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BIOL 600 > Unit 2 > Flashcards

Unit 2 Flashcards

1
Q

D-glucose and L-glucose are ____________.

A

enantiomers

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2
Q

The furanose form of fructose is generated by a form of a hemiketal involving the attack of the hydroxyl group on on carbon __ with carbon __.

A

5; 2

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3
Q

Formation of pyranose and furanose forms of sugar result in the generation of a new asymmetric carbon giving rise to alpha and beta forms of the sugars. The carbon at which this newly created asymmetric center is generated is referred to as ___________.

A

the anomeric carbon.

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4
Q

Cellulose is a polymer of glucose joined via ______________ linkages.

A

Beta 1, 4 glycosidic linkages

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5
Q

Fibrils of cellulose have high tensile strength, due to hydrogen bonds between _______________.

A

straight chains

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6
Q

Once formed, the alpha and beta forms of D-glucose are what?

A

interconvertible only through a linear, noncyclic intermediate with which they are both in equilibrium

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7
Q

What connects sugar molecules in both linear and branches of complex carbohydrates?

A

Glycosidic bonds

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8
Q

Human blood groups are the result of _______________.

A

differing glycotransferases

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9
Q

The amino acid R-groups that serve as sites for covalent attachment of glycoproteins to carbs include ____________.

A

hydroxyl-containing R-groups

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10
Q

Which two sugars are joined via an O-glycosidic bond to make lactose?

A

Beta-D galactose and alpha-D glucose, joined via 1 –> 4 glycosidic bond

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11
Q

Sorting which targets glycoproteins to their correct destination is done in what organelle?

A

Golgi apparatus

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12
Q

Diisopropylphosphofluoridate (DIPF) inactivates chymotrypsin by covalently modifying serine-195. This occurs because of what?

A

serine-195 is in environment which gives it a higher than normal reactivity with respect to DIPF

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13
Q

The observation of “burst” kinetic in rapid kinetic studies of the hydrolysis of N-acetyl-L-phenylalanine p-nitrophenyl ester by chymotrypsin is due to what?

A

The rate of the acylation reaction being faster than the deacylation reaction

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14
Q

TPCK inactivates chymotrypsin but not trypsin because

A

TPCK looks like the substrate for chymotrypsin and thus can bind in its active site and modify His-57

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15
Q

A competitive inhibitor often ____________ the substrate for the enzyme it inhibits.

A

resembles

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16
Q

The effects of a ____________ inhibitor can be overcome by increasing the concentration of the substrate.

A

competitive

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17
Q

Regarding the cleavage of peptide bonds by chymotrypsin being caused by a nucleophilic attack with an active-site residue, Serine is what?

A

Serine is a strong nucleophile because of the action of Asp and His in the active site.

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18
Q

Which type of inhibitor causes Vmax to decrease while Km stays the same?

A

Noncompetitive

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19
Q

Which type of inhibitor has no affect on Vmax while Km increases?

A

Competitive

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20
Q

Which type of inhibitor causes Vmax to decrease while Km decreases?

A

Uncompetitive

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21
Q

Which type of inhibitor binds at the active site?

A

Competitive

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22
Q

Which type of inhibitor binds to the ES?

A

Uncompetitive

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23
Q

Which type of inhibitor is allosteric?

A

Noncompetitive

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24
Q

Which type of inhibitor can only bind after the enzyme substrate complex has formed?

A

Uncompetitive

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25
Q

Why is penicillin called a suicide inhibitor for the biosynthesis of bacterial cell walls?

A

Penicillin forms a covalent intermediate which is enzymatically inactive.

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26
Q

The binding of oxygen to myoglobin and hemoglobin has what effect on the heme iron?

A

It causes the iron to move into the plane of the porphyrin ring

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27
Q

How do we know that the binding of oxygen to hemoglobin is cooperative?

A

A binding plot of Y (fraction of sites occupied) against pO2 is sigmoidal rather than hyperbolic.

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28
Q

Oxygen and 2,3-bisphosphoglycerate (2,3- BPG) cannot bind to hemoglobin at the same time because of what?

