General Biology Notes PDF

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These notes are for the General Biology class that is split by Professor Seyfried and Professor Annunziato. This was taught by Professor Annunziato....

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General Biology TA Office Hours 5-6 Tues/Thurs Higgins 210 Lecture 2: Life and the Universe How do we define “life”? a. Order EX: Pinecone b. Regulation EX: Lizard changing behavior to regulate temperature EX: Humans will sweat c. Growth and development d. Energy processing EX: Eating to convert energy … photosynthesis, too e. Response to the environment EX: Sunflower tracks the sun to face it f. Reproduction g. Evolution by natural selection Do viruses possess “Life”? They’re organized, reproduce, respond to environment, evolve by natural selection, they don’t really develop, they don’t regulate, they don’t process energy (eat) The Universe is ~13.75 billion years old Six Numbers (don’t memorize) -- see slides Stellar Fusion Series… elements cooked in stars… releasing energy that keeps star burning… when you get to iron, it’s a dead end… then BOOM! You get a Nova (if the energy is enough) Purple picture in slides … first SuperNova Matter - Matter occupies space and has mass (Mass DOES NOT EQUAL Weight) - Matter on earth has three physical states: solid, liquid and gas - Matter is composed of chemical ELEMENTS What is an “Element”? Antoine and Marie-Anne Lavoisier … worked in the arsenal during French Revolution and had access to chemicals and chemical equipment … did experiments… discovered oxygen and learned about elements and gasses - He was also a tax collector, so he was not popular, eventually killed at the guillotine His definition: Element - substance that cannot be broken down into another substance by CHEMICAL means - All (known) elements are listed in the Periodic Table

Chemical Composition by Weight: 65% oxygen Atoms - An ATOM is the smallest unit of matter than retains the properties of an ELEMENT - Atoms are composed of “subatomic particles” - Each element is composed of one kind* of atom (*some are isotopes with different numbers of neutrons) Atomic Structure - Protons and neutrons are in the atomic NUCLEUS (the atom’s central core) - Electrons orbit the central Nucleus Charles François de Cisternay du Fay (1698) - Discovered that there are two types of electricity o “vitreous” (positive) and “resinous” (negative) Proton = positive (+1) Neutron = no charge Electrons = negative (-1) Mass of a proton is almost equal to mass of a neutron Mass of an electron is 1/1800 of the mass of a proton (very small) Atomic Structure Experiment – Lord Rutherford of Nelson - Gold Foil Experiment: took thin gold foil and he fired positively charged particles at the gold… instead of going through a “Plum Pudding” model… some of the particles went at weird angles and some fired back at him o So we found that there’s a central positive charge surrounded by negative charges MOST of the mass (by far!) and ALL of the positive charge is in the atomic nucleus Helium: two diff. atomic models Planetary vs. Electron cloud (probability distribution “orbital”) -

If an atom were the size of a baseball stadium, the nucleus would be the size of a pea

How do elements differ? Each element has a UNIQUE number of protons - This is called the “Atomic Number” “Mass Number” = the sum of the number of protons AND neutrons - In table: top number is atomic number, bottom number is mass number - How it’s usually written: Mass Number top left, Atomic Number bottom left - Mass number is always bigger

8/30/19 Mendeleev’s Periodic Table Isotopes - alternative atomic mass forms of an element - Different isotopes of an element:  Have the SAME number of protons (and electrons)  Have DIFFERENT numbers of neutrons - Isotopes can be stable or radioactive Hydrogen (3 types happen naturally) 1: normal 2: in heavy water 3: radioactive Carbon 12, 13, 14 (14 is radioactive) Atomic mass of NATURALLY occurring carbon is about 12.011 Facts about atoms % electrons: - The VOLUME in which an electron is found 90% of the time = “orbital” - Each orbital holds up to 2 electrons Helium, again, has two atomic models: planetary and electron cloud (more correct) An atom’s energy levels are discrete = “SHELLS” Shells can hold one or more orbitals (2 electrons each) Second shell has 4 orbitals (8 electrons MAX) For these atoms, outer shells become “stable” with 8 electrons (or just 2 for first shell)  “OCTECT RULE” --- circle around Helium, Neon, and Argon Three Facts about Chemistry in Biological Systems: 1. Outermost shells are considered “filled” with 8 electrons (except for hydrogen atom, filled with 2) 2. Chemical properties of atom determined by # of electrons in outermost shell 3. Chemical properties of atoms are due to the “desire” to gain outermost shells w/ 8 electrons (except for hydrogen, which “wants” 2) “Chemical Compound” – consists of 2 or more elements in a fixed ratio (not a “mixture) Chemical Bonds 1: Ionic Bonds - Results from a complete transfer of electrons EX: NaCl

