Busm Biochemistry And Cell Biology Midterm

Front 1

Alanine

Back 1

What is the name of this amino acid?

Front 2

Arginine

Back 2

What is the name of this amino acid?

Front 3

Asparagine

Back 3

What is the name of this amino acid?

Front 4

Aspartate (Aspartic acid)

Back 4

What is the name of this amino acid?

Front 5

Cysteine

Back 5

What is the name of this amino acid?

Front 6

Glutamate (Glutamic acid)

Back 6

What is the name of this amino acid?

Front 7

Glutamine

Back 7

What is the name of this amino acid?

Front 8

Glycine

Back 8

What is the name of this amino acid?

Front 9

Histidine

Back 9

What is the name of this amino acid?

Front 10

Isoleucine

Back 10

What is the name of this amino acid?

Front 11

Leucine

Back 11

What is the name of this amino acid?

Front 12

Lysine

Back 12

What is the name of this amino acid?

Front 13

Methionine

Back 13

What is the name of this amino acid?

Front 14

Phenylalanine

Back 14

What is the name of this amino acid?

Front 15

Proline

Back 15

What is the name of this amino acid?

Front 16

Serine

Back 16

What is the name of this amino acid?

Front 17

Threonine

Back 17

What is the name of this amino acid?

Front 18

Tryptophan

Back 18

What is the name of this amino acid?

Front 19

Tyrosine

Back 19

What is the name of this amino acid?

Front 20

Valine

Back 20

What is the name of this amino acid?

Front 21

Glycine

Back 21

*Nonpolar/Aliphatic*
Gly
G

Front 22

Alanine

Back 22

*Nonpolar/Aliphatic*
Ala
A

Front 23

Proline

Back 23

*Nonpolar/Aliphatic*
Pro
P

Front 24

Valine

Back 24

*Nonpolar/Aliphatic*
Branched Chain
Val
V

Front 25

Leucine

Back 25

*Nonpolar/Aliphatic*
Branched Chain
Leu
L

Front 26

Isoleucine

Back 26

*Nonpolar/Aliphatic*
Branched Chain
Ile
I

Front 27

Phenylalanine

Back 27

*Aromatic*
Nonpolar
Phe
F

Front 28

Tyrosine

Back 28

*Aromatic*
More polar
Tyr
Y

Front 29

Tryptophan

Back 29

*Aromatic*
More polar
Trp
W

Front 30

Asparagine

Back 30

*Polar, Uncharged*
Asn
N

Front 31

Glutamine

Back 31

*Polar, Uncharged*
Gln
Q

Front 32

Serine

Back 32

*Polar, Uncharged*
Ser
S

Front 33

Threonine

Back 33

*Polar, Uncharged*
Thr
T

Front 34

Methionine

Back 34

*Sulfur Containing*
Met
M

Front 35

Cysteine

Back 35

*Sulfur Containing*
Cys
C

Front 36

Aspartate

Back 36

*Charged*
Negative (Acidic)
Asp
D

Front 37

Glutamate

Back 37

*Charged*
Negative (Acidic)
Glu
E

Front 38

Arginine

Back 38

*Charged*
Positive (Basic)
Arg
R

Front 39

Lysine

Back 39

*Charged*
Positive (Basic)
Lys
K

Front 40

Histidine

Back 40

*Charged*
Positive (Basic)
His
H

Front 41

phosphorylation targets?

Back 41

ser
thr

Front 42

Met is nearly always associated with ____________ of proteins

Back 42

hydrophobic cores

Front 43

What amino acids account for strong absorption at 280nm?

Back 43

aromatics:
phe
tyr
trp

Front 44

henderson hasselbalch equation?

Back 44

pH = pKa + log (base/acid)

Front 45

Approximate pKa for N-terminal? C-terminal group?

Back 45

N-terminal = ~7.6-10.6

COOH = ~3.0-5.5

Front 46

Approximate pKa for R group of:

arg

Back 46

12.5

Front 47

Approximate pKa for R group of:

cys

Back 47

8.5

Front 48

Approximate pKa for R group of:
His

Back 48

6

Front 49

Approximate pKa for R group of:

tyr

Back 49

10

Front 50

Approximate pKa for R group of:

asp

Back 50

3.8

Front 51

Approximate pKa for R group of:

glu

Back 51

4.2

Front 52

Approximate pKa for R group of:

lys

Back 52

10

Front 53

alpha helix

phi =?

psi=?

