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Welcome to BILD 1: The Cell

Gentry Patrick, PhDOffice hours:Weds: 9:30am to 11:00amPacific Hall rm 2222Agpatrick@ucsd.edu (BILD1 in subject line)

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Tu, Thu : 12:30pm - 1:50pm Warren Lecture Hall 2001

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•Textbook : Campbell “Biology in Focus”.•Biology by Campbell 9th 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: http://classes.biology.ucsd.edu/bild1.SP16•General Info, Syllabus, Announcements, lectures, handouts, problem sets including Problem Set Keys, regrade policy, etc.•Lectures will be podcasted: https://podcast.ucsd.edu

Course Logistics

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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

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•What is the grading system?

•Graded on a curve - Mean is B-/C+

Common Questions

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MIDTERM 1: Average 81.9

Frequency

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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, Crispr/Cas9, optogenetics 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

Adjustmentscrew

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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Microscopy driven by technology

Confocal Microscope: Patrick Lab

Microscopy driven by technology

Confocal Microscope: Patrick Lab

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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-

145656

#e- needed to fill outer shell

143232

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

H2.2

C2.5

N3.0

O3.4

N and O are electronegative in polar covalent bonds

δ- δ-

δ-

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

H2.2

C2.5

N3.0

O3.4

δ-

∆ 1.2

∆ 0.8 N-Hδ+

δ-

O-Hδ+

∆ 0.3

in contrastδ-

C-Hδ+

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

Hδ+

δ+

N

H

H

H

Remember they are reversible!

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Non-Covalent Bonds – Hydrogen Bonds

Specific Molecules

O

H

Hδ+

δ+

water

acceptor atom

donor atom

Donating and accepting H-bonds

donate and accept

O

CH2

Hδ+

CH3ethanol

* *

donate and accept

Dimethyl ether O

:

CH3H3C :

*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 PolarHydrophobic (water hating)

Ex. Butane (C4H10) C C C CH

H H H H

H

H H H H

Hydrocarbons

No H-bond donorNo H-bond acceptorNo electronegative atom

Can’t H-bond and therefore insoluble in water

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Van der waals attraction:

weak non-covalent interaction between non polar hydrophobic molecules1 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 proton11 e-

17 proton17 e-

11 proton10 e-

17 proton18 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

CO0HH3C 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

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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 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

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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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