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textbooks/bio/Biochemistry/Book%3A_Biochemistry_Free_For_All_(Ahern_Rajagopal_and_Tan)/01%3A_In_The_Beginning/1.01%3A_Introduction_-_Basic_Biology.txt | princeton-nlp/TextbookChapters | • 1.1: Introduction - Basic Biology
The most obvious thing about living organisms is their astounding diversity. Estimates put the number of eukaryotic species at about 8.7 million, while bacteria account for anywhere between 107 and 109 different species. The number of species of archaea is still uncertain, but is exp... |
textbooks/bio/Biochemistry/Book%3A_Biochemistry_Free_For_All_(Ahern_Rajagopal_and_Tan)/01%3A_In_The_Beginning/1.03%3A_Introduction_-_Water_and_Buffers.txt | princeton-nlp/TextbookChapters | Source: BiochemFFA_1_3.pdf. The entire textbook is available for free from the authors at http://biochem.science.oregonstate.edu/content/biochemistry-free-and-easy
When it comes to water, we’re literally drowning in it, as water is by far the most abundant component of every cell. To understand life, we begin the disc... |
textbooks/bio/Biochemistry/Book%3A_Biochemistry_Free_For_All_(Ahern_Rajagopal_and_Tan)/02%3A_Structure_and_Function/2.01%3A_Prelude_to_Structure_and_Function.txt | princeton-nlp/TextbookChapters | Thumbanil: Structure of human hemoglobin. The proteins α and βsubunits are in red and blue, and the iron-containing hemegroups in green. Image used with permission (CC BY-SA 3.0; Richard Wheeler).
02: Structure and Function
Source: BiochemFFA_2_1.pdf. The entire textbook is available for free from the authors at ht... |
textbooks/bio/Biochemistry/Book%3A_Biochemistry_Free_For_All_(Ahern_Rajagopal_and_Tan)/02%3A_Structure_and_Function/2.05%3A_Structure_and_Function-_Protein_Function_II.txt | princeton-nlp/TextbookChapters | Source: BiochemFFA_2_4.pdf. The entire textbook is available for free from the authors at http://biochem.science.oregonstate.edu/content/biochemistry-free-and-easy
To this point, the proteins we have discussed have not been catalysts (enzymes). The majority of proteins in cells, however, catalyze reactions. In this se... |
textbooks/bio/Biochemistry/Book%3A_Biochemistry_Free_For_All_(Ahern_Rajagopal_and_Tan)/02%3A_Structure_and_Function/2.06%3A_Structure_and_Function_-_Nucleic_Acids.txt | princeton-nlp/TextbookChapters | Source: BiochemFFA_2_5.pdf. The entire textbook is available for free from the authors at http://biochem.science.oregonstate.edu/content/biochemistry-free-and-easy
The nucleic acids, DNA and RNA, may be thought of as the information molecules of the cell. In this section, we will examine the structures of DNA and RNA,... |
textbooks/bio/Biochemistry/Book%3A_Biochemistry_Free_For_All_(Ahern_Rajagopal_and_Tan)/02%3A_Structure_and_Function/2.08%3A_Structure_and_Function_-_Lipids_and_Membranes.txt | princeton-nlp/TextbookChapters | Source: BiochemFFA_2_7.pdf. The entire textbook is available for free from the authors at http://biochem.science.oregonstate.edu/content/biochemistry-free-and-easy
Lipids are a diverse group of molecules that all share the characteristic that at least a portion of them is hydrophobic. Lipids play many roles in cells, ... |
textbooks/bio/Biochemistry/Book%3A_Biochemistry_Free_For_All_(Ahern_Rajagopal_and_Tan)/02%3A_Structure_and_Function/202%3A_Structure__Function_-_Amino_Acids.txt | princeton-nlp/TextbookChapters | Source: BiochemFFA_2_1.pdf. The entire textbook is available for free from the authors at http://biochem.science.oregonstate.edu/content/biochemistry-free-and-easy
All of the proteins on the face of the earth are made up of the same 20 amino acids. Linked together in long chains called polypeptides, amino acids are th... |
textbooks/bio/Biochemistry/Book%3A_Biochemistry_Free_For_All_(Ahern_Rajagopal_and_Tan)/02%3A_Structure_and_Function/203%3A_Structure__Function-_Proteins_I.txt | princeton-nlp/TextbookChapters | Source: BiochemFFA_2_2.pdf. The entire textbook is available for free from the authors at http://biochem.science.oregonstate.edu/content/biochemistry-free-and-easy
Proteins are the workhorses of the cell. Virtually everything that goes on inside of cells happens as a result of the actions of proteins. Among other thin... |
textbooks/bio/Biochemistry/Book%3A_Biochemistry_Free_For_All_(Ahern_Rajagopal_and_Tan)/03%3A_Membranes/3.01%3A_Basic_Concepts_in_Membranes.txt | princeton-nlp/TextbookChapters | Thumbnail: The cell membrane, also called the plasma membrane or plasmalemma, is a semipermeable lipid bilayer common to all living cells. It contains a variety of biological molecules, primarily proteins and lipids, which are involved in a vast array of cellular processes. It also serves as the attachment point for bo... |
textbooks/bio/Biochemistry/Book%3A_Biochemistry_Free_For_All_(Ahern_Rajagopal_and_Tan)/03%3A_Membranes/3.02%3A_Transport_in_Membranes.txt | princeton-nlp/TextbookChapters | Source: BiochemFFA_3_2.pdf. The entire textbook is available for free from the authors at http://biochem.science.oregonstate.edu/content/biochemistry-free-and-easy
Movement of materials across membranes
As noted earlier, it is essential for cells to be able to uptake nutrients. This function along with movement of io... |
textbooks/bio/Biochemistry/Book%3A_Biochemistry_Free_For_All_(Ahern_Rajagopal_and_Tan)/03%3A_Membranes/3.03%3A_Other_Considerations_in_Membranes.txt | princeton-nlp/TextbookChapters | Source: BiochemFFA_3_3.pdf. The entire textbook is available for free from the authors at http://biochem.science.oregonstate.edu/content/biochemistry-free-and-easy
There are many functions and factors relating to cell membranes that don’t fit into broad categories. Those items will be the focus of this section.
