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Biochemistry > Test 1 (Chapters 1-11) > Flashcards

Test 1 (Chapters 1-11) Flashcards

1
Q

What are Dr. Charlie Brenner’s two rules of Biochemistry?

A
  1. No violating physics and chemistry

2. Mutation and Selection

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2
Q

What are four classes of biomolecules?

A
  1. Proteins
  2. Nucleic acids
  3. Carbohydrates
  4. Lipids
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3
Q

Which biomolecules are polymers?

A

Proteins, nucleic acids and some carbohydrates (polysaccharides)

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4
Q

What is the monomer of a protein?

A

Amino acids

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5
Q

What is the monomer of a nucleic acid?

A

Nucleotide

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6
Q

What is the monomer of a polysaccharide?

A

Monosaccharide

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7
Q

Who and when proposed the Central Dogma of Molecular Biology?

A

Francis Crick 1958

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8
Q

Describe the Central Dogma of Molecular Biology

A

Information flows from DNA -> RNA -> Protein:

  1. DNA (self) replicates
  2. DNA can be transcripted to RNA
  3. RNA can be translated to protein
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9
Q

What are three (3) fundamental weak interactions of molecules

A
  1. Ionic bonds
  2. Hydrogen bond
  3. van der Waal
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10
Q

What law is the basis of the Hydrophobic Effect?

A

Second Law of Thermodynamics

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11
Q

What does the hydrophobic effect result in?

A

Nonpolar molecules cluster together

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12
Q

Why does the hydrophobic effect occur?

A
  1. Adding a nonpolar molecule decreases entropy of water molecules surrounding nonpolar molecules.
  2. Nonpolar molecules cluster to reduce surface area, freeing water molecules and increasing entropy.
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13
Q

The properties of amino acid lended by R-group functional groups fall into what four (4) categories?

A
  1. hydrophobic amino acids w/ nonpolar R groups
  2. polar amino acids w/ neutral R group but uneven charge distribution
  3. Positively charged amino acid w/ R group that have positive charge at physiological pH
  4. Negatively charged amino acid w/ R group that have negative charge at physiological pH
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14
Q

What is physiological pH?

A

7.4

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15
Q

Describe the structure of an amino acid

A

An alpha carbon attached to a hydrogen, carboxylic acid group, amino group and a distinctive side chain (R group).

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16
Q

Which amino acid does not have a chiral carbon and why?

A

Glycine because it doesn’t have 4 different groups attached to alpha carbon.

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17
Q

Describe the ionic state of an amino acid at physiological pH

A

The alpha amino group is protonated at pH less than 8-9; The alpha carboxyl group is deprotonated at pH greater than 3.1; it is a zwitterion.

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18
Q

What is a zwitterion?

A

A molecule with a dipole, having a full positive and a full negative charge on separate atoms.

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19
Q

What is unique about the structure of proline?

A

It is the only amino acid whose side chain is connected to both the alpha carbon and the nitrogen.

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20
Q

How does proline’s structure affect the structure of proteins?

A

It’s ring structured makes the protein more conformationally restricted than other amino acids.

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21
Q

Compare the reactivity of the sulfhydryl (-SH) and the hydroxyl (-OH) groups (2 components)

A
  1. Sulfhydryl is much more reactive; can react with itself. (Disulfide bonds)
  2. Sulfhydryl is deprotonated at a lower pH
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22
Q

How are the structures of asparagine and glutamine related?

A

They both contain a terminal carboxamide.

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23
Q

What is unique about the R group of lysine and arginine?

A

They have dual properties; the side chain contains a 3 or 4 carbon chain (nonpolar) and is topped by a positive charge (polar)

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24
Q

Histidine’s structure gives it what unique chemical property?

A

It can be charged or uncharged at neutral pH depending on the environment.

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25
Q

Which is the most acidic hydrogen on Histidine?

A

The sp2 nitrogen can accept and release a proton.

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26
Q

Histidine’s unique property causes it to be found where, and why?

A

In the active sites of enzymes where the ring will bind and release proteins in the course of the reaction.

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27
Q

How are asparagine and glutamine related to aspartate and glutamate?

A

The carboxamie of the former was replaced by a carboxylic acid of the latter.

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28
Q

What are five (5) nonpolar amino acids that have linear aliphatic side chains?

A
  1. Glycine
  2. Alanine
  3. valine
  4. Leucine
  5. Isoleucine
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29
Q

What are three (3) nonpolar amino acids that contain rings?

A
  1. Proline
  2. Phenylalanine
  3. Tryptophan
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30
Q

What is the nonpolar amino acid that contains a thioether (-S-) group?

A

Methionine

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31
Q

What are three (3) polar [neutral] amino acids that have a hydroxyl (-OH) group?

A
  1. Serine
  2. Threonine
  3. Tyrosine
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32
Q

What are two (2) polar [neutral] amino acids that have a carboxamide group?

A
  1. Asparagine

2. Glutamine

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33
Q

What is the polar [neutral] amino acid that has a sulfhydryl (-SH) group?

A

Cysteine

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34
Q

What are three (3) amino acids that are positively charged at neutral pH and what atom bears the positive charge?

A
  1. Lysine (nitrogen of terminal R-amino group)
  2. Arginine (carbon of terminal guanidinium group)
  3. Histidine (nitrogen adjacent to carbon attached to methylene group)
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35
Q

What are two (2) amino acids that are negatively charged at neutral pH and what atom bears the negative charge?

A
  1. Aspartate (carbon of terminal R-carboxylate)

2. Glutamate (carbon of terminal R-carboxylate)

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36
Q

What seven (7) amino acids have readily ionizable side chains?

A
  1. Tyrosine
  2. Cysteine
  3. Arginine
  4. Lysine
  5. Histidine
  6. Aspartic acid
  7. Glutamic acid
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37
Q

The seven ionizable amino acids have what two (2) chemical capabilities?

