Biochemistry Lecture Finals (S.Y. 2024 - 2025) PDF

BIOCHEMISTRY S.Y. 2024 – 2025 | FIRST SEMESTER LECTURE | FINALS o To name a nucleoside derived from a purine base, use the suffix “...

BIOCHEMISTRY S.Y. 2024 – 2025 | FIRST SEMESTER LECTURE | FINALS o To name a nucleoside derived from a purine base, use the suffix “- M6: NUCLEIC ACIDS osine.” NUCLEOSIDES & NUCLEOTIDES (INTRODUCTION) o For deoxyribonucleosides, add the prefix “deoxy-.” o Nucleic acids are unbranched polymers composed of repeating monomers called nucleotides. o Two types of nucleic acids: ▪ DNA (deoxyribonucleic acid): Stores the genetic information of an organism and transmits that information from one generation to another. ▪ RNA (ribonucleic acid): Translates the genetic information contained in DNA into proteins needed for all cellular function. o The nucleotide monomers that compose DNA and RNA consist of monosaccharide, N-containing base, and a phosphate group. o DNA molecules contain several million nucleotides, while RNA molecules have only a few thousand. o DNA is contained in the chromosomes of the nucleus, each chromosome having a different type of DNA. o Humans have 46 chromosomes (23 pairs), each made up of many genes. o A gene is the proportion of the DNA molecule responsible for the synthesis of a single protein. NUCLEOSIDES (JOINING A MONOSACCHARIDE & A BASE) o In RNA, the monosaccharide is the aldopentose D-ribose. o In DNA, the monosaccharide is the aldopentose D-2-deoxyribose. o The N-containing base is one of 5 types. NUCLEOTIDES (JOINING A NUCLEOSIDE WITH A PHOSPHATE) o Nucleotides are formed by adding a phosphate group to the 5’ -OH o Cytosine (C), uracil (U), and thymine (T) are all based on the structure of a nucleoside. of pyrimidine. o Adenine (A) and guanine (G) are based on the structure of purine. o DNA contains bases A, G, C, and T. o RNA contains bases A, G, C, and U. o A nucleoside is formed by joining the anomeric carbon of the monosaccharide with a N atom of the base. o To name a nucleoside derived from a pyrimidine base, use the suffix “-idine.”  BIOCHEMISTRY S.Y. 2024 – 2025 | FIRST SEMESTER LECTURE | FINALS o ADP is an example of a diphosphate: o The previous chain can be abbreviated: o ATP is an example of a triphosphate: NUCLEIC ACIDS o Nucleic acids (DNA and RNA) are polymers of nucleotides joined by phosphodiester linkages. o This polynucleotide would be named CATG, reading from the 5’ end to the 3’ end. DNA DOUBLE HELIX o The DNA model was initially proposed by Watson and Crick in 1953. o DNA consists of two polynucleotide strands that wind info a right- handed double helix. o The two strands run in opposite directions; one runs from the 5’ end to the 3’ end and the other runs from the 3’ end to the 5’ end. o The sugar-phosphate groups lie on the outside of the helix and the bases lie on the inside. o A polynucleotide contains a backbone consisting of alternating sugar and phosphate groups. o The identity and order of the bases distinguish one polynucleotide from another (primary structure). o A poly nucleotide has one free phosphate group at the 5’ end and one free OH group at the 3’ end. o In DNA, the sequence of the bases carries the genetic information of the organism.  BIOCHEMISTRY S.Y. 2024 – 2025 | FIRST SEMESTER LECTURE | FINALS o Formation of Replication Fork o Synthesis of Lagging Strand o The bases always line up so that a pyrimidine derivative can hydrogen bond to a purine derivative on the other strand. o Thus, there are complementary base pairs that always hydrogen bond together in a particular manner. o Adenine pairs with thymine with 2 hydrogen bonds to form an A—T base pair. o Cytosine pairs with guanine using 3 hydrogen bonds to form C—G base pairs. o The information stored in DNA is used to direct the synthesis of proteins. o Replication is the process by which DNA makes a copy of itself when a cell divides. o Transcription is the ordered synthesis of RNA from DNA; the genetic information stored in DNA is passed onto RNA. o Translation is the synthesis of proteins from RNA; the genetic o Final Product information determined the specific amino acid sequence of the protein. REPLICATION o The original DNA molecule forms two new DNA molecules, each of which contains a strand from the parent DNA and one new strand. o The identity of the bases on the template strand determines the order of the bases on the new strand. o A must pair with T, and G must pair with C. o A new phosphodiester bond is formed between the 5’ -phosphate of the nucleoside triphosphate and the 3’ -OH group of the new DNA strand. o Replication occurs in only one direction on the template strand, from the 3’ end to the 5’ end. o The new strand is either a leading strand, growing continuously, or a lagging strand, growing in small fragments. o Before Replication RNA o There are important differences between DNA and RNA. o In RNA, the monosaccharide is ribose. o The thymine (T) base is not present in RNA; instead, the uracil (U) base is used. o RNA is a single strand, and smaller than DNA. o Three types of RNA molecules: ▪ Ribosomal RNA (rRNA) provides the site where polypeptides are assembled during protein synthesis.  