Biochem exam script according to guidelines.pdf

Chemistry and structures of macromolecules 1. Principles of structure of organic molecules (bonds, main atoms) ★ Biomolecules are compounds of carbon with different functional groups ★ The main atom in organic molecule is carbon: - Carbon can have single bonds with hydrogen atoms,...

Chemistry and structures of macromolecules 1. Principles of structure of organic molecules (bonds, main atoms) ★ Biomolecules are compounds of carbon with different functional groups ★ The main atom in organic molecule is carbon: - Carbon can have single bonds with hydrogen atoms, single and double bonds with oxygen and nitrogen atoms - The most important thing is that a carbon molecule always has 4 four bonds ★ The four most important elements in the living organism is hydrogen, oxygen, nitrogen and carbon ★ Functional groups: ★ The “R” in a structure can mean anything that could be attached so a structure/functional group ★ Isomer: molecule which has the same molecular formula but different structural or spatial arrangement of atoms within the molecule ★ Constitutional isomerism: - Chain isomers: the carbon skeleton is arranged differentially  - Position isomers: the functional group has moved its place - Functional isomers: the functional group has changed ★ Stereo Isomerism: - Geometric: isomerism which most typically involves C=C and how they are oriented in space. There can be cis configuration and trans configuration: - Optical: isomers which contain a chiral center, which is a carbon with four different atoms (or groups of atoms) attached to it. 2. Carbohydrates, general chemical properties, structure ★ They are the most abundant biomolecules in nature ★ Produced via photosynthesis in plants ★ Most carbohydrates are water soluble due to the possibility of forming hydrogen bonds between hydroxyl groups and water molecules ★ They have a variety of important functions for the human body: - energy source and energy storage - structural component - informational molecules - carbon supply for the synthesis of cell components ★ There are simple and complex carbohydrates:  - Simple: monosaccharides, they contain one polyhydroxy aldehyde or ketone unit for example; glucose, fructose, galactose - Complex: Disaccharides, contain two monosaccharide units, for example; lactose, sucrose and maltose Oligosaccharides: contain 3-10 monosaccharide units,for example; raffinose Polysaccharides: contain long chains of hundreds or thousands of monosaccharide units for example; starch and cellulose ★ If the monosaccharide has an aldehyde has functional group it is an aldose ★ If the monosaccharide has a ketone as function group it is a ketose ★ To determine whether a monosaccharide is a D- or L- sugar you need to look at the last chiral carbon, if the OH group is on the right side it is a D-sugar and if it is on the left side it is a L-sugar. ★ The actual difference is in the cyclic structures: In the D the OH groups on the sides of the cyclic structure both point downwards and in L the OH group on the left side points upwards! ★ Most monosaccharides in the living organisms are D-isomers ★ Most common carbohydrates in biochemistry: ★ To determine whether a sugar is α-sugar or 𝛽-sugar you need to look at the orientation of the last carbon and the OH group on anomeric carbon:  ★ The relevance of a sugar being either α-sugar or 𝛽-sugar lays in the digestions of carbohydrates and which enzyme can break which bond. ★ The bond which is created when two monosaccharides undergo condensation is called glycosidic bond ★ To form a specific di- or polysaccharide, specific hydroxyl groups must undergo a condensation reaction ★ The glycosidic bond tells us; which two monosaccharide units are connected, whether the monosaccharides are alpha or beta and which hydroxyl groups of which carbon atoms are connected. ★ Natural carbohydrates are usually found as polymers ★ Glycogen: - is a branched homopolymer of glucose - the glucose molecules form bonds from alpha 1=>4 - Function as the main carbohydrate storage form ★ Starch: - A mixture of two glucose homopolysaccharides; Amylose, unbranched polymer which has alpha 1 =>4 linked residues, Amylopectin, branched - Main storage form of polysaccharides in plants ★ Cellulose: - Linear homopolysaccharide of glucose - Glucose monomers form beta 1=>4 linked chains - Most abundant polysaccharide in nature, water insoluble and though Chemical properties of carbohydrates: ★ Carbohydrate oxidation: the oxidation leads to increase in amount of C-O bonds and decrease in H-C bonds ★ Reducing sugars: - Is a sugar which as a free aldehyde or ketone which can act as a reducing agent - Have a free anomeric carbon - All monosaccharides and disaccharides (except sucrose) are reducing sugars - Fehling’s test or Tollen’s can be used to detect reducing sugars ★ Non-reducing sugars: sugar which does not contain a free aldehyde or ketone when the cyclic form is opened, they can’t act as a reducing agent. ★ Carbohydrate reduction: opposite happens then in oxidation ★ Condensation of carbohydrates ★ Hydrolysis of carbohydrates: mainly occurs with the help of enzymes, also the same thing can be achieved by heat and concentrated acid solutions ★ Biochemical processes involving carbohydrates: gluconeogenesis, glycolysis, glycogenesis, glycogenolysis, citric acid cycle, ETC, fructolysis, pentose phosphate pathway 3. Amino acids, general chemical properties, structure ★ Functions of proteins: - Catalysis  - transport - structure - motion ★ Amino acids are the building blocks of proteins ★ There can be α, 𝛽 and ɣ etc amino acids this depends on to which carbon the amino group is attached to ★ Alpha-amino acids: - most common amino acids - has 4 functional groups: acidic carboxyl group, basic amino group and a unique R-group which changes depending on the amino acid -There can be L and D alpha-amino acids -The amino acids are classed based on their R-group substituents -There are 8-9 essential amino acids, which cannot be produced by the human body. They are: Leucine, Isoleucine, Lysine, Methionine, Phenylalanine, Threonine, tryptophan, valine, (histamine) ★ Under normal conditions in the human body the amino acids and proteins are charged, amino group is in ionized form and so is carboxylic acid group 4. General bonds found in proteins, structure of proteins ★ Functions of proteins: - Structure - Transport - Energy - Maintaining colloid-osmotic pressure - Synthesis of peptide hormones - Regulating blood clotting - Immunoglobulins ★ Any two amino acids or peptide can undergo a condensation reaction where the carboxylic group reacts with the amino group forming a peptide bond ★ There is a N-terminal which is the end of the amino group and a C-terminal which is the end where the carboxylic group is located ★ The numbering and naming starts from the N-terminal ★ There are four levels to the protein structure: Primary, secondary, tertiary and quaternary ★ Proteins have specific three dimensional conformation which gives them a specific biological function to fulfill  ★ Primary structure: - It is a linear structure of amino acids which are bonded by peptide bonds - Rotation around the peptide bond is not allowed - Rotation around bond that are connected to the alpha carbon is allowed ★ Secondary structure: - Hydrogen bond interactions between peptide bonds - There is two common arrangements: alpha helix, beta sheet ★ Tertiary structure: - Refers to the overall spatial arrangement of atoms in the protein - It is stabilized by weak interactions between amino acid side chains - There is two major classes; fibrous and globular ★ Quaternary structure: - It is formed by the assembly of individual polypeptides into a larger functional cluster ★ Protein classification can be done based on various factors: - Chemical composition; simple,conjugated,derived - Shape; fibrous or globular - Biological function; enzymes, structural proteins, transport, carrier proteins etc - Solubility; can either be water-soluble or lipid-soluble ★ Proteins will fold to the lowest-energy fold ★ Denaturation: the protein loses structural integrity which is accompanied by loss of activity.  ★ Denaturation only affects the secondary,tertiary or quaternary structures! ★ Denaturation occurs when there is a disruption to the bonds that stabilize secondary,tertiary or quaternary structures ★ Denaturation can be caused by - Heat, it will disrupt the hydrogen bonds and hydrophobic attractions between R groups - Acids and bases, disrupt hydrogen bonds and salt bridges - Organic compounds, disrupt the hydrophobic interactions between R groups - Heavy metal ions, disrupt salt bridges, disulfide bonds - Agitation will disrupt hydrogen bonds and hydrophobic interaction between the R groups by stretching the polypeptide chain. 5. Lipids, general chemical properties, structure ★ They are organic molecules which are characterized by low solubility in water and being relatively hydrophobic ★ Classification of lipids: ★ Functions of lipids: - energy storage - insulation - water repellent - membrane structure - cofactors for enzymes - signaling molecules - antioxidants - hormone synthesis FATTY ACIDS: ★ Chains of hydrocarbons with a carboxylic acid group ★ Most have an even number of carbons and are unbranched ★ There can be saturated fatty acids, there are no double bonds between the carbons and then there can also be unsaturated fatty acids, which means there are double bonds between the carbons. ★ Furthermore they can be monounsaturated or polyunsaturated ★ ⍵-fatty acids (omgea fatty acids): - This shows the position of the first double bond in the hydrocarbon chain - The numbering starts from the hydrocarbon chain side  - Looks at a fatty acid from more of a biological or biochemical aspect, observing residue or fragments of a fatty acid left/bonded to a structure - There are three main types of omega fatty acids: ⍵-3, ⍵-6 and ⍵-9 - ⍵-3, ⍵-6 are both polyunsaturated fatty acids and they are essential fats because they aren’t produced by the human body - ⍵-9 are monounsaturated fatty acids, they can be produced by the human body ★ Δ-fatty acids: - this system shows all the double bonds in the hydrocarbon chain - The numbering if the carbons start from the main functional group - Looks at fatty acids from more of a classic chemical aspect ★ They can have cis- and trans- configuration ★ Their solubility in water will decrease as the hydrocarbon chain becomes longer ★ The melting point will decrease as the chain length decreases, also decreases when the amount of double bonds increase TRIACYLGLYCEROLS (TAGs): ★ Glycerol+fatty acids=TAGs ★ Formed via condensation reaction ★ There are ester bonds formed in TAGs ★ Fats= solid triacylglycerols ★ Oils= liquid triacylglycerols ★ TAGs is the main storage form of lipids in the body ★ The advantage of fats over polysaccharides: - Fatty acids carry more energy per carbon - Fatty acids carry less water per gram - Fats are for long-term energy needs GLYCEROPHOSPHOLIPIDS: ★ Glycerol base+two fatty acids+phosphate group+head-group substituent= glycerophospholipid ★ Phospholipids are the major class of membrane lipids SPHINGOLIPIDS: ★ sphingosine+fatty acid+head-group substituent ★ There is an amide linkage between the fatty acid and sphingosine ★ There are glycosphingolipids which can be used partly to determine the blood group, the type of sugars which are on the head groups are used. STEROLS and CHOLESTEROL: ★ The structure: ★ Cholesterol and related sterols are located in the membranes of most eukaryotic cells, their function is to: - modulate fluidity & permeability - thicken plasma membrane - cholesterol is used in the synthesis of steroid hormones ★ Cholesterol can be obtained in the food or it can be synthesized in the liver ★ Some other important lipids are: waxes, biologically active lipids (lipid soluble vitamins), terpenes & terpenoids 6. Polar, nonpolar functional groups, influence on hydrophobicity of molecule ★ The different properties of the functional groups usually determine the physiological role of the molecule and the type of reactions that occur. ★ Acidic groups: Contain a proton which can dissociate which leaves the remainder of the molecule as an anion, functional groups which are acidic: carboxylate group, phosphate group and sulfate group ★ Basic group: can accept an additional proton leaving them with a positive charge, for example amines ★ Polarity of a bond depends on the electronegativity of the atoms which form it. ★ A covalent bond is nonpolar when the atoms that form it are identical or of similar electronegativity. ★ A covalent bond is polar when the atoms that form it have different electronegativity. ★ “Lika löser lika”!  ★ Solubility of organic molecules in water depends on the portion of polar to nonpolar groups attached to the carbon-hydrogen skeleton and their relative positions inn the molecule - Polar groups or molecules are hydrophilic - Nonpolar groups or molecules are hydrophobic Properties of functional groups: ★ Alcohol: - There is primary, secondary and tertiary alcohols - Contain hydroxyl group - Exhibit intermolecular hydrogen bonding ★ Ketones and aldehydes - Both contain carbonyl group - Aldehydes have at least one hydrogen bonded to the carbonyl group - Ketones have two alkyl groups bonded to the carbonyl group - Ketone bodies are important for the body, they are derived from fatty acids through ketogenesis, three main ketone bodies: acetone, 3-beta-hydroxybutyrate and acetoacetate - ★ Carboxylic acids - Contain a carboxyl group - Proton donors - When dissolved in water there occurs an acid-base equilibrium; there will be formed a conjugate base so a carboxylate anion - When reacting with bases it will form water-soluble salts - In the body the most important one is carbonic acid which has a function in the respiratory system, it completes the chemical process that allows us to breathe. ★ Amines - Nitrogen containing compounds - They can be classified as primary, secondary or tertiary amines - Amines are bases - When reacting with water, the amine accepts a proton forming its conjugate acid - Amines importance in the human body: they are involved in amino acid synthesis, neurotransmitters, urea cycle ★ Amides and esters - Esters are carbonyl compounds which contain alkoxy group, COOR - Ester bonds are common in lipids - Amides are carbonyl compounds which contain nitrogen, CONR  - Amide bonds are also known as peptide bonds Main reactions of organic compounds: ★ Oxidation-reduction reactions ★ Substitution reactions ★ Elimination reactions ★ Hydrolysis ★ Condensation Enzymology 7.Enzymes: chemical nature, structure. Simple and complex enzymes ★ Enzymes are catalysts which means that they increase reaction rates without being used ★ Metabolites have many potential pathways for decomposition but enzymes make the desired one most favorable ★ Enzymes do not affect the equilibrium and they cannot either affect the free energy of the reaction ★ Enzymes can decrease the transition state, it will be more easily achieved ★ Some enzymes need cofactors in order for them to work ★ Cofactors which are tightly bound to the enzyme are called prosthetic groups ★ Holoenzyme= apoenzyme+cofactor ★ Simple enzyme: enzymes which are only composed of protein ★ Complex enzyme: enzymes which are composed of proteins plus a relatively small organic molecule, also known as holoenzyme ★ Catalytic mechanisms which enzymes may use: - acid-base catalysis: take or give protons - covalent catalysis: change the reaction paths - metal ion catalysis: usage of redox cofactors, 𝑝𝐾𝑎 shifters 8. Enzyme classification (7 classes) ★ Enzymes are divided into different types of classes depending on what type of mechanism they have Class Reaction catalyzed Enzyme example EC 1: oxidoreductases catalyze dehydrogenase, oxidase oxidation/reduction reactions; transferring H and O atoms or electrons  from one substance to another one EC 2: transferases transferring the functional transaminase, kinase group from one substance to another, the group can be a methyl-,acyl-, amino- or phosphate group EC 3: Hydrolases Formation of two lipase, amylase, products from a substrate peptidase, phosphatase by hydrolysis EC 4: Lyases Non-hydrolytic addition decarboxylase or removal of groups from substrates, bonds that may be cleaved: C-C, C-N, C-O or C-S EC 5: Isomerases Intramolecular isomerase, mutase rearrangement => isomerization changes in a molecule EC 6: Ligases Join together two Synthetase molecules by synthesis of new C-C, C-N, C-O or C-S bonds with simultaneous breakdown of ATP EC 7: Translocases Catalyze the movement of Transporter ions or molecules across the membranes or their separation within membranes 9. Enzyme activity and its influencing factors: temperature, pH, metal ions, [E], [S] ★ Factors which have an influence on the enzymes activity can be grouped as following: - Quantitative enzyme activity regulation : how much enzyme - Qualitative enzyme activity regulation: how well the enzymes work - Non-specific : all enzymes can be affected, for example temperature, strong acid or base, concentrated inorganic salt, organic solvent => denaturation of the enzyme - Specific: specific enzymes are affected, the enzymes can be either activated ( called activators, can increase enzyme activity) or inhibited ( called inhibitors and will decrease enzyme activity) - Reversible - Non-reversible  ★ The perfect temperature for enzymes is 37-38 degrees of celsius ★ pH also has an effect on the enzymes, every enzyme has an pH optimum 10. Enzyme substrate specificity (absolute, bond, group, stereo) ★ An enzyme can catalyze reactions with one or multiple substrates depending on the buildup of the active site. ★ Absolute substrate specificity: enzyme can only catalyze reactions with only one substrate, for example lactase ★ Relative substrate specificity: enzyme can catalyze reactions with several substrates, for example trypsin and chymotrypsin ★ Stereo specificity: enzymes which distinguish substrates based on optical or steric isomers, for example ɑ-amylase and cellulase which will only cleave beta 1,4 bonds ★ Bond specific enzymes: will act on particular type of chemical bonds regardless of the rest of the molecular structure, for example pancreatic lipase which can cleave ester bonds in various TAGs ★ Group specific enzymes: enzymes which will only act on molecule with specific functional groups, for example trypsin it will only cleave peptide bond if they are after basic amino acid ★ Exohydrolases: enzymes which will cleave bonds at the ends and starts of chains ★ Endohydrolases: enzyme which will cleave bonds in the middle of a chain 11. Enzyme kinetics Vmax, Km ★ Enzyme kinetics: study of the rate at which enzymes react ★ Factors which affect enzymatic reactions: - the enzyme - substrate - effectors - temperature ★ Vmax: the maximal velocity of enzyme, expressed in mol/min/mg of protein ★ Km: Michaelis constant, which is substrate concentration at which enzyme achieves half of its maximal speed, it is used to describe the enzymes affinity to the substrate ★ High Km means the enzyme has a low affinity to the substrate ★ Low Km means that the enzyme has a high affinity to the substrate ★ In competitive inhibition: no change in Vmax but Km will be increased, in Lineweaver-Burk: lines will cross at y-axis, affinity between enzyme and substrate is decreased ★ In uncompetitive inhibition: the Vmax will be decreased, Km will also be decreased, Lineweaver-Burk: lines are parallel, the affinity between enzyme and substrate is increased ★ Mixed inhibition: decreases Vmax and a noticeable change in Km will occur, the affinity between enzyme and substrate will be increased Uncompetitive Mixed  Competitive 12. Specific activators and inhibitors of E – proteolytic cleavage, covalent modification, etc /13. Specific inhibition of enzymes – reversible and irreversible, application in medicine ★ Proteolytic cleavage (activator): the enzyme is first secreted in inactive form and when the peptide bond is cleaved the enzyme will be active, this action is irreversible, for example trypsinogen (inactive)=> proteolytic cleavage => trypsin (active) ★ Covalent modification: additional structures are added to the enzyme by covalent bond which leads to a change in its structure, enzymes can be either activated or inhibited. This effect is usually reversible, for example phosphorylation, methylation ★ Competitive inhibition: there is another substance which is competing for the active site with substrate, depending on the bonds which are formed it can be reversible or irreversible. It is reversible if the bond is not strong and the enzyme is capable of getting rid of the other substance. It is irreversible