BIOCHEMISTRY BiOCHeMiSTRY

α-amylase Activity Measurement Method

An α-amylase solution (such as saliva) is added to a solution in which starch has been
dissolved inside a test tube. If an iodine solution is immediately added to this, before any
of the starch has been broken down, the starch will react with the iodine and produce a
blue-violet color. However, as time passes, the starch is broken down by the α-amylase,
and the color steadily changes (blue-violet  violet  red  orange  pale orange). Even-
tually, when all the starch has been broken down, the solution will become colorless. The
enzyme activity of α-amylase can be measured by using a spectrophotometer to quantify
the appearance of its color as a numeric value.

Color reaction

Starch When starch is present, it’s colored
blue-violet when it reacts with
iodine-potassium iodide.

α-amylase Iodine Reaction As the starch is broken down
solution is progresses by α-amylase, the color

added. steadily changes from blue-
violet to violet to red to

orange to pale orange and
finally becomes colorless.

α-amylase activity
measurement method

Molecular Biology and the Biochemistry of Nucleic Acids  237



* Projection Room *

Well, that's the end wham
of our lessons!

You two did a It's All
great job! thanks to you,

professor!

Um...by the way, The time
Professor... has come!

Now that we've Teach me the ultimate
finished our last secrets of dieting!

lesson... Epilogue 239

Silly girl—you've Wha-?
had the "secrets"

of dieting this
entire time!

Look... tap

This graph is the key! It's all right
Energy stored here in your
as fat
report.

Expended energy Eat moderately
Ingested energy and exercise
frequently!
If you expend more
calories than you Although there
ingest, you'll lose are endless fad
weight. diets out there, it
all really boils

down to that!

Guuuuuuh

And make sure you get Right, Kumi?
a good balance of Right?!

nutrients, of course! ...oh
dear.
You've learned that
proteins, saccharides,

and lipids are all
important to your body.
You must realize by now
that dieting by starving

yourself is complete
nonsense, right?

Stagger
Stagger

Well...I guess I Who am I kidding? I Calm down, Kumi!
learned some love food too much
valuable things. to watch what I eat!
I'll get fat for sure!
But...

Hmm, I
wonder...

Poor
Kumi

Waaaahhh

Doomed!

I'll eat cake and
pizza until I'm huge!

Kumi, you're being I'll turn into a
ridiculous. You've got a bloated, snack-
long way to go before scarfing manatee!

you're as big as a ...or maybe a
manatee. small bear
preparing for
If anything, heh hibernation,
you'd be more heh covered in
like a midsized heh winter fat.

sea lion... What?

squirm Hey! Hey, Professor...

squirm Fatty!

Ha ha ha ha

But you know...
if you think about
it, chubby animals
are almost always

the cutest, So
don't worry!

sob sob
sob

242 Epilogue

Give Kumi a break! Oh yeah? If you
have something to
Can't you see she's
too sensitive to stand say, you'd better
spill it!
up to this kind of
treatment?

sniff

First of all, I don't I will!
think Kumi's fat at all.
But even if she
GoaltD: holeow psnoewu5nitdlhsb!s! was fat, she'd still

be beautiful!

Epilogue 243

She's beautiful And she's extra
when she's stuffing beautiful in her

her face... bathing suit!

Hmmm...

Yum

She's beautiful
when she's poring
over her studies...

In fact... She's one of the
most beautiful girls

I've ever met! I'd
even go as far as

saying that...

Kumi is a total
dreamboat!

244 Epilogue

Well duuuuh!
You think I
don't know

that?

Huh?

Ne- Kumi is a cutie ...and the "fat
Nemoto? patootie! little bear"...

But...that "sea
lion" crack...

Just a little Worked like a charm,
reverse too. It's about time
Nemoto told you
psychology!
♪how he felt!
wink
Kumi, you studied
Yes, this lesson hard and learned
was a huge
some important
success, if I do things about your
say so myself.
body, right?

A trap... Definitely. No more
fad diets for me.

