Fall 24 Exam 1 Review PDF

Review Session recording will be uploaded to Canvas under “Zoom” tab! Unit 1 Test Review Sunday, September 22nd, 2024 Test Information Exam Date: Tuesday, September 24th ○ In person This...

Review Session recording will be uploaded to Canvas under “Zoom” tab! Unit 1 Test Review Sunday, September 22nd, 2024 Test Information Exam Date: Tuesday, September 24th ○ In person This is one of your 3 midterms ○ Worth 12% your total grade Exam will be a Canvas Quiz ○ Combination of 18 MC (1.5 pts each, 27 total) and 3 FRQs (33 pts total) - total of 60 pts Proctoring via Respondus ○ Make sure Respondus is running by taking the practice exam 60 minute exam from 9:30am to 10:30am (do NOT arrive late)! Check Canvas announcements for further detailed instructions  Week 2 Chemical Bonds, Water, Carbon and Isomers Terminology and Bonds Element: one type of atom (ex. Na) Compound: more than one type of atom (ex. NaCl) Covalent Bonds: a sharing of two valence electrons from two non-metals (ex. CH4 - methane) ○ Non-polar: equal sharing of electron pair(s) C-H bond is considered non polar. ○ Polar: unequal sharing due to significant differences of electronegativity EN: attraction of a given atom for electrons. Ionic: complete transfer of electrons to make ions (ex. NaCl - table salt - Na+ and Cl-) ○ Based on charge ○ Cation (+) and anion (-) Intermolecular Forces (AKA, weak bonds) Weak bonds are really important too! Interactions between different molecules, holding them together. ○ Van der Waals: due to transient dipoles between molecules Little attractions based on instantaneous changes in local partial charges Remember the gecko example ○ Hydrogen Bonds: occur when H covalently bound to F, O, or N interacts with F, O, or N covalently bound to H on another molecule. Super important for water, DNA, and much more. Q: What characteristic of F, O, and N makes them able to participate in hydrogen bonding? Why can’t carbon, for example, participate in hydrogen bonds? A: F, O, and N are considerably electronegative. When bound to H, they are partially negative, attracting a partially positive H from another molecule. Carbon is not electronegative enough. Bond Summary Water’s Emergent Properties Water’s ability to hydrogen bond allows for life to exist Cohesion: Water to water. ○ Helps transport water upward/against gravity ○ Surface tension Adhesion: Water to substance/surface. ○ Water can move up plant roots by adhering to cell walls High specific heat: Resists change in temp ○ Ocean takes up heat slower than sand/air. Evaporative cooling: Evaporation causes surface to cool ○ Due to water’s high heat of vaporization Expansion upon freezing: As temp decreases, number of H bonds increases ○ Ice floats on water and we get to have marine life Great solvent: δ- and δ+ allow water to surround many ionic or polar covalent molecules. ○ Note: nonpolar doesn’t dissolve in water ○ Terminology: put your solute into a solvent, which makes a solution Dissociation of Water Water dissociates to form hydroxide (OH-) and hydronium (H3O+) ions by transferring an H+ to another water molecule. ○ Water is continually dissociating and reforming Adding an acid to a solution increases [H+]; adding a base decreases [H+]. (opposite for pH) Buffer: helps reduce changes in pH ○ Acid-base pair that combines reversibly with H+. Q: Knowing that pH = –log[H+], what will Usually weak acid and its conjugate base happen to the pH of a solution if you ○ Shift equilibrium to either products or reactants to increase the concentration of H+ by a counteract pH change. factor of 1000? ○ Blood buffer system: ~7.4 A: The pH will decrease by 3. pH is logarithmic, meaning that one integer increase is equal to a tenfold change in concentration. Carbon: The Element of Life Can easily bond with oxygen ○ Important for energy storage and chemical reactions in our bodies Can form 4 bonds with any combination of single, double, or triple bonds. ○ Each bond = 1 pair of electrons Different lengths, branching, double bond positions, and rings ○ Rings are usually 5-6 carbons and non-polar. Q: Where have we seen rings with carbon so far? A: Nucleotides, sugars, etc Q: Where have we seen hydrocarbon chains so far? A: Fatty acids, phospholipids, etc Hydrocarbons Hydrocarbons: organic molecules made up of only C and H ○ Many organic molecules have hydrocarbon components, such as fats/lipids ○ Can store and release a large amount of energy Carbon burns with oxygen to give CO₂ and energy release Q: Why are fatty acid tails in Solid at phospholipids hydrophobic? room temp A: Because carbon isn’t super electronegative (electrons evenly distributed), there are Liquid at no charges in a hydrocarbon room temp to which water molecules can adhere.  Isomers: same molecular formula, different structures and properties Same covalent Different covalent bonds, but different bonds spatial arrangement of How are these atoms. atoms connected? How are these aka enantiomers bonds arranged? Geometric Isomers Cis/trans: same covalent bonds, but different spatial arrangement You cannot interconvert the compounds by rotation because of the double bond. Enantiomers Mirror images of each other The key to enantiomers: chiral centers! A carbon bound to four different substituents. Q: Biologically, why do we care about enantiomers? A: The specific arrangement of a molecule can have big consequences for its emergent properties. Our bodies are sensitive to even the subtlest changes. Functional Groups  Week 3 Monomers and Macromolecules Functional Groups, Bonds, Polarity Properties of organic molecules depend on the carbon skeleton and the functional group attached to it Polarity has huge ramifications for biological systems THINK