BioChem and Metabolism PDF

7 Conventional Definitions of Life: ​ Organization: being composed of one or more cells, which are the basic units of life ​ Reproduction: life has the ability to produce new organisms ​ Metabolism: life undergoes the chemical processes that are necessary for the maintenance of...

7 Conventional Definitions of Life: ​ Organization: being composed of one or more cells, which are the basic units of life ​ Reproduction: life has the ability to produce new organisms ​ Metabolism: life undergoes the chemical processes that are necessary for the maintenance of life ​ Catabolism: substances are broken down, providing energy ​ Anabolism: substances are synthesized using energy ​ Growth: life grows, it maintains a higher rate of building up than breaking down, progression from simpler to more complex ​ Homeostasis: life regulates the internal environment to maintain a constant ​ ​ Sweating to reduce body temp ​ ​ Shivering to increase body temp ​ Response to Stimuli: life has the ability to respond, to react to a stimulus ​ Adaptation: the ability to respond over a long period of time to one's environment Other Proposed Features of Life: ​ Carbon Containing: carbon is the chemical element that forms the basis of life on earth ​ Reliance on Water: water is a chemical substance needed for survival of all forms of life on earth ​ Genetic Information: uses DNA and RNA to store blueprint of an organism What is a Molecule: ​ Molecule: the smallest particle of a substance that retains the properties ​ ​ Can be composed of one or more atoms ​ Atom: the smallest particle of elements that retain the chemical property of the element 3 Molecular Characteristics of Life: ​ Life obeys the laws of thermodynamics ​ ATP is the common energy currency of life ​ Life is composed of similar biological molecules both large/small ​ 4 classes: proteins, lipids, carbs, nucleic acids Law of Thermodynamics: ​ 1rst: energy can neither be created nor destroyed, it can only change from one form to another ​ 2nd: all process increase entropy ​ Large molecules=less entropy ​ Smaller molecules=more entropy ATP is the Common Energy Currency of Life: ​ In biochemistry, there are multiple sources of energy and multiple types of work performed What is a Nutrient: ​ Any substance that is of nutritional value to an organism ​ Provide energy, provide building blocks to maintain, grow and repair itself ​ Some nutrients can be synthesized others cannot = essential Micronutrients vs Macronutrients: ​ Micronutrient: a nutrient required in small amounts ​ ​ Vitamins, microminerals ​ Macronutrient: a nutrient required in large amounts ​ Carbs, proteins, and lipids Vitamins: ​ Act as cofactors for enzymes, organic compounds that are loosely bound to the enzyme during reactions ​ Obtained in food Nucleic Acids: ​ Necessary to maintain, grow and repair our own DNA and RNA RNA: ​ Is the messenger that carries the instructions from DNA ​ Complementary to DNA and is single stranded ​ Uses uracil instead of thymine ​ Ribonucleotides are used to create new RNA Hydrocarbon Nomenclature: ​ Hydrocarbons are chemical compounds that contain hydrogen and carbon ​ Carbon being the chemical element that forms the basis of all life ​ Alkane: carbon-carbon are single bonds ​ Alkene: at least one carbon-carbon double bond ​ Alkyne: at least one carbon-carbon triple bond Methods of Drawing Hydrocarbons: ​ Structural: each straight line is a bond ​ Condensed: combine hydrogens with carbons ​ Skeletal: intersections = carbon atoms Naming Linear Hydrocarbons: Prefix # of Prefix # of Hydrocarbons Hydrocarbons Meth 1 Hex 6 Eth 2 Hept 7 Prop 3 Oct 8 But 4 Non 9 Pent 5 Dec 10 For Nomenclature rules refer to slide decs Refer to Slide deck for functional group rules Atomic Structure: ​ Have a central nucleus with protons and neutrons each having 1U ​ Circulating the nucleus are negatively charged electrons, having a mass of essentially Ou ​ Number of protons, neutrons and electrons is usually equal to the atomic number of the atom Electron orbitals: ​ Orbitals are filled inside to outside ​ First orbital contains 2e, second/third contain 8e ​ When the orbital is half filled or more, the atom attempts to gain electrons, when less than half filled, attempt to lose Bond Formation by Atoms: ​ Number of Bonds: which will be formed by these atoms depends on the number of electrons needed to fill the outermost partially filled orbital (½ full or more) ​ Number of Bonds: formed by these atoms depend on the number of electrons needed to be lost in order to empty the outermost partially-filled orbital (less than ½ full) Number of Bonds formed by Bioelemnments: Carbon-4 Nitrogen-3(4*) Hydrogen-1 Phosphorus-3(5*) Oxygen-2 Sulfur-2 Types of Chemical