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BIOC 2580 > Lecture Slides I > Flashcards

Lecture Slides I Flashcards

1
Q

What are some examples of small molecules? Why are small molecules seen in biochemistry?

A

Sugars, amino acids, nucleotides, carboxylic acid derivatives. They act as building blocks for macromolecules.

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2
Q

What are some examples of macromolecules and their subunits?

A

Proteins = chains of amino acids
Polysaccharides = chains of simple sugars
Nucleic acids = chains of nucleotides

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3
Q

What protein stores O2 in muscle tissue? Is this a macromolecule or a small molecule?

A

Myoglobin

Macromolecule

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4
Q

How large are most proteins?

A

10,000 to 100,000 g/mol

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5
Q

How large is a kilodalton (in terms of g/mol)?

A

1 kDa = 1000 g/mol

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6
Q

Is myoglobin a large or small protein?

A

Small - 16.5 kDa

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7
Q

Is P-glycoprotein a large or small protein?

A

Large - 170 kDa

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8
Q

What are the bonds between amino acids called?

A

Amide bonds

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9
Q

What are proteins made of?

A

Amino acids

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10
Q

What are the subunits of a protein linked by?

A

A peptide bond (type of amide bond).

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11
Q

Are the sequences of amino acids the same or different?

A

Each is unique, and that determines their properties.

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12
Q

Does the size/structure of a protein change?

A

No, it is well-defined.

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13
Q

What are some examples of the function of a protein?

A

Catalyzing reactions (enzymes) and forming complex subcellular structures

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14
Q

What is the basic amino acid structure?

A
  • Amino group
  • Carboxylate group
  • Each has a different side chain (R)
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15
Q

How many different amino acids are there?

A

20

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16
Q

What is condensation?

A

Removal of H2O from units being linked.

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17
Q

What is hydrolysis?

A

Regeneration of original carboxylic acid and amino group

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18
Q

What is the point of weakness in a peptide bond allowing H2O to attack?

A

C=O bond

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19
Q

What is a polypeptide?

A

A chain with many amino acids, usually a complete protein

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20
Q

What is an oligopeptide?

A

A chain with a few amino acids, usually a fragment

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21
Q

How can the alpha-carbon be described?

A

The central backbone atom

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22
Q

Describe the Beta-carbon.

A

The first atom of the side chain

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23
Q

What is the 2nd atom of a side chain referred to as?

A

Gamma-carbon

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24
Q

What is the order of greek letters representing carbons from the central backbone -> furthest away?

A

Alpha, beta, gamma, delta, epsilon

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25
Q

What are some important properties related to amino acids (3)?

A
  • Polarity
  • Charge
  • Hydrogen bonding ability
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26
Q

What are the 6 amino acids with very non-polar side chains?

A

Alanine (A Ala), Valine (V Val), Leucine (L Leu), Isoleucine (I Ile), Phenylalanine (F Phe) and Methionine (M Met)

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27
Q

What are the 5 amino acids with moderately non-polar side chains?

A

Glycine (G Gly), Cysteine (C Cys), Proline (P Pro), Tryptophan (W Trp) and Tyrosine (Y Tyr)

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28
Q

What are the 4 amino acids with polar but uncharged side chains?

A

Serine (S Ser), Threonine (T Thr), Asparagine (N Asn) and Glutamine (Q Gln)

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29
Q

What are the 3 amino acids with positively charged, very polar side chains?

A

Histidine (H His), Lysine (K Lys) and Arginine (R Arg)

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30
Q

What are the 2 amino acids with negatively charged, very polar side chains?

A

Aspartate (D Asp) and Glutamate (E Glu)

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31
Q

Are hydrocarbons polar/non-polar and hydrophobic/hydrophilic?

A

Hydrocarbons are non-polar and hydrophobic

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32
Q

What is polarity?

A

A consequence of having different electronegativities (or tendency to hold bonding electrons)

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33
Q

Place these in order of decreasing electronegativity:

C, H, N, O, S

A

O > N > S > C = H

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34
Q

How are electrons distributed between atoms with similar electronegativity?

A

They are shared equally and are therefore non-polar (ex. C-C or C-H)

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35
Q

How are electrons distributed when the electronegativities are quite different?

