page_content stringlengths 12 2.63M | metadata unknown |
|---|---|
#### **tertiary structure**
Complete three-dimensional structure of a fully folded protein.
#### **therapeutic cloning**
Procedure that uses nuclear transplantation to generate cells for tissue repair and other such purposes, as opposed to producing whole multicellular individuals.
#### **thioester bond**
H... | {
"Header 1": "Glossary",
"Header 3": "**RNA world**",
"token_count": 1333,
"source_pdf": "datasets/websources/biochem/Alberts_-_Essential_Cell_Biology__4th_ed._.pdf"
} |
Small, membrane-enclosed, spherical sac in the cytoplasm of a eukaryotic cell.
#### **vesicular transport**
Movement of material between organelles in the eukaryotic cell via membrane-enclosed vesicles.
#### **virus**
Particle consisting of nucleic acid (RNA or DNA) enclosed in a protein coat and capable of rep... | {
"Header 1": "Glossary",
"Header 3": "**vesicle**",
"token_count": 559,
"source_pdf": "datasets/websources/biochem/Alberts_-_Essential_Cell_Biology__4th_ed._.pdf"
} |
| A | actin-binding proteins 583β584, | adipocytes 442 |
|-------------------------------------------------------------------|-----------------------------------------|--------------------------------------|
| abbreviations an... | {
"Header 1": "Index",
"token_count": 1694,
"source_pdf": "datasets/websources/biochem/Alberts_-_Essential_Cell_Biology__4th_ed._.pdf"
} |
| Alu sequence 302, 303F, 309, 314F | glucose transport 393β394 | bacterial biosynthesis and 152F |
|------------------------------------|-----------------------------------------|---------------------------------------|
| AMD (age-related macular | model organisms 28β29, 32 ... | {
"Header 1": "Index",
"token_count": 2607,
"source_pdf": "datasets/websources/biochem/Alberts_-_Essential_Cell_Biology__4th_ed._.pdf"
} |
175 | pairing | CaM-kinase effects 549 |
| Avogadro's number 41 | bases (in solution) | energy consumption 409 |
| axons | basic side chain amino acids 74 | gene expression... | {
"Header 1": "Index",
"token_count": 1466,
"source_pdf": "datasets/websources/biochem/Alberts_-_Essential_Cell_Biology__4th_ed._.pdf"
} |
coli | blood groups 53, 71 | CaM-kinases (Ca2+/calmodulin |
| bacterial flagellae 459 | blood samples 336, 339F, 346, | dependent protein kinases) |
| bacteriophages 176, 310F | 707F | 549, 5... | {
"Header 1": "Index",
"token_count": 11651,
"source_pdf": "datasets/websources/biochem/Alberts_-_Essential_Cell_Biology__4th_ed._.pdf"
} |
coli | dividing mitochondrion 450F |
| DNA viruses 309, 310F | comparative genomics 306F | endoplamic reticulum 499F |
| DNP (2,4-dinitrophenol) 462β463 | DNA replication in 201β202, | Golgi apparatus 511F |
| dock... | {
"Header 1": "Index",
"token_count": 2785,
"source_pdf": "datasets/websources/biochem/Alberts_-_Essential_Cell_Biology__4th_ed._.pdf"
} |
coli |
| phospholipid synthesis at 366β367 | lysozyme 145F, 148F | estradiol 529T, 532 |
| possible origins 491 | enzymes | ethylene as a plant hormone 559,<br>560F ... | {
"Header 1": "Index",
"token_count": 24133,
"source_pdf": "datasets/websources/biochem/Alberts_-_Essential_Cell_Biology__4th_ed._.pdf"
} |
ethylene glycol 106
complementary 88β89
| precursor cells 705β706 | protein phosphorylation by 154 | lifetime and breakdown 250β252 |
|----------------------------------------|---------------------------------------|--------------------------------------|
| prereplicative complexes 617... | {
"Header 1": "Index",
"token_count": 14073,
"source_pdf": "datasets/websources/biochem/Alberts_-_Essential_Cell_Biology__4th_ed._.pdf"
} |
tropicalis 298, | |
| biologically significant properties | 609, 610F | |
| 48, 68β69 | xeroderma pigmentosum 211β212 | ... | {
"Header 1": "Index",
"token_count": 241,
"source_pdf": "datasets/websources/biochem/Alberts_-_Essential_Cell_Biology__4th_ed._.pdf"
} |
#### **Corporate Headquarters**
4840 Westfields Boulevard | Suite 500 | Chantilly, Virginia | 20151β2299 [phone] 1.800.832.2412 | [fax] 703.378.3819 | [web] [www.thegreatcourses.com](http://www.thegreatcourses.com)
#### **Copyright Β© The Teaching Company, 2019**
#### Printed in the United States of America
This... | {
"Header 1": "**Biochemistry and Molecular Biology**",
"Header 2": "**THE GREAT COURSES**",
"token_count": 204,
"source_pdf": "datasets/websources/biochem/Biochemistry-and-Molecular-Biology-9572.pdf"
} |
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 Ahe... | {
"Header 1": "**Kevin Ahern, PhD**",
"token_count": 657,
"source_pdf": "datasets/websources/biochem/Biochemistry-and-Molecular-Biology-9572.pdf"
} |
| | | INTRODUCTION |
|--|--|--------------|
| | | |
| | Professor Biography<br>i |
|----|--------------------------------------------------|
| | Course Scope<br>1 |
| | Acknowledgments<br>4 |
| | ... | {
"Header 1": "**Table of Contents**",
"token_count": 834,
"source_pdf": "datasets/websources/biochem/Biochemistry-and-Molecular-Biology-9572.pdf"
} |
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 testsβand are soon... | {
"Header 1": "**Course Scope**",
"token_count": 934,
"source_pdf": "datasets/websources/biochem/Biochemistry-and-Molecular-Biology-9572.pdf"
} |
Biochemistry is new, as the sciences go. Separately, the subjects of chemistry and biology have been around since the time of the ancient Greeks and Egyptians. But the idea of combining them is much more recent. About 200 years ago, there was no evidence that a science of biochemistry was even possible. Even 100 years ... | {
"Header 1": "**Biochemistry: A Young Science**",
"token_count": 525,
"source_pdf": "datasets/websources/biochem/Biochemistry-and-Molecular-Biology-9572.pdf"
} |
Biochemistry is mostly about molecules. The molecules of biochemistry are overwhelmingly built using primarily just 6 bonding elements: carbon, oxygen, nitrogen, and hydrogen, with supporting help from sulfur and phosphorus.