A
  1. Form ionic bonds

2. Acid-base catalysis

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38
Q

What is the pKa of terminal alpha-carboxyl group?

A

3.1

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39
Q

What is the pKa of terminal alpha-amino group?

A

8.0

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40
Q

What is the pKa of aspartic and glutamic acid terminal R-carboxyl group?

A

4.1

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41
Q

What is the pKa of Histidine?

A

6.0

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42
Q

What is the pKa of Cysteine?

A

8.3

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43
Q

What is the pKa of Tyrosine?

A

10.9

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44
Q

What is the pKa of Lysine

A

10.8

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45
Q

What is the pKa of Arginine

A

12.5

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46
Q

Despite an L and D isomer existing for all amino acids besides Glycine, proteins only contain which isomer?

A

L-amino acids.

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47
Q

What is a theory why only L amino acids are present in proteins?

A
  1. Pure L or D amino acids are slightly more soluble than a DL crystal.
  2. A small excess of L isomer, if appeared by chance, could amplify over time and dominate solution.
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48
Q

What is the primary structure of a protein?

A

The linear polymer formed by linking alpha-carboxyl group of one amino acid to the alpha-amino group of another amino acid.

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49
Q

What is the name of the bond between two amino acids?

A

Peptide bond (amide bond)

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50
Q

What molecule leaves during the formation of a dipeptide (two amino acids forming a peptide bond)?

A

H2O

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51
Q

Describe the equilibrium and kinetics of synthesis of peptide bonds.

A

Equilibrium lies on the side of hydrolysis (two amino acids is favored) so an input of free energy is required; Peptide bonds are stable kinetically because the rate of hydrolysis is extremely slow.

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52
Q

What is a polypeptide chain?

A

A series of amino acids joined by peptide bonds

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53
Q

What is each amino acid unit in a polypeptide called?

A

A residue

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54
Q

What is meant by the phrase “polypeptides have directionality?”

A

The ends are different: (1) one end is an alpha-amino group, (2) the other end is an alpha-carboxyl group.

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55
Q

Which end of the polypeptide is the “beginning” of the chain?

A

By convention, the amino end is the beginning of a polypeptide chain.

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56
Q

What are the two regions of a polypeptide chain?

A
  1. Main chain or backbone

2. Variable part, containing side chains

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57
Q

Describe the chemistry of the polypeptide backbone

A

It is rich in hydrogen bonding potential because each residue has a C=O and an N-H (proline does not have an N-H)

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58
Q

What are the most common covalent cross-link in a primary structure?

A

Disulfide bonds formed by oxidation of a pair of cysteine residues.

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59
Q

What is the name of the unit formed by the oxidation of a pair of cysteine residues?

A

Cystine

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60
Q

What are three (3) characteristics of a peptide bond?

A
  1. Planar
  2. Considerable double-bond character (resonance structures)
  3. Uncharged
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61
Q

What is a consequence of the double-bond character of the peptide bond?

A

Prevents rotation and constrains conformation of the peptide backbone.

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62
Q

What are the two possible conformations of a peptide bond and which is favored?

A

Cis or trans, related to the side the alpha carbons are on.

Trans is favored because it reduces steric hinderance.

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63
Q

Although the peptide bond is rigid, what two bonds of a residue are flexible?

A
  1. Bond between amino group and alpha-carbon atom

2. Bond between carbonyl group and alpha-carbon atom

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64
Q

How is the torsion angle Phi measured?

A

When viewing down the N-Calpha bond, it is the angle between (rotation of) the carbonyl carbons. Clockwise is positive, counterclockwise is negative.

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65
Q

How is the torsion angle Psi measured?

A

When viewing down the carbonyl-Calpha bond, it is the angle between (rotation of) the amino group. Clockwise is positive, counterclockwise is negative.

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66
Q

What is steric exclusion and how does it affect primary structures?

A
  1. the fact that two atoms cannot be in the same place at the same time
  2. restricts the number of possible peptide conformations
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67
Q

What is a Ramachandran diagram?

A

A two-dimensional plot of psi and phi torsion angles that shows possible combinations. Three-quarters of combinations are impossible because of steric exclusion.

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68
Q

What are three (3) most common secondary structures?

A
  1. Alpha-helices
  2. Beta-sheets
  3. Turns/Loops
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69
Q

What interactions form secondary structures?

A

Hydrogen bonds

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70
Q

Hydrogen bonds in an alpha-helix are between what atoms?

A

The carbonyl group of residue i and the NH group of residue i + 4.

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71
Q

An alpha-helix residue is spatially related to the next one in what two ways?

A
  1. A rise (translation) of 1.5 Å along helix axis (up)

2. A rotation of 100 degrees

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72
Q

How many amino acid residues are in each turn of a helix?

A

3.6

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73
Q

Define the pitch of an alpha-helix

A

The length along helix axis of one complete turn.

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74
Q

What is the pitch of an alpha helix in Å?

A

Product of translation (length per residue) * # of Residues per turn.

1.5 Å + 3.6Å = 5.4 Å

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75
Q

Define screw sense

A

The direction in which a helical structure rotates when viewed down its axis. Clockwise is right-handed, counterclockwise is left-handed.

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76
Q

What is the screw sense of essentailly all alpha-helices in proteins and why?

A
  1. Right-handed (clockwise)

2. Fewer steric clashes between side chain and backbone.

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77
Q

What are three (3) amino acid structures that disrupt an alpha-helix?

A
  1. Branching at beta-carbon atom.
  2. Hydrogen-bonding side chains close to main chain.
  3. Proline
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78
Q

What three (3) amino acids are not usually incorporated into an alpha-helix because of branching at beta-carbon atom?

A
  1. Valine
  2. Threonine
  3. Isoleucine
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79
Q

What three (3) amino acids are not usually incorporated into an alpha-helix because of hydrogen-bonding side chains close to the main chain?

