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CHEM > Module 4: Structures And Reactions Of Biological Molecules > Flashcards

Module 4: Structures And Reactions Of Biological Molecules Flashcards

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1
Q

Coenzyme

A

A small molecule which helps enzymes catalyse reactions

Important for building molecules such as fatty acids

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2
Q

What makes a molecule soluble in water?

A

Ionisable functional group(s)

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3
Q

R-OH

A

Alcohol

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4
Q

Example of an alcohol

A

Methanol

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5
Q

R-O-R

A

Ether

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6
Q

Example of an ether

A

Methyl ethyl ether

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7
Q

l
R-O-C-OH
l

A

Hemiacetal

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8
Q

l
R-O-C-O-R
l

A

Acetal

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9
Q

Which molecules are hemiacetal and acetal functional groups associated with?

A

Carbohydrates

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10
Q

O
ll
R-C-H

A

Aldehyde

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11
Q

Example of an aldehyde

A

Ethanal

Acetaldehyde

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12
Q

O
ll
R-C-R’

A

Ketone

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13
Q

Example of a ketone

A

Propanone (acetone)

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14
Q

O
ll
R-C-OH

A

Carboxylic acid

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15
Q

Example of a carboxylic acid

A

Ethanoic acid (acetic acid)

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16
Q

O
ll
R-C-OR’

A

Ester

Derivative of carboxylic acid

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17
Q

Example of an ether

A

Ethyl ethanoate

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18
Q

What molecules are carboxylic acids and esters associated with?

A

Lipids (and amino acids for carboxylic acid)

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19
Q

Are alcohols rare or common

A

Common

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20
Q

Are ethers rate or common?

A

Rare

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21
Q

Why are low molecular weight alcohols soluble in water?

A

Hydrogen bonding

This allows for bonding to active site of enzyme

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22
Q

Which nucleophilic reactions do alcohols undergo?

A

Substitution

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23
Q

Alcohols can combine with carboxylic acids to form _____

A

Esters

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24
Q

Primary alcohols are oxidised to form ____

A

Aldehydes

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25
Q

Aldehydes are oxidised to form _____

A

Carboxylic acids

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26
Q

Secondary alcohols are oxidised to form ____

A

Ketones

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27
Q

Which class of alcohol cannot readily be oxidised?

A

Tertiary alcohols

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28
Q

How does the silver mirror test distinguish an aldehyde from a ketone?

A

When placed in contact with a mild oxidant, an aldehyde will be oxidised, turning into a carboxylic acid

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29
Q

What molecules are used as oxidants for alcohols in the body? Give an example

A

Enzymes

Alcohol dehydrogenase to oxidise ethanol in the liver- turns into ethanal

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30
Q

Which is more reactive: ethers or esters? Why?

A

Esters

They are more easily cleaved by nucleophiles

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31
Q

What is an amine? Three classes

A

A nitrogen with 1-3 hydrocarbon groups bonded

Primary- 1 R
Secondary- 2 R
Tertiary- 3 R

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32
Q

What is an amide?

A

A nitrogen atom attached to three groups
- one of those is a C=O

Primary: C=O, H, H
Secondary: C=O, R’, H
Tertiary: C=O, R’, R”

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33
Q

What is an imine functional group?

A 
A nitrogen double bonded to a carbon, and single bonded to a hydrocarbon group
        R
\       /
 C=N
/
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34
Q

Main difference between amines and amides

A

Amines are significantly basic: they have a lone out of electrons on the nitrogen, available for bonding protons

Amides are not: their lone pair is not a available for bonding protons

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35
Q

Describe resonance in an amide

A

Amides have resonance because they flip between two structures

  • One where N has the lone pair
  • And one where O had the lone pair

The C=O bond is very polar, so O takes electrons from C, and in return C takes electrons from N

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36
Q

R-SH

A

Thiol

Alcohol analog

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37
Q

R-S-R’

A

Ether analog

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38
Q

R-S-S-R’

A

Disulfide

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39
Q

An oxidation reaction of thiol leads to what?

A

Disulfide

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40
Q 
O
       ll
HO-P-OH
        l
        OH
A

Phosphoric acid

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41
Q 
O
       ll
HO-P-OR
        l
        OH
A

Alkyl dihydrogen phosphate

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42
Q 
O
       ll
RO-P-OR
        l
        OH
A

Dialkyl hydrogen phosphate

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43
Q 
O
       ll
RO-P-OR
        l
        OR
A

Trialkyl phosphate

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44
Q

What do alkyl dihydrogen phosphates and dialkyl hydrogen phosphates have in common?