What matters for joining these atoms together is electrons. Chemical bonds always involve ele... | {
"Header 1": "**Biochemistry: A Young Science**",
"Header 3": "**Molecules and Minerals**",
"token_count": 1238,
"source_pdf": "datasets/websources/biochem/Biochemistry-and-Molecular-Biology-9572.pdf"
} |
Proteins are the workhorses of the cell. Proteins are polymers, which are long strings of molecules joined end to end. But there's more than one way to build a polymer.
Nonliving polymers, such as plastics, tend to repeat a single building block over and over. Such repetition provides uniformity: A sheet of plastic w... | {
"Header 1": "**Proteins and Enzymes**",
"token_count": 515,
"source_pdf": "datasets/websources/biochem/Biochemistry-and-Molecular-Biology-9572.pdf"
} |
Cells are the fundamental unit of life. Overall, you could think of cells as houses for molecular reactions. Like houses, cells have surrounding walls in
the form of a membrane. Some cellular houses are more like tents, with a simple design, small size, and only a single room for the re... | {
"Header 1": "**Proteins and Enzymes**",
"Header 3": "**Cells as Houses for Reactions**",
"token_count": 682,
"source_pdf": "datasets/websources/biochem/Biochemistry-and-Molecular-Biology-9572.pdf"
} |
The key to the behavior of water is in a property of atoms called electronegativity, which is a measure of the affinity of an atom's nucleus for its outermost electrons. You can think of it as how strongly the nucleus of the atom holds on to those electrons. Atoms whose nuclei hold on tightly to outer electrons have hi... | {
"Header 1": "**Water's Electronegativity**",
"token_count": 2028,
"source_pdf": "datasets/websources/biochem/Biochemistry-and-Molecular-Biology-9572.pdf"
} |
In other words, because water is held together by hydrogen bonds, water is an effective medium and solvent for the molecules important for life, both inside cells and in the fluids that surround them.
A solvent is a liquid that dissolves something. Ocean water is full of dissolved salts. Water uses its partial charge... | {
"Header 1": "**Water's Electronegativity**",
"token_count": 637,
"source_pdf": "datasets/websources/biochem/Biochemistry-and-Molecular-Biology-9572.pdf"
} |
Another property of water that is important in biological chemistry is water's own ability to ionize, or break into ions. This happens only to a very small number of water molecules, but it does occur and is important.
When water ionizes, it breaks into a positively charged hydrogen ion (H+ ), Only about one water mo... | {
"Header 1": "**Water's Ability to Ionize**",
"token_count": 1188,
"source_pdf": "datasets/websources/biochem/Biochemistry-and-Molecular-Biology-9572.pdf"
} |
There are 20 kinds of amino acids that are strung together in proteins. Because amino acids are the building blocks of all proteins, all cells need amino acids.
Amino acids found in proteins all have the same simple core structure: a central carbon, an amino group with $\mathrm{NH}_2$ , an acid group with COOH, and ... | {
"Header 1": "R Groups and Chiral Compounds",
"token_count": 704,
"source_pdf": "datasets/websources/biochem/Biochemistry-and-Molecular-Biology-9572.pdf"
} |
Alanine (Ala, A)
H O
| ||
H<sub>2</sub>N
$$-$$
C $-$ OH
CH<sub>3</sub>
Valine (Val, V)
H O
I ||
$$H_2N - C - C - OH$$
$H_3C - C - H$
$CH_3$
Hydrophobic amino acids, which have R groups that mostly contain carbons and hydrogens, include glycine, alanine, valine, leucine, and isoleucine. The degree of hydroph... | {
"Header 1": "R Groups and Chiral Compounds",
"Header 2": "**Nonpolar, Hydrophobic Amino Acids**",
"token_count": 2041,
"source_pdf": "datasets/websources/biochem/Biochemistry-and-Molecular-Biology-9572.pdf"
} |
It is also the most chemically interesting of the basic-charged amino acids. Histidine's ring contains 2 nitrogen atoms that share a proton when the pH is sufficiently low, giving the group as a whole its positive charge. Histidine's ring-shaped R group is the basic amino acid with the lowest pKa of 6, meaning at physi... | {
"Header 1": "R Groups and Chiral Compounds",
"Header 2": "**Nonpolar, Hydrophobic Amino Acids**",
"token_count": 327,
"source_pdf": "datasets/websources/biochem/Biochemistry-and-Molecular-Biology-9572.pdf"
} |
The English language has 26 letters in its alphabet, and we can construct every word in the language using different combinations of the letters. Likewise, the 20 amino acids can be used to create many different protein "words." When we write words, we know that which letters we use and the
order of the letters matte... | {
"Header 1": "FROM PEPTIDE BONDS TO PROTEIN STRUCTURE",
"Header 2": "The Amino Acid Alphabet",
"token_count": 754,
"source_pdf": "datasets/websources/biochem/Biochemistry-and-Molecular-Biology-9572.pdf"
} |
Proteins are made up of chains of amino acids that vary in length, the kinds, and the order of their constituent amino acids. This sequence of amino acids is referred to as the primary structure of a protein, and that determines its properties.