Endoc... |
textbooks/bio/Biochemistry/Book%3A_Biochemistry_Free_For_All_(Ahern_Rajagopal_and_Tan)/04%3A_Catalysis/4.01%3A_Basic_Principles_of_Catalysis.txt | princeton-nlp/TextbookChapters | Thumbnail: Enzyme changes shape by induced fit upon substrate binding to form enzyme-substrate complex. Hexokinase has a large induced fit motion that closes over the substrates adenosine triphosphate and xylose. Binding sites in blue, substrates in black and Mg2+ cofactor in yellow. (PDB: 2E2N, 2E2Q). Image used wit... |
textbooks/bio/Biochemistry/Book%3A_Biochemistry_Free_For_All_(Ahern_Rajagopal_and_Tan)/04%3A_Catalysis/4.02%3A_Control_of_Enzymatic_Activity.txt | princeton-nlp/TextbookChapters | A printable version of this section is here: BiochemFFA_4_2.pdf. The entire textbook is available for free from the authors at http://biochem.science.oregonstate.edu/content/biochemistry-free-and-easy
Regulation of enzyme activity
Apart from their ability to greatly speed the rates of chemical reactions in cells, enz... |
textbooks/bio/Biochemistry/Book%3A_Biochemistry_Free_For_All_(Ahern_Rajagopal_and_Tan)/04%3A_Catalysis/4.03%3A_Mechanisms_of_Catalysis.txt | princeton-nlp/TextbookChapters | A printable version of this section is here: BiochemFFA_4_3.pdf. The entire textbook is available for free from the authors at http://biochem.science.oregonstate.edu/content/biochemistry-free-and-easy
The magic of enzymes, as noted, is in their ability to create electronic environments conducive to initiation of a rea... |
textbooks/bio/Biochemistry/Book%3A_Biochemistry_Free_For_All_(Ahern_Rajagopal_and_Tan)/04%3A_Catalysis/4.04%3A_Blood_Clotting.txt | princeton-nlp/TextbookChapters | A printable version of this section is here: BiochemFFA_4_4.pdf. The entire textbook is available for free from the authors at http://biochem.science.oregonstate.edu/content/biochemistry-free-and-easy
Clotting is a process in which liquid blood is converted into a gelatinous substance that eventually hardens. The aim ... |
textbooks/bio/Biochemistry/Book%3A_Biochemistry_Free_For_All_(Ahern_Rajagopal_and_Tan)/05%3A_Energy/5.01%3A_Basics_of_Energy.txt | princeton-nlp/TextbookChapters | • 5.1: Basics of Energy
Living organisms are made up of cells, and cells contain a horde of biochemical components. Living cells, though, are not random collections of these molecules. They are extraordinarily organized or "ordered". By contrast, in the nonliving world, there is a universal tendency to increasing disor... |
textbooks/bio/Biochemistry/Book%3A_Biochemistry_Free_For_All_(Ahern_Rajagopal_and_Tan)/05%3A_Energy/5.03%3A_Energy_-_Photophosphorylation.txt | princeton-nlp/TextbookChapters | Source: BiochemFFA_5_3.pdf. The entire textbook is available for free from the authors at http://biochem.science.oregonstate.edu/content/biochemistry-free-and-easy
Photophosphorylation
The third type of phosphorylation to make ATP is found only in cells that carry out photosynthesis. This process is similar to oxidat... |
textbooks/bio/Biochemistry/Book%3A_Biochemistry_Free_For_All_(Ahern_Rajagopal_and_Tan)/05%3A_Energy/5.2%3A_Electron_Transport_and_Oxidative_Phosphorylation.txt | princeton-nlp/TextbookChapters | Source: BiochemFFA_5_2.pdf. The entire textbook is available for free from the authors at http://biochem.science.oregonstate.edu/content/biochemistry-free-and-easy
In eukaryotic cells, the vast majority of ATP synthesis occurs in the mitochondria in a process called oxidative phosphorylation. Even plants, which genera... |
textbooks/bio/Biochemistry/Book%3A_Biochemistry_Free_For_All_(Ahern_Rajagopal_and_Tan)/06%3A_Metabolism/6.01%3A_Metabolism_-_Sugars.txt | princeton-nlp/TextbookChapters | • 6.1: Metabolism - Sugars
• 6.2: Citric Acid Cycle & Related Pathways
The primary catabolic pathway in the body is the citric acid cycle because it is here that oxidation to carbon dioxide occurs for breakdown products of the cell’s major building blocks - sugars, fatty acids, and amino acids. The pathway is cyclic an... |
textbooks/bio/Biochemistry/Book%3A_Biochemistry_Free_For_All_(Ahern_Rajagopal_and_Tan)/06%3A_Metabolism/6.02%3A_Citric_Acid_Cycle__Related_Pathways.txt | princeton-nlp/TextbookChapters | Source: BiochemFFA_6_2.pdf. The entire textbook is available for free from the authors at http://biochem.science.oregonstate.edu/content/biochemistry-free-and-easy
Citric acid cycle
The primary catabolic pathway in the body is the citric acid cycle because it is here that oxidation to carbon dioxide occurs for breakd... |
textbooks/bio/Biochemistry/Book%3A_Biochemistry_Free_For_All_(Ahern_Rajagopal_and_Tan)/06%3A_Metabolism/6.03%3A_Fats_and_Fatty_Acids.txt | princeton-nlp/TextbookChapters | Source: BiochemFFA_6_3.pdf. The entire textbook is available for free from the authors at http://biochem.science.oregonstate.edu/content/biochemistry-free-and-easy
In the modern Western world, which is fat and getting fatter, there is a tremendous amount of interest in the metabolism of fat and fatty acids. Fat is the... |
textbooks/bio/Biochemistry/Book%3A_Biochemistry_Free_For_All_(Ahern_Rajagopal_and_Tan)/06%3A_Metabolism/6.04%3A_Other_Lipids.txt | princeton-nlp/TextbookChapters | Source: BiochemFFA_6_4.pdf. The entire textbook is available for free from the authors at http://biochem.science.oregonstate.edu/content/biochemistry-free-and-easy
Sugars are the building blocks of carbohydrates, amino acids are the building blocks of proteins and nucleotides are the building blocks of the nucleic aci... |
textbooks/bio/Biochemistry/Book%3A_Biochemistry_Free_For_All_(Ahern_Rajagopal_and_Tan)/06%3A_Metabolism/6.05%3A_Amino_Acids_and_the_Urea_Cycle.txt | princeton-nlp/TextbookChapters | Source: BiochemFFA_6_5.pdf. The entire textbook is available for free from the authors at http://biochem.science.oregonstate.edu/content/biochemistry-free-and-easy
In contrast to some of the metabolic pathways described to this point, amino acid metabolism is not a single pathway. The 20 amino acids have some parts of... |
textbooks/bio/Biochemistry/Book%3A_Biochemistry_Free_For_All_(Ahern_Rajagopal_and_Tan)/06%3A_Metabolism/6.06%3A_Nucleotides.txt | princeton-nlp/TextbookChapters | Source: BiochemFFA_6_6.pdf. The entire textbook is available for free from the authors at http://biochem.science.oregonstate.edu/content/biochemistry-free-and-easy
Diverse functions of nucleotides
Nucleotides are most often thought of as the building blocks of the nucleic acids, DNA and RNA. While this, is, of course... |
textbooks/bio/Biochemistry/Book%3A_Biochemistry_Free_For_All_(Ahern_Rajagopal_and_Tan)/07%3A_Information_Processing/7.01%3A_Prelude_to_Information_Processing.txt | princeton-nlp/TextbookChapters | The nature of biological information, how it is copied and passed on, how it is read and interpreted, and how it gives rise to the cellular activities that we can observe, is the subject of this chapter. Another kind of information is also considered, towards the end of the chapter- the molecular information that cells... |
