Foundations of Biology 1 Lecture 1.0: What is Life PDF

Welcome to Founda tions of Biology 1 L1. 1 what is life? with Dr. McSharr y! Lecture 1.0: intro & logistics  Two truths and a lie L1. 1 what is life?...

Welcome to Founda tions of Biology 1 L1. 1 what is life? with Dr. McSharr y! Lecture 1.0: intro & logistics  Two truths and a lie L1. 1 what is life? Turn to two neighbors and tell them three “facts” about yourself: two things that are true one thing that’s false Can they guess which one is the lie??  What I most hope you gain from this class Critical thinking skills Skills in transferring knowledge to new situations Confidence asking questions L1. 1 what is life? Adaptation of a new approach to studying At least one new friend A slightly new perspective about life/ the world we live in How exactly will I help you do those things?  A successful classroom is a team effort Your roles My roles Actively construct your own knowledge Facilitate intellectually active learning Be independent, curious, and Share control of learning L1. 1 what is life? purposeful Promote your thinking about Be metacognitive (think about your concepts and about learning own thinking) Make information deposits into the Be passive recipient of knowledge “bank” of your minds Be dependent on Dr. M for all Be in control of the pace and content information Be a purveyor of truth, knowledge, Accept information uncritically facts, and wisdom CROSS OUT THE BULLET POINTS THAT DON’T APPLY Think of me as your coach  What will our typical week look like? L1. 1 what is life? Weekly Quiz Due Friday 7pm Homework Due Monday 9am  What are study sessions? L1. 1 what is life? Please read the syllabus for more information on what we’ll do, who should come, what to bring, etc. L1. 1 what is life? How will my course grade be determined? Your lowest Module Exam score will be automatically dropped! Please see the syllabus for details!  BIOSC0150 Exams Tues Jan 28 Tues March 25 April 28, 10am Module 1 Exam Module 3 exam Cumulative Final Exam Module 2 Exam Module 4 Exam Tues Feb 25 Thurs Apr 17 Lecture 1.0 Course Intro & Logistics 8  How will my course grade be determined? L1. 1 what is life? Your lowest recitation homework/ attendance score will be automatically dropped! HW due Mondays at 9 am Upload homework to Canvas Mondays at 9am Recitation 1 begins next week There’s no homework due for recitation 1 Late work will never be accepted Posting any of the work from this class (exams, problem sets, Please see the syllabus for details! recitation work, etc) is a violation of copyright law  What should I bring to recitation? Completed homework submit on Canvas by 9am L1. 1 what is life? Collaborative mindset Questions!!!  How will my course grade be determined? L1. 1 what is life? Your lowest 2 weekly quiz scores will be automatically dropped Please see the syllabus for details!  How will my course grade be determined? Due on Top Hat by 8pm on Lecture Days L1. 1 what is life? Graded for correctness Your lowest 3 in-class problem scores will be automatically dropped! Please see the syllabus for details!  All lectures are recorded Lecture recordings will be posted on Panopto (in Canvas) by 10am each lecture day L1. 1 what is life? I’m only human  How will my course grade be determined? L1. 1 what is life? Please see the syllabus for details!  Science is an adventure! L1. 1 what is life? Journal Safari #1 due on Top Hat Thursday January 23rd at 8am  Many extra credit opportunities available throughout the semester Available now: Real World Bio 1: Study Skills (on Top Hat) 1 pt added to overall course grade L1. 1 what is life? Available soon: Research survey will open Monday 1/13 and closes 1/20 1 pt added to overall course grade  Percentage Letter Every single student can Grade Min Max earn an A! A+ 97.91 100 A 91.91 97.90 A- 89.91 91.90 An A is supposed to be challenging L1. 1 what is life? B+ 87.91 89.90 to achieve B 81.91 87.90 Please note that I will be strictly B- 79.91 81.90 adhering to this chart for final C+ 77.91 79.90 grades C 71.91 77.90 C- 69.91 71.90 D+ 67.91 69.90 D 61.91 67.90 A = outstanding D- 59.01 61.90 B = commendable F 0 59.00 C- satisfactory D = unsatisfactory F = failing Please read the syllabus for more details!  Schedule your time for the first 2 weeks now Weekly Quiz 1 due THIS FRIDAY Jan 10 at 7pm (covers today’s lecture) First recitation is MONDAY Jan 13! (Bring pen & paper; no HW) L1. 1 what is life? Weekly Quiz 2 due Fri Jan 17 Survey opens Monday; due Mon Jan 20 Recitation 2 HW due Mon Jan 20, 9am Real World Bio 1 is now available on Top Hat; due Fri Jan 17, 7pm ✓ Write these dates (and the dates of all assignments) in your planner! ✓ Schedule time to complete them NOW! o 2 hr per homework /Real-World Bio o 30 min per survey/ quiz  STOP If you are on the wait list for this course, you will not be excused from any work due before you were successfully registered. Email Dr. M immediately ([email protected]) to be added to Canvas!! L1. 1 what is life?  How will I succeed in this class? Come to class and be engaged Come to recitation and be engaged TL;DR Practice effortfully & frequently Read the textbook BEFORE class L1. 1 what is life? Do the assignments effortfully Ask questions Do as many practice questions as you can find (don’t start by re-reading the textbook) DON’T CRAM! Work in a group to talk out your ideas Write your own problems and exchange them with others  What conclusion might you draw from these data? *** 89.2% L1. 1 what is life? 72.7% p < 1x10-13 Present in Absent lecture from on a lecture random that day day  Four recommendations 1. Set a schedule and hold yourself accountable (COME TO CLASS) L1. 