BIS2A Notes PDF

Preview

Summary

Instructor: Marc Faccioti Biological Sciences 2ABIS2A NotesLecture 1 - January 4, 2021 (M)Lecturer: John D. Resources ● Canvas Homepage ● Contact info (Canvas mail) ● Assessment Dates (5 mini assessments) ● Final Exam on March 17, 10:30 AM - 12:30 PM ● No textbook required ● Discussion Manual ● Repo...

Description

1 Instructor: Marc Faccioti Biological Sciences 2A

BIS2A Notes Lecture 1 - January 4, 2021 (M) Lecturer: John D. Resources ● Canvas Homepage ● Contact info (Canvas mail) ● Assessment Dates (5 mini assessments) ● Final Exam on March 17, 10:30 AM - 12:30 PM ● No textbook required ● Discussion Manual ● Reporting Issues ● Syllabus Weekly Assignments ● Modules, per week, added on Friday of previous week. ● Each day has a “block” ○ Pre-class guide ○ NB reading ○ Lecture Video ○ Discussion assignment ● Pre-course guide ○ Contains learning goals/objectives ○ vocab ● post-course guide ○ Recommended exercises, assessment-style Q’s ○ Submitting course guides: initial in text box ● Readings

2 ○ NB Libretexts ○ Reading objectives ○ Interact + comment on material directly with comments ■ Highlight text ■ Hashtag specific parts, emojis ■ Ask for clarification/make observation ■ 3 good original comments/replies, 1 with emoji hashtag ● Biology ○ Carbon-conscious ○ Modern biology is engaging with energy systems/sustainability ○ Things all living things share ■ Cells ■ Evolved from a common ancestor ■ Genetic material ■ Reproduction ■ Responding to environment ■ Exchange matter and energy w/ environment ■ Death ○ What BIS2A covers ■ Molecular structures (atom → cell) ■ Scientific Method ● Make observation about the world ● Propose possible explanation ● Test explanation via experimentation ● If explanation disagrees, explanation is wrong ■ Design Challenge ● Identify problem(s) ● Determine criteria for success ● identify/imagine possible solutions

3 ● Evaluate proposed solutions against criteria for success ● Choose solution

Discussion 1 - January 5, 2020 (T) ● Outline ○ 10 Quizzes * 5 pts = 50 pts ○ 6 Assignments * 9 pts = 54 pts ○ 10 Attendance * 10 pts = 100 pts ○ Post-Assessment * 6pts = 6 pts ○ One dropped attendance score = 200 pts ● Characteristics of Life ○ C/H/O/N/P/S - main elements of life ○ Genetic code ○ Response to stimuli/environment ○ Evolution ○ Metabolism ○ Ability to reproduce ○ Descent from common ancestor ○ Discrete units/orders ○ Death ○ Maintain homeostasis ○ Not Living ■ Fire, but grows, reproduces, and metabolizes

4 ■ Crystals, has growth and order, not living ● Shrodinger’s What is Life? ○ Genetic molecule described as “aperiodic crystal,” thereby encodes info ● Traube Cell ○ Mortiz Traube, in 1867 designed artifiical cell w/ potassium feranocyanide to copper sulfate solution, forms film of copper ferranocyandide, “cells” expands as water enters ■ Grows, order/emembrane, not living ● Hypotheses of Origins of Life ○ Abiogenesis: Miller-Urey experiment, RNA World ● Scientific Method ○ Observation/Question: recognize problem, conduct research of what is already known ○ Hypothesis: statement anticipating result to previous question based on limited knowledge/observation ■ Testable ○ Good Experiment ■ Positive control: proves negative results are real ■ Negative control: shows positive results are real ■ Only one variable changes as a time (independant v. dependant variable)

Lecture 2 - January 6, 2021 (W)

5 Learning Goals: 1. Identify the location of the three core atomic elements (neutrons, protons, and electrons) from a basic model for an atom and describe their basic properties. 2. Define electronegativity and explain how it can be used to predict the type of bonds between 2 atoms. 3. Identify polar, covalent, and polar covalent bonds. 4. Recognize the basic core elements in biomolecules: CHONPS. 5. Interpret chemical and structural formulas of biomolecules. Chemistry, Molecules, and Basic Chemical Properties ● What is the “stuff”-of-life made of? ● How does that “stuff” interact with itself and things in its environment? ● How can those interactions be modulated/changed?