A

Both strong acids- ionised at physiological pH (soluble)

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45
Q

What properties do phosphate groups bring to compounds?

A

Help to solubilise them in water

Resistance to hydrolysis (repels nucleophiles due to negative charge)

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46
Q

What does a biological target (host) need to form interactions with a small molecule (guest)? (3)

A

Right polarity
Right shape
Right stereochemistry e.g. chirality

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47
Q

Carbonyl compounds

A

Ones containing a C=O functional group

Aldehydes and ketones

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48
Q

Which carbonyl functional group has two alkyl groups?

A

Ketone

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49
Q

Which carbonyl functional group has an alkyl group and a hydrogen?

A

Aldehyde

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50
Q

Which carbonyl functional group tends to be at the ends of a carbon chain? Why?

A

Aldehyde

Because it has an H attached

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51
Q

Suffix of an aldehyde

A

-al

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52
Q

Suffix of a ketone

A

-one

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53
Q

Which reactions is carbonyl chemistry dominated by?

A

Addition reactions

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54
Q

Steps in the addition reaction of a carbonyl, using a strong nucleophile

A

Two steps

  1. Rate determining attack of nucleophile (on C)
  2. Fast attack of electrophile (on O)
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55
Q

Bond breaks and formations in the addition reaction of a carbonyl, using a strong nucleophile

A

Attack of nucleophile breaks Pi bond of C=O and forms single bond to C

Attack of electrophile forms single bond to O

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56
Q

What are H, H+ and H-

A

H = hydrogen atom (one electron)

H+ = proton (no electrons)

H- = hydride (electron shell is full)

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57
Q

LiAlH4 can do what to carbonyl compounds?

A

Reduce them back to their corresponding alcohols

Because it contains hydride (H-) that can act as a nucleophile

Adding an acid (H+) gives an alcohol

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58
Q

Is there a reaction intermediate or transition state in the addition reaction of a carbonyl compound using a strong nucleophile?

A

Yes- once nucleophile attacks, before electrophile attacks, there is a negatively charged transition state

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59
Q

Can nucleophiles be neutral?

A

Yes- they just need a non-bonding electron pair

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60
Q

What do we need to do before reacting a weak electrophile with a carbonyl compound?

A

Increase the positive charge on C (of C=O) by adding the electrophile first

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61
Q

What transition state do we get after adding the electrophile (first) to the carbonyl compound?

A

Carbocation

This is very attractive to the weak nucleophile

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62
Q

What charge does the weak nucleophilic atom have after bonding to the carbocation? (Addition reaction of carbonyl)

A

+1

Because the electrophile attacked first, producing carbocation

Carbocation has +1 charge, weak nucleophile has 0 charge, so when it attacks, the charge is transferred to the nucleophile

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63
Q

What occurs due to the positive charge of the nucleophilic atom?

(In addition reaction of carbonyl using a weak nucleophile)

A

The Nu-H bond breaks (fast step)

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64
Q

What is the slow step in the addition reaction of a carbonyl using a weak nucleophile?

A

Attack of nucleophile to carbocation

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65
Q

Which is the more reactive carbonyl functional group? Why? (2)

A

Aldehydes

  1. Less steric hinderance (Only one alkyl group)
  2. Less stability due to less alkyl groups donating electrons to reduce positive charge on C
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66
Q

In the slow step of an addition reaction to a carbonyl compound (weak nucleophile), we go from a ____ hybridised carbon to a ___ hybridised carbon

A

sp2 (trigonal planar- 3 groups attached)

sp3 (tetrahedral- 4 groups attached)

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67
Q

What weak nucleophile is used to turn a carbonyl into a hemiacetal?

A

Alcohol

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68
Q

Adding alcohol to carbonyl can turn it into hemiacetal. What will further alcohol addition produce? What kind of reaction is this?

A

Acetal

Substitution

69
Q

Four steps in the substitution reaction to turn hemiacetal into acetal

A
  1. OH is a poor leaving group- so it’s protonated, forming carbocation
  2. Leaving group leaves (rate determining)
  3. Alcohol (nucleophile) attacks C, gaining its positive charge
  4. O-H bond is cleaved to get rid of positive charge, forming acetal
70
Q

Which carbohydrates exist in hemiacetal form?