A
  1. Serine
  2. Aspartate
  3. Asparagine
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80
Q

What are two (2) reasons why proline is not incorporated into alpha-helices?

A
  1. Lacks an NH group for hydrogen bonding.

2. Ring structures prevents the necessary Phi value to fit into an alpha-helix.

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81
Q

Describe the structure of Beta-sheets (2 components)

A
  1. Formed by linking two of more Beta strands with hydrogen bonds; typically 4-5, but as many as 10 or more.
  2. Sheets can be parallel or antiparallel, depending on if strands run in the same direction.
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82
Q

Describe the structure of Beta strands

A
  1. Polypeptide chain with a distance of 3.5Å between residues.
  2. Side chains of adjacent amino acids alternative above and below plane of strand.
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83
Q

What are the purpose of turns and loops in a protein?

A

Allows reversal of direction of chain to form compact globular shape.

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84
Q

Where are turns and loops located?

A

Always at the surface of proteins

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85
Q

Loops exposed to aqueous environments are composed of what kind of amino acids?

A

Amino acids containing hydrophilic R groups.

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86
Q

Describe the structure of a reverse turn in a polypeptide

A

The C=O group of residue i is hydrogen bonded to the NH group of residue i + 3, which stabilizes a turn.

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87
Q

According to the Ramachandran Plot, what are the typical values of Phi and Psi?

A
  1. Phi is usually negative

2. Psi is usually positive

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88
Q

What is meant by a superhelix protein?

A

A protein that is formed by the coiling of alpha-helices. These are typically fibrous proteins, like Keratin.

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89
Q

What is the most common mammalian protein?

A

Collagen

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90
Q

Describe the structure of collagen (3 components)

A
  1. It is a superhelical cable formed from three helical strands.
  2. The helical strands are stabilized not because of hydrogen bonds, but because twisting reduces steric hinderance from the proline rings.
  3. Every third residue is Glycine because it is the only amino acid small enough to fit within the interior of the coil.
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91
Q

The primary structure refers to what arrangement?

A

The sequence of amino acids

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92
Q

The secondary structure refers to what arrangement?

A

The simple repeating structures formed by hydrogen bonds of the peptide backbone.

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93
Q

The tertiary structure refers to what arrangement? (2 components)

A
  1. The spatial arrangement of amino acids that are far apart in the sequence
  2. Pattern of disulfide bonds
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94
Q

The tertiary structure arises from the interactions between what parts of amino acid residues?

A

Interactions between the R groups of the peptide chain.

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95
Q

Describe globular proteins (3 characteristics)

A
  1. Compact three-dimensional structure
  2. Water soluble
  3. Perform most of the chemical transactions in the cell
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96
Q

What is the apparent function of myoglobin?

A

To facilitate diffusion of oxygen from the blood to the mitochondria.

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97
Q

In general, the interior of a protein consists of what type of residues?

A

Nonpolar residues

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98
Q

What is the driving force of protein folding to form tertiary structures?

A

The hydrophobic effect

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99
Q

How does the variety of amino acids benefit the stability of the proteins?

A

The subtle differences in shapes and size allows the interior of a protein to be neatly packed to maximize van der Waal interactions.

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100
Q

How are proteins that exist in hydrophobic environments different from those that exist in aqueous environments?

A

In a hydrophobic environment, the interior of the protein contains hydrophilic side chains. These two types of proteins are “inside-out” of each other.

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101
Q

What is a motif?

A

Also called a supersecondary structure; a combination of secondary structures present in many proteins and also exhibit similar functions.

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102
Q

What are two examples of protein motifs?

A
  1. Helix-turn-helix

2. Domains (compact regions separated by flexible segment of chain)

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103
Q

Quaternary structure refers to what arrangement?

A

Arrangement of multiple polypeptide chains, called subunits.

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104
Q

What is the simplest quaternary structure?

A

Dimer, two identical subunits.

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105
Q

Describe the classic 1950s work of Christian Anfinsen (2 components)

A
  1. Native ribonuclease was destroyed [denatured] by urea (disrupt noncovalent bonds) and Beta-mercaptoethanol (cleaved disfulide bonds into sulfhydryl groups) [both reagents are called chaotropic agents]
  2. Once the chaotropic agents were removed, ribonuclease slowly regained enzymatic activity.
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106
Q

Anfinsen’s work revealed what key property of proteins?

A

sequence specifies conformation

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107
Q

Why does refolding not proceed efficiently for some proteins?

A

The unfolded protein molecules become tangled up and form aggregates.

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108
Q

How is the formation of aggregrates prevented in cellular protein synthesis?

A

Proteins called chaperones prevent tangling interactions.

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109
Q

What is the Levinthal paradox?

A

The difference between calculated (assuming the protein tries all possible conformations to find the energetically most favorable one) and experimental folding times of proteins.

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110
Q

Taken together, what does Levinthal’s paradox and Anfinsen’s results suggest?

A

Proteins do not test every possible conformation to find the most favorable, but rather go through progressively more stable intermediates.

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111
Q

What is the protein folding funnel?

A
  1. A two dimensional energy diagram to visualizing protein folding.
  2. Breadth of funnel are all possible conformations of the unfolded proteins.
  3. Depth of funnel is energy difference of folded and unfolded.
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112
Q

What are three models of protein folding pathways?

A
  1. Secondary structures form first (local) and then tertiary (long-range)
  2. The hydrophobic effect forms a globule first; because there is limited restriction on the globule conformation besides hydrophobic chains being on the interior, it is called a molten globule.
  3. Nucleation-condensation model: both local and long-range interactions take place to form the native state.
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113
Q

What are three (3) diseases related to protein misfolding?

A
  1. Alzheimers
  2. Parkinson disease
  3. Mad cow disease (prion disease)
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114
Q

What is the proteome?

A

the entire set of proteins expressed and modified

by a cell under a particular set of biochemical conditions (e.g. cell type, age, and environment)

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115
Q

What is an assay?

