Foundations Block I - Lecture 1

Front 1

Diels-Alder Reaction

Back 1

Front 2

Amino Acids make up ____% of the human body (excluding water)

Back 2

75

Front 3

Amino Acid Functions

Back 3

-95% of hormones

-100% of proteins

-Energy generation

-Neurotransmitters

-Nitric Oxide (NO) production

-MSG - Monosodium glutamate

-Nutritional Supplements

-Drugs

Front 4

Sickle Cell Anemia: approximately ____ US births/yr

Back 4

2000

Front 5

Sickle Cell Anemia: approximately ____ US citizens have it

Back 5

2 million

Front 6

Sickle Cell Anemia: mutation of _____ to _____ in the ______ _______.

Back 6

Glutamate, Valine, Hemoglobin, Beta-chain

Front 7

Glutamate is _______ while Valine is _________.

Back 7

hydrophilic, hydrophobic

Front 8

Amino acid structure

Back 8

Front 9

The chiral carbon in an amino acid is the _______

Back 9

alpha-carbon

Front 10

Only _____ amino acids are found in proteins.

Back 10

L-configuration

Front 11

Atomic priority (chirality)

Back 11

I > Br > Cl > S > O > N > C > H

Front 12

Amphoteric

Back 12

Contains acidic and basic groups

Front 13

At pH __ amino acids form a _____ ion

Back 13

7, dipolar (zwitterion)

Front 14

The acidic group of an amino acid

Back 14

COO-

Front 15

The basic group of an amino acid

Back 15

NH3+

Front 16

At a low pH, both amino acid groups are ________

Back 16

protonated

Front 17

At a high pH, both amino acid groups are ______

Back 17

deprotonated

Front 18

At a low pH, the amino acid has a net _____ charge

Back 18

positive

Front 19

At a high pH, the amino acid has a net ______ charge

Back 19

negative

Front 20

the L and D configurations are called

Back 20

stereoisomers

Front 21

Properties of Amino Acids

Back 21

-Size

-Charge

-Hydrophilicity

-Hydrophobicity

-Hydrogen-bonding capacity

-Side-chain reactivity

Front 22

The pKa of the carboxyl group of amino acids

Back 22

2.2

Front 23

The pKa of the amino group of amino acids

Back 23

9.4

Front 24

Families of Amino Acids

Back 24

-acidic

-basic

-uncharged polar

-nonpolar

Front 25

Glycine

Back 25

(Gly, G)

Nonpolar

Front 26

Alanine

Back 26

(Ala, A)

Nonpolar

Front 27

AA with simple nonpolar side chains:

Back 27

Glycine, Alanine

Front 28

AA with complex nonpolar side chains:

Back 28

Valine, Leucine, Isoleucine, Methionine

Front 29

AA with cyclic side chain

Back 29

Proline

Front 30

AA with nonpolar side chains:

Back 30

Glycine, Alanine, Valine, Leucine, Isoleucine, Methionine, Phenylalanine, Tryptophan, Cysteine

Front 31

Valine

Back 31

(Val, V)

Nonpolar

Front 32

Leucine

Back 32

(Leu, L)

Nonpolar

Front 33

Isoleucine

Back 33

(Ile, I)

Nonpolar

Front 34

Methionine

Back 34

(Met, M)

Nonpolar

Front 35

Proline

Back 35

(Pro, P)

Nonpolar

Front 36

AA with aromatic nonpolar side chains:

Back 36

Phenylalanine, Tyrosine, Tryptophan

Front 37

Phenylalanine

Back 37

(Phe, F)

Nonpolar

Front 38

Tyrosine

Back 38

(Tyr, Y)

Nonpolar

Front 39

Tryptophan

Back 39

(Trp, W)

Polar

Front 40

AA with uncharged polar side chains

Back 40

Serine, Threonine, Asparagine, Glutamate, Tyrosine

Front 41

Serine

Back 41

(Ser, S)

Uncharged Polar

Front 42

Threonine

Back 42

(Thr, T)

Uncharged Polar

Front 43

Cysteine

Back 43

(Cys, C)

Nonpolar

Front 44

AA with positive polar side chains

Back 44

Lysine, Arginine, Histidine

Front 45

Ionization of histidine

Back 45

Front 46

Lysine

Back 46

NH3 with + charge

(Lys, K)