if the bonds that are formed are strong => competitive. ★ Mixed inhibition: binds enzyme with or without substrate - binds to regulatory site - inhibits both substrate binding and catalysis ★ Uncompetitive inhibition: inhibitor only binds to ES complex - doesn’t affect substrate binding - inhibits catalytic function ★ Methotrexate is a competitive inhibitor and it is a chemotherapy agent and immune system suppressant. It is used to treat cancer, ectopic pregnancy etc. It stops the synthesis of tetrahydrofolic acid 14. Allosteric regulation and effectors ★ Allosteric site: additional binding site in an enzyme ★ These allosteric sites allow effectors to bind to proteins often causing a change in the conformation of the protein ★ Allosteric activators: effectors which enhance the proteins activity ★ Allosteric inhibitors: effectors which decrease the proteins activity ★ The allosteric effectors work in feed-back and feed-forwards loops Digestion 15. Digestion as an enzymatic hydrolysis ★ There are a lot of enzymes which are required to metabolize the different macronutrients we eat. ★ Different enzymes work on different types of bonds that keep the nutrients together ★ There are different organs which produce different types of enzymes, the organs that produce enzymes are: saliva, stomach, pancreas, gallbladder ★ Stomach: - Gastric juice is produced by secretion from parietal cells, chief cells, and mucous cells in the stomach wall lining - Parietal cells are responsible for secreting HCL - Gastric juice is highly acidic and its functions are: - kill microorganisms - denature proteins - activates enzyme pepsinogen to its active form pepsin - Gastric epithelium secretes intrinsic factor which is needed for the absorption of B12 - HCL secretion is stimulated by gastrin, histamine, parasympathetic nervous system - Gastrin secretion in turn is stimulated by protein, peptides and AAs ★ Pancreatic juice: - Composed mainly of water but also electrolytes and enzymes (glycosidases, peptidases, esterases) - The pH is 7.6-8.3 - The secretion of pancreatic juice is regulated by secretin and cholecystokinin ★ Cholecystokinin (CCK): - Produced by enteroendocrine cells in the small intestine - CCK secretion is stimulated by a mixture of amino acids and polypeptides, gastric acid and fatty acids - CCK in turn stimulates pancreatic juice secretion, gallbladder contraction, bile release, slows gastric emptying and inhibits food intake ★ Secretin: - Produced by S cells - Main task is to stimulate pancreatic juice secretion with a high concentration of bicarbonate content ★ Small intestine, intestinal juice: - Intestinal fluid is formed by pancreatic juice, intestinal juice and bile ★ Digestion enzymes belong to the enzyme class of hydrolases 16. Digestion of carbohydrates ★ Carbohydrates are broken down until monosaccharides and cannot be further hydrolyzed ★ Monosaccharides are the main form of carbs that are absorbed in our body ★ Glycogen is a storage form of carbohydrates, there is two forms in which it is stored: Muscle glycogen; it is used during exercise and liver glycogen; provides glucose to the cells throughout the body via the bloodstream  ★ There is two main steps to carbohydrate digestion: 1. Intraluminal hydrolysis of starch into oligosaccharides by pancreatic and salivary amylases 2. membrane digestion of oligosaccharides into monosaccharides by brush-border enzymes. DIGESTION: ★ Oral cavity: - The enzyme that is secreted here is salivary ɑ-amylase - The enzyme is a endoglycosidase (= breaks down internal bonds) - The bonds that are broken are: ɑ-1,4 linkages - The product will be disaccharides ★ Small intestines: - Pancreatic ɑ-amylase: - It is a endoglycosidase and it cleaves ɑ-1,4 linkages - The products are maltose and maltotriose from amylose and maltose, maltotriose and ɑ limit dextrins from amylopectin and glycogen - Glucoamylase: - It is a exoglycosidase and it cleaves ɑ-1,4 linkage - Products which are gotten ar shorter oligosaccharides and glucose - Sucrase-isomaltase complex: - Exoglycosidase which cleaves ɑ1-β2;ɑ-1,6, ɑ-1,4 linkages - Can also cleave disaccharide maltose with ɑ-1,4 glycosidic bond - β-glycosidase: - Exoglycosidase which cleaves β1-4 linkages - Trehalase: - Exoglycosidase which cleaves ɑ-1,1 linkages - It is absolute specific - The product will be 2 glucose molecules ★ Absorption of monosaccharides occurs in the small intestine ★ In the jejunum glucose, galactose and fructose are absorbed ★ Fructose is absorbed on the apical cell membrane surface by the GLUT5 transporter and glucose+galactose is absorbed SGLT1 transporter 17. Digestion of lipids ★ The enzymes which hydrolase the bonds in lipids are esterases ★ Oral cavity: Lingual lipase - It is more important for the breakdown of milk fats in newborns - Cleaves the fatty acyl ester bond at position 3 - Hydrolyzes short- and medium-chain fatty acids (containing 12 or fewer carbon atoms) ★ Stomach: Gastric lipase - Secreted by chief cells - Low pH, optimum is 4-6, and cleaves the bonds at position 3 - Activity is higher towards short-and medium chain fatty acids ★ Pancreatic enzyme: Pancreatic TAG lipase  - Is secreted in its active form - Needs a cofactor to function, known as colipase - It hydrolyzes ester bonds in TAGS at first and third position of the glycerol bond - Bile salts can inactivate ★ Phospholipase A2: - It is secreted from pancreas as a proenzyme and is activated by trypsin - Breaks down phospholipids into lysolecithin and fatty acid - It requires bile salts and calcium ions for activity ★ Pancreatic lipase related protein 2 - Breaks down galactolipids mostly ★ Carboxyl ester lipase - It is a pancreatic enzyme - Secreted in its active form and breaks down cholesterol esters into free cholesterol and fatty acids - It can also break down ester linkages in TAGs, galactolipids and phospholipids 18. Digestion of proteins ★ All the digestion enzymes belong to the group of hydrolases ★ There are endopeptidases and exopeptidases ★ To endopeptidases belong pepsin, trypsin, chymotrypsin and elastase ★ To exopeptidases belong; carboxypeptidases A&B, aminopeptidase, dipeptidase ★ Protein digestion begins on the stomach!!! ★ In the stomach: Pepsin - It is a endopeptidase - It is active when pH is 1-2 - Cleaves peptide bonds after aromatic AAs from N-terminus ★ Small intestines: Pancreatic peptidases - Endopeptidases (from the N-terminus): - Trypsin - Chymotrypsin, which cleaves aromatic AAs - Elastase, cleaves small AAs malabsorption. Carbohydrates 21. Glycolysis ★ The full oxidation of glucose yields a good amount of energy ★ The process is a catabolic process ★ Glucose is converted by many different enzymes into pyruvate ★ Pyruvate can then be further aerobically oxidized ★ Pyruvate can also be used as a precursor in biosynthesis ★ Glycolysis takes place in every single cell in the human body, especially in the brain and muscles ★ It takes place in the cytosol ★ Glycolysis is divided into two phases, the first one being the preparatory phase. ★ In the preparatory phase: glucose => glyceraldehyde 3-phosphate + dihydroxyacetone phosphate ★ The committed step of glycolysis is when fructose 6-phosphate is converted into fructose 1,6-phosphate ★ The second phase of glycolysis is the payoff phase, where glyceraldehyde 3-phosphate+dihydroxyacetone phosphate is converted into pyruvate ★ The rate limiting steps are: - glucose converted into glucose 6-phosphate by hexokinase  - fructose 6-phosphate converted into fructose 1,6-bisphosphate by phosphofructokinase-1 ★ The first step which yields energy is when GA3P is oxidized by glyceraldehyde-3-P dehydrogenase next step where there is energy given is when ATP is being made by phosphoglycerate kinase and next step where the 2nd ATP is generated is in the last step of glycolysis ★ The fate of pyruvate: in aerobic condition it will be made into acetyl-CoA, in anaerobic pyruvate will go into producing lactate ★ Regulation of glycolysis: Hexokinase: - Stimulated by glucose - Insulin stimulates; when blood glucose levels are down insulin is released in order to to promote glycolysis - Inhibited by glucose-6-P; feed-back inhibition - Glycogen inhibits; released when blood glucose levels are high to stimulate gluconeogenesis Glucokinase: - Glucose stimulates - Insulin stimulates; when blood glucose levels are down insulin is released in order to to promote glycolysis - Fructose-6-P inhibits Phosphofructokinase-1: - ADP/AMP, ribulose-5-P act as stimulators - Fructose-6-P acts as stimulator; in the presence of PFK II F6P will be converted into F2,6BisP and in turn will stimulate F6P =>more ATP - Insulin acts as a stimulator; it will dephosphorylate PFK-2 and F-2,6-BP. - stimulation of PFK-2 → F6P→ F-2,6-BP which will stimulate PFK-1 - ATP,PEP acts as inhibitors - Citrate is also an inhibitor: signals that there is a lot of CAC activity - Glucagon is a inhibitor; it inhibits PFK-2 by phosphorylation, glucagon will stimulate production of F-2,6-BP by phosphorylating it and this will lead to an increase of F-6-P and will ultimately inhibit PFK-1 Pyruvate kinase: - Alanine is an inhibitor: will signal that there is enough pyruvate - Glucagon will act as an inhibitor - ATP acts as an inhibitor - Acetyl-CoA acts as an inhibitor; signals high activity of CAC - Insulin acts as a stimulator; it increases pyruvate kinase synthesis and dephosphorylation - Fructose-1,6-BP acts as a stimulator; feed forward reaction. ★ Glycolysis produces 2 ATPS and 2 NADH:s 22. Anaerobic glycolysis and buffer systems ★ Anaerobic glycolysis = lactic acid fermentation ★ It is the reduction of pyruvate into lactate under anaerobic conditions, this is a reversible reaction ★ It occurs in vigorously contracting muscles and in erythrocytes (it is the only way for energy production to occur in erythrocytes because they lack mitochondria) ★ Lactate levels is a predictor for the survival of cancer patients ★ Anaerobic glycolysis: 2 Pyruvate ↔ 2 lactates under the influence of lactate dehydrogenase, NADH=>NAD+ ★ Regulation: - increased NADH/H+ stimulates - anaerobic conditions stimulate - breakdown of ethanol stimulates: it will stimulate the conversion of pyruvate into lactate - Increased levels of lactate will act as an inhibitor ★ Buffer systems are used to maintain the blood pH levels ★ ★ Acidosis is when the blood pH is 7.45 ★ Hemoglobin buffer system works