Two different proteins will never have the same sequence of amino acids. ... | {
"Header 1": "FROM PEPTIDE BONDS TO PROTEIN STRUCTURE",
"Header 2": "**The Primary Structure of a Protein**",
"token_count": 1233,
"source_pdf": "datasets/websources/biochem/Biochemistry-and-Molecular-Biology-9572.pdf"
} |
| | | | | T<br>E<br>E<br>H<br>A S<br>T<br>E<br>B | N<br>R<br>U<br>E T<br>RS<br>VE<br>RE | A<br>T<br>E<br>A β B<br>H<br>ALP |
|----------------------------------------------------------------------------------------------------------... | {
"Header 1": "FROM PEPTIDE BONDS TO PROTEIN STRUCTURE",
"Header 2": "**The Primary Structure of a Protein**",
"token_count": 1109,
"source_pdf": "datasets/websources/biochem/Biochemistry-and-Molecular-Biology-9572.pdf"
} |
The regular, repeating secondary structures of collagen and other fibrous proteins are very important. But most proteins are not fibrous, and in these proteins, secondary structures do not extend for long distances, as they do in fibrous proteins.
Instead, for nonfibrous proteins, secondary structures are local patte... | {
"Header 1": "FROM PEPTIDE BONDS TO PROTEIN STRUCTURE",
"Header 2": "**Tertiary Structure**",
"token_count": 737,
"source_pdf": "datasets/websources/biochem/Biochemistry-and-Molecular-Biology-9572.pdf"
} |
Proteins that are made up of more than one polypeptide have quaternary structure, which is defined by interactions among individual folded polypeptides. Quaternary structure can help regulate the activity of proteins.
Hemoglobin, for example, has 4 folded polypeptides that associate with each other to form the functi... | {
"Header 1": "**Quaternary Structure**",
"token_count": 453,
"source_pdf": "datasets/websources/biochem/Biochemistry-and-Molecular-Biology-9572.pdf"
} |
In the 1950s, the first experiments began by taking a protein out of the cell, unfolding it, and then seeing if it could refold in a test tube, independent of any cellular factors. The protein that Christian Anfinsen serendipitously chose was the enzyme ribonuclease (RNase) A, which is relatively smallβmade up of only ... | {
"Header 1": "**Protein Folding**",
"token_count": 1767,
"source_pdf": "datasets/websources/biochem/Biochemistry-and-Molecular-Biology-9572.pdf"
} |
Some of the most mysterious diseases result from protein folding gone wrong. These are the prion diseases, also known as transmissible spongiform encephalopathies (TSEs), which affect humans and other animals. They are a group of degenerative disorders that affect the brain. Mad cow disease, or bovine spongiform enceph... | {
"Header 1": "**Protein Folding**",
"Header 3": "**Protein Folding Gone Wrong**",
"token_count": 304,
"source_pdf": "datasets/websources/biochem/Biochemistry-and-Molecular-Biology-9572.pdf"
} |
Intrinsically disordered proteins (IDPs) have no fixed 3-D conformation in at least part of the protein. Surprisingly, this is not a harmful aberration. Numerous proteinsβperhaps 40% of all proteinsβmay have at least one region that is intrinsically disordered.
But if structure determines function, then why would so ... | {
"Header 1": "**Protein Folding**",
"Header 2": "**Flexible Proteins**",
"token_count": 827,
"source_pdf": "datasets/websources/biochem/Biochemistry-and-Molecular-Biology-9572.pdf"
} |
Our cells need oxygen to efficiently obtain energy from food. While some microbes survive in anaerobic conditionsβthat is, without oxygenβtheir use of foodstuffs is inefficient compared to ours. This is why animals have oxygen-carrying proteins to provide a steady supply of oxygen. Almost every vertebrate has hemoglobi... | {
"Header 1": "Carrying Oxygen",
"token_count": 733,
"source_pdf": "datasets/websources/biochem/Biochemistry-and-Molecular-Biology-9572.pdf"
} |
Besides carrying oxygen, hemoglobin has other functions. It also picks up 2 sets of molecular baggage in the tissues and dutifully hauls them back to the lungs.
- w Carbon dioxide is one type of baggage, a direct product of various oxidative processes in cells that create energy. Small quantities of carbon dioxide ca... | {
"Header 1": "**Carrying Protons and Carbon Dioxide**",
"token_count": 1952,
"source_pdf": "datasets/websources/biochem/Biochemistry-and-Molecular-Biology-9572.pdf"
} |
Enzymes are called catalytic for 2 reasons: They speed up the rate at which biochemical reactions happen in cells, and each enzyme molecule can be used over and over without being changed.
Enzymes are proteins. They contain amino acids, whose unique side chains play important roles in the mechanism of catalysis. But ... | {
"Header 1": "**Enzymes as Catalysts**",
"token_count": 547,
"source_pdf": "datasets/websources/biochem/Biochemistry-and-Molecular-Biology-9572.pdf"
} |
To look at what's happening in catalysis, we use Gibbs free energy (*G*), a measure of the amount of energy available to do useful work in a process. In a biochemical reaction, the work being done is the making and/or breaking of chemical bonds.
The energy changes for a reaction can be shown in a simple graph. On the... | {
"Header 1": "**Enzyme Energy**",
"token_count": 1591,
"source_pdf": "datasets/websources/biochem/Biochemistry-and-Molecular-Biology-9572.pdf"
} |
Enzyme velocities are measured in product made per time. If substrate is in short supply, the enzyme will spend time idling, and maximum velocity will not be reached. However, if the enzyme is saturated with substrateβmeaning that as soon as a product molecule is released, a new substrate is boundβthen the reaction wil... | {
"Header 1": "**Enzyme Velocity**",
"token_count": 645,
"source_pdf": "datasets/websources/biochem/Biochemistry-and-Molecular-Biology-9572.pdf"
} |
Cells regulate enzyme activity, exerting precise control over synthesis and breakdown of biomolecules, for every molecule they make. And they must do so continuously to maintain stable internal conditions, called homeostasis.