A

The are shared unequally. This leads to unbalanced charges and polar bonds (ex. O-H and N-H)

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36
Q

What is hydrophobicity related to?

A

Number of hydrocarbon groups (higher # of hydrocarbons, higher hydrophobicity)

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37
Q

What is unique about glycine?

A

It is the only non-chiral amino acid

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38
Q

What does it mean when the side chains are called ‘uncharged’?

A

They do not gain or lose H+ in aqueous solution at pH 7

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39
Q

What do the polar uncharged side chains have to do with hydrogen bonds?

A

All four (OH, NH2, =O) act as good hydrogen bond donors or receptors

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40
Q

What are hydrogen bonds?

A

Electrostatic attractions between an H-bond donor and acceptor. About 5-10% as strong as a covalent bond

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41
Q

What are good H-bond donors?

A

Highly polar -OH or -NH groups

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42
Q

What are good H-bond acceptors?

A

Electronegative atoms with an available lone pair of electrons (ex. O or N)

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43
Q

What happens to amino acids with positively charged side chains when placed in aqueous solution at neutral pH?

A

The weak bases gain H+ (or become protonated), and are positively charges (very-polar).

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44
Q

What happens to negatively charged amino acids at neutral pH in aqueous solution?

A

Lose H+ (become deprotonated). Carboxylic acid becomes carboxylate (negative and very polar).

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45
Q

Draw the dipeptide alanylserine (Ala-Ser)

A

O=C-NH2-

l

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46
Q

When an amino acid is ‘charged’, which part of the amino acid is being referred to?

A

The side chain (R)

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47
Q

Which of the following amino acids can accept/donate hydrogen bonds on its side chain? Val, Ala, Tyr, Phe

A

Tyrosine (OH)

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48
Q

Describe the polarity and charge of an amino acid with C=O and NH2.

A

Polar and uncharged

49
Q

What amino acid is present at the C-terminus of the following peptide?
QYTKLHSGAN

A

Asparagine

50
Q

What number in the side chain is the gamma-carbon of an amino acid?

A

2nd in the side chain

51
Q

What are free amino acids?

A

Weak electrolytes (acids/bases) due to their amino and carboxylate groups

52
Q

What is the Henderson-Hasselbalch equation and what is it useful for?

A

pH = pKa + log (deprotonated/protonated)

It is useful for determining how much deprotonated/protonated amino acid is present at a certain pH.

53
Q

What amino acids have ionizable side chains?

A

Aspartate, Glutamate, Arginine, Lysine, Histidine, Cysteine and Tyrosine

54
Q

What are the charges of the side chains of aspartate and glutamate when protonated/deprotonated?

A

Protonated: neutral
Deprotonated: -1

55
Q

What are the charges of the arginine, lysine, and histidine side chains when protonated/deprotonated?

A

Protonated: +1
Deprotonated: Neutral

56
Q

What are the charges of the cysteine and tyrosine side chains when protonated/deprotonated?

A

Protonated: Neutral
Deprotonated: -1

57
Q

What is the value of the pKa dependent on?

A

Chemical context. The pKa will be slightly different when part of a peptide chain.

58
Q

As pH is raised, is protonation or deprotonation more likely to occur? Why?

A

Deprotonation, because [H+] becomes less available.

59
Q

If pH is one unit or more higher than pKa, the group is fully ______.

A

Deprotonated

60
Q

If pH is equal to pKa, the group is ________.

A

50% deprotonated, 50% protonated

61
Q

If pH is one unit or more below the pKa, the group is fully ________.

A

Protonated

62
Q

Which amino acid is only partially charged at pH = 7?

A

Histidine

63
Q

What does the relationship between pH and pKa tell you?

A

Whether a group is protonated or deprotonated

64
Q

Groups that ionize O or S are _____ when protonated, and ______ when deprotonated.

A

Neutral

Negative

65
Q

Groups that ionize N are _______ when protonated, and ______ when deprotonated.

A

Positive

Neutral

66
Q

When is it needed to calculate the exact state of ionization?

A

When the pH is less than 1 unit away from pKa

67
Q

How can you find the fraction of molecules that are deprotonated?

A 
a = ratio/(1+ratio)
ratio = deprotonated/protonated
68
Q

What is the overall charge on the side chain of lysine when one third of the side chains are deprotonated?