in erythrocytes and it deals with the O2 levels and CO2 levels + ★ 𝐶𝑂2 + 𝐻2𝑂↔𝐻2𝐶𝑂3↔𝐻 + 𝐻𝐶𝑂3 lungs carbonic anhydrase liver ★ The buffer systems are regulated through gas exchange 23. Fermentation. Breakdown of ethanol by liver ★ Ethanol fermentation occurs in yeast and bacteria ★ ★ Humans lack pyruvate decarboxylase ★ Ethanol is broken down by the liver: ★ Short term consequences of alcohol intake: - Depletes the cellular supply of NAD+ - Hypoglycaemia - High levels of lactate - Oxidation of lactate to pyruvate is inhibited ★ Long term consequences of alcohol intake: - Addiction - Obesity - Liver cirrhosis - stomach ulcers 24. Oxidative decarboxylation of Pyruvate ★ Oxidative decarboxylation of Pyruvate is the process when pyruvate is converted into acetyl-CoA ★ It takes place in every single cell in the human body in the matrix of mitochondria  ★ ★ Enzyme 1: - will firstly decarboxylate pyruvate in to an aldehyde - secondly oxidation of hydroxyethyl to an acetate ★ Enzyme 2: - thirdly the formation of acetyl-CoA which is the first product of this pathway ★ Enzyme 3: - fourth step is reoxidation of lipoamide cofactor - fifth step is the regeneration of oxidized FAD cofactor and this produces NADH 25. Citric acid cycle ★ This is a catabolic process ★ ★ The conversion of oxaloacetate+acetyl-CoA to citrate by citrate synthase is a rate limiting step ★ The activity of the CAC largely depends on oxaloacetate ★ One turn of the CAC gives 10 ATPs and since there is 2 pyruvates and therefore 2 turns of the CAC will occur and give 10 ATPs  Regulation of CAC: ★ General mechanisms: - it is activated by substrate availability - it is inhibited by product accumulation - Any of the regulatory steps in the CAC can be rate limiting under specific conditions - It is affected by overall products produced by the pathway (ATP and NADH+H+) ★ Pyruvate dehydrogenase complex: - Inhibitors are: ATP,acetyl-CoA, NADH, fatty acids - Stimulators: AMP, CoA, NAD+ and calcium ions ★ Citrate synthase: - Inhibitors: NADH, succinyl-CoA, citrate and ATP - Stimulators: ADP ★ Isocitrate dehydrogenase: - Inhibitors: ATP - Stimulators: calcium ions and ADP ★ ɑ-ketoglutarate dehydrogenase complex: - Inhibitors: succinyl-CoA, NADH - Stimulators: calcium ions 26. Electron transport chain ★ Oxidation reactions are done by enzyme class oxidoreductases ★ Dehydrogenases use NAD and FAD:s as cofactors ★ Electrons in the cells are carried by NADH+H+ and FADH2 ★ ATP can be formed by substrate level phosphorylation or oxidative phosphorylation ★ The principle behind the ETC is oxidative phosphorylation ★ The ETC creates a electrochemical gradient which leads to the formation of ATP ★ There is 4 complexes which make up the ETC Complex I: NADH: Ubiquinone Oxidoreductase - It is a proton pump - It accepts 2 electrons from NADH=>NAD+ where the acceptor is FMN - FMN=>FMNH2 - About 4 protons are transported per on NADH Complex II: Succinate dehydrogenase: - It will accept 2 electrons from FADH2, oxidizing it back into FAD - It does not transport protons - FMN will pick up the 2 electrons making it FMNH2 ★ Both complex I and II transfer their electrons to a small mobile electron carrier which is called ubiquinone, it is reduced to QH2 and it travels through the membrane to deliver electrons to complex III Complex III: cytochrome c oxidoreductase - Here occurs the transfer of electrons from CH2 to cytochrome c, which is an electron carrier, this process is called the Q cycle  - cytochrome c will carry 1 electron from cytochrome 𝑏𝑐1complex to cytochrome oxidase Complex IV: Cytochrome Oxidase - It is a membrane protein - Contains copper ions: 𝐶𝑢𝐴 and 𝐶𝑢𝐵 - The electrons are transferred from cytochrome c to oxygen which is then reduced to water - 4 electrons are used to reduce 1 oxygen molecule into 2 water molecules - There are 4 additional protons picked up from the matrix and they are passed to the intermembrane space. ★ The ATP synthesis is driven by proton-motive force ATP synthase: - Has two functional units: F1: is the catalytic unit: catalyzes hydrolysis of ATP F0: proton pump, it transports H+ from IMS to the matrix → dissipating the proton gradient ★ The NADH can’t just freely enter the mitochondria, there is used two shuttles for this: the Malate-Aspartate shuttle and Glycerol-3-Phosphate shuttle  Regulation: - ADP acts as a stimulator - NADH/H+ acts as a stimulator - Inhibition of F1: will prevent hydrolysis of ATP during low oxygen ★ The inhibition of oxidative phosphorylation will lead to the accumulation of NADH and this causes a feed-back inhibition cascade up to PFK-1 in glycolysis ★ Each NADH+H+ will give 2.5 ATPs and each FADH2 will give 1.5 ATPs 27. Free radicals and antioxidants (enzymatic and non-enzymatic) ★ Free radical: it is a molecule or a part of a molecule which contains one or more unpaired electrons in the atomic or molecular orbitals ★ ROS (reactive oxygen species): an unstable molecule which contains oxygen and it reacts easily with other molecules in the cell. ★ Superoxide anion is considered a primary ROS, most of it is produced by the ETC,other sources include: NAD(P)H oxidases, ER, 𝑃450 ★ Oxidative stress is the result of an imbalance between levels of antioxidants and reactive oxygen species ★ Antioxidants: compounds which inhibit oxidation, there are enzymatic and non-enzymatic antioxidants ★ Endogenous antioxidants: antioxidants which are produced in our own body, for example superoxide dismutase, catalase ★ Exogenous antioxidants: antioxidants which are gotten from our diet, for example: beta-carotene, vitamin C, vitamin E etc ★ Enzymatic antioxidants: they work by breaking down and removing free radicals, they convert the dangerous oxidative products to hydrogen peroxide and then to water through a multi-step process. For example: superoxide dismutase, glutathione peroxidase and catalase ★ Non-enzymatic antioxidants: they work by interrupting free radical chain reactions, for example: vitamin C, E, carotenoids, glutathione ★ The reason for why free radicals are harmful is because they adversely alter lipids, proteins, and DNA and trigger a number of human diseases 28. Glycerol-3 phosphate shuttle and malate-aspartate shuttle Malate-aspartate shuttle:  ★ This shuttle is dominant in liver, kidney and heart ★ The reason for why we need these shuttle is to transport the electrons from NADH from the cytosol into the mitochondria Glycerol-3-Phosphate: ★ If the malate-aspartate shuttle is used the total yield of ATPs is 32 and if the glycerol-3-Phosphate shuttle is used the total yield of ATP is 30 29. Gluconeogenesis ★ It is the synthesis of glucose from noncarbohydrate precursors ★ It takes place primarily in the liver and to a small extent in the renal cortex and enterocytes ★ It follows the exact same pathway as glycolysis except for in these steps:  ★ Reversible reactions are used ★ There is no ATP generated during gluconeogenesis ★ Animals can produce glucose from: lactate, amino acids which can be converted to citric acid cycle intermediates and glycerol 30. Glycogen metabolism ★ Place of action: primarily in the liver and muscles in the cells cytosol ★ The function of glycogen in the muscles is to be a energy source ★ The function of glycogen in the liver is to regulate the blood glucose levels ★ Glycogenesis: the making of glycogen from glucose ★ The elongation of the glycogen chain occurs to make glycogen more soluble and to increase the number of non-reducing ends Glycogenolysis: the breakdown of glycogen ★ It ensures quick energy release ★ Importance: to give quick energy in the muscle or to rise the blood glucose levels incase they are low  ★ Regulation of Glycogen synthesis and degradaion: ★ Glycogen phosphorylase: it is active when phosphorylated and inactive when dephosphorylated Allosteric regulation: - Glucose-6-P acts as an inhibitor - Increased concentrations of ATP inhibits - High blood glucose levels will inhibit the synthesis in the liver - Increase concentrations of AMP will stimulate the breakdown - Calcium ions act as stimulators only in muscles Hormonal regulation: - Hormones will bind to G-receptors to stimulate cAMP which will activate protein kinase A when blood glucose levels are low - PKA stimulates phosphorylase kinase b => activates phosphorylase a => phosphorylates glycogen phosphatase => activates glycogen breakdown - Phosphoprotein phosphatases act as inhibitor => dephosphorylates phosphorylase kinase a => inactivation and also it dephosphorylates glycogen phosphorylase => inhibited ★ Glycogen synthase: wants to make glycogen, it is active when dephosphorylated and inactive when phosphorylated Allosteric regulation: - Glucose-6-P acts as a stimulator, blood glucose levels are high and we want to store glucose Hormonal regulation - Protein kinase A phosphorylates glycogen synthase => inactive  - Insulin (when blood glucose levels are high): activates of phosphoprotein phosphatase => dephosphorylates glycogen synthase => activated ★ Insulin stimulates glycogenesis ★ Epinephrine and glucagon stimulate glycogenolysis 31. Pentose phosphate pathway ★ Place of action: In every single cell in the human body but it has a higher importance in tissues which are rapidly dividing and exposed to ROS and synthesize fats more intensively ★ It takes place in the cells cytosol ★ The importance of Pentose phosphate pathway - Main products: ribose-5-phosphate and NADPH+H+ - reductive biosynthesis of fatty acids (occurs in liver, adipose tissue, lactating mammary glands), cholesterol and steroid hormones (occurs in liver, adrenal glands and gonads) - Repairs oxidative damage caused by ROS - Ribose-5-phosphate is a biosynthetic precursor for nucleotides: used in the synthesis of DNA & RNA or synthesis of coenzymes ★ There is two phases of this pathway: the non-oxidative phase and oxidative phase ★ Oxidative phase: 1. Oxidation 2. Hydrolysis 3. Oxidation and decarboxylation 4. Isomerization - This is the end point in rapidly dividing tissues  ★ Non-oxidative phase: - No energy is used in this phase Regulation: ★ The ratio of NADPH+H+/NADP determines glucose-6-P usage by PPP or glycolysis - Glucose-6-P dehydrogenase activity depends on NADPH+H+, if low levels enzyme will be stimulated and if high levels the enzyme will be inhibited ★ The oxidative phase is controlled by the level of NADP+ ★ The non-oxidative phase is controlled by the need of