do amino acids have a negatively charged group (-COO-) and a positively charged group (-NH3+), both attached to the a-carbon in humans?

A

At physiologic pH

183
Q

At physiologic pH, amino acids have a negatively charged group (-COO-) and a positively charged group (-NH3+), both attached to the a-carbon.

Which amino acids have additional potentially charged groups in their side chains?

A 
Glutamate
Aspartate
Histidine
Arginine
Lysine
184
Q

Why do glutamate, aspartate, histidine, arginine and lysine differ to other amino acids in terms of their electrical properties?

A

All amino acids have a negatively charged group (-COO-) and a positively charged group (-NH3+) attached to the a-carbon at physiologic pH.

These amino acids are acidic (glutamate, aspartate -COOH) and basic (histidine, arginine and lysine -NHx); therefore have additional potentially charged groups in their side chains.

185
Q

Amino acids can act as either acids or bases. What is the term to describe these?

A

Defined as amphoteric, and are referred to as ampholytes (amphoteric electrolytes).

186
Q

What does the word amphoteric mean?

A

A substance that can act as an acid or a base

187
Q

What is an ampholyte?

A

An amphoteric molecule (amphoteric electrolytes)

Amphoteric = substance that can act as an acid or base

188
Q

Give an example of an amphoteric molecule (ampholyte)

A

Amino acids

ESA 1 - Medical Cell Biology & Genetics (21 decks)

Brainscape helps you reach your goals faster, through stronger study habits.
© 2024 Bold Learning Solutions. Terms and Conditions