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Search Fundamentals of Biochemistry
RNA: Structure and Function
Ribonucleic acids are very similar in chemical structure to DNA except they contain ribose instead of deoxyribose. They also have the pyrimidine base uracil instead of thymine, as shown in Figures 1 and 2 above. These two small changes (but mostly the fi... | textbooks/bio/Biochemistry/Fundamentals_of_Biochemistry_(Jakubowski_and_Flatt)/01%3A_Unit_I-_Structure_and_Catalysis/08%3A_Nucleotides_and_Nucleic_Acids/8.02%3A_Nucleic_Acids_-_RNA_Structure_and_Function.txt |
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Now that we have an understanding of the structures of DNA and the structures and various functions of RNA, we can now more fully explore how their chemical similarities and difference contribute to different functions.
Chemical modifications of DNA and RNA
Post-translation modifi... | textbooks/bio/Biochemistry/Fundamentals_of_Biochemistry_(Jakubowski_and_Flatt)/01%3A_Unit_I-_Structure_and_Catalysis/08%3A_Nucleotides_and_Nucleic_Acids/8.03%3A_Nucleic_Acids_-_Comparison_of_DNA_and_RNA.txt |
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Chromatin
When stained and viewed in a microscope, eukaryotic nuclear DNA in nondividing cells is observed in two different states, heterochromatin (dark areas) and euchromatin (light areas), as shown in Figure \(1\).
The heterochromatin is darkly stained and found along the inner... | textbooks/bio/Biochemistry/Fundamentals_of_Biochemistry_(Jakubowski_and_Flatt)/01%3A_Unit_I-_Structure_and_Catalysis/08%3A_Nucleotides_and_Nucleic_Acids/8.04%3A_Chromosomes_and_Chromatin.txt |
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It is difficult to read newspapers and newsmagazines without encountering the CRISPR-Cas9 gene editing system that has the potential to make gene editing routine in disease diagnosis, treatment, and cure, as well as in genetic modification of organisms to improve their quality and q... | textbooks/bio/Biochemistry/Fundamentals_of_Biochemistry_(Jakubowski_and_Flatt)/01%3A_Unit_I-_Structure_and_Catalysis/08%3A_Nucleotides_and_Nucleic_Acids/8.06%3A_Enzymes_for_Genetic_modifications.txt |
• 9.1: DNA Isolation, Sequencing, and Synthesis
• 9.2: Bioinformatics
• 9.3: Cloning and Recombinant Expression
• 9.4: DNA Microarrays
A DNA microarray (also commonly known as DNA chip or biochip) is a collection of microscopic DNA spots attached to a solid surface. Scientists use DNA microarrays to measure the express... | textbooks/bio/Biochemistry/Fundamentals_of_Biochemistry_(Jakubowski_and_Flatt)/01%3A_Unit_I-_Structure_and_Catalysis/09%3A_Investigating_DNA/9.01%3A_DNA_Isolation_Sequencing_and_Synthesis.txt |
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Introduction
An unprecedented revolution has been observed in science with recent technological advances, which have provided a large amount of “omic” data. The crescent generation and availability of this information available in public databases were, and still are, a challenge f... | textbooks/bio/Biochemistry/Fundamentals_of_Biochemistry_(Jakubowski_and_Flatt)/01%3A_Unit_I-_Structure_and_Catalysis/09%3A_Investigating_DNA/9.02%3A_Bioinformatics.txt |
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A DNA microarray (also commonly known as a DNA chip or biochip) is a collection of microscopic DNA spots attached to a solid surface. Scientists use DNA microarrays to measure the expression levels of large numbers of genes simultaneously or to genotype multiple regions of a genome.... | textbooks/bio/Biochemistry/Fundamentals_of_Biochemistry_(Jakubowski_and_Flatt)/01%3A_Unit_I-_Structure_and_Catalysis/09%3A_Investigating_DNA/9.04%3A_DNA_Microarrays.txt |
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In situ hybridization (ISH) is a type of hybridization that uses a labeled complementary DNA, RNA, or modified nucleic acids strand (i.e., probe) to localize a specific DNA or RNA sequence in a portion or section of tissue (in situ) or if the tissue is small enough (e.g., plant seed... | textbooks/bio/Biochemistry/Fundamentals_of_Biochemistry_(Jakubowski_and_Flatt)/01%3A_Unit_I-_Structure_and_Catalysis/09%3A_Investigating_DNA/9.05%3A_In_Situ_Hybridization.txt |
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Introduction to Lipids
(Thanks to Rebecca Roston for providing a cohesive organizational framework and image templates)
Lipids are organic molecule molecules that are soluble in organic solvents, such as chloroform/methanol, but sparingly soluble in aqueous solutions. These solubi... | textbooks/bio/Biochemistry/Fundamentals_of_Biochemistry_(Jakubowski_and_Flatt)/01%3A_Unit_I-_Structure_and_Catalysis/10%3A_Lipids/10.01%3A_Introduction_to_lipids.txt |
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Single Chain Amphiphiles and Micelles
An understanding of lipids in simple solutions in the lab is incredibly helpful to understanding them in vivo. The same physical-chemical constraints would apply to the complex environment of the cell. What is different in the cell is that lipi... | textbooks/bio/Biochemistry/Fundamentals_of_Biochemistry_(Jakubowski_and_Flatt)/01%3A_Unit_I-_Structure_and_Catalysis/10%3A_Lipids/10.02%3A_Lipids_Aggregates_in_Water_-_Micelles_and_Liposomes.txt |
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An overview of lipid bilayers
A membrane bilayer consists of more than just two leaflets of amphiphilic leaflets. It also contains membrane proteins (which we will discuss in the next chapter) which can also be attached to carbohydrates. Most assuredly you have seen various represe... | textbooks/bio/Biochemistry/Fundamentals_of_Biochemistry_(Jakubowski_and_Flatt)/01%3A_Unit_I-_Structure_and_Catalysis/10%3A_Lipids/10.03%3A_Membrane_Bilayer_and_Monolayer_Assemblies_-_Structures_and_Dynamics.txt |
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Introduction
Lipids, although small compared to large biopolymers like proteins, nucleic acid, and large glycans, are very heterogenous in structure, given the large array of fatty acid and isoprenoid chain lengths, numbers of double bonds, etc that appear in different lipid classe... | textbooks/bio/Biochemistry/Fundamentals_of_Biochemistry_(Jakubowski_and_Flatt)/01%3A_Unit_I-_Structure_and_Catalysis/10%3A_Lipids/10.04%3A_Working_with_Lipids.txt |
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Introduction
One easily understandable function of membrane bilayers is to separate the inside and outside of the cell or intracellular organelles. Yet as we mentioned before, such barriers can not be so rigid and impenetrable that they prevent the movement of materials across the ... | textbooks/bio/Biochemistry/Fundamentals_of_Biochemistry_(Jakubowski_and_Flatt)/01%3A_Unit_I-_Structure_and_Catalysis/11%3A_Biological_Membranes_and_Transport/11.01%3A_Membrane_and_Membrane_Proteins.txt |
Learning Objectives
• Understand the structure and function of biological membranes.
• Describe the different types of diffusion and how they operate across a membrane.
• Explain the concept of concentration gradient and how it drives diffusion.