pentose - cells will enter the non-oxidative phase when it needs NADPH+H+ for synthesis of G6P 32. Metabolism of fructose ★ Place of action: high rate of fructose oxidation occurs in the liver, kidney and small intestines in the cells cytosol ★ Fructokinase C is an essential enzyme for fructose metabolism, it catalyzes the conversion of fructose → Fructose-1-P ★ Aldolase B is an essential enzyme also but in the liver, it catalyzes the rate limiting reaction of fructolysis ★ It replenishes glycogen stores ★ When there is excess it is used to synthesize TAGs which can lead to fatty liver in the long run 33. Metabolism of galactose ★ Place of action: almost only in the liver in the hepatocytes cytosol ★ Importance: produce intermediates of glycolysis/gluconeogenesis or glycogenesis 34. Most common pathologies related to carbohydrate metabolism ★ In tumor cells glycolysis takes place at an elevated rate ★ Cyanide is a poison because it causes the inhibition of complex IV in the ETC and this will lead to the stopping of the ETC and gradient would decrease ★ Symptoms of cyanide poisoning: dizziness, headache, nausea vomiting ★ Treatment for cyanide poisoning: remove clothing that may have cyanide on them, washing yourself , specific antidotes ★ If rotenone would be present in the mitochondria, complex I will be blocked which leads to 4 protons 4 less ★ Lactic acidosis: - Severe acidosis symptoms will lead to: labored and deep breathing, nausea,vomiting and diarrhea, generalized muscle weakness, headache and drowsiness  - Treatment: depends on what caused the acidosis, it is usually treated by dealing with the underlying conditions. For example: Diabetes - will administer insulin so that glucose is used to reduce the production of ketone bodies, Lung diseases - antibiotics and steroids ★ Pompe disease: - α-glucosidase deficiency affects the conversion of glycogen into glucose-1-P in lysosomes - Leads to weakening of muscles and accumulation of glycogen ★ Glycogen storage diseases: ★ Galaktosemia: - Deficiency of Galactokinase: - increased levels of galactose in blood and urine - There will be galactitol deposits in the lens (cataract in the lens) - Strict limitation in diet - Transferase deficiency: - There will be poor growth, speech abnormality, mental deficiency, liver damage - It can be fatal even if it is withheld from the diet - Epimerase deficiency: - It has similar symptoms as transferase deficiency - It is less severe if the diet is controlled ★ G-6-P dehydrogenase deficiency: - There is diminished NADPH+H+: - Detoxification is inhibited - Peroxidation of lipids destroys the cells membrane - Oxidation of proteins and DNA - Can cause hemolytic anemia and the symptoms of this include: pale skin, jaundice, dark-colored urine, fever etc ★ Essential fructosuria: - There is a mutation in the enzyme fructokinase - There is an impairment in the fructose metabolism which leads to increased excretion of fructose in the urine - There is no symptoms or no treatment necessary ★ Hereditary fructose intolerance: - There is a mutation in Aldolase B - Aldolase B deficiency leads to F1P build up which can cause local fructose toxicity, hypoglycemia - Symptoms: when the person ingests fructose causes: nausea, vomiting, restlessness, pallor, sweating, trembling, coma. If there is repeated ingestion of fructose it can lead to liver disease, kidney disease - Treatment: total elimination of fructose from the diet. Lipids 35. Types of lipids found in food and synthesized by body ★ Function of lipids in the body: - Energy storage - Cell membrane structure - Cofactors for enzymes - Signaling molecules - Steroid hormone synthesis - Antioxidants - Pigments - Insulation - Protection - Fat soluble vitamin transport and absorption ★ Fatty acids which are gotten through the diet are absorbed in the small intestine ★ Types of fats found in the food: TAGs, cholesterol, phospholipids ★ The types of lipids that are synthesized in the body are: free fatty acids, cholesterol, TAGs and ★ There is two types fat tissue in the body: white adipose tissue and brown adipose tissue ★ White adipose tissue: - It is made up of large spherical cells which are filled with one lipid droplet - All the other organelles are squeezed to the sides of the cell - Location: under skin, around deep blood vessels, in the abdominal cavity - Function: to fuel TAGs storage, carry out glycolysis through oxidative phosphorylation, convert acetyl-CoA into fatty acids, use FA to make TAGs and to release FA when other tissues might need them ★ Brown adipose tissue: - Smaller cells which contain multiple lipid droplets - Have more mitochondria and a richer supply of capillaries  - Location: around kidneys, spine and other vital organs which need support - Baby's have more BAT and the amount of BAT declines in childhood - Function: thermogenesis ★ More facts about lipids can be found if you scroll up! ★ 36. Energetic utilization of glycerol and glyceroneogenesis in adipose tissue ★ Place of action: mainly in the liver but the enzymes are expressed in all tissues, it takes place in the cells cytosol ★ Glycerol from fats enter either gluconeogenesis or glycolysis ★ ★ But before it can go forward it needs to be converted into fatty acyl-CoA ★ Glyceroneogenesis = making of glycerol-3-phosphate - It is a abbreviated version of gluconeogenesis in the liver and adipose tissue - It uses pyruvate, alanine, glutamine or any substances from the CAC as precursors for glycerol-3-phosphate 37. The carnitine – acylcarnitine shuttle ★ This transporter transports fatty acids with +14 carbons ★ ★ Acyl-carnitine/carnitine transporter belongs to group E7 enzyme class ★ 2 ATPs are used during this 38. Catabolism of fatty acids (saturated vs unsaturated, odd vs even, β-oxidation, α-oxidation, γ-oxidation) ★ Lipolysis - Place of action: TAGs which are stored in adipocytes, in the cells cytosol and lipid droplets.  - Hormones glucagon and epinephrine trigger the mobilization of stored TAGs: - Lipases cleave the fatty acids from the glycerol backbone of TAGs ★ Fatty acid oxidation can be divided into 3 stages: 1. Oxidative conversion of two carbon units into acetyl-CoA via beta-oxidation while there is generation of NADH+H+ and FADH2 2. Oxidation of acetyl-CoA into CO2 through the CAC where there is also generation of NADH+H+ and FADH2 3. Generation of ATP from NADH+H+ and FADH2 through the respiratory chain ★ β-oxidation: - Place of action: in every cell with mitochondria but at different rates, it takes place in the mitochondria  - - Each round of beta-oxidation produces one acetyl-CoA and the carbon chain is shortened by 2C - 4 ATPs are gained during this process ★ Long chain fatty acids are oxidized by a single trifunctional protein ★ Free fatty acid ATP calculations: - For example: If you have a 14C saturated free fatty acid To get the amount of beta-oxidation cycles you take 14:2-1=6 cycles To get amount of acetyl-CoA produced: 14:2=7 acetyl-CoA To get how much ATP is produced you take 6*4= 24 ATPs To get how much ATP is produced by the CAC you take 7*10=70 And then remember since this is a long chain free fatty acid it uses the acyl-carnitine shuttle so in total you get: 94-2= 92 ATPs from a 14 carbon long free fatty acid! If it is 14C unsaturated free fatty acid the total amount of ATP is 92-1.5 = 90,5 ATPs total that is produced If it is a 13C saturated free fatty acid: 3-10=10 C 10:2=5 acetyl-CoA 10:2=5 beta-oxidation cycles 5*10=50 ATP 5*4=20 ATP In total: 50+20+4=74 ATP but remember over 12 carbons so it uses the acyl-carnitine shuttle: 74-2=72 ATP  ★ Beta-oxidation in peroxisomes vs. mitochondria ★ The peroxisomal acyl-CoA dehydrogenase passes its electrons directly to molecular oxygen: - energy is released as heat - hydrogen peroxide will be eliminated by catalase ★ The peroxisomal beta-oxidation is mch more active on very long chain fatty acids, so fatty acids with more than 22 C ★ In the oxidation of unsaturated fatty acids there is two additional enzymes required to oxidized them: - Isomerase - Reductase ★ Monounsaturated fatty acids require isomerase and polyunsaturated fatty acids require both of the enzymes ★ The oxidation of unsaturated fatty acids results in 1 less FADH2 ★ ω- oxidation of fatty acids: - Occurs in liver and kidneys - Substrates which are preferred are fatty acids with 10C or 12C - It is important when beta-oxidation is defective - Product: fatty acid with carboxyl group at each end - The molecule will enter beta-oxidation for further oxidation and final 4C molecule can enter CAC ★ α-oxidation of branched chain fatty acids: - Occurs more in the liver and brain - Occurs in peroxisomes 39. Biosynthesis of fatty acids ★ It takes place in every cell with mitochondria, in the cells cytosol ★ Requires acetyl-CoA and malonyl-CoA and the reducing power of NADPH+H+ ★ The source for NADPH+H+: in adipocytes it is from the pentose phosphate pathway and malic enzyme and in hepatocytes & mammary glands also from pentose phosphate pathway  ★ The over all goal is to attach 2C units from malonyl-CoA to a growing chain and then reduce it ★ The reaction involves 4 cycles of enzyme-catalyzed steps: - condensation of the growing chain with the activated acetate group - reduction of carbonyl => hydroxyl - dehydration of alcohol => trans-alkene - reduction of alkene => alkane ★ The synthesis of fatty acids is tightly regulated through acetyl-CoA carboxylase ★ Glucagon, epinephrine trigger phosphorylation/inactivation which inhibits the acetyl-CoA carboxylase from working ★ Acetyl-CoA carboxylase is activated by citrate ★ ACC is inhibited by palmitoyl-CoA (feedback inhibition) 40. Ketogenesis, ketone utilization ★ Ketogenesis: - Place of action: in the liver, in the hepatocytes mitochondria - Occurs when oxaloacetate is depleted and acetyl-CoA is converted into ketone bodies - There are 3 types of ketone bodies: acetone, acetoacetate and beta-hydroxybutyrate  - Usage of ketone bodies: acetone is volatilized through lungs, acetoacetate and beta-hydroxybutyrate is used for energy for the skeletal and heart muscle, brain, renal cortex - The formation of ketone bodies: - Ketone bodies are used as fuel in the extrahepatic tissues 41. Cholesterol biosynthesis, functions  ★ 30% of cholesterol comes from the diet while 70% comes from the body itself by the synthesis of cholesterol ★ Functions of cholesterol: - It is a part