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biochem lecture 3 Flashcards

1
Q

reciprocal control

A

how are two opposing pathways regulated and under what conditions? can’t have them going simultaneously, so how do you see one pathway vs. another?

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2
Q

what is a strong component that controls regulation

A

hormones

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3
Q

how do hormones control metabolic activities

A

through activation/regulation of specific pathways

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4
Q

polysaccharides

A

sugar residues linked into a polymer

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5
Q

what are monomers of polysaccharides

A

monosaccharides

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6
Q

examples of monosaccharides

A

glucose, fructose, galactose

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7
Q

most abundant biomolecules in nature

A

cellulose

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8
Q

were is cellulose synthesized from

A

plants mainly

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9
Q

what are 2 main functions of polysaccharides

A

structure, energy/food source

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10
Q

describe the structural function of polysaccharide

A

polysaccharides (cellulose) make up cell wall in plants and some eukaryotes

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11
Q

describe the energy/food storage function of polysaccharides

A

serve as energy reservoirs/stores that can be tapped into and broken down to generate ATP

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12
Q

what types of polysaccharides are involved in energy/food storage

A

starches and glycogen

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13
Q

where is starch found

A

plant cells

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14
Q

where is glycogen found

A

animal cells

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15
Q

what are other uses for polysaccharides

A

proteins and lipids have carb units/polysaccharides attached to them

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16
Q

glycoproteins

A

proteins with carbs attached to them

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17
Q

glycolipids

A

lipids w/ carbs attached

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18
Q

where are glycoproteins/lipids found

A

cell surfaces (cell surface receptors, adhesion molecules, other cell surface proteins)

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19
Q

what is another function of polysaccharides

A

the heterogeneous array of polysaccharide containing components that make up the ECM

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20
Q

what is the ECM

A

holds us, our tissues, organs together; serves as a barrier and structure

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21
Q

what is a prime example of a structural polysaccharide

A

cellulose

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22
Q

what is the most abundant macro/biomolecule in nature

A

cellulose

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23
Q

where does the majority of cellulose come from

A

plants

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24
Q

where does a small portion of cellulose come from

A

algae, other eukaryotes w/ a cell wall

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25
Q

what is the equivalent of peptide bond for polysaccharides

A

glycosidic bond

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26
Q

what is a glycosidic bond

A

covalent bond that links together sugars

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27
Q

what are disaccharides

A

two sugars joined together via a glycosidic bond

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28
Q

sucrose

A

1,2 linked alpha glucose and beta fructose

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29
Q

what two monosaccharides make up sucrose

A

glucose and fructose

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30
Q

what kind of glycosidic linkage is found in sucrose

A

alpha-1,2-glycosidic linkage

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31
Q

what are sources of sucrose

A

sugar cane, sugar beet (common table sugar)

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32
Q

lactose

A

1,4 linked beta galactose and alpha glucose

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33
Q

what two monosaccharides make up lactose

A

glucose and galactose

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34
Q

what kind of glycosidic linkage is found in lactose

A

beta-1,4-glycosidic linkage

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35
Q

what are sources of lactose

A

milk

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36
Q

maltose

A

1,4 linked alpha glucose and alpha glucose

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37
Q

what two monosaccharides make up maltose

A

glucose and another glucose (2 glucoses)

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38
Q

what kind of glycosidic linkage is found in maltose

A

alpha-1,4-glycosidic linkage

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39
Q

what are sources of maltose

A

hydrolyzed starch

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40
Q

what is fructose

A

isomer of glucose

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41
Q

what does the alpha and beta designation have to do with

A

the orientation of the glycosidic bond

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42
Q

what is alpha configuration

A

cis configuration

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43
Q

what do the numbers in (alpha-1,2-glycosidic bond) mean

A

the specific carbons involved/linked together via this oxygen

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44
Q

describe a glycosidic bond

A

gonna have the carbon from one sugar, an oxygen, and the carbon from the linked sugar