textbooks/bio/Biochemistry/Book%3A_Biochemistry_Free_For_All_(Ahern_Rajagopal_and_Tan)/07%3A_Information_Processing/7.02%3A_Genes_and_Genomes.txt | princeton-nlp/TextbookChapters | Source: BiochemFFA_7_1.pdf. The entire textbook is available for free from the authors at http://biochem.science.oregonstate.edu/content/biochemistry-free-and-easy
Introduction
For many years, scientists wondered about the nature of the information that directed the activities of cells. What kind of molecules carried... |
textbooks/bio/Biochemistry/Book%3A_Biochemistry_Free_For_All_(Ahern_Rajagopal_and_Tan)/07%3A_Information_Processing/7.03%3A_DNA_Replication.txt | princeton-nlp/TextbookChapters | Source: BiochemFFA_7_2.pdf. The entire textbook is available for free from the authors at http://biochem.science.oregonstate.edu/content/biochemistry-free-and-easy
Copying instructions
The only way to make new cells is by the division of pre-existing cells. Single-celled organisms undergo division to produce more cel... |
textbooks/bio/Biochemistry/Book%3A_Biochemistry_Free_For_All_(Ahern_Rajagopal_and_Tan)/07%3A_Information_Processing/7.04%3A_DNA_Repair.txt | princeton-nlp/TextbookChapters | Source: BiochemFFA_7_3.pdf. The entire textbook is available for free from the authors at http://biochem.science.oregonstate.edu/content/biochemistry-free-and-easy
Safeguarding the genome
In the last section we considered the ways in which cells deal with the challenges associated with replicating their DNA, a vital ... |
textbooks/bio/Biochemistry/Book%3A_Biochemistry_Free_For_All_(Ahern_Rajagopal_and_Tan)/07%3A_Information_Processing/7.05%3A_Transcription.txt | princeton-nlp/TextbookChapters | Source: BiochemFFA_7_4.pdf. The entire textbook is available for free from the authors at http://biochem.science.oregonstate.edu/content/biochemistry-free-and-easy
In the preceding sections, we have discussed the replication of the cell's DNA and the mechanisms by which the integrity of the genetic information is care... |
textbooks/bio/Biochemistry/Book%3A_Biochemistry_Free_For_All_(Ahern_Rajagopal_and_Tan)/07%3A_Information_Processing/7.06%3A_RNA_Processing.txt | princeton-nlp/TextbookChapters | Source: BiochemFFA_7_5.pdf. The entire textbook is available for free from the authors at http://biochem.science.oregonstate.edu/content/biochemistry-free-and-easy
So far, we have looked at the mechanism by which the information in genes (DNA) is transcribed into RNA. The newly made RNA, also known as the primary tran... |
textbooks/bio/Biochemistry/Book%3A_Biochemistry_Free_For_All_(Ahern_Rajagopal_and_Tan)/07%3A_Information_Processing/7.07%3A_Translation.txt | princeton-nlp/TextbookChapters | Source: BiochemFFA_7_6.pdf. The entire textbook is available for free from the authors at http://biochem.science.oregonstate.edu/content/biochemistry-free-and-easy
Translation is the process by which information in mRNAs is used to direct the synthesis of proteins. As you have learned in introductory biology, in eukar... |
textbooks/bio/Biochemistry/Book%3A_Biochemistry_Free_For_All_(Ahern_Rajagopal_and_Tan)/07%3A_Information_Processing/7.08%3A_Gene_Expression.txt | princeton-nlp/TextbookChapters | Source: BiochemFFA_7_7.pdf. The entire textbook is available for free from the authors at http://biochem.science.oregonstate.edu/content/biochemistry-free-and-easy
The processes of transcription and translation described so far tell us what steps are involved in the copying of information from a gene (DNA) into RNA an... |
textbooks/bio/Biochemistry/Book%3A_Biochemistry_Free_For_All_(Ahern_Rajagopal_and_Tan)/07%3A_Information_Processing/7.09%3A_Signaling.txt | princeton-nlp/TextbookChapters | Source: BiochemFFA_7_8.pdf. The entire textbook is available for free from the authors at http://biochem.science.oregonstate.edu/content/biochemistry-free-and-easy
Up to this point we have considered how cells carry out biochemical reactions and how they regulate the expression of the genes in response to their intern... |
textbooks/bio/Biochemistry/Book%3A_Biochemistry_Free_For_All_(Ahern_Rajagopal_and_Tan)/08%3A_Basic_Techniques/8.01%3A_Cell_Lysis.txt | princeton-nlp/TextbookChapters | The environment of a cell is very complex, making it difficult to study individual reactions, enzymes, or pathways in situ. The traditional approach used by biochemists for the study of these things is to isolate molecules, enzymes, DNAs, RNAs, and other items of interest so they can be analyzed independently of the mi... |
textbooks/bio/Biochemistry/Book%3A_Biochemistry_Free_For_All_(Ahern_Rajagopal_and_Tan)/08%3A_Basic_Techniques/8.02%3A_Fractionation_and_Chromatography_Techniques.txt | princeton-nlp/TextbookChapters | Fractionation of samples, as the name suggests, is a process of separating out the components or fractions of the lysate. Fractionation typically begins with centrifugation of the lysate. Using low-speed centrifugation, one can remove cell debris, leaving a supernatant containing the contents of the cell. By using succ... |
textbooks/bio/Biochemistry/Book%3A_Biochemistry_Free_For_All_(Ahern_Rajagopal_and_Tan)/08%3A_Basic_Techniques/8.03%3A_Electrophoresis.txt | princeton-nlp/TextbookChapters | Electrophoresis uses an electric field applied across a gel matrix to separate large molecules such as DNA, RNA, and proteins by charge and size. Samples are loaded into the wells of a gel matrix that can separate molecules by size and an electrical field is applied across the gel. This field causes negatively charged ... |
textbooks/bio/Biochemistry/Book%3A_Biochemistry_Free_For_All_(Ahern_Rajagopal_and_Tan)/08%3A_Basic_Techniques/8.04%3A_Detection_identification_and_quantitation_of_specific_nucleic_acids_and_proteins.txt | princeton-nlp/TextbookChapters | While gel electrophoresis can be used to resolve molecules in a mixture, by itself, the technique does not permit the detection and identification of specific nucleic acid sequences or proteins. For example, the 2-D gel shown above clearly separates a large number of proteins in a sample into individual spots. However,... |
textbooks/bio/Biochemistry/Book%3A_Biochemistry_Free_For_All_(Ahern_Rajagopal_and_Tan)/08%3A_Basic_Techniques/8.05%3A_Transcriptomics.txt | princeton-nlp/TextbookChapters | Consider a matrix containing all of the known gene sequences in a genome. To make such a matrix for analysis, one would need to make copies of every gene, either by chemical synthesis or by using the polymerase chain reaction. The strands of the resulting DNAs would then be separated to obtain single-stranded sequences... |
