Molecules and Life (Ch.2 and 3)Levels of Organization of Life Biology can be visualized as a hierarchy of units that include molecules, cells, tissues, organs, organisms, populations, communities, and the biosphere. To understand organisms, biologists must study them at all levels of organization, from low to high Functions are mediated by molecules and allow life to happen Being able to multitask and functionseparately and coordinate to work togetherHierarchy of Organization Atoms simplest form of matter (~27 important in living organisms) 4 atoms make up ~96% of body: carbon, hydrogen, nitrogen, and oxygen Dont work by themselves form molecules or compounds Macromolecules large and complex (made of thousands of atoms) Most important b/c they allow life to occur Carbohydrates/sugars, lipids/fats, proteins, nucleic acid essential/necessary Cells smallest unit of life Characteristics of life: metabolism, responding to environment, chemical reactions, reproduction, growth Bacteria: single-celled Multicell: cluster Tissues layer of cells with common function4 types Organ group of tissue: heart, stomach, lungs, etc Organ system organs with common functions 11 systems OrganismNervous System Fast-acting control system Responds to internal and external changes Everything you do is initiated by nervous system Fuctions: Receives information from environment to brain Processing/ making sense of info Sending info out to other organs Organs: brain, spinal cord central nervous systemMuscular System Allows manipulation of environment Locomotion Facial expression Maintains posture Produces heat Functions: Use for form of communication (ex: facial expression) Heat production maintaining temperature (98.6F) 2 types of muscles smooth muscles and cardiac muscles, and skeletal musclesEndocrine System Sidekick to nervous system Controls chemically with hormones Glands secrete hormones that regulate growth, reproduction, and nutrient useCardiovascular System Blood vessels transport blood Carries oxygen and carbon dioxide Also carries nutrients and wastes Heart pumps blood Made of heart, blood vessels, blood Blood vessels are cavities for blood Picks up waste and carries nutrientsLymphatic/Immune System Picks up fluid leaked from blood vessels Houses white blood cells (lymphocytes) Mounts attack against foreign substances in the body (immunity) Circulatory fluid: accessory to cardiovascular system Functions Blood delivered picks up leaked fluid around cells and back to bloodRespiratory System Keeps blood supplied with oxygen Removes carbon dioxide Gas exchange occurs through walls of air sacs in the lungsDigestive System Breaks down food into absorbable units to supply blood with the food Indigestible foodstuffs eliminated as fecesUrinary System Eliminates nitrogenous wastes Regulates water, electrolyte, and acid-base balance Kidney, ureter, urinary bladder, urethraMale Reproductive System Overall function is to produce offspring Testes produce sperm and male sex hormones Produce sex cells and maintain sex cellsFemale Reproductive System Overall function is to produce offspring Ovaries produce eggs and female sex hormones Mammary glands produce milkPeriodic Table Carbon, oxygen, nitrogen, hydrogen ~92 elements, ~25 essential, 4 make up 96% of living matterAtoms: The Constituents of Matter Proton, neutrons, electrons Proton and neutron nucleus Electrons around nucleus positive/negative attraction Main mode of interaction Atomic number (P) ex. 2 Chemical symbol ex. He Atomic mass (P +N) ex. 4.003 Can infer # of N and EElectrons Sodium: 11 p+, 12 n, 11 e- Electrons organize around nucleus by being in specific shells Each shell has specific capacity (Ex. For Na:) First cell : 2e 2nd shell: 8e Third shell: 1e If outer shell is complete inert/does not react If outer shell is not complete reactive Electrons are naturally attracted to positive Inner shell: lowest potential energyChemical Bonds Electrostatic attractions (+ and attraction) Covalent: sharing of electrons Ionic: transfer of electrons Hydrogen Van der waalsCovalent Bonds Very strong bond H only has one electron needs to complete shell In constant random motion Each atom has 2 electron