1 what is life? 2. Take advantage of opportunities to work with others 3. Don’t give up!! 4. Take care of and be kind to yourself  Come to study sessions!! WRITE ONE IN YOUR CALENDAR RIGHT NOW L1. 1 what is life? Unlike Griffin, we do not bite!  What should I do if I have a question? FIRST do your own research Post it on the Canvas L1. 1 what is life? discussion board Ask in study sessions Ask at recitation Ask a peer  Important notes about my slide design Key terms are in pink/bold/underlined font Fill in the blank will help you follow along and identify key information/ terms that I expect you to use fluently on an exam L1. 1 what is life?  What is life? There is no right answer– this is is still up for debate!! L1. 1 what is life? L1. 1 what is life? The Scale of Life  _______________ is a unifying principle of biology Cells are the fundamental units of life. All organisms are made up of cells. L1. 1 what is life? All cells come from preexisting cells. Modern cells evolved from a common ancestor.  Components of all cells ____________: everything in the cell (except the nucleus, if applicable) ___________ are where proteins are made L1. 1 what is life? _______________: fluid cytoplasm not contained inside another compartment. Cell _______________ : outer boundary of every cell similar structure in all cells—a phospholipid bilayer with embedded proteins Site of entry into/ exit from the cell Determines what enters/ exits the cell  The _______________ is the site of cellular exchange of nutrients and waste for all cells a _______________ permeable barrier (more on this soon) constant internal environment L1. 1 what is life? communication with the environment/ other cells binding and adhering to adjacent cells  Two categories of cells _______________ human cell L1. 1 what is life? ________ Clostridium Bacteria Animals Archaea Plants Fungi Protists ~10 μm The main difference between prokaryotic/ eukaryotic cells: eukaryotic cells have ___________________________.  Eukaryotic cells have membrane-bound compartments called _______________ Membranes separate and concentrate molecules to favor their interactions in chemical reactions!!! L1. 1 what is life? We’ll learn about specific organelles later  Take a moment to imagine if there was only 1 door in… THE MALL OF AMERICA: 5,600,000 sq ft L1. 1 what is life? YOUR DORM ROOM: 150 sq ft THIS CLASSROOM: ~3,000 sq ft Square footage is a unit of _______________ : the amount of 3D space occupied by an object  Which one has a greater volume? Eukaryote human cell L1. 1 what is life? Prokaryote Clostridium ~10 μm Dr. M, what does this have to do with cells??????  Surface area is the area of all the surfaces of a 3D object L1. 1 what is life? A cell’s surface area is its cell membrane! Remember: the membrane is the site of transport (exchange)  Cellular intake of nutrients and release of waste products happens faster with a higher _______________ _______________ ratio L1. 1 what is life? The membrane is the site of exchange! https://ib.bioninja.com.au/standard-level/topic-1-cell-biology/11-introduction-to-cells/sa--vol-ratio.html If a cell was too big (SA:V ratio too small), it wouldn’t be able to carry out exchange; surface area (sites of exchange) limits how big a cell can get!  Substances found in living things Four types of biological macromolecules: _______________ L1. 1 what is life? Today Macromolecules: Very large molecules containing thousands or more atoms. Proteins, nucleic acids, and carbohydrates are all _____________ (comprised of smaller units called ___________) L1. 1 what is life? lipids  What do these items have in common? Butter Wax crayons L1. 1 what is life? Olive oil Animal fat Fish oil L1. 1 what is life? Lipids have many important biological functions! Thermal insulation Energy storage Electrical insulation Repel water Cell signaling  Lipids Are Defined by Their Insolubility in Water (1) _______________ are nonpolar hydrocarbons that have various roles in cells! L1. 1 what is life? ❖Fats and oils store energy. ❖Phospholipids—structural role in cell membranes. ❖Carotenoids and chlorophylls—capture light energy in plants. ❖Others  Fats and oils are _______________; they store energy 3 _______________ ______ + 1 _______________ linkage = _______________ L1. 1 what is life? ???? Thermal insulation Energy storage  Important questions we have to answer before moving on 1. How the heck do we get these molecules of fatty acids + glycerol together in the first place?? L1. 1 what is life? 2. What kind of bond forms between the atoms of in an ester linkage??  _______________ ________ reactions create polymers New bonds form between monomers and a water molecule is released L1. 1 what is life? They’re also called dehydration reactions L1. 1 what is life? The next question… How do we break molecules apart into monomers??  Polymers are broken down into monomers in _______________ reactions, which consume water L1. 1 what is life? Greek vocabulary Hydro- water Lysis - break  Important questions we have to answer before moving on 1. How the heck do we get these molecules of fatty acids + glycerol together in the first place?? CONDENSATION REACTION L1. 1 what is life? 2. What kind of bond forms between the atoms of in an ester linkage??  What is an ester linkage??? To answer this question we have to delve into chemistry condensation rxn 3 fatty acids + 1 glycerol Ester = triglyceride linkage L1. 1 what is life? Thermal insulation Energy storage  An _______________ is a substance comprised of only one kind of atom The number of protons in the atom (atomic ____________) identifies an element. L1. 