• Describe the mechanisms of passive and facilitated diffusion, including ... | textbooks/bio/Biochemistry/Fundamentals_of_Biochemistry_(Jakubowski_and_Flatt)/01%3A_Unit_I-_Structure_and_Catalysis/11%3A_Biological_Membranes_and_Transport/11.02%3A_Diffusion_Across_a_Membrane_-_Passive_and_Facilitated_Diffusion.txt |
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Introduction
If you punched a hole or pore in the membrane, depending on its size, multiple types of chemical species could flow through it simultaneously. We'll talk about pores in the next section. Let's focus on channels, which have much smaller openings, which are gated open to... | textbooks/bio/Biochemistry/Fundamentals_of_Biochemistry_(Jakubowski_and_Flatt)/01%3A_Unit_I-_Structure_and_Catalysis/11%3A_Biological_Membranes_and_Transport/11.03%3A_Diffusion_Across_a_Membrane_-_Channels.txt |
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Pores and Pore-Forming Proteins (PFPs)
If you form a pore in a cell bilayer, molecules of all sizes could move either way based on their electrochemical potential. They will move from regions of a higher to lower electrochemical potential in a thermodynamically favorable process. H... | textbooks/bio/Biochemistry/Fundamentals_of_Biochemistry_(Jakubowski_and_Flatt)/01%3A_Unit_I-_Structure_and_Catalysis/11%3A_Biological_Membranes_and_Transport/11.04%3A_Diffusion_Across_a_Membrane_-_Pores.txt |
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In the previous sections, we explored facilitated diffusion, diffusion through channels, and diffusion through larger pores. In each case, once a carrier/permease protein was available, or a channel (gated by ligand binding, change in membrane potential, lipid binding, or mechanical... | textbooks/bio/Biochemistry/Fundamentals_of_Biochemistry_(Jakubowski_and_Flatt)/01%3A_Unit_I-_Structure_and_Catalysis/11%3A_Biological_Membranes_and_Transport/11.05%3A__Active_Transport.txt |
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Pores and Pore-Forming Proteins (PFPs)
If you form a pore in a cell bilayer, molecules of all sizes could move either way based on their electrochemical potential. They will move from regions of a higher to lower electrochemical potential in a thermodynamically favorable process. H... | textbooks/bio/Biochemistry/Fundamentals_of_Biochemistry_(Jakubowski_and_Flatt)/01%3A_Unit_I-_Structure_and_Catalysis/11%3A_Biological_Membranes_and_Transport/11.4%3A_Diffusion_Across_a_Membrane_-_Pores.txt |
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Introduction
We have already discussed How Enzymes Work and Enzymatic Reaction Mechanisms in great detail in Chapter 6. Here we will focus on a lighter, less granular review of some key reaction mechanisms and the changes in Gibb's free energy associated with them, both in an uncat... | textbooks/bio/Biochemistry/Fundamentals_of_Biochemistry_(Jakubowski_and_Flatt)/02%3A_Unit_II-_Bioenergetics_and_Metabolism/12%3A_Bioenergetics_and_Biochemical_Reaction_Types/12.01%3A_Biochemical_Reactions_and_Energy_Changes.txt |
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ATP and Phosphoryl Transfer reactions
Biological oxidation reactions serve two functions, as described in the previous chapter. Oxidation of organic molecules can produce new molecules with different properties. For example, increases in solubility are observed on the hydroxylation... | textbooks/bio/Biochemistry/Fundamentals_of_Biochemistry_(Jakubowski_and_Flatt)/02%3A_Unit_II-_Bioenergetics_and_Metabolism/12%3A_Bioenergetics_and_Biochemical_Reaction_Types/12.02%3A_Phosphoryl_Group_Transfers_and_ATP.txt |
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The History of Oxygen
Oxygen may be considered one of the most important elements in chemistry. Not counting hydrocarbons, there is a greater diversity of molecules with oxygen than with carbon. Given its role in the molecular world, very little time is spent on the chemistry of ox... | textbooks/bio/Biochemistry/Fundamentals_of_Biochemistry_(Jakubowski_and_Flatt)/02%3A_Unit_II-_Bioenergetics_and_Metabolism/12%3A_Bioenergetics_and_Biochemical_Reaction_Types/12.03%3A_The_Chemistry_and_Biochemistry_of_Dioxygen.txt |
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General Oxidizing Agents
Before we consider common biological oxidizing agents, lets look back at ones you saw in other chemistry classes. Oxidizing agents are required to oxidize organic molecules. In organic lab, you never used dioxygen as an oxidizing agent. It is difficult to l... | textbooks/bio/Biochemistry/Fundamentals_of_Biochemistry_(Jakubowski_and_Flatt)/02%3A_Unit_II-_Bioenergetics_and_Metabolism/12%3A_Bioenergetics_and_Biochemical_Reaction_Types/12.04%3A_Biological_Oxidation-Reduction_Reactions.txt |
• 13.1: Glycolysis
In this section, we will provide you with a historical overview of glycolysis and introduce you to the 10 enzymatic reactions in the pathway. Our main goal is to understand how the oxidation of our major food molecules, sugars in the case of glycolysis, can lead to ATP synthesis.
• 13.2: Fates of Pyr... | textbooks/bio/Biochemistry/Fundamentals_of_Biochemistry_(Jakubowski_and_Flatt)/02%3A_Unit_II-_Bioenergetics_and_Metabolism/13%3A_Glycolysis_Gluconeogenesis_and_the_Pentose_Phosphate_Pathway/13.01%3A_Glycolysis.txt |
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Introduction to Fermentation
Fermentation is a process in which a fuel molecule is broken down anaerobically (or without oxygen) to meet ATP demands. One of the most notable pathways that can utilize fermentation is glycolysis, which we have just described. During glycolysis, gluco... | textbooks/bio/Biochemistry/Fundamentals_of_Biochemistry_(Jakubowski_and_Flatt)/02%3A_Unit_II-_Bioenergetics_and_Metabolism/13%3A_Glycolysis_Gluconeogenesis_and_the_Pentose_Phosphate_Pathway/13.02%3A_Fates_of_Pyruvate_under_Anaerobic_Cond.txt |
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Introduction
Gluconeogenesis is a metabolic pathway that results in the generation of glucose from non-carbohydrate carbon substrates such as lactate, glycerol, and glucogenic amino acids. It is one of the two main mechanisms humans and many other animals use to keep blood glucose ... | textbooks/bio/Biochemistry/Fundamentals_of_Biochemistry_(Jakubowski_and_Flatt)/02%3A_Unit_II-_Bioenergetics_and_Metabolism/13%3A_Glycolysis_Gluconeogenesis_and_the_Pentose_Phosphate_Pathway/13.03%3A_Gluconeogenesis.txt |
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Introduction
The pentose phosphate pathway (PPP), also known as the pentose phosphate shunt, is an important part of glucose metabolism. The PPP branches after the first step of glycolysis and consumes the intermediate glucose 6-phosphate (G6P) to generate fructose 6-phosphate (F6P... | textbooks/bio/Biochemistry/Fundamentals_of_Biochemistry_(Jakubowski_and_Flatt)/02%3A_Unit_II-_Bioenergetics_and_Metabolism/13%3A_Glycolysis_Gluconeogenesis_and_the_Pentose_Phosphate_Pathway/13.04%3A_Pentose_Phosphate_Pathway_of_Glucose_O.txt |
• 14.1: Regulation of Metabolic Pathways
Exquisite mechanisms have evolved that control the flux of metabolites through metabolic pathways to insure that the output of the pathways meets biological demand and that energy in the form of ATP is not wasted by having opposing pathways run concomitantly in the same cell.
