Basics : The structure of Cells

introduction:

introduction: am based on the book of dr Lehninger: “Principles of Biochemistry”

► All cells on Earth have some common structure: They have a cytosol containing metabolites , coenzymes , inorganic ions and enzymes; They all have a set of genes located in the nucleoid (bacteria and archaea ) or in the nucleus ( eukaryotes ).

this subject is discussed widely on the topic cell function and structure

► All creatures need a source of energy to carry out the biochemical processes taking place in their cells. Phototrophic organisms use the energy of sunlight, while chemotrophic organisms oxidize chemical compounds while transferring electrons to electron acceptors, including inorganic compounds , organic compounds and oxygen molecules.

► Bacterial and archaean cells contain cytosol , a nucleoid and plasmids , wrapped in the cell membrane. Eukaryotic cells have a nucleus, and the various processes take place in different sections of the cell. Researchers can isolate organelles from the whole cell and study them individually.

► The proteins of the cytoskeleton form long fibers that give the cell shape and solidity and work in the tracks along which the organelles move throughout the cell.

► Complexes of macromolecules, whose non-covalent bonds connect them to each other, are part of the hierarchy of structures in the cell. Some of these structures are so large that they can be seen with a light microscope. When one type of molecules is isolated from such a complex and studied in vitro , important interactions that occur in the living cell are probably lost.

1.2 Basics: Chemistry

► Thanks to its ability to form several types of bonds, carbon can form a wide variety of carbon-carbon skeletons with a variety of functional groups. These groups give biomolecules their characteristic biological and chemical properties.

► In all living cells we find an almost identical group of about a thousand small molecules. The main metabolic pathways in which these molecules are converted to each other have been conserved during evolution.

► Proteins and nucleic acids are linear polymers composed of subunits simple monomers . The sequences of these molecules contain the information that gives each molecule its spatial structure and biological function.

► The configuration of a molecule can only change following the breaking of covalent bonds . In a carbon atom to which four different modifiers ( chiral carbon ) are attached, the groups can be arranged in two different ways, creating stereoisomers with unique properties. Only one stereoisomer is biologically active. The conformation of a molecule is the position of its atoms in space, which can change due to rotation around single bonds, without breaking covalent bonds .

► Interactions between biomolecules are almost always stereospecific : they require spatial compatibility between the complementary structures of the molecules that bind to each other.

this subject is discussed widely on the topic CHEMICAL PRINCIPLES – Omanut Olam

1.3 Basics: Physics

► Living cells are open systems that exchange materials and energy with their environment, absorb and transport energy to exist in a dynamic stable state far from equilibrium. The cells produce energy from sunlight or chemical compounds and convert it from the energy of electron flow to ATP chemical bonds .

► The free energy change, AG , indicates the tendency of a chemical reaction to reach equilibrium. AG consists of two factors: the enthalpy change, AH , and the entropy change, AS . The formula expressing the relationship between these variables is

. AG=&H- Tks

When AG of a reaction is negative, the reaction is exergonic and tends to proceed to completion. When AG is positive, the reaction is androgenic and tends to progress in the opposite direction. When two reactions can be summed for a third reaction, n – AG of the total reaction is the sum AG of the two separate reactions.

The reactions in which ATP becomes b- ; bt p – ADP or b – AMP and Lech? They are very exergonic ( large and negative AG ). Many androgenic reactions occur in the cell thanks to their coupling, through a common intermediate, to these exergonic reactions.

The standard free energy change, ° AG , is a physical constant whose relation to the equilibrium constant corresponds to the formula AG ° = -RT 1nK .

cq

Most of the reactions that occur in cells progress at an effective rate only thanks to the enzymes that catalyze them. enzymes

Act by stabilizing the transition state, lowering the activation energy, AG

The catalytic activity of enzymes in cells is subject to control.

► Metabolism is the sum of many reaction sequences, which process and change metabolites and are related to each other through common intermediate products. Each of the reaction sequences is subject to control, so that the needs of the cell at every moment will be met and energy will be used only when it is needed.

1.4 Basics: genetics

►Genetic information is encoded in the linear sequence of four types

► DNA 3- deoxyribonucleotides .

► The H – DNA double helix molecule acts as an internal template for its own replication and repair.

► DNA molecules are very large, and their molecular weight reaches millions or billions.

► Despite the enormous size of the DNA molecules , the sequence of their nucleotides is very precise, and the preservation of this precise sequence over time is the basis for the genetic continuity of living beings.

► The linear sequence of amino acids in the protein, which is encoded by the DNA of the gene for this protein, is responsible for folding the protein into its unique spatial structure. The folding process also depends on the environmental conditions.

► Macromolecules that have an affinity for other macromolecules spontaneously assemble into supramolecular complexes .

1.5 Basics: Evolution

► Random inherited mutations create creatures that are better suited to survive and reproduce in a certain ecological niche, and their offspring become the majority in the population of that niche. The combination between mutations and selection is the basis of Darwinian evolution , which led from the first cells to all modern creatures. Many genes are common to all living things, hence the basic similarity between them.

► Life began about 3.5 billion years ago, probably as a membrane-wrapped vesicle that contained RNA that duplicated itself. It is possible that the components of the first cell were formed near hydrothermal vents at the bottom of the sea or due to the effect of lightning and high temperature on simple molecules in the atmosphere, such as NH3n co2 .

, DNAn proteins replaced RNA as catalysts and as the hereditary material, respectively.

► The eukaryotic cells acquired their ability to carry out photosynthesis and oxidative phosphorylation thanks to endosymbiosis with bacteria. In multicellular organisms , cells differentiate and specialize in performing one or more functions that are essential for the existence of the cell.

► Decoding the nucleotide sequence of the genomes of creatures from different branches of the phylogeny tree helps us chart the course of evolution and opens up a variety of possibilities in medicine.

Chapter 2- Water and a ladder acidity

Prior knowledge of general chemistry on PH , buffer systems , titration, solutions, interactions between molecules is required

2.1 Weak interactions in aqueous solutions

Due to the large difference between the electronegativity values of H and 0, the water molecule is very polar and can form hydrogen bonds with other water molecules or with solutes. Hydrogen bonds are temporary, mainly electrostatic and weaker than covalent bonds . Water is a good solvent for polar (hydrophilic) solutes, with which they form hydrogen bonds, and for charged solutes, with which they form electrostatic interactions.

► Non-polar (hydrophobic) compounds do not dissolve well in water. They cannot form hydrogen bonds with the solvent, and their presence forces the water molecules in the meeting areas into an arrangement that is not energetically beneficial. To reduce the area exposed to water, non-polar compounds such as lipids are organized into aggregates ( micelles ) whose hydrophobic groups are hidden on the inside and hydrophobic interactions are formed between them, and only the more polar groups are exposed to water.

► A large number of weak, non-covalent interactions have a large effect on the folding of macromolecules such as proteins and nucleic acids. The most stable conformations of macromolecules are those in which the number of hydrogen bonds within the molecule and between the molecule and the solvent is the greatest, and in which the hydrophobic groups face the inside of the molecule and not the aqueous solvent.

The physical properties of aqueous solutions are greatly influenced by the concentration of the solutes . When two compartments containing an aqueous solution are separated from each other by a semi-permeable membrane (such as the cell membrane that separates a cell from its environment), water passes through the membrane and thus reduces the gap between the osmolarity of the two compartments. This tendency of water to move through a semi-permeable membrane creates osmotic pressure.

2.2 “None of water, weak acids and weak bases

► Pure water ionizes only to a small extent, creating an equal number of hydrogen ions ( hydronium ions , + H3O ) and hydroxide ions. The equilibrium constant formula describing the degree of ionization is:

K = [H +][ 0H~]

eq [H2O]

From this constant we derive the product of the ion concentrations of the water, KW . in >° 25,

Kw = [][ OH55.5 ) = [- M)(Keq) = IO14 ־ M2

► The pH of an aqueous solution reflects, on a logarithmic scale, the concentration of hydrogen ions:

pH = log—=-10g[H+]

► The higher the acidity of a solution, the lower its pH . Weak acids partially ionize and release hydrogen ions, thus lowering the pH of the aqueous solutions. Weak bases accept hydrogen ions, thus raising the p – pH . The rate of these processes is typical for any acid or base, and it is customary to describe it using the decomposition constant of an acid:

► n – pKa expresses, on a logarithmic scale, the relative strength of a weak acid or base:

The stronger an acid is, the smaller its K is. The stronger a base, the greater its k . pKa can be measured experimentally: it is the equilibrium coefficient at the midpoint of the titration curve of an acid or base.

2.3 ” OK pH using buffers in biological systems

A mixture of a weak acid or a weak base with their salt reduces the changes of the reaction following the addition of + H or – OH . The mixture functions as a buffer .

Henderson – Hasselbach equation allows us to calculate the K of a solution of a weak acid or base with their salt :

► In cells and tissues, phosphate and bicarbonate buffer systems stabilize the K of the intracellular fluid and the extracellular at an optimal (physiological) level, usually close to 7 pH . Most enzymes function best at this pH .

Medical conditions that cause a drop in blood pH , i.e. acidosis, or that cause an increase in blood pH , i.e. alkalinity – may be life-threatening.

water as reactant

► Water acts both as a solvent, in which the metabolic reactions take place, and as a reactant in many biochemical processes, including hydrolysis, compression and redox reactions.

Chapter 3 Acids reliability peptides and proteins

3.1 Amino acids

The 20 amino acids common in proteins contain an m- carboxyl group , an m-amino group and a characteristic R group attached to the m carbon atom. The m carbon atom of all amino acids except glycine is asymmetric, so they have at least two stereoisomers . ( Stereochemistry ) Only stereoisomers appear in proteins L , whose configuration corresponds to the absolute configuration of the reference molecule. Glyceraldehyde .

There are also other amino acids, less common, that appear in proteins (through modification of common amino acids after protein synthesis) or as free metabolites.

The amino acids can be divided into five groups according to the polarity and charge (at 7 pH ) of their R groups .

1. Non-polar (hydrophobic) groups:
   Glycine (the smallest without a cyrillic carbon), alanine (small).
   Valine, leucine, isoleucine, proline (closes with an imino ring)
   
2. groups with aromatic rings
   Tryptophan, tyrosine, phenylalanine (absorbs UV radiation) phenylalanine is the lowest, then tyrosine, then tryptophan.
   
3. Polarity (hydrophilicity)
   Methreonine, serine: contain an OH end
   
4. Amino acids that contain a sulfur atom, methionine (sulfur as part of an allotopic and non-polar chain), cysteine (sulfur is polar and can form disulfide bonds)
   
5. Positively charged polarities (basicity): arginine, lysine, histidine (easily converted from an acid to a base, histidine is found in many receptors)
   5.2- Positive charges at a point above 7PH: glutamate and aspartate

3.2 Peptides and proteins

The amino acids differ from each other in their properties as acids or bases and in the characteristics of their titration curves. B ” low pH , mono-amino amino acids and monocarboxylic ( whose R groups are not ionized ) are diprotic acids (4 NCHWCOOH ), and when the pH increases they appear as several ions

► Amino acids linked to each other by peptide bonds Covalents form peptides and proteins. Most cells have thousands of different proteins, each of which has a different biological activity.

► There are proteins that are very long polypeptide chains , with from 100 to several thousand amino acid residues. In contrast, there are natural peptides that consist of only a few amino acids. There are proteins that consist of several polypeptide chains connected to each other in non-covalent interactions . These chains are called subunits .

► In the hydrolysis of simple proteins, only amino acids are obtained. Conjugated proteins contain additional components, such as a metal or an organic prosthetic group.

3.3 Protein research

► Researchers purify and separate proteins based on the differences between their properties. It is possible to selectively invest proteins by changing the equilibrium coefficient or the temperature, and especially by adding certain salts. Different types of chromatography take advantage of differences in size, binding affinity, charge, and other properties. These methods include ion exchange chromatography , chromatography based on size differences, affinity chromatography and high pressure liquid chromatography – HPLC .

► Electrophoresis separates proteins according to mass or charge. SDS wave electrophoresis and isoelectric focusing can be used separately or in combination, for sharper separation.