Back 53

phi = -57.8

psi = -47

Front 54

average alpha helix length (# of res)?

Back 54

10 residues

Front 55

alpha helix

residues per turn (crystallographic repeat)?

Back 55

c = 18 residues (5 x 3.6)

5 turns per repeat

Front 56

alpha helix residues per turn?

pitch?

rise?

Back 56

3.6 residues per turn

pitch = 0.54nm

rise = 0.15nm/residue

Front 57

The hydrogen bonding takes place between the carbonyl group of residue I and the hydrogen from the amide group ____ residues ahead

Back 57

The hydrogen bonding takes place between the carbonyl group of residue I and the hydrogen from the amide group four residues ahead (i+4)

Front 58

The most stretch helix will have the highest ____ and the lowest ________

Back 58

The most stretch helix will have the highest rise and the lowest number of residues per turn

Front 59

B-sheets are composed of __ or more different
stretches of at least ___to___ amino acids.

Back 59

B-sheets are composed of 2 or more different
stretches of at least 5-10 amino acids.

Front 60

residues per "turn" in a B-sheet?

phi =?

psi = ?

Back 60

n = 2 residues per turn

phi = -120

psi = +120

Front 61

distance between residues in B sheet for

anti-parallel?

parallel?

Back 61

antiparallel = 3.2A

parallel = 3.4A

Front 62

average length of a B-sheet?

Back 62

6 residues

Front 63

Turns are located primarily _______ and contain ________ residues

Back 63

Turns are located primarily on the protein surface and contain polar and charged residues

Front 64

Loops are located primarily _______ and contain ________ residues

Back 64

Loops are located primarily on the protein surface and contain polar and charged residues

Front 65

primary role of alpha-1-antitrypsin? why?

Back 65

inhibit neutrophil elastase so it doesn't break down elastic fibers of the lungs

Front 66

S mutation of alpha-1-antitrypsin

Back 66

Glu264 to Val

Front 67

Z mutation of alpha-1-antitrypsin

Back 67

Glu 342 to Lys

Front 68

hallmark of Z alpha-1-antitrypsin liver disease?

Back 68

acid-Schiff-positive inclusion bodies

Front 69

inactivation of neutrophil elstase occurs when

Back 69

inactivation of neutrophil elstase occurs when it moves from upper to lower pole of A-1-antitryp

Front 70

what major conformational change occurs in prion disease

Back 70

alpha helixes are converted to beta sheets

Front 71

fractional saturation of mgb equation?

Back 71

Front 72

Helix of the histidine that ligates heme( the 5th coordination site)?
residue # in mgb, b-chain, a-chain?

Back 72

Helix F8

mgb = residue 93
hgb b-chain = residue 92
hgb a-chain = 87

Front 73

6th coordination site in the deoxy state? helix and residue numbers?

Back 73

helix E7

mgb = residue 64
hgb b-chain = residue 63
hgb a-chain = residue 58

Front 74

fractional saturation of HGB

Back 74

Front 75

Hill equation of HGB

Back 75

Front 76

The _____ subunits of hgb may or may not be identical while the ____ subunits are identical

Back 76

alpha = maybe identical

beta = identical

Front 77

R state = ?

T state = ?

Back 77

R state = relaxed = oxy

T state = taut = deoxy

Front 78

What residue facilitates the rotation of the alpha/beta dimer when o2 binds?

Back 78

His F8

Front 79

Deoxy/T-state stabalizing interactions?

Back 79

-C-terminius of Beta HIS lies on top of helix C in alpha and interacts with Asp 94 of the same β2 by charge-charge interaction and with Lys 40 of the α1 through charge-charge interactions
-N-terminal (NH3 grp) residue of α1 interacts with the guanidinium group of carboxyl terminal residue (Arg) of α2 via charge-charge + Cl-
-guanidinium group of the C- terminal residue Arg141 of the α1 interacts with Asp126 of α2
-Tyr 140 of α1 hydrogen bonds to the carbonyl group of Val 93 in the same
subunit. Similarly, Tyr145 in the β subunit forms a hydrogen bond with the carbonyl group of Val98.