textbooks/bio/Biochemistry/Book%3A_Biochemistry_Free_For_All_(Ahern_Rajagopal_and_Tan)/08%3A_Basic_Techniques/8.06%3A_Isolating_Genes.txt | princeton-nlp/TextbookChapters | Earlier in this chapter, we discussed methods such as column chromatography that are used to purify proteins of interest. Using combinations of these methods, it is possible to isolate a protein to a high degree of purity, thus enabling us to study the protein’s activity and properties. This problem is harder to solve ... |
textbooks/bio/Biochemistry/Book%3A_Biochemistry_Free_For_All_(Ahern_Rajagopal_and_Tan)/08%3A_Basic_Techniques/8.07%3A_Polymerase_Chain_Reaction_%28PCR%29.txt | princeton-nlp/TextbookChapters | Molecular cloning was the first method available to isolate a gene of interest and make many copies of it to obtain sufficient amounts of the DNA to study. Today, there is a faster and easier way to obtain large amounts of a DNA sequence of interest -the polymerase chain reaction (PCR). PCR allows one to use the power ... |
textbooks/bio/Biochemistry/Book%3A_Biochemistry_Free_For_All_(Ahern_Rajagopal_and_Tan)/08%3A_Basic_Techniques/8.08%3A_Reverse_Transcription.txt | princeton-nlp/TextbookChapters | In the central dogma, DNA codes for mRNA, which codes for protein. One known exception to the central dogma is exhibited by retroviruses. These RNA-encoded viruses have a phase in their life cycle in which their genomic RNA is converted back to DNA by a virally-encoded enzyme known as reverse transcriptase. The ability... |
textbooks/bio/Biochemistry/Book%3A_Biochemistry_Free_For_All_(Ahern_Rajagopal_and_Tan)/08%3A_Basic_Techniques/8.09%3A_FRET.txt | princeton-nlp/TextbookChapters | Another method for detecting molecular interactions is Fluorescence resonance energy transfer (FRET) - also called Förster resonance energy transfer, resonance energy transfer (RET) or electronic energy transfer (EET). The technique is based on the observation that a molecule excited by the absorption of light can tran... |
textbooks/bio/Biochemistry/Book%3A_Biochemistry_Free_For_All_(Ahern_Rajagopal_and_Tan)/08%3A_Basic_Techniques/8.11%3A_Protein_Cleavage.txt | princeton-nlp/TextbookChapters | Because of their large size, intact proteins can be difficult to study using analytical techniques, such as mass spectrometry. Consequently, it is often desirable to break a large polypeptide down into smaller pieces. Proteases are enzymes that typically break peptide bonds by binding to specific amino acid sequences i... |
textbooks/bio/Biochemistry/Book%3A_Biochemistry_Free_and_Easy_(Ahern_and_Rajagopal)/01%3A_Cells_Water_and_Buffers/1.01%3A_Introduction.txt | princeton-nlp/TextbookChapters | In this chapter we introduce the subject and talk about the scientific aspects of the most important and most abundant liquid on the face of Earth - water.
01: Cells Water and Buffers
Biochemistry is a relatively young science, but the rate of its expansion has been truly impressive. This rapid pace of discoveries,... |
textbooks/bio/Biochemistry/Book%3A_Biochemistry_Free_and_Easy_(Ahern_and_Rajagopal)/01%3A_Cells_Water_and_Buffers/1.04%3A_Buffers_Keep_the_Cellular_Environment_Stable.txt | princeton-nlp/TextbookChapters | Water can ionize to a slight extent ($10^{-7}\; M$ is about 6 molecules per 100 million of pure water) to form $H^+$ (proton) and $OH^-$ (hydroxide). We measure the proton concentration of a solution with pH, which we define as the negative log of the proton concentration.
$pH = -\log[H^+] \label{1.4.1}$
If the proto... |
textbooks/bio/Biochemistry/Book%3A_Biochemistry_Free_and_Easy_(Ahern_and_Rajagopal)/01%3A_Cells_Water_and_Buffers/1.05%3A_Henderson-Hasselbalch_Approximation.txt | princeton-nlp/TextbookChapters | It is useful to be able to predict the response of the $HAc$ system to changes in $H^+$ concentration. The Henderson-Hasselbalch equation defines the relationship between pH and the ratio of $Ac^-$ and $HAc$. It is as follows
$pH = pK_a + \log \left(\dfrac{[Ac^-]}{[HAc]}\right) \label{1.5.1}$
This simple equation def... |
textbooks/bio/Biochemistry/Book%3A_Biochemistry_Free_and_Easy_(Ahern_and_Rajagopal)/02%3A_Energy/2.01%3A_Oxidative_Energy.txt | princeton-nlp/TextbookChapters | Living organisms are made up of cells, and cells contain many biochemical components such as proteins, lipids, and carbohydrates. But, living cells are not random collections of these molecules. They are extraordinarily organized or "ordered". By contrast, in the nonliving world, there is a universal tendency to increa... |
textbooks/bio/Biochemistry/Book%3A_Biochemistry_Free_and_Easy_(Ahern_and_Rajagopal)/02%3A_Energy/2.02%3A_Oxidation_vs_Reduction_in_Metabolism.txt | princeton-nlp/TextbookChapters | Biochemical processes that break things down from larger to smaller are called catabolic processes. Catabolic processes are often oxidative in nature and energy releasing. Some, but not all of that energy is captured as ATP. If not all of the energy is captured as ATP, what happens to the rest of it? The answer is simp... |
textbooks/bio/Biochemistry/Book%3A_Biochemistry_Free_and_Easy_(Ahern_and_Rajagopal)/02%3A_Energy/2.05%3A_Gibbs_Free_Energy.txt | princeton-nlp/TextbookChapters | Most of the time, ATP is the “storage battery” of cells (See also ‘Molecular Battery Backups for Muscles below). In order to understand how energy is captured, we must first understand Gibbs free energy and in doing so, we begin to see the role of energy in determining the directions chemical reactions take. Wikipedia ... |
textbooks/bio/Biochemistry/Book%3A_Biochemistry_Free_and_Easy_(Ahern_and_Rajagopal)/02%3A_Energy/2.06%3A_Cellular_Phosphorylations.txt | princeton-nlp/TextbookChapters | Formation of triphosphates is essential to meet the cell’s immediate energy needs for synthesis, motion, and signaling. In a given day, an average human being uses more than their body weight in triphosphates. Since triphosphates are the “currency” that meet immediate needs of the cell, it is important to understand ho... |
textbooks/bio/Biochemistry/Book%3A_Biochemistry_Free_and_Easy_(Ahern_and_Rajagopal)/02%3A_Energy/2.07%3A_Energy_Efficiency.txt | princeton-nlp/TextbookChapters | Cells are not 100% efficient in energy use; nothing that we know of is. Consequently, cells do not get as much energy out of catabolic processes as they put into anabolic processes. A good example is the synthesis and breakdown of glucose, something liver cells are frequently doing. The complete conversion of glucose t... |
textbooks/bio/Biochemistry/Book%3A_Biochemistry_Free_and_Easy_(Ahern_and_Rajagopal)/03%3A_Structure__Function/3.01%3A_Introduction_to_Structure__Function.txt | princeton-nlp/TextbookChapters | Function flows from structure. In order to understand the function of biomolecules, we must first understand their structures.