4 All purification methods require a way to identify and quantify the desired protein in the presence of other proteins. It is possible to monitor the cleaning by checking the specific activity.

3.4 The structure of proteins: primary structure

► Different proteins perform different functions because they differ from each other in the composition of the amino acids and their sequence. Not every change in the sequence of a protein necessarily affects its function.

► It is possible to find the amino acid sequences of polypeptides by breaking them down into smaller peptides with the help of reagents that cleave only certain peptide bonds ; Determining the amino acid sequence of each peptide using automated Adaman decomposition; and determining the order of the sequences found according to the overlap between fragments obtained by cutting with different reagents . It is also possible to deduce the sequence of a protein based on the nucleotide sequence of the corresponding 3- DNA gene , or by means of mass spectrometry .

► Short proteins and peptides (approximately up to 100 amino acid residues) can be synthesized by chemical methods. The peptide is built by adding amino acid after amino acid, with the elongating peptide bound to a solid substrate.

► Protein sequences are a rich source of information on the structure and function of proteins, as well as on the evolution of life on Earth. Researchers are developing sophisticated methods that allow them to reproduce the slow changes in the amino acid sequences of homologous proteins, and in this way – to chart the course of evolution.

Figure 3.36 Consensus tree of history ( consensus tree of life ). The tree in the figure is based on the analysis of many different protein sequences and leaking genomic information . In Ilan, only a small part of the information we have is presented – and only a few of the issues that still need to be clarified. Each of the existing groups appearing in Ilan is a complex evolutionary story in itself. LUCA is the common ancestor

Chapter 4 The structure the spatial of proteins

4.1 Overview of protein structure

4 A typical protein usually has one or more stable spatial structures that reflect its function. This spatial structure is also called conformation. There are proteins in which certain parts of their structure are disorganized.

4 The main factor that stabilizes the protein structure is a large number of weak bonds. Hydrophobic interactions, which result from an increase in the entropy of the aqueous environment when molecules

4.2 The secondary structure of proteins

► Secondary structure is the local spatial arrangement of the skeleton atoms in a certain section of the polypeptide chain .

►Among the regular error structures, the most common are the m helix, conformation p and torsion p .

► It is possible to describe the secondary structure of a segment of a polypeptide with absolute precision, if the 0 and – K angles of all its amino acids are known.

► Spectroscopy That’s enough rhyming Circular Dichroism is a method for estimating the proportion of common secondary structures in different proteins and for tracking their folding.

►        4.3 The tertiary and quaternary structure of proteins

► The tertiary structure is the spatial structure of the polypeptide chain . Many proteins belong to one of two large groups of proteins, according to their tertiary structure: fibrous proteins and globular proteins .

Fibrous proteins, which mainly play structural roles, are built from simple, repeating components of secondary structure.

► The tertiary structure of globular proteins is more complex, and in many of them we find several types of secondary structures in the same polypeptide chain . The first globular protein whose structure was deciphered, using x- ray diffraction , was myoglobin.

globular proteins can be analyzed by examining folding patterns called motifs (also called folds or secondary structures ). The thousands of known structures of proteins consist of a repertoire of only a few hundred motifs. Complexes are regions of the polypeptide chain that are able to fold independently and stably.

A quaternary structure is created due to interactions between subunits of proteins composed of several subunits ( multimers ) or of large protein aggregates. Many of the multimeric proteins are built from several identical units, each of which is a separate subunit or a combination of several subunits . Each of the identical units is called a protomer .

► There are proteins or parts of a protein that lack an organized structure. These proteins have a characteristic amino acid composition, which gives them structural flexibility. Some of these proteins act as structural components or as scavengers; Others can bind to a variety of other proteins, and serve as inhibitors or as central hubs in protein communication networks.

4.4 Denaturation and folding of proteins

► A cell in equilibrium has a variety of active cellular proteins. Maintaining stable amounts of these proteins is called proteostasis , and involves a large number of pathways and processes that fold, refold and disassemble polypeptide chains .

► Both the spatial structure and the function of most proteins are affected by denaturation , a fact that indicates a relationship between structure and function. There are proteins that are capable of spontaneous renaturation , that is, if they have been denatured – they reacquire their structure and biological activity without assistance. Hence the sequence of amino acids determines the spatial structure.

►        Protein folding in cells is mainly a hierarchical process . First, regions of secondary structure are formed, which fold into motifs and complexes. A multitude of intermediate forms rapidly converge to a single native conformation .

►        Chaperones from the Hsp70 family and the chaperonin family assist in the folding of many proteins. Unique enzymes catalyze the formation of disulfide bonds and isomerization Cis-trans of peptide bonds between Pro residues .

► Improper folding of proteins is the molecular basis of a variety of human diseases, including amyloid diseases .

Chapter 5 Their roles of proteins

5.1 Reversible binding of protein to ligand : oxygen-binding proteins

► Protein function often requires interactions with other molecules. A protein binds a molecule called a ligand at its binding site. Ligand binding may induce conformational changes in the protein, a process called induced conformation. In a multi -subunit protein , ligand binding One subunit may affect ligand binding to other subunits . Ligand binding is subject to control.

► Myoglobin contains a prosthetic group that binds oxygen. Heme consists of a single atom of + Fe2 coordinatively bound to porphyrin . Oxygen binds to myoglobin reversibly. You

This simple reversible binding can be described by the binding constant Ka or the dissociation constant Kd . In a monomeric protein like myoglobin, the relative part of the binding sites occupied by the ligand is a hyperbolic function of the concentration of the ligand .

► Normal hemoglobin of an adult is made up of four subunits containing two subunits a and two subunits P , whose structures are similar to each other and to the myoglobin structure. Hemoglobin has two alternative structural states, 1 T – R. The T state is most stable in the absence of oxygen. Oxygen binding promotes transition to the R state .

► Binding of oxygen to hemoglobin is both allosteric and cooperative. When 02 binds to one binding site, conformational changes occur in hemoglobin that affect other binding sites – an example of allosteric changes . Conformational changes between T and M states, mediated by interactions between subunits , cause cooperative binding. Cooperative binding is described by a sigmoid binding curve and can be analyzed using the Hill equation . Hill equation (biochemistry)

► Two main models , the coordinated model and the continuous model , offer an explanation for the cooperative binding of ligands to multi- subunit proteins .

►        Hemoglobin also binds + H and 002. Their binding creates ion pairs that stabilize the T state and reduce the affinity of the protein to 2s (Bohr effect). Another substance that regulates the binding of oxygen to hemoglobin is 3,2-bisphosphoglycerate, which binds to the T state and stabilizes it.

►        Sickle cell anemia is a genetic disease resulting from the replacement of a single amino acid ( Giu6 to ¥016) in each of the p chains of hemoglobin. The change creates a hydrophobic spot on the surface of the hemoglobin, which causes the molecules to coalesce into clusters of fibers. This homozygous condition causes severe medical complications.

5.2 Complementary interactions between proteins and ligands : the immune system and immunoglobulins

► The immune response involves interactions between an array of specialized leukocytes and the proteins associated with them.

T lymphocytes produce T cell receptors . Type B lymphocytes produce immunoglobulins . In a process called lineage selection, T cells help stimulate the culture of B cells that produce immunoglobulins , and of T cells Cytotoxic , expressing unique receptors that bind a specific antigen.

► In humans there are five groups of immunoglobulins , each of which has different biological functions. The most common group is 1 gG , Y -like proteins consisting of two heavy chains and two light chains. The complexes at the upper ends of the ¥ are characterized by great diversity among the wide population of 1 gG molecules , and create two antigen binding sites.

► A particular immunoglobulin usually binds only a part, called an epitope , of a larger antigen. In many pairs of antibody and antigen, the binding causes a change in the 1gG conformation – an induced adaptation of the antibody to the antigen.

► The high binding specificity of immunoglobulins is useful in research methods such as ELISA and immunoblotting.

5.3 Chemical energy regulates the interactions between proteins: actin, myo-vin and molecular motors

► Protein-ligand interactions in movement proteins have a special level of organization in space and time. Muscle contraction results from well-orchestrated interactions between myosin to actin which are conjugated to the hydrolysis of ATP by myosin .

► Myosin is composed of two heavy chains and four light chains, which form a fibrous coiled-coil complex (tail) and a globular complex (head). Myosin molecules are organized in thick filaments that slide over thin filaments composed mainly of actin . Hydrolysis of ATP bound to myosin coupled to a series of conformational changes in the myosin head , leading to the detachment of the myosin from one actin F subunit and its attachment to another further down the thin filament . In this way the myosin slides over the actin filaments .

► Release of Ca2 + ions from the sarcoplasmic reticulum triggers muscle contraction. Ca2 + ions bind to the troponin protein and cause a conformational change in the troponin – tropomyosin complex , which triggers a cycle of actin- myosin interactions .

Chapter 6 Enzymes

6.1 From enzymes

► Life depends on unique and powerful catalysts: the enzymes. Almost every biochemical reaction is catalyzed by an enzyme.

► Except for a few catalytic RNA molecules , all known enzymes are proteins. The catalytic activity of many enzymes requires non-protein coenzymes or cofactors .

► Enzymes are classified according to the type of reaction they catalyze. All enzymes have numbers. EC and official names. Most of them also have common names.

6.2 How enzymes work

►        Enzymes are very efficient catalysts, most speeding up reaction rates 105 to 1017 times.

►        Enzyme-catalyzed reactions are characterized by the formation of a complex between substrate and enzyme ( ES complex ). The substrate binds to a pocket in the enzyme called the active site.

► The function of enzymes and other catalysts is to lower the ΔG

the reaction rate. The enzyme does not affect the equilibrium of a reaction.

► A considerable part of the energy used by the enzyme to increase the reaction rate originates from weak interactions (hydrogen bonds and hydrophobic and ionic interactions) between the enzyme and the substrate. The active site of the enzyme is structured so that some of these weak interactions occur precisely in the transition state of the reaction, thus stabilizing the transition state. The need for many interactions is one of the reasons for the considerable size of enzymes. The binding energy, ΔGB , is used ΔG

For example, it can be used to lower the entropy of a substrate, remove a substrate from a solution or cause the enzyme’s conformation to change (induced conformation) . The binding energy is also responsible for the high specificity of enzymes for their substrates .

► Other catalytic mechanisms used by enzymes are general acid-base catalysis , covalent catalysis and catalysis by metal ions. In many reactions, catalysis involves temporary covalent interactions between the substrate and the enzyme, or the transfer of groups to or from the enzyme, creating a new, lower-energy reaction pathway. When the reaction is finished, the enzyme always returns to the free state.

6.3 Kinetics of enzymes as an approach to understanding mechanisms

► Most enzymes have certain kinetic properties in common. When a substrate is added to the enzyme, the reaction quickly reaches a steady state where the rate of formation of the ES complex balances with the rate of its decreasing. When [ S ] increases, the activity of an enzyme at a constant concentration and in a resistant state increases hyperbolically and approaches a characteristic maximum rate, and – max level when almost every molecule of the enzyme has formed a complex with the substrate.

► The concentration of the substrate at which the reaction rate is equal to half max is the Michaelis-Menten constant , Km , which is characteristic of any enzyme acting on a specific substrate. The Michaelis-Manten equation

Determines what the initial speed will be if certain [ S ] and “-k” are given according to the constant Km . Kinetics Michaelis – Manten is also called steady state kinetics .

The constant kcat , the cycle number, describes the limiting rate of an enzyme-catalyzed reaction at saturation. The ratio kcat /Km is a good measure of catalytic efficiency. The Michaelis-Menten equation can also be applied to two-substrate reactions that occur in triple complex or ” ping-pong ” (double substitution) pathways.

► Reversible inhibition of an enzyme can be competitive, uncompetitive or mixed. Competitive inhibitors compete with the substrate for reversible binding to the active site, but the enzyme does not act on them. Uncompetitive inhibitors bind only to the ES complex , a site that is not the active site. Mixed inhibitors bind to £ or £8, also to a site that is not the active site. In irreversible inhibition, an inhibitor forms a covalent bond or a very stable non- covalent interaction with the active site, thus binding to it permanently.