A

A test based on some unique identifying property that identifies/measures the protein of interest.

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116
Q

What is specific activity?

A

The ratio of enzyme activity (of interest) to total amount of protein.

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117
Q

Explain how an assay and specific activity are used to measure purification (3 components)

A
  1. The point of purification is to remove all proteins except the protein of interest.
  2. This means we want to maximize specific activity.
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118
Q

What is a homogenate?

A

The source of protein of interest that is a mixture of all of the components of the cell but no intact cells.

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119
Q

What are four (4) steps of protein purification?

A
  1. Source the protein (e.g. lyse a cell)
  2. Differential centrifugation
  3. Purification
  4. Assess purification
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120
Q

What is differential centrifugation?

A

Spinning a mixture in a centrifuge to create layers sorted by density.

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121
Q

What is the heavy material at the bottom of the centrifuge tube called?

A

Pellet

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122
Q

What is the lighter solution in the centrifugre called?

A

Supernatant

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123
Q

What are the pellet and supernatant referred to as collectively?

A

Fractions

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124
Q

What is the crude extract?

A

The centrifuged fraction that contains the most enzyme activity of interest.

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125
Q

What are four characteristics proteins can be separated from each other by?

A
  1. Solubility
  2. size
  3. Charge
  4. Binding affinity
126
Q

What are four (4) basic isolation techniques?

A
  1. Salting out
  2. Chromatography
  3. Isoelectric focusing
  4. 2D SDS-PAGE
127
Q

What is salting out?

A

The precipitation of protein out of solution at high salt concentration.

128
Q

What is the chemical basis for salting out?

A

Salt ions compete with the protein for solvating water. The concentration of salt this occurs at varies between proteins.

129
Q

What is dialysis?

A

The process of removing filtrate (e.g. salt in a protein-salt mixture) through a semi-permeable membrane.

130
Q

What are four (4) types of chromatography techniques used to isolate proteins?

A
  1. Gel-filtration chromatography
  2. Ion-exchange chromatography
  3. Affinity chromatography
  4. High-pressure liquid chromatography
131
Q

How does gel-filtration chromatography isolate proteins? (3 components)

A

By size:

  1. Porous, gel beads are placed in a column and protein mixture is added.
  2. The smaller the protein, the better able it is to enter the gel bead. The less able to enter a gel bead, the quicker the path the protein takes to the bottom of the column.
  3. The largest proteins exit first and smallest proteins exit last.
132
Q

How does ion-exchange chromatography isolate proteins?

A

By net charge:

  1. Determine charge of protein of interest.
  2. Fill column with beads of opposite charge.
  3. Protein will bind to column.
  4. Release protein from column by adding NaCl (salt) so that the cation Na+ exchanges with the protein.
133
Q

What pH is used for ion-exchange chromatography?

A

the pH of the mobile phase buffer must be between (1) the pI (isoelectric point) or pKa (acid dissociation constant) of the charged molecule and (2) the pKa of the charged group on the solid support (i.e. beads)

134
Q

What is the isoelectric point (pI)?

A

The pH at which a molecule has no charge.

135
Q

How does affinity chromatography isolate proteins?

A

By tendency to interact with specific molecules or functional groups.
Example: Concanvalin A can be purified by passing a crude extract through a column containing glucose residues because it has a high affinity for glucose. Concanvalin A can then be released from column by adding a glucose solution (competition frees it from the column).

136
Q

How does High-pressure liquid chromatography isolate proteins? (2 components)

A

This technique is an enhanced version of the other column chromatography techniques.

  1. Beads are more finely divided
  2. This creates more interaction sites, increasing resolving power.
137
Q

What is electrophoresis?

A

The movement of a charged molecule in an electric field.

138
Q

How does SDS-PAGE isolate proteins? (4 components)

A
  1. Sodium dodecyl sulfate (SDS) within gel denatures proteins and swamps the protein with negative charge. Proteins have same charge-to-mass ratio because 1 SDS binds for every 2 amino acids.
  2. Sulfhydryl agent reduces disulfide bonds and linearizes proteins
  3. Electric field is applied and proteins move from cathode to the anode.
  4. Small proteins move more rapidly through gel than large proteins.
139
Q

How does isoelectric focusing isolate proteins?

A
  1. Electrophoresis occurs in a pH gradient gel

2. Proteins will migrate until they reach the pH that is their pI and then stop.

140
Q

What is two-dimensional electrophoresis?

A

A technique that combines isoelectric focusing and SDS-PAGE.

141
Q

How does 2D-Electrophoresis isolate proteins?

A
  1. Isoelectric focusing is performed to separate proteins by their pI.
  2. The gel strip of proteins with the same pI is subjected to SDS-PAGE electrophoresis, separating them by mass.
  3. This technique separates proteins by both pI and mass on a two-dimensional plot.
142
Q

What are five parameters when evaluating a purification scheme?

A
  1. Total protein
  2. Total activity
  3. Specific activity
  4. Yield
  5. Purification level
143
Q

What is total protein? (2 components)

A
  1. The quantity of protein in a fraction.

2. Determined by multiplying protein concentration and multiplying by the volume.

144
Q

What is total activity? (2 components)

A
  1. The total enzyme activity (of interest) in a fraction.

2. Determined by multiplying specific activity determined by assay by total volume.

145
Q

What is specific activity? (2 components)

A
  1. Measurement of degree of purification

2. Determined by dividing total activity by total protein (also measured in assay)

146
Q

What is yield? (2 components)

A
  1. Measure of total activity retained as a percentage of activity in crude extract.
  2. Determined by dividing total activity by total activity of crude extract and converting to percent.
147
Q

What is purification level? (2 components)

A
  1. Measure of the increase in purity

2. Determined by dividing specific activity by the specific activity of crude extract.

148
Q

How can SDS-PAGE be used to assess purification?