One reason that biochemists care so much about the control of enzyme activity is that many m... | {
"Header 1": "ENZYME REGULATION IN CELLS",
"Header 3": "**How Cells Regulate Enzymes**",
"token_count": 583,
"source_pdf": "datasets/websources/biochem/Biochemistry-and-Molecular-Biology-9572.pdf"
} |
A simple, yet much more nuanced, mechanism for control is allosteric regulation, which works like a dimmer on a light to adjust brightness. In this form of regulation, the binding of a regulatory molecule in one part of the enzyme can adjust the enzyme's behavior. The binding of these regulatory molecules, called effec... | {
"Header 1": "**Allosteric Regulation**",
"token_count": 685,
"source_pdf": "datasets/websources/biochem/Biochemistry-and-Molecular-Biology-9572.pdf"
} |
Another common mechanism for enzyme regulation also acts like an on-off switch, but in this case, the switch is reversibleβwithout needing an inhibitor protein to cover the active site. How it works depends on the covalent addition or removal of what is usually a phosphate to the enzyme.
These enzymes exist in 2 stat... | {
"Header 1": "**Allosteric Regulation**",
"Header 3": "**Covalent Modification**",
"token_count": 1224,
"source_pdf": "datasets/websources/biochem/Biochemistry-and-Molecular-Biology-9572.pdf"
} |
Lipids do not play in the watery neighborhoods that other biomolecules do. Some lipids, such as fats and cholesterol, are fully phobic about water. Others, such as membrane lipids, are ambivalentβa part of them fears water, but another is drawn to it.
Unlike proteins, carbohydrates, and nucleic acids, lipids are not ... | {
"Header 1": "Fatty Acids",
"token_count": 672,
"source_pdf": "datasets/websources/biochem/Biochemistry-and-Molecular-Biology-9572.pdf"
} |
Our bodies can make most, but not all, of the fatty acids we need. Two classes of polyunsaturated fatty acids we cannot make are omega-3 and omega-6 fatty acids, and this makes them essential to get from the food we eat.
When the doctor checks your cholesterol, the lipid profile includes a number for your triglycerid... | {
"Header 1": "**Triacylglycerols**",
"token_count": 707,
"source_pdf": "datasets/websources/biochem/Biochemistry-and-Molecular-Biology-9572.pdf"
} |
A related group of molecules have only 2 fatty acids attached to a glycerol, and in the place of the third one, they have small molecules linked to a phosphate at that position. These are called glycerophospholipids, or phosphoglycerides. They have a family resemblance to the triacylglycerols but differ by featuring a ... | {
"Header 1": "**Glycerophospholipids**",
"token_count": 393,
"source_pdf": "datasets/websources/biochem/Biochemistry-and-Molecular-Biology-9572.pdf"
} |
Another important group of amphiphilic membrane lipids is the sphingolipids. These molecules get made by joining the amino acid serine to a 16-carbon fatty acid known as palmitic acid followed by several modifications. The amine of serine provides an attachment point for a second acyl group, so sphingolipids, like glyc... | {
"Header 1": "**Glycerophospholipids**",
"Header 3": "**Sphingolipids**",
"token_count": 773,
"source_pdf": "datasets/websources/biochem/Biochemistry-and-Molecular-Biology-9572.pdf"
} |
Biochemically, sugars are saccharides, a group of molecules with a particular chemical makeupβa simple carbohydrate. The general chemical formula for sugars is $CH_2O$ , with one carbon atom for every $H_2O$ water molecule.
In simple sugars, or monosaccharides, the number of carbons in the molecule equals the numb... | {
"Header 1": "What Are Sugars?",
"token_count": 401,
"source_pdf": "datasets/websources/biochem/Biochemistry-and-Molecular-Biology-9572.pdf"
} |
We have sweet receptors on our tongues, which are linked to pleasure centers in our brains. We also have sweet receptors in our guts. Our bodies reward us for eating sugar and enthusiastically encourage us to eat more. But why?
Sugars are full of energy, and eating high-energy foods is a simple recipe for survival. ... | {
"Header 1": "What Are Sugars?",
"Header 3": "**Why Do Sugars Appeal to Us?**",
"token_count": 1343,
"source_pdf": "datasets/websources/biochem/Biochemistry-and-Molecular-Biology-9572.pdf"
} |
Common sugars can cause problems. For example, consider lactose intolerance. Lactose is a disaccharide sugar found in milk that needs to be digested by the enzyme lactase into glucose and galactose to be used for energy.
Human babies make lots of lactase to help them digest the lactose... | {
"Header 1": "**Problems Caused by Sugar**",
"token_count": 1166,
"source_pdf": "datasets/websources/biochem/Biochemistry-and-Molecular-Biology-9572.pdf"
} |
ut how does life safely use and manage all the energy that's made in biochemical reactions? It's an incredible story of energy storage and transformation that centers on a molecule known as adenosine triphosphate (ATP).
#### **ATP and Oxidation**
Amazingly, we make and break down our weight in ATP each day! To unde... | {
"Header 1": "ATP AND ENERGY TRANSFORMATIONS IN CELLS",
"token_count": 565,
"source_pdf": "datasets/websources/biochem/Biochemistry-and-Molecular-Biology-9572.pdf"
} |
Recall that Gibbs free energy (*G*) is a measure of the amount of energy available to do useful work in a process. In biochemical reactions, the work being done is making or breaking chemical bonds. As biomolecules react with each other, there is a change in the available Gibbs free energy. The size of that free energy... | {
"Header 1": "**Using Thermodynamics**",
"token_count": 1182,
"source_pdf": "datasets/websources/biochem/Biochemistry-and-Molecular-Biology-9572.pdf"
} |
β*G* tells us a lot about reactions. How do we determine the value of β*G*? This turns out to be related to the equilibrium constant.
For temperature, scientists use the Kelvin temperature scale, which puts 0 K as absolute zero, so 25Β°C is 298 K.