Structure of an Atom - The Basics ● 3 core elements: neutron, proton, electron ● Human molecular make-up by mass: ○ 65% O, 18% C, 10%H, 3% N ● Understand how to read various representations of molecules

6

● C = Carbon, O = Oxygen, lines = bonds, double lines = double bonds

● 5 Carbons (each vertex), 12 Hydrogens. ● Each C can be bonded to 4 things.

Lecture 3 - January 8, 2021 (F) Learning Goals: 1. Given an image, identify and name the chemical structure of amino, carboxyl, hydroxyl, methyl, carbonyl, thiol, and phosphate groups. 2. Explain how functional groups influence the chemical properties of biomolecules. 3. Describe the key chemical properties of water and the importance of its H-bonds between water and other molecules. 4. Identify functional groups that act as good H-bond acceptors/donors. 5. Predict how water would interact with a given molecule based on its functional groups.

7 6. Describe solubility and how it is related to chemical properties. 7. Compare and contrast “polar” and “nonpolar” in terms of distribution of charge in a molecule and water solubility.

Functional Groups and their Interactions

Answer: 2 (NH2), H2 has polar bond with N

● Drug 2 is more soluble than Drug 1 because it has 2 OH groups, which means it has greater potential for H-bonding.

8

Lecture 4 - January 11, 2021 (M) Learning Goals: 1. Define the Law of Conservation of Mass 2. Describe the Equilibrium State 3. Discuss the Concept of reaction reversibility and its relationship to equilibrium. 4. Relate the magnitude of the equilibrium constant to the equilibrium position 5. Explain the effect of concentration change on a system at equilibrium 6. Apply the concept of chemical equilibrium and the equilibrium constant to describe the progress of a chemical reaction, initially out of equilibrium, towards equilibrium, and finally at equilibrium in terms of “forward” and “reverse” reaction rates and concentrations of chemical reactions 7. Define pH and understand the relationship between pH and the hydrogen ion concentration 8. Use the definition of pH to determine the difference in [H+] concentration between two aqueous solutions

pH and Equilibrium ● How can interactions be modulated/changed? ● Free hydrogen ions do not exist in water (H+) ● H2O ←> H+ + OH● Double arrows = reversibility of reaction, can go both ways to form/breakdown H2O

9 ● Reactants: H2O or H+ + OH-, depending on starting side ● Products: H+ + OH- or H2O, depending on starting side ● Typically, left → right when assigning reactants/products ● Given: H2O ←> H+. + OH-, define: pH = -log10[H+] ● -log inversely correlated to concentration of [H+] ● Example: comparing pH = 5 to pH = 7 ○ 5 has greater concentration of proton to 7 ○ 10-5 > 10-7 = 100x bigger concentration ● A+B←→D

● Chemical Equilibrium @ t = 25 b/c concentration no longer changes ● Keq = equilibrium constant ○ Keq = [D] / [A][B] ● Bases can pick off protons from a solution

10

Discussion 2 - January 12, 2021 (T) Welcome to Chemistry

Q: What are the Big 6 Elements in Biology? A: Carbon, Hydrogen, Oxygen, Nitrogen, Phosphorus, Sulfur Q: Most common in all living things? A: Carbon

Objectives: 1. Define 4 chemical bonds 2. Identify 4 types of biological macromolecules from drawings 3. Recognize common functional groups and describe properties 4. Describe polarity of bonds and molecules 5. Predict H-bond formation and effect of polarity on physical properties

Chemical Bonds ● Covalent: sharing of electron pairs (50-110 bond energy) ● Ionic Attraction: attraction of opposite charges (3-7 bond energy) ● Hydrogen-bond: electrical attraction b/w cov bonded H with an electronegative atom (3-7 bond energy)

11 ● Hydrophobic Interaction: interaction of nonpolar substances in presence of polar substances (especially water) (1-2 bond energy) ● Van der Waals interaction: interaction of e- of nonpolar substances (1 bond energy)

Chemical Compounds ● Letters represent compounds and elements (C, N, H2N, etc) ● Lines represent bonds. Solid lines = covalent ● Carbon ring = complete loop of bonds

Dipole Moment ● In a covalent bond, e- can be shared unequally ● Electronegativity ○ E- -loving ○ Some are more electronegative than others bc of size of e- cloud

● Strong electronegativity = small radii + high proton number ○ Increases going left → right, down → up ● Pointers on electronegativity

12 ○ Only difference of 0.5 or more in electronegativty makes a bond “polar” ○ C-H bond (2.5-2.1 = 0.4) and C-C is nonpolar ○ Where are electrons concentrated? ○ Polar: C-O, H-O, H-N, C-N ○ O = C = O → nonpolar, two negative charges pulling cancel each other out

○ H - O - H is polar, bent, angle = 105 degrees

○ Both H are good for H-bonding

13

○ H on bottom = H-donor, H on top: H receptor ● Q: How many H-bonds can one water molecule form? ○ A: 4 H-bonds total ● Q: How do the bonds affect the boiling/melting points of water? ○ A: raises the BP/MP ● Q: Due to so many H-bonds, what kind of molecules dissolve in water the best? ○ A: polar molecules ● Q: Besides the O-H bonds, in water, what other bonds can participate in H-bonding? ○ A:

Macromolecules ● Carbohydrates ○ CHO + OH Hydroxyl ○ Carbon rings with 1 O ○ Cn(H2O)n

14 ○ Similar numbers of C and O ○ Rarely other elements ○ Often in chains of rings ● Lipids ○ always : ■ Mostly non-polar (C-C and C-H) ■ Contains C and H ■ Amphipathic (one end is polar, other is non polar) ○ Mostly: ■ Have some O ■ = O, often in a carboxyl ■ Carbon rings ■ Carbon chains ● Proteins ○ Always: ■ CHON ■ Carboxyl at one end, amino acid on other ● Nucleic Acids ○ Always ■ CHONP ■ Nucleotides (nitrogenous bases (ACTGU) ■ Phosphate groups

15 ■ 5-C sugar rings

16

Lecture 5 - January 13, 2021 (W) Learning Goals 1. Define pKa 2. Explain the relationship bw pKa and pH, and apply those concepts to predict the protonation state of a functional group at diff. pH values 3. Describe how pH can influence the protonation state of functional groups in a biomolecule and how it can infuence protein function 4. Predict the potential influence of changes of pH on the structure and function of biomolecules

pKa Interactions, etc ● pH: measuring and quantifying hydrogen-ion concentration ● Deprotonation: H ion disconnected ● Predominantly biased to deprotonated form (negatively-charged state) ● When you breathe oxygen, O gets bound by protein, circulates ○ Sensing mechanism with protein to sense change in pH from lungs (pH 7.4) to tissue (pH 7.2) ● Deprotonation makes soln more basic ● pKa = -log10Ka = -log10 [A-][H+] / [HA] ○ Measurement of equilibrium condition, property of molecule ○ Determine relationship bw [AH] and [A-] when pH = pKa ○ When pH = pKa, [AH] = [A-]

17 ■ Balance points shifts when protons added/subtracted ● When pH > pKa, predominant form is deprotonated (remove protons) ● When pH < pKa, predominant form is protonated (add protons)

Discussion 3 - January 19, 2021 (T) Protein Structure and Function Review

ABDC Objectives: 1. Draw amino acid and label alpha-carbon, amino group, carboxyl group, and R-group 2. Categorize amino acids as polar/nonpolar/charged, describe properties of proline, cysteine and glycine. 3. Model formation of a peptide bond, explain why it is an endergeonic condensation reaction. 4. Differentiate among four levels of protein structure 5. Predict properties of amino acids Warm-Up ● Alpha-carbon: site of attachment

18

● Amino acids bind by connecting amino groups to carboxylic acid groups ● All amino acids can form proteins ● Peptide bond (NCC-NCC):

● H2O gets kicked out, bond solidifies with C-N (peptide bond)

● Condensation Reactions ● Amino Acid Structure ● Every amino acid has central (alpha) carbon with 4 single bonds

19 ○ Other end of 3 is always same ○ 4th is variable (R)

● pH at 50% of X’s are protonated ○ A. R-XH2 + H+ < - > R - XH3+ ○ B. R - X- + H+ < - > R - XH ○ Protonated form on right ○ Strong acid = weak base, strong base = weak acid ● pH > pKa = mostly deprotonated ● pH < pKa = mostly protonated

20 ● OH usually takes protons

● pH = 3 ○ Arginine carboxyl: deprotonated bc pKa > pH, negative ○ Arginine amino group: protonated bc pH > pKa, positive ○ Arginine functional group: protonated bc pH > pKa ○ Net charge: positive ● pH = 7 ○ Arginine carboxyl: deprotonated bc pH7 > 1.82pKa ○ Same w/ amino and functional groups, same as pH = 3 ○ Net charge: positive ○ Aspartic Acid ■ Amino acid: 9.90pKa > pH 7 = negative (deprotonated) ■ Protonated (pos) on R-group and carboxyl

21 ■ Net charge: positive ● pH = 11 ○ Arginine amino group: 11 > pKa 8.99, is deprotonated, negative ○ Net charge: neutral General Amino Acid Types: ● Nonpolar (all C and H), but also tryptophan and methionine ● Acidic: carboxyl group at end ● Basic: N at end, but not N close to O ● Polar, uncharged: -OH, =O groups outside of carboxyl groups, NH groups not at end ● Special ○ Glycine (very small) ○ Proline: R-group is covalently bonded to amino group N ○ Cysteine: accessible sulfur ● Proteins and amino acids are acids and bases at same time bc carboxyl = strong acid, amino acid = strong base ● Acids add protons to solutions (high pH) ● Bases accepts protons from solutions (low pH) ● pKa is 50% deprotonation/protonation ● At pH = 7, amino acid groups are positive and carboxyl groups are negatively charged ● Amino acids are joined by condensation RX’s Protein Structure ● Primary structure

22 ○ Amino acids, covalent/peptide bonds, single linear arrangements of amino acids, determined by mRNA codons at ribosomes ● Secondary structure ○ Peptide backbone -H and =O, H-bonds, alpha helices and beta sheets, determined by sequence of amino acids ● Tertiary structure ○ R-groups, H-bonds, ionic bonds, covalent bonds, van der Waals interactions, hydrophobic interactions, complex 3D shapes, determined by sequence of amino acids ● Quaternary structure ○ R-Groups and peptide backbones of different polypeptides, H-bonds, ionic bonds, weak interactions, 3D shapes, complex, determined by arrangement of amino acids on separate polypeptides Allostery + Protein-Substrate Interactions ●

Lecture 6 - January 20, 2021 (W) Learning Objectives 1. Create illustrations that serve as models of the 3D structures of proteins, carbohydrates, and phospholipid bilayers.

23 2. Create simple illustrations of carbohydrates that include the major functional groups, formation of glycosidic bonds, and the potential interactions of carbohydrates with water molecules or other molecules. 3. Diagram the pentose and hexose sugars, number their C atoms, and identify key functional groups on each molecule. 4. Identify a nucleotide from its molecular structure and decompose the molecule into 3 functional units. 5. Draw how water molecules might interact with lipid subparts. 6. Create a “parts-level” abstract sketch of a generic glycerophospholipid. 7. Classify common biomolecules as a lipid, protein, carbohydrate, or nucleic acid. 8. Describe the structure and all the parts of an amino acid and a polypeptide. 9. Given 2 or more amino acids, pKa values for functional groups, and a specified pH, draw a figure that depict the amino acids linked by peptide bonds. 10. Understand how the 1st sequence and how combinations of amino acids influence the 2nd, 3rd, and 4th structure. 11. Relate basic structures, such as alpha-helices and beta-pleated sheets to the tertiary structure of a protein. 12. Describe the interactions b/w amino acids in the primary, secondary, and tertiary levels of protein structure. 13. Describe and discuss the types of bonds and the portions of the amino acids that are responsible for the formation of the structures of a protein.

24 14. Create simple cartoon models depicting secondary, tertiary, and quaternary protein structures 15. Form hypotheses about how different types of changes at a molecular interface might influence binding. 16. Understand how changes to amino acids in the binding pocket can alter small molecules binding to proteins.