BIOCHEMISTRY S.Y. 2024 – 2025 | FIRST SEMESTER LECTURE | FINALS ▪ Messenger RNA (mRNA) carries the information from DNA to the ribosome ▪ Transfer RNA (tRNA) brings specific amino acids to the ribosomes for protein synthesis. o tRNA is drawn as a cloverleaf shape, with an acceptor stem at the 3’ end, which carries the needed amino acid, and an anticodon, which identifies the needed amino acid. TERMINATION o Translation continues until a stop codon (UAA, UAG, or UGA) is reached, which is called termination; the complete protein is released. o Transcription is the synthesis of mRNA from DNA. o The DNA splits into two strands, the template strand, which is used to synthesize RNA, and the informational strand which is not used. o Proceeds from the 3’ end to the 5’ end of the template. o Forms mRNA with a complementary sequence to the template DNA strand and an exact sequence as the informational DNA strand. o The difference between mRNA and the information DNA strand is that the base U replaces T on mRNA. THE GENETIC CODE o A sequence of three nucleotides (a triplet) codes for a specific amino acid. o Each triplet is called a codon. o For example, UAC is a codon for the amino acid serine; UGC is a codon for the amino acid cysteine. o Codons are written from the 5’ end to the 3’ end of the mRNA molecule. TRANSLATION AND PROTEIN SYNTHESIS o mRNA contains the sequence of codons that determine the order of MUTATIONS AND GENETIC DISEASE amino acids in the protein. o A mutation is a change in the nucleotide sequence in a molecule of o Individual tRNAs bring specific amino acids to the peptide chain. DNA. o rRNA contains binding sites that provide the platform on which protein synthesis occurs. o Some mutations are random, while others are caused by mutagens. o A point mutation is the substitution of one nucleotide for another. INITIATION o Initiation begins with mRNA binding to the ribosome. o A tRNA brings the first amino acid, always at codon AUG. o A deletion mutation occurs when one or more nucleotides is/are lost from a DNA molecule. ELONGATION o Elongation proceeds as the next tRNA molecule delivers the next amino acid, and a peptide bond forms between the two amino acids.  BIOCHEMISTRY S.Y. 2024 – 2025 | FIRST SEMESTER LECTURE | FINALS o An insertion mutation occurs when one or more nucleotides is/are o First, bacterial plasmid DNA is cut by the restriction endonuclease added to a DNA molecule. EcoRI, which cuts in a specific place. o A silent mutation has a negligible effect to the organism, because o This gives a double strand of linear plasmid DNA with two ends the resulting amino acid is identical. ready to bond called sticky ends. o A mutation that produces a protein with one different amino acid usually has a small to moderate effect on the protein overall. o Then, a second sample of human DNA is cut with the same EcoRI o Some proteins, such as hemoglobin, substitution of just one amino acid can result in the fatal diseases of sickle cell anemia. o If a mutation causes a big change, like producing a stop codon, the remainder of the protein will not be synthesized, which can have catastrophic results. o This forms human DNA segments with sticky ends that are complimentary to the plasmid DNA. o When a mutation causes a protein deficiency or defective protein synthesis, and this mutation is passed through generations, it is a genetic disease. o Cystic fibrosis results from defective cystic fibrosis transmembrane conductance regulator (CFTR); the effects are extremely thick lung o Combining the two pieces of DNA (with DNA ligase enzyme) forms mucus and low pancreatic secretions. DNA containing the new segment. o Galactosemia results from a deficiency of an enzyme needed for o This DNA chain is slightly larger because of its additional segment. galactose metabolism and can cause mental retardation. POLYMERASE CHAIN REACTION o Polymerase chain of reaction (PCR) amplifies a specific portion of a DNA molecule, producing millions of exact copies. o Four elements needed to amplify DNA by PCR: ▪ The segment of DNA that must be copied. ▪ Two primers – short polynucleotides that are complementary to the two ends of the segment to be amplified. ▪ A DNA polymerase enzyme to catalyze the synthesis of a complementary strand. ▪ Nucleoside triphosphates – the source of the A, T, C, and G needed to make a new DNA. RECOMBINANT DNA o Recombinant DNA is a synthetic DNA that contains segments from more than one source. o Three key elements are needed to form recombinant DNA: ▪ A DNA molecule into which a new DNA segment will be inserted ▪ An enzyme that cleaves DNA at specific locations. ▪ A gene from a second organism that will be inserted into the original DNA molecule.  