• 3.1: Introduction to Structure & Function
If we hope to understand function in biological systems, we must first understand structure.
• 3.2: Building Blocks
Biological macromolecules are al... |
textbooks/bio/Biochemistry/Book%3A_Biochemistry_Free_and_Easy_(Ahern_and_Rajagopal)/03%3A_Structure__Function/3.03%3A_Proteins.txt | princeton-nlp/TextbookChapters | Whereas nucleotides all are water soluble and have the same basic composition (sugar, base, phosphate) and the sugars also are water soluble and mostly contain 5 or 6 carbons (a few exceptions), the amino acids (general structure below) are structurally and chemically diverse.
Though all of the amino acids are, in fac... |
textbooks/bio/Biochemistry/Book%3A_Biochemistry_Free_and_Easy_(Ahern_and_Rajagopal)/03%3A_Structure__Function/3.04%3A_Nucleic_Acids.txt | princeton-nlp/TextbookChapters | Determination of the structure of the most common form of DNA, known as the B form, was one of the most important scientific advances of the 20th century. Using data from Rosalind Franklin, James Watson and Francis Crick initiated the modern era of molecular biology with their paper in the April 25, 1953 issue of Natur... |
textbooks/bio/Biochemistry/Book%3A_Biochemistry_Free_and_Easy_(Ahern_and_Rajagopal)/03%3A_Structure__Function/3.05%3A_Carbohydrates.txt | princeton-nlp/TextbookChapters | The last class of macromolecules we will consider structurally here is the carbohydrates. Built of sugars or modified sugars, carbohydrates have several important functions, including structural integrity, cellular identification, and energy storage.
Monosaccharides
Simple sugars, also known as monosaccharides, can g... |
textbooks/bio/Biochemistry/Book%3A_Biochemistry_Free_and_Easy_(Ahern_and_Rajagopal)/03%3A_Structure__Function/3.06%3A_Lipids_and_Membranes.txt | princeton-nlp/TextbookChapters | Lipids are a broad class of molecules that all share the characteristic that they have at least a portion of them that is hydrophobic. The class of molecules includes fats, oils (and their substituent fatty acids), steroids, fat-soluble vitamins, prostaglandins, glycerophospholipids, and sphingolipids. Interestingly, e... |
textbooks/bio/Biochemistry/Book%3A_Biochemistry_Free_and_Easy_(Ahern_and_Rajagopal)/04%3A_Catalysis/4.01%3A_Introduction_to_Catalysis.txt | princeton-nlp/TextbookChapters | In living systems, speed is everything. Providing the reaction speeds necessary to support life are the catalysts, mostly in the form of enzymes.
• 4.1: Introduction to Catalysis
• 4.2: Activation Energy
Notice that the reactants start at the same energy level for both conditions and that the products end at the same ... |
textbooks/bio/Biochemistry/Book%3A_Biochemistry_Free_and_Easy_(Ahern_and_Rajagopal)/04%3A_Catalysis/4.02%3A_Activation_Energy.txt | princeton-nlp/TextbookChapters | Figure 4.1.1 schematically depicts the energy changes that occur during the progression of a simple reaction. In the figure, the energy differences during the reaction are compared for a catalyzed (plot on the right) and an uncatalyzed reaction (plot on the left). Notice that the reactants start at the same energy leve... |
textbooks/bio/Biochemistry/Book%3A_Biochemistry_Free_and_Easy_(Ahern_and_Rajagopal)/04%3A_Catalysis/4.07%3A_Chymotrypsin.txt | princeton-nlp/TextbookChapters | Consider the mechanism of catalysis of the enzyme known as chymotrypsin. Found in our digestive system, chymotrypsin’s catalytic action is cleaving peptide bonds in proteins and it uses the side chain of a serine in its mechanism of catalysis. Many other protein- cutting enzymes employ a very similar mechanism and they... |
textbooks/bio/Biochemistry/Book%3A_Biochemistry_Free_and_Easy_(Ahern_and_Rajagopal)/04%3A_Catalysis/4.08%3A_Enzyme_Parameters.txt | princeton-nlp/TextbookChapters | Scientists spend a considerable amount of time characterizing enzymes. To understand how they do this and what the characterizations tell us, we must first understand a few parameters. Imagine I wished to study the reaction catalyzed by an enzyme I have just isolated. I would be interested to understand how fast the en... |
textbooks/bio/Biochemistry/Book%3A_Biochemistry_Free_and_Easy_(Ahern_and_Rajagopal)/04%3A_Catalysis/4.09%3A_Perfect_Enzymes.txt | princeton-nlp/TextbookChapters | Now, if we think about what an ideal enzyme might be, it would be one that has a very high velocity and a very high affinity for its substrate. That is, it wouldn’t take much substrate to get to \(V_{max}/2\) and the \(K_{cat}\) would be very high. Such enzymes would have values of \(K_{cat} / K_M\) that are maximum. I... |
textbooks/bio/Biochemistry/Book%3A_Biochemistry_Free_and_Easy_(Ahern_and_Rajagopal)/04%3A_Catalysis/4.11%3A_Enzyme_Inhibition.txt | princeton-nlp/TextbookChapters | Inhibition of specific enzymes by drugs can be medically useful. Understanding the mechanisms of enzyme inhibition is therefore of considerable importance. We will discuss four types of enzyme inhibition – competitive, non- competitive, uncompetitive, and suicide. Of these, the first three types are reversible. The las... |
textbooks/bio/Biochemistry/Book%3A_Biochemistry_Free_and_Easy_(Ahern_and_Rajagopal)/04%3A_Catalysis/4.12%3A_Control_of_Enzymes.txt | princeton-nlp/TextbookChapters | It is appropriate that we talk at this point about mechanisms cells use to control enzymes. There are four general methods that are employed. They include
1. allosterism
2. covalent modification
3. access to substrate
4. control of enzyme synthesis/breakdown
Some enzymes are controlled by more than one of these metho... |
textbooks/bio/Biochemistry/Book%3A_Biochemistry_Free_and_Easy_(Ahern_and_Rajagopal)/05%3A_Flow_of_Genetic_Information/5.01%3A_DNA_Replication.txt | princeton-nlp/TextbookChapters | As the cell’s so-called blueprint, DNA must be copied to pass on to new cells and its integrity safeguarded. The information in the DNA must also be accessed and transcribed to make the RNA instructions that direct the synthesis of proteins.