And you also
learned some
other important
information...hehe.

blush

246 Epilogue

So now that we're through But...but...I'm still
with our lessons, how about totally broke!

we go grab a bite to eat?

Yes!

Nemoto's treat, ...
of course.

Oh, I'm sure a smart kid like you
can figure something out.

I'll go get ready!

Um...Nemoto...

Epilogue 247

Thanks! For !
everything!

And now...

Let 's go
stuff our

faces!

248 Epilogue

Index

A atoms, 53 carbon bonds, 36
ATP (adenosine triphosphate), carbon dioxide
A (adenine), 206
ABO blood group system, 126 22–23, 82, 106 in carbon cycle, 46
acetyl-CoA, 72, 85, 115–117, autolysis, 216 fixation of, 51, 57–59
in photosynthesis, 32
120–122 B carboxyl group, 95
activation energy, 176 catalysts, 175
acyl-carnitine, 121 bad cholesterol, 100, 105 cells
acyl-CoA, 120–121 basal metabolism, 107 chemical reactions in, 26–35
adenine (A), 206 base catalysis, 216 interior of, 18–25
adenosine diphosphate (ADP), 82 base complementarity, 209–211 membrane of, 16
adenosine monophosphate base sequence, 219 origin of, 231
ß-oxidation, 119–120 structure of, 14–17
(AMP), 207 ß type, 143 cellular respiration, 37, 65
adenosine triphosphate (ATP), binary fission, 231 cellulose, 132, 142
biochemistry, definition of, 6, 8 centrifugation, 235
22–23, 82, 106 biochemists, 228–229 cerebral hemorrhage, 104
affinity chromatography, 233 biogeochemical cycle, 40–44 cerebral infarction, 104
affinity of enzymes, 181 biological catalyst, 175 chemical bonds, 140–144
alcohol, 20, 153 biopolymers, 36–37, 228 covalent, 36
aldoses, 83 blood double, 96
allosteric enzymes, 196–199 glycosidic, 138, 141–143, 173
a-amylase, 143, 144, 162, 163 ABO group system, 126 iconic, 36
a-amylase activity measurement glucosyltransferase, 169–171 metallic, 36
types of, 124–129, 169, 170 peptide, 155, 158
method, 237 blood sugar, 60, 63, 108 phosphodiester, 214
amino acids breathing, 64–65 chitin, 132
chlorophyll, 49–55
in carbon cycle, 45 C chloroplasts
overview, 154–157 overview, 17
primary structure of, 158 C (carbon). See carbon (C) photosynthesis and, 32
protein synthesis and, 27–28 C (cytosine), 206, 208 structure of, 49
quaternary structure of, 161 carbohydrates cholesterol
secondary structure of, 159 lipoproteins
tertiary structure of, 160 monosaccharides and cyclic
AMP (adenosine structure, 63 arteriosclerosis, 103–104
good and bad cholesterol,
monophosphate), 207 overview, 60–62
amphipathicity, 93 plants and, 48 105
amylopectin structure, 137–139 saccharides and -ose suffix, 63 overview, 102
amylose structure, 137–139 carbon (C) purpose of, 98–99
angina pectoris, 104 biogeochemical cycle and, 43 as steroid, 97
anticodon, 224 cycle of, 45–47
anti-nutritional factors, 193 fixation of, 57
antisense strand, 222 fundamentals of, 36
arteriosclerosis, 103–104