BIOCHEMISTRY S.Y. 2024 – 2025 | FIRST SEMESTER LECTURE | FINALS M7: BIOENERGETICS DIGESTION AND THE CONVERSION OF FOOD INTO ENERGY o Metabolism is the sum of all the chemical reactions that take place in an organism. o Catabolism is the breakdown of large molecules into smaller ones; energy is generally released during catabolism. o Anabolism is the synthesis of large molecules from smaller ones; energy is generally absorbed during anabolism. o Often, the process is a series of consecutive reactions called a metabolic pathway, which can be linear or cyclic. ▪ A linear pathway is the series of reactions that generates a final product different from any of the reactants. ▪ A cyclic pathway is the series of reactions that regenerates the DNA FINGERPRINTING first reaction. o The DNA of each individual is unique, so DNA can be used as a method of identification. o Any type of cell (skin, saliva, semen, blood, etc.) can be used to obtain a DNA fingerprint. o The DNA is first amplified by PCR and then cut by restriction enzymes. o The DNA fragments are then separated by size by gel electrophoresis. o Energy production occurs in the mitochondria. o DNA fragments can be visualized on X-ray film after they have been o Mitochondria are organelles within the cytoplasm of a cell. separated: o Mitochondria contain an outer membrane and an inner membrane with many folds. o The area between the two membranes is called the intermembrane space. o The area enclosed by the inner membrane is called the matrix, where energy production occurs. AN OVERVIEW OF METABOLISM VIRUSES o Stage – Digestion ▪ Carbohydrates are hydrolyzed into monosaccharides beginning o A virus is an infectious agent consisting of a DNA or RNA molecule with amylase enzymes in saliva and continuing in the small that is contained within a protein coating. intestine. o It is incapable of replicating alone, so it invades a host organism and makes the host replicate the virus. o Many prevalent diseases like the common cold, influenza, and herpes are viral in origin. o A vaccine is an inactive form of a virus that causes a person’s immune system to produce antibodies to the virus to ward off infection. o A virus with an RNA core is called a retrovirus. ▪ Protein digestion begins when stomach acid denatures the proteins, and pepsin begins to cleave the large protein backbone into smaller peptides ▪ Then, in the small intestines, trypsin and chymotrypsin cleave the peptides into amino acids. o Retroviruses invade a host and then synthesize viral DNA by reverse transcription. o The viral DNA can then be transcribed RNA, which then directs protein synthesis (new retroviral particles to infect other cells). o Acquired immune deficiency syndrome (AIDS) is caused by the retrovirus human immunodeficiency virus (HIV).  BIOCHEMISTRY S.Y. 2024 – 2025 | FIRST SEMESTER LECTURE | FINALS ▪ Triacylglycerols are emulsified by bile secreted by the liver, then GENERAL FEATURES OF ATP PHOSPHORYLATION hydrolyzed by lipase into 3 fatty acids and a glycerol backbone. o Phosphorylation is the reverse reaction, where a phosphate group is added to ADP. o Phosphorylation reforms ATP and requires 7.3 kcal/mol of energy. o Stage – Formation of Acetyl CoA o Any process (walking, running, and breathing) is fueled by the release of energy when ATP is hydrolyzed to ADP. ▪ Monosaccharides, amino acids, and fatty acids are degraded into acetyl groups, which are then bonded to coenzyme A o Energy is absorbed and stored in ATP when it is synthesized from ADP. forming acetyl-CoA. COUPLED REACTIONS ON METABOLIC PATHWAYS o Coupled reactions are pairs of reactions that occur together. o Stage – The Citric Acid Cycle o The energy released by one reaction is absorbed by the other ▪ The citric acid cycle is based in the mitochondria, where the reaction. acetyl CoA is oxidized to CO2. o Coupling an energetically unfavorable reaction with a favorable one ▪ The cycle also produces energy stored as a nucleoside that releases more energy than the amount required is common in triphosphate and the reduced coenzyme. biological reactions. o Stage – The Electron Transport Chain and Oxidative o The hydrolysis of ATP provides the energy for the phosphorylation of Phosphorylation glucose. ▪ Within the mitochondria, the electron transport chain and oxidative phosphorylation produce ATP (adenosine 5’- COENZYMES NAD+ AND NADH triphosphate). ▪ ATP is the primary energy-carrying molecule in the body. o A coenzyme acting as an oxidizing agent causes an oxidation reaction to occur, so the coenzyme is reduced. o When a coenzyme acts as an oxidizing agent, it gains H+ and e-. o A coenzyme acting as a reducing agent causes a reduction reaction to occur, so the coenzyme is oxidized. o When a coenzyme acts as a reducing agent, it loses H+ and e-. o Coenzyme NAD+ (nicotinamide adenine dinucleotide) is an oxidizing agent. GENERAL FEATURES OF ATP HYDROLYSIS o After gaining 1 H+ and 2 e-, the reduced form of NAD+ is NADH. o Hydrolysis of ATP cleaves 1 phosphate group. o This forms ADP and hydrogen phosphate (HPO42-), releasing 7.3 kcal/mol of energy. o Curved arrows are often used to depict reactions that use coenzymes as oxidizing agents.  