A

The structure of hemoglobin is changed when oxygen binds such that 2,3-BPG can no longer bind.

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29
Q

Because readily metabolizing tissues generate large amounts of protons and carbon dioxide, the oxygen-binding curve of hemoglobin does what?

A

Y vs pO2 is shifted to higher pO2 levels.

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30
Q

How is hemoglobin used to transport CO2 from the tissues to the lungs?

A

CO2 reacts with the terminal amino groups on hemoglobin in a reversible manner.

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31
Q

What is the relationship of the R-state and the T-states in oxygen binding?

A

Oxygen binds to the T-state, converting it into the R-state.

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32
Q

The difference between the “concerted” and “sequential” models of oxygen binding to hemoglobin is what?

A

whether the transition between T and R states is “all-or-nothing” or has intermediate states

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33
Q

Replacing beta subunits of hemoglobin with gamma subunits results in a higher affinity for oxygen due to what?

A

decreased binding to 2,3-BPG

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34
Q

The mutation of hemoglobin’s beta subunit to hemoglobin S as in sickle cell anemia results in the change of what?

A

a negatively charged amino acid R-group to a hydrophobic amino acid R-group

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35
Q

The molecular consequences of the hemoglobin S mutation are what?

A

hemoglobin S forms aggregates and fibrous precipitates when oxygen is released

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36
Q

Lipid molecules are said to be ___________.

A

amphipathic

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37
Q

Cis double bonds in fatty acids cause a ______ in the molecule.

A

bend

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38
Q

In phosphoglycerides, fatty acids are esterified at what?

A

glycerol carbons 1 and 2

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39
Q

Archaeal membrane lipids and those of other organisms both can have what?

A

a backbone other than glycerol

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40
Q

Archaeal membrane lipids’ fatty acid esters are replaced with what?

A

long chain alcohol enter links to the glycerol

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41
Q

Archaeal membrane lipids’ long hydrophobic tails are what?

A

branched rather than linear

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42
Q

Which major type of membrane lipid is not found in prokaryotes?

A

Cholesterol

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43
Q

What are the three major types of membrane lipids?

A

Phospholipids, glycolipids, and cholesterol

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44
Q

Decreasing the length of a fatty acid chain, does what to the Tm for a phospholipid bilayer?

A

lowers Tm

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45
Q

Unsaturating a carbon, does what to its Tm?

A

lowers Tm

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46
Q

Cis carbons have a _______ Tm compared to trans carbons.

A

lower

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47
Q

More carbon atoms in fatty acids, ___________ Tm

A

higher

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48
Q

________ van der Waals interactions lead to a higher Tm.

A

More

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49
Q

How many carbons do naturally occurring fatty acids have?

A

an even number, ranging from 14-24

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50
Q

Lipids are used by organisms for _________.

A

energy storage

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51
Q

Lipids can be attached to what and by what means?

A

Carbohydrates; covalent bonds

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52
Q

Riemann-Pick disease can result from lack of what?

A

sphingomyelinase

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53
Q

The HIV envelope protein is coated with what class of biomolecules?

A

Carbohydrates; sugars

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54
Q

These monosaccharides differ at a single asymmetric carbon

A

epimers

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55
Q

This is the most abundant organic molecule in the bioshphere

A

cellulose

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56
Q

What is the second most abundant molecule in the biosphere

A

chitin

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57
Q

The storage form of glucose in animals

A

glycogen

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58
Q

The storage form of glucose in plants

A

starch

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59
Q

Explain why cellulose and storage carbs have different structural properties.

A

The glucose polymers’ alpha hollow helix is more compact and easily accessible for storage. Cellulose’s beta formation is a rigid, strong structure because of the straight chains it creates.

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60
Q

These proteins bind to specific carb structures

A

lectins (selectin)

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61
Q

In n-linked glycoproteins, the carb portion is attached to this residue in the protein

A

asparagine

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62
Q

An o-linked glycoprotein is when the carb portion is attached to what?