Chemical Bonds 2: Covalent Bonds - Forms when two atoms SHARE one or more PAIRS of outer-shell electrons - Each single bond is ONE shared electron PAIR - Each double bond is TWO shared electron pairs - Each triple bond is THREE shared electron pairs Single covalent bonds have free rotation No free rotation around a double bond (important when it comes to things like trans-fat and other things we eat) and not around a triple bond either Some (not all) bonds have electrical “polarity” SLIDE First part labeled: None (“symmetry”) 2nd part: Partial polarity (electrons feel a stronger tug from the central Nitrogen) 3rd part: Extreme polarity (totally negative side, totally positive side… like magnet) Water is polar (electrons are pulled toward the oxygen) Polar covalent bond … KEY THING TO REMEMBER: H2O molecule as a WHOLE is neutral! - It’s the right number of electrons, it’s just that the electrons spend more time in one place than another Chemical Bonds 3: Hydrogen Bonds - Hydrogen bonds form BETWEEN water molecules … made/broken all the the time because electrons are constantly moving… they are overall attracted but they’re very weak because the charges are shifting - NOTE: NOT just for water! - There are hydrogen bonds between different molecules Water molecules form a network through H-bonds NOTE: O2- attracts two H+s

9/4 Lecture 4: Life’s Chemistry part 2: Carbon and Water 70-95% of the stuff of all living cells is water - Virtually all biochemical reactions take place in water - We probably wouldn’t recognize life that wasn’t water-based Properties of Water: 1. Cohesion – water molecules sticking to each other a. Cohesion results in “surface tension” b. Because of cohesion, evaporation pulls water UP from roots AGAINST gravity 2. Adhesion – water sticking to something else like glass Adhesion + Cohesion  Capillary Action

Heat and Temperature: - Heat is the amount of energy due to the movement of atoms and molecules in a body of matter - Temperature – measure of the warmth or coldness of an object (with reference to some standard value) SO: increased movement (kinetic energy) increases the heat 3. Water has a high Specific Heat* Specific Heat – amount of energy needed to raise the temperature of 1 gram of a substance 1 degree Celsius BUT – Hydrogen bonds must be BROKEN before water molecules can move - Water is slowly absorbing heat and slowly breaking H-bonds and eventually temperature begins to rise Because of hydrogen bonding, the melting point of water is 0 C, and boiling point is 100 C Without hydrogen bonding, something like sulfur, they easily come apart to melt/boil so it happens at extremely low temperatures below 0

3b. water has a HIGH Heat of Vaporization - Lots of heat needed to turn liquid water into a gas - This gas is water vapor or “steam” Evaporative Cooling (sweat and steam comes off your head to cool you down) Freezing WARMS the air** So why do you feel uncomfortable on a hot and HUMID day? - If you sweat and the air is already saturated with water, there’s nowhere for your sweat to go… the water is not leaving from your skin. So you feel sticky Why are burns from steam so severe? Because that steam of gaseous water, when it lands on your surface, it turns into liquid water and when this happens, all the energy that went to breaking the hydrogen bonds in the first place comes to your skin…extra energy and worse burn. Steam burns are worse than hot water burns 4. Ice floats (ice is less dense than liquid water) - Ice forms a crystal … stable hydrogen bonds that hold molecules apart, making ice less dense than water - In liquid water, the molecules are closer together

Definitions: Solution – a liquid containing a homogeneous mixture of 2 or more substances

Solvent – dissolving agent (dissolver) Solute – the substance that is dissolved 5. Water is a polar solvent (ex: for NaCl) – salt dissolves in water H2O molecules (O- and H+ atoms) surround Na+ and Cl- ions Water can dissolve molecules with polar groups EX: Sucrose (sugar) Water CANNOT dissolve nonpolar molecules EX: fats, oils, and nonpolar solvents (octane) The pH Scale measures the concentration of H+ ions in aqueous (water) solutions Base – high pH 8-14 Neutral – pH = 7.0 Acid – low pH 0-6 Carbon has 4 electrons in outer shell Needs 4 to get to “stable” 8 Carbon can form single bonds, double bonds, and triple bonds The 4 single bonds form a tetrahedron around C atom Carbon can form linear or ringed molecules Carbon nanotubes (very very thin!)