Positive Polar

Front 47

Arginine

Back 47

Partial double bond between double bond to N's with positive charge on carbon

(Arg, R)

Positive Polar

Front 48

Histidine

Back 48

(His, H)

Positive Polar

Front 49

AA with Polar negative side chains:

Back 49

Aspartate (Aspartic Acid), Glutamate (Glutamic Acid)

Front 50

Acidic Amino Acids:

Back 50

Aspartate (Aspartic Acid), Glutamate (Glutamic Acid)

Front 51

Asparagine

Back 51

(Asn, N)

Uncharged Polar

Front 52

Glutamine

Back 52

(Gln, Q)

Uncharged Polar

Front 53

Aspartate (Aspartic Acid)

Back 53

Partial double bond between O's (no H) with negative charge

(Asp, D)

Negative Polar

Front 54

Glutamate (Glutamic Acid)

Back 54

Partial double bond between O's (no H) with negative charge

(Glu, E)

Negative Polar

Front 55

AA with 2 Carbons

Back 55

Glycine

Front 56

AA with 3 Carbons

Back 56

Alanine, Serine, Cysteine

Front 57

AA with 4 Carbons

Back 57

Threonine, Aspartate, Asparagine

Front 58

AA with 5 Carbons

Back 58

Valine, Methionine, Proline, Glutamate, Glutamine

Front 59

AA with 6 Carbons

Back 59

Leucine, Isoleucine, Lysine, Arginine, Histidine

Front 60

AA with Sulfur in side chain

Back 60

Methionine, Cysteine

Front 61

AA with 9 carbons

Back 61

Phenylalanine, Tyrosine

Front 62

AA with 11 carbons

Back 62

Tryptophan

Front 63

AA with oxygen in side chain

Back 63

Tyrosine, Serine, Threonine, Aspartate, Glutamate, Asparagine, Glutamine

Front 64

AA with nitrogen in side chain

Back 64

Tryptophan, Lysine, Arginine, Histidine, Asparagine, Glutamine

Front 65

Asparagine or Aspartic Acid

Back 65

Asx, B

Front 66

Glutamine or Glutamic Acid

Back 66

Glx, Z

Front 67

pH =

Back 67

-log10[H+]

Front 68

pKa =

Back 68

-logKa=log(1/Ka)

Front 69

pKa of a _____ acid is the pH at which _____

Back 69

weak, it is half dissociated

Front 70

Ka =

Back 70

([A-][H3O+])/([HA][H2O])

Front 71

Buffers are:

Back 71

An acid base conjugate pair

Front 72

Buffer Function

Back 72

resist changes in pH

Front 73

Maximal buffering capacity occurs at ______

Back 73

pH = to pKa

Front 74

at ___ pH unit above or below ____ the buffering capacity is ____

Back 74

1, pKa, 10%

Front 75

major extracellular buffer system

Back 75

HCO3-/CO2

Front 76

major intracellular buffer system

Back 76

H2PO4-/HPO42-

Front 77

intracellular buffering system pKa

Back 77

6.86

Front 78

Henderson-Hasselbach Equation

Back 78

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

Front 79

Titration curve

Back 79

Front 80

Amino Acids with 3 pKa

Back 80

Aspartic Acid, Glutamic Acid, Lysine, Arginine, Histidine

Front 81

Amino Acids with pKa2 above 10

Back 81

Proline

Front 82

Amino Acids with pKa3 above 10

Back 82

Lysine, Arginine

Front 83

Amino Acids with pI (isoelectric point) below 4

Back 83

Aspartic Acid, Glutamic Acid

Front 84

Amino Acids with pI (isoelectric point) above 7

Back 84

Histidine, Lysine, Arginine

Front 85

pKa1 refers to

Back 85

alpha-carboxyl group

Front 86

pKa2 refers to

Back 86

alpha-NH3+ ion

Front 87

pKa3 refers to

Back 87

side chain group

Front 88

Terminal alpha-carboxyl group pKa

Back 88

3.1

Front 89

Terminal alpha-amino group pKa

Back 89

8.0

Front 90

Typical pKa1 values for AA

Back 90

1.8-2.8

Front 91

Typical pKa2 values for AA

Back 91

8.0-9.7

Front 92

Typical pI values for AA

Back 92

5.0-6.5

Front 93

Titration curve for Glycine

Back 93

Front 94

Isoelectric point (pI)

Back 94

pH which gives zero charge

Front 95

pI =

Back 95

(pK1+pK2)/2

Front 96

What is the pI of glutamic acid?

