Biochemistry MIDTERM REVIEWER 2024 PDF

MIDTERM EXAM REVIEWER – BIOCHEMISTRY LEC/LAB By Team Meow Meow = ( Halimeow and the three headed creature) DNA vs RNA Purine vs Pyrimidines Deoxyribonucleic acid (DNA) Found within the cell nucleus Stores an...

MIDTERM EXAM REVIEWER – BIOCHEMISTRY LEC/LAB By Team Meow Meow = ( Halimeow and the three headed creature) DNA vs RNA Purine vs Pyrimidines Deoxyribonucleic acid (DNA) Found within the cell nucleus Stores and transfers genetic information Passed from existing cells to new cells during cell division Ribonucleic Acid (RNA) Remember the mnemonic - Purines are double ring = if you are married you will say GA Occurs in all parts of a cell - pyrimidine remember - when you are single you CUT the Primary function is the synthesis of proteins relationship. Nucleoside formation C1 – the nitrogous base is connected C2 – where sugar is differentiated from H and OH C5 – Phosphate STRUCTURAL CHARACTERISTICS OF DNA DNA is composed of two polynucleotides, anti-parallel with each other (One strand runs from 5’ to 3’, while Components of Nucleic Acid the other strand runs from 3’ to 5’) = Opposite Nucleotide – nitrogen base + sugar + phosphate Direction nucleoside – nitrogen base + sugar o On the outside = Sugar-Phosphate Backbone o On the inside = Hydrophobic Bases Difference between ribose and deoxyribose sugar The two strands are connected by Hydrogen Bonding Deoxyribose = H in the second carbon between base pairs (Watson-Crick Base Pairs): Ribose = OH in the second carbon Adenine – Thymine = 2 Hydrogen Bonds (Easier to separate) Cytosine – Guanine = 3 Hydrogen Bonds (Harder to separate)  Base Pairing Steps in DNA replication A pyrimidine is always paired with a purine 1. helicase unwind the helix and separates the strands 2. primase anneals RNA primers A–T and G–C pairing is termed complementary 3. polymerase III copies each strands o Once continuously on leading stand and Okazaki Predict the sequence of bases in the DNA strand fragments on lagging strand complementary to the single DNA strand shown below: 4. polymerase I replaces the primers with DNA nucleotides 5. ligase seals everything up 5′ A–A–T–G–C–A–G–C–T 3′ Important enzymes of DNA replication 3’ T-T-A- C-G-T-C-G-A 5’ - DNA helicase- Breaks hydrogen bonds between DNA strands - DNA polymerase-Joins free nucleotides into a new strand of DNA - DNA ligase-Joins DNA segments on discontinuous strand CHARGAFF’S RULE: Content of A = Content of T Transcription - is the process of copying a segment of DNA into RNA. The Content of G = Content of C segments of DNA transcribed into RNA molecules that can encode Example: if G is 30 what is A, T ,C proteins are said to produce messenger RNA. RNA in Protein Synthesis (A= T) +(G=C) = 100 Type of RNA (20+20) +(30+30) = 100 Ribosomal RNA (rRNA) o Most abundant type of RNA Central Dogma o Structural component of the ribosome Replication: identical copies of DNA are made o Associates with ribosomal proteins to form the complete, functional ribosome Transcription: genetic messages are read and carried Transfer RNA (tRNA) out of the cell nucleus to the ribosomes, where o Second most abundant protein synthesis occurs. o Carry amino acids to the ribosome, where they will be Translation: genetic messages are decoded to make linked together during protein synthesis proteins. Messenger RNA (mRNA) o Carries information specifying the amino acid sequence of a protein to the ribosome o ONLY type of RNA that is translated o Very heterogeneous in size and base sequence Translation - mRNA is translated to protein - rRNA and tRNA translate the sequence of base triplets in mRNA into a sequence of amino acids Codon - A sequence of three mRNA nucleotides that codes for a specific amino acid - The order of codons in mRNA determines the order of amino DNA REPLICATION acids in a polypeptide chain - The doubling process of DNA molecules - The parent molecule unwinds, and two new daughter strands are Some codons signal the start or end of a gene built based on base pairing rules - A cell copies its DNA before mitosis or meiosis I - AUG (methionine) is a start codon - DNA replication takes place in the nucleus during interphase. - UAA, UAG, and UGA are stop codons - DNA repair mechanisms and proofreading correct most replication errors - New dna need to be made before cells can divide. The two daughter cells must each receive a complete set of DNA. The base sequences on the new DNA molecules must be identical with those on the original set.  Different forms of DNA B form - Most stable, right-handed double helix, Watson-Crick structure, predominant form in physiological conditions A form - Right-handed double helix, wider turn, favored in solutions lacking water Z form - Left-handed helix, zigzag appearance, elongated and slende Mutations - change in the usual DNA sequence at a particular gene locus. Although the term often has a negative connotation, mutations (including polymorphisms) can be harmful, beneficial, or neutral in their effect on cell function. Types of mutation Point mutation - a change in a single base pair in DNA, which is the genetic material of a cell o Silence mutation – causes no change in the activity of What is Lipid the protein. A lipid is an organic compound found in living organisms that is o Missense mutation – is a change in one DNA base pair insoluble (or only sparingly soluble) in water but soluble in non- that results in the substitution of one amino acid for polar organic solvents. another in the protein made by gene. o Nonsense mutation – is also a change in one DNA Unlike other biomolecules, lipids do not have common structural base pair. Instead of substituting one amino acid for feature that serves as the basis for defining such compounds. another, the altered DNA sequence prematurely signals the cell to stop building a protein which Classification: they are classified on the basis of solubility not on any results to a shortened protein that may function functional groups improperly or not at all o Insoluble or sparingly soluble in water Frameshift mutation – the addition or loss of DNA bases changes o Soluble in non-polar organic solvent a gene’s reading frame (consists of groups of 3 bases that code for amino acid). Resulting protein is usually nonfunctional. Deletions, insertions, duplications can all be frameshift mutations. o Deletion – it removes or lost a chromosomal segment. o Duplication – it repeats a segment; the deleted fragment may become attached as an extra segment to a sister o chromatid. o Inversion – reverses a segment within a chromosome; a chromosomal fragment may also reattach to the original chromosome but in a reverse orientation. o Translocation – moves a segment from one chromosome to a nonhomologous chromosome. In a reciprocal translocation, the most common type, nonhomologous chromosomes exchange fragments. Type of lipid 1. energy-storage lipids - triacylglycerols Polymerase chain reaction 2. membrane lipids - phospholipids, sphingoglycolipids, and Polymerase chain reaction, or PCR, is a technique to make many cholesterol copies of a specific DNA region in vitro. 3. emulsification lipids - bile acids (1) denaturation of the template into single strands; 4. chemical messenger lipids - steroid hormones (2) annealing of primers to each original strand for new andeicosanoids) strand synthesis; 5. protective-coating lipids - biological waxes (3) extension of the new DNA strands from the primers.  FATTY ACIDS Physical Properties structural components of all the lipids 1. Solubility Members of carboxylic acids: hydrocarbon chain with one 2. Melting temperature terminal carboxyl group (COOH). Determined by chain length and degree of saturation: Although the molecule as a whole is water-insoluble, the ▪ V # of Cs = V m.p. = less solubility negatively charged carboxylate is hydrophilic. Presence of double bond = X the melting point and boiling point Most fatty acid is even numbered up to 10C = soluble in water if greater than 10C = becomes less soluble to insoluble Unsaturated Fatty Acid = more soluble than their corresponding saturated fatty acid with the same number of carbon 1. Solubility ❖ Fatty acids are amphipatic- containing hydrophilic (carboxyl group) and hydrophobic (hydrocarbon chain) groups ❖ Short chain fatty acids ❖ are sparingly soluble in water due to polar carboxylic acid SATURATED VS UNSATURATED group (water soluble: C2-C10) ❖ The longer the hydrocarbon chain and the fewer double bonds, the lower the solubility in water Saturated fatty acids: ❖ The increasing number of double bonds has the effect of Bad cholesterol; (low density shortening the length of the hydrocarbon chain, therefore, lipoprotein) making it more soluble in water Solid at room temperature 2. Melting temperature ❖ longer chain length = more Van der Waals bonds present Unsaturated fatty acids ❖ increase chain length = increase in the melting temperature Good cholesterol ( high density ❖ Example: lipoprotein) Liquid at room temperature ▪ Stearic acid (18:0) = 69.9oC ▪ Oleic acid (18:1) = 13.4 o C Monounsaturated – one ❖ The degree of saturation also affects melting temperature by double bond; e.g.oleic (C16:1) determining te amount of van der waals forces between fatty Polyunsaturated – two or acid molecules more double bonds; e.g. arachidonic acid (C20:4) ❖ Saturation allows ordered formation with increased intermolecular attraction (nagdidikit-dikit yung faty acid chains)- result in increase melting temperature unsaturation induces disorder with decreased intermolecular attraction – FATTY ACID CLASSIFICATION results in decreased melting point (less clumping) short chain medium chain long chain ▪ less than 6 ▪ 6 to 12 C ▪ greater than 12 C C ▪ e.g. lauric (12) ▪ e.g. palmitic (16) ▪ e.g. butyric ▪ in coconut oil ▪ not water soluble (4) ▪ water soluble Note: The shorter carbon atom the shorter Boiling Point and Melting Point / the more double bonds lower melting point  Essential fatty acids (EFA) PROSTAGLANDINS Animals cannot insert double bonds at the methyl end of the fatty acid c20-fatty-acid derivative containing cyclopentane ring and oxygen- molecule, at n-6 and n-3. containing,functional groups Animals require n-6 and n-3 fatty acids in their diets. involved in raising body temperature, Most animals can carry out chain elongation and desaturation. These inhibiting the secretion of gastric juices, animals can use the 18 carbon EFA in their diets increasing the secretion of a protective mucus layer into the 18:2(n-6) and 18:3(n-3). stomach, relaxing and contracting smooth muscle, directing water Cats and some fish (carnivores) cannot carry out chain elongation and and electrolyte balance, intensifying pain, and enhancing desaturation. These animals require the long chain 20 and 22 carbon inflammation responses. EFA in their diet. Why do u drink aspirin during fever - aspirin reduces fever by inhibits an enzyme needed to make prostaglandins—those natural Cis vs trans fatty acids chemicals in our body that produce pain, inflammation and fever. Why do u need to eat before taking aspirin – it acts a neutralizer with the stomach acids since you will block the prostaglandins which inhibits mucus production and increase gastric secretion THROMBOXANES c20-fatty-acid derivative containing a cyclic ether ring and oxygen- containing functional groups promote platelet aggregation. act in the formation of blood clots and reduce blood flow to the site of a clot aspirin is contraindicated in dengue fever. This is explained by Why trans fatty acid is bad – because straighter and easily pack the anti-platelet and anticoagulant effects that make the bleeding caused by dengue fever uncontrollable, especially gastrointestinal HUFA: Higher unsaturated fatty acids PROSTANOIC ACID (C20) IS THE BASIC STRUCTURE IN LEUKOTRIENES PROSTAGLANDINS c20-fatty-acid derivative containing three conjugated double bonds 20:4(n-6) Arachidonic and hydroxyl groups 20:5(n-3) Eicosapentenoic (EPA) promote inflammato LTB4 – increase vascular permeablity , T- cell 22:6(n-3) Docosahexenoic (DHA) proliferation leukocyte aggregation IL-1, IL-2 , IFN-y The 20 carbon fatty acids are precursors of the eicosanoids consisting of LTC4 and LTD4 – increase bronchoconstriction , vascular two groups: prostaglandins and leukotrienes (slow reacting substances permeability ry and hypersensitivity (allergy) responses of anaphylaxis).. Eicosanoids act as “local hormones” Simple Glycerides They mediate a number of physiological responses, such as Esters of glycerol and a fatty acid. inflammation, anaphylaxis, smooth muscle contraction Principal function is energy storage - fat. DHA is apparently necessary for proper neural and visual function development eicosanoids arachidonic acid (20:4) derivatives: a. have profound physiological effects at extremely low concentrations. eicosanoids usually have a very short “life.” From 1 to 3 fatty acids may esterify with one glycerol. The acids may be the same or all different. 1 fatty acid gives a monoglyceride; 2 fatty acids gives a diglyceride; 3 fatty acids give a triglyceride. TRIACYLGLYCEROL major form by which energy is stored and found in adipose tissue Energy yield of 9cal/g is greater than that from carbohydrate or protein Compact in form and lighter because it has no water accompanying it Formed by esterification of 3 fatty acids to glycerol  Naming a triacylglycerol SPHINGOLIPIDS Mixed Triacylglycerol – when tere are different R groups or fatty Parent structure = sphingosine, an 18-carbon molecule acids attached to the glycerol A large number of sphingolipids have been identified at this point Simple Triacylglycerol - when the R groups or the fatty acids but only a few have well defined function. attached to glycerol are all the same. 25% of total lipids in man Functions: o Many are present in the plasma membrane of neurons – insulatory function o Some are recognition sites on surface of the cell o Anchors blood type carbohydrate into the membrane of RBC Glycolipids or glycosphingolipids are lipids a fatty acid, sphingosine and a carbohydrate Sphingosine with an addition of a fatty acid will produce a ceramide PHOSPHOLIPIDS lipids that contain a phosphate group lipid containing a fatty acid, an alcohol and a phosphatidic acid. They frequently have nitrogen containing bases and other substituents such as glycerol (glycerophospholipids) and sphingosine (sphingophospholipid) One of the most important structural lipid in the body. Main lipid constituent of membranes. Has a nonpolar tail ang polar head Parent structure = phosphatidic acid ▪ It is the basic structure found in all phosphoglycerides STRUCTURAL ROLE OF PHOSPHOLIPIDS Biological Membranes Cell and organelle membranes are composed of two layers - lipid CERAMIDE DERIVATIVES bilayers. Sphingomyelin = ceramide + phosphorylcholine Not any lipid will do. It must be one that has a polar portion and a ▪ Used primarily in nerve tissues as myelin sheath nonpolar portion on each molecule. Cerebroside = ceramide + sugar If sugar is glucose then it’s a glucocerebroside Galactose= galactocerebroside Lactose = lactocerebroside Sulfated sugar= sulfatide Ganglioside = ceramide + oligosaccharide (with sialic acid/NANA/neuramic acid) Cell Membrane Linkage of the oligosaccaride with ceramide and its further polymerization is through Beta linkages. The polar or ionic sites of a phospholipid are hydrophilic (water Linkage of NANA to the oligosaccharide is through Alpha linkage. loving). Can act as receptor in cholera and tetanus toxin, and influenza virus. The hydrocarbon part is hydro-phobic (water hating). Both are needed to make cell walls. Protein and cholesterol molecules are also imbedded in the cell wall SPHINGOMYELIN Used primarily in nerve tissue - myelin sheath. In humans, 25% of all lipids are sphingolipids The middle part above is sphingosine. CHOLESTEROL Vit. D3 – found in animal tissue. Major and best known steroid in the body Has 4 rings which is a derivative of cyclopentanoperhydropenanthrine with methyl side chains at C18 and C19, with an aliphatic side chain at C17 and with a double bond between C5 and C6 of ring B. Hormones From the adrenal Cortex A precursor of a large number of equally important steroids which includes: o Bile acids – steroids from cholesterol ▪ It acts as an emulsifier to fatty acids ▪ It is stored in the gallbladder ▪ Loss of double bond at ring B. ▪ Most important bile salts are: 1. Taurocholate – has taurin as its alipathic group at C17. 2. Glycocholate - has glycine as its alipathic group at C17. Sex Hormones Vitamin D Hormones 1. Vit. D2 – found in plant tissue. Important notes saturated fats are considered “bad fats” monounsaturated fats are considered “good fats” trans-monounsaturated fats are considered “bad fats” polyunsaturated fats can be both “good fats” and “bad fats” omega 3 and 6 are important “good fats” DIFFERENCE OF FATS AND OILS CHEMICAL REACTIONS OF TRIACYLGLYCEROLS 1. hydrolysis FATS OILS 2. saponification predominantly saturated predominantly unsaturated 3. hydrogenation solids or semisolids at room liquids at room temperature temperature 4. Oxidation Source – plant and fish oil Source -animal source and HYDROLYSIS OF TRIACYLGLYCEROL tasteless hydrolysis of triacylglycerols is the reverse of esterification reaction WAXES breaking of 1-2 ester bonds to give rise to mono- or Hydrophobic: Waxes are water-repellent and do not dissolve in diacylglycerol and fatty acid(s) water. This property makes them suitable for providing a protective within the human body, it is carried out by enzymes coating on surfaces. produced by the pancreas aka lipase Solid at Room Temperature: Most waxes are solid at typical room temperatures). However, they can melt at higher temperatures. Low Melting Point: Waxes generally have relatively low melting points, which means they can melt and flow easily when heated. Insulating: Due to their low thermal conductivity, waxes are used as insulators to slow down heat transfer. Lubricating: Waxes have lubricating properties and are used in SAPONIFICATION various applications where reduced friction is required. Chemically Stable: Waxes are relatively chemically stable and do hydrolysis in basic solution: produce salt of fatty acid and not readily react with other substances. glycerol Example Bees wax : secretion of abdominal glands of worker honey bees Lanolin or wool fat : Secretion of cutaneous glands and obtained from the wool of sheep -is frequently used in protective baby skin treatment and as a treatment for sore nipples in breastfeeding mothers Sebum : secretion of sebaceous glands of skin Cerumen : soft and brownish waxy secretion of the glands in the External auditory canal. Also called as Earwax OXIDATION Enzymes Enzymes – specialized protein catalysts that accelerate chemical double bonds in triacylglycerols are subject to reactions in biologic systems to about 105 to 1014 times faster than oxidation with oxygen in air (an oxidizing agent )-leads uncatalyzed reactions but are not consumed during the reaction to c=c breakage they catalyze remember that oxidation of alkenes may result into - at the end these are neither used up but are regenerated, two short chain molecules – an aldehyde or a recycled, reutilized - it is typically protein carboxylic acid: - They accelerate the reaction, but a. the aldehydes and/or carboxylic acids so produced o a. do not alter the reaction equilibrium often have objectionable odors - fats and oils are said o b. not consumed in overall reaction to be rancid o c. required only in very small quantities. b. to avoid this unwanted oxidation process - They have enormous power for catalysis. - Enzymes are highly specific for their substrate. antioxidants are added as preservatives, e.g., vitamin - Enzymes possess active sites at which interaction with c and vitamin e are good antioxidant preservatives substrate takes place. - Enzymes lower activation energy HYDROGENATION OF TRIACYLGLYCEROL double bonds in unsaturated fatty acids react with Apoenzyme – protein part of an enzyme; main enzyme; catalytically-active; cannot increase reaction rate hydrogen gas to produce carbon–carbon single bonds. Unsaturated fatty acids may be converted to Cofactor – small organic or inorganic molecules; either loosely or saturated fatty acids by the relatively simple tightly bound to apoenzyme, that participate in overall catalytic hydrogenation reaction. activity 3 cofactors: o Coenzymes – small organic molecules often derived from vitamins o Prosthetic group – an organic molecule attached to the apoenzyme o Metal ions – inorganic molecules Holoenzyme – consists of an apoenzyme and a cofactor; metabolically active form of enzyme CHEMICAL REACTIONS OF TRIACYLGLYCEROLS Metalloenzyme – enzymes that require metal in their composition; has very high affinity in binding and retaining metal atoms substrate of an enzyme are the reactants that are activated by the enzyme CATALYST A catalyst is a chemical that speeds up the reaction but is not used up in the reaction Lowers the activation energy needed to start a reaction Is not used up during the reaction Is unchanged after a reaction low-density lipoproteins (ldls) – lipoproteins that carry cholesterol from the liver high-density lipoproteins (hdls) – those that carry excess cholesterol from tissues back to the liver Statins are a widely prescribed class of drugs to lower cholesterol. Their mode of action is primarily via inhibition of HMG-CoA (hydroxymethylglutaryl-coenzyme A) reductase  CLASSIFICATION of Enzyme o Pyruvate Decarboxylase - cataylzes removal of - OXIREDUCTASES COO from pyruvate to synthesize acetaldehyde Transfer of electrons and hydrogen atoms (oxidation- and CO2 reduction reactions) from donors (reductants, hence o DOPA Decarboxyla, Histidine Decarboxylase oxidized) to acceptors (oxidized, hence reduced) Aldolase A, Citrate synthase Hydratase Oxidation - Loss of electrons; Reduction- Addition of electrons ISOMERASES Examples: Catalyze transfer of functional groups or double bonds o Lactate Dehydrogenase - transfer of H+ from within the same molecule (or catalyze racemization of lactate to NAD+ forming pyruvate optical or geometric isomers) o Oxidase - oxidation of substrate Examples: o Reductase - reduction of substrate o Alanine racemase - catalyzes transfer of amino o Dehydrogenase-introduction of double bond group on the left side of carbon 2 of alanine to the (oxidation) by formal removal of two hydrogen right side of the same carbon atoms from substrate, the H being accepted by a o Triosephosphate isomerase, coenzyme. phosphohexoisomerase, phosphoglycerate mutase, epimerase o Racemases - conversion of D to L isomer or vice TRANSFERASES versa. Transfer functional/ chemical groups (e.g. C-, N- or P-) from o Mutases - transfer of a functional group from one donors to acceptors position to another in the same molecule. Utilize 2 substrates to produce 2 products o Isomerase -catalyze reactions involving a Examples: structural rearrangement of a molecule. o Alanine Transaminase (an aminotransferace) - transfer of amino group from alanine to α- LIGASES ketoglutarate to form pyruvate and glutamate ▪ Catalyze ligation or joining of 2 substrates with covalent o Transaminases - transfer of an amino group bonds in a reaction coupled to the cleavage of a high- between substrates. energy phosphate bond in ATP or another nucleotide o Kinases -transfer of a phosphate group between ▪ Example: substrates. Pyruvate carboxylase - catalyzes condensation of pyruvate and CO2 (from biotin) HYDROLASES Synthetases formation of new bond between two Catalyze cleavage of chemical bonds by the addition of substrates with participation of ATP. H2O, producing 2 products o Carboxylases - formation of new bond between Examples: a substrate and CO2 with participation of ATP. o Pyrophosphatase - catalyzes cleavage of high Enzyme specificity energy phosphate bond in the presence of H2O, forming 2 inorganix phosphates o Lipase - hydrolysis of ester linkages in lipids o Proteases- hydrolysis of amide linkages in proteins. o Nucleases - hydrolysis of sugar phosphate ester bonds in nucleic acids. o Carbohydrases - hydrolysis of glycosidic bonds in carbohydrates. o Phosphatases - hydrolysis of phosphate- ester bonds. LYASES Cleave C-C, C-O or C-N bonds by means other than hydrolysis or oxidation Examples: o Dehydratases - removal of H20 from substrate o Decarboxylases -removal of CO2 from substrate o Deaminases - removal of NH3 from substrate o o Hydratase - addition of H2O to a substrate  MODELS OF SUBSTRATE-ENZYME BINDING 1. LOCK AND KEY MODEL Type of Effect on Effect on Substrate binds to a site whose shape Inhibition Definition Vmax Km Example complements its own (like lock and key) Inhibitor Does not take into account 3D flexibility of competes proteins with substrate Malonate for binding inhibiting to the succinate Competitive active site. No Increases dehydrogenase Inhibitor binds to a site other than the active site, changing 2. INDUCED FIT MODEL the Cyanide inhibiting Not rigid, undergoes a slight conformational Non- enzyme's cytochrome change (induced fit) on binding substrate induced competitive shape. Dec No oxidase by multiple hydrogen bonds forming a Inhibitor complementary shape or a “flexible pocket” that binds only approximates the shape of the substance to the Some heavy enzyme- metal ions Uncompetiti substrate inhibiting ve complex. Dec Dec enzymes Inhibitor binds to the enzyme and forms a covalent bond, Organophosphat permanentl e insecticides KINETICS OF ENZYME-CATALYZED REACTIONS y May or inhibiting An enzyme catalyzed reaction is like a second-order Suicide inactivating may not acetylcholinester reaction (Irreversible) it. Dec change ase With constant enzyme concentration, as substrate concentration is increased, the rate of the reaction increases Significance of Km Velocity slows down during the course of the reaction Significance of Km because the concentration of substrate is becoming 1. It is the substrate concentration at which half of the active sites of depleted or product is starting to accumulate the enzyme are filled up. 2. It is an inverse measure of the affinity of the substrate for the INHIBITION OF ENZYMATIC REACTIONS enzyme: Reversible – non-covalent bonding a. The lower the km, the higher is the affinity. (Lower concentration of substrate to attain Vmax) 1. Competitive – intersects at Y-axis Ex. Statins – group of b. The higher the km, the lower is the affinity. (Higher drugs that are adjunct with treatment of patients of concentration of substrate to attain Vmax) hypercholesterolemia 2. Non-competitive – decrease binding of substrate to active site of enzyme 3. Uncompetitive – parallel lines for uninhibited and inhibited reactions  Factors affecting Enzymes activity Importance of Proteins Factors Affecting Enzyme Activity Temperature: o Optimal temperature: Enzymes function best at a specific temperature. o Low temperature: Slows down enzyme activity. o High temperature: Can denature the enzyme, causing it to lose its shape and function. pH: o Optimal pH: Each enzyme has an optimal pH range. o Extreme pH: Can denature the enzyme. Substrate concentration: o Low concentration: Slows down reaction rate. o High concentration: Increases reaction rate up to a point of saturation. GENERAL STRUCTURE OF AMINO ACIDS Enzyme concentration: o Higher concentration: Faster reaction rate. Each amino acid has 4 different groups attached to α- carbon ( Presence of inhibitors or activators: which is C-atom next to COOH). These 4 groups are : amino o Inhibitors: Molecules that bind to the enzyme and group, COOH group, Hydrogen atom and side Chain (R) reduce its activity. o Activators: Molecules that bind to the enzyme and increase its activity. Salt concentration: o High salt concentration: Can denature the enzyme.. AMINO ACID AND PROTEIN ORGANIZATION ** SIDE CHAIN - determines the property of the amino acid. Amino Acid ZWITTERIONS “Alphabet” of protein structure Basic structural units Amino Acids are the building units of proteins. Proteins are Under normal cellular conditions amino acids are zwitterions polymers of amino acids linked together by what is called “ (dipolar ions): Peptide bond” through condensation There are about 700 amino acids occur in nature. Only 20 of them occur in proteins. It is essential to life, the proteins they form are involved in virtually all cell function Composed of carbocylic group, hydrogen, side chain, amino grou ISOELECTRIC POINT STEREOCHEMISTRY OF AMINO ACIDS The conditions of zwitterions are reliant on Mirror image pairs of amino acids are designated L (levo) and pH at which an amino acid solution has no net charge D (dextro) and are called enantiomers because an equal number of positive and negative charges Proteins are assembled from L-amino acids (a few D-amino are present acids occur in nature) The structure of an amino acid can change with the pH of the solution: ○ Lowering the pH of the solution causes the zwitterion to pick up a proton ○ Increasing the pH of the solution causes the zwitterion to lose a proton ** PROTEINS are generally L, CARBOHYDRATES are generally D. ABBREVIATIONS OF AMINO ACIDS CHIRALITY OF AMINO ACIDS 19 of the 20 common amino acids have a chiral α-carbon atom (Gly does not) Chiral carbons –have four different groups attached Glycine- no charial CLASSIFICATION OF AMINO ACID ** GLYCINE - only amino acid that is not chiral. GENERAL STRUCTURE OF AMINO ACIDS Threonine and isoleucine have 2 chiral carbons each (4 possible stereoisomers each) R GROUP : General properties like acidic, basic components, Stereoisomers-compounds that have the same molecular etc. formula but differ in the arrangement of atoms in space NUTRITION : “Do you need it or not?” CATABOLISM : “Is it ketogenic or glucogenic?” CLASSIFICATION OF AMINO ACID: SIDE CHAIN AMINO ACID WITH NONPOLAR SIDE CHAIN Contains uncharged hydrocarbon groups or benzene rings Does not gain or lose protons or participate in hydrogen or Maple syrup disease illness can’t syntheize branch amino acids ionic bonds Oily or lipid like -> Hydrophobic interaction ACCORDING TO METABOLIC PRODUCTS OF AMINO ACIDS Hydrophobic while polar is 1. Ketogenic amino acids: which give ketone bodies. Lysine and HYDROPHILIC: 1. Polar neutral side chain Leucine are the only pure ketogenic amino acids. Ketogenic ○ Have side chains with either a net positive or a net amino acids are a subset of amino acids that can be negative metabolized through acetyl coa ○ It is hydrophilic and soluble in water 2. Mixed ketogenic and glucogenic amino acids: which give both 2. Polar acidic side chain ketone bodies and glucose. These are isoleucine, phenyl ○ Contains 1 amino group and 2 carboxyl group alanine, tyrosine and tryptophan. ○ Side chain is negative and is –ic acid 3. Polar basic side chain 3. Glucogenic amino acids: Which give glucose. They include the ○ Contains 2 amino group and 1 carboxyl group rest of the amino acids. These amino acids by catabolism yield ○ Side chain is positive products that enter glycogen and glucose formation. OTHER AMINO ACIDS AND DERIVATIVES Glutamate: The primary excitatory neurotransmitter in the central nervous system. GABA (Gamma-Aminobutyric Acid): The primary inhibitory neurotransmitter in the central nervous system. Glycine: An inhibitory neurotransmitter, especially in the spinal cord. Aspartate: An excitatory neurotransmitter, often found in conjunction with glutamate. Catecholamines Dopamine: Derived from tyrosine.Involved in reward, CLASSIFICATION OF AMINO ACID motivation, and movement. Norepinephrine (Noradrenaline): Derived from dopamine Involved in attention, arousal, and the fight-or-flight response.. Epinephrine (Adrenaline): Derived from norepinephrine. Serotonin: Derived from tryptophan Involved in mood, sleep, and appetite Histamine: Involved in wakefulness and allergic reactions. PROTEINS: STRUCTURAL ORGANIZATION Protein Structural Organization Proteins have four levels of structural organization: 1. Primary Structure: o Linear sequence of amino acids linked by peptide bonds. o Determined by genetic information. 2. Secondary Structure: o Local folding patterns of the polypeptide chain. Protein Misfolding o Common secondary structures: ▪ Alpha helix: Spiral shape stabilized by Protein misfolding is a biological phenomenon in which a hydrogen bonds. protein adopts an abnormal three-dimensional structure, ▪ Beta pleated sheet: Folded sheet-like deviating from its native conformation. Proteins are essential structure stabilized by hydrogen bonds. macromolecules that carry out various functions in living 3. Tertiary Structure: organisms, and their proper function relies heavily on their o Overall three-dimensional shape of a polypeptide specific three-dimensional shape. chain. o Formed by interactions between R groups of amino acids: Hydrogen bonds,Ionic bonds,Disulfide bonds, Hydrophobic interactions Globular Proteins: Compact, spherical shape, often water-soluble. Examples: enzymes, hormones, antibodies. Fibrous Proteins: Long, fibrous shape, often insoluble in water. Examples: collagen, keratin. 4. Quaternary Structure: Subunits: Individual polypeptide chains. Interactions: Same as in tertiary structure (hydrogen Chaperones prevent proteins from folding incorrectly Proteins bonds, ionic bonds, disulfide bonds, hydrophobic interactions). that have problems achieving their native configuration are Examples: Hemoglobin (four subunits), insulin (two helped by chaperones to fold properly subunits). The misfolded proteins can be detected by quality-control mechanisms in the cell that tags them to be sent to the DIFFERENCE BETWEEN PEPTIDES AND PROTEIN cytoplasm, where they will be degraded The chains containing less than 50 amino acids are called “peptides”, while those containing greater than 50 amino Alzheimer's disease: Misfolding of proteins, such as amyloid- acids are called “proteins”. beta and tau, leads to the formation of toxic aggregates in the Each joined or linked to the next by a peptide bond brain, contributing to the development of Alzheimer's disease. ○ 2 amino acid – Dipeptide Parkinson's disease: Misfolding of the alpha-synuclein protein ○ 3 amino acid – Tripeptide leads to the formation of Lewy bodies, which are pathological ○ 10-20 amino acid – Oligopeptide protein aggregates found in the brains of Parkinson's disease ○ Long chain of amino acids - Polypeptide patients. PEPTIDE BOND Peptide bond - linkage between amino acids is a secondary Modification of Amino Acids: Protein Denaturation amide bond Denaturation of a protein means that it loses its natural shape ○ Formed by condensation of the α-carboxyl of one and cannot function properly. amino acid with the α-amino of another amino acid Factors that affect protein denaturation: (loss of H2O molecule) ○ Heat: ○ pH: ○ Organic solvents: ○ Chaotropic agents: ○ Heavy metals:  MIDTERM EXAM REVIEWER – BIOCHEMISTRY LEC/LAB By Team Meow Meow = ( Halimeow and the three headed creature) Tips for the lab Lipids ▪ Always do the guide questions and the simulation quizzes in the lab manual especially the online. ▪ Remember the positive result and what this test is for Protein test Test What is it used Positive result Reduced sulfur test cysteine and Black cystine Xanthoproteic Test Aromatic amino Yellow/ Orange acid like tyrosine or tryptophan Million’s test Tyrosine or phenol Red / pink group Biuret test Nitrogen in amino Purple acid Ninhydrin Test Amino acid Purple – amino acid Yellow – proline What is denaturation Factors that denature proteins heat Alcohol Acids Inorganic Organic Alkalis chemicals chemicals Grease spot test Acrolein test: This reaction is utilized to determine the presence of glycerine in a fat. Saponfication Saponification is the hydrolysis of an ester to form an alcohol and the salt of a carboxylic acid in acidic or essential conditions. Saponification is usually used to refer to the soap-forming reaction of a metallic alkali (base) with fat or grease Answer me and practice me http://amrita.olabs.edu.in/?sub=73&brch=3&sim=119&cnt=4 Staining of Nucleic Acid by Acetocarmine https://amrita.olabs.edu.in/?sub=79&brch=18&sim=476&cnt=4 Questions Why do we “crush” the kiwi/strawberry fruit? Why do we use shampoo? What does the salt do? Why do we need to cool the mixture? What does the cold ethanol do? Why can’t we use room temperature ethanol? Discussion Questions To extract DNA from cells, what must you isolate it from in the case of a plant such as strawberry? What steps did we use to extract the DNA? What is DNA used for when it is extracted?