• 5.1: DNA Replication
The only way to make new cells is by the division of p... |
textbooks/bio/Biochemistry/Book%3A_Biochemistry_Free_and_Easy_(Ahern_and_Rajagopal)/05%3A_Flow_of_Genetic_Information/5.02%3A_DNA_Repair.txt | princeton-nlp/TextbookChapters | Maintaining the Integrity of the Cell's Information: DNA Repair
In the last section we considered the ways in which cells deal with the challenges associated with replicating their DNA, a vital process for all cells. It is evident that if DNA is the master copy of instructions for an organism, then it is important not... |
textbooks/bio/Biochemistry/Book%3A_Biochemistry_Free_and_Easy_(Ahern_and_Rajagopal)/05%3A_Flow_of_Genetic_Information/5.03%3A_Transcription.txt | princeton-nlp/TextbookChapters | In the preceding sections, we have discussed the replication of the cell's DNA and the mechanisms by which the integrity of the genetic information is carefully maintained. What do cells do with this information? How does the sequence in DNA control what happens in a cell? If DNA is a giant instruction book containing ... |
textbooks/bio/Biochemistry/Book%3A_Biochemistry_Free_and_Easy_(Ahern_and_Rajagopal)/05%3A_Flow_of_Genetic_Information/5.04%3A_Regulation_of_Transcription.txt | princeton-nlp/TextbookChapters | The processes described above are required whenever any gene is transcribed. But what determines which genes are transcribed at a given time. What are the molecular switches that turn transcription on or off? Although there are entire books written on this one topic, the basic mechanism by which transcription is regula... |
textbooks/bio/Biochemistry/Book%3A_Biochemistry_Free_and_Easy_(Ahern_and_Rajagopal)/05%3A_Flow_of_Genetic_Information/5.05%3A_RNA_Processing.txt | princeton-nlp/TextbookChapters | So far, we have looked at the mechanism by which the information in genes (DNA) is transcribed into RNA. The newly made RNA, also known as the primary transcript (the product of transcription is known as a transcript) is further processed before it is functional. Both prokaryotes and eukaryotes process their ribosomal ... |
textbooks/bio/Biochemistry/Book%3A_Biochemistry_Free_and_Easy_(Ahern_and_Rajagopal)/05%3A_Flow_of_Genetic_Information/5.06%3A_Translation.txt | princeton-nlp/TextbookChapters | Translation is the process by which information in mRNAs is used to direct the synthesis of proteins. As you have learned in introductory biology, in eukaryotic cells, this process is carried out in the cytoplasm of the cell, by large RNA-protein machines called ribosomes. Ribosomes contain ribosomal RNAs (rRNAs) and p... |
textbooks/bio/Biochemistry/Book%3A_Biochemistry_Free_and_Easy_(Ahern_and_Rajagopal)/06%3A_Metabolism_I_-_Oxidative_Reductive_Processes/6.01%3A_Definitions.txt | princeton-nlp/TextbookChapters | The cost of living is energy and the producers and consumers of energy in the cell are the chemical reactions known collectively as metabolism. Metabolic processes are governed by the same laws of energy as the rest of the universe, so they must be viewed in the light of Gibbs free energy. For the most part, the driver... |
textbooks/bio/Biochemistry/Book%3A_Biochemistry_Free_and_Easy_(Ahern_and_Rajagopal)/06%3A_Metabolism_I_-_Oxidative_Reductive_Processes/6.02%3A_Perspectives.txt | princeton-nlp/TextbookChapters | We can view metabolism at several levels. At the highest level, we have nutrients, such as sugars, fatty acids and amino acids entering cells and carbon dioxide and other waste products (such as urea) exiting. Cells use the incoming materials for energy and substance to synthesize sugars, nucleotides, and other amino a... |
textbooks/bio/Biochemistry/Book%3A_Biochemistry_Free_and_Easy_(Ahern_and_Rajagopal)/06%3A_Metabolism_I_-_Oxidative_Reductive_Processes/6.04%3A_Gluconeogenesis.txt | princeton-nlp/TextbookChapters | The anabolic counterpart to glycolysis is gluconeogenesis, which occurs mostly in the cells of the liver and kidney. In seven of the eleven reactions of gluconeogenesis (starting from pyruvate), the same enzymes are used as in glycolysis, but the reaction directions are reversed. Notably, the \(\Delta\)G values of thes... |
textbooks/bio/Biochemistry/Book%3A_Biochemistry_Free_and_Easy_(Ahern_and_Rajagopal)/06%3A_Metabolism_I_-_Oxidative_Reductive_Processes/6.06%3A_Glyoxylate_Pathway.txt | princeton-nlp/TextbookChapters | A pathway related to the Citric Acid Cycle (CAC) is the glyoxylate pathway (Figure 6.6.1). This pathway, which overlaps all of the non-decarboxylation reactions of the CAC does not operate in animals, because they lack two enzymes necessary for the pathway – isocitrate lyase and malate synthase. Isocitrate lyase cataly... |
textbooks/bio/Biochemistry/Book%3A_Biochemistry_Free_and_Easy_(Ahern_and_Rajagopal)/06%3A_Metabolism_I_-_Oxidative_Reductive_Processes/6.09%3A_Ketone_Body_Synthesis.txt | princeton-nlp/TextbookChapters | In ketone body synthesis, an acetyl-CoA is split off from HMG-CoA, yielding acetoacetate, a four carbon ketone body that is somewhat unstable, chemically. It will decarboxylate spontaneously to some extent to yield acetone. Ketone bodies are made when the blood levels of glucose fall very low. Ketone bodies can be conv... |
textbooks/bio/Biochemistry/Book%3A_Biochemistry_Free_and_Easy_(Ahern_and_Rajagopal)/06%3A_Metabolism_I_-_Oxidative_Reductive_Processes/6.12%3A_Fatty_Acid_Synthesis.txt | princeton-nlp/TextbookChapters | Synthesis of fatty acids occurs in the cytoplasm and endoplasmic reticulum of the cell and is chemically similar to the beta-oxidation process, but with a couple of key differences. The first of these occur in preparing substrates for the reactions that grow the fatty acid. Transport of acetyl-CoA from the mitochondria... |
textbooks/bio/Biochemistry/Book%3A_Biochemistry_Free_and_Easy_(Ahern_and_Rajagopal)/07%3A_Metabolism_II/7.01%3A_Carbohydrate_Storage_and_Breakdown.txt | princeton-nlp/TextbookChapters | In the last chapter, we focused on metabolic pathways that played important oxidative/reductive roles relative to cellular energy. In this chapter, the pathways that we cover have lesser roles from an energy perspective, but important roles, nonetheless, in catabolism and anabolism of building blocks of proteins and nu... |
textbooks/bio/Biochemistry/Book%3A_Biochemistry_Free_and_Easy_(Ahern_and_Rajagopal)/07%3A_Metabolism_II/7.02%3A_Pentose_Phospate_Pathway.txt | princeton-nlp/TextbookChapters | The Pentose Phosphate Pathway (PPP) is one that many students are confused by. Perhaps the reason for this is that it does not really have a single direction in which it proceeds, as will be apparent below.
Portions of the PPP are similar to the Calvin Cycle of plants, also known as the dark reactions of photosynthesi... |
textbooks/bio/Biochemistry/Book%3A_Biochemistry_Free_and_Easy_(Ahern_and_Rajagopal)/07%3A_Metabolism_II/7.04%3A_C4_Plants.txt | princeton-nlp/TextbookChapters | The Calvin Cycle is the means by which plants assimilate carbon dioxide from the atmosphere, ultimately into glucose. Plants use two general strategies for doing so. The first is employed by plants called C3 plants (most plants) and it simply involves the pathway described above. Another class of plants, called C4 plan... |
textbooks/bio/Biochemistry/Book%3A_Biochemistry_Free_and_Easy_(Ahern_and_Rajagopal)/07%3A_Metabolism_II/7.08%3A_Amino_Acid_Catabolism.txt | princeton-nlp/TextbookChapters | Breakdown of glutamine by glutaminase is a source of ammonium ion in the cell. The other product is glutamate. Glutamate, of course, can be converted by a transamination reaction to alpha-ketoglutarate, which can be oxidized in the citric acid cycle.
• Asparagine can similarly be broken to ammonium and aspartate by as... |
textbooks/bio/Biochemistry/Book%3A_Biochemistry_Free_and_Easy_(Ahern_and_Rajagopal)/07%3A_Metabolism_II/7.11%3A_Purine_de_novo_Biosynthesis.txt | princeton-nlp/TextbookChapters | Synthesis of purine nucleotides differs fundamentally from that of pyrimidine nucleotides in that the bases are built on the ribose ring. The starting material is ribose 5-phosphate, which is phosphorylated by PRPP synthetase to PRPP using two phosphates from ATP. PRPP amidotransferase catalyzes the transfer of an amin... |
textbooks/bio/Biochemistry/Book%3A_Biochemistry_Free_and_Easy_(Ahern_and_Rajagopal)/08%3A_Signaling/8.01%3A_Cell_Signaling.txt | princeton-nlp/TextbookChapters | Cells must receive and respond to signals from their surroundings. Cellular signals and the pathways through which they are passed on and amplified to produce the desired effects on their targets are the focus of this section.
• 8.1: Cell Signaling
How do cells receive signals from their environment and how do they co... |
textbooks/bio/Biochemistry/Book%3A_Biochemistry_Free_and_Easy_(Ahern_and_Rajagopal)/08%3A_Signaling/8.02%3A_Ligand-gated_Ion_Channel_Receptors.txt | princeton-nlp/TextbookChapters | The simplest and fastest of signal pathways is seen in the case of signals whose receptors are gated ion channels. Gated ion channels are made up of multiple transmembrane proteins that create a pore, or channel, in the cell membrane. Depending upon its type, each ion channel is specific to the passage of a particular ... |
textbooks/bio/Biochemistry/Book%3A_Biochemistry_Free_and_Easy_(Ahern_and_Rajagopal)/08%3A_Signaling/8.04%3A_G-protein_Coupled_Receptors_%28GPCRs%29.txt | princeton-nlp/TextbookChapters | G-protein coupled receptors are involved in responses of cells to many different kinds of signals, from epinephrine, to odors, to light. In fact, a variety of physiological phenomena including vision, taste, smell and the fight-or-flight response are mediated by GPCRs.
What are G-protein coupled receptors?
G-protein ... |
textbooks/bio/Biochemistry/Book%3A_Biochemistry_Free_and_Easy_(Ahern_and_Rajagopal)/08%3A_Signaling/8.05%3A_Receptor_Tyrosine_Kinases_%28RTKs%29.txt | princeton-nlp/TextbookChapters | Receptor tyrosine kinases mediate responses to a large number of signals, including peptide hormones like insulin and growth factors like epidermal growth factor. Like the GPCRs, receptor tyrosine kinases bind a signal, then pass the message on through a series of intracellular molecules, the last of which acts on targ... |
textbooks/bio/Biochemistry/Book%3A_Biochemistry_Free_and_Easy_(Ahern_and_Rajagopal)/09%3A_Techniques/9.01%3A_Cell_Disruption.txt | princeton-nlp/TextbookChapters | The environment of a cell is very complex, making it very diffcult, if not impossible, to study individual reactions, enzymes, or pathways within it. For this reason, biochemists prefer to isolate molecules (enzymes, DNAs, RNAs, and other molecules of interest) so they can be analyzed without interference from the mill... |
textbooks/bio/Biochemistry/Book%3A_Biochemistry_Free_and_Easy_(Ahern_and_Rajagopal)/09%3A_Techniques/9.02%3A_Fractionation.txt | princeton-nlp/TextbookChapters | Fractionation of samples typically starts with centrifugation. Using a centrifuge, one can remove cell debris, and fractionate organelles, and cytoplasm. For example, nuclei, being relatively large, can be spun down at fairly low speeds. Once nuclei have been sedimented, the remaining solution, or supernatant, can be c... |
textbooks/bio/Biochemistry/Book%3A_Biochemistry_Free_and_Easy_(Ahern_and_Rajagopal)/09%3A_Techniques/9.08%3A_Electrophoresis.txt | princeton-nlp/TextbookChapters | DNA molecules are long and loaded with negative charges, thanks to their phosphate backbones. Electrophoretic methods separate large molecules, such as DNA, RNA, and proteins based on their charge and size. For DNA and RNA, the charge of the nucleic acid is proportional to its size (length). For proteins, which do not ... |
textbooks/bio/Biochemistry/Book%3A_Biochemistry_Free_and_Easy_(Ahern_and_Rajagopal)/09%3A_Techniques/9.09%3A_Protein_Cleavage.txt | princeton-nlp/TextbookChapters | Working with intact proteins in analytical techniques, such as mass spectrometry, can be problematic. Consequently, it is often desirable to break a large polypeptide down into smaller, more manageable pieces. There are two primary approaches to accomplishing this - use of chemical reagents or use of proteolytic enzyme... |
textbooks/bio/Biochemistry/Book%3A_Biochemistry_Free_and_Easy_(Ahern_and_Rajagopal)/09%3A_Techniques/9.11%3A_Blotting.txt | princeton-nlp/TextbookChapters | Blotting provides a means of identifying specific molecules out of a mixture. It employs three main steps. First, the mixture of molecules is separated by gel electrophoresis. The mixture could be DNA (Southern Blot), RNA (Nothern Blot), or protein (Western Blot) and the gel could be agarose (for DNA/RNA) or polyacryla... |
textbooks/bio/Biochemistry/Book%3A_Biochemistry_Free_and_Easy_(Ahern_and_Rajagopal)/09%3A_Techniques/9.14%3A_Lac_Z_Blue-White_Screening.txt | princeton-nlp/TextbookChapters | A powerful tool for biotechnologists is the lac Z gene. You may recall from an earlier section on the control of gene expression, that lac Z is part of the lac operon of E. coli and encodes the enzyme ß galactosidase. This enzyme catalyzes the hydrolysis of lactose into glucose and galactose, allowing the bacteria to u... |
textbooks/bio/Biochemistry/Book%3A_Biochemistry_Free_and_Easy_(Ahern_and_Rajagopal)/10%3A_Putting_It_All_Together/10.01%3A_Looking_Back.txt | princeton-nlp/TextbookChapters | With this chapter, we tie up a bunch of loose ends and ponder what lies in the future of biochemistry.