1 what is life? Number of protons and electrons determines how an element behaves in chemical reactions. Thi s Photo by Unknown Author i s l icensed under CC BY-SA  In the ___________ table, elements are organized by their physical and chemical L1. 1 what is life? properties  An element’s atomic structure determines its properties ___________ negative charge; negligible mass L1. 1 what is life? ___________ have a positive charge; mass = 1 dalton ___________ have no charge; mass = 1 dalton 1 dalton (Da) = 1.7 × 10–24 grams Generally, atoms are electrically neutral #electrons _____ #protons  How to learn about an element in the periodic table Atomic ___________ Mass number = protons + neutrons in 1 atom L1. 1 what is life? ___________: Forms of an element with different numbers of neutrons, and thus different mass numbers. Atomic ___________ = average of the mass numbers of a representative sample of atoms (accounts for isotopes)  Electrons are found in specific areas surrounding atoms Electrons are found in different shells around the atom Each shell has a different energy level L1. 1 what is life? Electron shells are comprised of orbitals ___________: Region where an electron is found at least 90% of the time. Orbitals are filled in a specific sequence. Electron shells are the blue rings; orbitals are not shown here.  Each shell holds a different number of electrons because it has a different number of orbitals Example: Nitrogen (atomic number = 7) 7 protons First shell (innermost): 1 orbital; 7 neutrons holds 2 electrons - - 7 electrons - - L1. 1 what is life? Second shell: 4 orbitals; holds 8 electrons - + - + + + + The farther a shell is from the + + nucleus, the higher the energy level of electrons in that shell. - (farther from the + nucleus) Nitrogen has 3 unpaired valence electrons  Electrons in the outermost (___________) shell determine how the atom behaves. Atoms with unpaired electrons in their valence shell are reactive L1. 1 what is life? This will determine how many bonds an atom can participate in If the outermost shell is full, the atom is stable; it won’t react with other atoms.  How many unpaired electrons does oxygen have in its valence shell? L1. 1 what is life?  Analysis of an atom 8 protons 8 neutrons 8 electrons L1. 1 what is life? Oxygen has 2 unpaired valence electrons  The most abundant elements in living things are H, C, N, S, O, and P L1. 1 what is life?  Atoms bond to form ___________ Chemical ___________: Attractive force that links atoms together to form molecules. L1. 1 what is life? Reactive atoms can share, lose, or gain electrons Result: atoms bond together to form stable molecules L1. 1 what is life?  ___________ Bond: atoms share 1 or more pairs of electrons so that their outer shells are filled Electron field L1. 1 what is life? Nucleus  Atoms Bond to Form Molecules In its excited state, carbon has 4 unpaired electrons in its valence shell; it can form 4 covalent bonds. L1. 1 what is life? When an atom of carbon reacts with four hydrogen atoms, methane forms. Because of equal electron sharing, the carbon atom and all 4 hydrogen atoms have full outer shells. Thi s Photo by Unknown Author i s l icensed under CC BY-NC Octet rule: Tendency of atoms to form stable molecules resulting in full valence shells. L1. 1 what is life? CH4 = methane Thi s Photo by Unknown Author i s l icensed under CC BY-NC L1. 1 what is life? Molecules formed by covalent bonds  Covalent bonds formed by the most abundant elements in living things L1. 1 what is life?  Bond energies are higher in multiple covalent bonds The energy input needed to break the bond is _____________ when _________ electrons are shared Triple bond (3 pairs of electrons shared): N N L1. 1 what is life? Double bond (2 pairs of electrons shared): C C Single bond (1 pair of electrons shared): C H Covalent bonds are very strong—it takes a lot of energy to break them.  Important questions we have to answer before moving on 1. How the heck do we get these molecules of fatty acids + glycerol together in the first place?? CONDENSATION REACTION L1. 1 what is life? 2. What kind of bond forms between the atoms of in an ester linkage??  What is an ester linkage??? To answer this question we have to delve into chemistry condensation rxn 3 fatty acids + 1 glycerol Ester = triglyceride linkage L1. 1 what is life? Thermal insulation Energy storage  An ____________ is a substance comprised of only one kind of atom The number of protons in the atom (atomic ____________) identifies an element. L1. 1 what is life? Number of protons and electrons determines how an element behaves in chemical reactions. Thi s Photo by Unknown Author i s l icensed under CC BY-SA  In the periodic table, elements are organized by their physical and chemical L1. 1 what is life? properties  An element’s atomic structure determines its properties ____________ negative charge; negligible mass L1. 1 what is life? ____________ have a positive charge; mass = 1 dalton ____________ have no charge; mass = 1 dalton 1 dalton (Da) = 1.7 × 10–24 grams Generally, atoms are electrically neutral #electrons ____ #protons  How to learn about an element in the periodic table Atomic ____________ ____________ number = protons + neutrons in 1 atom L1. 1 what is life? ____________ : Forms of an element with different numbers of neutrons, and thus different mass numbers. Atomic ____________ = average of the mass numbers of a representative sample of atoms (accounts for isotopes)  Electrons are found in specific areas surrounding atoms Electrons are found in different shells around the atom Each shell has a different energy level L1. 1 what is life? Electron shells are comprised of orbitals ____________ : Region where an electron is found at least 90% of the time. Orbitals are filled in a specific sequence. Electron shells are the blue rings; orbitals are not shown here.  