A

Monosaccharides e.g. glucose

71
Q

In which carbohydrates does acetal join adjacent sugars?

A

Complex- oligosaccharides and polysaccharides e.g. starch and cellulose

72
Q

How do amino compounds (R-NH2) act as nucleophiles?

A

Strong

Although they are neutral, the lone pair on nitrogen is more loosely held than the lone pair on an O, because N is less electronegative (orbital is further from the nucleus)

(Easier to share electrons)

73
Q

Is the product of nucleophilic addition of amino compound to a carbonyl compound stable or unstable?

What will further reaction form?

A

Unstable

Imine

74
Q

How is an imine formed from a nucleophilic addition product (from amino compound added to carbonyl)

What do equilibrium arrows between these steps mean?

A

OH is protonated

Leaving group (H2O) leaves forming a carbocation

Carbocation is deprotonated to form C=N double bond- amine

It’s a reversible process

75
Q

How does 11-cis retinal turn into 11-trans-retinal? (Vision)

A

On absorption of a photon, the molecule becomes high energy

Pi bond breaks between C11-C12, allowing free rotation (and forming radicals)

As it loses energy, the Pi bond reforms in the new shape (trans)

76
Q

What does the isomerisation of 11-retinal do in the body?

A

Triggers a series of events that send a signal form the eye to the brain

77
Q

How do we produce more 11-cis-retinal?

A

The isomerisation process is reversed by enzymes

78
Q

Most common form of monosaccharide

A

Aldose

79
Q

What is a 2D drawing of a 3D structure called?

A

Fischer projection

80
Q

What goes at the top of a Fischer projection?

A

The highest oxidised carbon

81
Q

In a Fischer projection, is the longest carbon chain bonded horizontally or vertically?

A

Vertically

82
Q

The bonds to the side of a Fischer projection project _____ the page

A

Out from the page

83
Q

The up and down bonds of a Fischer projection project _____ the page

A

Into the page

84
Q

How do we distinguish between D and L molecules in Fischer projections?

A

If the non-hydrogen atom points to the right= D

If it points to the left= L

85
Q

How can we draw carbohydrates (two forms)?

A

Open chain structure

Ring structure

86
Q

Why can a carbohydrate be drawn as a ring?

A

Because there’s free rotation about the single bonds

87
Q

Anomeric carbon

A

A carbon bonded to two oxygens

Can be an acetal or hemiacetal group

88
Q

5- membered ring

A

Furanose

89
Q

Six-membered rings

A

Pyranose

90
Q

Where do we draw oxygen in a carbohydrate ring?

A

Top right

91
Q

Alpha (anomeric carbon)

A

Group off anomeric carbon (OH or OR) is on the opposite side (of the plane) to the side chain

92
Q

Beta (anomeric carbon)

A

Group off anomeric carbon (OH or OR) is on the same side (of the plane) to the side chain

93
Q

Cyclic forms of sugars are always in equilibrium with ___ _______

What is this process of re-closure called?

A

Free aldehyde

Mutarotation

94
Q

What are the percentages of alpha, beta and open chain forms of sugar in solution?

A

37% alpha
63% beta
<1% open chain form

95
Q

How do we know the percentages of alpha and beta sugars in solution?

A

By the way they rotate plane polarised light

96
Q

Equatorial bonds

A

Bonds pointing slightly up and slightly down in a chair structure

97
Q

Axial bonds

A

Groups pointing north and south in a chair structure

98
Q

Which groups use equatorial bonds? Why?

A

Generally all groups: H atoms use axial bonds

Axial bonds aren’t suitable for larger groups because there’d be too much repulsion, raising the energy and making it more unstable

99
Q

Reducing sugar

A

A hemiacetal sugar

- there must be free -CHO in solution to reduce silver

100
Q

Why are acetals stable in the absence of H+?

A

OR is a poor leaving group

Would need to be protonated

101
Q

Glycoside

A

Cyclic acetal

102
Q

What is the bond between anomeric carbon and OR group called in a glycoside?

A

Glycosidic linkage

103
Q

How can the substitution reaction of glucose with methanol produce both alpha and beta acetals?