► Every enzyme has an optimal pH or range of pH values , where its activity is maximum.

6.4 Examples of enzymatic reactions

Chymotrypsin is serine A protease whose mechanism of action has been well studied and involves general acid-base catalysis, covalent catalysis and transition state stabilization.

Hexokinase is an excellent example of induced fit as a means of utilizing the binding energy of a substrate.

The enolase reaction occurs via metal ion catalysis.

Lizozyme uses covalent catalysis and a general acid environment to promote two successive nucleophilic displacement reactions .

Deciphering enzyme mechanisms enables the development of drugs that inhibit enzyme activity.

6.5 Control enzymes

► The cells monitor the activity of certain enzymes, thus controlling the rate of operation of the metabolic pathways.

► The activity of an allosteric enzyme is slowed down or accelerated following reversible binding of a specific modulator to a control site. A modulator can be the substrate itself or another metabolite , and the effect of the modulator can be stimulatory or inhibitory. The kinetic characteristics of allosteric enzymes reflect the cooperative interactions between the enzyme subunits.

► Other control enzymes are regulated by covalent modification of a specific functional group necessary for their activity. Phosphorylation of specific amino acid residues is a particularly common way to control the activity of an enzyme. ► Many proteolytic enzymes are synthesized as inactive precursors called zymogens , which are activated by cleavage of small peptide segments .

zymogens / proenzyme

Chapter 7 Carbohydrates and glycobiology

7.1 Monosaccharides and disaccharides

► Sugars (also called saccharides ) are compounds with an aldehyde or ketone group and two or more hydroxyl groups .

► Monosaccharides usually have several chiral carbons , so they have several different stereochemical forms , which can be presented on paper as structural formulas. Epimers are sugars that differ in the configuration of only one carbon atom.

► Monosaccharides usually form internal hemiacetals or micetals , where the aldehyde or ketone group binds to the hydroxyl group of the same molecule and forms a ring structure; This structure can be presented on paper using the Warat projection . The carbon atom originally found in the aldehyde or ketone group (the anomeric carbon ) can adopt one of two configurations , a or p , which alternate between them in a microrotation . In the linear form of the monosaccharide , which is in equilibrium with the ring forms, the anomeric carbon is easily oxidized, so the compound is a reducing sugar.

► The anomeric carbon of one monosaccharide can bind to the hydroxyl group of another monosaccharide and form an acetal called a glycoside . In such a disaccharide, the glycosidic bond protects the anomeric carbon from oxidation and turns the sugar into a non-recyclable sugar .

► Oligosaccharides are short polymers of several monosaccharides linked by glycosidic bonds . At one end of the chain, the repeating end, there is a monosaccharide unit whose anomeric carbon is not involved in a glycidic bond .

4 According to the accepted method of naming disaccharides And for oligosaccharides , the order of the monosaccharide units , the configuration at each carbon number and the carbon atoms involved in the glycosidic bond or bonds must be specified .

the last from which all other life forms dangled. The blue arrow and the green arrow indicate endomybiotic assimilation of certain types of bacteria in eukaryotic cells . The assimilated bacteria became mitochondria and chloroplasts , respectively (see Figure 1.38).

7.2 Polysaccharides

► Polysaccharides ( glycans ) serve as fuel stores and structural carbohydrates of cell walls and the extracellular matrix .

► The homopolysaccharides starch and glycogen are fuel stores in plants, animals and bacterial cells. They consist of m-glucose whose units are connected to each other by bonds (4<-al ) , and both are branched.

► The homopolysaccharides cellulose, chitin and dextran play structural roles. Cellulose, which consists of s-glucose residues linked by bonds (41?/), gives rigidity and strength to plant cell walls. Chitin, a polymer of #-acetylglucosamine units linked together

In bonds (4<-1?0), strengthens the exoskeletons of arthropods . Dextran forms a sticky shell around certain bacteria.

► Homopolysaccharides fold into a three-dimensional structure . The chair shape of the pyranose ring is quite rigid, so the conformation of the polymers is determined by the rotation around the bonds between the ring and the oxygen atom in the glycosidic bond . Starch and glycogen form helical structures with hydrogen bonds within each chain; Cellulose and chitin form long, straight chains that interact with adjacent chains.

► Heteropolysaccharides – peptidoglycans in bacteria and agar in red algae – contribute to the strength of cell walls. The repeating disaccharide in peptidoglycan is 0’11(41?/):>10S; in agar the repeating disaccharide is D-Gal(/? i ->4)3,6-anhydro-L-Gal .

► Glycosaminoglycans are heteropolysaccharides Extracellular in which one of the two monosaccharide units is uronic acid ( creatin sulfate is an exception to this rule), and the other is an acetyl -linked amino sugar . Ester sulfate on some of the hydroxyl groups and the amine group of some glucosamine residues with heparin And heparin sulfate gives these polymers a high density of negative charge, causing them to adopt extended conformations . These polymers ( hyaluronan , chondroitin sulfate, dermatan sulfate and keratin sulfate) give the extracellular matrix viscosity, stickiness and tensile strength.

7.4 Carbohydrates in information molecules: the sugar code

Monosaccharides can be assembled into an almost infinite variety of oligosaccharides , which differ from each other in their stereochemistry and the position of the glycosidic bonds , in the type and orientation of the permanent groups, and in the types and number of branches. The information density in glycans is much higher than in nucleic acids or proteins.

► Lectins, which are proteins with highly specific carbohydrate-binding complexes, are usually found on the outer cell surface, where they initiate interactions with other cells. In vertebrates, the lectins The “readers ” of the oligosaccharide markers control the rate of degradation of certain peptide hormones , of proteins carried in the blood and of blood cells.

► Pathogenic bacteria and viruses, as well as certain eukaryotic parasites , adhere to the animal cells they recognize as targets by binding to the pathogens ‘ lectins to oligosaccharides on the surface of target cells.

► X- ray crystallography analysis of lectin-sugar complexes reveals the details of the conformation between the two molecules, which is behind the specificity and strength of the interaction of lectins with carbohydrates

7.5 Carbohydrate research

4- Deciphering the complete structure of oligosaccharides And polysaccharides require determination of the linear sequence, the location of the branches, the configuration of each monosaccharide unit and the positions of the glycosidic bonds – a more complex task than the analysis of proteins and nucleic acids.

►        Deciphering the structure of oligosaccharides And polysaccharides usually require a combination of several methods: hydrolysis by specific enzymes to determine the stereochemistry of the glycosidic bonds and create smaller fragments for further analysis; methylation ( Hoffman elimination) to place glycosidic bonds ; and gradual decomposition to determine the sequence and configuration of anomeric carbons .

►        Mass spectrometry and spectroscopy High-resolution NMR of small samples of carbohydrates provides essential information about the sequence, the configuration of anomeric and other carbons, and the positions of glycosidic bonds .

►        Solid substrate synthesis methods are used to produce defined oligosaccharides , which are of great value in the study of interactions between lectins and oligosaccharides and may prove to be of medical importance.

► Microarrays of pure oligosaccharides are used to determine the specificity and affinity of lectin binding to certain oligosaccharides .

Chapter 8 Nucleotides and acids nucleus

8.1 Some basic facts

► A nucleotide consists of a nitrogenous base ( purine or pyrimidine ), a sugar which is a pentose and one or more phosphorus groups. Nucleic acids are polymers of nucleotides, linked by phosphodiester bonds between the 5-monophosphorylation group of one pentose and the 3-hydroxyl group of the following pentose .

► There are two types of nucleic acids: DNA and RNA . The n – RNA nucleotides contain jam and the common pyrimidine bases are uracil and cytosine . DNA , the nucleotides contain 2-deoxyribeh, and the common pyrimidine bases are thymine and cythine . The major purines in both DNA and RNA are adenine and guanine .

8.2 Structure of nucleic acids

► Various types of evidence have shown that rw – DNA carries genetic information. Some of the earliest evidence came from the Avery – McLeod-McCarty experiment , which showed that DNA isolated from one strain of bacteria could infect another strain of bacteria and give it some of the heritable characteristics of the ” donor ” strain. The Hershey- Zeiss experiment showed DNA from a bacterial virus, but Not least its protein coat, carries the genetic message for the multiplication of the virus in the host cell.

► Watson and Crick summarized the existing data and posited natural DNA constructed of two strands arranged in a right-handed double helix of opposite polarity. Complementary base pairs, G= cn A=T , are formed by hydrogen bonds within the helix. The base pairs are stacked on top of each other perpendicular to the longitudinal axis of the double helix. The distance between the base pairs is 3.4 A and each turn of the coil has 10.5 bases.

DNA ► can exist in several structural forms. Two variations of the Watson-Crick form , or B-DNA , are A-DNA and Z-DNA . There are sequence-dependent structural variations that cause bends in the DNA molecule . DNA strands with an appropriate sequence can form pinhead or cross-like structures, or DNA Three-stranded or four-stranded . Messenger RNA transmits genetic information DNA ™ to ribosomes for protein synthesis. RNA guides RNA Ribosomes are also involved in protein synthesis. RNA can be a complex structure; A single strand of RNA can fold into hairpins, double-stranded regions , or complex loops.

8.3 Chemistry of nucleic acids

Heating or extreme pH conditions cause the loosening and separation (fusion) of natural DNA strands . The melting points of DNA molecules rich in G=c pairs are higher than those of DNA molecules rich in A=T pairs .

Single DNA strands that have been denatured and originate from two different biological species can form a double-hybrid strand . The degree of hybridization depends on the degree of similarity between the sequences. Hybridization is the basis of important methods used to study and isolate specific genes and RNA molecules .

► DNA is a relatively stable polymer. Spontaneous reactions such as deamination of certain bases, hydrolysis of sugar-base glycosyl bonds, formation of pyrimidine dimers induced by radiation and oxidative damage occur at a very slow rate , but they are important due to the high sensitivity of cells to changes in the genetic material.

► There are a variety of modern methods for DNA sequencing .

►  It is possible to synthesize oligonucleotides with a certain sequence quickly and accurately.

Tri-phosphorus (Ev 8.36). The three phosphorylation groups are marked as m , p and { from the ribose direction . Hydrolysis of triphosphate nucleosides provides chemical energy that drives many cellular reactions. For this purpose, adenosine 5-triphosphate, ATP , is mainly used , but in some reactions GTP, UTP and O1 are also used. Nucleosides Triphosphates are also used as activated starting materials in the synthesis of DNA and RNA .

to the energy released in the hydrolysis of ATP and the nucleosides The other triphosphates are responsible for the structure of the triphosphate group . The connection between the jam and the a phosphor is an ester connection . The bonds y,p -\ p,a are phosphoanhydrides (Figure 8.37). Under standard conditions, hydrolysis of the ester bond releases D -14 kJ/m01 while hydrolysis of each of the anhydride bonds releases D -30 kJ /m01 . ATP hydrolysis often plays an important thermodynamic role in biosynthesis . When hydrolysis of ATP Coupled to a reaction with a positive free energy change, it shifts the equilibrium of the overall process towards the product (remember the relationship between the equilibrium constant and the free energy change described in equation 6.3 in chapter 6).

8.4 Additional functions of nucleotides

► ATP is a major carrier of chemical energy in cells. The presence of an adenosine residue in a variety of enzyme cofactors may be related to the need for binding energy.

4 Cyclic AMP , which forms ATP in a reaction catalyzed by the enzyme adenylyl Cyclase is a common secondary messenger that is formed in response to hormones and other chemical signals.

9.1 Study of genes and their products

► DNA cloning and genetic engineering include cutting DNA and assembling DNA segments in new combinations – DNA Recombinant .

► In the cloning process, DNA is cut into segments using enzymes; Select and sometimes change the section you are interested in; insert the DNA fragment into a suitable cloning vector; transfer the vector with the DNA from the chamber to a host cell for multiplication; Identify and select cells containing the DNA segment .

► Key enzymes in gene cloning include DNA cleavage enzymes (mainly type 11). Ligaz .

► Cloning vectors include plasmids , and for cloning from the longest DNA chambers – bacterial artificial chromosomes ( BACS ) and yeast artificial chromosomes ( YACS ).