Each shell holds a different number of electrons because it has a different number of orbitals Example: Nitrogen (atomic number = 7) 7 protons First ___________ (innermost): 7 neutrons 1 orbital; holds 2 electrons - - 7 electrons - - L1. 1 what is life? Second shell: 4 orbitals; holds 8 electrons - + - + + + + The farther a shell is from the + + nucleus, the higher the energy level of electrons in that shell. - (farther from the + nucleus) Nitrogen has 3 unpaired valence electrons  Electrons in the outermost (_____________________) shell determine how the atom behaves. Atoms with unpaired electrons in their valence shell are reactive L1. 1 what is life? This will determine how many bonds an atom can participate in If the outermost shell is full, the atom is stable; it won’t react with other atoms.  Atoms bond to form molecules Chemical ____________ : Attractive force that links atoms together to form molecules. L1. 1 what is life? Reactive atoms can share, lose, or gain electrons Result: atoms bond together to form stable molecules  An ester linkage is one type of covalent bond! L1. 1 what is life?  ________________ Bond: atoms share 1 or more pairs of electrons so that their outer shells are filled Electron field L1. 1 what is life? Nucleus  Atoms Bond to Form Molecules In its excited state, carbon has 4 unpaired electrons in its valence shell; it can form _____ covalent bonds. L1. 1 what is life? When an atom of carbon reacts with four hydrogen atoms, methane forms. Because of equal electron sharing, the carbon atom and all 4 hydrogen atoms have full outer shells. Thi s Photo by Unknown Author i s l icensed under CC BY-NC Octet rule: Tendency of atoms to form stable molecules resulting in full valence shells. L1. 1 what is life? CH4 = methane Thi s Photo by Unknown Author i s l icensed under CC BY-NC L1. 1 what is life? Molecules formed by covalent bonds  The most abundant elements in living things are H, C, N, S, O, and P L1. 1 what is life?  Covalent bonds formed by the most abundant elements in living things L1. 1 what is life?  Bond energies are higher in multiple covalent bonds The energy input needed to break the bond is _____________ when _____________ electrons are shared Triple bond (3 pairs of electrons shared): N N L1. 1 what is life? Double bond (2 pairs of electrons shared): C C Single bond (1 pair of electrons shared): C H Covalent bonds are very strong—it takes a lot of energy to break them.  In a triglyceride, the ester linkage is a covalent bond between the indicated O of glycerol and C of a fatty acid condensation rxn 3 fatty acids + 1 glycerol = triglyceride Ester linkage L1. 1 what is life? Carboxylic acid More specifically, it’s the connection between the OH of an alcohol and a carboxylic acid with an alipathic/ aromatic group  The two types of fatty acids differ in the presence of double-bonds between composite carbon atoms L1. 1 what is life? Fats are solid at room temperature Oils are liquid at room temperature  __________________ of vegetable oils is carried out to produce a more solid substance than from found in plants L1. 1 what is life? hydrogenation  Lipids Are Defined by Their Insolubility in Water (1) Lipids are nonpolar hydrocarbons; they are insoluble in water Fats and oils store energy. L1. 1 what is life? Phospholipids—structural role in cell membranes.  Triglycerides vs ___________________ L1. 1 what is life?  Phospholipids: 2 fatty acids bound to glycerol, but a phosphate group replaces one fatty acid. L1. 1 what is life? Phospholipids are _____________: “Head” is a phosphate group—hydrophilic. “Tails” are fatty acid chains—hydrophobic.  What is hydrophilic vs hydrophobic? L1. 1 what is life? L1. 1 what is life? Is the sharing of electrons always equal? This Photo by Unknown Author is licensed under CC BY  Sharing of electrons in a covalent bond is not always equal. ________________: Extent of the attractive force that an atomic nucleus exerts on electrons. (its ability to win tug of war) L1. 1 what is life? Hydrogen Oxygen electrons The greater an atom’s electronegativity, the _______ it attracts electrons. Chandler is less electronegative than Joey  When atoms of different electronegativities form a covalent bond, the electrons are drawn more to one nucleus than to the other L1. 1 what is life? Electronegativity (χ) of Oxygen: 3.5 χ Hydrogen: 2.1 Difference between atoms’ electronegativities influences the nature of the covalent bond  Electrons in a _______ _____________ bond spend more time near the nucleus of the atom with the greater electronegativity Electrons are drawn more to the nucleus of the atom with greater electronegativity L1. 1 what is life? The participating atom has a partial negative charge (____) if it “hogs” electrons The participating atom has a partial positive charge (____) if it loses out on electrons  Electrons in a _________ _____________ bond are shared equally (atoms have similar electronegativity). Electrons are Electrons are L1. 1 what is life? near-equally more likely to be likely to be found near the found near the nucleus of O nucleus of C or H than of H χC 2.5 χO 3.5 χH 2.1 χH 2.1  can be polar or nonpolar L1. 1 what is life?  χ Na = 0.9 χCl= 3.1 _____________ bonds form when one atom is much more electronegative than L1. 1 what is life? the other, and a complete transfer of electrons occurs This results in two ions with full outer shells. Ions are electrically charged particles formed when atoms lose or gain one or more electrons. Cations—positive (Na+); lost an electron Anions—negative (Cl-); gained an electron  _____________ are ionically bonded compounds (eg, NaCl = table salt!) In solids, ionic bonds are strong because ions are close together. But what happens when you add salt to water? L1. 