Biochemistry

All amino acids are L except cysteine. L-amino acids are (S) configuration.

We do not digest D-amino acids, cellulose, or dietary fiber.

Glucose and ketones makes ATP in the brain.

The most abundant polymer on Earth is cellulose. Cellulose makes up 90% of cotton, and 40 to 50% of wood. Lignin is the 2nd most abundant organic polymer on Earth, which makes wood heavy. RuBisCO is the most abundant protein in leaves.

The density of crystalline cellulose 1.63 g/cm³, and amorphous cellulose 1.47 g/cm³.

Starch can be divided into 2 structures: branches amylopectin and linear amylose. Most starches contain 10-20% amylose and 80-90% amylopectin, though the ratio can vary greatly.

When there's lots of lysine on surfaces of proteins, that is a headache, as lysine chemistry is scary (bad selectivity). Out of 8 amino acids commonly found on the surface of proteins, having lysine on them is the worst selectivity, followed by arginine. The amine group on lysine is highly nucleophilic and reacts with electrophiles, making it easy to modify, but hard to control. Modifying lysines (such as acetylation and methylation) alters charge and structure, which can impact protein folding, interactions, or and activity. Histidine, on the other hand, has pH-dependent selectivity, meaning it is reactive in specific pH conditions. Serine and threonine can be modified selectively, such as via phosphorylation.

Rare sugars.

Sugars that are found in plants or bacteria, but not found in humans or mammals, are called rare sugars, and there are over 800 of them.

Examples of where they are found in plants include apiose found in the pectins of celery and parsley, allulose (D-psicose) found in wheat and figs, tagatose found in some fruits and trace amounts in dairy, xylose found in wood and corn husks, and L-fucose found in seaweed and human breast milk.

Examples of where they are found in bacteria include KDN (keto-deoxynonulosonic acid) found in bacteria and algae, colitose found in Gram-negative bacteria such as Salmonella and E. coli, abequose found in Salmonella, and tyvelose found in Salmonella, Shigella, and others.

Examples of both include L-rhamnose (the most common of all rare sugars), and sedoheptulose found in plants and cyanobacteria.

Anti-oxidants.

Vitamin E is the primary chain-breaking anti-oxidant in cell membranes. The generic term vitamin E refers to at least 8 structural isomers of tocopherols or tocotrienols. Among these, a-tocopherol is the best known and possesses the most anti-oxidant activity. Growing evidence suggests that some of the beneficial effects of vitamin E in cells resides in its ability to regulate gene expression of proteins.

Similar to vitamin E, carotenoids (such as ß-carotene) are lipid-soluble anti-oxidants located primarily in the membranes of tissues. The antioxidant properties of carotenoids come from their structural arrangement consisting of long chains of conjugated double bonds. This arrangement permits the scavenging of several different ROS species including superoxide and peroxyl radicals. Because of their cellular location and their radical scavenging capacity, carotenoids are efficient biological anti-oxidants against lipid peroxidation.

Weight lifting and oxidative stress.

It is a paradox in metabolism that oxygen is necessary for survival, yet causes oxidative stress. The 1st suggestion that physical exercise results in free radicals damaging tissues appeared in 1978. It is now well established that both resting and contracting skeletal muscles produce reactive oxygen species (ROS) and reactive nitrogen species (RNS). Intense and prolonged exercise can result in oxidative damage to proteins and lipids in the contracting myocytes.

Muscle fibers contain both enzymatic and non-enzymatic anti-oxidants that work as a complex unit to regulate ROS. Within the fiber, these anti-oxidants are strategically compartmentalized throughout the cytoplasm and within various organelles (such as mitochondria), and exist in both the extracellular and vascular space. Collectively, these anti-oxidants protect muscle fibers from oxidative injury during periods of increased oxidant production (such as intense or prolonged exercise).

Numerous anti-oxidant strategies exist and can be used to protect against ROS toxicity. For example, some agents (such as catalase) convert ROS into less active molecules and prevent the transformation of these less active species to a more deleterious form. Another anti-oxidant strategy is to minimize the availability of pro-oxidants such as iron and copper ions via metal binding proteins. Numerous low molecular weight agents are capable of scavenging ROS species. Examples of this antioxidant strategy include endogenously synthesized molecules such as glutathione, uric acid, and bilirubin along with agents found in the diet such as ascorbic acid and vitamin E.

Hydrogen peroxide is unable to oxidize DNA or lipids directly but can inactivate some enzymes. The cytotoxicity of hydrogen peroxide primarily occurs through its ability to generate hydroxyl radical through metal-catalyzed reactions, such as the Fenton reaction (changing Fe(II) to Fe(III).

Lysozymes.

Lysozymes (muramidase) is an abundant cationic anti-microbial protein that plays an important role in pulmonary host defense. Lysozymes are defined by the FAO and WHO as a polypeptide obtained from consisting of 129 amino acids, with a molecular weight of 14,700.

Lysozymes act mostly on Gram-positive bacteria and a few Gram-negative bacteria. Gram-positive bacteria are more susceptible to the action of lysozymes because their cell wall contains up to 90% peptidoglycan, and also that the outer membrane of Gram-negative bacteria occludes the passage of molecules generally with a molecular weight greater than 650. (Lysozymes degrade peptidoglycan in the bacterial cell wall.). Examples of Gram-positive bacteria susceptible to are Micrococcus, Sarcina, Lactobacillus, and Bacillus. Examples of Gram-negative bacteria susceptible to are Salmonella, Pseudomonas, Aeromonas, E. coli, Clostridium botulinum, and Listeria monocytogenes. Lysozymes also inhibit viruses, parasites, and fungi.