• ... | textbooks/bio/Biochemistry/Fundamentals_of_Biochemistry_(Jakubowski_and_Flatt)/02%3A_Unit_II-_Bioenergetics_and_Metabolism/14%3A_Principles_of_Metabolic_Regulation/14.01%3A_Regulation_of_Metabolic_Pathways.txt |
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Introduction to Metabolic Control Analysis
Enzyme kinetics may seem difficult given the complicated mathematical derivations, the number of chemical species involved (an enzyme and all its substrates and products), the number of steps in the mechanism, and a large number of rate, k... | textbooks/bio/Biochemistry/Fundamentals_of_Biochemistry_(Jakubowski_and_Flatt)/02%3A_Unit_II-_Bioenergetics_and_Metabolism/14%3A_Principles_of_Metabolic_Regulation/14.02%3A_Basic_Principles_of_Metabolic_Control_Analysis_%28MCA%29.txt |
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Introduction
Metabolic control analysis (MCA) is one method used to address the complexity of dynamic changes of species in a complex metabolic system. As such, an understanding of MCA would apply to complex signal transduction pathways as well as to other emerging areas in systems... | textbooks/bio/Biochemistry/Fundamentals_of_Biochemistry_(Jakubowski_and_Flatt)/02%3A_Unit_II-_Bioenergetics_and_Metabolism/14%3A_Principles_of_Metabolic_Regulation/14.03%3A_The_Flux_Control_Coefficient.txt |
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Concentration Control Coefficients
The Concentration control coefficient ($C_{E_{i}}^{S}$), a global property of the system, gives the relative fractional change in metabolite concentration $S_j (dS_j/S_j)$, where $S_j$ is the concentration of any metabolite in the system and as su... | textbooks/bio/Biochemistry/Fundamentals_of_Biochemistry_(Jakubowski_and_Flatt)/02%3A_Unit_II-_Bioenergetics_and_Metabolism/14%3A_Principles_of_Metabolic_Regulation/14.04%3A_Concentration_Control_and_Elasticity_Coefficients.txt |
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Introduction
We have studied binding interactions in Chapter 5, kinetics in Chapter 6, and principles of metabolic control in this chapter. We've learned the following:
Binding Reactions
• for simple binding of a ligand to a macromolecule, graphs of fractional saturation of the ... | textbooks/bio/Biochemistry/Fundamentals_of_Biochemistry_(Jakubowski_and_Flatt)/02%3A_Unit_II-_Bioenergetics_and_Metabolism/14%3A_Principles_of_Metabolic_Regulation/14.5%3A_Metabolism_and_Signaling%3A__The_Steady_State_Adaptation_and_Home.txt |
• 15.1: Insulin Signaling in the Liver
In this section, we will discuss insulin signaling and glycogen synthesis.
• 15.2: Glycogenesis
The process of forming glycogen is called glycogenesis and it requires the activity of six enzymes. Some of these, we have already discussed including the hexokinase that phosphorylates... | textbooks/bio/Biochemistry/Fundamentals_of_Biochemistry_(Jakubowski_and_Flatt)/02%3A_Unit_II-_Bioenergetics_and_Metabolism/15%3A_Glucose_Glycogen_and_Their_Metabolic_Regulation/15.01%3A_Insulin_Signaling_in_the_Liver.txt |
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Introduction
The process of forming glycogen is called glycogenesis and it requires the activity of six enzymes as illustrated in Figure $1$. We have already discussed several including hexokinase which phosphorylates the 6'-OH of glucose and phosphoglucomutase which converts gluc... | textbooks/bio/Biochemistry/Fundamentals_of_Biochemistry_(Jakubowski_and_Flatt)/02%3A_Unit_II-_Bioenergetics_and_Metabolism/15%3A_Glucose_Glycogen_and_Their_Metabolic_Regulation/15.02%3A_Glycogenesis.txt |
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In the previous section, you learned that glucagon signaling down-regulates glycogen synthesis. Now let's look at glycogen breakdown, called glycogenolysis, and its control by two hormones, glucagon, and epinephrine. Only two enzymes are required for the breakdown of glycogen, the g... | textbooks/bio/Biochemistry/Fundamentals_of_Biochemistry_(Jakubowski_and_Flatt)/02%3A_Unit_II-_Bioenergetics_and_Metabolism/15%3A_Glucose_Glycogen_and_Their_Metabolic_Regulation/15.03%3A_15.3_Glycogenolyis_and_its_Regulation_by_Glucagon_a.txt |
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There are three major enzymatic control points within the glycolytic pathway. These include hexokinase, phosphofructokinase, and pyruvate kinase reactions. Key drivers for regulating the pathway are energy demand within the cell as determined by local indicators such as ATP and AMP,... | textbooks/bio/Biochemistry/Fundamentals_of_Biochemistry_(Jakubowski_and_Flatt)/02%3A_Unit_II-_Bioenergetics_and_Metabolism/15%3A_Glucose_Glycogen_and_Their_Metabolic_Regulation/15.04%3A_Regulation_of_Glycolysis.txt |
The citric acid cycle – also known as the TCA cycle or the Krebs cycle – is a series of chemical reactions to release stored energy through the oxidation of acetyl-CoA derived from carbohydrates, fats, and proteins.
16: The Citric Acid Cycle
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Introduction
Let's do a short review... | textbooks/bio/Biochemistry/Fundamentals_of_Biochemistry_(Jakubowski_and_Flatt)/02%3A_Unit_II-_Bioenergetics_and_Metabolism/16%3A_The_Citric_Acid_Cycle/16.01%3A_Production_of_Acetyl-CoA_%28Activated_Acetate%29.txt |
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Introduction
The acetyl-CoA formed by the pyruvate dehydrogenase complex (PDC) now enters a cyclic, non-linear pathway called the citric acid cycle, tricarboxylic acid (TCA) cycle, or the Kreb's cycle after Hans Krebs who discovered it. The cycle is shown in Figure \(1\) in wedge/d... | textbooks/bio/Biochemistry/Fundamentals_of_Biochemistry_(Jakubowski_and_Flatt)/02%3A_Unit_II-_Bioenergetics_and_Metabolism/16%3A_The_Citric_Acid_Cycle/16.02%3A__Reactions_of_the_Citric_Acid_Cycle.txt |
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Overview
Entry of pyruvate into the citric acid cycle leading to the aerobic production of energy and intermediates for biosynthesis is a key metabolic step. Hence both the pyruvate dehydrogenase complex and key enzymes in the cycle are targets for regulation. This occurs through s... | textbooks/bio/Biochemistry/Fundamentals_of_Biochemistry_(Jakubowski_and_Flatt)/02%3A_Unit_II-_Bioenergetics_and_Metabolism/16%3A_The_Citric_Acid_Cycle/16.03%3A_Regulation_of_the_Citric_Acid_Cycle.txt |
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Citric Acid Cycle Shunts and Bypasses
Evolution has allowed variants in the citric acid cycle to produce new functionalities in organisms. Let's consider a few.