1 what is life? This Photo by Unknown Author is licensed under CC BY-ND  Water molecules surround ions, keeping them separate Na+Cl— L1. 1 what is life? Salts dissolve in water!  Electron density in covalent vs ionic bonds L1. 1 what is life? L1. 1 what is life?  Hydrogen bonds can form between two atoms with opposite partial charges between 2 molecules or within 1 molecule L1. 1 what is life? L1. 1 what is life?  Polar molecules like HCl can form H-bonds with (and therefore dissolve freely in) water; they’re ______________________ L1. 1 what is life?  Nonpolar molecules can’t form hydrogen bonds with water; they’re hydrophobic _________________ are comprised of only C and H ____________ molecules like hexene, don’t have partial charges (C and H have approximately equal electronegativities) L1. 1 what is life? We call them ______________ (“water-fearing”) because they can’t Why does this happen?? form hydrogen bonds with water; they clump together instead. In the presence of a polar substance, hydrophobic substances aggregate with each other = hydrophobic interactions L1. 1 what is life? One molecule can have polar and nonpolar regions When in water, a molecule with a polar head and long nonpolar tail will form a structure called a micelle. The force that drives the tails into the center of the micelle is a hydrophobic interaction. L1. 1 what is life?  Phospholipids: 2 fatty acids bound to glycerol, but a phosphate group replaces one fatty acid. L1. 1 what is life? Phospholipids are _____________: “Head” is a phosphate group—hydrophilic. “Tails” are fatty acid chains—hydrophobic.  Phospholipids organize to form the __________________, which comprises the L1. 1 what is life? membrane that surrounds all cells What forces hold the hydrophobic tails of these phospholipids together? L1. 1 what is life?  Electrons are extremely dynamic–at one moment, a dipole can be temporarily created even in a nonpolar bond L1. 1 what is life? T=1 T=2 T=3 δ- δ+ The temporary dipole causes even more dipoles in molecules that are close by!  van der Waals forces are weak interactions between nonpolar molecules that are close together L1. 1 what is life? temporary δ+ / δ- identities (dipoles) are determined by electron locations these interactions are brief and weak but can be substantial when summed over a large molecule. Important when hydrophobic regions of molecules, such as an enzyme and a substrate, come together.  Lipids Are Defined by Their Insolubility in Water (1) Lipids are nonpolar hydrocarbons Fats and oils store energy. L1. 1 what is life? Phospholipids—structural role in cell membranes. Carotenoids and chlorophylls—capture light energy in plants.  Carotenoids: light-absorbing pigments, e.g., β-carotene traps light energy for photosynthesis. In humans, β-carotene breaks down into Vitamin A. L1. 1 what is life? This Photo by Unknown Author is licensed under CC BY  Lipids Are Defined by Their Insolubility in Water (1) Lipids are nonpolar hydrocarbons Fats and oils store energy. L1. 1 what is life? Phospholipids—structural role in cell membranes. Carotenoids and chlorophylls—capture light energy in plants. Steroids add to membrane integrity, function as hormones (cell signaling) Cell signaling  In steroids, multiple rings share carbon atoms. Cholesterol is an important component of animal membranes L1. 1 what is life? Other steroids are hormones “messenger” molecules secreted by animal or plant cells to regulate specific processes eg Insulin, which is not a steroid!  Lipids Are Defined by Their Insolubility in Water (1) Lipids are nonpolar hydrocarbons Fats and oils store energy. Phospholipids—structural role in L1. 1 what is life? cell membranes. Carotenoids and chlorophylls— Repel water capture light energy in plants. Waxes can repel water, keep tissues from drying out, etc. Waxes: long-chain alcohol bound to an unsaturated fatty acid. L1. 1 what is life? Polar or nonpolar  Electron density in covalent vs ionic bonds Water is polar: it is one molecule, but different parts of it have opposite PARTIAL charges L1. 1 what is life? Roughly equal eletronegativities Different eletronegativities L1. 1 what is life? L1. 1 what is life? Hydrogen bonds can form between 2 molecules… L1. 1 what is life? Hydrogen bonds can form between 2 molecules or within 1 molecule  Hydrogen bonding influences the properties of water Turning liquid water to gas requires a lot of energy input (to break the H bonds) It has a high ___________________________ Sweating allows organisms to dissipate excess heat Ice floats because it’s less dense than liquid water L1. 1 what is life?  Hydrogen bonding influences the properties of water Liquid water molecules stick to each other, and resist coming apart = cohesion and surface tension L1. 1 what is life? Key Concept 2.4 The Properties of Water Are Critical to the Chemistry of Life L1. 1 what is life? Water is the dominant component of virtually all living organisms Water has many unusual properties resulting from its polarity and ability to form hydrogen bonds. Most biochemical reactions take place in water (aqueous solution) Water can act as an acid or as a base  Most biochemical reactions take place in an aqueous (watery) solution Cells are mostly water Solution: substance (solute) dissolved in a liquid (solvent). L1. 1 what is life? Dissolved molecules don’t lose their identity and properties; they can still react.  __________ release H+ In an aqueous solution (like a cell), an acid reacts with water to release a H+ → L1. 1 what is life? What is another name for H+?  