PROTEINS 2 Lipids NOT actually a polymer b/c it’s not made up of monomer subunits, but rather smaller units made up of different kinds (fatty acids and glycerol) More Lipids 3 types: fats, phospholipids, sterols ○ Fats: ester linkage bonds hydroxyl group of glycerol to the carboxyl group of the fatty acids (3 fatty acids:1 glycerol) ○ Phospholipid: 2 fatty acids and phosphate head bound to a glycerol ○ Steroids: 4-carbon ring lipids; NO fatty acids Cholesterol: a precursor from which other steroids are synthesized More Lipids Saturated vs: unsaturated fats: ○ Saturated: SOLID at room temp, linear structure ○ Unsaturated: LIQUID at room temp, cis bonds cause kinks in fatty acids Phospholipid bilayer: ○ Form due to water’s polarity ○ Hydrophobic tails INSIDE ○ Hydrophilic heads OUTSIDE Membrane fluidity: ○ Amphipathic nature of phospholipids crate spontaneous bilayers ○ Fluidity affected by temperature, lipid packing, saturation of fatty acids, and cholesterol Proteins 20 amino acids differing in R groups (side chains) are found in peptides and proteins Peptide bond: form from dehydration, joining 2 amino acids together Makes up >50% of cell’s dry mass Which two functional groups make up an amino acid? More Proteins 4 levels of structure: ○ Primary: unique sequence of amino acids ○ Secondary: coils and folds in the polypeptide ○ Tertiary: determined by interactions among various side chains (R-groups) ○ Quaternary: results when a protein consists of multiple polypeptide chains Shape/structure determine function ○ Affected by pH, salt concentration, temperature, or other environmental factors, causing protein to denature ○ What would be an ideal pH for enzymes found in our stomach? Nucleic Acids Polymers of nucleotides joined by covalent bonds ○ Phosphodiester linkages join nucleotides through dehydration Nucleic acids store, transmit, and help express hereditary information Central dogma of biology: DNA → RNA → protein ○ 1. DNA stores information ○ 2. RNA uses information to make proteins ○ 3. Proteins do the work in the cell More Nucleic Acids Adenine Thymine Cytosine Guanine Binds with: T A G C Purine or Purine (2 Pyrimidine (1 Pyrimidine (1 Purine (2 pyrimidine: carbon rings) carbon ring) carbon ring) carbon rings) # of TOTAL 2 (A & T bond 3 (G & C bond hydrogen together) together) bonds when bonded w/ respective nucleotide: More Nucleic Acids RNA vs. DNA: DNA RNA Double-stranded helix Single-stranded THYMINE, adenine, URACIL, adenine, guanine, guanine, cytosine cytosine Read from 5’ → 3’ Read from 5’ → 3’ direction direction Bases attached to Bases attached to ribose deoxyribose sugar sugar Serves as a template for Molecule can fold back on both DNA and RNA itself to adopt 3D shape More Nucleic Acids 3 main types of RNA: ○ Messenger RNA (mRNA): encodes amino acid sequence of a polypeptide ○ Ribosomal RNA (rRNA): ribosomes-organelles that translate mRNA ○ Transfer RNA (tRNA): brings amino acids to ribosomes during translation DNA reverse complementation: What would be the reverse complementation RNA strand of DNA strand 5’TCACGGTAC3’? Summary Summary  Week 4 Prokaryotes and Eukaryotes, Origin of Life, and Cell Structures and Function Geological Record Sedimentary rocks deposited into layers called strata Fossil record: major boundaries between eras correspond to major extinction events in fossil records ○ Biased in favor of species that Exist for a long time Were abundant and widespread Had hard parts such as shells or skeletons Origin of Life Abiotic synthesis of small organic molecules ○ What Miller-Urey experiment proved Molecules → Macromolecules ○ RNA monomers have been produced spontaneously from simple molecules Molecules packaged into “Protocells” ○ Vesicles formed from lipids - experience growth, reproduction, and metabolism Origin of self replicating molecules (RNA) ○ Single strand → bending → ability to self replicate ○ RNA’s catalytic ability - Ribozymes O2 Accumulation Cyanobacteria: photosynthesis -> released O2 Oxygen revolution: significant rise in O2 levels (2.4 billion year ago) Great opportunity and great problem to early prokaryotes ○ Opportunity: using oxygen for aerobic respiration -> more usable energy ○ Problem: oxygen and side products react with bonds, inhibit enzymes, damage cells -> wiped out many prokaryotic groups Affected development of life at all levels Prokaryotes → Colonization of land 1. Prokaryotes: 4. Multicellular eukaryotes: Cyanobacteria Multicellularity & specialization 2. Atmospheric oxygen: 5. Animals: oxygen revolution Cambrian Explosion 3. Single-celled eukaryotes: 6. Colonization of land: endosymbiosis Plants and fungi began Prokaryotes vs. Eukaryotes Eukaryotes Prokaryotes - nuclear membrane - no nucleus - more than 1 - single circular - cytosol chromosome chromosome - chromosome - membrane- - no - ribosomes bound organelles membrane-bound - plasma - generally larger organelles membrane - *unicellular Prokaryotes Biofilm formation: thick layer of prokaryotes that have aggregated to form a colony Lack compartmentalization Reproduce by binary fission Categorized by energy/carbon sources Surface Characteristics Fimbriae: stick to a substrate, surface, or other individuals Pili: allow exchange of DNA Flagella: motility - move toward or away from a stimulus Cilia: microtubule-based hair-like organelles that extend from the surface of almost all cell types of the human body - also used for motility Eukaryotes Free vs. Bound Ribosomes Free Ribosomes: Bound Ribosomes: Cytosol Outside of the ER or nuclear envelope Synthesize proteins mostly for use within Synthesize proteins for export (secretion) the cell from the cell  Review Session recording will be Questions? uploaded to Canvas under “Zoom” tab!