A

+0.67

69
Q

What is the overall charge on the side chain of aspartate when 1/4 of the side chains are deprotonated?

A

-0.25

70
Q

Calculate the net charge of the side chain of Arg at pH 11.8 (pKa = 12.5).

A

+0.83

71
Q

What are the two processes involved in amino acid analysis?

A

1 - Separation of a mixture of components

2 - Detection of the components of interest (can be qualitative/quantitative/preparative)

72
Q

What is partition chromatography?

A
  • Stationary phase = Particles of a solid (e.g. silica gel) with a specific property.
  • Mobile phase = Non-polar liquid solvent/buffer flows
  • Amino acids exchange between phases
  • Polar move slowly
  • Non-polar move quickly with solvent
73
Q

What is thin layer chromatography?

A
  • Silica gel
  • Solvent moves upwards
  • Very polar amino acids have a low relative mobility (Rf), while non-polar amino acids have a high Rf
74
Q

What is column chromatography?

A
  • Elution volume = volume of buffer needed to move compound through column
  • Compounds identified by elution volume
75
Q

What is the purpose of ninhydrin?

A

Detection of amino acids (reacts with primary/secondary amines to give purple colour or yellow for proline).
Colour intensity is proportional to quantity of amino acid

76
Q

What is an alternative to ninhydrin? Why might it be used instead?

A

Fluorescamine can detect 10^-10 moles, which is smaller than the 10^-8 moles ninhydrin can detect

77
Q

What is ion exchange chromatography?

A

Separates on the basis of charge

  • Stationary phase = charge resins
  • Elution by competition with high ion concentration or change pH (altering charge)
78
Q

What do cation exchanger resins bind?

A

Positive molecules (cations)

79
Q

What do anion exchanger resins bind?

A

Negative molecules (anions)

80
Q

What technique is frequently used to separate protein mixtures?

A

Ion exchange (as the charge can show large differences between peptides).

81
Q

Calculate the overall net charge of the following polypeptide at pH = 12.8.
Ile-Gln-His-Arg-Trp-Asp

A

-1.67

82
Q 
Which of the following peptides would bind most tightly to a cation-exchange column, at neutral pH?
CAMILLA
EDWARD
HARRY
PHILIP
WILLIAM
A

HARRY

83
Q

What is metal affinity chromatography?

A
  • His clusters bind to Ni2+ or Co2+

- Column is made up of Ni2+ resin

84
Q

What are his-tags?

A
  • Protein artificially reproduced by gene insertion into cells
  • Gene can be modified to include 6-8 extra His residues (His tag)
  • Bind tightly to Ni2+ resin
85
Q

How is the his-tagged protein eluted?

A
  • By adding imidazole (structurally similar to His) to the buffer
  • Out-competes His-tag, and protein no longer binds
  • High degree of purification in one step
86
Q

What is gel filtration/molecular exclusion chromatography?

A
  • Separation of proteins on basis of molecular size
  • Gel filtration can also be used to measure size of an unknown protein
  • Beads of hydrated gel (polymer with water-filled pores)
  • Proteins enter pores if they fit, so large proteins are passed quicker
87
Q

How can gel filtration be used to measure the molar mass of proteins?

A
  • Measure elution volume of known proteins
  • Elution volume = volume of buffer needed to move protein from top to bottom
  • Ve is a linear function of log molar mass (-ve slope)
  • Measure elution volume of unknown and project back to log mass axis
88
Q

What is ultracentrifugation?

A
  • Protein placed in ultracentrifuge (force of 10000-500000 g)
  • Molecules sediment at rate dependent on size/shape
  • Time consuming
89
Q

What can you find using sedimentation velocity from ultracentrifugation?

A

Molecular mass of a protein

90
Q

What is electrophoresis?

A
  • Separation based on movement of charged molecules in an electric field
  • Carried out in porous gel (buffer is immobilized, porous enough to let proteins through)
91
Q

What does the rate of movement in electrophoresis depend on?

A
  • Size
  • Shape
  • Charge
92
Q

What is polyacrylamide gel?

A
  • 5-15% polymer and 90-95% water with conductive buffer

- Right porosity for proteins 10 kDa - 1000 kDa

93
Q

What is SDS-PAGE?