BIOCHEMISTRY S.Y. 2024 – 2025 | FIRST SEMESTER LECTURE | FINALS o In this reaction, isocitrate is oxidized to oxalosuccinate while NAD+ is SPECIFIC STEPS OF THE CITRIC ACID CYCLE reduced to NADH. COENZYMES FAD AND FADH2 o Coenzyme FAD (flavin adenine dinucleotide) is an oxidizing agent as well. o Step reacts acetyl CoA with oxaloacetate to form citrate, and it is o After gaining 2 H+ and 2 e-, the reduced form of FAD is FADH2. catalyzed by citrate synthase. COENZYMES NADH AND FADH2 o Step isomerize the 3o alcohol in citrate to the 2o alcohol in o NAD+ and FAD both act as oxidizing agents. isocitrate; it is catalyzed by aconitase. o Their reduced forms, NADH and FADH2, both acts as reducing agents. COENZYME A o Coenzyme A (HS-CoA) is neither an oxidizing nor a reducing agent. o Step isocitrate loses CO2 in a decarboxylation reaction catalyzed by isocitrate dehydrogenase. o Also, the 2o alcohol of isocitrate is oxidized by the oxidizing agent NAD+ to form the ketone α-ketoglutarate and NADH. o When an acetyl group reacts with the sulfhydryl end of coenzyme A, the thioester acetyl CoA is formed. o When the thioester bond is broken, 7.5 kcal/mol of energy is released. o Step releases another CO2 with the oxidation of a-ketoglutarate THE CITRIC ACID CYCLE by NAD+ in the presence of coenzyme A to form succinyl CoA and o The citric acid cycle is a cyclic metabolic pathway that begins with the NADH. addition of acetyl CoA to a four-carbon substrate. o This step is catalyzed by α-ketoglutarate dehydrogenase. o The cycle ends when the same four-carbon substrate is formed as a product 8 steps later. o The citric acid cycle produces high-energy compounds for ATP synthesis in stage of catabolism. OVERVIEW OF THE CITRIC ACID CYCLE o In step , the thioester bond of succinyl CoA is hydrolyzed to form succinate, releasing energy that converts GDP to GTP. o In step , succinate is converted to fumerate with FAD and succinate dehydrogenase; FADH2 is formed. o In step , water is added across the C=C; this transform fumerate into malate, which has a 2o alcohol. o The citric acid cycle begins when 2 Cs of acetyl CoA react with a four- carbon substrate to form a six-carbon product (step ). o 2 C atoms are sequentially removed to form 2 CO2 molecules (steps and ). o 4 molecules of reduced coenzymes (3 NADHs and 1 FADH2) are formed (steps , , , and ). o In step , the 2o alcohol of malate is oxidized by NAD+ to form the o 1 mole of GTP is made in step ; GTP is similar to ATP. ketone portion of oxaloacetate and NADH.  BIOCHEMISTRY S.Y. 2024 – 2025 | FIRST SEMESTER LECTURE | FINALS o The product of step is the starting material for step. ATP SYNTHESIS BY OXIDATIVE PHOSPHORYLATION o Each NADH entering the electron transport chain produces enough energy to make 2.5 ATPs. o Each FADH2 entering the electron transport chain produces enough energy to make 1.5 ATPs. o The citric acid cycle produces overall: THE CITRIC ACID CYCLE HYDROGEN CYANIDE o If any one step of the electron transport chain or oxidative phosphorylation is disrupted, an organism cannot survive. o Hydrogen cyanide (HCN) produces —CN, which irreversibly binds to the FE3+ portion of the cytochrome oxidase. o Cytochrome oxidase is a key enzyme of complex IV of the electron transport chain. o The overall citric acid cycle yields: o This prevents the FE3+ from being reduced to FE2+, halting the ▪ 2 CO2 molecules electron transport chain and energy production. ▪ 3 NADH and 1 FADH2 molecules o ATP in not synthesized, and cell death occurs. ▪ 1 GTP molecule o The main function of the citric acid cycle is to produce reduced M8: CARBOHYDRATE, LIPID, AND PROTEIN METABOLISM coenzymes (NADH and FADH2). o These molecules enter the electron transport chain and ultimately BIOCHEMICAL REACTIONS produce ATP. o The daily operations of the cell are accomplished through the biochemical reactions that take place within the cell. THE ELECTRON TRANSPORT CHAIN o Reactions are turned on and off or sped up and slowed down o The electron transport chain is a multistep process using 4 enzyme according to the cell’s immediate needs and overall functions. complexes (I, II, III, and IV) located along the mitochondrial inner o The numerous pathways involved in building up and breaking down membrane. cellular components are monitored and balanced in a coordinated fashion such that the cells organize reactions into various enzyme- powered pathways. o The management of biochemical reactions with enzymes is an important part of cellular maintenance. o The enzymatic activity allows a cell to respond to changing environmental demands and regulate its metabolic pathways, both which are essential to cell survival. o The reduced coenzymes (NADH and FADH2) are reducing agents and can donate e- when oxidized. o NADH is oxidized to NAD+ and FADH2 is oxidized to FAD when they GLYCOLYSIS enter the electron transport chain. o Glycolysis is a series of reactions extracting energy from glucose by o The e- donated by the coenzymes are passed down from complex to splitting it into two three-carbon molecules called pyruvate. complex in a series of redox reactions, which produces some energy. ▪ It is the first stage in the cellular respiration that occurs in the o These e- and H+ react with inhaled O2 to form water. cytoplasm under the anaerobic condition which does not o This process is aerobic because of the use of O2. require oxygen. o Mature mammalian red blood cells do not have mitochondria and ATP SYNTHESIS BY OXIDATIVE