► Genetic engineering methods change cells so that they express and/or change cloned genes.

4 It is possible to connect proteins or peptides to the desired protein by changing the cloned gene that codes it and thus create a fusion protein. The additional peptide segments can be used to identify the protein or to purify it using convenient methods of affinity chromatography .

► The polymerase chain reaction ( PCR ) makes it possible to amplify selected DNA or RNA segments , so that they can be carefully studied or cloned.

9.2 Using methods based on DNA to understand the function of proteins

► It is possible to study proteins at the level of phenotypic function , at the level of cell function or at the molecular level.

► DNA libraries may be an opening for many types of studies that yield information about protein function.

► By fusing the desired gene with genes that code for a green fluorescent protein or epitope tags , researchers can observe the cellular location of the gene product, directly or through immunofluorescence .

► It is possible to study protein interactions with other proteins or with RNA using epitope tags and immunoprecipitation or using affinity chromatography . Yeast two-hybrid analysis allows the disclosure of molecular interactions in vivo .

DNA chips can reveal expression patterns of genes that change in response to cell stimulation, developmental stage or environmental conditions.

9.3 Genomics and human history

► A new generation of sequencing methods has greatly shortened the time needed to obtain complete genome sequences.

► About 30% of DNA in the human genome is in exons and introns of genes that code for proteins. The origin of almost half of DNA is from parasitic transposons . remainder

► DNA mostly encodes many types of RNA . Simple sequence repeats assemble centromeres and telomeres .

►        Some of the changes in the genes that define humans can be distinguished through comparative genomics with the genomes of other primates.

► Comparative genomics is also used to locate changes in genes that cause hereditary diseases, and it can be used to study evolution and migration of our ancestors over thousands of years.

in them as detectors for identifying sequence segments from ancient samples that coincide with the sequences of the known segments. The possible problem of contamination with very similar modern human DNA can be overcome by examining mitochondrial DNA . Human populations have haplotypes (series of distinct genomic differences ; see Figure 9.30) that can be identified in their mitochondrial DNA , and an examination of Meanderthal samples showed that their mitochondrial DNA contained unique haplotypes . Another proof of finding non-human hominid gene sequences is the presence of some differences in base pairs that are found in the chimpanzee database but not in the human one – in Neanderthal samples .

The completion of this challenging task is already visible on the horizon. The draft Neanderthal genome sequence published in early 2009 included more than 60% of the genomic sequences . Only a little more time should be devoted to completing the sequence. The data provide proof that about 700 years ago, the modern man and the Neanderthal man, who were the source of this DNA , had a common ancestor (Figure 2). Mitochondrial DNA analysis suggests that the two groups continued on the same path, with a certain degree of gene transfer between them, during about 300 more years. The branches diverged when anatomically modern man appeared, although today there is evidence of mixing between the two branches a little later as well.

Expanded DNA libraries Neanderthals from other collections of remains should eventually allow an analysis of the genetic diversity of the Neanderthals and perhaps also of their migration, thus opening a porthole through which we can glimpse our fascinating hominid past .

Chapter 10 Lipids Sea lipid of accumulation

10.1     Structural lipids in Mambats

10.2     Lipids in signaling molecules, as cofactors and as dyes

10.3     Working with lipids

Biological lipids are a chemically diverse group of compounds whose defining and common characteristic is insolubility in water. The biological roles of lipids are as diverse as their chemistry. Fats and oils are the main compounds used for energy storage in many organisms. Phospholipids And sterols are key components of biological membranes. Other lipids, although found in a relatively small amount, play vital roles and serve as cofactors of enzymes, electron carriers, light-absorbing dyes, hydrophobic anchors for proteins, spherons that help the folding of membrane proteins , emulsifying factors in the digestive system, hormones and intracellular messengers . This chapter describes representative lipids of each of the groups, organized according to the functions of the groups, and highlights the chemical structure and physical properties of the lipids belonging to them. Although our discussion will stick to the organization according to function, the thousands of different lipids can also be classified into eight categories according to their chemical structure (see Table 10.3). In Chapter 17 we discuss the energy-generating oxidation of lipids.

10.1 Storage lipids

► Lipids are water- insoluble cellular components with a variety of structures, and they can be extracted from tissues using non-polar solvents .

► Almost all fatty acids, which are the hydrocarbon component of many lipids, have an even number of carbon atoms (usually 12 to 24); They are saturated or unsaturated , and the double bonds in them are almost always in configuration Cis .

► Triacylglycerols contain three molecules of fatty acids linked by an ester bond to three hydroxyl groups of glycerol. Simple triacylglycerols contain only one type of fatty acid; Mixed triacylglycerols contain two or three types. Triacylglycerols are primarily storage fats; They are found in many foods.

► Partial hydrogenation of vegetable oils in the food industry converts some of the cis double bonds to the trans configuration . Trans fatty acids in the diet are a major risk factor for the development of coronary heart disease.

10.2 Lipids from BNM in membranes

► The polar lipids, with polar heads and non-polar tails, are central components of membranes. The most common are the glycerophospholipids , which contain fatty acids linked by an ester bond to two hydroxyl groups of glycerol, and a second alcohol, the head group, is linked by an ester bond to the third hydroxyl of glycerol in a phosphodiester bond . Other polar lipids are the sterols .

► Glycerophospholipids differ from each other in the structure of their head group; Phosphatidylethanolamine and phosphatidylcholine are common glycerophotolipids . At an equilibrium factor close to 7, the polar heads of glycerophospholipids carry a charge.

► Membranes of chloroplasts are rich in galactolipids , consisting of diacylglycerol to which one or two residues of galactose are bound, and sulfolipids , diacylglycerols to which a sulfonate sugar residue is bound , therefore their head group carries a negative charge.

► There are archaeons that have unique membrane lipids with long-chain alkyl groups linked at both ends to glycerol by an etheric bond and with sugar and/or phosphate residues attached to glycerol and giving them a polar or charged head group. These lipids are resistant to the extreme conditions in which the archaeons live .

► The sphingolipids contain sphingosine , a long-chain ellipsoidal amino alcohol , but they do not contain glycerol. Sphingomyelin has, besides phosphoric acid and choline , two long hydrocarbon chains, one of which is contributed by a fatty acid and the other by sphingosine . Three other groups of sphingolipids are cerebrosides , globosides and gangliosides , whose composition includes sugar.

► Sterols consist of four fused rings and a hydroxyl group . Cholesterol, the main sterol in animals, is a structural component of membranes and a starting material for a variety of steroids.

10.3 Lipids in signaling molecules, as cofactors and as dyes

► Some types of lipids, despite their small amount, play essential roles as cofactors or signaling molecules.

► Phosphatidylinositol Bisphosphate is hydrolyzed into two intracellular messengers : diacylglycerol and inositol             4,1,C-trisphosphate. Phosphatidylinositol

5,4,3-trisphosphate is a nucleation point for supramolecular protein complexes involved in biological signaling.

► Prostaglandins , thromboxanes And leucterians ( eicosanoids ), which originate from archidont , are powerful hormones .

► Steroid hormones , such as mating hormones, are derived from sterols . They are used in powerful biological signaling molecules that change gene expression in target cells.

► Vitamins E, A, D and & are fat-soluble compounds consisting of isoprene units . Everyone has important roles

Most in animal metabolism and physiology. Vitamin D is a derivative of a hormone that regulates calcium metabolism. Vitamin A provides the color of vision in the eyes of vertebrates and regulates gene expression during growth of epithelial cells, vitamin E protects membrane lipids from oxidative damage and vitamin K is essential for blood clotting.

►        Ubiquinones And plastoquinones , which are also isoprenoid derivatives , are electron carriers in mitochondria and chloroplasts , respectively.

►        Dolichols activate sugars and anchor them in cellular membranes; The sugar groups are then used to synthesize complex carbohydrates, glycolipids and glycoproteins .

►        Dianes Conjugated lipids are used as colorants in flowers and fruits and give the feathers of birds striking colors.

Polyketides are natural products widely used in medicine.

Chapter 11 Membranes biology and beyond

Materials

11.1     The composition and architecture of membranes

11.2     Dynamics of membranes

11.3     Passage of solutes through membranes

11.1 The composition and architecture of membranes

► Biological membranes define cell boundaries, divide cells into separate compartments, organize complex sequences of reactions and play a role in signal reception and energy conversions.

► Membranes are composed of lipids and proteins in variable combinations unique to each species, cell type and organelle. The double layer The lipid is the basic structural unit.

► Peripheral membrane proteins are loosely bound to the membrane through electrostatic interactions and hydrogen bonds or through covalently bound lipid anchors . Integral proteins bind tightly to membranes through hydrophobic interactions between the bilayer the lipid and the side chains of their non-polar amino acids . facing out from the protein towards the hydrophobic medium. Amphitropic proteins bind to membranes reversibly.

► Many membrane proteins cross the bilayer the lipid several times; Hydrophobic sequences of about 20 amino acids form helices a Transmembrane . barrels p Multistrands are also common in integral proteins in bacterial membranes. The 1yr and 1¥ residues of transmembrane proteins are usually found in the lipid-water contact area.

► The lipids and proteins of membranes are arranged in the membrane with specific laterality; This is the reason why membranes are structurally and functionally asymmetric . Glycoproteins of the cell membrane are always arranged when the oligosaccharide-bearing complex is on the extracellular surface .

11.2 Dynamics of membranes

► Lipids in biological membranes can exist in an ordered liquid state or in a disordered liquid state ; In the disordered liquid state, thermal movement of acyl chains make the interior of the bilayer liquid . This fluidity is affected by temperature, fatty acid composition and sterol content .

► Flip -flop diffusion of lipids between the inner leaflet and the outer leaflet of a membrane is very slow , unless it is specifically catalyzed by flipases , flipases or scramblelases .

► Lipids and proteins can undergo lateral diffusion within the plane of the membrane, but this mobility is limited by interactions of membrane proteins with internal structures of the cytoskeleton and by interactions of lipids with lipid rafts . One group of lipid rafts contains sphingolipids and cholesterol with a subset of membrane proteins linked to I?s or attached to several long-chain fatty acyl residues.

► Cabolin is an integral membrane protein that binds to the inner leaflet of the cell membrane and forces it to curl and form vesicles , which are apparently involved in membrane movement within cells and signaling.

BAR complexes cause a local curvature of the membrane and serve as mediators in the fusion of two membranes, which takes place in processes such as endocytosis , exocytosis and virus invasion.

► Integrins are proteins that cross the cell membrane

Small molecules that mask the ion charge and allow them to diffuse through the bilayer the torch Except in very few cases, the movement of small molecules through the cell membrane is done with the help of proteins such as channels, carriers and transmembrane pumps . Different compartments within the eukaryotic cell contain different concentrations of ions and metabolic products and intermediates, and these too must cross intracellular membranes in processes in which proteins act as mediators and are carefully regulated.

Chapter 12 Signaling biological Properties general of transfer signals

12.1     G protein- coupled receptors and secondary messengers

12.2     Receptortyrosine Kinases

12.3     Guanylyl receptor Cyclase , CGMP and protein kinase G

12.4     Multivalent adapter proteins and membrane rafts

12.5     Gated ion channels

12.6     Integrins : two- way cell adhesion receptors

12.7     Transcriptional control by nuclear receptors for hormones

12.8     Signaling in microorganisms and plants

12.9     Sensory transmission in the sight, smell and taste systems

12.10   Cell cycle control by protein kinases

12.11   Oncogenes , tumor suppressor genes and programmed cell death

12.1 General characteristics of signal transmission

All cells have specific and highly sensitive signal transduction mechanisms that have been conserved during evolution.

A wide variety of stimuli act through receptors for specific proteins found in the cell membrane.

The receptors bind the signaling molecule and start a process that amplifies the signal, combines it with input from other receptors and transmits the information throughout the cell. If the signal persists, the receptor undergoes desensitization which reduces or terminates the response.