after covalent bond For hydrogen atoms: Electron of each H is attracted to its nucleus Electron is attracted to the nucleus of the other atom; atoms get close to each other The 2 electrons become shared in a covalent bond Valence shell is complete Sharing depends on types of atom Polar covalent: unequal sharing Nonpolar covalent: equal sharing, not shifted to one sideIonic Bond Strong bond; complete transfer of electrons Na and Cl both have incomplete shells When the 2 atoms get close to each other, the electron from Na is attracted to the 17 atoms of Cl (stronger pole/attraction) Ending result: Na has 11 protons, 11 electrons (+) charge/cation; Cl (-) charge/anion Ion: atom with loss/gain of electrons Sodium chloride salt strong bond In water: Na and cl becomes less attracted b/c water interferes Water surrounds Na and Cl ions hydration shell ***Brain functions- how ions move, how electrical activity worksHydrogen Bonds Weak bonds Non covalent interaction between specific polar bonds A hydrogen atom and nitrogen A hydrogen atom and oxygenVan der Waals Weak bonds Non covalent interaction between nonpolar bonds Carbon and hydrogen Do not have strong poleProperties of Molecules Polar molecules tend to be hydrophilic substances that are ionic or polar often dissolve in water due to hydrogen bonds Nonpolar molecules are called hydrophobic because they tend to aggregate with other non-polar molecules Amphipathic molecules Both hydrophilic and hydrophobic Partly polar, partly nonpolar Ex: cell membrane Hydrophilic water-loving molecules (polar) dissolves in water Hydrophobic do not interact with water (ex: lipids) nonpolarWater: Structure and Properties Due to its shape, polarity, and ability to form hydrogen bonds, water has some unusual propertiesWater Properties Cohesive and surface tension Strong surface tension liquid- gas phase strong attractive force Respiratory system Solvent of life 60% of life Temperature moderation cooling the body Water stores and releases heat into the air Controls changes in body temperature High specific heat Existence in multiple states solid, liquid, gas Changes in hydrogen bonds between the liquid state and solid state Ice is less dense than waterAcids and Bases Hydrogen ions may leave a water molecule Leads to the formation of hydroxide ions H2O H+ + OH- The hydrogen ion may bond to a water molecule forming hydronium ion H3O+ This water chemical reaction is rare, but when it occurs it will affect biological systems Other molecules may donate or accept hydrogen ions Some substances dissolve in water and release hydrogen ions (H+) acids Other substances dissolve in water and release hydroxide ions (OH-) basespH Scale pH is the measure of hydrogen ion concentration defined as the negative log of the hydrogen ion concentration in moles/liter indicates the strength of a solution of an acid or base pH 7 means the concentration of hydrogen ions is 1X10^-7 M of water pH of lower value acidic; pH of higher value basic human blood: pH of 7.4 slightly basic chemical reactions favorable Pollution and pH acid rain: H2SO4, sulfur dioxide, nitrogen oxide normal rain ~5.6, acid rain ~4.3 pH in human body ~7.4, in stomach: 1-2 as long as high acidity is contained in stomach, its not noticeable pills contain lo of base to neutralize acidsAtoms and Medicine important for understanding diseases Thyroid gland part of endocrine system produces thyroid hormone for regulating metabolism- activity in cells Iodine always added to salt chemical ingredient to synthesize thyroid hormones Hyperthyroidism: thyroid gland overly active radiolabeled