cholesterol ester, 101 DNA (deoxyribonucleic acid), 17, reaction measurement of
chromatography of columns, 202–203, 218–219 a-amylase activity
method, 237
232–233 DNA polymerase I, 212 DNA polymerase activity
citric acid cycle (TCA cycle), 67, DNA polymerase activity mea- method, 236
overview, 236
71–73, 115 surement method, 236
CoA (coenzyme A), 85 double bonds, 96 substrates and, 162–165
transferases
acetyl-CoA, 72, 85, 115–117, E
120–122 determining blood type,
EC Number (Enzyme Commission 169–171
acyl-CoA, 120–121 Number), 166
malonyl-CoA, 116–117 overview, 168
succinyl-CoA, 72 ecosystems using graphs to understand
column chromatography, biogeochemical cycle, 40–44
carbon cycle, 45–47 activation energy, 176
232–233 calculating Vmax and Km,
competitive inhibition, 193 electron transport chain, 52–55,
complementarity 67, 74–78 182–192
chemical reactions,
configurations, 211 electrophoresis, 233–234
concentration gradient force, 77 endoplasmic reticulum, 16, 17 175, 177
consumers, 48 endothelial cells, 113 maximum reaction
covalent bonds, 36 energy
cycles rate, 178
ATP, 82 Michaelis-Menten equation
biogeochemical, 40–44 creation of
carbon, 45–47 and Michaelis constant,
citric acid, 71–73 citric acid cycle, 71–73 180–181
cyclic structure, 61, 63, 141 electron transport chain, overview, 174
cytidine monophosphate, 208 essential fatty acids, 95
cytoplasm, 16 74–78 ether extraction, 204
cytosine (C), 206, 208 glucose decomposition by eukaryotes, 227
cytosol, 16, 30 exons, 219, 227
glycolysis, 68–70 expended energy, 106–110
D overview, 66–67 experiments
fat used as, 118–122 centrifugation, 235
deoxyadenosine ingested and expended, column chromatography,
monophosphate, 207 232–233
106–110 electrophoresis and western
deoxycytidine metabolism, 38 blots, 233–234
monophosphate, 208 Enzyme Commission Number (EC enzyme reaction measurement
a-amylase activity
deoxyguanosine Number), 166 measurement
monophosphate, 208 enzymes method, 237
DNA polymerase activity
deoxyribonucleic acid (DNA), 17, classifications of, 166–167 measurement
202–203, 218–219 DNA polymerase, 212–214 method, 236
fundamentals of, 37 overview, 236
deoxyribose, 207 hydrolases, 172–173 lectin blotting, 234–235
deoxythymidine inhibitors and overview, 232
external respiration, 37, 65
monophosphate, 208 allosteric enzymes,
deoxyuridine monophosphate, 208 196–199
detoxification, 21
D-form isomers, 84 overview, 193–195
diacylglycerol, 92 lipoprotein lipase, 112
dietary fiber, 142 proteins and
digestion, 7
amino acids, 154–161
overview, 150–151,

