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Welcome to BILD 1: The Cell

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

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Textbook : Biology Campbell and Reece 9th Edition (8th is OK) 18 Lectures

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

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

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)

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.

Course Logistics 04-2-13: Lecture 1

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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

Common Questions 04-2-13: Lecture 1

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What is the grading system?

Graded on a curve - Mean is B-/C+

Common Questions

Curve for Fall-BILD1 Midterm 1

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Num

ber

of S

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nts

A B C

Ex.

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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, etc.

Healthy curiosity about who/what we are!

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BILD 1: Basic Course Ideas Biology is/uses a language

Science is about questions

the most powerful tool you can hone is the willingness to

we will learn about 300 new terms & a conceptual basis by which they are used

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

Adjustment screw

Base plate

Lens (eye piece)

Specimen holder

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

Robert Hooke built a more advanced microscope (added more light)

Cork

What was the significance of this image?

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3 Domains of Life

Eubacteria Archea Eukarya

Prokaryotic Eukaryotic

: 2 cell types

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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Containment Problem

Specificity Problem

Information Problem

The Cell: 3 Problems to solve!

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Small Molecules and Chemical Bonds

Elements:

92 naturally occuring elements; 25 are essential to life

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

Elements properties depends on the structure of its atoms

+

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 (H) Carbon (C) Nitrogen (N) Oxygen (O) Phosphorus (P) Sulfur (S)

#Valence e-

1 4 5 6 5 6

#e- needed to fill outer shell

1 4 3 2 3 2

In order to fill outermost shell atoms share electron pairs

+ +

H2

+ +

H H

+

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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: Electrons are shared equally

Polar covalent bonds: Electrons are not shared equally

Polar or Non polar?

Non polar

Non polar

Non polar

Polar Why?

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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 2.5

N 3.0

O 3.4

N and O are electronegative in polar covalent bonds

- -

-

Because they have unshared electron pairs

N O

The most important biological molecule is________. H20 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 2.5

N 3.0

O 3.4

-

1.2

0.8 N-H +

-

O-H +

0.3

in contrast -

C-H +

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

Hydrogen Bond (H-bond)

O H

H +

+

N H

H H

Remember they are reversible!

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Non-Covalent Bonds Hydrogen Bonds

Specific Molecules

O H

H +

+

water

acceptor atom

donor atom

Donating and accepting H-bonds

donate and accept

O CH2

H +

CH3 ethanol

* * donate and accept

Dimethyl ether O :

CH3 H3C :

* accept only

Whose more soluble in water? 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)

Ex. Butane (C4H10) C C C C H H H H H

H H H H H

Hydrocarbons

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 e-

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Water can Ionize also

H20 0H- H+ + Hydroxide ion Hydrogen ion

[H+] = 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

CO0H H3C COO- H3C H+ + Acetic acid Donates more H+ to water increases [H+] to [10-3 M] ; pH = 3

NH3 OH- + Ammonia steals H+ from water to liberate OH-decreases [H+] to [10-10 M] ; pH = 10

NH4 +

ammonium ion

acetate ion

hydroxide ion

hydrogen 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 NH2

COOH

NH3+

COO-

+ H+

+ H+ carboxyl

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 bound to.

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Solving the Containment Problem!

Amphipathic molecules: Hydrophobic and hydrophilic

+

Sulfate

Dodecylsulfate

(hydropholic) Dodecane

(hydrophobic)

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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