Front 80

Bohr effect in terms of specific residue

Back 80

excess protons protonate C terminus B2 146 His and stabalize the deoxy/T state

Front 81

where does carbamation happen? effect?

Back 81

carbamation happens N-terminus and stabalizes the salt bridge formation between alpha and beta chains

Front 82

what residue is replaced by ser in fetal gamma subunit? effect?

Back 82

his 143 is replaced by ser in fetal gamma subunit = positive charge replaced by negative = repels BPG = fHgb has less affinity for BPG = fHgb has higher O2 affinity

Front 83

amino acid residues involved in binding 2,3BPG are

Back 83

Lys82, His143, His2, and the N-terminal amino group of the β- chains?

Front 84

substitution in sickle cell

Back 84

β6 Glu -> Val

Front 85

Sickle cell hgb on electrophoresis?

Back 85

runs slower; close to the anode

Front 86

Codes for Glu and Val

Back 86

Glu = GAG

Val = GTG

Front 87

β6 Glu -> Ala

Back 87

• Changes in helix A of β6 from Glu to Ala produces insignificant sickling. Ala, due to its small size,
probably does not fit in the hydrophobic EF pocket of the β chain very well.

Front 88

β121 Glu -> Lys

Back 88

• Enhanced sickling
• The reason for this enhanced sickling is that switching from Glu (negative charge) to Lys (positive charge) causes charge- charge interactions with β6 Glu.

Front 89

His, F8, αchain (α87) -> Tyr

Back 89

• Replacement of His with Tyr results in ligating the ferrous atom in the heme and the Fe+2 becomes susceptible to oxidation to the ferric state (Fe+3)and no longer binds oxygen, resulting in reduced oxygen binding affinity.

Front 90

Arg 141 (α chain) -> His

Back 90

This variant is characterized by increased oxygen affinity (smaller p50) favoring the R state.

This is attributed to the elimination of the interactions between Arg and Asp126 of α chain in deoxyHb.

Front 91

• β Gly74 -> Asp.

Back 91

introducing a negatively charged residue in this region reduces the binding of 2,3-bisphosphoglycerate to Hb resulting in higher affinity Hb.

Front 92

• β His146 -> Asp

Back 92

Since this residue is critical for the Bohr effect and it plays a role in deoxy to Oxy Hb switching, the changes to Asp results in formation of Hb with high affinity for oxygen

Front 93

β His (F8) -> Gln

Back 93

This variant does not hold on to its heme because Gln does not coordinate well with the ferrous atom in the heme, opening the hydrophobic crevice for polar solvent.

Front 94

β 42 Phe -> Ser

Back 94

• This variant is unstable and loses its heme.
• replacement of the more hydrophobic amino acid residue Phe with Ser, which is hydrophilic and polar, opens the pocket for water and results in loss of heme.

Front 95

Pro (α chain) -> Arg

Back 95

• The loss of Pro results in a change of the geometry of the subunit and therefore alters subunit interactions due to continuation of the helix. This results in Hb dissociation into subunits.

Front 96

Leu136 (α chain) -> Pro

Back 96

Since introduction of proline into the helix interrupts the helix, it results in dissociation of the tetramer and results in high oxygen binding affinity.

Front 97

alpha genes are on chromosome?

beta genes are on chromosome?

Back 97

alpha = 16

beta = 11

Front 98

How many residues in alpha chain of HGB?

How many residues in beta chain of HGB?

Back 98

alpha = 141

beta = 146

Front 99

the plane of ______ and ______ is rotated to avoid collision with the heme

Back 99

valFG5 and leuFG3

Front 100

relative rotation of alpha-beta units in hgb?

Back 100

15degrees

Front 101

His F8 function in hgb?

Back 101

proximal his that binds Fe(II)

Front 102

His E7 function in hgb?

Back 102

Distal histidine, protects the heme and forces O2 to bind at an angle

Front 103

Phe CD1 function in hgb?

Back 103

Heme contact

Front 104

Leu F4 function in hgb?

Back 104

Heme contact

Front 105

Gly B6 function in hgb?

Back 105

Allows approach of B and E helices

Front 106

Pro C2 function in hgb?

Back 106

Terminates the helix

Front 107

Tyr HC2 function in hgb?

Back 107

hydrogen bond between H and F helices

Front 108

On assuming the R state the iron moves down ____ angstroms into the same plane as the porphyrin.

Back 108

0.6A

Front 109

Enzyme classification number:

First number?

Fourth number?

Back 109

first = n1 = type of reaction

last = n4 = substrate

Front 110

Enzyme classifications:

n1 = 1

Back 110

Oxidoreductase

Oxidation-reduction: Transfer of electrons from one molecule (donor, reductant) that is oxidized to another (acceptor, oxidant) that is reduced

Front 111

Enzyme classifications:

n1 = 2

Back 111

Transferase

Transfer of functional group (C-, N-, P-containing) from one molecule to another

Front 112

Enzyme classifications:

n1 = 3

Back 112

Hydrolase

Cleavage of bonds by hydrolysis

Front 113

Enzyme classifications:

n1 = 4

Back 113

Lyase

Addition or removal of groups to form double bonds

Front 114

Enzyme classifications:

n1 = 5

Back 114

Isomerase

Isomerization: Intramolecular group transfer

Front 115

Enzyme classifications:

n1 = 6

Back 115

Ligase

Joining two molecules by covalent bonds with breakdown of ATP

Front 116

Cosubstrate is _______ by a rxn

prosthetic group is _________ by a rxn

Back 116

Cosubstrate is loosely bound and changed by a rxn

prosthetic group is tightly or covalently bound and unchanged by a rxn

Front 117

standard free energy change equation

Back 117

Front 118

Chymotrypsin cleaves peptide bonds selectively on the ______ side of _________ amino acids (methionine)

Back 118

Chymotrypsin cleaves peptide bonds selectively on the carboxyl side of aromatic (tryptophan, tyrosine, phenylalanine ) and large hydrophobic amino acids (methionine)

Front 119

Chymotrypsin Catalytic triad?

Back 119

Ser 195, His 57, Asp 102

Front 120

michaelis-menten equation

Back 120

Front 121

active sites filled equation?

Back 121

[ES]/[E]t = v/vmax = [S]/Km+[S]

Front 122

When [S] is >>>> Km?

[S] <<< Km

Back 122

S > Km = zero order; usually [S] = 20Km

S <<<Km = zero order V proportional to [S]

Front 123

When [S] = Km?

Back 123

When [S] = Km:

v = 0.5vmax

Front 124

Michaelis-Menten 5 assumptions?

Back 124

1) Formation of ES complex between enzyme and substrate
2) No back reaction from product buildup: k4 = 0 at t ~ 0
3) Initial velocities used for analysis (t ~ 0)
4) Steady-state assumption for [ES] = [ES] doesnt change
5) Negligible depletion of substrate: [S] >> [E]

Front 125

Small Km = ?

Back 125

Small Km = high affinity

Large Km = low affinity

Front 126

catalytic efficiency?

Back 126

kcat/Km

You always want the highest kcat

Front 127

Lineweaver Burk plot equation

Back 127

Front 128

Competitive Inhibition:

Binds?
Ki = ?
Km, app = ?
Vm, app =?
Effect on Km? Vmax? catalytic efficiency?

Back 128

Binds only to active site

Ki = [E][I]/[EI]

Km, app = 1 + ([I]/Ki)

Km increases, Vmax doesn't change, cat-eff decreases

Front 129

Uncompeitive Inhibition:

Binds?
Ki = ?
Km, app = ?
Vm, app =?
Effect on Km? Vmax? catalytic efficiency?

Back 129

Binds only ES complex

Ki = [ES][I]/[ESI]

Km, app = Km/{1 + ([I]/Ki)}

Vm,app = Vm/{1 + ([I]/Ki)}

Km decreases, Vmax decreases, cat-eff no change

Front 130

Noncompeitive Inhibition:

Binds?
Ki = ?
Km, app = ?
Vm, app =?
Effect on Km? Vmax? catalytic efficiency?

Back 130

Binds to E or ES at a place different than active site

Ki = [E][I]/[EI] = [ES][I]/[ESI]

Km, app = Km

Vmax, app = Vm/{1 + ([I]/Ki)}

Km doesnt change, Vm decreases, Cat-eff decreases

Front 131

succinyl CoA + glycine --> ? enzyme?

Back 131

succinyl CoA + glycine --> delta aminolevulinic acid (ALA)

ALA synthase

Front 132

ALA x 2 --> ? enzyme?

Back 132

ALA x 2 --> porphobilinogen (PBG)

ALA dehydrase

Front 133

PBG x 4 --> ? enzyme?

Back 133

PBG x 4 --> hydroxymethyl bilane (bilane)

PBG deaminase

Front 134

bilane --> ? enzyme?

Back 134

bilane --> uroporphyrinogen III (uro’gen III)

urogen III cosynthase

Front 135

uro’gen III --> ? enzyme?

Back 135

uro’gen III --> coproporphyrinogen III (copro’gen III)

uro’gen III decarboxylase

Front 136

copro’gen III --> ? enzyme?

Back 136

copro’gen III --> protoporphyrinogen IX (proto’gen IX)

copro’gen III decarboxylase

Front 137

proto’gen IX --> ? enzyme?

Back 137

proto’gen IX --> protoporphyrin IX (proto IX)

proto’gen dehydrogenase

Front 138

proto IX --> ? enzyme?

Back 138

proto IX --> heme

ferrocheletase

Front 139

Starting reactants in order for Heme synthesis?

Back 139

1. succinyl CoA + glycine
2. ALA x 2
3. PBG x 4
4. bilane
5. uro’gen III
6. copro’gen III
7. proto’gen IX
8. proto IX

Front 140

Acute Intermittent Porphyria (AIP)? Enzyme defect? Step? Photosensititve?

Back 140

Step 3 = PBG deaminase

NOT photosensitive

Front 141

Hereditary Coproporphyria (HC) Enzyme defect? Step? Photosensititve?

Back 141

Step 6 = Coprogen III Decarboxylase

PHOTOsensitive

Front 142

Porphyria Cutanea Tarda (PCT) Enzyme defect? Step? Photosensititve?

Back 142

Step 5 = Urogen III Decarboxylase

PHOTOsensitive

Front 143

Variegate Porphyria (VP) Enzyme defect? Step? Photosensititve?

Back 143

Step 7 = Protogen IX Dehydrogenase

PHOTOsensitive

Front 144

Urine/Stool findings for the Acute Porphyrias?

Treatment?

Back 144

Rx = IV Heme

Urine:
ALA
PBG
Uro
Copro

Stool:
Copro
Proto

Front 145

Factors associated with PCT?

Back 145

• Chronic hepatitis C infection
• Alcohol use
• Iron overload (Increased hepatic iron inhibits UROD activity)
• HIV infection

Front 146

Diagnostic signs for PCT

Back 146

• Characteristic rash
• Increased uroporphyrin int he urine
• Emission peak on plasma flourescence
• Check for genetic hemochromatosis

Front 147

treatment for PCT?

Back 147

Based on cause:
-Chloroquinone
-Blood draw
-No sun or alcohol
-Treat HepC

Front 148

1/3 of all amino acid residues in collagen are?

Back 148

glycine

Front 149

1/4 of all amino acid residues in collagen are?

Back 149

proline

Front 150

1/2 of all proline residues are

Back 150

hydroxylated at carbon 3 or 4 to form hydroxyproline

Front 151

The repeating polypeptide of collagen is Gly-X-Y where X is usually? and Y is usually?

Back 151

X is usually Pro

Y is usually hydroxyproline

Front 152

Polarity of Gly-Pro-Y and Gly-X-Y

Back 152

Gly-Pro-Y is usually non-polar
Gly-X-Y is most often polar

Front 153

Microheterogeneity

Back 153

different parts of the peptided are hydroxylated

Front 154

MW of collagen is 300,000 Da, how many residues? residues/chain?

Back 154

3,000 residues

1,000 residues/chain

Front 155

Proline helix?

Back 155

Type II trans helix = left handed polyproline helix with pyrrolidine rings

Front 156

poly-proline helix:

rise?

Back 156

2.8A

Front 157

Tight binding of alpha chains is facilitated by

Back 157

Gly at every 3rd position

Front 158

Function of N-terminal leader sequence in transcripted alpha chain>

Back 158

signals translation by rER ribosomes

Front 159

Enzyme that post-translationally modifies proline residues? cofactor? primarily at what carbon? where in cell?

Back 159

prolyl hydroxylase hydroxilates mainly at C4

cofactor = ascorbate

in the ER

Front 160

Enzyme that hydroxylates lys? what carbon? where do hydroxylysines usually appear in the collagen polymer?

Back 160

Lysyl hydroxylase
5th carbon
Hydroxylysines frequently occur at the Y-position in the sequence (Gly-X- Y)

Front 161

Unique reactant needed for prolyl and lysyl hydroxylase?

byproducts?

Back 161

reactant O2 (and ascorbate)

byproducts = succinate and CO2

Front 162

Once in the __________, some _________ residues are glycosylated with galactose monosaccharides or glucosylgalactose disaccharides.

Back 162

Once in the Golgi apparatus, some hydroxylysine residues are glycosylated with galactose monosaccharides or glucosylgalactose disaccharides.

Front 163

Does procollagen have disulfide bonds?

Back 163

Yes in the C-terminal extensions

Front 164

Does tropocollagen have disulfide bonds?

Back 164

usually no

Front 165

Tropocollagens align with ___ stagger in a non-symmetrical way with ____nm gaps between tropocollagens. Adjacent rows are displaced by ___nm, and the structure repeats every ___ rows.

Back 165

Tropocollagens align with 1⁄4 stagger in a non-symmetrical way with 40nm gaps between tropocollagens. Adjacent rows are displaced by 68nm, and the structure repeats every 5 rows.

Front 166

Fibers are stabilized by the covalent cross-linking of the constituent collagen molecules. The cross-links result from the ________ in lysine (or hydroxylysine) into an _______ by the enzyme ________

Back 166

Fibers are stabilized by the covalent cross-linking of the constituent collagen molecules. The cross-links result from the oxidation of the amino group in lysine (or hydroxylysine) into an aldehyde by the enzyme lysyl oxidase (LOX).

Front 167

hydroxypyridinium ring (pyridinoline) forms between ?

Back 167

two hydroxylysyl and one lysyl residues.

Front 168

BAPN?

Back 168

suicide inhibitor of LOX, and the resulting reduced cross-linkage of collagen fibers caused by BAPN is reflected by severe abnormalities in the physiology of bones, joints and blood vessels.

Front 169

MMPs?

Back 169

matrix metalloproteinase’s (MMPs) enzymes cleave the collagen triple helix about three quarters from the N-terminus, thus decreasing the Tm from slightly above 37°C to about 30°C.

Front 170

elastin is a ____ molecule and is ___ glycosylated. About one third of the amino acid residues are ____, and about one half are ___

Back 170

elastin is a single molecule and is not glycosylated. About one third of the amino acid residues are Gly, and about one half are Pro

Front 171

do gly and pro elastin form a regular secondary structure

Back 171

no

Front 172

Each molecule is about 70kDa and contains_______ regions that participate in _______ interactions.

Back 172

70,000Da (~100 residues)

valine-rich non-polar regions that participate in hydrophobic interactions.

Front 173

Function of lysyl oxidase on elastin?

Back 173

cross-links to form highly insoluble elastin fibres

Front 174

cross-linking requires lysyl oxidase to form ________ residues that react with the _______, unaltered lysine residue to form a _______

Back 174

cross-linking requires lysyl oxidase to form three allylysine residues that react with the amino group of a fourth, unaltered lysine residue to form a desmosine

Front 175

Prolyl hydroxylase example of disease?

Back 175

scurvy

Front 176

Lysyl hydroxylase example of disease?

Back 176

Ehlers-Danlos type VI

Front 177

Lysyl oxidase example of disease

Back 177

Osteolathyrism Copper deficiency Vitamin B6 deficiency Menkes kinky-hair syndrome D-Penicillamine Ehlers-Danlos type V

Front 178

Requirements for the function of prolyl hydroxilase?

Back 178

ascorbate
alpha ketoglutarate
Molecular O2
Ferrous

Front 179

Requirements for function of lysyl hydroxylase?

Back 179

ascorbate
alpha ketoglutarate
Molecular O2
Ferrous

Front 180

Requirements for function of Lysyl oxidase

Back 180

Copper
Pyridoxal phosphate
Molecular oxygen

Front 181

Proteoglycans are extracellular proteins with covalently bound glycosaminoglycans (GAGs) O-linked to _____

charge?

Back 181

serine residues.

very negative

Front 182

Is hyaluronic acid linked to proteins?

Back 182

no

it is the exception of proteoglycans