Multicellular organisms are characterized by six general types of signaling mechanisms: proteins in the cell membrane that act through G proteins , tyrosine receptor Kinase , guanylyl receptor Cyclases that work through protein kinases , ion channels with gates, adhesion receptors that transmit information between the extracellular material and the cell skeleton, and nuclear receptors that bind steroids and change gene expression. 12.2 G protein- coupled receptors and secondary messengers

► GPCRS (G ) protein- coupled receptors have the same structural organization of seven transmembrane helices , and they act through G proteins Heterotrimeric . Upon ligand binding , GPCRS catalyze the exchange of GDP with K1s on the G protein and cause the dissociation of the subunit Ga , which continues and stimulates or inhibits the activity of an effector enzyme while changing the level of the second messenger it creates.

► The adrenergic receptor activates a stimulating G protein, GS , and thus activates Andylyl cyclase and increases the concentration of the second messenger, cyclic AMP.CAMP causes cAMP- dependent protein kinase to phosphorylate important target enzymes while changing their activity.

12.3 Tyrosine receptor Kinases

►        The insulin receptor, INSR , is the prototype for enzymatic receptors with tyrosine activity Keynes . With the binding of insulin, each ap unit of INSR Phosphorylates the p subunit of its partner, activating the tyrosine activity receptor kinase . The kinase catalyzes phosphorylation of Tyr residues on other proteins such as 1- IRS .

►        Phosphotyrosine residues 1-1- IRS serve as binding sites for proteins with SH2 complexes . Some of these proteins, such as Grb2 , contain two or more protein binding complexes and can act as adapters that bring two proteins together.

Sos ◄ bound to 0<2 catalyzes GDP-GTP exchange on Ras (a small G protein ), which in turn activates a transduction chain MAPK that results in the phosphorylation of target proteins in the cytosol and nucleus. The result is specific metabolic changes and changes in the expression of genes.

► The P13K enzyme , which is activated by interaction with 1- IRS , turns the membrane lipid b PIP2 – P1P3 , and it becomes a point of deprivation for proteins in the second and third branch of the insulin signaling process.

► In the          JAK-STAT signaling system , protein tyrosine Keynes Tax ( JAK ) is activated by contacting a receptor and phosphorylates the transcription factor STAT , which then enters the nucleus and changes the expression of a series of genes.

►        Between the signaling pathways there are extensive mutual connections that allow integration and targeting of multiple hormonal effects.

12.4 Guanylyl receptor Cyclase , CGMP and protein kinase G

► There are signals, including a natriuretic growth factor and guanylin , which work through receptor enzymes with guanylyl activity Cycles . The cGMP produced in this way is a second messenger that activates the clock – dependent protein kinase [ 00 ( PKG ). This enzyme alters metabolism by phosphorylating specific target enzymes.

► Nitric oxide is a short-lived messenger that stimulates guanylyl Cyclase diverts and in the process raises [ CGMP ] and stimulates PK

Multivalent adapter proteins and membrane rafts

► Many signaling proteins contain complexes that bind Ser, Tyr or Thr residues Phosphorylation of other proteins; The binding specificity of each compound is determined by sequences adjacent to the phosphorylated residue in the substrate.

► PTB SH2 complexes bind to proteins that contain Tyr – © residues ; Other complexes bind Ser -® and At-® residues in different contexts.

PHn SH3 complexes bind the phospholipid the membranous

. PIP3

► Many signaling proteins are multivalent , and have several different binding modules . Cells form a large number of multiprotein signaling complexes by combining the substrate specificities of protein kinases Different with the specificity of complexes that bind Thr , Ser or Tyr residues phosphorylated and with phosphatases that can quickly disable a signaling pathway.

► Membrane and intracellular rafts isolate groups of signaling proteins in small areas of the cell membrane, thereby enhancing their interactions and optimizing the signaling process.

12.6 Gated ion channels

► Ion channels with gates that depend on the membrane potential or on ligands play a central role in signaling processes in neurons and other cells.

► Channels + K+n Na Voltage dependences in the membranes of neurons carry the action potential along the axon as a wave of depolarization (inflow of Na + ) followed by repolarization (outflow of K + ).

► The mechanism of opening and closing the gates of the voltage-dependent channels includes the movement, perpendicular to the plane of the membrane, of a peptide transmembrane with high charge density as a result of the presence of Arg or other charged residues.

► The arrival of an action potential at the distal (remote) end of a presynaptic neuron causes the release of a neurotransmitter. The neurotransmitter (for example acetylcholine ) diffuses into the other synaptic nerve cell (or into the muscle cell at the nerve-muscle junction), binds to specific receptors in the cell membrane and causes a change in 4

► The acetylcholine receptor in neurons and muscle cells is a ligand- dependent ion channel ; Binding of acetylcholine causes a conformational change that opens the channel for Na + ,’-‘ Ca2 ions .

► Neurotoxins produced by many organisms attack ion channels in neurons, which is why they are fast-acting and deadly.

12.7 Integrins : two-way cell adhesion receptors

► Integrins are a family of dimeric receptors ( op ) in the cell membrane that interact with extracellular macromolecules and with the cell skeleton while carrying signals into and out of the cell.

The 4 active and inactive forms of integrin differ from each other in the conformation of their extracellular complexes . Intracellular signals and events can make the active conformation inactive and vice versa.

► Integrins mediate various aspects of the immune response, blood coagulation and angiogenesis , and they act in the metastasis of tumors.

12.8 Transcriptional control by nuclear hormone receptors

►        Steroid hormones enter cells and bind to specific receptor proteins.

► The hormone-receptor complex binds to specific regions of DNA , the components of the response to hormones, and interacts with other proteins to regulate the expression of nearby genes.

►        Certain effects of steroid hormones can occur through a different and faster signaling pathway.

12.9 Signaling in microorganisms and junctions

► Bacteria and eukaryotic microorganisms are equipped with a variety of sensory systems that allow them to sample their environment and respond to it. In the two-component system , the His receptor Kinase senses the signal and self- phosphorylates the His residue and then phosphorylates the Asp residue of the response regulator.

4 Plants respond to many environmental stimuli and use hormones and growth factors to coordinate the development and metabolic activities of their tissues. Plant genomes encode hundreds of signaling proteins, including some that closely resemble mammalian signaling proteins.

Two-component signaling mechanisms common in bacteria are also found in adapted forms in plants, and are used to detect chemical and light signals.

4> In plants, receptor-like kinases ( RLKs ) participate in the detection of a wide variety of stimuli, including brassinosteroids , peptides derived from pathogens and developmental signals. RLKs self -phosphorylate on Ser / Thr residues , then activate downstream proteins, which in some cases are MAPK chains . The end result is increased transcription of certain genes.

12.10 Sensory transmission in the sight, smell and taste systems

► The sight, smell and taste systems in vertebrates use GPCRS , which are modified by means of G proteins Heterotrimeric the membrane potential of a sensory neuron.

4 In the rod and spindle cells of the retina, light activates rhodopsin , which activates a G protein called transducin . The subunit a of transducin that is released, activates cGMP phosphodiesterase , and it lowers [ cGMP ] and thus closes cGMP- dependent ion channels in the outer segment of the neuron. The resulting hyperpolarization of the barrel or spindle cell carries the signal to the next neuron in the pathway and eventually to the brain.

► In olfactory neurons , odor stimuli, which act through GPCRS and G receptors , cause an increase in [ cAMP ] (by activating adenylyl cycle ) or to increase in [+032] (by PLC activation ). These secondary messengers affect ion channels and thus the membrane potential.

4 neurons of the sense of taste ( gustatory ) contain GPCRS that respond to taste molecules by changing D – CAMP levels , which changes the membrane potential by opening and closing ion channels.

4 There is a high degree of conservation of signaling proteins and transmission mechanisms among different signaling systems and among different species.

12.11 Cell cycle control by protein kinases

► The progression through the cell cycle is regulated by protein kinases Cyclin-dependent kinases ( CDKS ), which act at certain points in the cycle, phosphorylate key proteins and change their activity. The catalytic subunit of CDKs is not active unless it is bound to the regulatory subunit of cyclin .

► The activity of the cyclin-1M0 complex changes during the cell cycle through differential synthesis of CDKS , specific degradation of cyclin , phosphorylation and dephosphorylation of critical CDK residues and binding of inhibitory proteins to specific cyclin-tax complexes .

► The targets phosphorylated by cyclin – CDK complexes include proteins of the nuclear envelope and proteins that are necessary for cytokinesis and repair. DNA

12.12 Oncogenes , tumor suppressor genes and programmed cell death

►        Oncogenes encode defective signaling proteins. By continuously producing the signal for cell division, they lead to the formation of tumors. Oncogenes are genetically dominant, and they can encode growth factors, G proteins , protein kinases or nuclear transcription control factors .

►        Tumor suppressor genes encode control proteins that normally inhibit cell division; Mutations in these genes are genetically recessive but they may lead to the formation of tumors.

►        Cancer is usually the result of the accumulation of mutations in oncogenes and tumor suppressor genes.

►        When stability genes, which encode proteins needed to repair genetic damage, are mutated, other mutations remain uncorrected , including mutations in proto-oncogenes and tumor suppressor genes, which can lead to cancer.

► Apoptosis is a programmed and controlled cell death that operates during normal development and maturity to eliminate unnecessary, damaged or contaminated cells. Apoptosis can be activated by extracellular signals such as TNF , which act through receptors in the cell membrane.

 

► Chains of enzymatic processes, in which a single hormone molecule activates a catalyst that activates another catalyst and so on, lead to a large amplification of the signal, which is characteristic of hormone receptor systems.

4> Cyclic AMP concentration is eventually reduced by CAMP A phosphodiesterase , Gsn turns itself off by hydrolyzing GTP bound to it to Cs ; This reaction acts as a binary switch that enables self-limitation.

► When the epinephrine signal persists, adrenergic receptor- specific protein kinase ?/- and arrestin temporarily desensitize the receptor and cause it to move into vesicles Intracellular .

► There are receptors that stimulate adenylyl cyclization using GS ; Others inhibit it using ! G. ​Thus [ CAMP ] cells reflect the combined input of two (or more) signals.

Non-catalytic adapter proteins such as AKAPS hold together proteins that are involved in a signaling process, increasing the efficiency of their interactions and in some cases limiting the process to a specific location in the cell.

► There are GPCRS that act through phospholipase c In the cell membrane, the cleft PIP2 to diacylglycerol and 3ts. IP3 increases [+ Ca2 ] in the cytosol by opening + Ca2 channels in the endoplasmic reticulum . Diacylglycerol Ca2+n co-activate protein kinase C , which phosphorylates and changes the activity of certain proteins in the cell. The concentration of Ca2 + in the cell also regulates (sometimes frequently using calmodulin ) many other enzymes and proteins involved

Part B

13.1 Bioenergetics and thermodynamics

► Living cells perform work all the time. They require energy to maintain their carefully arranged structures, to synthesize cell components, to generate electrical currents, and for many other processes.

► Bioenergetics is the quantitative study of energetic relationships and energy conversions in biological systems. Biological transformations of energy obey the laws of thermodynamics .

► All chemical reactions are affected by two forces: the tendency to reach the most stable binding state (it is convenient to express it through enthalpy, H ) and the tendency to reach the highest degree of randomness, which is expressed as entropy, S. The net driving force in the reaction is AG , the change in free energy, which represents their net effect of these two factors: AG = AH – TAS .

► The standard free energy change, ° AG , is a physical constant that characterizes a given reaction, and it is possible to calculate from the equilibrium constant of the reaction: AG ‘ ° = – RT in K eq .

► The actual free energy change, AG , is a variable that depends on ° AG and the concentrations of the reactants and products:

)] RT ln )]products[/]reactants + ° AG = AG .

► When – AG is large and negative, the reaction tends to move towards the products; When AG is large and positive, the reaction tends to proceed in the opposite direction; And when 0 = AG , the system is in equilibrium.

► The change in the free energy of a reaction does not depend on the pathway in which the reaction occurs. Free energy changes are additive; The total change in the free energy of the net chemical reaction resulting from successive reactions with a common intermediate is equal to the sum of the AG values of the separate reactions

13.2 Chemical logic and common biochemical reactions

► Living systems use a large number of chemical reactions that can be divided into five general types.