9/6/19 Lecture 5: Carbohydrates -

Carbon skeletons can be branched/unbranched, may have double bonds in various locations, and may be arranged in rings - Monosaccharides (simple sugars) o 3 to 6 carbon atoms 3 = triose 4 = tetrose 5 = pentose 6 = hexose ALPHA-Glucose ring … one carbon is outside the ring (important) Glucose and Fructose are “structural isomers”  have same chemical formula, but different structures  OH groups are polar

Corn Starch is processed by enzymes to produce High Fructose Corn Syrup (HFCS) - Starch from corn! – break down starch from these enzymes and then convert glucose to fructose Disaccharides and Polysaccharides: Building a Polymer with a Dehydration Reaction (separate water to make the chain) - BREAK by adding water BACK (hydrolysis … hydrolyze it to add water back) Disaccharide is formed from two Monosaccharides (slide) – shows a dehydration reaction Maltose is a disaccharide, made from glucose -

When carbon is in the ring, single bonds don’t have free rotation (blue highlighted parts, H cannot spin) … but in the linear format, they can spin

Remember: alpha-1,4 glycosidic bond – in the 1 and 4 position Sucrose (disaccharide) = glucose + fructose ** notice that 2 carbons are outside of the ring, this bond causes this Polysaccharides are made from 100’s and 1000’s of monosaccharides -

Storage (EX: starch; glycogen) Structure

Starch stores glucose in plants (long chain of glucose) Glycogen stores glucose in muscles (very branched, but it’s the same thing) (these are alpha-1,4 glycosidic bonds to link the chains … but the first is linear, second is branched) Starch and glycogen do NOT pass through cell membranes Cellulose also is made from glucose monomers (links made by the dehydration reaction, but it’s slightly different)

Alpha and Beta Glucoses: Interchanged by going through the linear form Maltose is a disaccharide, made from ALPHA-glucose - H- comes from an –OH group … both the OH are below

BETA glucose: OH is above, hydrogen below … we don’t have the enzymes to digest this… so this is why we cannot live on wood

Alpha: Starch & glycogen Beta: Cellulose Lipids are Hydrophobic: fats and oils Fats are made from glycerol (has 3 carbon atoms) and 1, 2, or 3 Fatty Acids (on the right: triglycerides) Fatty acid, remove molecule of water, links to glycerol Fatty Acids will always have a C=O double bond, but that’s normal for the chemistry Fatty acids differ in length (short to very long) and presence or absence of double bond Saturated (no C=C double bonds in the fatty acid)* Monounsaturated (one C=C double bond in fatty acid) Polyunsaturated (many C=C double bonds in the fatty acid) *Saturated fatty acids are saturated with Hydrogen atoms Next slide: A monounsaturated fat - Double bond causes the bottom chain to bend A SATURATED fat (no C=C double bonds) - All fatty acids are straight SO all saturated fats are solid at room temperature Unsaturated fats are liquids at room temperature (plant oils) Why? Because of the bend… they cannot close-pack their molecules Double bonds – are they cis-bond or trans-bond? Food producers may “hydrogenate” oils to obtain solids - Put oils through chemical reactions that move double bonds… oils become solid at room temperature - “Partially Hydrogenated Oil”  doughnuts - problem with this process: normal double bond you would see (cis-bond) … inevitably, the process creates TRANS double bonds (hydrogen above and below) – this is a trans-

fat … these are not biological for the most part and your body does not know what to do with them Association with consuming trans-fats and heart disease Certain fatty acids are “essential” - omega-3, omega-6, and polyunsaturated fatty acids (walnuts, salmon, seafood) - helpful for membrane function, healthy skin, brain function, heart health ~75% of world’s population is lactose intolerant (as an adult) - as we age, the enzyme gene that lets us digest it shuts off A study was done in Finland… what causes/does not cause lactose intolerance? What keeps lactase gene on? (don’t memorize) They took a guy from Finland, they isolated DNA from a large population of people, and they found on chromosome 2 is where the lactase gene resides … huge stretch of DNA away (14,000 base pairs) they found a mutation C to a T, or T to a C … T yields tolerance (gene is on), C  gene is off 9/9/19 Protein functions: 1. Defense (antibodies) 2. Enzymes (help chemical reactions… aka Lactase) Enzymes are “catalysts” that increase the rates of chemical reactions - enzymes bind their substrate targets - hallmark of all enzymes: Enzymes are not permanently changed by the reaction! (recycled) - Proteins are Polymers of Amino Acids o Amino Acid: Amino group, Carboxyl group (these two do not change), and side group o Amino Acids have different classes: hydrophobic (nonpolar), hydrophilic (polar, uncharged and charged) o Amino acids are essential to our diet - Amino acids are linked by Peptide Bonds (to form a polypeptide chain) (dehydration reaction) – know that a peptide bond links an amino group and carboxyl group ALL PROTEINS ARE POLYPEPTIDES - Not all polypeptides are called “proteins” – Why? Some are too short Proteins are made up of 40 or more polypeptides Protein Primary Structure: (Kinds, order, and total number of amino acids) - Which amino acids? How many? And what is the sequence? - Exact order is critical – could make difference in being functional and non-functional

EX: A single amino acid change can cause sickle cell disease (hydrophilic turning into hydrophobic) – HbS causes red blood cells to assume stretched, sickle shape -