Suppose you start with a 1-liter solution of *A* and *B*, 50% of each... | {
"Header 1": "**Determining** β*G*",
"token_count": 1393,
"source_pdf": "datasets/websources/biochem/Biochemistry-and-Molecular-Biology-9572.pdf"
} |
Cells act on glucose in 10 steps in glycolysis. Glucose contains 6 carbons and gets broken down to 2 identical molecules of pyruvate, each with 3 carbons. Other sugars can be oxidized here as well. In the process, glucose is oxidized. This involves a release of energy, which is partly stored in the phosphate bonds of A... | {
"Header 1": "Sugar Glycolysis",
"token_count": 2031,
"source_pdf": "datasets/websources/biochem/Biochemistry-and-Molecular-Biology-9572.pdf"
} |
Sugars are not the only sources of energy in our bodies. In fact, they are not even the primary energy storage molecules. Those would be fats, also known as triglycerides or triacylglycerols. A triacylglycerol is a molecule that binds 3 fatty acids (3 acyls) to a glycerol. To get energy out of a fat, the acyls in it mu... | {
"Header 1": "**Fatty Acid Oxidation**",
"token_count": 1443,
"source_pdf": "datasets/websources/biochem/Biochemistry-and-Molecular-Biology-9572.pdf"
} |
Glycolysis generates some ATP, but its main role is to deliver molecules that can be further oxidized to extract more energy. This is where the citric acid cycle comes in, providing a second stage for the efficient production of energy from food.
Like glycolysis, the citric acid cycle extracts energy and provides int... | {
"Header 1": "The Role of Energy Extraction",
"token_count": 952,
"source_pdf": "datasets/websources/biochem/Biochemistry-and-Molecular-Biology-9572.pdf"
} |
By whichever means it got there, acetyl-CoA enters the citric acid cycle, which is comprised of 8 reactions. Though the pathway is a circle, the reactions are numbered starting from the entry point for acetyl-CoA.
- 1 Acetyl-CoA transfers its 2-carbon acetyl group to a 4-carbon molecule of oxaloacetate, which comes f... | {
"Header 1": "**Reactions of the Citric Acid Cycle**",
"token_count": 1106,
"source_pdf": "datasets/websources/biochem/Biochemistry-and-Molecular-Biology-9572.pdf"
} |
The citric acid cycle links to many pathways, feeding intermediates into some and being fed by others. In its role as a hub for many pathways, portions of the cycle can operate independently, and some molecules can enter and exit the cycle without going all the way around.
w Step 1 of the citric acid cycle combines a... | {
"Header 1": "**Connections to Other Metabolic Pathways**",
"token_count": 1142,
"source_pdf": "datasets/websources/biochem/Biochemistry-and-Molecular-Biology-9572.pdf"
} |
14
he innermost, liquid-filled region of mitochondria, the matrix, is where the reactions of the citric acid cycle and fatty acid oxidation pathways occur, leading to the final phase in energy harvesting.
#### The Structure of Mitochondria
The structure of mitochondria is key to energy generation. Mitochondria ar... | {
"Header 1": "ENERGY HARVESTING IN ANIMALS AND PLANTS",
"token_count": 417,
"source_pdf": "datasets/websources/biochem/Biochemistry-and-Molecular-Biology-9572.pdf"
} |
Electrons move through the ETC in 4 steps in a process managed by 2 small shuttle systems and 4 large protein bundles called complex I through IV. Through these carriers, electrons start a journey that ultimately brings them to their final destination: molecular oxygen (O2).
Oxygen's role as the final electron accept... | {
"Header 1": "**The Electron Transport Chain**",
"token_count": 653,
"source_pdf": "datasets/websources/biochem/Biochemistry-and-Molecular-Biology-9572.pdf"
} |
Compared to electron transport, oxidative phosphorylation is simple. All of the magic occurs within a remarkable protein machine called ATP synthase, also known as complex V. ATP synthase is made up of 2 connected multiprotein assemblies, which together look like a mushroom. The base of the stalk is rooted in the mitoc... | {
"Header 1": "**Oxidative Phosphorylation**",
"token_count": 537,
"source_pdf": "datasets/websources/biochem/Biochemistry-and-Molecular-Biology-9572.pdf"
} |
In both the ETC and oxidative phosphorylation processes, oxidation creates activated electron carriers to pass on to the ETC. As electrons move through the ETC on their way to making water by combining with molecular oxygen, they generate a proton gradient, and protons flowing back into the matrix through ATP synthase ... | {
"Header 1": "**Oxidative Phosphorylation**",
"Header 3": "**Oxygen: Key to Both Processes**",
"token_count": 369,
"source_pdf": "datasets/websources/biochem/Biochemistry-and-Molecular-Biology-9572.pdf"
} |
Early in the history of life, the atmosphere had very little oxygen in it. It was only when a group of tiny organisms called cyanobacteria began to perform photosynthesis almost 3 billion years ago that oxygen levels gradually began to rise.
The availability of abundant oxygen was dangerous because of the damage that... | {
"Header 1": "**Oxidative Phosphorylation**",
"Header 2": "**The Light Reactions of Photosynthesis**",
"token_count": 1183,
"source_pdf": "datasets/websources/biochem/Biochemistry-and-Molecular-Biology-9572.pdf"
} |
Glucose is produced through a pathway known as gluconeogenesis, which means "new synthesis of glucose." The body needs a continual supply of glucose, which is stored as the polymer glycogen, which is broken down to provide glucose as needed. But we only have about a 24-hour supply of glycogen in our bodies, so keeping ... | {
"Header 1": "Gluconeogenesis",
"token_count": 1400,
"source_pdf": "datasets/websources/biochem/Biochemistry-and-Molecular-Biology-9572.pdf"
} |
Glycogen is made when glucose supplies are abundant. It is stored in skeletal muscle and the liver. Making glycogen only requires 3 reactions:
- 1 G6P from glycolysis is converted to glucose 1-phosphate (G1P).
- 2 G1P reacts with the nucleotide uridine triphosphate (UTP) to make the high-energy intermediate known as ... | {
"Header 1": "**Glycogenesis**",
"token_count": 334,
"source_pdf": "datasets/websources/biochem/Biochemistry-and-Molecular-Biology-9572.pdf"
} |
Glucose is only one of the sugars our bodies need. Sugars with 5 carbons, called pentoses, are needed for RNA and DNA. The pathway for the synthesis of sugars and related compounds is known as the pentose phosphate pathway (PPP).