A

serine or threonine

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63
Q

The influenza virus recognizes this acidic sugar molecule found on glycoproteins that are present on human cell surfaces. What functional group makes this sugar acidic?

A

Sialic acid; carboxylic acid

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64
Q

Mostly, the pentasaccharide core of N-linked glycoproteins is made of ________ and ________.

A

manose; N-acetyl glucosamine

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65
Q

What is the difference between proteoglycans and glycoproteins?

A

Proteoglycans are more sugar than protein and play a structural role. Glycoproteins are more protein than sugar and are used for communication.

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66
Q

A surface protein of influenza virus that binds to a sugar residue on the host cell membrane.

A

Hemagglutinnin

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67
Q

A surface protein of influenza virus that cleaves glycosidic bonds

A

neuraminidase

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68
Q

Draw the chair structure of beta-D-glucose.

A

(oxygen right corner, CH2OH equatorial, alternating OHs equatorially)

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69
Q

Most fatty acids have odd or even number of carbon atoms and why?

A

Even, C2 is required to make fatty acids, therefore, only in pairs

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70
Q

What are the 3 major types of membrane lipids?

A

Phospholipids, Glycolipids, Cholesterol

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71
Q

What features are common to other macromolecules but not lipids?

A

inability to form polymers; can bendefined by solubility

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72
Q

Lipids which contain carbs

A

glycolipids

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73
Q

Type of lipid with two acyl-chains, a glycerol backbone, and a phosphate head-group.

A

phosphoglyceride

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74
Q

Flat hydrophobic 4-ring molecule that is precursor to many steroidal hormones

A

Sterol ring or steroid nucleus

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75
Q

Name the enzyme reversible inhibitors

A

competitive, uncompetitive, and noncompetitive

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76
Q

What are the 4 categories of irreversible inhibitors?

A

Group-specific reagents, affinity labels, suicide inhibitors, and transition-state analogs

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77
Q

Lipid bilayers are formed how?

A

The bilayers are formed by phospholipids and glycolipids due to the hydrophobic effect.

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78
Q

How many amino acids does it take to span a lipid bilayer?

A

20

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79
Q

What is the melting temperature?

A

Temperature when a membrane transitions from highly ordered to very fluid

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80
Q

Longer chains of fatty acids have _________ Tm and therefore, _________ membrane fluidity.

A

higher; lower

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81
Q

Cis Tm __ Trans Tm and why?

A

Cis Tm

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82
Q

Cholesterol __________ Tm

A

broadens

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83
Q

An increase in temperature has what affect on chain length and unsaturation?

A

Longer; less

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84
Q

What must happen for beta strands with polar groups to pass through a membrane.

A

The polar groups must hydrogen bond with water

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85
Q

What is prostaglandin?

A

membrane protein that participates in inflammatory response

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86
Q

The prostaglandin active site within the membrane can be inhibited by _______________.

A

Salicylic acid

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87
Q

Enzyme that facilitates flip-flopping.

A

flipase

88
Q

What is the ion gradient needed for?

A

nerve impulse

89
Q

Digitalis inhibits what?

A

Na+ and K+

90
Q

What is the ABC transporter?

A

ATP-binding cassette is an ion pump involved in drug efflux.

91
Q

What is the explanation for bigger molecules passing through an ion channel when smaller molecules cannot?

A

The bigger molecules strip the K+ ions of water because of their hydrogen backbone.

92
Q

Phospholipids spontaneously form _________.

A

bilayers

93
Q

The driving force for the formation of membrane bilayers

A

hydrophobic effect

94
Q

_______ has a high permeability through lipid bilayers.

A

Water

95
Q

_________ proteins are only removed from a membrane with detergents

A

integral

96
Q

This substance inhibits prostaglandin H2 synthase-1 by blocking the channel through which the substrate, arachidonate, travels

A

Aspirin

97
Q

The type of amino acid found in the transmembrane helix of an integral protein

A

nonpolar

98
Q

This is the process by which lipids and proteins move in the membrane layer.

A

lateral diffusion

99
Q

These membrane components contain carbohydrates.

