PCCH104 Biochemistry Lecture Midterms PDF

PCCH104 Amino Acids Biochemistry Lecture ➔ Organic compounds containing an amino PCCH104-1-22 group (NH2) and a carboxylic acid group 1st Semester Midterms | P...

PCCH104 Amino Acids Biochemistry Lecture ➔ Organic compounds containing an amino PCCH104-1-22 group (NH2) and a carboxylic acid group 1st Semester Midterms | Prof. Salazar (COOH) ◆ Basic - amino group/amine ◆ Acidic - carboxylic acid group MODULE 4 ➔ Building blocks of protein. ➔ *monomers of proteins. Proteins ➔ *proteins are good buffers Protein Digestion Diseases Associated with Proteins PROTEINS What makes up proteins? WHAT ARE PROTEINS? Proteins ➔ A group of complex organic macromolecules that contain carbon, hydrogen, oxygen, nitrogen, and usually 20 COMMON AMINO ACIDS sulfur. ➔ Linear polymers of amino acids connected by peptide bonds. ➔ Diverse abundant class of biomolecules. ➔ The most important of all biological compounds. Amino Acids ➔ Derived from the Greek word proteios, which Most amino acids are chiral molecules. means first of importance. ○ Chiral carbon centers are carbon atoms ➔ Constitutes about 50% of the dry weight of that are attached to four different cells. substituents. ➔ Unlike lipids and carbohydrates, proteins are not stored, so they must be consumed daily. ➔ Current recommended daily intake for adults is 0.8 grams of protein per kg of body weight. ➔ Dietary protein usually comes from eating Most common amino acids are α-amino meat and dairy products. acids. All amino acids in the body are L-isomers. WHAT MAKES UP PROTEINS? ♡  *location of N ang titingnan Left side N = L-isomer Right side N = D-isomer ○ Exemptions: Glycine ❖ Peptides and proteins are formed when amino acids are joined together by amide ➔ It is the simplest amino acid. bonds. The amide bond is called peptide ➔ It is the only achiral amino acid. bond. Proline ❖ A dipeptide has two amino acids joined together by one peptide bond. ❖ Polypeptides have many amino acids, while proteins have more than 40 amino acids. ➔ It is an imino acid. ➔ It is a secondary amine. All amino acids are amphiprotic compounds. ○ They have an acidic and basic EXAMPLE OF AMINO ACIDS component. * Acidic = Carboxyl Group Basic = Amino Group FORMATION OF PEPTIDE BONDS All amino acids are zwitterions Peptide Bonds are formed by a condensation ○ Zwitterions have a positive and negative reaction end ○ Water is removed. ○ Zwitterions are neutral. ○ Zwitterion can only exist at a specific pH If the amino acid is in zwitterion form: ○ Isoelectric point is a pH at which amino 1. Remove an oxygen from the first amino acids have equal positive and negative acid. (*never remove double bonded O, charges. only single bonded O) *at a specific isoelectric point, 2. Remove two hydrogens from the second amino acids have no charge. amino acid. 3. Connect the two amino acids. ♡  Remove a hydrogen from the second amino acid. Connect the two amino acids. EXAMPLE EXERCISE Create a dipeptide: Ala-Gly - Count the number of amino acids present. Remove an oxygen from the first amino acid. > five Remove two hydrogens from the second amino acid. - Connect the two amino acids. If the amino acid is uncharged: 1. Remove an oxygen and a hydrogen from the first amino acid. 2. Remove a hydrogen from the second amino acid. 3. Connect the two amino acids. CLASSIFICATION OF AMINO ACIDS EXAMPLES Create a dipeptide: Gly-Ala *amino acids depend on their polarity. 