A
  • Protein is pre-treated with detergent sodium dodecyl sulfate (SDS), causing molecules to extend and give uniform charge per unit size
94
Q

What is isoelectric focussing?

A
  • Separation based on isoelectric point of proteins
  • High pH: deprotonated and moves toward + electrode
  • Passes through gradient of decreasing pH, becomes protonated, net -ve charge decreases
  • When net charge = 0, protein stops moving
  • Become separated along pH gradient
95
Q

What is the isoelectric point?

A
  • pH at which the net charge on a protein is 0
96
Q

What are two-dimensional gels?

A
  • Isoelectric focusing and SDS electrophoresis

- Can separate individual proteins in complex mixtures

97
Q

What is mass spectrometry and what is its function?

A
  • Way to identify proteins (in conjunction with electrophoresis)
  • Protein is vaporized, yielding charged particles which travel toward detector
  • Velocity depends inversely on mass (larger = slower)
  • The time of flight yields a very accurate mass measurement
  • Compare with catalog of proteins of known mass
98
Q

What does the ribbon in a diagram show you?

A

The path of the polypeptide backbone

- Side chains fill the spaces

99
Q

What colour is the N-terminal and what colour is the C-terminal in diagrams?

A 
N-terminal = blue
C-terminal = red
100
Q

How is the ribbon arranged in myoglobin?

A
  • Eight spiral/helical segments
101
Q

What is the primary structure of proteins?

A
  • Linear sequence of amino acids
102
Q

What is the secondary structure of proteins?

A
  • Regular repetitive patterns

- Ex. helical sections (5-20 AAs)

103
Q

What is the tertiary structure of proteins?

A
  • Overall pattern of 3D folding of the whole polypeptide
104
Q

What is the quaternary structure of proteins?

A
  • Only some proteins
  • Combination of subunits
  • Ex. hemoglobin is a complex of 4 globin units which act cooperatively to improve O2 transport
105
Q

How do we find out what amino acids are present and in what sequence?

A
  • Hydrolysis of peptide bonds
  • Help of digestive enzymes called proteases
  • Amino acids can be analyzed by chromatography (how much is present)
106
Q

What are the conditions of acid hydrolysis? How long does it take? What is destroyed?

A
  • 6M HCl 110deg.
  • 24-72 hrs
  • Trp is destroyed
  • Asn and Gln side chain converted to carboxylic acid form (releasing amino group as ammonia)
107
Q

What are the conditions of base hydrolysis? How long does it take? What is destroyed?

A
  • 4M NaOH 110deg.
  • 16 hrs
  • Trp is not destroyed, but some other amino acids may be
108
Q

What does chemical reactivity arise from?

A
  • An unbalanced distribution of valence electrons
109
Q

What atoms are involved in reactions?

A
  • Atoms with unshared electrons (lone pairs)
  • Electron deficient
  • Pull electrons toward them due to electronegativity
110
Q

What initiates many biochemical reactions?

A
  • Nucleophiles
111
Q

What is a nucleophile?

A
  • Atom with a lone pair of electrons available to share

- They seek out other groups that are electron deficient

112
Q

What are 3 ways that an atom may use its lone pair?

A
  • As an H-bond acceptor (if it simply attracts O-H or N-H)
  • As a base (if it captures H+)
  • As a nucleophile when it shares its lone pair with another electron deficient atom to make a new bond
113
Q

What is nucleophilic substitution/displacement?

A
  • Incoming nucleophile attacks target atom to displace leaving group
114
Q

What is nucleophilic addition?

A
  • Incoming nucleophile attacks double bond to create a single bond with target atom
115
Q

What is hydrolysis?

A
  • Attack by H2O as nucleophile on the electron deficient carbon of the peptide bond (AKA nucleophilic displacement)
116
Q

Is carbon an electrophile or a nucleophile in a peptide bond?

A
  • Electrophile b/c electronegative O bonded to C pulls electrons away from it
  • Lets C take incoming electron pair
117
Q

What is the stability of the transition state?

A
  • Semi-stable (compressed spring)
118
Q

What is the leaving group in hydrolysis of a peptide bond?

A
  • Amino N (allowing peptide bond to break)

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