PHOSPHORYLATION are not capable of aerobic respiration so that glycolysis is their only source of ATP. o The electron transport chain provides the energy to pump H+ ions o If glycolysis is interrupted, the red blood cells lose their ability to across the inner membrane of the mitochondria. maintain their sodium-potassium pumps, which require ATP to o The concentration of H+ ions in the intermembrane space becomes function, and eventually, they die. higher than that inside the matrix. o This creates a potential energy gradient, much like potential energy of water stored behind a dam. PYRUVATE o To return to the matrix, H+ ions travel through a channel in the ATP o Pyruvate is a versatile molecule that feeds into several pathways. synthase enzyme. o It is then converted to acetyl CoA under the aerobic conditions which o ATP synthase is the enzyme that catalyzes the phosphorylation of have numerous metabolic destinations including the TCA cycle. ADP into ATP. o It can also be converted into lactate under an anaerobic condition o The energy released as the H+ ions return to the matrix is the energy that enters the Cori cycle to undergo gluconeogenesis. stored in the ATP molecule. o It is called oxidative phosphorylation because the energy used to GLUCONEOGENESIS transfer the phosphate group results from the oxidation of the o Translated as ‘the production of new glucose’. coenzymes. o It is a metabolic pathway that results in the generation of glucose from non-carbohydrate carbon substrates such as lactate, glycerol, and glucogenic amino acids.  BIOCHEMISTRY S.Y. 2024 – 2025 | FIRST SEMESTER LECTURE | FINALS o Occurs beyond around 8 hours of fasting when liber glycogen stores o beta (β)-hydroxybutyrate is oxidized to acetoacetate and NADH is start to deplete, and an alternative source of glucose is required. released. o It occurs mainly in the liver and the kidney (to a lesser extent in the o An HS-CoA molecule is added to acetoacetate, forming acetoacetyl cortex). CoA. o Three main precursors: o When ketones are produced faster than they can be used, they can ▪ Lactate from anaerobic glycolysis in exercising muscle and red be broken down into CO2 and acetone. The acetone is removed by blood cells via the Cori Cycle. exhalation. ▪ Glycerol which is released from adipose tissue breakdown of o One symptom of ketogenesis is that the patient’s breath smells sweet triglycerides like alcohol. ▪ Amino acids (mainly amine) o This effect provides one way of telling if a diabetic is properly o Gluconeogenesis has a close relationship with glycolysis. controlling the disease. o Glycolysis is the breaking of glucose; gluconeogenesis is the creation o The carbon dioxide produced can acidify the blood, leading to of glucose. diabetic ketoacidosis, a dangerous condition in diabetics. o However, gluconeogenesis is not as simple as reversing glycolysis, as there are irreversible steps in glycolysis. THE CATABOLISM OF TRIACYLGLYCEROLS Example: GLUCONEOGENESIS o The Cori Cycle, or glucose-lactate cycle, was discovered by Carl How much ATP is formed by the complete catabolism of steric acid Ferdinand Cori and Gerty Theresa Radnitz, a husband-and-wife team, C18H36O2. in the ‘30s and ‘40s of the last century. o Step : Converting the fatty acid into the fatty acyl CoA uses up to 2 o They demonstrated the existence of metabolic cooperation between ATP. the skeletal muscle working under low oxygen conditions and the liver. o This cycle can be summarized as follows: o Step : Next, add up the ATP from the reduced coenzymes made ▪ The conversion of glucose to lactid acid, or lactate, by anaerobic during b-oxidation. glycolysis in skeletal muscle cells. ▪ The diffusion of lactate from muscle cells into the bloodstream, by which it is transported to the liver. ▪ The conversion of lactate to glucose by hepatic gluconegenesis. o Step : Finally, add up the ATP synthesized from each acetyl CoA. ▪ The diffusion of glucose from the hepatocytes into the bloodstream, by which it is transported back to the skeletal muscle cells, thereby closing the cycle. o Part of the lactate produced in skeletal muscle is converted to glucose in the liver and transported back to the skeletal muscle. AMINO ACID CATABOLISM o The importance of this cycle is demonstrated by the fact that it may o Metabolism of the 20 common amino acids are considered from the account for about 40% of plasma glucose turnover. origins and fates of their: ▪ Nitrogen atoms LIPID METABOLISM ▪ Carbon skeletons o Lipid metabolism entails the oxidation of fatty acids to either o For mammals: generate energy or synthesize new lipids from smaller constituent ▪ Essential amino acids must be obtained from diet molecules. ▪ Nonessential amino acids can be synthesized o It is associated with carbohydrate metabolism, as products of glucose o Amino acids from degraded proteins or from diet can be used for the (such as acetyl CoA) can be converted into lipids. biosynthesis of new proteins. o During starvation, proteins are degraded to amino acids to support BREAKDOWN OF FATTY ACIDS glucose formation. o First step is often removal of the a-amino group. o During fatty acid