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45
Q

describe the glycosidic bond on sucrose

A

C1 carbon of glucose and C2 carbon of fructose are linked together via the glycosidic bond –> alpha-1,2-glycosidic linkage

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46
Q

where is the beta configuration found on

A

lactose

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47
Q

where else do we see a beta-1,4-glycosidic linkage (besides lactose)

A

cellulose

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48
Q

lactose vs. cellulose

A

lactose is a disaccharide, cellulose is a polysaccharide

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49
Q

what is cellulose made up of

A

glucose units

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50
Q

most diverse biomolecules in nature

A

polysaccharides

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51
Q

why are polysaccharides the most diverse biomolecules in nature?

A

because they have 6 chiral centers —> potential for many isomeric forms

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52
Q

why are polysaccharides more diverse/abundant than proteins?

A

amino acids only have 1 chiral center, so its more restricted in terms of isomeric forms of those building blocks [basically due to 1 vs. 6 chiral centers, AAs can’t have as many isomeric forms]

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53
Q

what is cellulose

A

massive polymer of glucose units linked together via a beta-1,4-glycosidic bond

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54
Q

what is cellulose basically

A

structural polysaccharide from glucose

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55
Q

where is cellulose found

A

plant cell walls (primarily), but also bacteria, algae, fungi, seed hairs, animals

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56
Q

why can’t we digest cellulose?

A

humans don’t have enzymes that can break down the beta-1,4-glycosidic bonds found in cellulose

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57
Q

who does have enzymes that can break down the beta-1,4-glycosidic bonds

A

certain bacteria, fungi, protozoa, etc.

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58
Q

what is cellulose made of

A

glucose units linked together via beta-1,4-glycosidic bonds

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59
Q

who is an exception to this enzyme thing

A

ruminants; certain livestock like cows sheep have microorganisms in their gut that have enzymes

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60
Q

what enzyme breaks down beta-1,4-glycosidic bond in cellulose

A

cellulase

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61
Q

what is interesting about this situation

A

we have lactase, capable of breaking down the beta-1,4-glycosidic bond in lactose

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62
Q

why can’t lactase break down cellulose?

A

lactase is a disaccharide which lactase can easily accommodate; cellulose is WAYYY too large, can’t be broken down easily

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63
Q

what is cellulose an abundant source of

A

abundant energy source

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64
Q

can cellulose be metabolized by humans?

A

no

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65
Q

what can be metabolized by humans unlike cellulose

A

starch

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66
Q

what do starches provide

A

bulk of the energy we get from grains, potatoes etc.

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67
Q

why can we utilize starch as an energy source and not cellulose

A

unlike cellulose, we possess the enzymes capable of breaking the glycosidic bonds in starches

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68
Q

what is starch

A

major energy source form of polysaccharides in plants

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69
Q

what serves a parallel function as starches in animals

A

glycogen

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70
Q

what are 2 types of starches

A

amylose, amylopectin

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71
Q

what are both amylopectin and amylose made up of

A

glucose monosaccharide units linked together via alpha-1,4-glycosidic bonds

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72
Q

what is the primary difference between these 2 forms of starch

A

branch points/ amount of branching

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73
Q

what do alpha-1,4-glycosidic bonds generate

A

linear chains of glucose polymers (unbranched)

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74
Q

are alpha-1,4-glycosidic linkages branched or unbranched

A

unbranched glucose chains

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75
Q

how does a branch point occur

A

alpha-1,6-glycosidic bond

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76
Q

what does an alpha-1,6- bond do vs. alpha-1,4

A

positions the adjoining glucosyl units in a different orientation/position

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77
Q

how does this branching occur from the different types of bonds

A

the linkage occurs between diff carbons (1,4 vs. 1,6)

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78
Q

are alpha 1,4 and alpha-1,6 linkages also found in glycogen

A

yes

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79
Q

what does amylose tend to be

A

straight, linear, unbranched

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80
Q

what does amylopectin tend to have

A

more branching, because of its alpha-1,6 linkage

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81
Q

what delineates the amylose and amylopectin?