of the cell membrane, in which it prevents the solidifying of FA tails and prevents permeability to some solutes - Precursor for steroid hormones - Precursor for bile acids - Precursor for vitamin D ★ Place of action: primarily in the liver but can occur everywhere in the human body, in the cell it occurs primarily in the endoplasmic reticulum but also in peroxisomes and in the cytosol. ★ Cholesterol synthesis: ★ Uses 36 ATPs ★ HMG-CoA reductase is a common target for cholesterol-lowering drugs Regulation of cholesterol transport and synthesis: ★ Short term: 1. Covalent modification of HMG-CoA reductase ★ Long term: 2. The transcriptional regulation of HMG-CoA reductase gene 3. Proteolytic degradation of HMG-CoA reductase 4. Activate acyl-CoA-cholesterol acyl transferase which will increase the esterification for storage 5. Transcriptional regulation of LDL receptor ★ AMP dependent protein kinase:  - when the AMP levels rises, protein kinase phosphorylates the enzyme => decrease in activity and cholesterol synthesis - Glucagon acts as a inhibitor - Insulin stimulates - Epinephrine acts as a inhibitor 42. Lipid transport in lipoproteins ★ Lipids are transported in the blood as lipoproteins ★ There are 4 major classes of lipoprotein particles: Type of lipoprotein Composition Characteristic Lipid transport from apolipoproteins => to (most important) Chylomicrons TAG, phospholipids, Apo-B48 Intestines→liver cholesteryl esters, Apo-CII Exogenous pathway proteins and free Apo-E cholesterol VLDL( very low TAGs 50%, ApoH Liver→periphery density lipoproteins) phospholipids, ApoB-100 Endogenous cholesteryl esters, ApoE pathway proteins and free cholesterols HDL (high density Protein 55%, Apo-I Periphery→Liver lipoprotein) phospholipids, Apo-D Reverse cholesterol cholesteryl esters, ApoA-II transport TAGs, free cholesterol LDL(low density Cholesteryl esters ApoB-100 Liver→periphery lipoprotein) 37%, proteins, Endogenous phospholipids, TAGs pathway and free cholesterol ★ Apolipoproteins: refer to the protein part of lipoprotein, their function is to ensure the transport of various lipids between organs ★ Each of the lipoprotein classes have a specific function determined by its place of synthesis, lipid composition and apolipoprotein content ★ There are three primary routes: 1. Exogenous pathway 2. Endogenous pathway 3. Reverse cholesterol transport  ★ Summaries of lipoproteins and activation and mobilization: 43. Most common pathologies related to lipid metabolism ★ X-linked adrenoleukodystrophy: - This disease affects boys after the age of 10 - Symptoms: loss of vision, behavioral disturbances and death within a few years - Affects mainly the nervous system and the adrenal glands, the myelin covering the nerves in the brain and spinal cord tends to deteriorate ★ Diabetic ketoacidosis: - DKA develops when the body doesn’t have enough insulin to allow blood sugar into your cells for energy usage and instead your body breaks down fat for fuel (ketogenesis) and this produces ketones. When there is too many ketones produced in the body too fast the levels of ketones increase to dangerous levels in the body - Most common for people with diabetes type 1 - Symptoms: fast, deep breathing, flushed face, headache, fruity-smelling breath, being very tired, dry skin and mouth - Treatment: giving fluids, electrolyte replacement, insulin therapy  ★ Hyperosmolar hyperglycemic state: - It is a metabolic complication of diabetes mellitus which is characterized by severe hyperglycemia, extreme dehydration, hyperosmolar plasma and altered consciousness - Occurs most often in people with diabetes type 2 - Treatment: Vigogours intravenous rehydration, electrolyte management, intravenous insulin - Symptoms: high blood sugar(over 600 mg/dl), confusion, hallucinations, drowsiness or passing out, fever, frequent urination, blurred vision or loss of vision. ★ Ketonuria: - Medical condition in which ketone bodies are present in the urine - Causes: diabetes, renal glycosuria or glycogen storage disease, fasting, starvation - Treatment: for people with diabetes you give insulin injections, in other conditions you treat it with appropriate diet, medication, or therapy for the underlying condition ★ Ketonemia: - Refers to the abnormal increase of ketone bodies in the blood - Causes: increased production of ketone bodies in the liver, decreased utilization in muscle and reduced volume of distribution ★ Cardiovascular disease: - It is a multifactorial disease - Very high LDL-cholesterol levels have a tendency to correlate with atherosclerosis - -Treatment to prevent artherosclertoic plaque formation we use statins which inhibit HMG-CoA reductase and thus reducing cholesterol synthesis ★ Familial Hypercholesterolemia: - It is caused by a mutation in the LDL receptor which causes impairment of receptor mediated uptake of cholesterol from LDL - Causes cholesterol to accumulate in the blood and in foam cells - Symptoms: atherosclerosis, corneal arcus, xanthelasma and tendon xanthoma - Treatment: statins, PCSK9 inhibitors Amino acids 44. Transamination of amino acids ★ Transamination: transfer of amino group ★ The transamination of amino acids allow the transfer of an amine to a common metabolite and generate a trafficable amino acid ★ Ammonia is captured by a series of transaminations ★ There is four amino acids which play a central role in the nitrogen metabolism: 1. glutamate 2. glutamine 3. alanine 4. aspartate ★ The enzymes which perform transamination are aminotransferases (=transaminase) ★ They use pyridoxal phosphate as cofactor ★ Usually it is ɑ-ketoglutarate that accepts amino groups: - When one amino group is transferred glutamate is made - When a second amino group is transferred glutamine is made ★ Glutamine transports safely ammonia in the bloodstream  ★ Overview of the amino acid synthesis: 45. Deamination of amino acids ★ It is the removal if an amino group from a molecule ★ It primarily occurs in the liver but also in the kidney ★ Once the proteins are degraded into amino acids they are treated in the same way in accordance to the organisms energy needs: 1. Recycled into new proteins 2. Oxidized for energy ★ Overview of amino acid catabolism:  ★ There are ketogenic amino acids which can be converted into ketone bodies, these are: Ile, Leu,Trp,Lys,Phe,Trp,Tyr ★ There are glucogenic amino acids which can be converted into glucose, these are: Ile, Leu,Trp,Lys,Phe,Trp,Tyr, Asp,Met,Vat,Arg,His,Gln,Ala,Cys,Gly,Hyp,Ser,Thr,Pro 46. Urea (ornithine) cycle ★ Takes place almost exclusively in the liver ★ In the hepatocytes it occurs party in the matrix of the mitochondria and the cytosol ★ There is 3 ATPs used  ★ The Aspartate-Argininosuccinate shunt links the urea cycle with CAC also called Krebs bicycle: ★ Regulation of urea cycle: - Glucagon will increase the efficacy of urea synthesis 47. Detoxification ways of ammonia ★ Ammonia impacts the blood pH ★ It depletes alpha-ketoglutarate and glutamate stores (this impairs neurotransmission) ★ Alanine and glutamine are nontoxic transport molecules for ammonia ★ The free ammonia that is released from transamination and deamination is quickly recaptured into carbamoyl phosphate and excreted through the urea cycle in the form of urea 48. Neurotransmitters (general principles of synthesis and breakdown; functions) ★ Dopamine: - Acts as a neurotransmitter in the brain and hormone when secreted into the blood  - It is derived from tyrosine - In the central nervous system: coordinates body movements, motivation, reward, reinforcement, sleep, mood and attention etc - Outside of the CNS it works as a local paracrine messenger: - In the kidneys it increases sodium excretion and urine output - in the pancreas it decreases insulin production - In the digestive system it reduces motility, protects intestinal mucosa - In the immune system it decreases the activity of lymphocytes - Degraded by MAO and COMT ★ Norepinephrine: - It is the most common neurotransmitter in the sympathetic nervous system and it mostly acts on alpha-receptors - It is derived from tyrosine - Mostly it acts as a neurotransmitter - Effects: it will increase heart rate, regulate sleep and wakefulness, attention and feeding behavior - It is degraded by MAO and COMT  ★ Glutamate: - It is the most important excitatory neurotransmitter in the CNS - The excess glutamate is metabolized in the mitochondria of hepatocytes ★ GABA - Most important inhibitory neurotransmitter - It is derived from glutamate 49. Heme and bilirubin (general principles of synthesis and breakdown; functions) ★ It is porphyrin which makes up the heme of hemoglobin  ★ The synthesis of heme: (Don’t need to know it by heart just roughly how it is made) ★ If there is mutations or misregulation of enzymes in the heme synthesis it can lead to porphyrias ★ Heme from red blood cells is degraded into bilirubin, there is two steps involved here: 1. Heme oxygenase will linearize heme which will create biliverdin, which is a green compound 2. Biliverdin reductase will convert biliverdin to bilirubin, a yellow pigment ★ Bilirubin is then excreted from the liver 50. Other nitrogen containing compounds (carnitine, creatine, glutathione) ★ Creatine is an intermediate which is produced by glycine and arginine ★ Phosphocreatine is the end product of the synthesis ★ Creatine can be used as a energy source ★ Phosphocreatine is an important energy buffer in skeletal muscles ★ Glutathione is derived from glutamate,cysteine, glycine ★ Glutathione is present in most cells and in high amounts, it is a reducing agent/antioxidant: - removes toxic peroxides - it keeps the redox enzymes in a reduced state - it keeps proteins, metal ions reduced ★ Nucleotides have many important roles in our body: - act as precursors of DNA and RNA - components of coenzymes - they are a energy currency, driving anabolic processes - carriers in biosynthesis - they are key allosteric modulators of enzymes in the metabolism - Second messengers in important signaling pathways ★ Two types of synthesis of nucleotides: De novo synthesis and Salvage pathways  ★ Glycine is the precursor for purines and Aspartate is precursor for pyrimidines 51. Most common pathologies related to protein/amino acid metabolism ★ If a person has any genetic defects in any of the enzymes involved in the urea formation they cannot tolerate protein-rich diets ★ The toxic ammonia