A

glycolipids

100
Q

__________ are bilayer lipid vesicles with an aqueous compartment.

A

Liposomes

101
Q

________ membrane proteins are bound primarily by electrostatic and hydrogen bond interactions with the head groups of lipids.

A

Peripheral

102
Q

Some proteins are anchored to the membrane by being covalently attached to a ________ or ________ group by a thirster linkage to a specific cysteine residue.

A

farnicyl; palmytic

103
Q

An increase in the amount of unsaturated fatty acid chains in a membrane ________ the fluidity of the membrane.

A

increases

104
Q

Which 3 classes of lipids make up cell membranes

A

Phospholipids, glycolipids, and steroids

105
Q

Triacylglycerol serves what purpose?

A

Storage of fatty acids that provides energy

106
Q

Which class of lipid is a hormone precursor?

A

Free fatty acids

107
Q

What are the beginnings and ends of fatty acid chains called?

A

alpha and omega

108
Q

Type of fatty acid in vegetable oils

A

unsaturated, cis

109
Q

Which fatty acid is naturally occurring in animals

A

Palmitate C16 saturated

110
Q

What factors determine the melting point of fatty acids?

A 
# of carbons
# of double bonds
111
Q

Draw Glycerol

A

3 Cs w/ OH and H

112
Q

Triacylglycerols pack 6 times more _______ than glycogen by weight

A

energy

113
Q

Phosphoglyceride components

A

Glycerol backbone with 2 non polar fatty acids and polar phosphate attached to alcohol

114
Q

What are carbohydrates?

A

Hydrated carbons

115
Q

What functional classification does dihydroxyacetone have?

A

ketose

116
Q

What functional classification does D-Glyceraldehyde have?

A

Aldose

117
Q

What functional classification does L-Glyceraldehyde have?

A

aldose

118
Q

D-Glucose and D-mannose are _________.

A

epimers differing at C2

119
Q

What are anomers?

A

Isomers that differ at a new asymmetric carbon atom formed on ring closure

120
Q

What is the difference between ribose and deoxyribose?

A

C2 in ribose is hydrated whereas C2 in deoxyribose has 2H’s

121
Q

Fructose and Galactose have how many carbons?

A

6

122
Q

A ketone and an alcohol form what?

A

A hemiketal in which the hydrogen atom from the alcohol bonds with the ketone and the R group and oxygen from the alcohol form their own side chain.

123
Q

An aldehyde and an alcohol form what?

A

A hemiacetal in which the alcohol hydrogen bonds to the aldehyde oxygen and the alcohol’s oxygen and R group create their own side chain

124
Q

How is the cyclic form of D-glucose created?

A

The glucose reacts with its own hydroxyl and can form anomer because the reaction can occur from top or bottom.

125
Q

What is the sugar of fruits?

A

D-fructose: 6 carbon ketose

126
Q

Draw D-glucose

A

O at corner with CH2OH next to it in equitorial and OHs alternating

127
Q

The sugars that reduce Cu 2+ into Cu2O have what type of ends?

A

aldose

128
Q

Carbohydrates form _______ linkages to phosphates.

A

ester

129
Q

maltose is made of what?

A

two glucose molecules bound together by an alpha-1,4-glycosidic bond

130
Q

Glycosyltransferases

A

make sugars

131
Q

Humans don’t have enzymes to break what?

A

Glycosidic bonds

132
Q

Proteins, DNA, and RNA all have what in common?

A

They are unbranched

133
Q

Starch and Glycogen cannot what?

A

Pack well due to their alpha-1,4 linkages

134
Q

Cellulose packs to what degree?

A

It packs well because of its beta-1, 4 linkages and H bonding

135
Q

Steroids are what class of carb?

A

Glycoprotein

136
Q

Why did the aids vaccine fail?

A

N-linked Glycoproteins

137
Q

Lance Armstrong

A

Erythropoietin

138
Q

Glycoproteins function

A

cell-cell recognition and signaling

139
Q

Which class of carbs function as shock absorbers for joints?