A

this alpha-1,6 linkage which causes branching

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82
Q

describe amylose

A

straight chain

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83
Q

describe amylopectin

A

branch point; alpha-1,6

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84
Q

what does a-1,6 give rise to in amylopectin

A

these branch points

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85
Q

what emanates from these branch points

A

more linear chains

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86
Q

how are reducing and non-reducing ends oriented

A

on opposite sides

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87
Q

how do you induce branch points vs. straight chains

A

when you form a 1,4-alpha linkage vs. an alpha-1,6, you can see that there’s a diff positioning of one sugar relative to others

88
Q

what occurs at non-reducing end

A

enzymes that break down glycogen work at the non-reducing end

89
Q

what are enzymes that break down glycogen

A

glycogen phosphorylase, debranching enzymes, etc.

90
Q

what are major sites of glycogen storage (glycogen stores)

A

liver and muscle

91
Q

what is the major energy storage form of polysaccharides in animals

A

glycogen

92
Q

what is glycogen

A

polymer, polysaccharide

93
Q

how is glycogen stored

A

glycogen granules; glucose units are linked together to form glycogen, concentrations are so high that they form a granule

94
Q

why do we store glucose in polymeric form (glycogen granules) and not as glucose monmers

A

glucose is soluble; if there’s to much it can swell and cause cell to burst

95
Q

polymers of glucose

A

glycogen

96
Q

describe solubility of glycogen (glucose polymers)

A

insoluble

97
Q

what does this insolubility mean

A

will have minimal effects on the osmotic state of the cell

98
Q

what does glucose’s solubility (in monomeric form) mean

A

can affect the osmotic state of the cell; high solute concentration inside the cell vs. outside the cell means more water outside the cell than inside the cell…. water would flow from outside to inside, cause the cell to swell up and burst

99
Q

glycogen

A

stored form of glucose

100
Q

glycogenin

A

enzyme that initiates the formation of glycogen from glucose through synthesizing the primer

101
Q

what protein serves as a mean to initiate glycogen protein formation

A

glycogenin

102
Q

what is glycogenin important for

A

synthesis of a short piece of glucose polymer, eight glucosyl residue know as the primer

103
Q

besides the primer, is the rest of this particle made by glycogenin?

A

no; made by 2 other enzymes: glycogen synthase and branching enzyme

104
Q

how does glycogenin form the primer

A

2 steps; first reaction involves transfer of UDP-glucose to glycogenin (glucosyl transferase reaction); second reaction is series of attachments of additional UDP glucose residues, up to 8 glucosyl residues

105
Q

describe the first step of glycogenin forming the primer

A

attachment/transfer ofa UDP-glucose to glycogenin protein

106
Q

how does this attachment of UDP-glucose to glycogenin occur

A

glycogenin is going to cleave UDP from glucose, and at the same time links the glucose to the glycogen and tyrosine residue

107
Q

what happens to the UDP

A

it’s eliminated; goes away

108
Q

what serves as a link/tether between UDP-glucose and glycogenin

A

tyrosine–194

109
Q

what happens when you attach a UDP molecule to glucose

A

glucose has been biochemically activated; enables it to participate in some biochemical reaction

110
Q

what is UDP glucose going to be acted on

A

by glycogenin

111
Q

what is the 2nd reaction

A

transfer of glucosyl residues to existing glucose(n)-glycogenin (attachments of additional UDP glucose residues)