Acids release H+ (protons) HCl (hydrochloric acid) is a strong acid; it ionizes fully in water: HA → H+ + A– L1. 1 what is life? HCl → H+ concentration is increased; the resulting solution is acidic. The reaction doesn’t often go backwards (it’s ______________)  Strong acids vs weak acids HCl is a ___________ acid because it fully ionizes in water; the reaction only proceeds in this direction: HCl → H+ + Cl– L1. 1 what is life? A ___________ acid like CH3COOH (acetic acid) will react reversibly with water/ some of the ions reassociate: HA ⇌ H+ + A– CH3COOH ⇌ H+ + CH3COO– Acetic acid  Many biological molecules have a carboxyl group = are acids Many biological molecules have a ___________ group: R—COOH ⇌ H+ + R—COO– L1. 1 what is life? What happens to this proton?? Weak acids: Not all the acid molecules dissociate into ions (e.g., when acetic acid CH3COOH is added, only some will fully dissociate). REMEMBER: Strong acids like hydrochloric acid (HCl) ionize completely.  ___________ accept H+ (protons) When an acid releases a proton in water, the proton is accepted by water, creating a hydronium ion. L1. 1 what is life? HA + H2O → H3O+ + A– In this reaction, water acts as a base because it accepts a proton!  Water acts as both a weak acid and a weak base Water has a slight tendency to ionize (1/500 million): L1. 1 what is life? Ionization of water is important because of the abundance of water in living systems and the reactive nature of the H+ ions.  Strong bases vs weak bases NaOH is a ___________ base because it fully ionizes in water; the reaction only proceeds in this direction: NaOH → Na+ + OH– L1. 1 what is life? A ___________ base like HCO3– (bicarbonate) will react reversibly with water: HCO3– + H+ ⇌ H2CO3 — carbonic acid! The direction in which a reversible reaction proceeds will be determined by the concentrations Bicarbonate of reactants and products.  ________ is a measure of the concentration of H+ pH = –log[H+] oH+ concentration of pure water is 10–7 M, so its pH = 7 L1. 1 what is life? oH+ concentration of 1M HCl is 1 (100) M, so its pH = 0 oH+ concentration of 1M NaOH is 10-14M, so its pH = 14 Lower pH numbers mean higher H+ concentration (greater acidity).  In living systems, buffers help maintain constant pH Organisms must maintain ________ (constant internal conditions including temperature, pH, etc.) L1. 1 what is life? ________ : a mixture of a weak acid + its conjugate base (or vice versa) e.g., bicarbonate ion (HCO3–) + carbonic acid (H2CO3): HCO3– + H+ ⇌ H2CO3 When both are present in a solution, small increases in [H+] or [OH-] will not change the pH of the solution because it won’t change the concentration of free H+.  Buffers illustrate the law of mass action Addition of reactant on one side of a reversible system drives the system in the direction that uses up that compound. L1. 1 what is life? Addition of an acid drives the reaction in one direction; addition of a base drives the reaction in the other direction. HCO3– + H+ ⇌ H2CO3 Addition of an acid will shift the reaction toward the _____ Addition of a base will shift the reaction toward the _____  In biological systems, buffers are critical to minimize changes in pH, but a solution may still still become saturated L1. 1 what is life? Solution with buffer Test yourself: What would this graph look like if Solution without buffer you added an acid instead? answer in Achieve  pH is a measure of the concentration of H+ pH = –log[H+] oH+ concentration of pure water is 10–7 M, so its pH = 7 L1. 1 what is life? oH+ concentration of 1M HCl is 1 (100) M, so its pH = 0 oH+ concentration of 1M NaOH is 10-14M, so its pH = 14 Lower pH numbers mean higher H+ concentration (greater acidity).  Common acids and bases to (look up* and) memorize Acids Bases Hydrochloric acid Ammonia L1. 1 what is life? Carbonic acid Sodium hydroxide (NaOH) Nitric acid Potassium hydroxide Acetic acid Methyl amine Phosphoric acid Sodium hypochlorite (NaOCl), the Sulfuric acid active ingredient in bleach *Draw the chemical structure and know whether each is a strong or weak acid/ base and write the reaction that occurs when you put it in water (identify acidic H or basic groups and conjugate acid/ base)  L1.3 Substances can pass membranes by passive processes L1. 1 what is life?  Today’s agenda! Chemistry of phospholipids Summary of chemical bonds and interactions Summary of lipids as a macromolecule L1. 1 what is life? Chemistry of water H-bonding and properties of water pH How substances move across membranes without help (passive transport) L1. 1 what is life? One molecule can have polar and nonpolar regions When in water, a molecule with a polar head and long nonpolar tail will form a structure called a micelle. The force that drives the tails into the center of the micelle is a hydrophobic interaction. L1. 1 what is life?  Phospholipids: 2 fatty acids bound to glycerol, but a phosphate group replaces one fatty acid. L1. 1 what is life? Phospholipids are _____________: “Head” is a phosphate group—hydrophilic. “Tails” are fatty acid chains—hydrophobic.  Phospholipids organize to form the __________________, which comprises the L1. 1 what is life? membrane that surrounds all cells What forces hold the hydrophobic tails of these phospholipids together? L1. 1 what is life?  Electrons are extremely dynamic–at one moment, a dipole can be temporarily created even in a nonpolar bond L1. 1 what is life? T=1 T=2 T=3 δ- δ+ The temporary dipole causes even more dipoles in molecules that are close by!  van der Waals forces are weak interactions between nonpolar molecules that are close together L1. 1 what is life? temporary δ+ / δ- identities (dipoles) are determined by electron locations these interactions are brief and weak but can be substantial when summed over a large molecule. Important when hydrophobic regions of molecules, such as an enzyme and a substrate, come together.  