can’t be converted into urea inside the liver which leads to the accumulation of ammonia in the liver which is the not good ★ Enzyme deficiency can cause hyperammonemia ★ Hyperammonemia: - Metabolic condition which is characterized by raised levels of ammonia - It is caused by a defect in detoxification or the over production of ammonia - Symptoms: irritability, headache, vomiting, ataxia, seizures, encephalopathy, coma - Treatment: antibiotics, hemodialysis ★ PKU (Phenylketonuria): - Genetic condition in which the levels of phenylalanine and phenylpyruvate accumulate in the body, the degradation of phenylalanine is defective since the enzyme phenylalanine is not working or is absent - It impairs the neurological development which leads to intellectual deficits  - The treatment for this is limiting the dietary intake of Phe or you can administer a medication called sapropterin dihydrochloride to breakdown phenylalanine in the body ★ Maple syrup urine disease: - Caused by deficiency of branched-chain alpha-keto acid dehydrogenase complex - Symptoms: poor feeding, vomiting, lethargy, abnormal movement and delayed development, urine & sweat, or earwax which smells like maple syrup or burnt sugar - Treatment: low-protein diet which has low levels of three amino acids ( leucine, isoleucine and valine), dialysis, give glucose & insulin through IV to adjust levels of amino acids in the body ★ Jaundice: - It is the yellowing of the skin and the eyeballs - Jaundice can be caused by impaired liver, blocked secretion, insufficient glucuronyl bilirubin transferase - Jaundice can be pre-, post- or intrahepatic - These impairments causes bile to be leaked into the blood which leads to the yellowing of the skin - Prehepatic jaundice: increased production or impaired hepatic uptake of bilirubin  - Intrahepatic jaundice: impaired hepatic metabolism or secretion of bilirubin - Posthepatic jaundice: obstruction to biliary excretion ★ Gout: - Caused by excess uric acid - Causes painful joints due to deposits of sodium urate crystals - It also affects the kidneys since uric acid can be deposited in the kidney tubules - Treatment: avoidance in purine-rich food (seafood, liver) or avoidance of fructose, can also be treated with xanthine oxidase inhibitor allopurinol General metabolism 52. Vitamins as cofactors ★ Vitamins are molecules which are needed for enzymatic reactions ★ Fat-soluble vitamins are A, D, E and K, they are stored in tissues. ★ Vitamin A and D work more like hormones while as vitamin K works as a cofactor ★ Vitamin A is important in eyesight, vitamin D is important in the calcium homeostasis, vitamin E is an important antioxidant and vitamin K is important not only as a cofactor for glutamate carboxylation but also in blood clotting. ★ Water-soluble vitamins are B1, B2, B3, B5, B6, B7 (biotin), B9 (folic acid), B12 and vitamin C ★ B12 is the only water-soluble vitamin that the body can store, it is stored in the liver. ★ All other water-soluble vitamins must be supplied through diet ★ B complex vitamins work as coenzymes ★ Side note: coenzyme: non-protein molecule which is necessary for the functioning of an enzyme, cofactor: chemical compounds that are bound to proteins ★ B1-Thiamine: - Important in carbohydrate metabolism - Needed as a prosthetic group to transfer two carbon units - For example: pyruvate dehydrogenase - Can’t be synthesized by animals - Foods in which it can be found: whole grains, meat, yeast etc - When there is not enough thiamine in the diet the first symptoms that will appear are in the nervous system and heart. - Example diseases: beriberi, wernicke-korsakoff syndrome ★ B2-Riboflavin: - It is a part of FADH2 which is a reducing cofactor and is used by oxidoreductases - Belongs to the enzyme class oxidoreductases  - For example: succinate dehydrogenase - Food source: leafy vegetables, mushrooms, milk - Deficiencies are rare ★ B3-Niacin: + + - It is a part of NADH+𝐻 and NADPH+𝐻 - Also used by dehydrogenases and belongs to the enzyme class oxidoreductases - For example: malate dehydrogenase, 3-hydroxyacyl-CoA dehydrogenase - Deficiency will cause pellagra: diarrhea, skin changes and mental disorders ★ B5-Pantothenic acid: - It is a part of coenzyme A, which is needed in the fatty acid synthesis and citric acid cycle - For example: acyl-CoA synthetase, thiolase - The reaction it catalyzes the enzyme will belong to EC 6 enzyme class ★ B6-Pyridoxine: - Pyridoxal is the prosthetic group which is involved in the elimination or addition of different functional groups - It is mostly observed in deamination, transamination and decarboxylation of different types of amino acids - The enzymes which uses pyridoxine as coenzyme belong to the transferases enzyme class ★ B7-Biotin: - Prosthetic group used in carboxylation reactions in lipogenesis, gluconeogenesis and the metabolism of branched amino acids - For example: pyruvate decarboxylase, acetyl-CoA carboxylase - If there is deficiency of this vitamin it will cause: seizures, muscle weakness, breathing problems, hearing loss, visual disturbances etc - Biotinidase deficiency is screened in newborns ★ B9- folate and B12- cobalamin: - Folate will form tetrahydrofolate which is a methyl carrier in the cell - Cobalamin is the second cofactor used in methylation - Folate deficiency is the most common vitamin deficiency - During pregnancy the demand for folate increases a lot - Cobalamin is gotten by eating dirty plants and then the bacteria will become a part of the intestinal microflora ★ Vitamins C and B are antioxidants ★ Vitamin C can act both as a substrate and cofactor - in the synthesis of collagen, carnitine, dopamine, tyrosine metabolism 53. Hormone classes (precursors, action mechanisms) ★ Autocrine: the hormone affects the cell where it is produced, for example: cytokines ★ Paracrine: the hormone is released into the extracellular space and diffuses into neighboring target cells, for example: eicosanoids  ★ Endocrine: the hormone is released into the bloodstream and carried to the target cells, for example: insulin, glucagon ★ The hormone-receptor interactions are specific and high-affinity ★ Different cells have different set of receptors which have different set of responsiveness to hormones ★ Different cells with the same receptors can have different intracellular targets and thus the downstream effect of a hormone can be different for the same hormone ★ There are 5 types of downstream events which follow after a hormone binds to it: 1. A secondary messenger cascade (cAMP, IP3): this regulates the allosterically enzymes 2. A receptor Tyr kinase is activated: this results in changes in the membrane potential 3. An adhesion receptor sends information to the cytoskeleton 4. A hormone-gated ion channel is either opened or closed 5. A steroid bound to receptor protein in nucleus alters the gene transcription: this results in changes in protein expression Peptide Biogenic Eicosanoids Steroid Thyroid Lipid soluble hormones amines hormones hormones vitamin derivatives Examples insulin, dopamine, Prostaglandi cortisol, T3 and T4 Vitamin D, glucagon noradrenali ns, testosterone retinoid hormones ne, thromboxane , adrenaline, s, lipoxins, aldosterone serotonin, leukotrienes histamine and GABA Precursor Amino single arachidonic Cholesterol Thyroglobuli cholesterol molecules acids amino acid acid n Inactive Storage in None Produced Inactive Inactive Inactive vitamins forms/storage the form of when needed while they while bound prohormone are bound to a , activated to transport transport by protein protein proteolytic cleavage Endocrine/ Endocrine Endocrine Paracrine endocrine Endocrine Endocrine paracrine and paracrine  Half life short half Very short short-half Long Long long life life Effects Generalized Localized Localized Generalized Generalized Generalized and generalized Functions Depends on act as play a role Depends on ↑basal Depends on the the neurotrans in the hormone metabolic hormone hormone mitters and inflammatio rate hormones, n, smooth ↑protein muscle synthesis contraction, regulate platelet bone growth function and neural maturation permissivene ss for catecholami nes Degradation Proteasome Proteasome Not known ubiquitin ubiquitin: system De-aminati on: MOA Methylation : MET ★ Peptide, catecholamine and eicosanoid hormones will bind to specific receptors on the plasma membrane of the target cells, altering the level of an intracellular second messenger cascade ★ Steroid, vitamin D, retinoid and thyroid hormones are bound to transport proteins and enter target cells and alter the gene expression by interacting with specific nuclear receptors 54. Hormonal regulation (effects of most common hormones, e.g. insulin, glucagon, epinephrine, on metabolic processes) ★ There is top down and bottom up hormonal signaling ★ Top down: the signals originate in the brain and then the signal is sent out to the body, for example: oxytocin, vasopressin, cortisol ★ Bottom up: The signals originate from somewhere in the body and will be sent to the brain, for example: insulin, leptin and epinephrine ★ Insulin: - Secreted in response to increased blood glucose levels - It binds to receptors located in muscle, brain, liver, adipose tissue and other fuel-metabolizing tissues - In muscle insulin will facilitate glucose uptake - In liver insulin will promote glycogen synthesis - In adipocytes insulin will promote glycerol synthesis and inhibits breakdown of fats - Metabolic effects: upregulates glycolysis, glycogenesis, lipogenesis and protein synthesis and glucose uptake in tissues ★ Epinephrine: - Primarily it acts as a hormone - It is derived from tyrosine - Metabolic effects: ↑glycogen breakdown in muscle and liver ↓glycogen synthesis in the muscle and liver ↑gluconeogenesis in the liver => the overall effect of these is to increase the production of glucose as fuel ↑Glycolysis in the muscle ↑Fatty acid mobilization ↑Glucagon secretion ↓ Insulin secretion - Degraded by MAO and COMT ★ Glucagon: - Involved in glucose homeostasis - Rises the blood glucose levels when they are low - Stimulates gluconeogenesis - Stimulates glycogenolysis - Stimulates lipolysis and beta-oxidation - Stimulates proteolysis - Stimulates ketogenesis - During exercise the secretion increases, it promotes liver glycogen breakdown and glucose formation from amino acids during rest ★ Melatonin: - Hormone which is