153–154
roles of, 151–152

250 Index

F glucosyltransferase, 169–171 inhibitors
glycocalyx, 125 allosteric enzymes, 196–199
fat glycogen, 132 overview, 193–195
ingested and expended energy, glycolipids, 94
106–110 glycolysis insulin, 108
overview, 106 internal respiration, 37, 65
saccharides in energy production, 30 introns, 219, 223, 227
fat used as energy source, glucose decomposition by, invertase, 133, 134
118–122 ionic bonds, 36
overeating and weight 68–70
gain, 123 in respiration, 67 K
overview, 111–117 glycosidic bond, 138,
ketoses, 83
fatty acids, 45, 95–96 141–143, 173 Krebs cycle (citric acid cycle), 67,
foam cells, 103 glycosyltransferase, 169
free cholesterol, 101 golgi apparatus, 16, 17 71–73, 115
fructofuranose, 83 good cholesterol, 100, 105
fructopyranose, 83 granums, 49 L
fructose, 59, 61, 116 graphs
fruit lactose, 61
activation energy, 176 LDL (low-density lipoproteins),
becoming sweet, 133–135 chemical reactions, 175, 177
saccharides, 131–132 maximum reaction rate, 178 101–105
sugar in, 130 Michaelis-Menten equation, lectin blotting, 234–235
furanose, 83 leptin, 109, 110
180–181, 191–192 L-form isomers, 84
G overview, 174 Lineweaver-Burk reciprocal plot,
reciprocals, 186–190
G (guanine), 206, 208 guanine (G), 206, 208 183–184, 192
galactose, 62 guanosine monophosphate, 208 lipids
genes
H cholesterol, 97–99
DNA, 17, 202–203, 218–219 fatty acids, 95–96
exons, 219, 227 HDL (high-density lipoproteins), lipoproteins
introns, 219, 223, 227 101–105
overview, 19 arteriosclerosis, 103–104
RNA. See RNA heme, 160 good and bad
hemiacetal, 63
(ribonucleic acid) hemoglobin, 161 cholesterol, 105
genetic material of cells, 202 high-density lipoproteins (HDL), overview, 100–102
global environment, 40–41 overview, 88–90
globin, 161 101–105 types of, 91–94
glucofuranose, 83 hydrocarbon chain, 95 lipogenesis, 29
gluconeogenesis, 29–30 hydrogen acceptor, 54 lipoprotein lipase enzyme, 112
glucose hydrolases, 119, 172–173 lipoproteins
hydrolysis, 173 arteriosclerosis, 103–104
in carbon cycle, 45 hydrophilic, 16, 93 good (HDL) and bad (LDL)
composition of, 62 hydrophobic, 16, 93
cyclic (ring) form, 61 cholesterol, 105
decomposition by glycolysis, I overview, 100–102
liquid scintillation counter, 236
68–70 ingested energy, 106–110 low-density lipoproteins (LDL),
in energy production, 30 ingested lipids, 112
in food, 59 inhibition 101–105
open-chain form, 61 lysosome, 16–17
competitive, 193
non-competitive, 194

Index 251

M enzyme reaction P
measurement, 236–237
macrophages, 103 palmitic acid, 116
malonyl-CoA, 116–117 lectin blotting, 234–235 pepsin, 162
maximum reaction rate, 178–179 overview, 232 peptide bonds, 155, 158
messenger RNA (mRNA), genes peptidyl transfer, 158
DNA, 218–219 phagocyte, 103
222–223 RNA, 220–227 phosphate, 205
metabolism, 38, 107, 231 molecular biology phosphodiester bond, 214
metabolism first theory, 231 and biochemistry, 228–230 phospholipids, 16, 93, 95
metallic bonds, 36 origin of cells, 231 phosphopantetheine group, 85
methane, 46 recombinant DNA phosphorylation, 56
Michaelis constant, 180–181
Michaelis-Menten equation, techniques, 229–230 photophosphorylation reaction,
nuclein, 204 50–56
180–181, 191–192, 196 overview, 199–203
Miescher, Friedrich, 204 nuclein, 204 photosynthesis
milk sugar, 63 nucleosides, 205 carbon dioxide fixation, 57–59
mitochondria, 16–17, 31, 116 nucleotides chloroplast structure, 49
molecular biology base complementarity overview, 79–81
photophosphorylation reaction,
and biochemistry, 228–230 and DNA structure, 50–56
origin of cells, 231 209–211 plants, 48
recombinant DNA techniques, DNA replication and enzyme
DNA polymerase, photosystem I, 55
229–230 212–214 photosystem II, 55
monoacylglycerol, 92 overview, 205–208 Phytolacca americana plant, 228
monosaccharides RNA structure, 214–217 pokeweed, 228
nucleus, 16, 17, 204 polynucleotides, 209–210
aldoses and ketoses, 83 polypeptide chain, 158
D-form and L-form, 84 O polysaccharides, 131–132, 137
pyranose and furanose, 83 post-genome era, 230
in respiration, 62–63 obesity precursor mRNA, 223
structure of, 131–132 ingested and expended energy, primary structure, 158
mRNA (messenger RNA), 106–110 producers, 48
overview, 106 product, defined, 37
222–223 saccharides progesterone, 98
multicellular organisms, 15 fat used as energy source, protease, 204
myocardial infarction, 104 118–122 protein catabolism enzymes,
overeating and weight
N gain, 123 164, 165
overview, 111–117 proteins
NADH molecule, 54–55, 75
NADPH molecule, 54–55 oligosaccharides, 131–132, 137 amino acids
neutral fat, 91 open-chain glucose form, 61 overview, 154–157
neutral lipids, 91 organelles, 16 primary structure of, 158
non-competitive inhibition, -ose suffix, 63 quaternary structure of, 161
overeating, 123 secondary structure of, 159
194–195 oxidation-reduction, 37 tertiary structure of, 160
nucleic acids. See also nucleotides oxidized, defined, 37
oxygen, 77, 216 created by cells, 18
conducting experiments overview, 150–151, 153–154
centrifugation, 235 roles of, 151–152
column chromatography,
232–233
electrophoresis and
western blots, 233–234