The PPP has at least 2 important possible ouputs:
- 1 Hexose sugars like glucose can b... | {
"Header 1": "**The Pentose Phosphate Pathway**",
"token_count": 402,
"source_pdf": "datasets/websources/biochem/Biochemistry-and-Molecular-Biology-9572.pdf"
} |
Fatty acids are the simplest of lipids, with a carboxyl group of COOH at one end and a long nonpolar hydrocarbon tail with a CH3 methyl group at what is called the omega end. Fatty acids are the acyl groups joined to glycerol to make fats, also known as triacylglycerols.
Though lipids have many sizes, shapes, and fun... | {
"Header 1": "**The Synthesis of Fatty Acids**",
"token_count": 1167,
"source_pdf": "datasets/websources/biochem/Biochemistry-and-Molecular-Biology-9572.pdf"
} |
The first step in cholesterol synthesis starts with acetyl-CoA moleculesβthe same molecules that are used for fatty acid synthesis and are obtained from the breakdown of numerous molecules. The pathway to cholesterol from acetyl-CoA is long, involving 28 steps, but many cause only very minor changes. Most of the action... | {
"Header 1": "**Key Steps in Cholesterol Synthesis**",
"token_count": 673,
"source_pdf": "datasets/websources/biochem/Biochemistry-and-Molecular-Biology-9572.pdf"
} |
Probably the most important role for cholesterol is in its presence in cellular membranes to help manage their fluidity. The rigid, planar structure of cholesterol fits nicely in the gaps between the hydrophobic tails of the fatty acids, making membranes stiffer at moderate temperatures.
It also helps to significantl... | {
"Header 1": "**Key Steps in Cholesterol Synthesis**",
"Header 2": "**Cellular Membranes**",
"token_count": 919,
"source_pdf": "datasets/websources/biochem/Biochemistry-and-Molecular-Biology-9572.pdf"
} |
Membranes need cholesterol, and cells need other lipids as well. In order for cholesterol to do its magic, or for fat to provide energy to hungry cells, these water-hating molecules must first overcome their hydrophobic urges and travel through the body of an organism that is mostly water. Doing this takes extra steps,... | {
"Header 1": "**Lipoprotein Complexes**",
"token_count": 1520,
"source_pdf": "datasets/websources/biochem/Biochemistry-and-Molecular-Biology-9572.pdf"
} |
Ways that enzymes can be controlled include allosteric regulation, where the binding of a molecule modifies an enzyme's activity; covalent modification, where a phosphate group gets chemically linked to specific side chains in an enzyme protein to turn it on or off; and control of whether or not a cell even makes an en... | {
"Header 1": "**Regulation of Metabolic Pathways**",
"token_count": 1099,
"source_pdf": "datasets/websources/biochem/Biochemistry-and-Molecular-Biology-9572.pdf"
} |
The movement of electrons through the electron transport chain pumps protons out of the mitochondrial matrix, creating a proton gradient. The terminal acceptor of electrons during electron transport is molecular oxygen. The proton gradient generated by electron transport is used by ATP synthase to create ATP from ADP a... | {
"Header 1": "**The Role of Electron Transport**",
"token_count": 747,
"source_pdf": "datasets/websources/biochem/Biochemistry-and-Molecular-Biology-9572.pdf"
} |
When people exercise vigorously, their bloodstream has difficulty supplying all the oxygen the muscles could optimally use to generate ATP. And when cells have insufficient oxygen, electron transport slows and NAD+ levels fall and that could be a problem.
Fortunately, there's a backup: fermentation. In fermentation, ... | {
"Header 1": "**Fermentation**",
"token_count": 998,
"source_pdf": "datasets/websources/biochem/Biochemistry-and-Molecular-Biology-9572.pdf"
} |
The Calvin cycle constitutes the second phase of photosynthesis, where the light energy is used to build the molecules that make up the plants, support their growth, and feed the rest of the world.
In biochemical terms, carbon dioxide is being chemically reduced to a carbohydrate. When a molecule is reduced, it accep... | {
"Header 1": "**The Calvin Cycle**",
"token_count": 782,
"source_pdf": "datasets/websources/biochem/Biochemistry-and-Molecular-Biology-9572.pdf"
} |
Plants don't make food or produce oxygen for our benefit; they need glucose for their own cellular reactions. Extra glucose is stored as starch in tubers like potatoes and in the seeds of grain plants like wheat. Plants also use glucose to make cellulose, which is a polymer of glucose that makes up the plant cell wall.... | {
"Header 1": "**Photorespiration**",
"token_count": 1316,
"source_pdf": "datasets/websources/biochem/Biochemistry-and-Molecular-Biology-9572.pdf"
} |
In addition to the 2 primary things plants do for usβfood and oxygen there are 3 families of secondary metabolites that plants also make. By definition, secondary metabolites are not essential for plant growth and reproduction. But they often serve to protect plants against pests. It just so happens that many of these ... | {
"Header 1": "**Secondary Metabolites**",
"token_count": 704,
"source_pdf": "datasets/websources/biochem/Biochemistry-and-Molecular-Biology-9572.pdf"
} |
To be absorbed and used by animals or plants, nitrogen in the air must be converted to forms of nitrogen that plants can useβeither ammonia (NH $_3$ ) or nitrate (NO $_3$ ). Converting nitrogen to ammonia is no easy task. The industrial process for making ammonia from nitrogen requires 400Β°C to 500Β°C and more than 200 ... | {
"Header 1": "Nitrogen Fixation",
"token_count": 811,
"source_pdf": "datasets/websources/biochem/Biochemistry-and-Molecular-Biology-9572.pdf"
} |
Plants and bacteria synthesize all 20 of the amino acids for making proteins, but animals, including humans, make only some of them, with the rest coming from diet.
Amino acids have a characteristic structure: The alpha carbon is attached to an amino group, a carboxyl group, and a hydrogen, plus an R group, or side c... | {
"Header 1": "**Amino Acids**",
"token_count": 1652,
"source_pdf": "datasets/websources/biochem/Biochemistry-and-Molecular-Biology-9572.pdf"
} |
In addition to its other roles, glutamine is also the nitrogen control point for creation of nucleotides, which are the building blocks of nucleic acids, another critical area of nitrogen metabolism.
Nucleotides have 3 components: a sugar, one or more phosphates, and a nitrogenous base.