A

The fewer bands after electrophoresis, the more pure the extract.

149
Q

What is the value of immunological techniques for purifying and characterizing proteins?

A

Provides a way to detect proteins that have no enzymatic activity.

150
Q

What is the biochemical basis for the power of immunological purification techniques?

A

The high specificity of the antigen-antibody interaction.

151
Q

To what part of the antigen does the antibody bind?

A

A specific sequence of amino acids called the antigenic determinant or epitope.

152
Q

What are polyclonal antibodies?

A

A mixture of different antibodies that bind to the same antigen at different epitopes.

153
Q

What are monoclonal antibodies?

A

A pure antibody that binds to one epitope of an antigen.

154
Q

What are three (3) biochemical techniques involving antibodies?

A
  1. Western blot
  2. ELISA
  3. Immunoprecipitation
155
Q

What is immunoprecipitation?

A

A technique for precipitating a protein antigen out of a solution by binding its antibody.

156
Q

What are two (2) advantages of western blotting?

A
  1. Allows detection of very small quantities of protein of interest
  2. Allows determination of size of target protein
157
Q

What are the three (3) general steps of western blotting?

A
  1. SDS-PAGE separate proteins
  2. Resolved proteins transferred to a sheet and antibody is added.
  3. Second, fluorescent antibody is added that is specific for antibody that is specific for protein of interest.
158
Q

What is an advantage of ELISA?

A

The method uses an enzyme that produces a colored product in the presence of protein of interest. [The degree of color change is proportional to the amount of target protein.]

159
Q

What is amino acid composition?

A

Simply the amino acids present in protein.

160
Q

What is amino acid sequence?

A

The sequence of amino acids in protein.

161
Q

How is amino acid composition determined? (3 steps)

A
  1. Peptide is hydrolyzed into constitudent amino acids by heating in strong acid.
  2. Ion-exchange chromatography separates amino acids
  3. Treatment with fluorescamine determines concentration, as fluorescence is proportional to concentration.
162
Q

How is amino acid sequence determined?

A

Edman degradation

163
Q

Describe the technique of Edman degredation (3 steps)

A
  1. Phenyl isothiocyanate reacts with terminal amino group of the peptide, breaking it of and leaving a peptide shorted by one amino acid.
  2. The cyclic PTH-amino acid can be identified with chromatography.
  3. Repeat for all amino acids
164
Q

What are three steps in the proteomics work-flow?

A
  1. Proteolysis
  2. Liquid chromatography
  3. Mass spectroscopy
165
Q

Describe proteolysis in proteomics

A

An enzyme digests a target protein into smaller peptides.

166
Q

Describe liquid chromatography in proteomics

A

Peptides are separated by physical characteristics (e.g. hydrophobicity or charge)

167
Q

Describe mass spectroscopy in proteomics

A

Mass-to-charge ratio is measured precisely and compared to database to determine amino acid sequence of peptide.

168
Q

What are enzymes?

A

(typically) protein catalysts that can accelerate the rate of a
reaction by factors of as much as a million or more.

169
Q

What are cofactors?

A

Small molecules that some enzymes require for activity.

170
Q

What is a proteolytic enzyme?

A

An enzyme that catalyzes hydrolysis of peptide bonds.

171
Q

What are six (6) major classes of Enzymes?

A
  1. Oxidoreductases
  2. Transferases
  3. Hydrolyases
  4. Lyases
  5. Isomerases
  6. Ligases
172
Q

What is the function of oxidoreductase?

A

Catalyze oxidation-reduction reactions

173
Q

What is the function of transferases?

A

Move functional groups between molecules

174
Q

What is the function of hydrolyases?

A

Cleave bonds with the addition of water (proteases)

175
Q

What is the function of lyases?

A

Add atoms to double bonds or remove atoms to form double bonds

176
Q

What is the function of isomerases?

A

Move functional groups within a molecule

177
Q

What is the function of ligases?

A

Join two molecules at the expense of ATP

178
Q

What are two (2) main classes of cofactors?

A
  1. Coenzymes - organic molecules derived from vitamins

2. Metals

179
Q

What is a prosthetic group?

A

A tightly-bound coenzyme

180
Q

What is a holoenzyme?

A

an enzyme with its cofactor

181
Q

What is an apoenzyme?

A

an enzyme without its cofactor

182
Q

What is Free Energy (G)?

A

A measure of energy capable of doing work

183
Q

What is ΔG?

A

The free energy difference between reactants and products

184
Q

What information does ΔG provide and what information does ΔG not provide?

A
  1. Provides information about spontaneity.

2. Does not provide information about rate of reaction.

185
Q

What is ΔG º’

A

the standard free energy change at pH 7 (1 M and 298 K).

186
Q

What is an exergonic reaction?

A

A reaction in which ΔG is

187
Q

What is the ΔG at equilibrium?

A

Zero.

188
Q

What is an endergonic reaction?

A

A reaction in which ΔG is > 0.

189
Q

The difference between ΔG and ΔG º’ can be attributed to what?

A

A difference in the concentrations of the reactants and products. The reaction can be made spontaneous by changing concentrations.

190
Q

The equilibrium position is a function of what parameter?

A

The free energy difference between reactants and products.

191
Q

What is steady state in regards to kinetics?

A

The rates of forward and reverse reactions are equal.

192
Q

What is the free energy of activation?

A

The difference in free energy between transition state and substrate.

193
Q

How do enzymes increase the rate of product formation?

A

They lower the activation energy (i.e. decrease energy of transition state).

194
Q

What is an enzyme-substrate (ES) complex?

A

Interaction between enzyme and substrate at particular region of enzyme called active site.

195
Q

What are six (6) common characteristics of active sites of enzymes?

A
  1. 3D cleft/crevice/pocket
  2. Small volume
  3. Unique microenvironment
  4. Weak interactions with substrate
  5. Provides specificity through 3D structure
  6. Active site residues can be far apart in sequence
196
Q

Why is the lock and key analogy of enzymes no longer valid?