112
Q

when is the primer formed

A

when you get up to 8 glucosyl residues, that forms the 8 glucosyl primer

113
Q

how are these glucosyl residues linked

A

via alpha-1,4-glycosidic bonds; once you reach 8, that forms primer

114
Q

what does primer serve as

A

scaffold/starting point for building the rest of the polymer

115
Q

what is the synthesis of the primer due to the actions of

A

protein glycogenin

116
Q

is glycogenin involved in any other parts of the particle

A

no, just in synthesis of initial primer

117
Q

how many chains of glycogen exist in tiers

A

glycogen chains of 12-14 residues exist in tiers

118
Q

describe inner chains

A

at least 2 apha-1,6 branches / branch points

119
Q

describe outer chains

A

unbranched

120
Q

how many tiers in mature particles

A

12

121
Q

how are the 12-14 glucosyl residues subdivided

A

inner and outer tiers

122
Q

what does it mean whenever you see a branch

A

it’s an alpha-1,6 glycosidic bond

123
Q

what color is the linear chain

A

purple

124
Q

what is emanating off of linear chains

A

the primer w/ branch point

125
Q

describe outer and inner tiers

A

inner tiers have branch points, outer tiers are unbranched

126
Q

describe a mature glycogen particle

A

upwards of 12 tiers, 55,000 individual glycogen residues; huge

127
Q

how many individual glycogen residues in a mature glycogen particle

A

upwards of 55,000

128
Q

what is the primer made up of

A

8 glucose units linked via 1,4-glycosidic bonds

129
Q

describe structure of glycogen particle

A

glycogenin-glucose chain in the center

130
Q

what is primer important for

A

formation of the particle; can’t build particle w/o primer

131
Q

what are the 2 catabolic pathways

A

glycogenolysis and glycolysis

132
Q

what is glycogenolysis

A

breakdown of glycogen into individual units in form of glucose-6-phosphoate units (glycogen –> glu-6-p)

133
Q

what is glycolysis

A

breakdown of glucose (glu-6-p) into pyruvate (glu-6-p –> pyruvate)

134
Q

what are the anabolic pathways

A

gluconeogenesis and glycogenesis

135
Q

what is gluconeogenesis

A

synthesis of glucose from pyruvate/lactate

136
Q

what is glycogenesis

A

synthesis of glycogen from glucose

137
Q

what enzymes are involved in glycogen breakdown (glycogenolysis)

A

glycogen phosphorylase, phosphoglucomutase, glucose-6-phosphatase

138
Q

what enzyme carries out the breakdown of glycogen

A

glycogen phosphorylase

139
Q

what is phosphorylase gonna do

A

acts on glycogen, removes glucose units one at a time

140
Q

how does phosphorylase work

A

takes a phosphate group, transfer that phosphate group to the glucose units that its releasing

141
Q

what two reactions does phosphorylase do simultaneously

A

removes glucose units from glycogen AND simultaneously phosphorylates that glucose

142
Q

what do you end up with after phosphorylase does its job

A

glucose-1-phosphate monomers AND ALSO glycogen has been shortened by one glucose unit

143
Q

what does phosphoglucomutase do

A

takes glucose-1-phosphate monomers (released from glycogen) and isomerizes G-1-P to G-6-P

144
Q

why does phosphoglucomutase isomerize G1P to G6P

A

G6P is the first intermediate in glycolysis; G-1-P can’t be directly fed into glycolysis, needs to undergo isomeization to go thru it

145
Q

what happens to glucose-6-phosphate once it’s formed

A

it will either go through glycolysis or released into the blood stream

146
Q

what happens to glucose-6-phosphate in the muscle

A

G6P is fed into glycolysis, gets oxidized to generate ATP in the muscle

147
Q

what happens to glucose in the muscle

A

stays in the muscle; like vegas

148
Q

what happens to glucose in the liver

A

released into the bloodstream

149
Q

what helps release glucose in liver into the bloodstream

A

glucose-6-phosphatase

150
Q

why do we phosphorylate glucose (G1P)

A

keeps the glucose trapped inside the cell, less likely for glucose to be transported out of the cell (what happens in vegas stays in vegas)

151
Q

are there situations where you wanna transport glucose out of the cell

A

yes, especially if it’s in the liver (glucose-6-phosphatase helps with that)