oxidation, triglycerides can be broken down into o Carbon chains are altered for entry into central pathways of carbon acetyl CoA molecules and used for energy when glucose levels are metabolism. low. o Acetyl CoA is used to create lipids, triglycerides, steroid hormones, cholesterol, and bile salts. DIETARY PROTEINS o Digested in intestine KETOGENESIS o By peptidases o Transport of amino acids o If excessive acetyl CoA is created from the oxidation of fatty acids and o Active transport coupled with Na+ the Krebs cycle is overloaded and cannot handle it, the acetyl CoA is diverted to create ketone bodies. o These ketone bodies can serve as a fuel source if glucose levels are too low in the body. o Ketones serve as fuel in times of prolonged starvation or when patients suffer from uncontrolled diabetes and cannot utilize most of the circulating glucose. DIETARY PROTEINS o In both cases, fat stores are liberated to generate energy through the Krebs cycle and will generate ketone bodies when too much acetyl o Proteins are continuously synthesized and degraded (turnover) (half- CoA accumulates. lives minutes to weeks). o Ketones oxidize to produce energy for the brain. o Lysosomal hydrolysis degraded some proteins.  BIOCHEMISTRY S.Y. 2024 – 2025 | FIRST SEMESTER LECTURE | FINALS o Some proteins are targeted for degradation by a covalent attachment o Pyridoxal phosphate co-factor (through lysine residues) of ubiquitin (C terminus). o Proteasome hydrolyzes ubiquitinated proteins. SCHIFF BASE o Cellular protein o Ping pong o Proteasome degrades protein with Ub tags. o Keto acid o T ½ determined by amino terminus residue. o Stable: Ala, Pro, Gly, & Met (greater than 20 h). o Unstable: Arg, Lys, His, & Phe (2-30 min). UBIQUITIN SERINE AND THREONINE DEAMINATION o Dehydratase reaction o Remove H2O first o Serine -> pyruvate o Threonine -> a-ketobutyrate o Ubiquitin protein: 8.5 kD o Highly conserved in yeast/humans. o Carboxy terminal attaches to E-lysine amino group. o Chains or 4 or more Ub molecules target protein for destruction. DEGRADATION — PROTEASOME o Proteasome degrades protein with Ub tags. OXIDATIVE DEAMINATION o 26s: two subunits, 20s (catalytic), and 19s (regulatory). o Glutamate transferred to mitochondria. o Releases peptides 7-9 units long. o Glutamate dehydrogenase DEAMINATION UREA CYCLE o In liver o Glutamate dehydrogenase o CPS I o Bicarbonate and ammonia react o Collect NH3 from tissues. o In mitochondria: reactions o Alanine from muscle o Cytosolic reactions o Glutamine from other tissues o Arginase release urea o Glutamate from liver o Remove waste products o Tied to TCA cycle TRANSAMINATION o Transfer of an amino group from an a-amino acid to an a-keto acid. o In amino acid biosynthesis, the amino group of glutamate is transferred to various a-keto acids generating a-amino acids. o In amino acid catabolism, transamination reactions generate o Mitochondria reactions glutamate or aspartate. o Cytosolic reactions o Cytosol of liver o Collect in glutamate o Glutamate transferred to mitochondria MECHANISM  BIOCHEMISTRY S.Y. 2024 – 2025 | FIRST SEMESTER LECTURE | FINALS MITOCHONDRIAL REACTIONS o CPS I o Bicarbonate and ammonia react o Orinithine transcarbamolyse o Citrulline transported to cytosol CYSTOSOLIC REACTIONS INBORN ERRORS OF AMINO ACID METABOLISM o Arginase releases urea o Remove waste products: ammonia/bicarbonate o Tied to TCA cycle UREA CYCLE AND TCA CYCLE M9: NUTRITION MACRONUTRIENTS o Macronutrients are substances that provide calories or energy and are required in large amounts to maintain body functions and carry out daily activities. o There are three broad classes of macronutrients: carbohydrates, proteins, and fats. UREA CYCLE AND TCA CYCLE o Glucogenic amino acids can supply gluconeogenesis pathway via DIETARY FIBER pyruvate or citric acid cycle intermediates. o Dietary fiber is that part of food that cannot be digested by human o Ketogenic amino acids can contribute to synthesis of fatty acids or enzymes. ketone bodies. o It is found in edible plant foods such as cereals, fruits, vegetables, o Some amino acids are both glucogenic and ketogenic. dried peas, nuts, lentils, and grains. o Dietary fiber helps keep the gut healthy and reduce the risk of CARBON SKELETONS OF AMINO ACIDS diseases such as diabetes, coronary heart disease, and bowel cancer. o Glucogenic o Soluble Fiber: o Ketogenic ▪ It is found in foods like fruits, oats, bean, and barley. o Phenylalanine example ▪ It forms a gel-like substance in water. o Autosomal genetic defect ▪ It supports the growth of bacteria needed to help maintain a healthy gut. ▪ It slows down the time it takes for food to pass through the stomach into the small intestine o Insoluble Fiber: ▪ Insoluble fiber does not dissolve in water. ▪ It is found in foods like wholewheat bread, wheat bran, vegetables, and nuts. ▪ It adds bulk to the stool by absorbing water and helps to keep regular bowel movement. PHENYLALANINE METABOLIC DEFECT o Genetic defect DIETARY FATS o Recessive o Hydroxylase defect o Dietary fat is the fat obtained from food. It is essential for energy o Minor pathways produce Phenylpyruvic acid