► Carbonyl groups play a special role in reactions that create or cleave C—C bonds . Carbanionic intermediates are common and are stabilized by adjacent carbonyl groups; or, more rarely, by certain imines or cofactors .

► Redistribution of electrons can lead to internal rearrangement, isomerization and elimination. Such reactions include intramolecular oxidation-reduction , a change in the cis -trans arrangement around a double bond, and a change in the position of double bonds.

► Homolytic cleavage of covalent bonds to form free radicals occurs in one of the pathways, such as in certain isomerization , decarboxylation , reductase and rearrangement reactions.

► Reactions in which the transfer of a phosphoryl group occurs are a particularly important type of group transfer in cells that is required for the activation of molecules for reactions that would otherwise be highly unfavored .

► Redox reactions involve the loss or addition of electrons: one reactant gains electrons and undergoes redox, while the other loses electrons and is oxidized. Oxidation reactions usually release energy, and are important in catabolism .

13.3 ATP and transfers of phosphoryl groups

► ATp is the chemical link between catabolism for anabolism . It is the energy currency of the living cell. Exergonic conversion of 1 ADP ATP – Pi or <-1 AMP – ppi , coupled to many androgenic reactions and processes .

► Direct hydrolysis of ATp is the source of energy in some of the processes driven by conformational changes; However, in general, the transfer of a phosphoryl , pyrophosphoryl or adenylyl group D – ATP It is the substrate or the enzyme that attaches the energy from the breakdown of ATp to androgenic transformations of substrates , and not the hydrolysis of ATp .

► Through these reactions in which group transfer occurs, ATp provides the energy for anabolic reactions, including the synthesis of macromolecules of information, and for the transfer of molecules and ions through membranes against concentration cascades and electric potential cascades.

► To maintain a high potential for group transfer, ATp concentrations must be maintained well above the equilibrium concentration through energy-yielding catabolic reactions .

► Cells contain other metabolites with large and negative free energies for hydrolysis, including phosphoenolpyruvate , 3,1-bisphosphoglycerate and phosphocreatine . These high-energy compounds, similar to ATP , have a high potential for transferring phosphoryl groups . Thioesters also have high free energies of hydrolysis.

► Polyphosphate Inorganic , found in all cells, can be used as a reservoir of phosphoryl groups with a high group transfer potential

13.4 Biological redox reactions

► In many organisms, a central energy-conserving process is oxidation in the stages of glucose <- CO2 , where part of the oxidation energy is stored in ATP with the transfer of electrons to 02.

► Biological redox reactions can be described in terms of two half-reactions , each of which has a characteristic standard redox potential, ° E .

► When connecting two electrochemical half-cells , each of which contains the components of a half-reaction , electrons tend to flow to the half-cell with the higher redox potential. The strength of this tendency is proportional to the difference between the two redox potentials ( AE ), and is a function of the concentrations of the oxidized derivative and the reduced derivative.

► The standard free energy change for an oxidation-reduction reaction is proportional to the difference in the standard redox potentials of the two half-cells : °’ n F AE – = ° AG .

► Many biological oxidation reactions are dehydrogenations in which one or two hydrogen atoms (- H+ + e ) are transferred from a substrate to an electron acceptor. Redox reactions in living cells involve specialized electron carriers.

are used as coenzymes of dehydrogenases NADP -! NAD ◄

many and diffuse freely. Both NAD + and NADP + gain two electrons and one proton.

► 1 FAD – JMN The flavin nucleotides are used as prosthetic groups of strongly bound flavoproteins . They can have one or two electrons and one or two protons. Flavoproteins also serve as photoreceptors in cryptochromes and in photolyases .

14.1 Glycolysis

► Glycolysis is an almost universal pathway in which a glucose molecule is oxidized to obtain two pyruvate molecules , and energy is conserved ATP !- NADH .

► All ten glycolytic enzymes are found in the cytosol , and all ten intermediate compounds are phosphorylated compounds with three to six carbons.

► In the preparatory phase of glycolysis , ATP is expended to turn glucose into fructose 6,1-bisphosphate. The bond between 3- C and 4S is then broken to obtain two molecules of triose phosphate.

► In the gain phase, each of the two glyceraldehyde 3-phosphate molecules derived from glucose undergo 1-1- C oxidation ; The energy of this oxidation reaction is conserved in the form of one NADl and two ATP for each triose phosphate that is oxidized. The net equation of the total process is:

► Glycolysis is subject to strict control in coordination with other pathways of energy production to ensure a stable supply of

. ATP

► In type 1 diabetes, impaired uptake of glucose by muscle and adipose tissue has a profound effect on carbohydrate and fat metabolism.

14.2 Pathways that fuel glycolysis

► Endogenous starch and glycogen , storage forms of glucose, enter glycolysis in a two-step process . Phosphorolytic cleavage of a glucose residue at the end of the polymer, generating glucose 1-phosphate, catalyzed by glycogen phosphorylase or starch phosphorylase . Phosphoglucomatase converts the glucose 1-phosphate to glucose 6-phosphate, and it can now enter the glycolysis pathway .

► Polysaccharides And digested disaccharides are converted into monosaccharides by hydrolytic enzymes in the intestine, and the monosaccharides enter intestinal cells and are transported to the liver or other tissues.

► A variety of m- hexoses , including fructose, galactose and mannose , can be routed into glycolysis . Each is phosphorylated and converted to glucose 6-phosphate, fructose 6-phosphate or fructose 1-phosphate.

► The conversion of galactose 1-phosphate to glucose 1-phosphate includes two nucleotide derivatives : npto-UDPn nvp >:1-UDP . Genetic defects in any of the three enzymes that catalyze the conversion of galactose to glucose 1-phosphate lead to galactosemias of varying degrees of severity.

14.3 The fate of pyruvate in anaerobic conditions : fermentation

► NADH formed in glycolysis must be cycled to regenerate NAD + , which is required as an electron acceptor in the first reaction of the profit phase. Under aerobic conditions, electrons pass from D – NADH to 02 in mitochondrial respiration.

► Under anaerobic or hypoxic conditions , many organisms regenerate NAD + by transferring electrons D – NADH to pyruvate , while forming lactate . Other organisms, such as yeast, regenerate NAD + by pyruvate reduction to ethanol and 2ss. In these anaerobic processes (fermentations), there is no net oxidation or reduction of the carbon atoms of glucose.

► A variety of microorganisms can ferment sugar in fresh foods, a process that leads to changes in taste and texture and preserves the food from spoilage. Fermentations are used in industry to produce a wide variety of commercially valuable organic compounds from inexpensive starting materials.

14.4 Gluconeogenesis

► Gluconeogenesis is a multi-step process that takes place everywhere, in which glucose is produced from lactate , pyruvate , or oxaloacetate or from any compound that can transform it into one of these intermediate compounds (including intermediate compounds of the citric acid cycle). Seven of the gluconeogenesis reactions are catalyzed by the same enzymes that are used in glycolysis ; These are the reversible reactions.

► Three irreversible reactions Glycolysis is bypassed by reactions catalyzed by gluconeogenic enzymes : (1) conversion of pyruvate < -PEP through oxaloacetate , a reaction catalyzed by pyruvate carboxyls I – PEP carboxykinase ; (2) Fructose 6,1-bisphosphate pattern by 1- FBPase ; and (3) glucose 6-phosphate pattern by glucose 6-phosphatase.

► The formation of one molecule of glucose from pyruvate requires 4 molecules 2 , ATP , GTP molecules and 2 NADH molecules ; This is an expensive reaction.

► Gluconeogenesis in the liver, kidneys and small intestine of mammals provides glucose for use by the brain, muscles and red blood cells.

► Acetyl – CoA activates pyruvate carboxylase while increasing the rate of gluconeogenesis when the cell has a sufficient supply of other substrates (fatty acids) for energy production.

► Animals cannot convert acetyl – CoA derived from fatty acids into glucose; Plants and microorganisms can do this.

► Glycolysis and gluconeogenesis are subject to mutual control to prevent wasteful activation of both pathways at the same time.

14.5 The pentose phosphate pathway of glucose oxidation

► The oxidative pentose phosphate pathway ( the phosphogluconate pathway or the hexose pathway). Monophosphate (results in oxidation and decarboxylation in 1-) of glucose 6-phosphate, while reducing + NADP to ADP1 \ and creating pentose phosphates.

► NADpH provides redox power for biosynthetic reactions , and ribose 5-phosphate is a starting material in the synthesis of nucleotides and nucleic acids. Rapidly growing tissues and tissues that perform active biosynthesis of fatty acids, cholesterol, or steroid hormones send more glucose 6-phosphate through the pentose phosphate pathway than tissues with a reduced demand for pentose phosphates and redox capacity.

► The first step in the pentose phosphate pathway consists of two oxidations that convert glucose 6-phosphate to ribulose 5-phosphate and recycle + NAPDH NADP . The second stage consists of non-oxidative reactions that convert pentose phosphates to glucose 6-phosphate, which starts the cycle again.

► In the second step, transketolase (with Tpp As a cofactor ( and transaldoles catalyze the interconversion of three-, four-, five-, six- and seven- carbon sugars , along with the reversible conversion of six pentose phosphates to five hexose phosphates. In carbon assimilation reactions in photosynthesis, the same enzymes catalyze the reverse process, the pentose pathway Reductive Phosphate: Conversion of five hexose phosphates to six pentose phosphates .

► A genetic defect in transketolase that reduces the affinity of the enzyme <- TPP aggravates the Wernicke-Korsakoff syndrome .

► The entry of glucose 6-phosphate into glycolysis or the pentose phosphate pathway is largely determined by the relative concentrations of

. NADPH”! NADP +

15.1 Control of metabolic pathways

► In a metabolically active cell that is in a resistant state, intermediate compounds are created and consumed at the same rate. When a transient disturbance changes the rate of formation or consumption of a certain metabolite , changes in the activity of enzymes compensate for this and return the system to the resistant state.

► Cells regulate their metabolism with the help of a variety of mechanisms that operate in time frames between less than a millisecond and days, by changing the activity of existing enzyme molecules or changing the number of molecules of a specific enzyme.

► Different signals activate or deactivate transcription factors , which act in the nucleus to regulate gene expression. Changes in the transcriptome lead to changes in the proteome and ultimately to changes in the metabolism of a cell or tissue.

► In multi-step processes such as glycolysis , certain reactions are actually in steady state equilibrium; The rate of these reactions increases and decreases depending on the concentration of the substrate. Other reactions are far from equilibrium; These steps are usually the control points of the overall route.

► Control mechanisms maintain almost constant levels of central metabolites such as I ATP – NADH in the cells and glucose in the blood, while adjusting the use or production of glucose to the changing needs of the organism.

ATP and AMP concentrations are a highly sensitive reflection of the energy state in the cell, and when the ratio [ATP]/[AMP] decreases, protein kinase Activated by AMP (AMPK) triggers a variety of cellular reactions aimed at raising [ ATP ] and lowering [ AMP ].

15.2 Analysis of metabolic control

► Analysis of metabolic control shows that control of the flux rate of a metabolite in a pathway is shared between several of the enzymes in the same pathway.

► The flux control coefficient, C , is an experimentally determined measure of the effect of the concentration of an enzyme on flux in a multi-enzyme pathway. The coefficient is characteristic of the entire system, and is not specific to the enzyme.

► The elasticity coefficient, 8, of an enzyme is an experimentally determined measure of the reactivity of the enzyme to changes in the concentration of a metabolite or a control molecule.

► The response coefficient, R , is a measure of the experimentally determined change in pathway flux in response to a control hormone or second messenger. The coefficient is a function of C and 8: 8 • R = C.

► Some regulatory enzymes control the flux in the pathway, while others rebalance the level of metabolites in response to a change in flux. The first activity is control ; the second activity, of rebalancing, is regulation .

► Analysis of metabolic control predicts, and experiments confirm, that it is possible to increase the flux towards a particular product most efficiently by increasing the concentration of all enzymes in the pathway.