152
Q

what does glucose-6-phosphatase do

A

removes the phosphate group from G6P to form glucose and inorganic phosphoate

153
Q

is glucose-6-phosphatase in muscle or liver

A

liver, not found in muscle

154
Q

does muscle have glucose-6-phosphatase

A

no

155
Q

why does it make sense for liver to have glucose-6-phosphatase

A

because glycogen in liver is gonna serve as an energy reservoir for entire body

156
Q

where does glucose used in the brain or other tissues come from

A

glucose from diet or glucose synthesized (via gluconeogenesis) or glucose released from liver [unless we’re talking about muscle]

157
Q

what does it mean in terms of transport if glucose is phosphorylated

A

it’s trapped, can’t really transport to different parts of the body

158
Q

if you want to release glucose from liver into bloodstream what do you need to do

A

need to dephosphorylate it (cuz if it’s phosphorylated it’s trapped)

159
Q

why is phosphatase so important

A

glucose in the liver is all about its distribution to other parts of the body; can’t do that unless you dephosphorylate glucose first

160
Q

describe steps of glycogen breakdown

A

glucose that’s released from glycogen via glycogen phosphorylase produces glucose-1-phosphate.

glucose-1-phosphate gets isomerized into glucose-6-phosphate

in muscle, G6P gets directed to glycolysis
in liver, G6P gets dephosphorylated by phosphatase, glucose is released into bloodstream (to other tissues and organs)

161
Q

what’s another enzyme involved in glycogen breakdown

A

debranching enzyme

162
Q

what are the two activities associated w/ debranching enzyme

A

debranching activity and alpha-1,6 glucosidase activity

163
Q

describe the debranching activities of the enzyme

A

it helps remove the branch points when glycogen is being broken down.

164
Q

what kinds of linkages are in glycogen

A

alpha-1,4 linked glucose units (straight chains) AND alpha-1,6 branch points

165
Q

what breaks down glycogen

A

glycogen phosphorylase

166
Q

is glycogen phosphorylase able to break down a branch point

A

no; that’s where debranching enzyme comes in

167
Q

what does the debranching enzyme do (1st function)

A

transfers 3 of the 4 terminal glucosyl residues at the branch point to the adjacent straight chain

168
Q

what is still remaining after the transfer of 3 of the residues

A

there is still one remaining glucosyl residue at the alpha-1,6 branch point

169
Q

what is the other activity of the debranching enzyme

A

alpha-1,6 glucosidase activity

170
Q

describe the alpha-1,6-glucosidase activity

A

removes the 4th residue at the branch point, removing the branch point entirely

171
Q

what is the debranching enzyme known as

A

a tandem enzyme

172
Q

what is a tandem enzyme

A

enzyme that possesses 2 activities within the same polypeptide

173
Q

how are these two functions carried out

A

in sequence

174
Q

why do you need a debranching enzyme

A

phosphorylase is only able to act on straight chain polymers of glucose, not at a branch point

175
Q

what enzymes are involved in glycogen breakdown

A

glycogen phosphorylase, phosphoglucomutase, glucose-6-phosphatase, debranching enzyme

176
Q

what is glycogen phosphorylase

A

releases glucose monomers from glycogen in the form of glucose 1-P

177
Q

what is phosphoglucomutase

A

converts glucose 1-P into glucose 6-P which can feed into glycolysis

178
Q

what is glucose-6-phosphatase

A

converts glucose 6-P to glucose, allows glucose release into the bloodstream

179
Q

what is debranching enzyme

A

removes a-1,6 branch points and ‘linearizes’ glucose chain (2 activities in 1 enzyme)

180
Q

does phosphorylase act on straight or branched chains

A

straight chains; linear chains

181
Q

describe how phosphorylase and debranching enzymes work together

A

imagine phosphorylase chews on linear chain indefinitely until it hits a branch point, at which point the debranching enzyme acts on it