Lipids Are Defined by Their Insolubility in Water (1) Lipids are nonpolar hydrocarbons Fats and oils store energy. L1. 1 what is life? Phospholipids—structural role in cell membranes. Carotenoids and chlorophylls—capture light energy in plants.  Carotenoids: light-absorbing pigments, e.g., β-carotene traps light energy for photosynthesis. In humans, β-carotene breaks down into Vitamin A. L1. 1 what is life? This Photo by Unknown Author is licensed under CC BY  Lipids Are Defined by Their Insolubility in Water (1) Lipids are nonpolar hydrocarbons Fats and oils store energy. L1. 1 what is life? Phospholipids—structural role in cell membranes. Carotenoids and chlorophylls—capture light energy in plants. Steroids add to membrane integrity, function as hormones (cell signaling) Cell signaling  In steroids, multiple rings share carbon atoms. Cholesterol is an important component of animal membranes L1. 1 what is life? Other steroids are hormones “messenger” molecules secreted by animal or plant cells to regulate specific processes eg Insulin, which is not a steroid!  Lipids Are Defined by Their Insolubility in Water (1) Lipids are nonpolar hydrocarbons Fats and oils store energy. Phospholipids—structural role in L1. 1 what is life? cell membranes. Carotenoids and chlorophylls— Repel water capture light energy in plants. Waxes can repel water, keep tissues from drying out, etc. Waxes: long-chain alcohol bound to an unsaturated fatty acid. L1. 1 what is life? Polar or nonpolar  Electron density in covalent vs ionic bonds Water is polar: it is one molecule, but different parts of it have opposite PARTIAL charges L1. 1 what is life? Roughly equal eletronegativities Different eletronegativities L1. 1 what is life? L1. 1 what is life? Hydrogen bonds can form between 2 molecules… L1. 1 what is life? Hydrogen bonds can form between 2 molecules or within 1 molecule  Hydrogen bonding influences the properties of water Turning liquid water to gas requires a lot of energy input (to break the H bonds) It has a high ___________________________ Sweating allows organisms to dissipate excess heat Ice floats because it’s less dense than liquid water L1. 1 what is life?  Hydrogen bonding influences the properties of water Liquid water molecules stick to each other, and resist coming apart = cohesion and surface tension L1. 1 what is life? Key Concept 2.4 The Properties of Water Are Critical to the Chemistry of Life L1. 1 what is life? Water is the dominant component of virtually all living organisms Water has many unusual properties resulting from its polarity and ability to form hydrogen bonds. Most biochemical reactions take place in water (aqueous solution) Water can act as an acid or as a base  Most biochemical reactions take place in an aqueous (watery) solution Cells are mostly water Solution: substance (solute) dissolved in a liquid (solvent). L1. 1 what is life? Dissolved molecules don’t lose their identity and properties; they can still react.  __________ release H+ In an aqueous solution (like a cell), an acid reacts with water to release a H+ → L1. 1 what is life? What is another name for H+?  Acids release H+ (protons) HCl (hydrochloric acid) is a strong acid; it ionizes fully in water: HA → H+ + A– L1. 1 what is life? HCl → H+ concentration is increased; the resulting solution is acidic. The reaction doesn’t often go backwards (it’s ______________)  Strong acids vs weak acids HCl is a ___________ acid because it fully ionizes in water; the reaction only proceeds in this direction: HCl → H+ + Cl– L1. 1 what is life? A ___________ acid like CH3COOH (acetic acid) will react reversibly with water/ some of the ions reassociate: HA ⇌ H+ + A– CH3COOH ⇌ H+ + CH3COO– Acetic acid  Many biological molecules have a carboxyl group = are acids Many biological molecules have a ___________ group: R—COOH ⇌ H+ + R—COO– L1. 1 what is life? What happens to this proton?? Weak acids: Not all the acid molecules dissociate into ions (e.g., when acetic acid CH3COOH is added, only some will fully dissociate). REMEMBER: Strong acids like hydrochloric acid (HCl) ionize completely.  ___________ accept H+ (protons) When an acid releases a proton in water, the proton is accepted by water, creating a hydronium ion. L1. 1 what is life? HA + H2O → H3O+ + A– In this reaction, water acts as a base because it accepts a proton!  Water acts as both a weak acid and a weak base Water has a slight tendency to ionize (1/500 million): L1. 1 what is life? Ionization of water is important because of the abundance of water in living systems and the reactive nature of the H+ ions.  Strong bases vs weak bases NaOH is a ___________ base because it fully ionizes in water; the reaction only proceeds in this direction: NaOH → Na+ + OH– L1. 1 what is life? A ___________ base like HCO3– (bicarbonate) will react reversibly with water: HCO3– + H+ ⇌ H2CO3 — carbonic acid! The direction in which a reversible reaction proceeds will be determined by the concentrations Bicarbonate of reactants and products.  ________ is a measure of the concentration of H+ pH = –log[H+] oH+ concentration of pure water is 10–7 M, so its pH = 7 L1. 1 what is life? oH+ concentration of 1M HCl is 1 (100) M, so its pH = 0 oH+ concentration of 1M NaOH is 10-14M, so its pH = 14 Lower pH numbers mean higher H+ concentration (greater acidity).  In living systems, buffers help maintain constant pH Organisms must maintain ________ (constant internal conditions including temperature, pH, etc.) L1. 