1. Non-polar ➔ Leucine, Isoleucine, Proline, Alanine, Valine, Methionine, Phenylalanine, Tryptophan 2. Polar uncharged (neutral) ➔ Glycine, Serine, Asparagine, Glutamine, Tyrosine, Threonine, Cysteine 3. Polar acidic ➔ Aspartic Acid, Glutamic Acid ➔ *has 2 COOH Remove an oxygen and a hydrogen from the first amino acid. ♡ 4. Polar basic ➔ Promotes the repair of tissues. ➔ Histidine, Lysine, Arginine ➔ Helps with energy prevision. ➔ *has excess nitrogen group ➔ Regulates blood sugar levels. ➔ Assists with normal growth and development. ➔ Stimulates the central nervous system. ➔ Builds muscle mass. ➔ Helps with stress management. ESSENTIAL AMINO ACIDS ➔ Regulates the immune system. ❖ Essential amino acids are amino acids that Tryptophan cannot be produced by the body. ❖ There are 10 essential amino acids: Phenylalanine* Valine Threonine Tryptophan Isoleucine Methionine** ➔ Required to produce serotonin and Histidine*** melatonin. Arginine**** ➔ Improves sleep quality. Semi-essential ➔ Supports the immune system, metabolism, Tinatanggal sa ibang circulation, CNS, and enzyme production. references/books. ➔ Needed for the manufacture of vitamin B3 Leucine (niacin). Lysine ➔ Assists with the regulation of blood sugar. ➔ Stops free radical damage. Phenylalanine ➔ Prevents cholesterol buildup. ➔ Production of tyrosine. ➔ It is required if one’s diet does not contain enough tyrosine. ➔ Formation of neurotransmitters and Threonine hormones. ◆ Norepinephrine ◆ Epinephrine ◆ Dopamine ◆ Thyroid Hormones ➔ Helps with depression. ➔ * fight or flight responde ➔ Helps maintain the balance of protein in the body. Valine ➔ Supports normal growth and development. ➔ Supports the central nervous system, cardiovascular system, immune function, and liver function. ➔ Produces the amino acids serine and glycine. ♡ ➔ Helps to process fatty acids and prevent liver ➔ Essential for maintaining energy and blood failure when combined with methionine and supply as well as detoxification of heavy aspartic acid. metals. ➔ Regulation of the blood pH and wound Isoleucine healing. Arginine ➔ Involved in muscle development and repair. ➔ Insufficient levels of this amino acid within the body can produce symptoms that are similar to those experienced by people suffering ➔ * can be produced by the body. from hypoglycemia. ➔ Improves the burning of excess fat. ➔ Decreases cholesterol levels. Methionine ➔ It is converted in the body into nitric oxide. ➔ Preterm infants are unable to synthesize arginine. ➔ A semi-essential amino acid. ➔ The rate of synthesis is too slow. ➔ Stimulates the release of growth hormone and insulin. ➔ Improves the circulation. ➔ Sulphur-containing essential amino acid. ➔ strengthens the immune system. ➔ Helps in effectively processing and removing ➔ Enhances male libido. fat. ➔ Accelerates the rate of wound healing. ➔ Prevents liver damage in acetaminophen poisoning. Lysine ➔ Improves wound healing. ➔ Produces the amino acids: ◆ Taurine ◆ Cysteine ◆ Glutathione Histidine ➔ Helps to build a healthy immune system. ➔ Involved in the development of antibodies and has important antiviral properties. ➔ Assists with the formation of collagen and muscle tissue. ➔ Aids in growth and maintenance of bones. ➔ Essential for infants to ensure the regulation ➔ Lowers cholesterol. of growth and natural development and ➔ * this and zinc are important in vitamins. repair mechanisms. ➔ Production of histamine, glutamate, ferritin and hemoglobin. ♡  Chief constituents of skin, bones, hair, Leucine and nails. ★ Examples: ○ Collagen ○ Keratin ○ Elastin ○ Fibroin → proteins that constitute silk fibers ➔ The 4th most concentrated amino acid found KERATIN within muscle. ➔ Keratins comprise the type I and type II ➔ Helps to maintain nitrogen balance and intermediate filament-forming proteins and energy supply. occur primarily in epithelial cells. ➔ Support muscle building. ➔ Found on epithelial cells, which line the inside ➔ Decreases muscle wasting. and outside surfaces of the body. ➔ Lowers cholesterol and LDL levels. ➔ Keratins help form the tissues of the hair, ➔ Reduces the risk of atherosclerosis. nails, and the outer layer of the skin. Limiting Amino Acid The amino acid that is in shortest supply in relation to need. Essential amino acids that are present in relatively small amounts and are below the amino acid requirements. COLLAGEN ○ Shortage inhibits protein synthesis ➔ Most abundant protein in the body. ○ Usually from incomplete proteins. ➔ Its is used to make connective tissue. Plant-food sources and gelatin. ➔ It is a major component of bone, skin, Examples of Limiting Amino Acid muscles, tendons, and cartilage. ➔ It is composed of three chains, wound together in a tight triple helix. ➔ It helps to make tissues strong and resilient. ELASTIN ➔ Elastin is a key extracellular matrix protein that is critical to the elasticity and resilience of many vertebrate tissues including large arteries, lung, ligament, tendon, skin, and elastic cartilage. WHAT ARE THE FUNCTIONS OF PROTEINS? Functions of Proteins 1. Structure Proteins provide strength to cells and tissue. ♡ 2. Catalysis Reactions in the body are catalyzed by enzymes. Enzymes speed up reactions by lowering the activation energy. ★ Example: Amylase (for digesting 4. Transport carbohydrates), Lipase (for digesting Proteins transport other substances lipids), Protease (for digesting ★ Examples: proteins) ○ Hemoglobin 3. Movement ○ serum albumin Muscles are made up of protein ○ Lipoproteins molecules HEMOGLOBIN ★ Example: ➔ Carries oxygen from the lungs to the body’s ○ Myosin tissues and returns carbon dioxide from the ○ Actin tissues back to the lungs. ○ Tropomyosin (regulate the ➔ Made up of four globulin chains. interaction of actin and myosin) ➔ Each globulin chain contains heme. ○ Troponin ➔ Responsible for the color of blood. MYOSIN ➔ Maintains the shape of the red blood cells. ➔ Thick filament ◆ Head and tail ➔ Motor protein ➔ Generates the force in a muscle contraction. ACTIN SERUM ALBUMIN ➔ Spherical protein ➔ Serum Albumin is the largest protein ➔ Thin filament component of human blood (50-60%) ◆ 2 long chains ➔ It is an important factor in the regulation of ➔ Each actin has a myosin-binding site. plasma volume and tissue fluid balance. TROPOMYOSIN ➔ Blocks myosin binding sites on actin molecules, preventing cross-bridge formation. ➔ Prevents contraction in a muscle without 5. Hormones nervous input. Chemical messengers released in the bloodstream. TROPONIN Endocrine glands ➔ Globular protein. ★ Examples ➔ Protein complex that binds to tropomyosin. ○ Insulin ➔ Helps position tropomyosin on the actin ○ Erythropoietin molecule. ○ Somatotropin ○ Vasopressin ○ Oxytocin ♡ ERYTHROPOIETIN ➔ Growth hormone ➔ Glycoprotein hormone ➔ Secreted by the anterior lobe of the pituitary ➔ It is naturally produced by the peritubular gland. cells of the kidney ➔ It stimulates the growth of essentially all ➔ It acts on red blood cells to protect them tissues of the body. against destruction. ➔ Keeps blood glucose levels within set levels. ➔ It stimulates stem cells of the bone marrow to ➔ Decreases the rate of glucose uptake and increase RBC production. metabolism ➔ EPO doping increases an athlete’s performance ability and endurance. VASOPRESSIN ➔ Antidiuretic hormone ➔ Produced in the hypothalamus. ➔ Helps control blood pressure by acting on the kidneys and the blood vessels. ➔ Conserves body water by reducing the loss of water in urine. OXYTOCIN ➔ It is a neurotransmitter ➔ Produced in the hypothalamus ➔ It is released in response to activation of sensory nerves during labor, breastfeeding, sexual activity, positive interaction between DOPAMINE adults or between humans and animals. ➔ It is a neurohormone ◆ well-being and anti-stress effects ➔ Produced in the hypothalamus ➔ Provides an intense feeling of reward. ➔ Pleasure and Addiction ➔ Low dopamine levels are associated with diseases including Parkinson’s disease, restless legs syndrome and attention deficit hyperactivity disorder (ADHD) SOMATOTROPIN ♡ SEROTONIN ➔ It is a neurohormone ➔ Mostly found in the gut ➔ It influences learning, memory, happiness as well as regulating body temperature, sleep, sexual behavior and hunger. ➔ Lack of enough serotonin is thought to play a CIRCADIAN RHYTHM role in depression, anxiety, mania and other ➔ Physical, mental, and behavioral changes an health conditions organism experiences over a 24-hour cycle. ➔ Body clock ◆ *may specific na hormones na narerelease per cycle. MELATONIN ➔ Sleep hormone ➔ Initiates and maintains sleep ➔ Produced in response to darkness. ➔ Pineal gland ➔ Being exposed to light at night can block melatonin production. ➔ It helps with sleep-wake cycle ➔ Circadian rhythm ➔ Immune system health ➔ Antioxidant 6. Protection When a protein from an outside source or some other foreign substance (antigen) enters the body, the body makes its own proteins (antibodies) to counteract the foreign protein. ★ Examples ○ Immunoglobulin (*antibodies) ○ Fibrinogen ○ Thrombin 7. Storage Proteins provide a reservoir of an essential nutrient. ♡  They also provide sufficient nitrogen in ➔ Connected by peptide bond and times of need. hydrogen bonds ★ Examples ➔ Alpha-helix; beta pleated; random coil ○ Ovalbumin ○ Casein ○ Ferritin MYOGLOBIN ➔ Monomeric protein found mainly in muscle tissue ➔ It serves as an intracellular storage site for 3. Tertiary Structure oxygen. ➔ The complete 3D arrangement of the ➔ The primary function of myoglobin is to atoms in a protein supply oxygen to the muscle. ➔ Held together by: ◆ peptide bonds ➔ * “myo” = muscle ◆ hydrogen bonds ➔ * red meat - high in myoglobin (e.g. beef, ◆ disulfide bonds pork, chicken thigh and legs.) ◆ salt bridges ➔ * white meat - low in myoglobin and this is healthier (e.g. chicken breast and wings) OVALBUMIN ➔ The major egg white protein synthesized in the hen's oviduct ➔ It is responsible for egg white formation. ➔ It accounts for about 54% of the total proteins of egg albumen. 4. Quaternary Structure FERRITIN ➔ The spatial relationship and interactions ➔ Ferritin is a protein complex that stores iron in between subunits in a protein that has a soluble, non-toxic form. more than one polypeptide chain ➔ Low levels of ferritin lead to iron-deficiency ➔ Held together by peptide bonds, anemia. hydrogen bonds, disulfide bonds, salt ➔ High levels of ferritin can damage your joints, bridges heart, liver, and pancreas. ➔ * dalawang tertiary structure na pinagsama ➔ *ferrous - ginagamit natin na iron sa body. HOW ARE PROTEINS CLASSIFIED? Levels of Proteins Structure 1. Primary Structure LEVELS OF PROTEIN STRUCTURES ➔ Linear sequence of amino acids. ➔ A small protein has at least 60 amino acids residues. ➔ Connected by peptide bonds. 2. Secondary Structure ➔ A repetitive conformation of the protein According to Shape backbone ♡ 1. Fibrous According to Nutritional Basis ➔ Long and narrow ➔ Used mainly for structural purposes 1. Complete Proteins ➔ Repetitive amino acid sequences ➔ Contains an adequate amount of all the ➔ Less sensitive to changes in pH and essential amino acids that should be temperature incorporated in the diet ➔ Insoluble to water ➔ Even if the protein contains all the *structural protein – for movement (e.g. essential amino acids, they must be in myosin, keratin, etc.) equal proportion in order to be considered complete ➔ Generally comes from animal and fish products ★ Source: meat, fish, dairy, egg 2. Incomplete Proteins ➔ Any protein that lack one or more essential amino acids in correct proportion 2. Globular ➔ Also called partial proteins ➔ Round / spherical ★ Source: grains, nuts, beans, seeds, peas, ➔ Used for non-structural purposes corn ➔ Irregular amino acid sequence ➔ More sensitive to changes in pH and temperature ❖ Combining two or more incomplete ➔ More or less soluble to water proteins to create a complete protein *most proteins are globular (e.g. ❖ Complementary proteins compensate hemoglobin, lipase, melatonin, etc.) for each other’s lack of amino acids *partner for limited amino acids PROPERTIES OF PROTEIN Protein Denaturation Denaturation ➔ the loss of the secondary, tertiary and According to Composition quaternary structures of a protein by a chemical or a physical agent 1. Simple Proteins ➔ the primary structure remains intact ➔ composed of amino acids ➔ also called homoproteins ★ Examples: albumins, globulins, glutelins, albuminoids, histones, protamines, collagen, and keratin 2. Conjugated Proteins ➔ contains a prosthetic group or a non-protein part in addition to protein. ★ Examples: Glycoprotein, Phosphoprotein, Lipoprotein, Chromoprotein 3. Derived Proteins ➔ Proteins derived from simple or conjugated proteins by physical or chemical means. FACTORS THAT CAUSE PROTEIN DENATURATION ★ Examples: denatured proteins and 1. Heat – cleaves hydrogen bonds peptides ♡ 2. Detergents – opens up hydrophobic regions 3. Acids and bases – affects salt bridges and Discussion H-bonds - Enzymes needed to break down protein are 4. Salts – affects salt bridges and H-bonds produced inactive form (meaning hindi sila 5. Reducing agents – breaks disulfide bonds active pag pinoproduce ng katawan). 6. Heavy metal ions – attacks SH group Because pag palaging active, palaging 7. Alcohol – Hydrogen bonds gagana and uubusin organs. Dapat 8. Mechanical Stress inactive talaga siya. Protein Hydrolysis It only becomes active once acetylcholine and gastrin are produced, and the pH of the Breaking the peptide bonds by treatment stomach drops to 1.5-2.0 (we release with aqueous acid, base, or certain enzymes. gastric juice). The primary structure of protein is cleaved by the addition of water. Pepsin ○ Gastric chief cells - pepsinogen Acetylcholine Gastrin pH 1.5-2.0 PROTEIN DIGESTION Discussion - Protein → speeds up chemical reactions. Enzymes → biological catalyst. Trypsin ○ Pancreas - Trypsinogen Start of Digestion: Carbohydrates – begins in the mouth ○ Enterokinase (Positive feedback) Lipid – Adults sa stomach, Babies sa mouth Chymotrypsin ○ Pancreas - Chymotrypsinogen ○ Trypsin ORGANS INVOLVED IN PROTEIN DIGESTION Elastase ○ Acinar cells - Proelastase Stomach ○ Trypsin ○ Start of protein digestion Pancreas Discussion Small Intestine ○ Major digestion of protein - Lahat galing sa pancreas and inactive. Once chyme enters the small intestine, it is neutralized and maaactivate ang trypsin, chymotrypsin, and elastase. Carboxypeptidase ○ Pancreas - Procarboxypeptidase ○ Aromatic amino acids ○ Branched amino acids Aminopeptidase ○ Small intestine - Proaminopeptidase ENZYMES INVOLVED IN PROTEIN DIGESTION ♡  DISEASES ASSOCIATED WITH PROTEINS Discussion - Anything that has something to do with blood or enzymes is related to proteins. 1. Protein Deficiency ➔ A state of relative or absolute deficiency of body proteins or one or more of the essential amino acids. ➔ Hypoproteinemia DIGESTION OF PROTEINS ➔ A state of relative or absolute deficiency of body proteins or one or more of the essential Digestion of proteins begins in the stomach amino acids. ○ HCl denatures proteins ➔ Rare in developed countries ○ Pepsin cuts proteins into smaller ◆ * most prevalent kapag hindi tama or polypeptides kulang ang kinakain. The small intestine releases hormones to stimulate the digestive process ○ Secretin - Sodium bicarbonate ○ Cholecystokinin - pancreatic enzymes Majority of protein digestion occurs in the small intestine Signs of Protein Deficiency ABSORPTION OF PROTEINS In adults, essentially all protein is absorbed as tripeptides, dipeptides or amino acids ○ Happens in the duodenum ○ via Facilitated diffusion or active process Amino acids are transported to the liver via 2. Protein Energy Malnutrition the hepatic portal vein ○ through the Enterohepatic circulation ➔ Protein-energy undernutrition ➔ A condition arising from inadequate intake of food rich in energy and protein, characterized by marked weight loss and failure to grow ◆ Kwashiorkor ◆ Marasmus PEM IN THE PHILIPPINES ❖ For nearly thirty years, there have been almost no improvements in the prevalence of undernutrition in the Philippines. ♡ ❖ In September 2020, after seven months of ◆ Phenylalanine hydroxylase breaksdown community quarantine, 31% of families phenylalanine reported experiencing hunger in the past 30 ➔ Phenylalanine can build up in the blood and days, and 9% were suffering severe hunger. brain. ➔ Does not usually cause any symptoms if 3. Marasmus treatment is started early. ◆ Without treatment, PKU can damage the ➔ Severe undernutrition — a deficiency in all the brain and nervous system, which can macronutrients that the body requires to lead to learning disabilities. function, including carbohydrates, protein ➔ behavioral difficulties and fats. ◆ frequent temper tantrums and episodes ➔ Marasmus causes visible wasting of fat and of self-harm muscle under the skin, giving bodies an ➔ fairer skin, hair and eyes than siblings emaciated appearance. ➔ eczema ➔ It causes stunted growth in children. ➔ jerking movements in arms and legs ➔ tremors 4. Kwashiorkor ➔ epilepsy ➔ musty smell to the breath, skin and urine ➔ Severe form of malnutrition ◆ Severe protein malnutrition ➔ Bilateral extremity swelling ➔ Usually affects infants and children. ◆ Poverty-stricken regions ◆ Diets based mainly on maize, cassava, or rice ➔ Previously believed to be due to protein deficiency and low levels of antioxidants and aflatoxins. ➔ Too much fluid in the body's tissues, which causes swelling under the skin (edema). ➔ Usually begins in the legs, but can involve the whole body, including the face. ➔ Marked muscle atrophy ➔ Abdominal distension ➔ Round face ➔ Subcutaneous fat retention with loose inner inguinal skin folds ➔ Thin, dry, peeling skin with areas of scaling and hyperpigmentation ➔ Dry, full, hypopigmented hair that falls out or is easily plucked ➔ Growth retardation ➔ Psychic changes (anorexia, apathy) ➔ Skin lesions/dermatitis (perineum, groin, limbs, ears, armpits) 5. Phenylketonuria ➔ a rare inherited disorder that causes an amino acid called phenylalanine to build up in the body. ➔ PKU is caused by a change in the phenylalanine hydroxylase (PAH) gene. ♡