Glyoxylate Shunt
What if you were a microorganism that has evolved to use acetate (2C) as a source (if not the sole sou... | textbooks/bio/Biochemistry/Fundamentals_of_Biochemistry_(Jakubowski_and_Flatt)/02%3A_Unit_II-_Bioenergetics_and_Metabolism/16%3A_The_Citric_Acid_Cycle/16.04%3A_Variants_of_the_Citric_Acid_Cycle.txt |
Fatty acid catabolism is the mechanism by which the body accesses energy stored as triglycerides.
• 17.1: Digestion, Mobilization, and Transport of Fats
In this chapter we will discuss the breakdown of fats to produce useful energy for biosynthesis and for ATP production.
• 17.2: Oxidation of Fatty Acids
Fatty acids, ... | textbooks/bio/Biochemistry/Fundamentals_of_Biochemistry_(Jakubowski_and_Flatt)/02%3A_Unit_II-_Bioenergetics_and_Metabolism/17%3A_Fatty_Acid_Catabolism/17.01%3A_Digestion_Mobilization_and_Transport_of_Fats.txt |
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Introduction
Fatty acids, esterified to glycerol in triacylglycerols, are the major source of stored energy in organisms. As we burn fossil fuels to produce energy to drive our society, so can we "burn" fatty acids to indirectly produce for heat, ATP to drive biosynthetic reactions... | textbooks/bio/Biochemistry/Fundamentals_of_Biochemistry_(Jakubowski_and_Flatt)/02%3A_Unit_II-_Bioenergetics_and_Metabolism/17%3A_Fatty_Acid_Catabolism/17.02%3A_Oxidation_of_Fatty_Acids.txt |
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Much of the material below derives from Kolb et al. BMC Medicine (2021) 19:313 https://doi.org/10.1186/s12916-021-02185-0. Creative Commons Attribution 4.0 International License, http://creativecommons.org/licenses/by/4.0/.
Introduction
Ketone bodies are the name given to two mole... | textbooks/bio/Biochemistry/Fundamentals_of_Biochemistry_(Jakubowski_and_Flatt)/02%3A_Unit_II-_Bioenergetics_and_Metabolism/17%3A_Fatty_Acid_Catabolism/17.03%3A_Ketone_Bodies.txt |
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Introduction
Organic chemistry is usually described as the chemistry of carbon-containing molecules. But isn't that definition a bit carbon-centric, especially since the prevalence of oxygen-containing molecules is staggering? What about nitrogen? We live in a dinitrogen-rich atmos... | textbooks/bio/Biochemistry/Fundamentals_of_Biochemistry_(Jakubowski_and_Flatt)/02%3A_Unit_II-_Bioenergetics_and_Metabolism/18%3A_Nitrogen_-_Amino_Acid_Catabolism/18.01%3A_The_Biochemistry_of_Nitrogen_in_the_Biosphere.txt |
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From the previous section on the nitrogen cycle, it should be clear that NH3/NH4+ has a central role in metabolism. Nature's fertilizer for plants is ammonium derived from bacterial nitrogenase and human-derived Born-Haber process. Animals get their ammonia mostly from ingested plan... | textbooks/bio/Biochemistry/Fundamentals_of_Biochemistry_(Jakubowski_and_Flatt)/02%3A_Unit_II-_Bioenergetics_and_Metabolism/18%3A_Nitrogen_-_Amino_Acid_Catabolism/18.02%3A_Metabolic_Fates_of_Amino_Groups.txt |
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The Urea Cycle
Now we are in a position to see what happens to excess NH3/NH4+ that accumulates in the liver mitochondria. The ammonia that is formed in the liver through oxidative deamination by glutamate dehydrogenase, ends up in urea. Alternatively, it could be added to glutamic... | textbooks/bio/Biochemistry/Fundamentals_of_Biochemistry_(Jakubowski_and_Flatt)/02%3A_Unit_II-_Bioenergetics_and_Metabolism/18%3A_Nitrogen_-_Amino_Acid_Catabolism/18.03%3A_Nitrogen_Excretion_and_the_Urea_Cycle.txt |
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Amino acid degradation
We saw how nitrogen is removed from amino acids to produce urea or NH4+ in the previous chapter section. What are the fates of the carbon skeletons that remain? This section is where students might get overwhelmed by the diversity of amino acid degradation pa... | textbooks/bio/Biochemistry/Fundamentals_of_Biochemistry_(Jakubowski_and_Flatt)/02%3A_Unit_II-_Bioenergetics_and_Metabolism/18%3A_Nitrogen_-_Amino_Acid_Catabolism/18.04%3A_An_overview_of_amino_acid_metabolism_and_the_role_of_Cofactors.txt |
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Introduction
In previous sections, we saw how nitrogen is removed from amino acids to produce urea or NH4+, that some amino acids are glucogenic, ketogenic, or both, and the role of tetrahydrofolate derivatives and S-adenosylmethionine in 1C transfer reactions. Now we can focus on ... | textbooks/bio/Biochemistry/Fundamentals_of_Biochemistry_(Jakubowski_and_Flatt)/02%3A_Unit_II-_Bioenergetics_and_Metabolism/18%3A_Nitrogen_-_Amino_Acid_Catabolism/18.05%3A_Pathways_of_Amino_Acid_Degradation.txt |
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An Overview of Mitochondrial Electron Transport
The main oxidizing agent used during aerobic metabolism in the citric acid cycle is NAD+ (although FAD is used in one step). In the process, these oxidizing agents get reduced to form NADH (and FADH2). Unless NAD+ is regenerated, glyc... | textbooks/bio/Biochemistry/Fundamentals_of_Biochemistry_(Jakubowski_and_Flatt)/02%3A_Unit_II-_Bioenergetics_and_Metabolism/19%3A_Oxidative_Phosphorylation/19.01%3A_Electron-Transfer_Reactions_in_Mitochondria.txt |
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Introduction
ATP synthase, also called F1FoATPase, is a rotary motor enzyme. This enzyme is found in the inner membrane of mitochondria, the analogous thylakoid membranes of chloroplasts, and the cell membrane of bacteria. The enzyme consists of two parts, the membrane-bound Fo whi... | textbooks/bio/Biochemistry/Fundamentals_of_Biochemistry_(Jakubowski_and_Flatt)/02%3A_Unit_II-_Bioenergetics_and_Metabolism/19%3A_Oxidative_Phosphorylation/19.02%3A_ATP_Synthesis.txt |
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Introduction
The main function of oxidative phosphorylation (oxphos) is to produce, under aerobic conditions, lots of ATP. It should make sense that to a first approximation, the regulation of oxphos depends primarily on the energy state of the cell, which is reflected by the ADP/A... | textbooks/bio/Biochemistry/Fundamentals_of_Biochemistry_(Jakubowski_and_Flatt)/02%3A_Unit_II-_Bioenergetics_and_Metabolism/19%3A_Oxidative_Phosphorylation/19.03%3A_Regulation_of_Oxidative_Phosphorylation.txt |