A

Proteoglycans

140
Q

N-linked glycoprotein

A

Asn

141
Q

O-linked glycoprotein

A

Ser, Thr, Tyr

142
Q

Glycosylation of erythropoietin ______________ of the protein in the blood.

A

enhances the stability

143
Q

Proteoglycans have what charge?

A

Negative

144
Q

How do proteoglycans function as a shock absorber?

A

They absorb water and then release it upon compression

145
Q

What is the difference between O, A, and B blood antigens?

A

O is missing and alpha-1,3 link. A has GalNAc at its alpha-1,3 link. B has Gal at its alpha-1,3 link.

146
Q

Which amino acids are used for the attachment of carbohydrates to proteins?

A

Asparagine, Serine, Threonine, Tyrosine

147
Q

Tay Sachs is the result of what?

A

Failure to degrade glycoproteins sugars that accumulate in the lysosomes.

148
Q

What is the flu virus surface protein?

A

Hemagglutinin

149
Q

What does the flu virus bind to?

A

Sialic acid

150
Q

What does hemoglobin do?

A

O2 carrier for red blood cells

151
Q

Does myoglobin or hemoglobin have a quaternary structure?

A

hemoglobin

152
Q

What does myoglobin do?

A

O2 storage, exponential graph

153
Q

What are some key characteristics of hemoglobin?

A

Tetra shape, exhibits cooperativity and is therefore sigmoidal

154
Q

Max Perutz

A

molecular structure of hemoglobin

155
Q

Addition of what to deoxyhemoglobin creates flat structured oxyhemoglobin?

A

O2 binding to Heme

156
Q

Deoxyhemoglobin and oxyhemoglobin are associated with what states respectively?

A

T state; R state

157
Q

What happens upon O2 binding to the T state?

A

A conformational change occurs forming the R state which includes a smaller space in the middle.

158
Q

What are the differences between hemoglobin with and without BPG?

A

Hemoglobin with BPG has a lower affinity for O2 and hemoglobin without BPG has a higher affinity for O2.

159
Q

What does the binding of BPG to hemoglobin do?

A

Stabilizes the T state

160
Q

How does BPG bind to hemoglobin?

A

BPG is negatively charged and binds to the positively charged residues of the hemoglobin.

161
Q

Why does fetal hemoglobin have a tighter affinity to O2?

A

The alpha chain is replaced with a gamma chain.

162
Q

What happens in sickle cell?

A

Soluble fibrils deform cells so that they cannot flow through capillaries

163
Q

More CO2 –> _________ pH

A

lower

164
Q

What affect does CO2 have on hemoglobin?

A

Hemoglobin reacts with N-terminus to stabilize deoxy T-State.

165
Q

What kind of bonds occur in reversible inhibitors?

A

non covalent

166
Q

Sulfa drug is what type of inhibitor?

A

Competitive inhibitor

167
Q

Which type of inhibitor binds at the active site?

A

Competitive

168
Q

Which type of inhibitor binds at the ES?

A

Uncompetitive

169
Q

Which type of inhibitor has allosteric binding?

A

Noncompetitive

170
Q

Which type of inhibitor raises Km?

A

Competitive

171
Q

Which type of inhibitor lowers Km?

A

Uncompetitive

172
Q

Which type of inhibitor does Km remain steady in?

A

noncompetitive

173
Q

Which type of inhibitor has no effect on Vmax?

A

competitive

174
Q

Which type of inhibitor lowers Vmax?

A

Uncompetitive and noncompetitive

175
Q

What is an example of a suicide inhibitor?

A

Penicillin

176
Q

What is an example of a group specific reagent?

A

DIPF

177
Q

What is an example of affinity labels?

A

TPCK

178
Q

Bacterial cell walls have __________ cell walls.

A

D amino acid

179
Q

How does penicillin work?

A

It forms covalent bonds to inhibit the enzyme that forms bacterial cell walls.

180
Q

Chymotripsin will cleave what?

A

Amino acid after big amino acid

181
Q

What is the catalytic triad?

A

Asp, His, Ser connected by peptide bonds

182
Q

DIPF means _________.