Bonds: ​ Intramolecular: bonds within a molecule (covalent/ionic) ​ Intermolecular: bonds between molecules (hydrogen/ Van Der Waals/ Hydrophobic) Relative Chemical Bond Strengths: ​ Intramolecular: more energy stored in bond, greater energy required to form, greater energy released when bond is broken ​ Intermolecular: Bonds are weaker than intermolecular Covalent Bonds: ​ Sharing of electron pair between bonded atoms ​ Very stable, very strong ​ Each of the two bonding atoms will end up with a full outer orbital after the bond is formed Ionic Bonds: ​ One or more electrons removed from one atom and added to another atom ​ Electrons are not shared but transferred from one atom to another ​ One fills outer shell by going, while other fills by losing electrons Hydrogen Bonds: ​ Force of attraction between hydrogen atom in molecule 1 and an atom such as oxygen in molecule 2 ​ Only 5% to 10% of the strength of a covalent bond Van Der Waals Forces: ​ Force generated by any two molecules with electron shells that are almost touching ​ Temporary situation, since electrons are always moving in orbit ​ Electrostatic attraction between opposite charges similar to hydrogen bonds through water Hydrophobic Force: ​ Hydrophobic (non-polar) molecules do not interact well with water and tend to seek each other out and avoid water Determination of Intramolecular bond Type by Electronegativity: ​ Electronegativity: the ability of an atom to attract electrons ​ High electronegativities exert a strong attraction on electrons ​ Low electronegativities exert a weak attraction on electrons ​ Result in unequal sharing of electrons between atoms, electrons spend more time closer to the atom with higher electronegativity Bond Polarity Spectrum: ​ Non-Polar Covalent: 0 - 0.4 ​ Polar Covalent: 0.4-1.1 (slightly) 1.1-2.0 (highly) ​ Ionic: more than 2.0 Electronegativity vs Polarity: ​ Electronegativity: ability of an atom to attract electrons ​ Polarity: Charge in a bond/molecule resulting from unequal sharing of electrons ​ The amount of bond polarity is proportional to the difference in electronegativities of the atoms forming the bond Polar Bond vs Polar Molecule: ​ Molecular polarity: is a sum of all bonds in that molecule ​ If that bond is polar, then the character of the whole molecule is polar (only one bond) ​ Overall polarity will be determined by the number of polar bonds and shape of molecule (multiple bonds) Water: ​ Is a very important polar molecule in biochemistry ​ Oxygen is more electronegative than hydrogen ​ Oxygen has partial negative charge ​ Hydrogens will have partial positive charges Importance of Polarity in Solubility: ​ Polar molecules will dissolve in a solution of other polar molecules ​ Non-polar will dissolve in a solution of other non-polar molecules ​ Non-polar molecules will not dissolve in a solution of polar molecules Water and pH: ​ Ionization of Water: there is a measurable tendency for the hydrogen ion to jump to an adjacent water molecule Acids and Bases: ​ Are molecules which can change the pH of water by affecting the concentration of hydronium ions ​ Acids: acts as a proton donor ​ Bases: act as a proton acceptor Acids and Bases in the Body: ​ pH balance is extremely important for biological function ​ pH of blood is maintained from 7.35-7.45 ​ Increased presence of acids and bases is a feature of some diseases Isomers: ​ Are two molecules with the same chemical formula but a different arrangement of atoms ​ Two types structural and spatial ​ Structural: differing bonds between atoms even though the total number of atoms of each element are identical ​ Spatial: same bonding arrangement between atoms but a different spatial arrangement Structural Isomers: ​ Different bonding arrangement of atoms Spatial Isomers: ​ Same bonding arrangement but different spatial positioning of atoms around chiral carbon Platin: ​ Cis-platin: prevents replication of cancer cells by binding to DNA (leads to apoptosis) ​ Trans-Platin: quickly broken down before it can reach target site (ineffective) Energy: ​ Thermal, potential, kinetic, nuclear, solar, chemical Chemical Energy: ​ Energy that exists in the bonds between atoms ​ When bonds are broken chemical energy is released - catabolism Energy in Biochemistry: ​ Energy is neither created or destroyed but changes form (1rst thermodynamics) ​ It can be transferred: chemical - kinetic ​ The energy in a biochemical reaction can be defined by the Enthalpy or heat content of a molecule ​ Involving a transfer of heat between a molecule and its surrounding Enthalpy: ​ Represented by H ​ Change in enthalpy is : delta H= Final-Hinitial ​ Heat can be lost or gained by a molecule ​ When heat is lost, Final is lower than Initial and deltaH is negative ​ When heat is gained, Final is higher than Hinitial and deltaH is positive Negative DeltaH - Exothermic Reaction: ​ The molecule loses heat, giving off heat to environment ​ Final product(p) temperature(H) is lower than initial reactant(r) ​ Heat lost by the molecule is transferred to the surroundings ​ Surroundings gain heat Positive deltaH - Endothermic Reaction: ​ The molecule gain heat, taking heat from environment ​ Final product (p) temperature(H) is higher than initial reactant(r) ​ Heat gained by molecule is transferred from the environment surroundings lose heat Negative deltaH - Spontaneous Reaction: ​ If the reaction loses heat, if the reaction has a -ve delta H, the reaction will proceed spontaneously ​ The reacting molecules provide the energy to drive the reaction but if the reaction has a positive deltaH needs to take energy in form the environment to proceed What else determines of a Reaction is Possible: ​ 2nd Law of Thermodynamics: all processes try to increase entropy in the universe ​ The energy change in a system, reaction can also be defined by its entropy(s), the disorder of molecules in a system ​ Higher entropy - less energy in the system ​ Lower entropy - more energy in a system Entropy: ​ Changes in entropy: deltaS = Final - Initial ​ 3 factors: arrangement, number and motion of molecules Arrangement of Molecules: ​ Tightly packed arrangement - less entropy in the system ​ Loose arrangement - more entropy in the system Number of Molecules: ​ More molecules - more entropy ​ Fewer molecules - less entropy Motion of Molecules: ​ More motion - more entropy in the system ​ Less motion - less entropy in the system ​ Less pressure - more motion ​ More pressure - less motion Gibbs Free Energy: ​ Combines the concepts of enthalpy and entropy into the term delta G= deltaH -T* deltaS / deltaG = GFinal-GInitial ​ Represents the maximum amount of energy available t do work ​ Gibbs free energy can be lost - negative delta G, or gained - positive deltaG Exergonic vs Endergonic: ​ Delta G is negative: exergonic reaction, releases energy, reaction occurs spontaneously ​ Delta G positive: endergonic reaction, requires energy, reaction occurs non-spontaneously Conditions that Favour Exergonic Reactions: ​ Reactions that lose heat and gain entropy will be energetically favourable and will be spontaneous ​ Loss of heat - loss of entropy ​ Gain of heat - gain of entropy DeltaG vs DeltaG॰: ​ DeltaG is not only affected by temperature, but also by pH and the concentration of the reactants and products ​ DeltaG: Gibbs free energy represents the maximum amount of energy available to do work ​ Represents what is actually happening in a living cell ​ DeltaG॰ Bibbs standard free energy is measured under standard lab conditions usually DeltaG॰ is given in biochemistry, since deltaG is hard to measure accurately in dynamic in vivo conditions How DeltaG Values are Obtained: ​ Delta: standard free energy measured under standardized lab conditions constant temperature, pH and concentration Energy in Food - Gross Energy: ​ Gross Energy: the total energy found in food ​ Gross energy is the measurement of heat produced by combustion of food Non-useable Energy: ​ 3 types: fecal, urinary, and gaseous energy Useable Energy: ​ Metabolize Energy: energy available to the organism to do work. Used for growth, cell/tissue maintenance, and repair and reproduce Energy Out: ​ Energy expenditure: measured in calories over 24 hrs ​ BMR(basal metabolic rate) = BW(in lbs) x 10 Cal/lb/24h ​ Thermic effect of food (TEF)= food intake(cal) x 10% ​ Activity level of the person: BMR x Activity Level (%) 3 factors affecting Obesity Epidemic: ​ Intake of fast food ​ Intake of added sugar ​ Intake of large portion sizes Amino Acid: ​ Are the building blocks of protein ​ 20 standard amino acids all with the same general structural formula ​ Half aa’s are essential and required in diet ​ Dietary aa’s are not usually found individually but in the form of dietary proteins Protein Peptides: ​ Protein dimers, trimers and oligomers ​ Dipeptide: 2 amino acids ​ Tripeptide: 3 amino acids ​ Oligopeptide: 4-50 amino acids ​ Linear linkages, joined by peptide bond Protein Polymers: ​ Polypeptide: >50 amino acids, less than 100 amino acids ​ Linear linkages between amino acids ​ We consider polypeptides to be linear Biological Proteins: ​ Usually contain 100’s to 1000’s of amino acids ​ Can consist of several different proteins ​ Complex globular/folded structure - usually needed to be functional Complete vs Incomplete: ​ Complete protein: contains all the essential amino acids (animal proteins) ​ Incomplete protein: is missing some of the essential amino acids (plant protein) Protein Structure: ​ Described as 4 potential levels