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Primary Structure is Flexible This allows for the folding of the structure into higher order structures – like a secondary structure Secondary Structures: 1. Beta-pleated sheet – protein chain assumed pleated form, H up and down, and Hydrogen bonds link the chains together to form a sheet (found in silk fibers, whether a spider or silk worms) 2. Alpha-helix – picture is WRONG! Because the helix is going the wrong way a. The alpha-helix is right handed … side toward you should be rising from left to right Protein Tertiary Structure (polypeptide 3D shape) – taking helices and pleated sheets and making them into another structure Tertiary Structure: Myoglobin Another way to show protein folding: helixes, beta-strands, and loops… always amino terminus to C-terminus Beginning of protein is amino terminus at helix and then the end green on the left is the C-terminus Forces that shape proteins: o Hydrophobic interactions – non-polar amino acids o Hydrogen bonds – polar o Ionic bonds – polar, charged

Rule of protein folding (folding in water) – aqueous solution - When a protein folds up in water, the polar side chains want to be on the outside of the molecule and the hydrophobic amino acids want to hide and they form a core region on the inside Some proteins have Quaternary Structure – 2 or more polypeptides form ONE functional protein - It has more than one polypeptide chain, but together they make one functional protein - EX blue and white pic: hemoglobin Mis-folded proteins can cause disease EX: Bovine spongiform encephalopathy (mad cow disease; analogous disease would be Creutzfeldt-Jakob Disease in humans) - Caused by infectious “prions” – not virus, not bacteria – it is an infectious protein in itself - C-J Disease is normally in a form with alpha-helices … but it can flip into beta-sheet form and this makes it infectious … the beta form causes the alpha form to assume the beta form when they interact - What does it do? It tends to precipitate in brain cells (beta-form) and causes plaques that cause your brain to become like a sponge… cells start to burst (no cure)

- Transmitted through eating a protein in the beta-form STUDY: protein structure summary slide Malaria mosquito (anopheles gambiae) - Mosquito bites: into blood stream, goes to liver, red blood cells, stomach, into salivary gland One copy of “sickle cell trait” affords some malaria resistance – most of the worldwide distribution of this HbS allele is where a lot of the malaria is 9/11/19 Scientific Discovery - Observation - New Theory of idea - Union of them, yielding testable hypotheses (with predictive value) Antonie van Leeuwenhoek - Developed a way to create very small and powerful lenses) - Discovered bacteria, protozoa, and capillaries Robert Hooke - Discovered cells (Hooke invented name) Robert Brown - Discovered the cell nucleus Matthias Schleiden and Theodor Schwann - Developing the “Cell Theory” - Tadpole cells drawings “All living things are composed of cells and cell products” – Theodore Schwann Francesco Redi – had very different ideas from the two guys before where cells came from Schleiden thought non-living items could spontaneously gain life … Redi disagreed Redi – “omne vivum ex vivo” – all living things come from living things Redi’s “Maggot” Experiment on Spontaneous Generation - theory at time was that rotting meat was creating flies - put meat in closed jar … no flies - living flies come from other flies who have laid their eggs on the meat What about micro-organisms? Where do they come from?

Louis Pasteur (1822-1895) Pasteur’s “Swan Neck Flask” - Even the microorganisms that I’m seeing must be coming from outside the flask… not coming from the broth inside - Spontaneous generation is a dream

Robert Remak and Rudolf Virchow “Omnis cellula e cellula” – All cells come from cells Virchow didn’t believe Remak for a while, but then he stole his data and published it So Virchow received all credit to this … so he’s a loser Meter: the length of the path travelled by light in vacuum during a time interval of 1/299,792,458 of a second

All cells are either: Prokaryotic or Eukaryotic Eukaryotic -- “true” nucleus – have a membrane-enclosed nucleus Prokaryotic – Lack a membrane-enclosed nucleus Prokaryotic cells are smaller, simpler, and lack most organelles Eukaryotic cells are bigger, more complex, and have many organelles Organisms are either: - Single-celled, such as most prokaryotes and protists OR … ( look at notes )

The Three Domains of Life Prokaryotes (1. domain Bacteria, 2. domain Archaea) 3. Domain Eurkarya (Eukaryotes) Domain Evolution Bacteria to Archaea to Eukaryotes - Common single-celled ancestor Penicillin was discovered by Alexander Fleming in 1928 MRSA (drug-resistant Staph aureus) – resistant to almost all antibiotics Does Antibiotic Treatment CAUSE resistance, or SELECT for resistance?

Replica-Plating Technique - Each colony came from one cell - Felt experiment - Sterile felt, press against plate, and recreate pattern of colonies on other plates from the master plate Predicted results if resistance is present BEFORE exposure to penicillin? The resist...