A

The ethanol can attack from either above or below the plane

104
Q

Non-reducing sugar

A

Acetal sugar

No reaction possible when there’s no open chain form

105
Q

Which group links monosaccharides? At which points of the sugars?

A

Acetals

Anomeric carbon of one
OH of two

106
Q

What is the reverse of acetal formation reaction?

A

Glycoside hydrolysis

Breaking the glycosidic linkage

107
Q

How can monosaccharides differ? (5)

A 
Number of carbons
Stereochemistry
Functional groups
Ring size
Orientation of groups
108
Q

How do blood types differ?

A

By their extra sugar (or lack of)

109
Q

Four examples of carboxylic acid derivatives

A

Ester
Amide
Acid anhydride
Acid chloride

110
Q

Which L group of a carboxylic acid derivative has the strongest influence on the polarity of C?

Which has the weakest influence?

A

Chloride (in an acid chloride) and RCOO (in an acid anhydride)

R’HN (in an amide)

111
Q

Why is an amide the least reactive carboxylic acid derivative?

A

The lone pair of electrons on the nitrogen create a Pi bond (N=C)

Reduces positive dipole on C

112
Q

What two things does the substitution reaction of a carboxylic acid derivative depend on?

A

Strength of nucleophile

Reactivity of acid derivative

113
Q

Oh which acid derivatives does the nucleophile strength not matter in a substitution reaction? Why?

A

Acid chlorides and acid anhydrides

Because the induced dipole on C is sufficient to attract weak and strong nucleophiles

114
Q

Which acid derivatives require a strong nucleophile for substitution? Why?

A

Amides
Carboxylic acids
Esters

Positive dipole on C isn’t strong enough

115
Q

What is the slow step, and intermediate in a substitution reaction of an acid derivative?

A

Addition of nucleophile

Unstable tetrahedral carbocation (wants to get rid of group with weakest bond)

116
Q

Are the alkyl groups single or double bonded in fats?

A

Single

117
Q

Are the alkyl groups single or double bonded in oils?

Why?

A

Double

Kinks in the tails make molecule more fluid and oil like

118
Q

What is done to fats to prepare soaps?

A

Hydrolysis

119
Q

What structures does soap form?

How do these work?

A

Micelles

Hydrophobic hydrocarbon chains cluster in the middle

Hydrophilic (polar) carboxylate groups are on the surface

Oil and dirt and trapped and dissolve in non-polar part of micelle

120
Q

How is a liposome formed? What are they good for?

A

Lipid bilayer is unsaturated and folds into a liposome (double membraned micelle)

Drug delivery

121
Q

Protease

A

Breaks down proteins (enzyme)

122
Q

Amylase

A

Enzymes which break down starches

123
Q

Lipases

A

Enzymes which break down fats and bread

124
Q

Which two functional groups do amino acids contain?

A

NH2 amine

COOH carboxylic acid

125
Q

What do the 20 naturally occurring amino acids have in common? (2)

A

All have a chiral carbon (except one)

All have same 3D arrangement around this chiral carbon

126
Q

Alpha amino acid

A

An amino acid which has both amine and carboxylic acid groups on the chiral carbon

127
Q

Do naturally occurring amino acids have R or S configuration?

Which fisher label do they have?

A

S (except cysteine)

L (including cysteine)
- NH2 group points to the left

128
Q

What is the difference between amino acids?

A

Their side chain R

It can make them non-polar or polar, and acidic or basic

129
Q

Acid-base properties of amino acids come from ______

A 
The amine (base)
The carboxylic acid (acid)
130
Q

When we’re talking about the pKa of the amine group of an amino acid (pKa2), what should we keep in mind?

A

It is the pKa of it’s conjugate base NH3+

131
Q

In a titration of an amino acid with a base, which groups react and in what order?

A

COOH ——> COO-
- first because COOH is the strongest acid

NH3+ ——> NH2
- once COOH has run out

132
Q

What are the states of the amino acid groups in a zwitterion?

A

NH3+ and COO-

133
Q

What do zwitterionic amino acids behave like?

A

Ionic salts

  • high melting points
  • solids
  • soluble in water
134
Q

pI

A

Isoelectric point

The pH at which the max number of molecules have a net zero charge (first equivalence point)

135
Q

Where is the pI for simple amino acids?

