Biochemistry and Molecular Biology: How Life Works

414 Pages·22.492 MB·English

by  Kevin Ahern

Topic Subtopic
Science & Mathematics Biochemistry
Biochemistry
and Molecular Biology
How Life Works
Course Guidebook
Professor Kevin Ahern
Oregon State University
Published by
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Kevin Ahern, PhD
Professor of Biochemistry and
Biophysics
Oregon State University
Kevin Ahern is a Professor of Biochemistry and Biophysics at Oregon
State University (OSU). He received BS and MS degrees from Oklahoma
State University and a PhD in Biochemistry and Biophysics from OSU.
Trained as a molecular biologist, Professor Ahern’s primary area of scholarly
activity is in biochemistry instruction. He has served on the OSU faculty
in Biochemistry/Biophysics since the mid‑1990s, teaching undergraduate
and graduate courses and serving as head advisor of the department. A
passionate supporter of undergraduate research, Professor Ahern served for
14 years as director of OSU’s Howard Hughes Medical Institute Summer
Undergraduate Research Program and for 3 years as OSU’s first Director for
Undergraduate Research. He is also the principal investigator and has served
since 2014 as director of OSU’s National Science Foundation–funded STEM
Leaders Program, which uses research experiences as tools for retention of
underrepresented minority students in STEM disciplines.
PROFESSOR BIOGRAPHY i
Professor Ahern coauthored 3 popular biochemistry textbooks: Biochemistry
(3rd edition with Christopher K. Mathews and Kensal E. van Holde),
Biochemistry Free and Easy, and Biochemistry Free for All. The last 2 books
were cowritten with Indira Rajagopal and are open educational resources that
have been downloaded more than 1/4 of a million times.
Paralleling his academic career, Professor Ahern had an extensive career in
scientific publishing, serving as a contributing editor to Science magazine,
Genetic Engineering & Biotechnology News, and BioTechniques. He has written
and published more than 700 articles, including 39 in Science magazine
and 42 in Biochemistry and Molecular Biology Education. Professor Ahern’s
approach to classroom teaching is novel. He writes and performs music,
verses, and limericks to help students learn complicated material. He has more
than 100 metabolic melodies he sings to, and with, students in his classes.
Professor Ahern’s efforts have been recognized with numerous local, regional,
and national awards. He was a 2‑time national finalist for Baylor University’s
prestigious Robert Foster Cherry Award for Great Teaching and was OSU’s
nominee for the US Professor of the Year Award in 2009. Professor Ahern
received OSU’s highest teaching recognition, the Elizabeth P. Ritchie
Distinguished Professor Award, and is an Eminent Professor of OSU’s
Honors College. He was named an OSU top professor by students a record
14 times and was inducted into OSU Libraries’ Open Access Hall of Fame in
2013. In 2019, Professor Ahern was the recipient of a Fulbright US Scholar
Award that provided funding for him to teach biochemistry at the University
of Malta.
As an academic advisor, Professor Ahern won every university award given
in that field. His mentoring of students was also recognized regionally with
the Oregon Health & Science University Foundation’s Medical Research
Foundation Mentor Award and nationally with the National Academic
Advising Association’s Outstanding Advising Award. u
ii Biochemistry and Molecular Biology
Table of Contents
INTRODUCTION
Professor Biography i
Course Scope 1
Acknowledgments 4
GUIDES
1 Biochemistry Is the Science of Us 5
2 Why Water Is Essential for Life 17
3 Amino Acids: 20 Building Blocks of Life 29
4 From Peptide Bonds to Protein Structure 40
5 Protein Folding, Misfolding, and Disorder 52
6 Hemoglobin Function Follows Structure 63
7 Enzymes’ Amazing Speed and Specificity 74
8 Enzyme Regulation in Cells 84
9 Fatty Acids, Fats, and Other Lipids 92
10 Sugars: Glucose and the Carbohydrates 100
11 ATP and Energy Transformations in Cells 110
12 Breaking Down Sugars and Fatty Acids 120
13 Metabolism Meets at the Citric Acid Cycle 132
14 Energy Harvesting in Animals and Plants 143
15 How Animals Make Carbs and Fats 154
16 Cholesterol, Membranes, Lipoproteins 165
TABLE OF CONTENTS iii
17 Metabolic Control during Exercise and Rest 176
18 How Plants Make Carbs and Other Metabolites 185
19 Recycling Nitrogen: Amino Acids, Nucleotides 195
20 Eating, Antioxidants, and the Microbiome 206
21 Hormones, Stress, and Cell Division 216
22 Neurotransmitters, the Brain, and Addiction 225
23 The Biochemistry of Our Senses 235
24 From Biochemistry to Molecular Biology 244
25 DNA and RNA: Information in Structure 255
26 DNA Replication in Bacteria; PCR in the Lab 265
27 Chromosome Replication, Telomeres, Aging 275
28 DNA Mismatch and Excision Repair 284
29 DNA Recombination, Gene Editing, CRISPR 293
30 Transcribing DNA to RNA 305
31 Translating RNA into Proteins 316
32 Protein‑Synthesis Controls and Epigenetics 328
33 Human Genetic Disease and Gene Therapy 337
34 Cancer Mechanisms and Treatments 348
35 Biotechnology, Stem Cells, Synthetic Biology 358
36 Omics: Genomics, Proteomics, Transcriptomics 367
SUPPLEMENTARY MATERIAL
Answers 377
Bibliography 402
iv Biochemistry and Molecular Biology
Course Scope