A

It is now known that the active sites of some enzyme assume a shape that is complementary only after the substrate has been bound. This is called induced fit.

197
Q

What is binding energy?

A

Free energy released by weak interactions between complementary enzyme and substrate.

198
Q

When does maximum binding energy occur?

A

The most weak interaction occurs – i.e, the maximum binding energy occurs – when the substrate is in its transition state.

199
Q

What is a first-order reaction?

A

A reaction in which the rate (velocity) is directly proportional to a single reactant concentration.

200
Q

What is the unit of a first-order rate constant?

A

S^-1

201
Q

What is a second-order reaction?

A

A reaction in which the rate (velocity) is proportional to two reactant concentrations.

202
Q

What is the unit of a second-order rate constant?

A

M^-1 S^-1

203
Q

What is a pseudo-first-order reaction?

A

A second-order reaction in which one of the reactants is in such great excess that the reaction appears to be first order with respect to the limited reactant.

204
Q

What is a zero order reaction?

A

A reaction in which the velocity is independent of reactant concentrations.

205
Q

When are zero order reactions observed?

A

Some enzyme-catalyzed reactions approximate zero order reactions under certain conditions.

206
Q

What is the Michaelis-Menten model?

A

A model that describes the kinetics of many enzymes according to this equation:

E+S ES E + P

207
Q

What are the two (2) assumptions of the Michaelis-Menten Model?

A
  1. Measure activity when [P] is about equal to 0.

2. The ES complex is a necessary intermediate.

208
Q

What is the initial velocity in the Michaelis-Menten Model

A

The number of moles of product formed per second shortly after the reaction has begun

209
Q

What is the Michaelis-Menten Equation?

A

Initial velocity = (Max Velocity*[S])/([S] + Km)

210
Q

What does the Michaelis-Menten constant, Km, represent?

A

describes the efficiency of selecting and

converting S to P

211
Q

When initial velocity is half of maximum velocity, what do we know about [S]?

A

[S] = Km

212
Q

Km varies according to what two parameters?

A

Enzyme and Substrate

213
Q

What are two (2) advantages of having Km approximately equal to the substrate concentration normally available to an enzyme?

A

At these concentrations the enzyme (1) displays significant catalysis and (2) is still sensitive to concentrations in [S] and can be manipulated.

214
Q

Describe the Lineweaker-Burke equation?

A

A linear equation resulting from manipulation of the Michaelis-menten Equation.

215
Q

What is the “y” of the Lineweaker-Burke equation?

A

1/initial velocity

216
Q

What is the slope of the Lineweaker-Burke equation?

A

Km/Vmax

217
Q

What is the “x” of the Lineweaker-Burke equation?

A

1/[S]

218
Q

What is the y-intercept of the Lineweaker-Burke equation?

A

1/Vmax

219
Q

What is the x-intercept of the Lineweaker-Burke equation?

A

-1/Km

220
Q

What information does the kcat or turnover number provide?

A

the number of substrate molecules converted to product per second when enzyme is fully saturated with substrate (tells how good the enzyme is)

221
Q

How is catalytic efficiency measured?

A

kcat/Km because

  1. kcat measures rate of catalysis
  2. Km related to nature of enzyme-substrate interaction
222
Q

Define allostery

A

a change in the shape and activity of a protein (i.e. enzyme) that results from combination with another substance at a point other than the active site

223
Q

What is a function of allosteric enzymes?

A

They control the flux of interconnecting biochemical reactions in pathways.

224
Q

What molecules limit the activity of allosteric enzymes?

A

Products of the pathway under their control.

Example: An allosteric enzyme may convert A -> B, and MM enzymes will convert B -> C -> D -> E. E may limit the activity of the allosteric enzyme.

225
Q

What is feedback inhibition?

A

When the activity of an enzyme is lessened by an increase in product of the pathway under its control.

226
Q

What is the committed step of a pathway?

A

The committed step is the step under control of the alloseric enzyme. Once the reaction takes place, the product is committed to finishing the pathway because it will be under MM enzyme control.

227
Q

What is the name of the site at which feedback inhibition occurs on an allosteric enzyme?

A

Regulatory site (NOT active site.)

228
Q

Describe the curve of the initial velocity of an allosteric enzyme with respect to [S]

A

Sigmoidal curve with a “threshold” near Km

229
Q

Describe the structure of all allosteric enzymes (2 components)

A
  1. Quaternary structures

2. Multiple active sites and regulatory sites

230
Q

What are the two states of an active site of an allosteric enzyme?

A

R (relaxed) and T (tense)

231
Q

Describe the R state of an allosteric enzyme

A

Enzymatically more active than T state and greater affinity for substrate.

232
Q

Describe the T state of an allosteric enzyme

A

Less enzymatically active but more thermodynamically favorable

233
Q

Describe the equilibrium of R and T states of an allosteric enzyme

A

T/R&raquo_space;> 1

234
Q

What is the symmetry rule in the concerted model of allosteric enzymes?

A

All active sites must be in the same state, R or T.

235
Q

What happens when a substrate binds to an active site R in a allosteric enzyme in the concerted model? (3 components)

A
  1. Other active sites are trapped in R state. [Symmetry rule]
  2. That molecule of enzyme is removed from equilibrium, allowing more conversion of T state to R state.
  3. Cooperativity: This facilitates binding of more substrate.
236
Q

What is the homotropic effect?

A

The disruption of R T equilibrium by substrate binding at active sites.

237
Q

What is the heterotropic effect?

A

The disruption of R T equilibrium by regulator molecules at regulatory sites.

238
Q

What are two (2) types of regulator molecules and what do they do?

A
  1. Inhibitors stabilize the T state

2. Activators stabilize the R state

239
Q

What is the biggest difference between concerted and sequential models of allosteric enzymes?