A

serine is present

183
Q

TPCK will only react with __________.

A

histidine forming keto group

184
Q

Chymotripsin has a ______ pocket with ______ van der Waals forces.

A

large, weak

185
Q

An enzyme that temporarily undergoes covalent catalysis as part of its mechanism.

A

chymotrypsin

186
Q

The type of reaction catalyzed by proteases

A

hydrolysis

187
Q

The inhibitor which binds only to the ES complex and lowers the Vmax and Km

A

uncompetitive

188
Q

The enzyme inhibition that can be overcome by increasing concentration of substrate.

A

competitive

189
Q

The shape of the kinetic plot of an enzyme that exhibits cooperative binding

A

sigmoidal

190
Q

An enzyme catalyst mechanism that uses a molecule other than water to accept or donate a proton.

A

Acid-Base Catalysis

191
Q

A catalytic mechanism that forces two substrates into proximity

A

Catalysis by approximation and orientation

192
Q

The sulfa drug is an example of what kind of inhibitor?

A

Competitive

193
Q

An uncompetitive inhibitor will have _________ lines on a double reciprocal plot.

A

parallel

194
Q

A _________ inhibitor binds irreversibly to the active site of an enzyme

A

suicide

195
Q

The ____________ stabilizes the intermediate of the hydrolysis of a peptide bond by chymotrypsin.

A

oxyanion hole

196
Q

A __________ inhibitor has a structure similar to the substrate and reversibly binds to the active site of the enzyme.

A

competitive

197
Q

Which three amino acids play the most important role at the active site in chymotrypsin?

A 
Serine (-OH)
Histidine (pentagon with nitrogen bottom left and top and double bonds bottom right and top left)
Aspartic acid (Cooh-ch2)
198
Q

The mechanism of chymotrypsin involves the formation of an unstable ________-shaped intermediate that is stabilized by the oxyanion hole

A

tetrahedral

199
Q

This is the organic portion of the heme group in hemoglobin

A

porphyrin

200
Q

This is the chemical form in which most of the CO2 is transported in the blood.

A

Bicarbonate

201
Q

This type of hemoglobin is composed of two alpha chains and two gamma chains.

A

Fetal Hb

202
Q

This is the molecule whose function is to store oxygen in muscle cells.

A

myoglobin

203
Q

A type of covalent bond that attaches the heme in myoglobin and hemoglobin

A

metal coordination bond

204
Q

This type of binding is indicated by a sigmoidal-shaped binding curve.

A

Cooperative

205
Q

This condition is a result of a single point mutation in the beta chain of hemoglobin.

A

Sickle cell

206
Q

Under normal conditions the heme iron in myoglobin and hemoglobin is in the ___ oxidation state

A

Fe 2+

207
Q

The ability of myoglobin to bind oxygen depends on the presence of this bound prosthetic group

A

heme

208
Q

In hemoglobin, the iron of the heme is bonded to the four nitrogens of porphyrin and to the proximal ____ residue of the global chain.

A

Histidine

209
Q

The biding of 2-3-bisphosphogycerate to hemoglobin _________ its affinity of oxygen binding

A

decreases

210
Q

The effect of pH on oxygen-binding of hemoglobin is referred to as the ________.

A

Bohr effect

211
Q

Carbon dioxide reacts with the amino terminal groups of hemoglobin to form carbamate goups, which carry a _______ charge.

A

negative

212
Q

The T-state of hemoglobin is stabilized by a salt bridge between Beta 1 Asp 94 and the C-terminal ________ of the Beta 1 chain

A

Histidine

213
Q

In normal adult hemoglobin, HbA, the Beta6 position is a glutamate residue whereas in sickle cell anemia hemoglobin, HbS, it a _____ residue.

A

Val

214
Q

As the presence of carbon increases, the affinity of oxygen binding to hemoglobin ___________.

A

decreases

215
Q

2,3-Bisphosphoglycerate binds only to the ________ form of hemoglobin.

A

Deoxy or Tstae

BIOL 600 (5 decks)

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