15.3 Coordinated control of glycolysis and gluconeogenesis

► to the gluconeogenesis pathways And glycolysis has seven enzymes in common that catalyze the reactions that are infinitely reversible. For the other three steps, the forward and reverse reactions are catalyzed by different enzymes, and these are the control points of the two pathways.

► The kinetic properties of hexokinase iV ( glucokinase ) are related to its special role in the liver: releasing glucose into the blood when the blood glucose level is low and glucose absorption and glucose metabolism when the blood glucose level is high.

► 1- PFK is allosterically inhibited by ATP and citrate . In most mammalian tissues, including the liver, fructose 6,2-bisphosphate is an allosteric activator of this enzyme.

► Pyruvate Kinase is allosterically inhibited by ATP , and liver isozyme is also inhibited by 1- cAMP- dependent phosphorylation .

► The process of gluconeogenesis is regulated at the level of pyruvate Carboxylase ( which is activated by acetyl – m (CoA -1- FBPase ) (which is inhibited by fructose 6,2-bisphosphate AMPn ).

► To limit the cyclic turnover of substrate between glycolysis For gluconeogenesis , both pathways are subject to mutual allosteric control , which is obtained mainly from the opposing effects of fructose 6,2-bisphosphate on 1- PFK and

. FBPase-1

► Glucagon or epinephrine lower the concentration of 6,2- proteacose bisphosphate by increasing [ cAMP ] and phosphorylating the bifunctional enzyme 2- PFK-2/ FBPase . Insulin increases the concentration of fructose 6,2-bisphosphate through phosphoprotein activation A phosphatase that performs phosphorylation and thus activates 2- PFK .

► Xylulose 5-phosphate, an intermediate compound in the pentose phosphate pathway, activates the phosphoprotein phosphatase PP2A , which phosphorylates several target proteins, including 2- PFK-2/ FBPase and tilts the balance towards glucose uptake, glycogen synthesis and lipid synthesis in the liver.

► Transcription factors , including FOXO1A SREBP, CREB, ChREBP act in the nucleus to regulate the expression of specific genes that encode enzymes that participate in glycolysis pathways and gluconeogenesis . Insulin and glucagon act antagonistically in the activity of these transcription factors , thus turning many genes on and off.

15.4 The metabolism of glycogen in animals

► Glycogen is stored as large particles in muscle and liver. The enzymes participating in glycogen metabolism and the control enzymes are inside the particles.

► Glycogen Phosphorylase catalyzes phosphorolytic cleavage at the non-recycling ends of glycogen chains , thus producing glucose 1-phosphate. A debranching enzyme transfers branches to central chains and releases the residue at the branching point (61 a ) as free glucose. Enter glycolysis or turn, in the liver, into free glucose with the help of glucose 6-phosphatase found in the endoplasmic reticulum , and then be released and raise the glucose concentration in the blood.

► The sugar nucleotide npto -UDP donates glucose residues to the non-recycling end of glycogen in a glycogen- catalyzed reaction Synthesis . A separate branching enzyme creates the (6 < 1 a ) bonds at the branching points.

New glycogen particles are formed from the autocatalytic formation of a glycosidic bond between the glucose of npto -UDP and the Tyr residue in the glycogenin protein , after which some glucose residues are added to form a primer on which the enzyme glycogen Synthesis can work.

Acetyl production – ( activated acetate )

► Pyruvate , the product of glycolysis , is converted to acetyl – CoA , the starting material of the citric acid cycle , by the pyruvate complex Dehydrogenase .

The PD1 complex consists of copies of three enzymes: pyruvate Dehydrogenase , E1 (with its associated cofactor , TPP ); dihydrolipoyl transacetyls , E2 (with a lipoyl group covalently bound to it ) and dihydrolipoyl Dehydrogenase , E3 (with its cofactors FAD !- NAD ).

► E1 first catalyzes carboxylation of pyruvate , which results in the formation of hydroxyethyl -, and then catalyzes oxidation of the hydroxyethyl group to an acetyl group . The electrons from this oxidation recycle the disulfide of lipoate bound to £2 and the acetyl group moves into a thioester bond with the SH -one group of recycled lipoate .

► E2 catalyzes the transfer of the acetyl group to coenzymes A , to form acetyl – CoA .

► E3 catalyzes the re-formation of the disulfide (oxidized) form of lipoate ; Electrons first pass through FAD , and then + NAD .

► The long lipolysyl arm oscillates from the active site of E2 E1 to £3 and leaves the intermediate compounds bound to the enzyme complex. This mode allows channeling of substrates .

► The organization of the 1C1(1C1) complex is very similar to the organization of the complexes that catalyze the oxidation of a – ketoglutarate and the a – keto acids

16.2 The reactions of the citric acid cycle

citric acid cycle (Krebs cycle, TCA cycle ) is an almost universal central catabolic pathway , in which compounds derived from the breakdown of carbohydrates, fats and proteins are oxidized <- CO2 , and most of the oxidation energy is temporarily stored in the electron carriers FADH2 !- NADH . During aerobic metabolism, these electrons are transferred to 02 and the energy of the electron flow is captured in the form of ATP .

► Acetyl – CoA enters the citric acid cycle (in the mitochondria of eukaryotes , in the cytosol of bacteria); Citrate Synthesis catalyzes its compression with oxaloacetate to form citrate .

► The citric acid cycle converts citrate to oxaloacetate and releases two Co2 in seven successive reactions, which include two decarboxylations . The cycle is cyclic since the intermediate compounds of the cycle are not utilized; For every molecule of oxaloacetate consumed in the pathway, one molecule of oxaloacetate is produced.

► For each acetyl – CoA that is oxidized in the citric acid cycle , the energy gain consists of three molecules of NADH , one molecule of FADH2 and one molecule of nucleoside Triphosphate ( ATP ) or GTP

► Besides acetyl – CoA , any compound that leads to an intermediate compound in the citric acid cycle that has four or five carbons—for example, the breakdown products of many amino acids—can be oxidized in the cycle.

► The citric acid cycle is amphibolic , meaning it is used in both catabolism and anabolism ; Intermediate compounds of the cycle can be pumped out of the cycle and serve as starting materials for a variety of biosynthetic products .

► When intermediate compounds are diverted from the citric acid cycle to other pathways, their inventory in the cycle is renewed with the help of some encephalotropic reactions, which produce four-carbon intermediate compounds through the carboxylation of three-carbon compounds ; These reactions are catalyzed by pyruvate Carboxyls , PEP Carboxykinase , PEP carboxylase and malic enzyme (see Table 16.2). Enzymes that catalyze carboxylations usually use biotin to activate Co2 and carry it to receiving compounds such as pyruvate or phosphoenolpyruvate .

Citric acid circuit control

citric acid cycle is controlled by the conversion rate of pyruvate to acetyl – CoA and by the flux of citrate Synthesis , isocitrate Dehydrogenase and a – ketoglutarate Dehydrogenase . These fluxes are determined to a large extent by the concentrations of substrates and products: the final products NADHn ATP have an inhibitory effect, and the substrates + NAD and C1(1\■•. – a stimulating effect.

► Production of acetyl – CoA for the citric acid cycle by the 1C1 complex is allosterically inhibited by metabolites that signal sufficient metabolic energy ( ATP , acetyl – NADH, CoA and fatty acids) and stimulated by metabolites that indicate reduced energy supply

.) CoA, NAD +, AMp (

► Complexes of successive enzymes in the pathway allow the routing of substrates between them. 16.4 The glyoxylate cycle

► The glyoxylate cycle is active in the germinating seeds of certain plants and in certain microorganisms that can live with acetate as a sole carbon source. In plants, the pathway occurs in shoot glyoxysomes. It includes several enzymes of the citric acid cycle and two additional enzymes: isocitrate Liaz and Malat Synthesis .

► In the glyoxylate cycle , bypassing the two decarboxylation reactions of the citric acid cycle allows the net formation of succinate , oxaloacetate and other intermediate compounds of the acetyl – CoA cycle . The oxaloacetate formed in this way can be used for the synthesis of glucose through gluconeogenesis .

glyoxylate cycle and they cannot synthesize glucose from acetate or the fatty acids that lead to acetyl – CoA .

► The distribution of isocitrate between the citric acid cycle and the glyoxylate cycle is controlled by the level of isocitrate Dehydrogenase , regulated by reversible phosphorylation

17.1 Digestion, movement and transport of fats

► The fatty acids of triacylglycerols provide a large part of the oxidation energy in animals. Triacylglycerols from the food undergo milking by bile salts in the small intestine, undergo hydrolysis by lipases in the intestine, are absorbed by epithelial cells in the intestine, are converted back to triacylglycerols and finally bind to specific apolipoproteins and become chylomicrons .

► Chylomicrons carry triacylglycerols to the tissues, where they are lipoproteins Lipase breaks them down and releases free fatty acids that enter the cells. Triacylglycerols stored in adipose tissue are mobilized thanks to the activity of triacylglycerol Lipez was sensitive to the hormone. The released fatty acids bind to albumin in the blood serum and are carried to the heart, skeletal muscles and other tissues that use fatty acids as fuel.

► After entering the cells, fatty acids are activated in the outer membrane of the mitochondrion by converting them into fatty thioesters of 2 K <- C0A . 2 K <- C0A Fatty destined for oxidation enters the mitochondria in three stages, via the carnitine shuttle .

17.2 Oxidation of fatty acids

► In the first stage of p- oxidation , each cycle of four reactions catalyzes the removal of an acetyl – CoA unit from the carboxyl end of saturated fatty < -CoA : (1) dehydrogenation of carbons a and C-2) p and 3-s) by <- CoA dehydrogenases which are related to FAD (2) from the day of the trans A2 double bond obtained in step 1 by CoA->w hydratase , (3) dehydrogenation of pm – hydroxyacyl – CoA obtained in step 2 by p – hydroxyacyl – CoA Dehydrogenase to which NAD is bound and (4) cleavage by thiolase of the rop -p -<- CoA obtained in step 3. Acetyl – CoA and fatty acyl- CoA shortened by two carbons are obtained. The shortened fatty acyl- CoA enters another p -oxidation cycle .

► In the second step in the oxidation of fatty acids, acetyl – CoA is oxidized to 2S in the citric acid cycle . A large part of the theoretical yield of free energy from the oxidation of fatty acids is obtained as ATP In oxidative phosphorylation , the last step in the oxidation pathway.

► CoA- Pn’dn , an early intermediate compound in the synthesis of fatty acids, inhibits carnitine acyltransferase I and prevents the entry of fatty acids into the mitochondria. In this way, it blocks the breakdown of fatty acids during synthesis.

► Genetic defects in acyl- CoA Medium-chain dehydrogenases lead to serious diseases in humans, as do mutations in other components of the p- oxidation system .

unsaturated fatty acids requires two additional enzymes: enoyl -S isomerase and 4,2-dienoyl- CoA reductase . Unpaired fatty acids are oxidized in the p- oxidation pathway and acetyl – CoA and a CoA molecule are obtained . This compound undergoes carboxylation , CoA’drnK which undergoes isomerization CoA in the reaction catalyzed by methylmalonyl – CoA Mutase , an enzyme that needs a coenzyme for its action B12 .

► Peroxisomes of plants and animals, and glyoxisomes of plants, carry out p- oxidation in a cycle of four steps similar to those in the mitochondrial pathway in animals. However, in the first oxidation step, electrons are transferred directly to O2 and H2O2 is obtained . Peroxisomes in animal tissues specialize in oxidizing fatty acids with very long chains and branched fatty acids. In glyoxysomes , in germinating seeds, p- oxidation is one of the steps in the conversion of lipid stores into a variety of intermediate compounds and products.

► Oxidation reactions m , which occur in the endoplasmic reticulum , form intermediate acyl dicarboxylic compounds that can undergo p oxidation at each of the two ends and yield short dicarboxylic acids, such as succinate .

► Oxidation reactions break down branched fatty acids, such as phytic acid .

17.3 Ketone bodies

► The ketone bodies — that is, acetone, acetoacetate I – pD – hydroxybutyrate – formed in the liver. The last two compounds are used as fuel molecules in extrahepatic tissues, by oxidation to acetyl – CoA and entering the citric acid cycle .

