04-2-13: Lecture 1

Welcome to BILD 1: The Cell

Tu, Thu : 2:00pm-3:20 pm Warren Lecture Hall 2001

Gentry Patrick, PhD

Office hours: Mondays: 11am-12:30pm Weds: 9:30am to 11:00am Pacific Hall rm 2222A gpatrick@ucsd.edu (BILD1 in subject line)
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Course Logistics
Textbook : Biology Campbell and Reece 9th Edition 18 Lectures 6 Problem Sets Handouts or additional helpful readings Discussion Sections (http://sections.ucsd.edu/) 2 Midterms (Thursday - 4/25 & Thursday 5/16) Final Comprehensive (Tuesday 6/11) Exam Reviews: prior to midterms and final
lecture
(8th is OK)

Style - powerpoint; student version (sv) posted on website prior to

Website: http://www.biology.ucsd.edu/classes/bild1-2.FA11/ General Info, Syllabus, Announcements, lectures, handouts, problem sets including Problem Set Keys, regrade policy, etc. 2

Review Session Dates: Evenings of 04/23 and 05/14 (Midterms 1 and 2 Review; 7pm-10pm; Peterson 108) and 06/08 (Final Review; 11am 2pm; WLH 2001)

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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
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Common Questions
What is the grading system? Graded on a curve - Mean is B-/C+
Curve for Fall-BILD1 Midterm 1
50 45 40
Number of Students

35 30 25 20 15 10

Ex.

5 0

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BILD 1: The Cell WHY?

Usual reasons cell multi cell 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, etc. Healthy curiosity about who/what we are!
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mol bio, pre-med, research, etc

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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!
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Dawn of Cellular Thinking

1600s Anton Van Leeuwenhoek
(skilled lens grinder) first to identify and describe single cell organisms

Lens (eye piece) Specimen holder Base plate Adjustment screw

Pond water

Animalcules protazoans

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Dawn of Cellular Thinking

1600s Anton Van Leeuwenhoek
(skilled lens grinder) first to identify and describe single cell organisms (added more light)

Robert Hooke built a more advanced microscope

Cork What was the significance of this image?

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3 Domains of Life : 2 cell types

Eubacteria Archea Eukarya Eukaryotic

Prokaryotic

All solve 3 basic problems!

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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

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

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Small Molecules and Chemical Bonds

Elements: 92 naturally occuring elements; 25 are essential to life Elements properties Atom
depends on the structure of its atoms

is the smallest unit of matter that retains properties of an element

Electron

Proton , Neutron

What is this name of this atom? Hydrogen

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

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Chemical properties of an atom is most related to the number of electrons in the outer most shell Most Common Atoms in Biological organisms Hydrogen Carbon Nitrogen Oxygen Phosphorus Sulfur (H) (C) (N) (O) (P) (S) #e- needed to #Valence e- fill outer shell 1 4 5 6 5 6 1 4 3 2 3 2

In order to fill outermost shell atoms share electron pairs

+
H

+
H

+
H2

+
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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)

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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
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Covalent Bonds Polar and Non polar molecules Electronegativity of an atom dictates equal or unequal sharing of electron pairs

H 2.2

C N O 2.5 3.0 3.4

N N and O are electronegative in polar covalent bonds Because they have unshared electron pairs

2 The most important biological molecule is________.

H 0

Why?

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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

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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 N O 2.5 3.0 3.4

0.8 1.2

N-H O-H
+

in contrast - + 0.3 C-H

Therefore the H atom that slightly positive can form a weak non-covalent interaction with electron rich (electronegative) atom of another molecule.

H O H + H

Hydrogen Bond (H-bond) Remember they are reversible!

N H H

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Non-Covalent Bonds Hydrogen Bonds Donating and accepting H-bonds Specific Molecules water acceptor atom

O H + H

donor atom

donate and accept

*O H *
ethanol

CH3 CH2 * H3C O

:

donate and accept

Dimethyl ether

CH3

accept only

Whose more soluble in water? 20 Ethanol because it donates and accepts H-bonds; polar molecule (water loving)

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Molecules that can not form Hydrogen Bonds Non Polar Hydrophobic (water hating) H Ex. Butane (C4H10) H C H Hydrocarbons H H C C H H H C H H

No H-bond donor No H-bond acceptor No electronegative atom

Cant H-bond and therefore insoluble in water

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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)

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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 e23

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Water can Ionize also

H20 [H+]

0HHydroxide ion

H+
Hydrogen ion

= 10-7 M at neutral pH [H+] = -Log [10-7 M] = 7 (pH inside cell)

pH = -Log

Acids and bases can ionize inside the cell Acetic acid

Donates more H+ to water increases [H+] to [10-3 M] ; pH = 3 Ammonia

H3C CO0H NH3

H3C COO- + H+
+

acetate ion

hydrogen ion

ammonium ion

steals H+ from water to liberate OH-decreases [H+] to [10-10 M] ; pH = 10

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NH4

+ OH-

hydroxide ion

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

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Functional Groups Many of the functional groups that we will discuss have properties that involve acid base chemistry amine carboxyl NH2

H+

NH3+ COO-

COOH

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 27 bound to.

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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?
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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?
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Solving the Containment Problem! Micelles create a space where water cant 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

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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

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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!
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