Biochemistry is a fascinating subject that explains how all life on Earth
functions. Unfortunately, the details of biochemistry often cause students
to get lost, and consequently, they don’t get to see the big picture. Without
connections to real life, the details simply become things to memorize for
tests—and are soon forgotten.
These lectures were designed to help everyone learn and enjoy biochemistry
using explanations of real‑world biochemistry problems as tools to understand
the subject—while still introducing college‑level biochemistry and not
dumbing it down. And without any need for memorization, you won’t spend
your time memorizing facts, giving much more time to listen to explanations
and think through the concepts.
Biochemistry combines biology—the science of life—and chemistry, the
science of molecules. Biochemistry, then, is the molecular basis of life. Every
single thing that makes people alive is due to biological molecules and
their interactions.
The first 24 lectures of this course focus on biological molecules and
metabolism, the thousands of different biochemical reactions that are
occurring in human cells. You’ll start by learning some basics about water,
the most abundant molecule in the body, in lecture 2. You’ll then move on
to amino acids, proteins, and enzymes in lectures 3 through 8. Along the
way, you’ll discover how the flexibility of proteins enables everything from
speeding up reactions to meeting the body’s needs for oxygen.
Lectures 9 and 10 introduce other major biomolecules: lipids and
carbohydrates. You’ll learn what metabolic energy is in lecture 11 and how
much of it you go through. Then, in lectures 12 and 13, you’ll discover how
COURSE SCOPE 1
cells break down dietary and stored carbs and fats to generate the energy
your body needs. Lecture 14 will bring all of the cell’s energy considerations
together under one umbrella, and you’ll learn how photosynthesis—the
capture of solar energy by plants—is related to metabolic energy generation
in humans.
Lectures 15 through 19 complete the tour of metabolism by examining
how human cells build carbs, fats, amino acids, and cholesterol. In lectures
20 through 24, you apply your biochemical knowledge to fascinating topics
that take you well beyond individual cells. These lectures discuss healthy
eating and fad diets, the language of cellular communication, the incredible
speed of neurotransmission, and the 5 manifestations of neurotransmission
that give rise to your senses.
The last 12 lectures of the course delve into biological information—
specifically, the specifications for building an organism and how that
information is stored in molecules to be used, maintained, and transmitted
to future generations. This is often called molecular biology. Whereas
biochemistry focuses on biomolecular reactions, molecular biology covers the
underlying cellular architecture that gives rise to the proteins that enable all of
the biochemical reactions.
DNA’s role in this process is dissected in lectures 25 through 29. Prepare to be
surprised at how you have DNA that is different from both of your parents’
and how little DNA would be needed to store all of the world’s computer
information. Lecture 30 illuminates the role of another information molecule,
RNA, in making proteins and how it may have played additional roles in early
life on Earth. The actual process of making proteins, and the many ways cells
control when and how much of each protein to make, is the subject of lectures
31 and 32.
Beginning with lecture 33, you’ll apply knowledge you’ve acquired to
understand human genetic diseases. You’ll also learn about some clever
and promising approaches to fixing some of them. Lecture 34 covers the
molecular basis of cancer and its treatment. The last 2 lectures (35 and
2 Biochemistry and Molecular Biology
36) focus on exciting, modern applications of biochemistry knowledge—
especially on medicine that is personalized and that works at the molecular
level to cure disease.
You can skip around a bit, if you like, but you’ll probably benefit more from
following the topics sequentially in each of the 2 modules—biochemistry and
molecular biology—as the lectures were created to build on lessons learned
from preceding lectures. The biochemistry and molecular biology modules
have also been structured to be independent so that watching the first
24 lectures isn’t essential to understanding the last 12. And if you want to go
deeper at any point in your biochemical journey, there is an extensive reading
list in the Bibliography and 2 biochemistry textbooks you can download for
free at www.davincipress.com/freeforall.html. u
COURSE SCOPE 3
Acknowledgments
The effort that went into putting these lectures together was enormous. I can
take credit for what is said in front of the camera, but much more happened
behind the scenes. Major credit for the scripts goes to Indira Rajagopal and
Jay Tate. Video production, editing, and graphics were the product of a
talented team led by Trish Golden, Kristen Westphal, and Trisa Barnhill.
Finally, I’d like to acknowledge Christopher Mathews for giving me the
opportunity to bring my teaching ideas to life, George Pearson for being an
incredible mentor and friend, and Neal Gladstone for inspiring me to write
lyrics and verse. u
4 Biochemistry and Molecular Biology