derived from tryptophan - It acts as both a neurotransmitter and a hormone in the brain - It regulates sleep-wake cycle ★ Serotonin: - It is a intermediate in the synthesis of melatonin - It can also acts as a neurotransmitter - It regulates mood, memory processing, sleep and cognition - It is released from platelets and serves as a vasoconstrictor and regulates blood clotting - It is metabolized by MAO and AD  ★ Histamine: - It is produced in mast cells, basophils, eosinophils - It generates an allergic response and it mediates attention and arousal - Can act as a neurotransmitter also - It is derived from histidine - It is metabolized by methyltransferase, MAO and DAO ★ Cortisol: - Levels will first drop a bit and then increase during the first 30 to 45 min of exercise - Increases protein catabolism, which frees amino acids to be used within the liver for gluconeogenesis ★ Growth hormone: - Increase the mobilization of FFAs and decreases the cellular uptake of glucose ★ Thyroid hormones: - Stimulate glucose catabolism and fat metabolism 55. Energy systems during physical activity ★ Which energy system that is used during physical activity depends on the the duration, intensity and recruited muscle mass ★ During physical activity there are three energy systems which interact with each other to ensure our activity. ★ Depending on the type of activity and oxidative capacity of the muscle different systems are used 1. ATP stores -2 sec 2. ATP/PC system - 10 sec, used in skeletal muscle, heart, brain, used also during a sprint 3. Lactic acid system - 60 sec, anaerobic glycolysis 4. Aerobic system - lasts for a long time, pathways which are used during this time is oxidation of fatty acids & full oxidation of carbohydrates => CAC and ETC to make more ATP available ★ The energy metabolism in the muscle cell: During light activity and at rest the main energy source for the muscle cells come from fatty acids, ketone bodies and blood glucose and these produce CO2 as a bi-product. During bursts of heavy activity or during fight/flight muscle glycogen is  used from the stores as an energy source and lactate is produced as a bi-product. Also phosphocreatine is used during bursts of heavy activity and a bi-product of using this is creatine. All of these will also produce ATP which will eventually lead to muscle contraction. ★ Phosphocreatine system: - It is the end product which is derived from glycine and arginine - Creatine which is a intermediate can be gotten from food sources like meat and dairy products - The place of synthesis is primarily occurring in the liver and kidney - Place of use: mostly in the skeletal muscle, heart muscle and brain - You can take creatine as a supplement but it is of no use you don’t exercise enough - Creatine increases muscle mass, improves performance in high-intensity, short-duration workouts ★ Anaerobic glycolysis: - Occurs during short and high intensity workouts, for example when transitioning from walking into a full on sprint - Used during the start of any exercise - Used also once the intensity increase above the lactate threshold ★ Aerobic system: - Fat oxidation uses more oxygen it is a system which is used mostly during low intensity workouts - Protein oxidation accounts for about 5% of the energy requirements during prolonged exercise - When you eat a CHO-rich meal before exercise it will increase the muscle glycogen and maintain blood glucose late in exercise - Metabolic pathways which ensure aerobic oxidation of carbs, lipids and proteins are: CAC, ETC, ketolysis, glycolysis, lipolysis etc  ★ The relative contribution of carbohydrates and fat as fuel sources during exercise: The longer you spend time exercising the more fat will be used as a energy substrate ★ Adaptation to aerobic and anaerobic exercise occur on physiological level and on cellular level, including upregulation of enzyme activity which are responsible for ATP production 56. Major regulators of obesity and insulin resistance ★ An imbalance in food intake and energy expenditure leads to increase in body weight and obesity ★ When the storage capacity of WAT becomes saturated the fat will be accumulated in the peripheral organs ★ When the peripheral organs can’t store more fat the excess lipids will enter in non-oxidative pathways which results in the production of reactive toxic lipid species => tissue specific damage => lipotoxicity ★ Adipose tissue is also an endocrine organ, it releases hormones called adipokines ★ Adipokines: - Carry information to the brain about fuel stores and other tissues - Leptin and adiponectin are adipokines - In normal situations these will produce changes in the fuel metabolism and feeding behavior so that there is reestablished adequate fuel reserves and maintain body mass - If it is over- or under-produced it can result in life threatening diseases ★ Leptin: - Is a appetite suppressing hormone => decreases appetite - It is sent from the adipose tissue to the brain ★ Neuropeptide Y: - It is an orexigenic hormone = appetite stimulating hormone - It will send signals to eat - Levels will rise during starvation - It is inhibited by leptin and insulin ★ ɑ-melanocyte-stimulating hormone: - It is an anorexigenic hormone = appetite suppressing hormone - It will send signals to stop eating - The release is stimulated by leptin and insulin ★ Ghrelin: - It is a short time orexigenic hormone which is secreted in the stomach - It increases hunger - Prader-Willi syndrome is associated with high amounts of ghrelin ★ Adiponectin: - Made by adipose tissue - Makes organs more sensitive to insulin - It has an effect on fatty acid metabolism and carbohydrate metabolism in liver and muscle: ↑FA oxidation in muscle and glucose uptake&catabolism in muscle and liver, inhibits FA synthesis and gluconeogenesis in liver  ★ There are receptors called peroxisome proliferator-activated receptors (PPARs) and they alter the expression of genes for fat and carbohydrate metabolism ★ There are PPARɣ, PPARɑ, PPARδ ★ The microbiome in the gut have an influence on obesity ★ The microbes function as big endocrine glands affecting metabolism, feeding behavior and body mass ★ Obese people and lean people have different gut microbial flora ★ Type 1 diabetes: caused by autoimmune reaction where the body's immune system attacks insulin producing beta-cells in the pancreas. The result is that the body produces very little or no insulin at all, life long treatment is needed. ★ Type 2 diabetes: it is the most common type of diabetes and it is the result of the body not being able to fully respond to the insulin leading to insulin resistance. It can be reversed by making lifestyle modifications and medication ★ Metabolic syndrome: it is the intermediate stage before developing diabetes type 2, inorder for a person to be having metabolic syndrome some criteria must be fulfilled: - Elevated TAGs >1,7mM - Low HDL, 85 mmHg - Elevated fasting glucose >5,6mM or diagnosed type 2 diabetes - Abdominal adiposity The patient must have abdominal adiposity or BMI >30 and 2 of the other for the patient to have metabolic syndrome  ★ Treatment for diabetes 2: weight loss. exercise, bariatric surgery, ★ Irisin has shown promise in understanding and managing metabolic syndrome and obesity ★ Pathophysiology of metabolic syndrome: 57. Major contributors to cancer development and treatment ★ Cancer is a disease which is characterized by cell in the body which function abnormally and are uncontrollably proliferating ★ Cancer cells are usually the result of accumulation of many damages in the DNA. The damage can be cause by: degradation, mutation or epigenetic changes ★ Accumulation of ROS and NOS which leads to oxidative stress can cause cancer because it increases DNA mutations and DNA damage ★ Obesity has been shown to be linked with chronic diseases and reduction of life and it also increases the risk for getting different types of cancers, for example: stomach, pancreatic, liver cancers ★ High body fatness change hormone profiles: - ↑insulin concentration => ↑ IGF-1, which stimulates hormones and creates an imbalance => ↑ risk for breast cancer - ↑ IGF-1 => inhibition of apoptosis of the cell and ↑ cell proliferation - Visceral fatness => ↑ inflammatory response = > ↑ risk of colorectal cancer ★ Red meat can cause cancer due to either high fat percentage or how it is prepared: - High temperature => forms heterocyclic amines and polycyclic aromatic hydrocarbons => carcinogenic effects  - Meat contains heme iron => ↑ lipid peroxidation and formation of N-nitroso compounds => colorectal tumorigenesis - Processed meats are rich in fat ★ Salt: - 90% of stomach cancers are attributed to helicobacter pylori - The bacteria will accumulate and infect the lower stomach => inflammation of gastric mucosal lining and ↑↑ acid => ulcer => can lead to gastric cancer development - Also this bacteria has been shown to secrete Cag A which is an oncogenic agent ★ Alcohol: - The impact depends on cancer type and how much someone has consumed and the frequency of consumption - Mechanisms: Alcohol increases formation of ROS, alcohol changes the metabolism , alcohol acts as membrane crossing enhancer for molecules which can be carcinogenic compounds and when alcohol is metabolized it produces acetaldehyde which is is toxic and can disrupt DNA synthesis and DNA repair ★ To minimize the risk of getting cancer it is recommended to live a healthy lifestyle which includes eating a lot of different fruits & vegetables, daily exercise, avoiding red meat, not consuming too much salt or alcohol ★ MDR: - Multidrug resistance, it is the resistance of an organism to at least one drug (decrease or loss of therapeutic activity) ★ DDI: - drug-drug interactions occur in multidrug treatments when one drug inhibits the therapeutic action of another one - Metabolic enzymes CYP and UGT and membrane transporters for drug influx or efflux SLC and ABC have been involved in both MDR and DDI - SLC and ABC are very important in drug influx and efflux, if there are any problems with these transporters it may impair the drug efflux and lead to toxicity ★ Food-drug interactions: - phytochemicals can modulate activity/expression of CYP or SLC/ABC transporter => modulate systemic active drug clearance - After food intake when the phytochemicals are in the bloodstream they can interact with hepatic or renal transporter: