Welcome to BILD 1: The Cell. Gentry Patrick, PhD

Transcription

1 Welcome to BILD 1: The Cell Tu, Thu : 12:30pm - 1:50pm Warren Lecture Hall 2001 Gentry Patrick, PhD Office hours:weds: 9:30am to 11:00am Pacific Hall rm 2222A gpatrick@ucsd.edu (BILD1 in subject line) 1

2 Course Logistics : Lecture 1 Textbook : Campbell Biology in Focus. Biology by Campbell 9 th or earlier edition is ok to use for the course please cross check continuity of content. 18 Lectures Style - powerpoint; student version (sv) posted on website prior to lecture 6 Problem Sets Handouts or additional helpful readings Discussion Sections 2 Midterms (04/21 & 05/12 (Thursdays) during regular class time in WLH 2001) Final Comprehensive (Thursday 06/06) 11:30am to 2:30pm WLH 2001 Exam Reviews: prior to midterms and final Review Session Dates: 4/19 and 5/10 (Midterms 1 and 2 Review) and 06/04 (Final Review); Time and location TBD. Website: General Info, Syllabus, Announcements, lectures, handouts, problem sets including Problem Set Keys, regrade policy, etc. Lectures will be podcasted: 2

3 Common Questions What do we need to know for the exam? What I cover in class is your responsibility to know! Text should be read as a supplement to lectures but things not covered in class will not be on the exams. Problem sets are a great way to study Go to discussion section and utilize office hours 3

4 Common Questions What is the grading system? Graded on a curve - Mean is B-/C+ 70 MIDTERM 1: Average Frequency

5 BILD 1: The Cell WHY? Usual reasons cell multi cell mol bio, pre-med, research, etc EBE, field biology, etc Increasing impact of biology on our lives PCR, HIV, Humane Genome Project, Mad Cow Disease, Genetically engineered crops, Neurodegenerative diseases, Smart mice, children, Crispr/Cas9, optogenetics etc. Healthy curiosity about who/what we are! 5

6 BILD 1: Basic Course Ideas Biology is/uses a language we will learn about 300 new terms & a conceptual basis by which they are used Science is about questions the most powerful tool you can hone is the willingness to CONVINCE YOURSELF! & CONVINCE YOURSELF AGAIN! 6

7 Dawn of Cellular Thinking : Lecture s Anton Van Leeuwenhoek (skilled lens grinder) first to identify and describe single cell organisms Lens (eye piece) Specimen holder Pond water Base plate Adjustment screw Animalcules protazoans 7

8 Dawn of Cellular Thinking : Lecture s Anton Van Leeuwenhoek (skilled lens grinder) first to identify and describe single cell organisms Robert Hooke built a more advanced microscope (added more light) Cork What was the significance of this image? 8

9 Microscopy driven by technology Confocal Microscope: Patrick Lab

10 Microscopy driven by technology Confocal Microscope: Patrick Lab

11 3 Domains of Life : 2 cell types Eubacteria Archea Eukarya Prokaryotic Eukaryotic All solve 3 basic problems! 11

12 The Cell: Basic unit of Life Self-contained collection of aqueous reactions and processes. Uptake of material from the environment Conversion of these materials into energy Production of exact replicas of the cell 12

13 The Cell: 3 Problems to solve! Containment Problem Specificity Problem Information Problem 13

14 Small Molecules and Chemical Bonds Elements: 92 naturally occuring elements; 25 are essential to life Elements properties depends on the structure of its atoms Atom is the smallest unit of matter that retains properties of an element Electron + Proton, Neutron What is this name of this atom? Hydrogen 14

15 Chemical properties of an atom is most related to the number of electrons in the outer most shell Valence Electrons 15

16 Chemical properties of an atom is most related to the number of electrons in the outer most shell Most Common Atoms in Biological organisms #Valence e- #e- needed to fill outer shell Hydrogen Carbon Nitrogen Oxygen Phosphorus Sulfur (H) (C) (N) (O) (P) (S) In order to fill outermost shell atoms share electron pairs H H H 2 16

17 Covalent Bonds Electrons are shared Stable and strong 50 to 200 kcal/mole atoms very close (~0.1 to 0.2 nm apart) Usually represented by, : (usually a line) 17

18 Covalent Bonds Non polar covalent bonds: Polar covalent bonds: Electrons are shared equally Electrons are not shared equally Polar or Non polar? Non polar Non polar Polar Why? Non polar 18

19 Covalent Bonds Polar and Non polar molecules Electronegativity of an atom dictates equal or unequal sharing of electron pairs H 2.2 C 2.5 N 3.0 O 3.4 δ - δ - δ - N O N and O are electronegative in polar covalent bonds Because they have unshared electron pairs The most important biological molecule is. H 2 0 Why? 19

20 Non-Covalent Bonds Binding interactions that do not involve shared electrons Weak bonds: 1 7 kcal/mole Distance between atoms: ~0.3nm Reversible Hydrogen Bonds Van der Waals Attraction Hydrophobic Effect Ionic Bonds 20

21 Non-Covalent Bonds Hydrogen Bonds When a H atom is covalently bond to an electronegative atom (N and O), the H atom becomes slightly polarized and slightly positive in charge H 2.2 C 2.5 N 3.0 O in contrast δ - δ + δ - N-H 0.3 C-H δ - δ + O-H δ + Therefore the H atom that slightly positive can form a weak non-covalent interaction with electron rich (electronegative) atom of another molecule. H Hydrogen Bond (H-bond) δ + O H H δ+ N H H Remember they are reversible! 21

22 Non-Covalent Bonds Hydrogen Bonds Donating and accepting H-bonds Specific Molecules acceptor atom water ethanol δ + CH 3 O H H δ+ δ + * O H* CH 2 donor atom donate and accept donate and accept Dimethyl ether H 3 C * O : : CH 3 accept only Whose more soluble in water? 22 Ethanol because it donates and accepts H-bonds; polar molecule (water loving)

23 Molecules that can not form Hydrogen Bonds Non Polar Hydrophobic (water hating) H H H H Ex. Butane (C 4 H 10 ) H C C C C H H H H H Hydrocarbons No H-bond donor No H-bond acceptor No electronegative atom Can t H-bond and therefore insoluble in water 23

24 Van der waals attraction: weak non-covalent interaction between non polar hydrophobic molecules 1 kcal/mole Hydrophobic Effect Molecules that can not form H-bonds with water will form a separate phase (e.g. oil and water) 24

25 Ionic bonds Non-covalent - no electrons shared One atom donates electron to another Fills outer shell of both atoms produces positive and negative ion 3-7 kcal/mole 11 proton 11 e- 17 proton 17 e- 11 proton 10 e- 17 proton 18 e- 25

26 Water can Ionize also H 2 0 0H - H + + [H+] Hydroxide ion Hydrogen ion = 10-7 M at neutral ph ph = -Log [H+] = -Log [10-7 M] = 7 (ph inside cell) Acids and bases can ionize inside the cell Acetic acid Ammonia acetate ion H 3 C CO0H H COO - 3 C + H + Donates more H+ to water increases [H+] to [10-3 M] ; ph = 3 ammonium ion + NH 3 NH + OH - 4 hydroxide ion hydrogen ion steals H+ from water to liberate OH - decreases [H+] to [10-10 M] ; ph = 10 26

27 A little chemistry helps to understand a lot of biology Biology is the interplay between covalent and non-covalent chemistry Covalent bonds - define the spatial arrangements of atoms in biological molecules Non covalent bonds - define interactions between molecules or parts of a molecule Specifically, the covalent arrangement of atoms in a biological molecule determine the non-covalent interactions and behavior that define the functions of that molecule! 27

28 Functional Groups Found in many types of organic molecules especially macromolecules 28

29 Functional Groups Many of the functional groups that we will discuss have properties that involve acid base chemistry amine NH 2 + H + NH 3 + carboxyl COOH COO - + H + At physiological ph = ~7 Functional Groups that are always negatively charged at physiological ph phosphate sulfhydryl - Note: Especially at a set ph, the functional groups we will study BEHAVE with AUTONOMY. Their chemical properties occur independently of exactly who they are 29 bound to.

30 Solving the Containment Problem! Amphipathic molecules: Hydrophobic and hydrophilic + Sulfate (hydropholic) Dodecane (hydrophobic) Dodecylsulfate Amphipathic molecule: water loving and water hating What Happens if you put this molecule in water? 30

31 Solving the Containment Problem! Covalent structure creates the potential for this non-covalent interaction. Very general solution to amphipathic molecules in water! How does this solve the CONTAINMENT PROBLEM for cells? 31

32 Solving the Containment Problem! Micelles create a space where water can t enter Amphipathic molecules of the same size will form a ball But cells need a wall not a ball to contain an aqueous environment! Phospholipids: the solution to the containment problem 32

33 Phospholipids and the phospholipid bilayer: the solution to the containment problem! Many, many variations but they all form the same structure: A sheet of amphipathic molecules! Cross section 33

34 Phospholipids and the phospholipid bilayer: the solution to the containment problem! Closed structure occurs so that there are no water hating (hydrophobic) edges Inner aqueous environment separated from outer aqueous environment: WHY? Bilayer is poorly permeable to ions and to big molecules Stable formation but not to stable! 34