1 what is life? ________ : a mixture of a weak acid + its conjugate base (or vice versa) e.g., bicarbonate ion (HCO3–) + carbonic acid (H2CO3): HCO3– + H+ ⇌ H2CO3 When both are present in a solution, small increases in [H+] or [OH-] will not change the pH of the solution because it won’t change the concentration of free H+.  Buffers illustrate the law of mass action Addition of reactant on one side of a reversible system drives the system in the direction that uses up that compound. L1. 1 what is life? Addition of an acid drives the reaction in one direction; addition of a base drives the reaction in the other direction. HCO3– + H+ ⇌ H2CO3 Addition of an acid will shift the reaction toward the _____ Addition of a base will shift the reaction toward the _____  In biological systems, buffers are critical to minimize changes in pH, but a solution may still still become saturated L1. 1 what is life? Solution with buffer Test yourself: What would this graph look like if Solution without buffer you added an acid instead? answer in Achieve  pH is a measure of the concentration of H+ pH = –log[H+] oH+ concentration of pure water is 10–7 M, so its pH = 7 L1. 1 what is life? oH+ concentration of 1M HCl is 1 (100) M, so its pH = 0 oH+ concentration of 1M NaOH is 10-14M, so its pH = 14 Lower pH numbers mean higher H+ concentration (greater acidity).  Common acids and bases to (look up* and) memorize Acids Bases Hydrochloric acid Ammonia L1. 1 what is life? Carbonic acid Sodium hydroxide (NaOH) Nitric acid Potassium hydroxide Acetic acid Methyl amine Phosphoric acid Sodium hypochlorite (NaOCl), the Sulfuric acid active ingredient in bleach *Draw the chemical structure and know whether each is a strong or weak acid/ base and write the reaction that occurs when you put it in water (identify acidic H or basic groups and conjugate acid/ base)  Today’s agenda! Chemistry of phospholipids Summary of chemical bonds and interactions Summary of lipids as a macromolecule L1. 1 what is life? Chemistry of water H-bonding and properties of water pH How substances move across membranes without help (passive transport) L1. 1 what is life? What property of the membrane does this diagram illustrate?  _____________________: the process of random movement of a solute from a region of higher concentration to a region of lower concentration L1. 1 what is life? Particles move randomly in a solution; when they are evenly distributed, they are at _______________ (but still move!) L1. 1 what is life? Diffusion works very well over short distances (eg, within a small cell)  Concentration is the number of particles in a given volume; The unit of concentration is ____________________ (M) L1. 1 what is life? 1 mol dissolved in 1 L 1 mol dissolved in 0.25 L 1 mol / 1 L = ______ M 1 mol / 0.25 L = _____ M You don’t need to calculate molarity, but you should know that a solution with higher molarity is more concentrated  Lipid-soluble substances can cross membranes by diffusion Molecules move across a permeable membrane until concentration is equal on both sides. L1. 1 what is life? Molecules will continue to diffuse across the membrane, but there will be no net change in concentrations. Energy for passive transport comes from the ____________________. VERY IMPORTANT TERM!  The concentration gradient decreases over time as the dye particles become more evenly distributed in the solution L1. 1 what is life? Polar and charged molecules diffuse across the membrane with concentration gradients. Diffusion is the net movement from regions of greater concentration to regions of lesser concentration.  The rate at which substances diffuse in a solution depends on several factors: Concentration gradient Size and mass of the molecules or ions L1. 1 what is life? Temperature of the solution Density of the solution Area and distance L1. 1 what is life? Water diffuses across a membrane in a process called ___________________ The rate of water movement across the membrane depends on the relative concentrations of solute molecules on either side. ________________: equal solute concentrations inside and outside the cell ________________: lower solute concentration outside the cell ________________: higher solute concentration outside the cell Hyper – higher Hypo – lower  Animal cells may burst when placed in a hypotonic solution, or shrink in a hypertonic solution. Isotonic = ideal! L1. 1 what is life? Cell swells Cell shrinks  The cell membrane is selectively permeable LIPID BILAYER WITH _____________________ HYDROCARBON TAILS ________ fluidity L1. 1 what is life? LIPID BILAYER WITH __________________ HYDROCARBON TAILS ________ fluidity  Some substances can cross membranes by passive transport, which does NOT require energy input L1. 1 what is life?  In a cell, water moves across the membrane through _____________ (transmembrane tunnels made of protein) called aquaporins _____________ diffusion is carried out by protein channels or carriers that increase the _____________ of diffusion L1. 1 what is life?  Ion _____________ penetrate the membrane and have hydrophilic pores Most are gated—can be closed or open to ion diffusion. The gate opens when the protein is stimulated to change shape by… L1. 1 what is life? a chemical signal (ligand) or an electrical charge difference (voltage- gated). a mechanical signal (force)  _____________ proteins transport polar molecules, such as glucose, across membranes in both directions. L1. 1 what is life?  Glucose transporters can become saturated (all occupied) L1. 1 what is life? All transporters are in use  Substances can cross membranes by passive processes Passive transport does not require energy input. Occurs through: Simple diffusion through the membrane, or L1. 1 what is life? Facilitated diffusion through channels or carriers