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Introduction
We have seen how we can transduce the chemical potential energy stored in carbohydrates, into the chemical potential energy of ATP. This occurs namely through coupling the energy released during the thermodynamically favored oxidation of carbon molecules through interm... | textbooks/bio/Biochemistry/Fundamentals_of_Biochemistry_(Jakubowski_and_Flatt)/02%3A_Unit_II-_Bioenergetics_and_Metabolism/20%3A_Photosynthesis_and_Carbohydrate_Synthesis_in_Plants/20.01%3A_Light_Absorption_in_Photosynthesis_-_An_Overvie.txt |
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Introduction
We have just seen how photoexcitation of the non-reaction center chlorophyll turns that molecule into a good reducing agent, which transfers its electron to the nearest excited state level of the reaction center chlorophyll. If you count both steps together, the non-re... | textbooks/bio/Biochemistry/Fundamentals_of_Biochemistry_(Jakubowski_and_Flatt)/02%3A_Unit_II-_Bioenergetics_and_Metabolism/20%3A_Photosynthesis_and_Carbohydrate_Synthesis_in_Plants/20.02%3A_The_Kok_Cycle_and_Oxygen_Evolving_Complex_of_Ph.txt |
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Introduction
In the previous sections, we studied light absorption by chlorophylls, the transfer of energy to the reaction center of photosystem II, the oxidation of H2O by the oxygen-evolving complex (OEC), and the transfer of electrons from these events to the lipophilic carrier ... | textbooks/bio/Biochemistry/Fundamentals_of_Biochemistry_(Jakubowski_and_Flatt)/02%3A_Unit_II-_Bioenergetics_and_Metabolism/20%3A_Photosynthesis_and_Carbohydrate_Synthesis_in_Plants/20.03%3A_Plant_Electron_Transport_and_ATP_Synthesis.txt |
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The source for the organization and some of the text derives from: Sindayigaya and Longhini. https://www.peoi.org/Courses/Courses...chem/biochem18 CC - https://creativecommons.org/licenses...sa/3.0/deed.en
Introduction
We focused on the light reactions of photosynthesis. Now let's... | textbooks/bio/Biochemistry/Fundamentals_of_Biochemistry_(Jakubowski_and_Flatt)/02%3A_Unit_II-_Bioenergetics_and_Metabolism/20%3A_Photosynthesis_and_Carbohydrate_Synthesis_in_Plants/20.04%3A_CO_uptake_-_Calvin_Cycle_and_C3_organisms.txt |
Search Fundamentals of Biochemistry
The source for the organization and some of the text derives from Sindayigaya and Longhini. https://www.peoi.org/Courses/Courses...chem/biochem18 CC - https://creativecommons.org/licenses...sa/3.0/deed.en
The C4 Pathway
Photorespiration, caused by the oxygenase activity of RuBisCo... | textbooks/bio/Biochemistry/Fundamentals_of_Biochemistry_(Jakubowski_and_Flatt)/02%3A_Unit_II-_Bioenergetics_and_Metabolism/20%3A_Photosynthesis_and_Carbohydrate_Synthesis_in_Plants/20.05%3A__CO2_uptake_-_C4_and_CAM_Pathways.txt |
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Now that we have seen how carbon is captured and fixed into 3C trioses, which can be converted to fructose and glucose and their derivative, we can now explore the synthesis of the key plant carbohydrates we all know, sucrose, starch, and cellulose.
The source for the organization ... | textbooks/bio/Biochemistry/Fundamentals_of_Biochemistry_(Jakubowski_and_Flatt)/02%3A_Unit_II-_Bioenergetics_and_Metabolism/20%3A_Photosynthesis_and_Carbohydrate_Synthesis_in_Plants/20.06%3A_Biosynthesis_of_Starch_Sucrose_and_Cellulose.txt |
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Introduction
We present the full fatty acid synthase pathway based on the structure of the yeast fatty acid synthase (FAS) complex, whose full structure is known. Then we will explore each step in more detail. The mammalian FAS complex is a bit different and we will summarize those... | textbooks/bio/Biochemistry/Fundamentals_of_Biochemistry_(Jakubowski_and_Flatt)/02%3A_Unit_II-_Bioenergetics_and_Metabolism/21%3A_Lipid_Biosynthesis/21.01%3A_Biosynthesis_of_Fatty_Acids_and_Eicosanoids.txt |
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by William (Bill) W. Christie and Henry Jakubowski.
This section is an abbreviated and modified version of material from the Lipid Web, an introduction to the chemistry and biochemistry of individual lipid classes, written by William Christie.
Introduction
All eukaryotic organism... | textbooks/bio/Biochemistry/Fundamentals_of_Biochemistry_(Jakubowski_and_Flatt)/02%3A_Unit_II-_Bioenergetics_and_Metabolism/21%3A_Lipid_Biosynthesis/21.02%3A_Biosynthesis_of_Triacylglycerols.txt |
Search Fundamentals of Biochemistry
by William (Bill) W. Christie and Henry Jakubowski.
This section is an abbreviated and modified version of material from the Lipid Web, an introduction to the chemistry and biochemistry of individual lipid classes, written by William Christie.
Introduction
In this section will be... | textbooks/bio/Biochemistry/Fundamentals_of_Biochemistry_(Jakubowski_and_Flatt)/02%3A_Unit_II-_Bioenergetics_and_Metabolism/21%3A_Lipid_Biosynthesis/21.03%3A_Biosynthesis_of_Membrane_Glycerolipids.txt |
Search Fundamentals of Biochemistry
by William (Bill) W. Christie and Henry Jakubowski.
This section is an abbreviated and modified version of material from the Lipid Web, an introduction to the chemistry and biochemistry of individual lipid classes, written by William Christie.
Sphingolipids
Introduction:
The sph... | textbooks/bio/Biochemistry/Fundamentals_of_Biochemistry_(Jakubowski_and_Flatt)/02%3A_Unit_II-_Bioenergetics_and_Metabolism/21%3A_Lipid_Biosynthesis/21.04%3A_Biosynthesis_of_Membrane_Sphingolipids.txt |
Search Fundamentals of Biochemistry
By William (Bill) W. Christie and Henry Jakubowski.
This section is an abbreviated and modified version of material from the Lipid Web, an introduction to the chemistry and biochemistry of individual lipid classes, written by William Christie.
Sterols: Cholesterol and Cholesterol ... | textbooks/bio/Biochemistry/Fundamentals_of_Biochemistry_(Jakubowski_and_Flatt)/02%3A_Unit_II-_Bioenergetics_and_Metabolism/21%3A_Lipid_Biosynthesis/21.05%3A_Biosynthesis_of_Cholesterol_and_Steroids.txt |
Search Fundamentals of Biochemistry
By William (Bill) W. Christie and Henry Jakubowski.
This section is an abbreviated and modified version of material from the Lipid Web, an introduction to the chemistry and biochemistry of individual lipid classes, written by William Christie.
Isoprenoids: 1. Tocopherols and Tocot... | textbooks/bio/Biochemistry/Fundamentals_of_Biochemistry_(Jakubowski_and_Flatt)/02%3A_Unit_II-_Bioenergetics_and_Metabolism/21%3A_Lipid_Biosynthesis/21.06%3A_Biosynthesis_of_Isoprenoids.txt |
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Introduction
Organic chemistry is usually described as the chemistry of carbon-containing molecules. But isn't that definition a bit carbon centric, especially since the prevalence of oxygen-containing molecules is staggering? What about nitrogen? We live in a dinitrogen-rich atmos... | textbooks/bio/Biochemistry/Fundamentals_of_Biochemistry_(Jakubowski_and_Flatt)/02%3A_Unit_II-_Bioenergetics_and_Metabolism/22%3A_Biosynthesis_of_Amino_Acids_Nucleotides_and_Related_Molecules/22.01%3A_Overview_of_Nitrogen_Metabolism.txt |
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Introduction
By the time many students get to the study of amino acid biosynthesis, they have seen so many pathways that learning new pathways for the amino acids seems daunting, even though they can be clustered into subpathways. Most know that from a nutrition perspective, amino ... | textbooks/bio/Biochemistry/Fundamentals_of_Biochemistry_(Jakubowski_and_Flatt)/02%3A_Unit_II-_Bioenergetics_and_Metabolism/22%3A_Biosynthesis_of_Amino_Acids_Nucleotides_and_Related_Molecules/22.02%3A_Biosynthesis_of_Amino_Acids.txt |
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Introduction
Once made or ingested, amino acids have many metabolic fates. Of course, they are used for the synthesis of proteins. Aspartate and glutamate (and indirectly glutamine) can be converted to oxaloacetate and α-ketoglutarate, respectively, and used in the citric acid cycl... | textbooks/bio/Biochemistry/Fundamentals_of_Biochemistry_(Jakubowski_and_Flatt)/02%3A_Unit_II-_Bioenergetics_and_Metabolism/22%3A_Biosynthesis_of_Amino_Acids_Nucleotides_and_Related_Molecules/22.03%3A_Molecules_Derived_from_Amino_Acids.txt |
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Introduction
We conclude our exploration of metabolic pathways with the biosynthesis and breakdown of nucleotides, the monomers that comprise nucleic acids. We can't also forget the important role of ATP as the universal carrier of biological free energy, as well as the nucleotides... | textbooks/bio/Biochemistry/Fundamentals_of_Biochemistry_(Jakubowski_and_Flatt)/02%3A_Unit_II-_Bioenergetics_and_Metabolism/22%3A_Biosynthesis_of_Amino_Acids_Nucleotides_and_Related_Molecules/22.04%3A_Biosynthesis_and_Degradation_of_Nucle.txt |
• 23.1: Gene Mapping and Chromosomal Karyotypes
Genes provide instructions to build living organisms and each specific gene maps to the same chromosome in every cell. This physical gene location within the organism's chromosomes is called the gene loci. If two genes are found on the same chromosome, especially when the... | textbooks/bio/Biochemistry/Fundamentals_of_Biochemistry_(Jakubowski_and_Flatt)/03%3A_Unit_III-_Information_Pathway/23%3A_Chromosome_Structure/23.01%3A_Gene_Mapping_and_Chromosomal_Karyotypes.txt |
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Introduction
Eukaryotic genomes contain an abundance of repeated DNA, and some repeated sequences are mobile. Transposable elements (TEs) are defined as DNA sequences that can move from one location to another in the genome. TEs have been identified in all organisms, prokaryotic an... | textbooks/bio/Biochemistry/Fundamentals_of_Biochemistry_(Jakubowski_and_Flatt)/03%3A_Unit_III-_Information_Pathway/23%3A_Chromosome_Structure/23.02%3A_DNA_Transposable_Elements.txt |
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Some of the material in this chapter section comes from Chapter 8.4, Chromosomes and Chromatin, as it was important to describe it earlier in the structure/function unit. In addition, some biochemistry courses might not get to the material in a late chapter in a text. Repetition of ... | textbooks/bio/Biochemistry/Fundamentals_of_Biochemistry_(Jakubowski_and_Flatt)/03%3A_Unit_III-_Information_Pathway/23%3A_Chromosome_Structure/23.03%3A_Chromosome_Packaging.txt |
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Introduction
The elucidation of the structure of the double helix by James Watson and Francis Crick in 1953 provided a hint as to how DNA is copied during the process of DNA replication. Separating the strands of the double helix would provide two templates for the synthesis of new... | textbooks/bio/Biochemistry/Fundamentals_of_Biochemistry_(Jakubowski_and_Flatt)/03%3A_Unit_III-_Information_Pathway/24%3A_DNA_Metabolism/24.01%3A_DNA_Replication.txt |
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The integrity of the DNA structure for cell viability is underscored by the vast amounts of cellular machinery dedicated to ensuring its accurate replication, repair, and storage. Even still, mutations within the DNA are a fairly common event.
DNA Mutations
Mutations are random ch... | textbooks/bio/Biochemistry/Fundamentals_of_Biochemistry_(Jakubowski_and_Flatt)/03%3A_Unit_III-_Information_Pathway/24%3A_DNA_Metabolism/24.02%3A_DNA_Mutations_Damage_and_Repair.txt |
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Homologous Recombination
Homologous recombination is a type of genetic recombination in which genetic information is exchanged between two similar or identical molecules of double-stranded or single-stranded nucleic acids (usually DNA as in cellular organisms but may be also RNA in... | textbooks/bio/Biochemistry/Fundamentals_of_Biochemistry_(Jakubowski_and_Flatt)/03%3A_Unit_III-_Information_Pathway/24%3A_DNA_Metabolism/24.03%3A_DNA_Recombination.txt |
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Types of RNA
Structurally speaking, ribonucleic acid (RNA), is quite similar to DNA. However, whereas DNA molecules are typically long and double-stranded, RNA molecules are much shorter and are typically single-stranded. A ribonucleotide within the RNA chain contains ribose (the p... | textbooks/bio/Biochemistry/Fundamentals_of_Biochemistry_(Jakubowski_and_Flatt)/03%3A_Unit_III-_Information_Pathway/25%3A_RNA_Metabolism/25.01%3A_DNA-Dependent_Synthesis_of_RNA.txt |
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Post-transcriptional modifications of rRNA and tRNA will be topics of Chapter 27 as their structure and function in protein synthesis will be a focal point. Thus, this section will focus on post-transcriptional modifications of mRNA. We'll spend most of our time on eukaryotic RNA pr... | textbooks/bio/Biochemistry/Fundamentals_of_Biochemistry_(Jakubowski_and_Flatt)/03%3A_Unit_III-_Information_Pathway/25%3A_RNA_Metabolism/25.02%3A_RNA_Processing.txt |
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RNA Viruses
Infections with RNA viruses place a constant burden on our healthcare systems and economy. Over the past century, this has been particularly true for infections with the Human immunodeficiency virus 1 (HIV-1), Influenza A virus (IAV), Rotavirus (RotaV), West Nile virus ... | textbooks/bio/Biochemistry/Fundamentals_of_Biochemistry_(Jakubowski_and_Flatt)/03%3A_Unit_III-_Information_Pathway/25%3A_RNA_Metabolism/25.03%3A_RNA-Dependent_Synthesis_of_RNA_and_DNA.txt |
<h210.6refs">26.4.6 References
1. Parker, N., Schneegurt, M., Thi Tu, A-H., Lister, P., Forster, B.M. (2019) Microbiology. Openstax. Available at: https://opentextbc.ca/microbiologyopenstax/
2. Palazzo, A., and Lee, E.S. (2015) Non-coding RNA: what is function and what is junk? Frontiers in Genetics 6:2 Available at: f... | textbooks/bio/Biochemistry/Fundamentals_of_Biochemistry_(Jakubowski_and_Flatt)/03%3A_Unit_III-_Information_Pathway/25%3A_RNA_Metabolism/25.04%3A_26.4_References.txt |
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Overview of Translation
Within this chapter, we will cover the details of prokaryotic and eukaryotic translation. Translation is the process of converting the information housed in mRNA into the protein sequence. Essentially, you are translating the language of nucleotides into the... | textbooks/bio/Biochemistry/Fundamentals_of_Biochemistry_(Jakubowski_and_Flatt)/03%3A_Unit_III-_Information_Pathway/26%3A_Protein_Metabolism/26.01%3A_The_Genetic_Code.txt |
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Prokaryotic Initiation
The small subunit of the ribosome (the 30S) interprets the genetic information by selecting aminoacyl-tRNAs cognate to the mRNA codons in the decoding center. The large subunit (the 50S) carries the catalytic peptidyl transferase center where amino acids are ... | textbooks/bio/Biochemistry/Fundamentals_of_Biochemistry_(Jakubowski_and_Flatt)/03%3A_Unit_III-_Information_Pathway/26%3A_Protein_Metabolism/26.02%3A_Protein_Synthesis.txt |
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Regulation of Translation
Heterogeneity of Ribosome Structure
Over the years, many studies performed in eukaryotes presented evidence that ribosomes can vary in their protein and rRNA complement between different cell types and developmental states. These observations culminated i... | textbooks/bio/Biochemistry/Fundamentals_of_Biochemistry_(Jakubowski_and_Flatt)/03%3A_Unit_III-_Information_Pathway/26%3A_Protein_Metabolism/26.03%3A_Translational_Regulation_and_Protein_Degradation.txt |
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Introduction
Each nucleated cell in a multicellular organism contains copies of the same DNA. Similarly, all cells in two pure bacterial cultures inoculated from the same starting colony contain the same DNA, except for changes that arise from spontaneous mutations. If each cell in... | textbooks/bio/Biochemistry/Fundamentals_of_Biochemistry_(Jakubowski_and_Flatt)/03%3A_Unit_III-_Information_Pathway/27%3A_Regulation_of_Gene_Expression/27.01%3A_Regulation_of_Gene_Expression_in_Bacteria.txt |
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As seen in Chapter 26, the initiation of transcription requires the assembly of a multitude of transcription factors (TF) localized at the promoter region. Transcription can also utilize far-reaching interactions of enhancers, that bind at a distant DNA site and loop back around to ... | textbooks/bio/Biochemistry/Fundamentals_of_Biochemistry_(Jakubowski_and_Flatt)/03%3A_Unit_III-_Information_Pathway/27%3A_Regulation_of_Gene_Expression/27.02%3A_Regulation_of_Gene_Expression_in_Eukaryotes.txt |
These questions derive from the Research Literature Module - Carbon Capture Using Carbonic Anhydrase
Question $1$
Using the equation below, at what ratio of CO2/[HCO3-] would the rate for the forward reaction (CO2 sequestration) be cut in half?
v_0=\frac{V_M S}{K_M\left(1+\frac{I}{K is}\right)+S}
If you need some he... | textbooks/bio/Biochemistry/Fundamentals_of_Biochemistry_(Jakubowski_and_Flatt)/Fundamentals_of_Biochemistry_Vol._V_-_Problems/Enzyme_Kinetics_Problems/Carbonic_Anydrase_Inhibition.txt |
Introduction
Instead of presenting a litany of end-of-chapter or end-of-book questions that are not linked in content or concepts, we will present a number of problem-solving assessments linked to research literature that deal with key challenges that face the world today. We will call these research literature module... | textbooks/bio/Biochemistry/Fundamentals_of_Biochemistry_(Jakubowski_and_Flatt)/Fundamentals_of_Biochemistry_Vol._V_-_Problems/Global_Challenges_-_Literature-Based_Guided_Assessments_(LGAs)/1.__Global_Challenges%3A_Literature-based_Guided.txt |
Research Literature Module - Carbon Capture Using Carbonic Anhydrase
Critical World Challenges
Climate Change
Key Words, Concepts: protein structure, structure/function relationships, enzyme kinetics, enzyme mechanisms, reaction mechanisms, Western blot analysis, site-directed mutagenesis, biomolecular visualization, c... | textbooks/bio/Biochemistry/Fundamentals_of_Biochemistry_(Jakubowski_and_Flatt)/Fundamentals_of_Biochemistry_Vol._V_-_Problems/Global_Challenges_-_Literature-Based_Guided_Assessments_(LGAs)/2.__Global_Challenges_-_Climate_Change%3A__Carbo.txt |
Under Construction
Glutamatergic transmission has been implicated in the pathophysiology of PTSD, particularly in the effects of N-methyl-D-aspartate receptor (NMDAR) signaling on the synaptic plasticity underlying learning and memory [13]. NMDARs comprise two GluN1 subunits and two GluN2 (A-D) or GluN3 (A, B) subunit... | textbooks/bio/Biochemistry/Fundamentals_of_Biochemistry_(Jakubowski_and_Flatt)/Fundamentals_of_Biochemistry_Vol._V_-_Problems/Signal_Transduction_Problems/NMDA_Receptor_-_Under_Construction.txt |
Disulfide engineering
The first set of questions below are based on this reference as noted: Craig, D.B., Dombkowski, A.A. Disulfide by Design 2.0: a web-based tool for disulfide engineering in proteins. BMC Bioinformatics 14, 346 (2013). https://doi.org/10.1186/1471-2105-14-346. Creative Commons Attribution License (... | textbooks/bio/Biochemistry/Fundamentals_of_Biochemistry_(Jakubowski_and_Flatt)/Fundamentals_of_Biochemistry_Vol._V_-_Problems/Structure%2F%2FFunction_-_Protein_Problems/Disulfide_Bonds.txt |
Written by Henry Jakubowski, Emily Schmitt Lavin, Arthur Sikora, and Subhasish Chatterjee
Introduction
Eukaryotic voltage-gated sodium (NaV) channels generate and sustain action potentials in nerve and muscle cells by moving Na+ ions from the outside to the inside of the cell. This increases and makes positive the t... | textbooks/bio/Biochemistry/Fundamentals_of_Biochemistry_(Jakubowski_and_Flatt)/Fundamentals_of_Biochemistry_Vol._V_-_Problems/Structure%2F%2FFunction_-_Protein_Problems/LGA%3A_Voltage-Gated_Sodium_Channel_-_Students_082423.txt |
Carbonic Anhydrase
Engineered Stability
We have already encountered this enzyme before (Chapter 6.1). It catalyzes the hydration of CO2 (g) as shown below.
CO2 (g) + H2O ↔ H2CO3 (aq) ↔ HCO3- (aq) + H+ (aq)
It is among the fastest of all enzymes, with a kcat of 106 s-1 and a kcat/Km of 8.3 x 107 M-1s-1 (reference). ... | textbooks/bio/Biochemistry/Fundamentals_of_Biochemistry_(Jakubowski_and_Flatt)/Fundamentals_of_Biochemistry_Vol._V_-_Problems/Structure%2F%2FFunction_-_Protein_Problems/Literature-based_Guided_Assessments%3A__Protein_Stability_-_Carbonic.txt |
File, Retrieve by ID
MMDB
• MMDB (Molecular Modeling Database) files from the NCBI
• derived from PDB atomic coordinates but with …
• Database information (quaternary struct, molecular interactions, SNPs, conserved domains, clinical variants – i.e related structure info, not just xyz coord
PDB
• xyz coordinates
R... | textbooks/bio/Biochemistry/Fundamentals_of_Biochemistry_(Jakubowski_and_Flatt)/Fundamentals_of_Biochemistry_Vol._V_-_Problems/iCn3D_Molecular_Modeling_Tutorials/iCn3D_Basics%3A_File_Types.txt |
B. Rendering Full Proteins
Pick one of the proteins below that has both alpha helices and beta sheets. You will then change the protein style (rendering) to see the same protein in different ways to illustrate different properties of the proteins.
Monomeric proteins with alpha (helices) and beta (sheets)
1HDO
Hu... | textbooks/bio/Biochemistry/Fundamentals_of_Biochemistry_(Jakubowski_and_Flatt)/Fundamentals_of_Biochemistry_Vol._V_-_Problems/iCn3D_Molecular_Modeling_Tutorials/iCn3D_Intro_Tutorial_B%3A_Rendering_a_Protein.txt |
Use iCn3D to model the binding of one of the psychoactive/analgesic drug to their receptor (either the 5HT or cannabinoid receptor). Paste the final model in the space shown.
Serotonin (5-hydroxytryptamine) receptors
5-HTreceptors are indirectly involved in the mechanism of action of antidepressant drugs. Most antide... | textbooks/bio/Biochemistry/Fundamentals_of_Biochemistry_(Jakubowski_and_Flatt)/Fundamentals_of_Biochemistry_Vol._V_-_Problems/iCn3D_Molecular_Modeling_Tutorials/iCn3D_Intro_Tutorial_D%3A__Modeling_Psychoactive_Drugs_in_Target_Proteins.txt |
Superimpose and annotate active (phosphorylated) form of cyclin-dependent kinase 2 (1JST) and inactive (1FIN)
Description
1JST (active)
• PHOSPHORYLATED CYCLIN-DEPENDENT KINASE-2 BOUND TO CYCLIN A. Has bound Mn2+ and ATPγS.
• pT160 is on the regulatory T-loop of CDK2. It is mostly buried and neutralized by 3 Arg s... | textbooks/bio/Biochemistry/Fundamentals_of_Biochemistry_(Jakubowski_and_Flatt)/Fundamentals_of_Biochemistry_Vol._V_-_Problems/iCn3D_Molecular_Modeling_Tutorials/iCn3D_Skill%3A__Aligning_two_structures.txt |
Structure
• PDB ID: 3UBB
• Protein: Rhomboid intramembrane serine protease GlpG (3UBB) with phosphonofluoridate inhibitor
• Activity: Integral membrane serine protease
• Description: Single chain transmembrane protease from E. coli bound to a phosphonofluoridate inhibitor, which is covalently bonded to the catalyti... | textbooks/bio/Biochemistry/Fundamentals_of_Biochemistry_(Jakubowski_and_Flatt)/Fundamentals_of_Biochemistry_Vol._V_-_Problems/iCn3D_Molecular_Modeling_Tutorials/iCn3D_Skill%3A__Creating_and_Saving_Selections.txt |
Analysis: Mutation
A simple way to change 1 amino acid to another
PDB ID: 1xww
Description: human B-form low molecular weight protein tyrosine phosphatase (has single domain) with bound sulfate (SO4) and glycerol (GOL)
Instructions
1. File, Retrieve by ID, MMDB
2. Analysis, Mutation
3. Input the desired mutation ... | textbooks/bio/Biochemistry/Fundamentals_of_Biochemistry_(Jakubowski_and_Flatt)/Fundamentals_of_Biochemistry_Vol._V_-_Problems/iCn3D_Molecular_Modeling_Tutorials/iCn3D_Skill%3A__Mutations.txt |
Protein:Protein Interface
PDB ID: 3S9D
• binary complex between interferon alpha 2 (IFNa2) and its recetor IFNAR2
• Cyan: IFN, blue IFN receptor
Instructions
1. Retrieve by ID, MMDB
2. Analysis, Seq. & Annotationsm, Details Tab.
3. Select magenta IFN alpha chain: 3s9d_A
4. Select, Save Selections INF
5. Repeat w... | textbooks/bio/Biochemistry/Fundamentals_of_Biochemistry_(Jakubowski_and_Flatt)/Fundamentals_of_Biochemistry_Vol._V_-_Problems/iCn3D_Molecular_Modeling_Tutorials/iCn3D_Skill%3A__Showing_a_Protein-Protein_Interface.txt |
Protein Kinase B (AKT)
A more complicated protein with multiple domains and at least two major conformations with different PDB structures: Protein Kinase B (aka AKT)
PDB files:
• 3CQW (active)
• 3O96 (inactive)
• 1UNQ PH domain
A. Exploration of AKT – Domain Structure
• PDB ID: 1UNQ
• Description: Pleckstrin H... | textbooks/bio/Biochemistry/Fundamentals_of_Biochemistry_(Jakubowski_and_Flatt)/Fundamentals_of_Biochemistry_Vol._V_-_Problems/iCn3D_Molecular_Modeling_Tutorials/iCn3D_Tutorial%3A__Protein_Kinase_B_%28AKT%29.txt |
BIOMOLVIZ
Promoting Molecular Visualization Literacy
The BMV framework is used with permission from BioMolViz.Org
Copy the appropriate row when assigning a theme, goal, and objective to a designated iCn3D or other biomolecular visualization assessment
Atomic Geometry (AG) Three‐atom and four‐atom (dihedral) angles,... | textbooks/bio/Biochemistry/Fundamentals_of_Biochemistry_(Jakubowski_and_Flatt)/Fundamentals_of_Biochemistry_Vol._V_-_Problems/iCn3D_for_Biomolecular_Visualization_Learning_Themes_and_Goals/BioMolViz_Framework.txt |
It is not only important to visualize pre-rendered models of biomolecules, but it is also important to be able to create them to address key aspects of structure and function. These efforts should be guided by a clear set of learning goals and objectives that target student understanding of structure and function. So... | textbooks/bio/Biochemistry/Fundamentals_of_Biochemistry_(Jakubowski_and_Flatt)/Fundamentals_of_Biochemistry_Vol._V_-_Problems/iCn3D_for_Biomolecular_Visualization_Learning_Themes_and_Goals/BioMolViz_Theme%3A_Alternate_Renderings_%28AR%29.txt |
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Introduction to Cell Signaling
Cell signaling is at the heart of biology. A cell must know how to respond to chemical signals in its environment. These signals control every aspect of cell life and interactions. A cell must sense when to grow, divide and die. It must sense the pres... | textbooks/bio/Biochemistry/Fundamentals_of_Biochemistry_(Jakubowski_and_Flatt)/Unit_IV_-_Special_Topics/28%3A_Biosignaling_-_Capstone_Volume_I/28.01%3A_General_Features_of_Signal_Transduction.txt |
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Introduction
We are going to start a more detailed description of cell signaling where it begins, at the cell membrane, and move inward, toward intracellular organs, where we will end at the nucleus and changes in gene expression mediated by the signal. Of course, this end is somew... | textbooks/bio/Biochemistry/Fundamentals_of_Biochemistry_(Jakubowski_and_Flatt)/Unit_IV_-_Special_Topics/28%3A_Biosignaling_-_Capstone_Volume_I/28.02%3A_At_the_cell_membrane-_receptors_and_receptor_enzymes.txt |
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