► Excess production of ketone bodies in a situation of uncontrolled diabetes or very reduced calorie consumption may lead to acidosis or lactose . The metabolic fate of amino groups

► In the human body, only a small part of the energy produced in oxidation processes is obtained in the catabolism of amino acids. Amino acids are created in the normal breakdown ( metabolism ) of cell proteins, in the breakdown of proteins from food and in the breakdown of body proteins instead of other fuel sources during starvation or untreated diabetes.

► Proteases break down proteins from food in the stomach and small intestine. Most proteases are first synthesized as inactive zymogens.

► An early step in the catabolism of amino acids is the separation of the amine group from the carbon skeleton. In most cases, the amine group is transferred to α – ketoglutarate and glutamate is obtained . This transamination reaction requires the presence of the coenzyme Pyridoxal Phosphate.

► Glutamate is transported to the mitochondria in the liver, where glutamate Dehydrogenase releases the amine group as an ammonium ion (+ NH4 ). Ammonia produced in other tissues is transported to the liver as the amide nitrogen of glutamine or, when it is transported from the skeletal muscles, as the amine group of alanine .

► Pyruvate produced in the deamination of alanine in the liver is converted to glucose, which is transported back to the muscle as part of the glucose-alanine cycle .

18.2 Nitrogen excretion and the urea cycle

► Ammonia is extremely toxic to animal tissues. In the urea cycle, ornithine binds to ammonia, in the form of carbamoyl phosphate, and citrulline is obtained . A second amine group is transferred from aspartate to citrulline and arginine is obtained – the immediate precursor of urea. Arginase catalyzes the hydrolysis of arginine to urea and ornithine ; Ornithine is thus regenerated in each round of the cycle.

► The urea cycle leads to the net conversion of oxaloacetate For fumarate , two intermediate compounds in the citric acid cycle . The two circles are therefore related to each other.

► The urea cycle activity is controlled at the level of enzyme synthesis and through allosteric control of the enzyme that catalyzes the formation of carbamoyl phosphate.

18.3 Decomposition pathways of amino acids

► After the removal of the amino groups, the carbon skeletons of the amino acids are oxidized to compounds that can enter the citric acid cycle and oxidize <- CO2 and 20 and 1. The reactions in these pathways require several cofactors , including tetrahydrofolate and 5-adenosylmethionine in one-carbon transfer reactions and tetrahydrobiopterin in the oxidation of phenylalanine by phenylalanine hydroxylase .

► Depending on their final breakdown product, certain amino acids can become ketone bodies, others can become glucose, and others – both. The breakdown of amino acids is thus integrated into intermediate metabolism and may be of crucial importance in survival under conditions where amino acids are a major source of metabolic energy.

► The carbon skeletons of amino acids enter the citric acid cycle through five intermediate compounds: a, CoAK – ketoglutarate , r2p10 <- C0A , fumarate and oxaloacetate . Some of them are also broken down into pyruvate , which can turn into acetyl – CoA or oxaloacetate .

► The amino acids converted to pyruvate are alanine , cysteine , glycine , serine , threonine and tryptophan. Leucine , lysine , phenylalanine and tryptophan become acetyl – CoA through acetoacetyl – CoA . Isoleucine , leucine , threonine and tryptophan also become directly acetylated . CoA

► Arginine, glutamate , glutamine, histidine and proline become α – ketoglutarate ; Isoleucine , methionine , valine and threonine become succinyl -€; Four carbon atoms of phenylalanine and tyrosine become fumarate ; and asparagine and aspartate become oxaloacetate .

► The branched chain amino acids ( isoleucine , leucine ). Valine (, unlike the other amino acids, undergoes decomposition only in extrahepatic tissues .

► Genetic defects in the enzymes involved in the catabolism of amino acids are responsible for several serious diseases in humans.

19.1 Electron transfer reactions in mitochondria

► The chemiosmotic theory provides the theoretical principles that explain many types of biological energy transformations, including oxidative phosphorylation and photophosphorylation . The energy coupling mechanism is similar in both processes: the energy of electron flow is conserved through the simultaneous pumping of protons through the membrane, creating an electrochemical cascade, the protonic driving force .

► In mitochondria, hydride ions removed from substrates (such as α – ketoglutarate and malate ) by dehydrogenases associated with NAD donate electrons to the respiratory chain (electron transfer), which transfers the electrons to molecular 02, while reducing it to 1 and 20.

► D – NADH reducing equivalents are transported through a series of Fe-S centers to ubiquinone , which transfers the electrons to cytochrome b , the first carrier in complex III . In this complex, electrons travel in two separate paths through two b- type cytochromes and cytochrome c1 to the Fe-S center . The n – Fe-S center transfers the electrons, one by one, through cytochrome c and into complex IV , cytochrome Oxidase . This copper-containing enzyme also contains cytochromes a and a3 , accumulates electrons and transfers them to 02, while reducing the oxygen to 1120.

► Some of the electrons enter this carrier chain in alternative pathways. Succinate is oxidized by succinate Dehydrogenase (complex II ), which contains a flavoprotein that transfers electrons through several Fe-S centers to ubiquinone . Electrons obtained from the oxidation of fatty acids pass to ubiquinone via the flavoprotein the electron transporter .

► Active derivatives of oxygen, which are produced in the mitochondria and can cause damage, become inactive thanks to a series of protective enzymes, which includes superoxide dismutase and glutathione Peroxidase .

► Plants, fungi and eukaryotes Unicellular organisms are equipped, in addition to the typical cyanide-sensitive electron transfer pathway, also with an alternative pathway for NADH oxidation , resistant to cyanide 19.2 ATP synthesis

► The flow of electrons through complexes I-III, I – IV leads to the pumping of protons through the inner membrane of the mitochondria, which makes the matrix basic relative to the intermembrane space . This proton cascade provides the energy (in the form of the proton motive force) for the synthesis of D ATP -1 ADP – pi by ATP synthesis ( FoF1 complex) in the inner membrane.

► ATp Synthesis performs “rotational catalysis”, where the flow of protons through Fo causes each of the three nucleotide-binding sites a – F1 to pass from the binding form ( ADP + Pi ) to the form binding ATp and from there to the form lacking the nucleotide.

► The creation of ATp on the enzyme requires little energy; The proton motive force is needed to push the G1’1\ molecule from its binding site on the synthesis .

ATP molecules synthesized and the number of 1/202 units converted to 20 and 1 (the 0/ P ratio ) is about 2.5 when the electrons enter the respiratory chain in complex I , and about 1.5 when the electrons enter through ubiquinone . This ratio may be slightly different in different organisms, depending on the number of subunits c in the complex Fo .

► Energy conserved in the proton cascade can drive the transport of solutes through a membrane up the concentration cascade.

► The inner membrane of the mitochondria is impermeable to 1(1\\) and 1(1\\), but equivalents of NADH are transferred from the cytosol to the matrix by one of two shuttles. Equivalents of NADH that reach the matrix with the help of the malate -aspartate shuttle enter the respiratory chain in complex I and ratio n – their P/O is 2.5; those that reach the matrix with the help of the glycerol 3-phosphate shuttle enter the respiratory chain through ubiquinone and their P/O ratio is 1.5.

19.3 The control of oxidative phosphorylation

► Oxidative phosphorylation is regulated according to the energy requirements of the cell.

[ ADP ] in the cell and the mass action ratio ([ ATP]/([ADP][Pi ]) are measures of the energy state of the cell.

► In hypoxic cells (suffering from a lack of oxygen), an inhibitory protein blocks the hydrolysis of ATP by reverse ATP activity synthesis , and prevents a drastic decrease in 1- [ ATP ].

► The adaptation reactions to hypoxia , in which 1-11 and 1 act as a mediator, slow down the transfer of electrons to the respiratory chain and change complex IV so that it works more efficiently at low oxygen concentrations.

ATP and C1(1c) concentrations determine the rate of electron transfer through the respiratory chain through a series of integrated controls on the respiratory processes, glycolysis and the citric acid cycle

19.4 Mitochondria in thermogenesis , steroid synthesis and programmed cell death

► In brown adipose tissue of newborns, the coupling between electron transfer and ATP synthesis is canceled, and the energy obtained from fuel oxidation is dissipated as heat.

► The hydroxylation steps in the synthesis of steroid hormones in steroid-producing tissues (adrenal gland, gonads, liver and kidneys) occur in specialized mitochondria.

► Cytochrome c Mitochondrial released into the cytosol participates in the activation of caspase-9, one of the proteases involved in apoptosis .

19.5 Mitochondrial genes: origin and effect of mutations

► A small part of the human mitochondrial proteins, 13 in total, are encoded in the mitochondrial genome and synthesized in the mitochondria. About 1,100 mitochondrial proteins are encoded in nuclear genes and are imported into the mitochondria after their synthesis.

► The evolutionary origin of mitochondria is in aerial bacteria, which entered into an endosymbiotic relationship with primitive eukaryotes .

► Mutations in the mitochondrial genome accumulate during the life of the organism. Mutations in the genes that encode the components of the respiratory chain, ATP Synthesis and the system that receives ROS , and even in genes <- tRNAs , may cause a variety of diseases in humans. The muscles, heart, brain, and p cells of the pancreas are usually most severely affected.

19.6 General characteristics of photophosphorylation

► Photosynthesis occurs in the chloroplasts of algae and plants. Chloroplasts are structures wrapped in double membranes and filled with stacks of membrane discs ( thylkoid membranes) that contain the biological molecules responsible for photosynthesis.

► The light reactions of photosynthesis are those that depend directly on light absorption; The resulting photochemistry takes electrons from 120 and passes them through a series of membrane-bound carriers. At the end of the process NADPH !- ATP are obtained .

► The carbon assimilation reactions of photosynthesis recycle C02 with the help of electrons D – NADPH and energy n – ATP . Trioses , hexoses and a wide variety of carbohydrates derived from them are obtained .

19.7 Light absorption

► A photon of visible light has enough energy to cause photochemical reactions, which in photosynthetic organisms ultimately lead to ATP synthesis .

► In the light reactions of plants, the absorption of a photon excites chlorophyll molecules and other pigments (auxiliary pigments), which direct the energy to reaction centers in the thylakoid membranes . In the reaction centers, excitation by light leads to a separation of charges that produces a strong electron donor (reducer) and a strong electron acceptor.

19.8 The main photochemical event: light drives the flow of electrons

► Bacteria have a single reaction center; In purple bacteria, this reaction center is of the pheophytin-quinone type , and in green sulfur bacteria it is of the Fe-S type .

► The study of the structure of the reaction center of purple bacteria yielded information about the flow of electrons driven by light from a special pair of

ATP synthesis through photophosphorylation

► In plants, both the water splitting reaction and the flow of electrons through the cytochrome complex b6 f involve pumping protons through the thylakoid membrane . The resulting proton motive force drives ATP synthesis by the CFoCF1 complex , which is similar to the mitochondrial FoF1 complex .

► The catalytic mechanism of CFoCF1 is very similar to that of ATP Synthesis in mitochondria and bacteria. Physical rotation driven by a proton cascade involves the synthesis of ATP at sites that pass through three conformations , one with a strong affinity <- ATP , one with a strong affinity <- ADP + Pi and one with a low affinity for both nucleotides. 19.10 The evolution of oxygenic photosynthesis

► The modern cyanobacteria evolved from an ancient organism that had two light systems, one of the type found today in purple bacteria and the other of the type found in green sulfur bacteria .

► Many photosynthetic microorganisms obtain electrons for photosynthesis not from water, but from donors such as H2S .

► Blues with light systems that operate in a column, and water fission activity that releases oxygen into the atmosphere, appeared on Earth about 2.5 billion years ago.

► Chloroplasts , like mitochondria, evolved from bacteria that lived in endosymbiosis in early eukaryotic cells . n – ATP Synthesis of bacteria, cyanobacteria, mitochondria and chloroplasts have a common evolutionary ancestor and a common enzymatic mechanism.

► In the modern archaeons , a completely different mechanism was developed to convert light energy into a proton cascade. In this mechanism, the light-absorbing pigment is retinal .