Back 96

pI = (pK1+pKR)/2

Front 97

pKa can _____ in a protein due to the ______

Back 97

vary greatly, environment

Front 98

Elution profile to determine amino acid composition (increasing pH)

Back 98

D T S E P G A C V M I L Y F K H NH3 R

Front 99

______ react with _____ to give a colorized product

Back 99

amines, ninhydrin

Front 100

ninhydrin can be used _______ or ________

Back 100

qualitatively, quantitatively

Front 101

alpha-amino acids typically give a ______ product (reaction with ninhydrin)

Back 101

blue-purple

Front 102

_____ gives a ________ product (reaction with ninhydrin

Back 102

proline, yellow-orange

Front 103

ninhydrin can be used for visualization of _____

Back 103

fingerprints

Front 104

ninhydrin reaction with amino acids

Back 104

Front 105

These amino acids absorb strongly near ______

Back 105

280 nm, (Tryptophan, Tyrosine)

Front 106

Amino Acids can be detected and sequences using the ________

Back 106

Edman degradation

Front 107

Labeling compound used in Edman Degradation

Back 107

Phenyl isothiocyanate

Front 108

Edman degradation

Back 108

Front 109

Edman Degradation: After labeling and release, ________ can be rapidly separated by ________

Back 109

PTH-amino acids, high-pressure liquid chromatography (HPLC)

Front 110

The linking of 2 amino acids is called a:

Back 110

peptide bond

Front 111

Peptide bond formation

Back 111

Front 112

Peptides have a _______ terminus and a ______ terminus

Back 112

carboxyl, amino

Front 113

Polypeptide chain

Back 113

Front 114

2 _____ residues can form a ________ bond

Back 114

cysteine, disulfide

Front 115

The formation of a disulfide bond is a _______ reaction

Back 115

oxidation

Front 116

Removal of a disulfide bond is a _______ reaction

Back 116

reduction

Front 117

Oxidation is the _____ of electrons

Back 117

loss

Front 118

Reduction is the _____ of electrons

Back 118

gain

Front 119

Disulfide bonds can link together two ______ or two _______

Back 119

amino acids in one peptide, peptides

Front 120

Selenocysteine

Back 120

(Sec, U)

Codon UGA

Front 121

Selenocysteine is present in _______ enzymes

Back 121

eukaryotic

Front 122

There are ______ selenoproteins in the human genome

Back 122

25

Front 123

Selenium (Se) is a ______ in animals and humans

Back 123

vital nutrient

Front 124

Health effects of Selenium deficiency

Back 124

hypothyroidism, myocardial necrosis, cartilage degeneration

Front 125

Selenium is found in ______ (food)

Back 125

broccoli

Front 126

Pyrrolysine

Back 126

(Pyl, O)

Codon UAG

Front 127

Pyrrolysine is found in proteins of _________ __________

Back 127

methanogenic archaebacteria

Front 128

Non-protein Amino Acids

Back 128

5-Hydroxylysine, 4-Hydroxyproline, Ornithine, Penicillamine, Thyroxyine, GABA (gamma-aminobutyric acid), gamma-carboxyglutamic acid

Front 129

Non-protein amino acids in collagen

Back 129

5-Hydroxylysine, 4-Hydroxyproline

Front 130

Non-protein amino acid that plays a role in urea cycle

Back 130

ornithine

Front 131

non-protein amino acid used as a form of immunosuppression to treat arthritis

Back 131

penicillamine

Front 132

non-protein amino acid that is a major hormone secreted by thyroid

Back 132

thyroxyine

Front 133

non-protein amino acid that is a neurotransmittter

Back 133

GABA (gamma-aminobutyric acid)

Front 134

non-protein amino acid that is found in blood clotting factors

Back 134

gamma-carboxyglutamic acid

Front 135

Formation of a peptide bond is a _____ reaction

Back 135

condensation