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All of the amino acids, except cysteine has a _____ configuration. Cysteine has a ____ configuration.

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1

All of the amino acids, except cysteine has a _____ configuration. Cysteine has a ____ configuration.

L; R

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2

Non-polar amino acids are found in the interior or exterior of proteins?

Interior

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3

Polar molecules amino acids are found in the interior or exterior of proteins?

Exterior

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4

Acidic residues have an additional _______ charge beyond the C terminus

negative

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5

Basic residues have an additional _______ charge beyond the N terminus

positive

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6

At low pH, amino acids are more ___________ with a net ______ charge

protonated; positive

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7

At high pH, amino acids are more __________ with a net ______ charge

deprotonated; negative

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8

At 7.4 pH, amino acids exist in dipolar, _________, form. Why?

zwitterionic, b/c the N terminus is protonated (NH3+) and the C terminus is deprotonated (COO-)

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9

List the non-polar amino acids:

Glycine, Leucine, Alanine, Methionine, Valine, Isoleucine, Proline, Tryptophan, Phenylalanine (GLAM VIP WF)

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10

List the uncharged, polar amino acids:

Glutamine "Queen Glutamine", Threonine, Serine, Tyrosine ("Y, Try, Tyrosine"), Asparagine ("Asparagus iN my diet"), Cysteine (QT SYNC)

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11

Which of the polar amino acids have an -OH in the side chain?

Tyrosine, Threonine, and Serine (YTS)

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12

List the acidic and basic amino acids:

Glutamate, Aspartate (ED) (Every Dog)

Histidine, Arginine, Lysine (HRK) (Hates Red Kool-Aid)

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13

What does it mean when pH=pka

Half are protonated and half are deprotonated

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14

If the pka of the carbonyl group is 3.1 , what happens when the pH is above and below the pka?

Above pka = conjugate base will predominate (COO-)

Below pka = acid will predominate (COOH)

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15

If the pka of the amino group is 8, what happens when the pH is above and below the pka?

Above the pka = conjugate base will predominate (NH2)

Below the pka = acid will predominate (NH3+)

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16

How are amino acids linked together?

Peptide bonds

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17

The forward reaction of peptide bond formation is a _______________ reaction

dehydration

<p>dehydration</p>
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18

Peptide bonds are thermodynamically ______________

favorable

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19

How does the forward reaction occur in peptide bond formation?

Use of ATP

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20

Peptide bonds are kinetically _____________

unfavorable

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21

What is acid hydrolysis?

Splitting a peptide bond with heat; nonspecific

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22

Proteolysis

specific cleavage certain bonds-- can choose which peptide bond to cleave

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23

Why is the trans configuration favored in peptide bonds?

- More stable (less steric hindrance than cis configuration, no electrostatic repulsion)

- Lower in energy

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24

Secondary structure

Primary structure folds and forms either alpha helix or beta sheets

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25

Where is the backbone located on the alpha helix?

Inner portion

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26

Where is the side chain (R group) located on the alpha helix?

Outer portion

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27

What type of bond/interactions occur between amino acid backbones in secondary structures?

Hydrogen bonding (N-H and C=O)/Non-covalent interactions

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28

How frequently does hydrogen bonding in the alpha helix occur?

Every 4 units

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29

Which two amino acids disrupt the alpha helix?

Proline and glycine

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30

Why is the right-hand alpha helix preferred?

Less steric hindrance between side chains

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31

Which type of beta sheets are most common?

Antiparallel beta sheet

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32

Antiparallel beta sheets consist of:

2 linear polymers in opposite direction

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33

Parallel beta sheets consist of:

2 linear polymers in same direction

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34
<p>What are beta turns?</p>

What are beta turns?

180 degree turns by 4 amino acids and stabilized by a hydrogen bond of the C=O and N-H

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35

What two amino acids are common in beta turns?

Proline and glycine

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36

What types of bonds are in the tertiary structure?

- Ionic bonding

- Hydrogen bond

- Disulfide bonds

- Dispersion forces

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37

Which type of bond is the only covalent bond in the tertiary structure?

Disulfide bond

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38

What type (covalent/noncovalent) of bonds are in the quaternary structure?

non-covalent

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39

Isoelectric point (pI) equation for neutral amino acid:

pI = (pka NH + pka COOH)/2

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40

pI equation for acidic amino acid:

pI = (pka R group + pka COOH)/2

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41

pI equation for basic amino acid:

pI = (pka R group + pka NH)/2

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42

Cofactors are…

Nonprotein enzyme helpers

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43

Do cofactors bind to the enzyme?

No

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44
<p>Apoenzyme is the…</p>

Apoenzyme is the…

Inactive portion of the protein

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45
<p>Apoenzyme + cofactor =</p>

Apoenzyme + cofactor =

holoenzyme

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46

Coenzymes:

Small organic compounds that loosely/strongly bind to the active site of the enzyme

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47

What is the difference between cofactors and coenzymes?