• 10.1: Looking Back
Thousands of enzymes and their substrates have been identified, and hundreds of metabolic pathways traced. The structure of hundreds of proteins is known down to the position of every atom. Follo... |
textbooks/bio/Biochemistry/Book%3A_Biochemistry_Free_and_Easy_(Ahern_and_Rajagopal)/10%3A_Putting_It_All_Together/10.02%3A_Looking_Forward.txt | princeton-nlp/TextbookChapters | Toward the end of the twentieth century, new methods began to change the face of biochemistry. The launching of the Human Genome Project and the development of faster and cheaper sequencing technologies provided biochemists with entire genome sequences, not only of humans, but of numerous other organisms. Huge database... |
textbooks/bio/Biochemistry/Fundamentals_of_Biochemistry_(Jakubowski_and_Flatt)/01%3A_Unit_I-_Structure_and_Catalysis/01%3A_The_Foundations_of_Biochemistry/1.01%3A_Cellular_Foundations.txt | princeton-nlp/TextbookChapters | Search Fundamentals of Biochemistry
Introduction
You have probably studied the cell many times, either in high school or in college biology classes. There are many websites available that review both prokaryotic (bacterial and archaeal cell types) and eukaryotic cells (protist, fungi, plant, and animal cell types). A... |
textbooks/bio/Biochemistry/Fundamentals_of_Biochemistry_(Jakubowski_and_Flatt)/01%3A_Unit_I-_Structure_and_Catalysis/01%3A_The_Foundations_of_Biochemistry/1.02%3A_Chemical_Foundations.txt | princeton-nlp/TextbookChapters | Search Fundamentals of Biochemistry
Organic Molecules
On Earth, all carbon-containing molecules have originated from biological, living organisms causing them to be termed organic compounds. The number of known organic compounds is quite large. In fact, there are many times more organic compounds known than all the o... |
textbooks/bio/Biochemistry/Fundamentals_of_Biochemistry_(Jakubowski_and_Flatt)/01%3A_Unit_I-_Structure_and_Catalysis/01%3A_The_Foundations_of_Biochemistry/1.03%3A_Physical-Chemical_Foundations.txt | princeton-nlp/TextbookChapters | Search Fundamentals of Biochemistry
The types and numbers of chemical reactions that occur in biological cells are staggering. Compared to both physical and chemical reactions that occur in a controlled and closed environment, biological reactions occur in open systems with input and output of both energy and chemical... |
textbooks/bio/Biochemistry/Fundamentals_of_Biochemistry_(Jakubowski_and_Flatt)/01%3A_Unit_I-_Structure_and_Catalysis/01%3A_The_Foundations_of_Biochemistry/1.04%3A_Genetic__Foundations.txt | princeton-nlp/TextbookChapters | Search Fundamentals of Biochemistry
Introduction
The development of complex biological organisms on our planet has arisen through the evolutionary mechanism of natural selection. The British naturalist, Charles Darwin proposed the theory of biological evolution by natural selection in his book, ‘On the Origins of Spe... |
textbooks/bio/Biochemistry/Fundamentals_of_Biochemistry_(Jakubowski_and_Flatt)/01%3A_Unit_I-_Structure_and_Catalysis/01%3A_The_Foundations_of_Biochemistry/1.05%3A_Chapter_1_Questions.txt | princeton-nlp/TextbookChapters | Section 1 Questions
Question \(1\)
In Figure 1.2, two examples of types of enzyme-substrate binding are shown: the Lock-and-Key model and Induced-Fit. What are some situations in which one style of the enzyme would be favored over the other?
Answer
Lock and key enzymes are highly specific for their substrate and th... |
textbooks/bio/Biochemistry/Fundamentals_of_Biochemistry_(Jakubowski_and_Flatt)/01%3A_Unit_I-_Structure_and_Catalysis/02%3A_Water_and_its_Role_in_Life/2.01%3A_The_multiple_roles_of_water.txt | princeton-nlp/TextbookChapters | Search Fundamentals of Biochemistry
“Nothing in the world is as soft and yielding as it,
Yet nothing can better overcome the hard and strong,
For they can neither control nor do away with it.
The soft overcomes the hard,
The yielding overcomes the strong;”
These words come from the Tao Te Ching by Lao Zu. Let’s conve... |
textbooks/bio/Biochemistry/Fundamentals_of_Biochemistry_(Jakubowski_and_Flatt)/01%3A_Unit_I-_Structure_and_Catalysis/02%3A_Water_and_its_Role_in_Life/2.02%3A_Weak_Acids_and_Bases_pH_and_pKa.txt | princeton-nlp/TextbookChapters | Search Fundamentals of Biochemistry
The previous section described the general acid/base properties of water. There are many functional groups in both small and large biomolecules that act as acids and bases. Common weak acids are carboxylic acids and derivatives of phosphoric acid which become negatively charged on d... |
textbooks/bio/Biochemistry/Fundamentals_of_Biochemistry_(Jakubowski_and_Flatt)/01%3A_Unit_I-_Structure_and_Catalysis/02%3A_Water_and_its_Role_in_Life/2.03%3A_Buffering_against_pH_Changes_in_Biological_Systems.txt | princeton-nlp/TextbookChapters | Search Fundamentals of Biochemistry
Introduction
As one way to ensure homeostasis, the pH is maintained between 7.35 and 7.45 in humans. (Much lower pH values, around 4.5, are found in the lysosome). Lower pH values are associated with metabolic and respiratory acidosis while higher pH values are characteristic of me... |
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