A

The symmetry rule is not enforced in sequential model, so subunits undergo sequential changes in structure.

240
Q

What are four (4) common catalytic strategies

A
  1. Covalent catalysis
  2. General acid-base catalysis
  3. Metal ion catalysis
  4. Catalysis by approximation and orientation
241
Q

Describe covalent catalysis

A

Active site contains a nucleophile that is covalently modified

242
Q

Describe general acid-base catalysis

A

A molecule other than water donates or accepts a proton

243
Q

Describe three (3) ways meta ions catalyze reactions

A
  1. stabilize negative charge
  2. generate a nucleophile
  3. bind substrate
  4. serve as electrophilic catalyst
244
Q

Describe catalysis by approximation and orientation

A

Enzyme brings two substrates into an orientation that facilitates catalysis

245
Q

What is the molecular basis for enzymes having an optimum temperature? (2 components)

A
  1. As temperature increases, Brownian motion increases and facilitates reaction.
  2. At a point, the thermal jostling breaks weak bonds holding 3D structure together and denatures protein.
246
Q

What is the molecular basis for enzymes having an optimum pH?

A

Enzymes depend on particular ionizations of their side chains. The optimum pH is the pH at which the majority of proteins are ionized properly.

247
Q

What is enzyme inhibition?

A

Enzyme activity is decreased by binding of small molecules and ions.

248
Q

What are two (2) types of enzyme inhibition?

A
  1. Reversible inhibition

2. Irreversible inhibition

249
Q

What are three (3) types of reversible inhibition?

A
  1. Competitive inhibition
  2. Uncompetitive inhibition
  3. Noncompetitive inhibition
250
Q

Describe competitive inhibition

A

The inhibitor binds to the active site, preventing the actual substrate from binding.

251
Q

Describe uncompetitive inhibition

A

the inhibitor binds only to the enzyme-substrate complex

252
Q

Describe noncompetitive inhibition

A

the inhibitor binds either the enzyme or the enzyme-substrate complex to reduce the overall number of enzyme molecules

253
Q

Describe the kinetic effect (change to Vmax and Km) of competitive inhibition

A
  1. Vmax is unchanged

2. Km is increased (inhibition is reversible by increasing [S])

254
Q

Describe the kinetic effect (change to Vmax and Km) of uncompetitive inhibition

A
  1. Vmax is decreased because ESI is unproductive (less product).
  2. The KM is decreased. ES is depleted (it becomes ESI); to maintain E/ES equilibrium, more S binds E resulting in lower [S] and [ES] needed to reach ½ Vmax
255
Q

Describe the kinetic effect (change to Vmax and Km) of noncompetitive inhibition

A
  1. Vmax is decreased because ESI and EI reduce enzyme (less product).
  2. KM is unchanged; E and ES are depleted proportionately. The reaction appears to be occurring at a lower enzyme concentration.
256
Q

What is chymotrypsin?

A

A proteolytic enzyme secreted by pancreas

257
Q

What are irreversible inhibitors?

A

Inhibitors that bind very tightly to enzymes (covalently or noncovalently)

258
Q

What are four (4) types of irreversible inhibitors?

A
  1. Group-specific
  2. Affinity label (substrate analog)
  3. Suicide inhibitors (mechanism based)
  4. Transition state analogs
259
Q

What is the catalytic triad of of chymotrypsin active site?

A

Ser195-His57-Asp102

260
Q

What are the two (2) steps of chymotrypsin action?

A
  1. Fast step resulting in acyl-enzyme

2. Slow step of deacylation back to native enzyme.

261
Q

What are the steps of the fast step of the chymotrypsin mechanism? [acylation]

A
  1. His deprotonates Ser forming alkoxide
  2. Alkoxide attacks carbon of C=O [transition state, negative charge on oxygen]
  3. His protonates substrate to form a stable leaving group (e.g. HCl, NH3)
262
Q

What are the steps of the slow step of the chymotrypsin mechanism? [deacylation]

A
  1. H2O binds to C=O of acyl group
  2. His deprotonates water and electorns between Ser and Acyl group collapse onto oxygen
  3. carboxylic acid product released
263
Q

What is the function of Asp102 in the catalytic triad of chymotrypsin?

A

Orients His57 to make it a better proton acceptor

264
Q

Describe the intermediate of the chymotrypsin mechanism

A

Tetrahedral intermediate with a negative charge on carbonyl oxygen atom.

265
Q

How is the intermediate of the chymotrypsin mechanism stabilized?

A

A site termed the oxyanion hole that stabilizes intermediate with NH groups.

266
Q

What site accounts for the specificity of chymotrypsin?

A

the S1 pocket

267
Q

What type of enzyme is Hemoglobin?

A

Allosteric enzyme

268
Q

Describe the heme group

A

A prosthetic group consisting of protoporphyrin (four linked pyrrhole rings and a central iron ion in the Fe2+ state)

269
Q

What is the proximal histidine?

A

The histidine residue in myoglobin to which the iron ion is coordinated

270
Q

Describe the structure of hemoglobin

A

Quaternary structure consisting of two alpha chains and two beta chains (alpha-beta dimers)

271
Q

How does the oxygen-binding curve indicate oxygen is binding cooperatively?

A

It is sigmoid shaped

272
Q

Describe the structural differences of the T (deoxyhemoglobin) and R (oxyhemoglobin) state of hemoglobin

A
  1. The position of the iron atom shifts upwards.

2. The two alpha-beta dimers rotate by approximately 15 degrees in the transition from the T to the R state.

273
Q

What are three (3) allosteric regulators of hemoglobin?

A

H+, CO2 and 2,3-BPG

274
Q

What affinity difference allows oxygen transfer from maternal to fetal blood?

A

Fetal hemoglobin binds oxygen more tightly than adult hemoglobin due to weaker 2,3-BPG binding.

275
Q

How does 2,3-BPG regulate oxygen affinity of hemoglobin?