A

Halfway between pKa1 and pKa2

136
Q

Where is the pI for amino acids with acidic or basic R groups?

A

Between the two most similar pKa values

137
Q

Name of the technique that discriminates molecules based on their overall charge

A

Electrophoresis

138
Q

Amide bond formation involves which groups of an amino acid?

A

Amine NH2 of one bonding with the carboxylic acid COOH of the other

139
Q

Peptide bond

A

Bond between two amino acids

140
Q

What are the ends of amino acids that aren’t involved in the peptide bond called?

A

N-terminal and C-terminal

141
Q

Are amides reactive to nucleophiles? Why?

A

They’re relatively unreactive

Resonance (due to lone pair on nitrogen) makes the central carbon less positive

142
Q

What influence does the peptide bond have on molecule shape?

A

It has double bond character- restricted rotation

So the shape of the molecule is flat (in the same plane)

143
Q

Peptide

A

Linear polymer of amino acids

144
Q

Which terminus is written on the left when drawing a peptide?

A

N

C on the right

145
Q

Why are peptides referred to as peptide chains?

A

Because the individual units can move in respect to each other (bond rotation)

146
Q

How many amino acids does a molecule need to be considered a protein?

A

> 75

147
Q

Four levels of protein structure

A

Primary- sequence of aa’s

Secondary- segments off structure along the chain

Tertiary structure- secondary elements fitting together

Quaternary structure- proteins/ peptide chains fitting together

148
Q

Why do peptides adopt secondary structures?

A

To expose polar side chains, and bury non-polar ones

149
Q

How are secondary structural elements in a peptide chain stabilised? What does this cause?

A

Hydrogen bonding

Kinks and turns in the chain

150
Q

What shapes can be formed from peptide chains? (2)

A

Alpha-helices

Beta-sheets

151
Q

What other bonding (other than H) can influence the shape of peptides?

A

Disulfide linkages

Thiol groups in cysteines can be oxidised by to give disulfide-linked dimer

152
Q

Structure of insulin

A

Two peptide chains joined by disulfide bridges

153
Q

To synthesise a peptide from two amino acids, what must we do before reacting them together?

A

Protect the group on each amino acid we don’t want to bond

154
Q

Protecting group

A

Protects amino acid group we don’t want involved in next reaction

Examples: BOC, OMe (ester)

155
Q

What role does an activator such as DCC play in peptide synthesis?

A

Facilitates the joining of two amino acids

156
Q

How can reactivity of a peptide be achieved?

A

Heating with strong aqueous acid

157
Q

Why do we need to hydrolyse peptide bonds?

A

To liberate amino acids we ingest

158
Q

Apart from the low pH in our stomach, how do we hydrolyse peptide bonds?

A

Proteases (enzymes) catalyse the reaction

159
Q

What does the enzyme chymotrypsin recognise?

A

Aromatic amino acid side chains

160
Q

What do aromatic rings contain?

A

Benzene (C6H6)

161
Q

What does the hydrophobic binding pocket in chymotrypsin do?

A

Recognises the aromatic ring and positions the peptide bond at the catalytic triad

162
Q

What three molecules make up the catalytic triad?

A

Serine
Histadine
Aspartic acid

163
Q

Which part of the catalytic triad acts as the nucleophile for the peptide bond?

A

O- of serine (OH bond cleaved)

164
Q

Why does the chain of electron transfers along the catalytic triad start?

A

Aspartic acid exists as its conjugate base at physiological pH

It has an O- that shares electrons with H of histadine

165
Q

What two main steps occur in peptide hydrolysis by chymotrypsin?

A

Peptide bond breaks, forming an intermediate ester

Intermediate ester is hydrolysed by ‘activated water’

166
Q

Three key factors of carboxypeptidase and its role in hydrolysing peptide bonds

A

Holds reactants close together

Zn2+ makes C=O more susceptible to nucleophile attack

Deprotonates H2O to form OH- (much better nucleophile)

167
Q

What part of a peptide does carboxypeptidase recognise?

A

The C-terminal of the amino acid

168
Q

Why is OH of phenol (in tyrosine) more acidic than an OH group in another alcohol?

A

It’s conjugate base is very stable- at equilibrium there’ll be more of it

These is because the charge of the electrons is delocalised around the aromatic ring

CHEM (3 decks)

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