252 Index

proteios, 154 RNA (ribonucleic acid) sugar, 60–61, 116, 130
pyranose, 83 in creation of proteins, 203 sugar chain, 126
pyrimidine bases, 206 mRNA, 222–223
pyruvate, 68, 72 overview, 220–221 T
pyruvic acid, 29–30 ribozymes, 226–227
rRNA and tRNA, 223–225 T (thymine), 206, 208
Q self-splicing, 227 TCA cycle (citric acid cycle), 67,
structure of, 214–217
quaternary structure, 161 71–73, 115
rRNA (ribosomal RNA), 223–225 templates, DNA replication, 211
R tertiary structure, 160
S testosterone, 98
rate-limiting reaction, 117 thylakoid membrane, 52
reaction rate, 178 saccharides thylakoids, 49
reciprocals, 186–190 aldoses and ketoses, 83 thymine (T), 206, 208
recombinant DNA techniques, in carbon fixation, 58 thymus, 228
D-form and L-form transcription, 222
229–230 isomers, 84 transferases
reduced, defined, 37 excess, transformation into fat,
reducing agents, 37 111–117 glucosyltransferase and blood
replication first theory, 231 in fruits, 133–135 type, 169–171
replication of DNA, 211, 212–214 -ose suffix and, 63
reproduction, 231 overeating and weight overview, 168
respiration gain, 123 transfer RNA (tRNA), 223–225
photosynthesis and, 25 triacylglycerol, 92, 113–114
breathing, 64–65 pyranose and furanose, 83 tRNA (transfer RNA), 223–225
carbohydrates types of, 131–132
using fat as energy source, U
monosaccharides and cyclic 118–122
structure, 63 U (uracil), 206, 208
secondary structure, 159 unicellular microorganisms, 15
overview, 60–62 self-replication, 231 unsaturated carbons, 96
saccharides and -ose sense strand, 222 unsaturated fatty acids, 96
side chain, 159 uracil (U), 206, 208
suffix, 63 sigmoid curve, 196 uridine monophosphate, 208
energy creation by specific gravity, 101
spliceosome, 227 V
citric acid cycle, 71–73 splicing, 223
electron transport chain, starch, 66, 132, 136 very low-density lipoproteins
steroids, 97 (VLDL), 113
74–78
glucose decomposition by steroid hormone, 98 vitalism theory, 229
steroidal skeleton, 97 Vitamin D, 99
glycolysis, 68–70 stroma, 57
overview, 66–67 substance metabolism, 38 W
fundamentals of, 37 substrates, 37, 162–165
overview, 79–81 subunit, 161 weight gain, 123
ribonucleic acid (RNA). See RNA succinyl-CoA, 72 western blots, 233–234
(ribonucleic acid) sucrose, 59, 61–63 wine, 21
ribosomal RNA (rRNA), 223–225 sucrose-phosphate synthase,
ribosomes
in cells, 16–19 133–134
defined, 37
in protein synthesis, 27–28
ribozymes, 226–227
rice starch, 136–137
ring structure of glucose, 61, 141

Index 253

Notes

Notes

Notes

Notes

About the Author

Masaharu Takemura, PhD, is currently an Associate Professor at the Tokyo University of
S­ cience. His specialties are molecular biology and biology education.

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