Digital Subtraction Angiography Look or symptoms of cardiovascular disease Disease of blood vessels Inhale xenon (g) binds to hemoglobin Goes to lungs, then to blood vessels Imaging blood cells in blood vessel Picture: bottom arrow: narrowing of the artery; top arrow: artery supplying the heartDrugs Most drugs are manufactured as salts because they are stable when dry They dissociate easily when dissolved in water Pills in water break down easily because ionic bondsBiological Molecules Four major types: Proteins Carbohydrates Nucleic acids LipidsBiological Macromolecules vs. Individual Units Macromolecules Proteins amino acids (20 different types) Carbohydrates glucose, fructose, galactose Nucleic acids nucleotides (5 different types) Lipids fatty acids and glycerols Not big enough to be a macromoleculeBiological Molecules The functions of these biological molecules are related to their shape and the chemical properties of their monomers Some of the roles of macromolecules include: Energy storage Structural support Transport Protection and defense Regulation of metabolic activities Means for movement, growth, and development HeredityCondensation Either connected together or apart Polymer/monomerHydrolysis Splitting covalent bond as well as water moleculeProteins Most diverse Proteins range in size from a few amino acids to thousands of them Insulin (51 amino acids) for sugar regulation; titin found in muscles (30,000 amino acids) Folding is crucial to the function of a protein and is influenced largely by the sequence of amino acids Needs proper 3D shape to functionAmino Acid Structure Amino group; carbon; carboxyl group; R-group gives it specific function Classify based on how much they interact with water Positive charged, negative charged, neutral water solubleAmino Acid Types A. Amino acids with electrically charged hydrophilic side chains Positive Arginine (Arg) (R) Histidine (His) (H) Lysine (Lys) (K) Negative Aspartic Acid (Asp) (D) Glutamic acid (Glu) (E) B. Amino acids with polar but uncharged side chains (hydrophylic) Serine (Ser) (S) Threonine (Thr) (T) Asparagine (Asn) (N) Glutamine (Gln) (Q) Tyrosine (Tyr) (Y) C. Special cases: Cysteine (Cys) C) Glycine (Gly) (G) Proline (Pro) (P) D. Amino acids with nonpolar hydrophobic side chains Alanine (Ala) (A) Isoleucine (Ile) (I) Leucine (Leu) ( L) Methionine (Met) (M) Phenylalanine (Phe) (F) Tryptophan (Trp) (W) Valine (Val) (V)Essential Amino Acids Methionine Tryptophan Leucine Phenylalanine Threonine Valine Isoleucine Lysine HistidineAmino Acids Polymerization Making proteins or breaking proteins into amino acids Peptide bond covalent bond btw carboxyl group and amino group condensation Four levels of protein structure: Primary Secondary Tertiary QuaternaryPrimary Establishing sequence/ order of folding Repeating units of N-C-C-N-C-CSecondary Stabilized by the hydrogen bonds that form between different amino acids (carboxyl group and amino group) The R-group extends outward Starting to take specific shape Alpha-helix; beta-pleated sheetTertiary May be final functioning product R-groups interaction Hydrophobic interaction (van der waals) Hydrogen bonds Ionic interaction Covalent bondsQuaternary Hemoglobin has 4 subunits (structures)Why do we need proteins? Shape is crucial to the functioning of some proteins: Enzymes need certain surface shapes in order to bind substrates correctly Chemical facilitators Carrier proteins in the cell surface membrane allow substance to enter the cell Doors and windows Chemical signals such as hormones bind to proteins on the cell surface membraneCan Proteins Become Non-Functional? Native: correct shape net = -3.9 kcal/molBiochemical Reaction Thermodynamics refers to the free energy (G) Kinetics refers to the rate of the reaction Speed is important Maltose + H2O no reaction Maltose + H2O + enzyme glucose + glucoseActivation Energy Energy needed to start a reaction Chemical reactions cannot proceed without an aid G determines the direction of a reaction but not its rate To initiate a reaction E_a is needed The rate of the reaction depends on the activation energy Enzymes lowers activation energy to speed up reaction Not changed during chemical reactionEnzymes Cells can control the speed of reactions by using protein catalysts called enzymes Enzymes enhance the speed of biochemical reactionsEnzyme Properties The enzymes are not changed They alter the rate of the reaction Lower activation energy of the reaction They do not change G (the outcome) With enzyme catalyzed Without enzyme uncatalyzedInduced Fit Chemical binding Substrate will fit into active site induced fit when substrate binds, the enzyme changes conformation Enzyme back to original structure so it can function properlyEnzyme-Substrate Interaction