production and cell growth. o Dietary lipids are 90% triglycerides. o The remaining percentage includes cholesterol esters, phospholipids, essential fatty acids, and fat-soluble vitamins. o Dietary fats provide long-lasting energy and help create a feeling of fullness after eating. o They also help the body make hormones, form part of the brain and nervous system, form cell membranes for every cell in the body,  BIOCHEMISTRY S.Y. 2024 – 2025 | FIRST SEMESTER LECTURE | FINALS transport vitamins throughout the body, and regulate body FAT-SOLUBLE VITAMINS temperature. o Short-Chained Fatty Acids (SCFA) o Vitamin A ▪ Fatty acids with fewer than 6 carbon atoms. ▪ Vitamin A includes fat-soluble retinoids, including retinol, ▪ They are produced when the friendly gut bacteria ferment fiber retinal, and retinyl esters. in the colon. ▪ It is found preformed (retinoids) in animal products, or in ▪ The main source of energy for the cells lining the colon. precursor form (carotenoids) from plant foods. ▪ Involved in the metabolism of carbs and fat. ▪ Vitamin A is mainly stored in the liver. o Monounsaturated Fatty Acids (MUFA) ▪ It is involved in immune function, vision, reproduction, and ▪ Type of fat found in a variety of foods and oils. cellular communication. ▪ Improves blood cholesterol levels. ▪ It is an essential component of rhodopsin. ▪ Improves wound healing, increases the elimination of ▪ It supports cell growth and differentiation. pathogens, and is associated with protection against ▪ It is important in the maintenance of normal skin and mucus autoimmune diseases. membrane., as well as normal iron metabolism. o Polyunsaturated fatty acids (PUFA) o Vitamin D ▪ Type of fat found mostly in plant-based foods and oils, and cold- ▪ Bioactive vitamin D (calcitriol) is a steroid hormone. water fish. ▪ It is produced endogenously when UV rays from sunlight strike ▪ Improves blood cholesterol levels the skin. ▪ Decrease the risk of heart disease and type 2 diabetes. ▪ Vitamin D is mainly stored in fat and muscle tissue. o Saturated Fatty Acids ▪ Vitamin D is biologically inert and must undergo two ▪ Mainly from animal sources (i.e. red meat, poultry, and full-fat hydroxylations in the body for activation. dairy products) ▪ It promotes calcium absorption and maintains adequate serum ▪ Raises total blood cholesterol levels and LDL levels. calcium and phosphate concentrations. ▪ Increase the risk of cardiovascular disease. ▪ It promotes bone growth and bone remodeling. o Trans Fat ▪ It also modulates cell proliferation regulation, differentiation, ▪ Occurs naturally in some foods in small amounts. and apoptosis. ▪ Made from oils subjected to partial hydrogenation. o Vitamin E ▪ Increase LDL cholesterol levels. ▪ The collective name for a group of fat-soluble compounds with ▪ Lower HDL cholesterol. distinctive antioxidant activities. ▪ Increase the risk of cardiovascular disease. ▪ Naturally occurring vitamin E exists in eight forms. ▪ However, α-tocopherol is the only form of vitamin E recognized to meet human requirements. LIMITING AMINO ACIDS ▪ Vitamin E is partially stored in the liver. o These are amino acids that are in the shortest supply in relation to ▪ It protects cells from the damaging effects of free radicals. need. ▪ It stops the production of ROS formed when fat undergoes o These are found in the shortest supply from incomplete proteins - oxidation. proteins from plant food sources and gelatin ▪ It enhances vasodilation. o Incomplete proteins must be paired up with complementary proteins ▪ It also protects vitamins A and C, red blood cells, and essential in order to have sufficient amino acid supply needed by the body. fatty acids from destruction. o Vitamin K VITAMINS ▪ Vitamin K was discovered as a result of investigations into the o Vitamins are a group of organic nutrients required in small quantities cause of a bleeding disorder in some animals on a fat-free diet. for a variety of biochemical functions. ▪ Vitamin K is partially stored in the liver. o Most vitamins cannot be synthesized by the body and must, ▪ It promotes blood clotting. therefore, be supplied in the diet. ▪ It prevents bone breakdown. o They regulate metabolism and help convert energy from fat, ▪ It prevents arteriosclerosis by keeping calcium out of the carbohydrate, and protein into ATP. arterial linings. o They also promote growth and reproduction. ▪ It also protects cells from oxidative stress. TYPES OF VITAMINS WATER-SOLUBLE VITAMINS o Fat-Soluble Vitamins o Thiamin (B1) ▪ These vitamins require bile and dietary fat for absorption. ▪ Thiamin helps release energy from foods. ▪ Fat-soluble vitamins are absorbed in the duodenum and are ▪ It promotes normal appetite and is important in maintaining transported with fats through the lymphatic system in proper cardiovascular and nervous system function. chylomicrons. o Riboflavin (B2) ▪ They are stored in body fat and cannot be easily excreted. ▪ Riboflavin helps release energy from foods. ▪ They are toxic when taken excessively. ▪ It promotes good vision and healthy skin. o Water-Soluble Vitamins ▪ It also helps to convert tryptophan into niacin. ▪ Water-soluble vitamins are comprised of B complex and vitamin o Niacin (B3) C. ▪ Niacin can be synthesized in the body from tryptophan. ▪ They function as enzyme cofactors. ▪ It is involved in energy production and enzyme activity. ▪ They are absorbed with water and enter directly into the ▪ It is also involved in digestion, promoting normal appetite, bloodstream through the portal vein. healthy skin, and nerves. ▪ They are mostly absorbed in the duodenum and jejunum. ▪ It is toxic in excess. ▪ Excess intake is excreted through the urine. o Pantothenic Acid (B5) ▪ Pantothenic acid is involved in energy production.  