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BB 490 > Final Exam > Flashcards

Final Exam Flashcards

1
Q

Equation for K of Water

A

K = [H+][OH-]/[H2O]

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2
Q

pH =

A

pH = -log[H+]

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3
Q

Equation for Ka

A

Ka = K[H2O] = [H+][A-]/[HA]

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4
Q

pH at titration midpoint =

A

pK

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5
Q

At titration midpoint, [HA] = ?

A

[A-]

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6
Q

Carbonic anhydrase equation

A

CO2 + H2O <–> H2CO3 <–>HCO3- + H+

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7
Q

Purines

A

Adenine & guanine

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8
Q

Pyrimidines

A

Cytosine, uracil, & thymine

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9
Q

How does deoxyribose differ from ribose?

A

Deoxyribose lacks the 2’ -OH group

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10
Q

What is the effect of ribose’s 2’ -OH group on RNA?

A

Decreases stability
Discourages double helix formation
Allows RNA to undergo chemical rxns

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11
Q

Nucleoside

A

A nitrogenous base bound to a sugar

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12
Q

Phosphodiester bonds are formed via ________ reactions.

A

Condensation

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13
Q

How many hydrogen bonds does A-T form?

A

2

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14
Q

How many hydrogen bonds does G-C form?

A

3

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15
Q

The DNA double helix is ______-handed.

A

right-handed

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16
Q

How do bacteria use restriction endonucleases?

A

They methylate their own DNA, then purge bacteriophages by having restriction endonucleases cleave any unmethylated DNA.

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17
Q

Hydrophobic AAs

A

Cys, Leu, Ala, Met, Ile, Val (CLAMIV)

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18
Q

Aromatic AAs

A

Tyr, Phe, Try (TPT)

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19
Q

Basic AAs

A

His, Arg, Lys (HAL)

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20
Q

Acidic AAs

A

Asp, Glu (AG)

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21
Q

Neutral AAs

A

Thr, Asn, Gln, Ser (TAGS)

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22
Q

What are unique properties of Pro?

A

Conformationally restricted
No NH

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23
Q

What are unique properties of Gly?

A

Smallest
Achiral
Conformationally most free

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24
Q

AAS are ______, with ______-handedness being more common.

A

Chiral, with left-handedness being more common

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25
Q

Peptide bond formation is a _________ reaction

A

condensation

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26
Q

Is the cis or trans form preferred in peptide bonds?

A

Trans

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27
Q

Phi describes the __ bond

A

CO bond

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28
Q

Psi describes the __ bond

A

CN

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29
Q

Torsion angles are ____ when the polypeptide backbone is fully extended.

A

180*

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30
Q

Secondary structure

A

Encompasses backbone, but not side chains.

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31
Q

Tertiary Structure

A

Encompasses the 3D shape of the polypeptide

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32
Q

The alpha helix is _____-handed.

A

right-handed

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33
Q

Where do side chains project in the alpha helix?

A

Outwards and downwards from the helix

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34
Q

Where does H bonding occur in beta sheets?

A

Between the peptide strands

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35
Q

How many peptide strands are contained within a beta sheet?

A

2-22 (average of 6)

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36
Q

How many residues per strand in a beta sheet?

A

Up to 15 (average 6)

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37
Q

Supersecondary structures

A

Groupings of secondary structural elements.

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38
Q

Beta-Alpha-Beta Motif

A

Alpha helix connects two parallel beta sheets

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39
Q

Beta hairpin motif

A

Antiparallel beta strands connected by tight reverse turns

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40
Q

Alpha-Alpha motif

A

Two alpha helices, connected and inclined towards one another (side chains can intermesh)

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41
Q

Greek Key motif

A

A beta hairpin is folded over to form a 4-stranded antiparallel beta sheet

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42
Q

Structure of collagen

A

Right-handed triple helix

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43
Q

Structure of keratin

A

2 alpha helices coiled around one another (coiled coil)

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44
Q

Structure of myoglobin

A

8 alpha helices arranged into a globular protein

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45
Q

Where is myoglobin’s heme complex manufactured?

A

The mitochondria

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46
Q

p50 of myoglobin

A

2.8 Torr (fully saturated at physiological pO2)

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47
Q

Myoglobin has a ________ binding curve.

A

Hyperbolic

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48
Q

What role does His64 play in myoglobin?

A

It sterically blocks the linear arrangement, preventing CO from binding

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49
Q

Structure of hemoglobin

A

Alpha-beta tetramer (dimer of dimers)

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50
Q

p50 of hemoglobin

A

26 Torr (10x that of myoglobin)

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51
Q

Which protein has T and R states?

A

Hemoglobin

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52
Q

T state

A

“Tense” state, low O2 affinity (better for release of O2 in the muscles)

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53
Q

R state

A

“Relaxed” state, high O2 affinity (better for O2 pickup in the lungs)

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54
Q

The Bohr effect

A

Hemoglobin binds more O2 at a higher pH

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55
Q

Hemoglobin has a _______ binding curve.

A

sigmoidal

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56
Q

Function of molecular chaperones

A

Lift folding polypeptides out of false minima in the folding funnel, prevent misfolding and aggregation

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57
Q

Which protein does BPG interact with?

A

Hemoglobin

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58
Q

How does BPG impact hemoglobin?

A

Stabilizes the T state, promoting oxygen release

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59
Q

What is the relationship between fetal hemoglobin and BPG?

A

Fetal hemoglobin has a low affinity for BPG

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60
Q

What molecule is impacted by altitude adaptation?

A

BPG - increased BPG at altitude helps with release of O2 in the body

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61
Q

What is modified in the hemoglobin of an SCA patient?

A

A residue is converted to a hydrophobic valine

62
Q

How does hydroxyurea impact the body?

A

It increases the quantity of cells containing fetal hemoglobin

63
Q

Fatty acids

A

Carboxylic acids with long-chain hydrocarbon side groups.

64
Q

__ and __ are the two most common fatty acid types in higher plants and animals.

A

C16 & C18

65
Q

Where does the first double bond of an unsaturated fatty acid occur?

A

Between C9 and C10

66
Q

Do bacteria have polyunsaturated fatty acids?

A

No

67
Q

Triglycerides

A

Fatty acid triesters of glycerol.

68
Q

What suffix is used for fatty acids in a triglyceride?

A

-oyl

69
Q

Phospholipids

A

Molecules of glycerol-3-phosphate whose C1 and C2 have been esterified with fatty acids.

70
Q

Simplest form of phospholipid

A

Phosphatidic acids

71
Q

C1 of a phospholipid is typically __________.

A

saturated

72
Q

C2 of a phospholipid is typically __________.

A

Unsaturated

73
Q

What do phospholipases do?

A

They excise the C2 fatty acid residue of phospholipids, leaving a lysophospholipid.

74
Q

Sphingolipids

A

Fatty acid derivatives of sphingosines; major membrane components.

75
Q

What is notable about the structure of sphingosine?

A

Its alkene is trans

76
Q

Ceramides

A

N-acyl fatty acid derivatives of sphingosines. A sphingosine with an attached fatty acid.

77
Q

What is unique about the properties of cholesterol?

A

Weakly amphiphilic
Greater rigidity than other membrane lipids

78
Q

Do plants have cholesterol?

A

They have little cholesterol, and synthesize other sterols.

79
Q

Do yeast and fungi have cholesterol?

A

No, they synthesize their own unique sterols.

80
Q

Do prokaryotes contain cholesterol?

A

Very rarely

81
Q

How many residues in the hydrophobic regions of integral membrane proteins?

A

18-23

82
Q

Which molecules carry out passive-mediated transport?

A

Ionophores, porins, ion channels, aquaporins, & transport proteins

83
Q

Valinomycin

A

A carrier ionophore that transports K across the membrane.

84
Q

What coordinates K within valinomycin?

A

Carbonyl groups of its six Val residues (can only coordinate K)

85
Q

What makes valinomycin lipid-soluble?

A

Projecting methyl and isopropyl side chains

86
Q

KcsA K+ Channel

A

A channel ionophore that moves K and water.

87
Q

Which transport component is known for its selectivity filter?

A

The KcsA K+ channel

88
Q

What is a prominent example of a voltage-gated channel? What kind of transport does it facilitate?

A

The Kv channel; voltage-gated channels facilitate passive transport

89
Q

GLUT1

A

A uniport that moves glucose across the membrane.

90
Q

SGLT

A

A symport that moves glucose and Na+ simultaneously.

91
Q

What does the Na+-K+ ATPase move across the membrane?

A

3 Na+ ions out of the cell, 2 K+ into the cell

92
Q

E1 of Na-K ATPase

A

High Na affinity, dephosphorylated

93
Q

E2 of Na-K ATPase

A

Low Na affinity, phosphorylated

94
Q

What direction do Na and glucose move in the SGLT transporter?

A

Na+ moves with its gradient
Glucose moves against its gradient

95
Q

Why are SGL2 inhibitors used to treat diabetes?

A

They prevent glucose uptake in the kidneys.

96
Q

Process of glucose-induced signal transduction in pancreatic beta cell insulin secretion

A
  • Glucose enters the cell, and is metabolized to ATP.
  • High intracellular ATP triggers closing of ATP-dependent K channels.
    *Buildup of K causes depolarization, opening up Ca2+ channels.
    *Rise in intracellular Ca2+ triggers release of secretory vesicles & insulin.
97
Q

How do sulfonylureas work?

A

They bind to ATP-dependent K channels and inhibit them, triggering a rise in intracellular Ca2+ and subsequent insulin release.

98
Q

What does the cardiac ATPase/Ca2+ exchanger do?

A

It swaps Na+ for Ca2+, getting rid of extra Ca2+ in the cell.

99
Q

How does digoxin work?

A

It inhibits the Na-K ATPase, which causes the NCX to not have enough energy to swap Na and Ca2+. The rise in intracellular Ca2+ improves cardiac function.

100
Q

What do aldehydes and ketones react with to form hemiacetals and hemiketals?

A

Alcohols

101
Q

D sugars have the same absolute configuration as _________.

A

D-glyceraldehyde

102
Q

The ________ points to the right in D sugars.

A

C5 -OH

103
Q

Alpha anomer

A

The anomeric -OH is on the opposite side of the ring as the CH2OH

104
Q

Beta anomer

A

The anomeric -OH is on the same side of the ring as the CH2OH

105
Q

Mutarotation

A

Carbohydrate anomers freely interconvert in aqueous solution.

106
Q

Formation of a glycosidic bond is a ________ reaction.

A

Condensation

107
Q

Lactose

A

Galactose + Glucose

108
Q

Sucrose

A

Glucose + Fructose

109
Q

Structure of cellulose

A

Up to 15,000 glucose residues connected via B(1–>4) bonds

110
Q

Amylose structure

A

A linear polymer of several thousand glucose residues connected via A(1—>4) bonds

111
Q

_________ is an isomer of cellulose

A

Amylose

112
Q

Amylopectin structure

A

A(1–>4) linked glucose residues with A(1–>6) branch points every 24-30 residues

113
Q

Glycogen structure

A

Resembles a more branched form of amylopectin (branching every 8-10 residues)

114
Q

What does glycogen phosphorylase do?

A

Cleaves A(1–>4) bonds sequentially from nonreducing ends

115
Q

What does glycogen debranching enzyme do?

A

Cleaves A(1–>6) bonds

116
Q

Heparin activates ________, which inhibits __________.

A

Activates anti-thrombin, which inhibits thrombin.

117
Q

N-linked glycosylation

A

Oligosaccharides are linked to Asn (Asn-X-Ser or Asn-X-Thr)

118
Q

Where does N-linked glycosylation occur?

A

Endoplasmic reticulum

119
Q

O-Linked Glycosylation

A

Oligosaccharides are attached to Ser or Thr

120
Q

Which form of glycosylation occurs cotranslationally?

A

N-linked glycosylation

121
Q

Where does O-linked glycosylation occur?

A

Golgi

122
Q

What is the size range of O-linked glycosylation additives?

A

1 galactose up to 1,000 disaccharides

123
Q

Which levels of protein structure dictate glycosylation sites?

A

Secondary and tertiary

124
Q

Proteoglycan structure

A

“Bristles” noncovalently attached to a hyaluronate backbone. A highly hydrated gel forms within the bristles.

125
Q

Which part of the body notably contains proteoglycans?

A

Cartilage (collagen fibrils are filled in with proteoglycans)

126
Q

Hyaluronate is a prominent _____________.

A

Glycosaminoglycan

127
Q

Where in the body is hyaluronate found?

A

Synovial fluid, vitreous humor, connective tissue

128
Q

Which molecule fulfills the function of hyaluronate in plants?

A

Pectin

129
Q

What are the 5 mechanisms of enzyme catalysis?

A

Acid-base catalysis
Covalent catalysis
Metal ion cofactors
Orientation and proximity effects
Preferential binding of transition state

130
Q

Acid catalysis

A

Proton transfer from an acid lowers the free energy of a reaction’s transition state.

131
Q

Covalent catalysis

A

Transient formation of a catalyst-substrate covalent bond.

132
Q

During covalent catalysis, the enzyme acts as a _________, and the substrate as a _________.

A

The enzyme acts as a nucleophile, and the substrate as an electrophile.

133
Q

What are the three ways that metal ion cofactors catalyze reactions?

A
  • Bind to substrates and orient them
  • Mediate redox reactions (by changing their own oxidation states)
  • Electrostatically stabilizing or shielding negative charges
134
Q

What metal ion does carbonic anhydrase use in mediating blood pH?

A

Zn2+

135
Q

What are the four ways that proximity and orientation effects catalyze reactions?

A
  • Bring substrates in contact with catalytic groups
  • Bind substrate at proper orientations
  • Charged groups stabilize TSs
  • Freeze out relative translational and rotational movement
136
Q

The Michaelis-Menten equation describes a ___________.

A

rectangular hyperbola

137
Q

Vmax

A

The maximum reaction velocity

138
Q

Km

A

The substrate concentration when the reaction velocity is half of its maximum.

139
Q

Lower Km indicates _____ substrate affinity.

A

Lower Km = Higher affinity

140
Q

What enzyme is associated with competitive inhibition?

A

Succinate dehydrogenase/fumarate

141
Q

How are Km and Vmax impacted by competitive inhibition?

A

Km increases, Vmax stays constant

142
Q

How are Km and Vmax impacted by noncompetitive inhibition?

A

Km stays constant, Vmax decreases

143
Q

What is the rate-determining step of glycolysis?

A

Phosphorylation of F6P to F1,6BP by phosphofructose kinase

144
Q

What are the two high-energy intermediates seen in glycolysis?

A

2,3-BPG and PEP

145
Q

How does ATP impact PFK?

A

It is an allosteric inhibitor - it preferentially binds to the T state, reducing binding of F6P

146
Q

Substrate cycling

A

F6P and FBP are both active in resting muscle (cycling); PFK activity is dominant in active muscle, increasing GADP/DHAP output.

147
Q

Where do animals use substrate cycling and for what purpose?

A

They use substrate cycling in the muscles and liver to generate heat (nonshivering thermogenesis).

148
Q

In the ___ state of hemoglobin, the Fe is out of the heme plane.

A

T state

149
Q

When oxygen binds to heme, the oxygen forms a hydrogen bond with ____.

A

His E7

150
Q

What is indicated by the pKa of an amino acid?

A

The pH at which the side chain will be 50% protonated and 50% deprotonated.

151
Q

What does Kcat represent?

A

The number of substrate molecules converted to product per enzyme molecule per second at Vmax (rate constant for conversion of substrate to product).

152
Q
A

BB 490 (1 decks)

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