The fit of a substrate to the enzyme is highly specific based on shape, H-bonds, hydrophobic interactions Different chemical bonds: Ionic Hydrogen bond Polar NonpolarSpecific Enzymatic Action G to G6P hexokinase adds phosphate group to carbon number 6 Pancreas, liver, small intestine all play a role in glucose processing Alpha (glucagon) and beta cells (insulin) antagonistic (opposite) hormones Every time we consume a meal, insulin lowers sugar level When not consuming food, glucagon raises sugar level Glucostat measures glucose level by monitoring hexokinase level Glucose important b/c energy source Glucose stored and release in liver Affects glycogen storageOptimal Conditions pH and temperature regulated pH is a range pepsin (in stomach) narrow ranged for perfect function acidic important for protein digestion chief cells release pepsins needs acidic environment to function Salivary amylase neutral pH digest sugar Arginase formation of urine nitrogen waste Temperature Optimal temperature 98.6FInhibiting Enzymes Natural Artificial Enzymes arent active all the time activation only when neededCompetitive Inhibition Something in addition to the substrate competing for the active site. Concentration dependent for which is going to win Turns on enzymes when binded (substrate)Noncompetitive Inhibition Inhibitor has a different active site Concentration independent Inhibitor locks active site makes active site not availableRegulation of Proteins What would happen if proteins are inhibited or over activated? Protein activity can be affected Naturally When needed, proteins turn on/off Artificially Genetically GeneticsSickle Cell Anemia Oxygen inadequately delivered to cells Major ingredient for ATP Erythrocytes = red blood cells Hemoglobin: 250 million in each red blood cell Sickle-cell phenotype cell changes shape Creates traffic jams blocks oxygen from going to cells Hemoglobin still attached to each other Glutamic acid valineFH (Familial Hypercholesterolemia) Cardiovascular disease Cholesterol made in body (lipid) packaged in LDL vesicles Taken to liver Receptor messed up not going to liver stays in bloodPKU Phenylketonuria, a disease caused by mutation in the enzyme phenylalanine hydroxylase in the liver Converts phenylalanine to tyrosine Mostly from protein accumulated Have to have low protein diet Very rare autosomal recessive diseaseSynapse Brain made of neurons lots of communication One sends signal, one receives signal (presynaptic and postsynaptic) Neurotransmitter (chemical) signal sent and it binds to the postsynaptic ligand gated channels activation Limit time b/c dont want neurons to be constantly active Key to turn off: neurotransmitters broken down by degrading enzyme, then more neurotransmitters released to unlock Reuptake protein resynthesize neurotransmitterChronic Depression Chemical imbalance due to a decrease in serotonia release In certain areas, not enough neurotransmitters produced Fluoxetine medication that interferes with a particular protein in brain Some interfere with degrading enzyme, some the reuptake protein Changing duration Selective serotonin reuptake inhibitor Phenelzine (Nardil) manipulate breakdown Monoaminooxidase (MAO) inhibitorCaffeine Stimulant makes brain more aware delay need for sleep Adenosine receptor antagonist Caffeine is inhibitor of adenosine receptors Increase dopamine activity so it stays longer interfering with durationCocaine Stimulant and appetite suppressant Dopamine reuptake inhibitor Dopamine transporter protein blocker make dopamine available longer Cocaine and caffeine acts on different proteins not the sameMuscles Neuromuscular junction junction between neuron and junction Acetylcholine released Acetylcholine receptor muscle contracts when activated by acetylcholine Acetylcholine esterase (degrading enzyme) turn off muscle by degrading neurotransmitterCurare Blocks ACh receptors Used to be used as poison b/c it stops muscles Used as a relaxant with anesthetic agents Anesthesia: Put patient to sleep Contains pain suppressant Contains muscle relaxant Anesthesia awareness Patient feels pain but cannot wake up to do anything about itDIPF Diisopropylphosphofluoridate