All nucleotides are initiall... | {
"Header 1": "**Nucleotides**",
"token_count": 663,
"source_pdf": "datasets/websources/biochem/Biochemistry-and-Molecular-Biology-9572.pdf"
} |
We begin to age the moment we are born. And this is primarily because of events in our cells that occur in the course of normal metabolism.
A cellular cause of aging is the production of free radicals: unstable atoms or molecules with one or more unpaired electrons. Electrons like to be in pairs, so atoms with unpair... | {
"Header 1": "EATING, ANTIOXIDANTS, AND THE MICROBIOME",
"Header 2": "Free Radicals",
"token_count": 1226,
"source_pdf": "datasets/websources/biochem/Biochemistry-and-Molecular-Biology-9572.pdf"
} |
Oxidative stress may be a factor in aging and is believed to play a role in the development of a whole slew of diseases. For example, emphysema arises from oxidative damage to a critical protective protein in the lungs called alpha-1 antitrypsin. Reactive oxygens have been implicated in atherosclerosis, stroke, arthrit... | {
"Header 1": "EATING, ANTIOXIDANTS, AND THE MICROBIOME",
"Header 2": "**Oxidative Stress**",
"token_count": 1759,
"source_pdf": "datasets/websources/biochem/Biochemistry-and-Molecular-Biology-9572.pdf"
} |
Cellular communications always involve sensing and signaling. It has long been known that even bacteria sense and move toward food sources and away from toxic substances. Even more interesting, bacteria talk to each other, kind of like teenagers at a mall, to find out how many "friends" are nearby.
Plants sense and c... | {
"Header 1": "**Cellular Signals**",
"token_count": 640,
"source_pdf": "datasets/websources/biochem/Biochemistry-and-Molecular-Biology-9572.pdf"
} |
In some types of membrane receptor signaling, enzyme activities are altered. Affected enzymes include protein kinases, which phosphorylate target proteins, and phosphatases, which remove phosphates. Adding and removing phosphates is an easy way to control whether cellular proteins are active or not.
A good example of... | {
"Header 1": "**The Stress-Response System**",
"token_count": 1007,
"source_pdf": "datasets/websources/biochem/Biochemistry-and-Molecular-Biology-9572.pdf"
} |
There is another category of signaling in which external signals can induce changes in cells that tell them to divide. This pathway also relies on receptor binding, relaying of the message through various go-betweens, and finally activating kinases that bring about changes in the cell.
A classic example of such a sig... | {
"Header 1": "**The Stress-Response System**",
"Header 3": "**Cell Division**",
"token_count": 886,
"source_pdf": "datasets/websources/biochem/Biochemistry-and-Molecular-Biology-9572.pdf"
} |
The nervous system can be divided into 2 main parts:
- 1 The central nervous system (CNS) is made up of the brain and the spinal cord.
- 2 The peripheral nervous system (PNS) consists of all the nerves that branch off from the spinal cord and extend to all parts of the body.
Fast-acting hormones like adrenaline tak... | {
"Header 1": "The Nervous System",
"token_count": 1267,
"source_pdf": "datasets/websources/biochem/Biochemistry-and-Molecular-Biology-9572.pdf"
} |
Neurotransmitters are small molecules made by neurons to cross the gap of the synaptic cleft. In the absence of a signal, neurotransmitters are stored in small membrane sacs called synaptic vesicles near the axon terminals. The arrival of the action potential at an axon terminal is a signal to vesicles containing the n... | {
"Header 1": "The Nervous System",
"Header 2": "**Neurotransmitters**",
"token_count": 654,
"source_pdf": "datasets/websources/biochem/Biochemistry-and-Molecular-Biology-9572.pdf"
} |
Some neurotransmitters affect the way we see the world. Serotonin is popularly associated with happiness and well-being. The vast majority of serotonin in the body is produced and acts in the gastrointestinal system, where it is necessary for normal gut function. Pathogenic amoebas producing their own serotonin can cau... | {
"Header 1": "The Nervous System",
"Header 2": "**Neurotransmitters**",
"Header 3": "**Serotonin and Dopamine**",
"token_count": 778,
"source_pdf": "datasets/websources/biochem/Biochemistry-and-Molecular-Biology-9572.pdf"
} |
e can understand the power of molecules for the thousands of reactions in biochemistry, but most of those reactions largely occur outside our everyday awareness. The most important group of biochemical signals that we notice is the molecular reactions that give rise to our 5 sensesβthe signals that give us virtually al... | {
"Header 1": "THE BIOCHEMISTRY OF OUR SENSES",
"token_count": 627,
"source_pdf": "datasets/websources/biochem/Biochemistry-and-Molecular-Biology-9572.pdf"
} |
The sense of smell, known as olfaction, is enormously important to animals not just for enjoying food, but also for warning of danger and even selecting mates. It occurs as a result of the binding of odorant molecules to olfactory receptor cells in the nasal cavity.
Smells reach receptors by 2 routes. The primary one... | {
"Header 1": "THE BIOCHEMISTRY OF OUR SENSES",
"Header 3": "**Smell**",
"token_count": 419,
"source_pdf": "datasets/websources/biochem/Biochemistry-and-Molecular-Biology-9572.pdf"
} |
The detection of light and the ability to distinguish detail by our eyes involves an amazing convergence of optics, light-sensitive proteins, nerve signaling, and brain processing. About 130 million photoreceptors in the retina absorb light and transmit visual signals to the brain.
The anatomy of the eye is such that... | {
"Header 1": "**Vision**",
"token_count": 566,
"source_pdf": "datasets/websources/biochem/Biochemistry-and-Molecular-Biology-9572.pdf"
} |
The sense of hearing is remarkable in its range. People with normal hearing can detect sounds of pitches, or frequencies, between 20 and 20,000 hertz. Normal, everyday speech has a mix of low- and high-frequency sounds that is generally in the 250 to 6000 hertz range. The length of time it takes our nervous system to r... | {
"Header 1": "**Vision**",
"Header 2": "**Hearing**",
"token_count": 412,
"source_pdf": "datasets/websources/biochem/Biochemistry-and-Molecular-Biology-9572.pdf"
} |
The most mysterious sense is touch. Touch stimuli can be mechanical signals, where low-threshold mechanoreceptors sense contact with the skin. Low-threshold mechanoreceptors detect pressure, vibration, stretching of the skin, and movement of hair follicles in the skin. These receptors respond by triggering action poten... | {
"Header 1": "**Vision**",
"Header 2": "**Touch**",
"token_count": 459,
"source_pdf": "datasets/websources/biochem/Biochemistry-and-Molecular-Biology-9572.pdf"
} |
When you wake up in the morning, your body has already been preparing for the day. Levels of your fast-acting stress hormones epinephrine and norepinephrine are rising, your slower-acting cortisol is getting into the act, and your body is getting primed for action.
Your body seeks energy, having been asleep for a lon... | {
"Header 1": "FROM BIOCHEMISTRY TO MOLECULAR BIOLOGY",
"Header 2": "Caffeine",
"token_count": 363,
"source_pdf": "datasets/websources/biochem/Biochemistry-and-Molecular-Biology-9572.pdf"
} |
Coffee is not the only thing that tinkers with sugar levels in your body. While the buzz from caffeine is fairly innocuous, the buzz from other foods and drinksβespecially items containing high-fructose corn syrupβis not.
There are 2 issues to keep in mind: the overconsumption of sugar in general and the effects of h... | {
"Header 1": "**Fructose**",
"token_count": 1017,
"source_pdf": "datasets/websources/biochem/Biochemistry-and-Molecular-Biology-9572.pdf"
} |
Alcohol is metabolized by alcohol dehydrogenase into acetaldehyde, which is toxic. So, your body summons up another dehydrogenase enzyme to convert acetaldehyde into acetate, which can give you a horrid headache. But unlike acetaldehyde, at least it won't give you palpitations, shortness of breath, blurred vision, and ... | {
"Header 1": "**Alcohol**",
"token_count": 326,
"source_pdf": "datasets/websources/biochem/Biochemistry-and-Molecular-Biology-9572.pdf"
} |
When you exercise, the harder you push yourself, the more heavily you breathe. Contrary to what you might think, when you're so out of breath that you can't speak, that is not aerobic exercise in a biochemical sense.
When your muscles are working hard, you are starting to go anaerobic because the muscles are using ox... | {
"Header 1": "**Exercise**",
"token_count": 1360,
"source_pdf": "datasets/websources/biochem/Biochemistry-and-Molecular-Biology-9572.pdf"
} |
**25**
olecular biology is the part of biochemistry that explains how living things reproduce. The fertilized egg that gives rise to each individual contains DNA, which is copied each time a cell divides, with a copy of the information passed on to every one of the trillions of cells in a human baby. In each generati... | {
"Header 1": "**Exercise**",
"Header 2": "DNA AND RNA: INFORMATION IN STRUCTURE",
"token_count": 1038,
"source_pdf": "datasets/websources/biochem/Biochemistry-and-Molecular-Biology-9572.pdf"
} |
One major function of the information in DNA is to provide instructions for making proteins, which are built from amino acids. The information for amino acids arises directly from the sequence of the bases in DNA, so the sequence of bases in DNA stores instructions for making proteins.
Information that is securely st... | {
"Header 1": "**Instructions for Making Proteins**",
"token_count": 554,
"source_pdf": "datasets/websources/biochem/Biochemistry-and-Molecular-Biology-9572.pdf"
} |
Double-stranded DNA molecules have 2 features that make copying it easy. First, the base sequences of the 2 strands are complementary: The As are always connected by 2 hydrogen bonds with Ts, while Gs are always connected by 3 hydrogen bonds with Cs. This is called base pairing.
When the 2 strands of a DNA molecule a... | {
"Header 1": "**Instructions for Making Proteins**",
"Header 2": "**Storing and Copying Information**",
"token_count": 424,
"source_pdf": "datasets/websources/biochem/Biochemistry-and-Molecular-Biology-9572.pdf"
} |
The information for making a protein is encoded in the base sequence of DNA, but DNA does not serve as the direct template for building the protein. Instead, the information in the gene is copied into the closely related molecule, ribonucleic acid (RNA), which directs the synthesis of proteins.
Like DNA, RNA has a ba... | {
"Header 1": "**RNA**",
"token_count": 909,
"source_pdf": "datasets/websources/biochem/Biochemistry-and-Molecular-Biology-9572.pdf"
} |
In their 1953 paper, James Watson and Francis Crickβbenefitting from Erwin Chargaff's observations and the unacknowledged work of Rosalind Franklinβdescribed a model for DNA structure. They proposed that the DNA molecule had 2 intertwined strands with As across from Ts and Gs across from Cs. They noted that their struc... | {
"Header 1": "DNA Replication",
"token_count": 738,
"source_pdf": "datasets/websources/biochem/Biochemistry-and-Molecular-Biology-9572.pdf"
} |
Bacteria like *E. coli* have a relatively small DNA genome, with 5 million base pairs wrapped in just one chromosome. And unlike our chromosomes, which are linear, *E. coli*'s single chromosome is circular.
DNA replication in all organisms is carried out by a large number of proteins that act together as a complex pr... | {
"Header 1": "DNA Replication",
"Header 3": "**Replication in Bacteria**",
"token_count": 971,
"source_pdf": "datasets/websources/biochem/Biochemistry-and-Molecular-Biology-9572.pdf"
} |
Human ingenuity has harnessed the power and speed of DNA replication in a way that has revolutionized how genes are studied. Its inventor, Kary Mullis, won a Nobel Prize for it.
Called polymerase chain reaction (PCR), this procedure makes millions of copies of any DNA that we need in a few hours by replicating the de... | {
"Header 1": "**PCR in the Lab**",
"token_count": 968,
"source_pdf": "datasets/websources/biochem/Biochemistry-and-Molecular-Biology-9572.pdf"
} |
Subsets and Splits
No community queries yet
The top public SQL queries from the community will appear here once available.