  • Cofactors are inorganic compounds, and coenzymes are organic

  • Cofactors do not bind to the enzyme, and coenzymes do bind loosely to the enzyme

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48

What are tightly bound coenzymes called?

Prosthetic groups

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49

How do active sites establish microenvironments?

Create non-polar environments where bonds can break/form more easily

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50

How do substrates bind reversibly through active sites?

Non-covalent interactions: hydrogen bonding, electrostatic interactions, and hydrophobic interactions

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51

What are allosteric sites?

non-catalytic regions of the enzyme that bind regulators

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52

Lock and Key model

Substrates fit precisely into active sites

*No alteration to tertiary or quaternary structure needed

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53

Induced fit model

Substrate induces change on enzyme shape--requires energy; therefore, endergonic

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54

Products form __________ when there is a high enzyme concentration.

Quickly

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55

The addition of more substrate _______ the rate of reaction

Increases

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56

If substrates outnumber enzymes, then the reaction reaches ____________

Saturation

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57

If the reaction reaches saturation, then the enzyme is working at ________________

maximum velocity; vmax

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58

How do you increase the vmax?

Increase the enzyme concentration

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59

When the reaction rate is equal to half of vmax:

Km = [S]

<p>Km = [S]</p>
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60

What does Km represent?

  • Michaelis constant

  • Measures the affinity an enzyme has for a substrate

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61

Increase Km means . . .

Enzyme has low affinity for substrate

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62

Decrease Km means . . .

Enzyme has high affinity for substrate

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63

Where does the inhibitor bind to in the enzyme in competitive inhibition?

Active site

<p>Active site</p>
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64

How does competitive inhibition affect Km?

Increases Km

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65

Does competitive inhibition affect Vmax?

No

<p>No</p>
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66

Where does the inhibitor bind to in the enzyme in noncompetitive inhibition?

Allosteric site

<p>Allosteric site</p>
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67

How does noncompetitive inhibition affect Km?

No change

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68

Does noncompetitive inhibition affect Vmax?

Decreases

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69

Where does the inhibitor bind to in the enzyme in uncompetitive inhibition?

Allosteric site

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70

How does uncompetitive inhibition affect Km?

Decreases

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71

Does noncompetitive inhibition affect Vmax?

Decreases

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72

Competitive inhibitors bind only to ____________

free enzymes [E]

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73

Uncompetitive inhibitors bind only to _____________

enzyme-substrate complex [ES]

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74

Noncompetitive inhibitors have equal binding affinity for

free enzymes [E] and enzyme-substrate complex [ES]

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75

Mixed inhibitors bind to ______________

both, free enzymes [E] and enzyme-substrate complex [ES]

*can have a higher affinity for one over the other

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76

A mixed inhibitor is more competitive when…

Ki [E] < Ki [ES]

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77

A mixed inhibitor is more uncompetitive when…

Ki [E] > Ki [ES]

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78

What does Ki mean?

Similar to Kd, Ki is binding affinity for inhibitors.

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79

Low Ki means…

Strong affinity

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80

High Ki means…

Weak affinity

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81

How is Km affected when a mixed inhibitor is more competitive?

Increased

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82

How is Km affected when a mixed inhibitor is more uncompetitive?

Decreased

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83

How is Vmax affected when a mixed inhibitor is competitive?

Decreased

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84

How is Vmax affected when a mixed inhibitor is uncompetitive?

Decreased

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85

Cell adhesion molecules (CAM)

Allow cells to bind to other cells or surfaces

Cadherins

Integrins

Selectins

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86

Cadherins

calcium-dependent glycoproteins that hold similar cells together

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87

Integrins

Two membrane-spanning chains and permit cells to adhere to proteins in the extracellular matrix.

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88

Selectins

Allow cells to adhere to carbohydrates on the surfaces of other cells

Commonly used in the immune system

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89

Voltage-gated channels

open and close in response to changes in membrane potential

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90

Ligand-gated channels

Respond to neurotransmitters or hormones

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91

Ligand-binding domain

Stimulated by ligand and induces a conformational change that activates the catalytic domain

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92

Activation of the catalytic domain can trigger a second messenger, which relays what?

a signal from the cell surface to the intracellular target

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93

What are G protein-coupled receptors?

Cell surface receptors that transmit extracellular signals into intracellular responses

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94

What do G-protein-coupled receptors do?

Modulates intracellular signaling pathways and influence physiological processes

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95

Where do negative charged molecules migrate to in electrophoresis?

Anode

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96

Where do positive charged molecules migrate to in electrophoresis?

Cathode

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97

If a molecule is small in size, how fast will it migrate in electrophoresis?

Fast

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98

If a molecule is large in size, how fast will it migrate in electrophoresis?

Slow

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99

What does native PAGE analyze?

  • Proteins are in native state

  • Compare molecular size or charge of proteins

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100

What are the limitations of native PAGE?

Many proteins experience same migration

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