Primary 1॰ Tertiary 3॰ Secondary 2॰ Quaternary 4॰ 1॰ Structure of Proteins: ​ Order of aa in the polypeptide ​ Determined by DNA sequence - RNA sequence ​ Becomes the bones for all other levels of structure that give the protein its chemical and physiological properties 2॰ Structure of Proteins: ​ Arrangement of 1॰ string of aa into 2॰ structure by hydrogen bonds that form between backbone atoms of aa ​ Two different structures produced: a-helices, B-pleated sheets 2॰ Structure: the a-helix: ​ C double bond O of each peptide bond is aligned to form a hydrogen bond with the N-H of the fourth amino acid from it ​ Forms a helical cylinder with the R side chains projecting outwards with no space in the cylinder 2॰ Structure: the B pleated sheet: ​ Hydrogen bonding between the C double bonded O and N-H groups of adjacent chains ​ If chain runs in the same direction amino to carboxyl - parallel sheet ​ If chains n in opposite direction - called an antiparallel sheet ​ R side chains alternate sticking out on either side of B-sheet ​ R side chains can attach to other Bsheets or a-helixes 3॰ Structure of Protein: ​ The folding of these 2॰ structures into compact globular proteins is 3॰ ​ Structure and is determined by interactions between the side chains of various amino acids 4 Main Forces Hold 3॰ Structure Together: ​ Disulfide Bond: between two S atoms in adjacent cysteine aa’s ​ Hydrogen Bond: between partial positive and partial negative ​ Salt bridges: weak bonds between positive and negative side chains ​ Hydrophobic: interactions between two or more non-polar side chains 4॰ Structure of Proteins: ​ Combining of multiple protein subunits already folded into their 3॰ structure ​ Many proteins don't have a 4॰ structure ​ Protein subunits can be the same protein, or different 4॰ structure is linked together by same kinds of forces that contribute to 3॰ structure Protein Denaturation: ​ Proteins can be found in native or denatured ​ Denaturation disrupts the 2॰,3॰ and 4॰ structure of proteins ​ Denaturation could occur by: heating, treating with acids/bases, organic compounds, heavy metals Dynamic vs Static Proteins: ​ Dynamic: not fixed to one spot in the body (transport proteins, peptide, hormones, enzymes) ​ Static: fixed to one spot in the body (elastin, collagen, fibronectin, proteoglycans, actin/myosin) Serum Albumins: ​ A group of water soluble proteins that compromise 60% of the proteins found in blood plasma ​ Functions: maintenance of osmotic pressure, regulation of blood volume transporter of non polar substances Globulins: ​ Group of water soluble proteins that comprise most of the other 40% of proteins found in blood plasma ​ Functions: transport, binding, elimination of specific foreign particles Hemoglobin: ​ Not a blood plasma protein, contained within red blood cells ​ Contains 4 subunits of globin protein and a non-protein heme prosthetic group ​ Bound together by weak non-covalent bonds Myoglobin: ​ Muscle equivalent of hemoglobin and is contained within muscle cells ​ Only detected in blood after muscle injury- such as heart attack Insulin: ​ Hormone produced when blood glucose levels are high, released as active monomer which binds to insulin receptor ​ Signaling events takes place leading to the translocation of GLUT4 glucose transporter proteins to cell membrane and glucose uptake Thyroid Hormones: ​ T3 and T4 are produced in thyroid gland and circulated in blood ​ Normally TH inhibit the brain pathways that cause their own production ​ Low TH levels remove inhibition- greater production Somatropin: ​ Also known as human growth hormone, and is produced in pituitary gland and circulated blood ​ Promotes lipolysis and gluconeogenesis ​ Promotes protein synthesis, increase in muscle cells, bone growth Collagen: ​ Three strands of procollagen cross linked via hydrogen bonds ​ Most abundant protein in mammals Elastin: ​ Multiple cross linked tropoelastin molecules ​ Crosslinks are covalent bonds between cysteine amino acids ​ Very important: arteries, lungs, skin, bladder, elastic ligaments/cartilage Proteoglycans: ​ Found in many tissues: blood vessels, skin cartilage ​ Consists of a core protein with many polar CHO side chains Fibronectin: ​ Are extracellular matrix proteins that crosslink other matrix proteins such as a collagen and proteoglycans ​ Labels actually increase with age making connective tissue less flexible Actin and Myosin: ​ Actin: globular actin protein molecules polymerize into long thin filaments ​ Myosin: protein run between actin filaments muscle fiber has head groups that reach out to contact actin Dietary Proteins: ​ Of 20 amino acids, our body only makes 10-12 ​ Does not store protein in an easily accessible way ​ Percentage of total intake: 10–35%