Life’s Biomolecules - Carbohydrates, Lipids, Proteins Carbohydrates ● Hydrated ● Mostly H - C - OH ● Ring form and linear form ○ Carbon - water - carbon - water ● Monomers join through condensation RX (glycosidic bond) Lipids ● Fatty acids ○ Long tail of unhydrated carbons ○ Lots of hydrogens, has “head” ○ Combines w/ glycerol carbohydrate to form triacylglycerol ○ Properties dominated by tails ● Glycerophospholipid ○ Head with tails

25 ○ R-group + Phosphate + glycerol in head, tails of saturated and unsaturated fatty acids ○ Saturated = all C’s bonded with H ○ Unsaturated = some H’s taken away Proteins ● Many different functions ○ Enzymes, transports, structural, hormones, defense, contractile, storage ● Amino acids ○ Amino group + alpha carbon (+ R-group + H) + carboxyl group ○ Alpha carbon first ○ Condensation synthesis forms peptide bonds ■ Carboxyl + amino group, H gets removed from NH2 ○ N-Terminus = N at end, C-Terminus = C at end ○ Aminos always in N-C-C pattern

26 ● Alpha helix: backbone continues into spiral pattern ● Secondary structure composed of alpha helices ● Spiral held together by polar/H-bonds w/ N-H - O=C ● Proteins folding into tertiary structure, driven by hydrophobic effect ● Quaternary structure composed of multiple 3D tertiary structures

Lecture 7 - January 22, 2021 (F) Learning Goals: 1. Describe the concept of equilibrium in the context of reaction coordinate diagram. 2. Interpret reaction coordinate diagrams and associate changes in Gibbs enthalpy and AE with relative rates of RX, equilibrium conditions, and whether a RX is endergonic or exergonic. 3. Understand how to use the equation deltaG = deltaH - TdeltaS 4. Interpret a biochemical transformation and predict whether or not the RX is spontaneous using a Gibbs enthalpy reaction coordinate diagram. 5. Develop an energy story about a biological or biochemical RX using the first and second laws of thermodynamics. 6. Explain the first law of thermodynamics. 7. Explain the second law of thermodynamics. 8. Describe the relationship bw free energy and chemical equilibrium using the equation deltaG* = -RTlnKEQ invoking appropriate initial and final states.

27 9. Apply the energy story rubric to describe a transformation in biology, explicitly describing initial, intermediate, and final states of matter and energy. Thermodynamics and Energy Story ● Process of turning one state into another state Energy Story 1. 2 states (start/end) 2. Identify and list matter in system and states at start and end 3. Account for location of energy, start and end 4. Describe transformation of matter 5. Describe the transfer of energy during process 6. Identify and describe mechanisms responsible for mediating the transformation of matter and transfer of energy Energy ● Property of all physical system ● Change in energy leads to change in system ● Can be transferred, is conserved: ○ EFINAL = EINITIAL in the Universe ● Maybe be transferred, but cannot be destroyed or created ● Avoid “energy is lost” ● Not strictly “ability to do work”

28

Entropy ● Property of physical system ● Related to ways to disperse energy in microstates of system ● Always increases in the universe ○ SFINAL > SINITIAL in the universe ● A local decrease is compensate by equal or greater increase elsewhere ● When barriers are overcome, energy spontaneously disperse

● deltaE = EF - EI ● deltaS = SF - SI

29 Enthalpy ● Total Energy in a system ● H = EINTERNAL + pV ● H ~ EINTERNAL ● deltaH = HFINAL - HINITIAL ● Ethanol + Oxygen = Water + Carbon Dioxide ● Initial entropy increases with universe ● -deltaG = evolved energy ● deltaSUNIVERSE associated, therefore: -deltaG/T ● -(deltaG/T)SYSTEM = -(deltaH/T)SYSTEM + deltaSSYSTEM ○ Therefore: deltaG = deltaH - TdeltaS ● deltaG refers to quantity of energy that can be dispersed to universe ● If deltaG is negative → RX is spontaneous ● If deltaG is positive → RX is not spontaneous ● Spontan...