In mammals, lysozymes are found in abundance in the blood and liver, and in secretions of tears, urine, saliva, and milk, at mucosal surfaces (where it can reach concentrations as high as 1 mg/mL), and in professional phagocytes such as macrophages, neutrophils, and dendritic cells.

Proteins.

Some examples of proteins that have a repeating sequence of amino acids are elastin, keratin, ankyrin proteins, spider silk, and collagen.
Some examples of proteins that do not have a repeating sequence of amino acids are actin and tubulin.

Proteins may have evolved from self-assembled peptides (self-assembled homo-oligomers). Assembly of peptides can display protein-like properties. Peptoids are a synthetic sequence-defined oligomer (such as N-substituted glycines).

Membrane proteins facilitate the transfer of information across lipid bilayers, comprise approximately 25% of a typical proteome, and represent over half of all drug targets.

Proteins that cause cancers.

Approximately 5% of all human cancers are attributed to infections by Human Papillomaviruses (HPVs). The HPV E6 and E7 proteins are the major carcinogenic drivers, and they function by subverting key signaling pathways including those governed by the p53, PTPN14, and retinoblastoma (Rb) tumor suppressor proteins.

Proteomics.

Proteomics is the large-scale study of proteins, where proteomes are the entire set of proteins produces or and modified by an organism. But proteomics often refers specifically to protein purification and the mass spectrometry of it. In protein analysis, mass spectrometry can be used to determine the masses of peptides and proteins. The m/z vs. intensity chart allows researchers to identify protein fragments or whole proteins by comparing the mass spectrum to known databases.

Protein turnover refers to the continuous process of synthesizing new proteins and degrading existing proteins.

Embryos generally would not survive being placed in pure water because they require a specific balance of ions, nutrients, and proper osmotic conditions to survive and develop. The water itself can disrupt the delicate balance of these conditions, leading to cell death due to osmotic stress, lack of nutrients, or other factors.

There is an N-end rule in biology, which suggests that the lifespan (or half-life) of a protein is influenced by the identity of the amino acid at its N-terminus (the N-terminal amino acid). This concept is part of the broader N-end rule pathway, which links the degradation rate of proteins to their N-terminal residues, often determining how quickly a protein is recognized and targeted for degradation by the cell's protein degradation machinery. The N-end rule helps determine how long a protein will remain active in the cell before being degraded. The specific amino acid at the N-terminus can act as a signal for stability or degradation, influencing the protein's overall lifespan.

The N-end rule was discovered in the 1980s and is part of the ubiquitin-proteasome system, where proteins destined for degradation are tagged with a small protein called ubiquitin. This tagging signals the proteasome (a large protein complex) to break down the tagged proteins. N-terminal amino acids act as signals (or "degrons") that can either stabilize a protein or mark it for rapid degradation.

Stabilizing amino acids include methionine (Met) and glycine (Gly). Destabilizing amino acids include Arg, Lys, and His for primary destabilizers, Asp and Glu for secondary stabilizers (these are modified to create degradation signals), and Gln and Asn for tertiary stabilizers (these proteins are targeted for degradation after they undergo modifications).

Chromatin.

Chromatin is a highly dynamic polymer that is embedded in a viscoelastic solvent and subject to active, far-from equilibrium forces. As a result, chromatin exhibits dynamics at multiple time scales, ranging from the sub-second scale thermal motion of the chromatin polymer to minutes and hours long reorganization in response to developmental programs and external chemical and mechanical stimuli.

Molecular biology.

Boxes.

Boxes are conserved sequence motifs, or specific, conserved regions (domains) of the protein that play critical roles in the protein's function, often involved in its structural stability or interaction with other molecules. These motifs are typically short sequences of amino acids that are highly conserved across different members of a protein family.

F box: This refers to a specific protein motif found in some proteins. The F box is typically involved in protein-protein interactions, particularly in the context of ubiquitination, where it helps target proteins for degradation.

N box: typically contains conserved residues that are crucial for the catalytic activity or the structural stability of a protein. In histidine kinases for example, which are part of two-component signaling systems in bacteria, the N box often includes a histidine residue that plays a key role in phosphorylation during signal transduction. This histidine becomes phosphorylated and then transfers the phosphate group to a response regulator, triggering downstream effects.

G1 box: often associated with nucleotide-binding domains, particularly those that bind GTP or ATP. In histidine kinases, the G1 box typically contains conserved residues like tryptophan and glutamic acid that are important for binding and hydrolyzing ATP. This ATP binding and hydrolysis is essential for the kinase activity, providing the energy required for the phosphorylation events.

Ho box: found in G-proteins, contains a conserved histidine residue crucial for GTPase activity. The histidine acts in the hydrolysis of GTP to GDP, a process central to G-protein function in signal transduction.

C box: often found in proteins with enzymatic functions, contains conserved cysteine residues that may participate in catalytic activities, such as forming disulfide bonds or acting as nucleophiles in enzymatic reactions.

Walker A and B boxes: commonly found in ATPases and GTPases, these motifs are involved in nucleotide binding and hydrolysis. The Walker A box (P-loop) binds the phosphate groups of ATP or GTP, while the Walker B box is involved in coordinating the magnesium ion necessary for nucleotide hydrolysis.

S box: found in proteins that bind SAM (S-adenosylmethionine), a common cofactor involved in methylation reactions. This motif plays a role in recognizing and binding SAM.

D box (destruction): found in proteins targeted for degradation via the ubiquitin-proteasome pathway, the D box is recognized by specific ubiquitin ligases, which tag the protein with ubiquitin molecules, marking it for degradation.