182
Q

what happens after the debranching enzyme transfers

A

the straight chain has been lengthened by 3 residues

183
Q

at when end do enzymes that break down glycogen work at

A

non-reducing ends

184
Q

what kind of sugar is glucose

A

a reducing sugar

185
Q

how do you define one end of glycogen molecule vs. another

A

glycogen phosphorylase acts at the non-reducing end

186
Q

what are reducing sugars

A

sugars that reduce mild oxidizing agents

187
Q

examples of mild oxidizing agents

A

ferric (Fe2+) or cupric (Cu2+) ions

188
Q

what kind of functional group is formed when sugars reduce mild oxidizing agents

A

aldehyde is oxidized to form a carboxyl group

189
Q

what is Fehling’s reaction

A

and old test trying to test for the presence of glucose in urine of patients (test for diabetes or high glucose levels in urine)

190
Q

how does Fehling’s reaction work

A

if glucose is present in a specimen, mix it w/ Fehling’s reagent (iron or copper ions) –> it will reduce those copper ions

191
Q

what would be reduced to what

A

Cu2+ is reduced to Cu+ (for example)

192
Q

how can you tell that the reaction has occurred

A

a color change

193
Q

why is glucose able to do this?

A

it can cycle from this cyclical form to a linear form

194
Q

what happens to glucose in this reaction

A

by virtue of the fact that it reduces the copper ion, glucose becomes oxidized from glucose into D-gluconate

195
Q

basically what ends up happening

A

goes from aldehyde to a carboxyl group (results from oxidation reaction)

196
Q

what is necessary in sugars for this reaction to happen

A

sugars able to do this have a free/accessible C1 carbon

197
Q

what sugars can’t participate in this reaction

A

sugars that have C1 carbons tied up in some way

198
Q

what does phosphoglucomutase act on

A

acts on glucose-1-phosphate monomers generated from the glycogen phosphorylase

199
Q

how are the glucose units released from glycogen released as

A

glucose-1-phosphate

200
Q

what does phoshporylase transfer

A

transfers an inorganic phosphate to each of the glucose/glucosyl residues that are released/cleaved from glycogen

201
Q

phosphoglucomutase

A

converts glucose-1-phosphate to glucose-6-phoshpate

202
Q

are mutases the same as isomerases

A

no, their catalytic mechanisms are kinda different than isomerase reactions

203
Q

what is interesting about phosphoglucomutase

A

in its active site it has a catalytically relevant serine residue that undergoes phosphorylation

204
Q

why is the phosphorylation of the serine within the active site of the enzyme significant

A

essential for enabling the isomerization of glucose-1-phosphate to glucose-6-phosphate

205
Q

how is the serine phosphorylation relevant

A

catalytic action of mutase is a 2 step rpocess

206
Q

what is the 1st step in catalytic action of mutase

A

transfer of phosphate group from serine of active site to G1P, produces di-phosphorylated intermediate glucose-1,6 bisphosphate

207
Q

what is the intermediate

A

glucose-1,6-bisphosphate

208
Q

what is the 2nd step in catalytic action of mutase

A

generate the glucose-6-phosphate product AND regenerate phosphorylated serine

209
Q

how is the phosphorylated serine regenerated

A

there’s going to be a second phosphoryl group transfer reaction here carried out within enzyme’s active site; phosphate at C1 position of glucose is transferred to serine

210
Q

what phosphate is transferred where

A

phosphate at C1 position of glucose is transferred to serine

211
Q

what does this process do

A

regenerates the enzyme, so that once it encounters the second G-1P molecule it can carry out the same reaction again

212
Q

what would happen without the regeneration of phosphorylated serine within the active site of enzyme

A

it wouldn’t be able to perform another round of catalysis

213
Q

what is the significance of G6P

A

it’s a usable form of glucose that can be fed into glycolysis

214
Q

can G1P be directly used in glycolysis

A

no; has to go through an isomerization reaction

215
Q

what is another significance of the phosphorylation of glucose

A

it traps the glucose inside the cell

216
Q

when would the glucose not want to be trapped

A

glucose in the liver; it wants to be released to the bloodstream and spread to other tissues/organs

217
Q

what has to happen for the glucose to be released

A

phosphorylated glucose has to undergo a round of dephosphorylation

biochem (15 decks)

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