A

2,3-BPG binds tightly to the T state but not the R state, stabilizing T state and lowering oxygen affinity.

276
Q

What is the Bohr effect?

A

Oxygen-binding properties of hemoglobin are markedly affected by pH (H+) and carbon dioxide.

277
Q

How does increasing [H+] affect oxygen affinity of hemoglobin?

A

Decrease oxygen affinity of hemoglobin due to protonation of amino termini and certain histidine residues which stabilize T state.

278
Q

How does increasing [CO2] affect oxygen affinity of hemoglobin? (2 mechanism)

A
  1. CO2 -> H2CO3 -> H+ + HCO3- (increases [H+] decreases affinity)
  2. CO2 adds to amino termini of hemoglobin to form carbamates (negative charged groups). These stabilize deoxyhemoglobin.
279
Q

How does the Bohr effect help release oxygen into tissues?

A

[H+] and [CO2] is greatest in rapidly metabolizing tissues (which require the most oxygen). Hemoglobin in this environment will release oxygen due to decreases oxygen affinity.

280
Q

Is the binding of Myoglobin cooperative?

A

No!!

281
Q

What are two types of stereoisomers?

A
  1. Enantiomers (one asymmetric carbon)

2. Diastereomers (more than one asymmetric carbon)

282
Q

What are two (2) types of diastereomers and describe them

A
  1. Epimers (differ in configuration at 1 asymmetric center)

2. Anomers (differ in configuration at asymmetric center produced by ring closure)

283
Q

What is the chemical basis for carbohydrate ring formation? (2 situations)

A
  1. Aldehyde + Alcohol Hemiacetal

2. Ketone + Alcohol Hemiketal

284
Q

Explain the alpha-beta designation of the anomeric carbon for pyranoses

A
  1. Alpha means anomeric carbon hydroxyl group points oppositely from flag
  2. beta means anomeric carbon hydroxyl group points same direction as flag
285
Q

Explain the alpha-beta designation of the anomeric carbon for furanoses

A
  1. Alpha means anomeric carbon hydroxyl group points opposite from flag on carbon on other side of -O-
  2. Beta means anomeric carbon hydroxyl group points same as flag on carbon on other side of -O-
286
Q

What is a reducing sugar?

A

A sugar that can be oxidized… contains an aldehyde in its open-chain form.

287
Q

Explain the forms of fructose

A
  1. Fructose exists as a furanose in fructose derivatives

2. Fructose exists as a pyranose when fructose is free in solution

288
Q

What is an O-glycosidic bond?

A

A bond between an anomeric carbon and an alcohol.

289
Q

What is an N-glycosidic bond?

A

A bond between an anomeric carbon and an amine.

290
Q

How do carbohydrates interact with phosphates?

A

Carbohydrates form ester linkages to phosphates (phosphoesters)

291
Q

What are four (4) common modifications of monosaccharides?

A
  1. Addition of methyl group
  2. Addition of N-acetyl group
  3. Addition of N-acetyl group AND glycerol group
  4. Addition of Phosphate
292
Q

What is the function of glycosyltransferases?

A

Catalyze formation of glycosidic bonds

293
Q

What is the function of Uridine Diphosphate (UDP)?

A

Activate monosaccharides for catalysis by glycosyltransferases

294
Q

What are three (3) common disaccharides?

A
  1. Sucrose
  2. Maltose
  3. Lactose
295
Q

What is a homopolymer?

A

A polymer in which all monomers are the same

296
Q

What is the storage form of glucose in animal cells? in plants?

A
  1. Glycogen

2. Starch

297
Q

Describe the branching (the glycosidic bonds) in glycogen (3 components)

A
  1. Mostly alpha-1,4-glycosidic bonds
  2. every 10 glucose units is an alpha-1,6-glycosidic bond
  3. form hollow cylinders suited for storage
298
Q

Describe the branching (the glycosidic bodns) in cellulose (2 components)

A
  1. Homopolymer of glucose with Beta-1,4-glycosidic bonds

2. yields straight chain capable of interacting with other molecules and forming fibrils

299
Q

What are three (3) main classes of glycoproteins?

A
  1. Glycoproteins
  2. Proteoglycans
  3. Mucins/mucoproteins
300
Q

Describe glycoproteins

A

Protein and carbohydrate. Protein is the largest component by weight

301
Q

Describe proteoglycans

A

Protein and carbohydrate. Carbohydrate is the largest component by weight.

302
Q

Describe mucins/mucoproteins

A

A proteoglycan in which the protein is attached to the carbohydrate by N-acetylgalactosamine

303
Q

How many carbohydrates be linked to proteins in glycoproteins? (2 ways)

A
  1. Attached to nitrogen atom in the side chain of Asparagine (N-linkage)
  2. Attached to oxygen atom in the side chain of Serine or Threonine (O-linkage)
304
Q

Define a lipid

A

Water-insoluble molecule that are soluble in organic solvents

305
Q

Describe the structure of a fatty acid

A

Hydrocarbon chains of various lengths and degrees of unsaturation that terminate with carboxylic acid group

306
Q

Describe Triacylglycerols (2 components)

A
  1. Storage form of fatty acids

2. Composed of three fatty acids esterified to a glycerol backbone.

307
Q

What are three (3) common types of membrane lipids?

A
  1. Phospholipids
  2. Glycolipids
  3. Cholesterol
308
Q

Describe the structure of Phospholipids

A

Glycerol backbone, two fatty acid chains and a phosphorylated alcohol

309
Q

Describe the structure of glycolipids

A

Sugar-containing lipids derived from sphingosine. Carbohydrate is on the extracellular surface

310
Q

Describe the structure of cholesterol

A

Constructed from steroid nucleus

311
Q

What is a common featured to all membrane lipids?

A

Amphipathic molecules containing both hydrophobic and hydrophilic ends.

Biochemistry (7 decks)

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