BIOCHEMISTRY S.Y. 2024 – 2025 | FIRST SEMESTER LECTURE | FINALS ▪ It aids in the formation of hormones and the metabolism of fats, ▪ It is also necessary for nerve transmission and muscle proteins, and carbohydrates from food. contraction. o Pyridoxine (B6) o Sodium ▪ Pyridoxine aids in protein metabolism and red blood cell ▪ Sodium is needed for proper fluid balance. formation. It is also involved in the production of insulin and ▪ It helps control the blood volume. hemoglobin. ▪ It is also necessary for nerve transmission and muscle o Biotin (B7) contraction. ▪ Biotin is also known as Vitamin H or Coenzyme R. o Sulfur ▪ It helps release energy from carbohydrates. ▪ Sulfur is found in protein molecules. ▪ It aids in the metabolism of fats, proteins, and carbohydrates ▪ It helps regulate gene expression. from food. ▪ Plays a role in building and repairing DNA. o Folate (B9) ▪ It also helps the body metabolize food. ▪ Folate promotes red blood cell formation and lowers the risk for neural tube birth defects. TRACE MINERALS ▪ It aids in protein metabolism. o Iron ▪ It plays a role in controlling homocysteine levels, thus reducing ▪ Iron is part of hemoglobin found in red blood cells. the risk of coronary heart disease. ▪ It is needed for energy metabolism. o Cobalamin (B12) ▪ It is critical for motor and cognitive development. ▪ Cobalamin aids in the building of genetic material. o Copper ▪ It helps in the production of normal red blood cells and plays a ▪ Copper is necessary for iron absorption and incorporation of role in the maintenance of the nervous system. iron into hemoglobin. o Ascorbic Acid (Vitamin C) ▪ It is very essential for tyrosinase activity. ▪ Vitamin C holds cells together through collagen synthesis. ▪ It is the co-factor for vitamin C requiring hydroxylation. ▪ It aids in wound healing. ▪ Copper increases the level of high-density lipoprotein and ▪ It helps bone and tooth formation, as well as strengthens blood protects the heart. vessel walls. o Zinc ▪ Vitamin C improves immune system function. ▪ Zinc promotes immunity and resistance to infection. ▪ It also increases the absorption and utilization of iron. ▪ It helps in proper growth and development of the nervous ▪ It works with vitamin E as an antioxidant. system. o Fluoride MINERALS ▪ Fluoride is well known for its protective effect on caries. o Minerals are solid crystalline, chemical elements that cannot be o Selenium decomposed and synthesized by ordinary chemical reactions. ▪ Selenium is an antioxidant. o They are present in both plants and animals to execute specific o Manganese functions. ▪ Manganese-activated enzymes play important roles in o Deficiencies of most minerals are shown by reduced appetite and the metabolism of carbohydrates, amino acids, production, slow growth, and occasionally death. and cholesterol. ▪ Manganese superoxide dismutase (MnSOD) is the MAJOR MINERALS principal antioxidant enzyme in the mitochondria. o Molybdenum o Calcium ▪ Molybdenum functions as a prosthetic group in some enzymes. ▪ Plays a role in bone and tooth formation. ▪ Its main function is removing toxins from the metabolism of ▪ Responsible for the excitation and contraction of muscle fibers. sulfur-containing amino acids. ▪ Transmission of the nerve impulse from presynaptic to o Iodine postsynaptic region. ▪ Iodine is found in the thyroid hormone, which regulates ▪ Required in the activation of some clotting factors. growth, development, and metabolism. o Chloride ▪ It is one of the most important minerals required by a fetus for ▪ Chloride is needed for proper fluid balance. brain and cognitive development. ▪ It is also an important component of stomach acid. o Chromium ▪ Sources of chloride include table salt, soy sauce, processed ▪ Chromium works closely with insulin to regulate blood sugar foods, milk, bread, meats, and vegetables levels. o Phosphorus ▪ It stimulates fatty acid and cholesterol synthesis. ▪ Plays a key role in the formation of tooth and bone. ▪ Production of high energy phosphate compounds such as ATP, CTP, GTP etc. ▪ Synthesis of nucleotide co-enzymes such as NAD and NADP. ▪ Formation of phosphodiester backbone structure for DNA and RNA synthesis. ▪ Plays a role in acid-base balance. o Magnesium ▪ It is needed for making protein. ▪ Lowers irritability of neuromuscular tissues. ▪ Magnesium supplementation improves glucose tolerance. ▪ Promotes muscle contraction and nerve transmission. ▪ Improves immune system health. o Potassium ▪ Potassium is needed for proper fluid balance.