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Welcome to

BILD1: The CellSpring 2010

Dr. Amy Kiger

Assistant Professor, Cell & Developmental BiologyNatural Sciences Building 6109

akiger@ucsd.edu

All information is on website!! http://www.biology.ucsd.edu/classes/bild1.SP10/

BILD1: The CellGOALS:

1. Learn the structures and mechanisms of actionfor the smallest unit of life - the cell

Terminology (what is it?)Functional Concepts (how does it work? themes?)

Hierarchy, Connectivity (how do parts fit together?)

2. Learn Cell Biology is an Experimental Science

How do we know what we know?What new questions are raised still to be tested?

3. Prepare you for future biology courses and for afuture in medicine or science

http://www.biology.ucsd.edu/classes/bild1.SP10/ Course Meetings

• Lectures Syllabus posted on websiteMonday / Wednesday, 5:00-6:20 PM, Solis 107

NOTE! No Office Hours or Sections this week

• Midterm Exams In class - Same time, Same place#1 Wednesday, April 14#2 Wednesday, May 5

• Final Exam place to be determinedFriday, June 11, 7:00-10:00 PM

http://www.biology.ucsd.edu/classes/bild1.SP10/

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• Weekly Sections, starting Monday, April 5- 10 TA-led Discussion Section options (see website for schedule)- Review Problem Sets, Chapter reading, Q&A- Sign-up at first meeting, attendance taken- Not Required, but Highly Recommended!- TA input on attendance/participation can affect grades

• Exam Review SessionsTA-led Reviews and Q&A prior to all Exams.

Course Meetingshttp://www.biology.ucsd.edu/classes/bild1.SP10/

Course TAs

Divya AhujaKristin Carr

Jonathon ChangThao Dang

Arpi HambarchyanArek HidirsahAubri Kottek

Hong LawPatricia Villegas

Debra Yeh

http://www.biology.ucsd.edu/classes/bild1.SP10/

Course Etiquitte

• Arrive on Time• Turn off phones• Do not disturb others• Participate!

– Questions will be fielded and are also welcome

http://www.biology.ucsd.edu/classes/bild1.SP10/

• Reading of assigned text, as on syllabusBiology, 8th Edition, Campbell & Reece http://www.aw-bc.com/campbell/

- Recommended to pre-read prior to lecture

NOTE! Students responsible for conversions if using old editions

• Problem Sets, to be posted on website- Not for credit, but Highly Recommended!- Announced in class when posted on the website- Reviewed in Sections the following week

NOTE! Some questions will be re-used verbatim on exams

Course Workhttp://www.biology.ucsd.edu/classes/bild1.SP10/

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Exams

• NO MAKE UPS!Check your exam schedules now! No rescheduled exams given

• Only pen and ID allowed, closed book and notes

• Regrade policies– Only exams taken in pen, No whiteout or correction tape– Cover letter must indicate which problem and describe dispute– Provide full name and email– Entire exam will be regraded– Subset of exams will be copied before returned

• Zero tolerance for cheating of any kind

http://www.biology.ucsd.edu/classes/bild1.SP10/Academic Integrity

• Absolutely no cheating tolerated

• UCSD Policies enforced

All work must be done by the student to whom it isassigned, without any unauthorized aid of any kind

http://blink.ucsd.edu/Blink/External/Topics/Policy/0,1162,19400,00.html

http://www.biology.ucsd.edu/classes/bild1.SP10/

• Grading by curveAverage at B-/C+Curve used to rescale (lowers cut-offs, to your advantage)Your grade is independent of other student grades

• Your Final Grade:• 25% Midterm Exam 1• 25% Midterm Exam 2• 50% Final Exam (Comprehensive)

Borderline grades are influenced by participation in Sections

Course Gradinghttp://www.biology.ucsd.edu/classes/bild1.SP10/

• Weekly Professor Office Hours

– Tuesdays, 3:00-4:30 PMNote: this and next week, Wednesday 3:30-5:00 PM instead

Natural Science Building Room 6109

- By appointment, when necessary

• Weekly TA Office Hours

- 10 options each week, as posted on website- Extra office hours will be held during exam weeks

Resourceshttp://www.biology.ucsd.edu/classes/bild1.SP10/

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• Please join Google Groups - BILD1 message board

– Free membership– Set-up options to receive emails with new postings– Read, post, reply– Students, TAs, Instructors

Resources

http://groups.google.com/group/bild1sp10

http://www.biology.ucsd.edu/classes/bild1.SP10/

• From Instructor to Student […did you receive my email?]

Students must have functional email account- working account as listed on TritonLink- make sure instructor’s email not seen as spam- make sure inbox is not full

• From Student to Instructor

- Include BILD1 in subject line- Use proper English- Include full name in note- Do not expect instant replies. Please come to instructor office

hours for most certain and immediate replies.

Email Contacthttp://www.biology.ucsd.edu/classes/bild1.SP10/

Biology Student AffairsUndergraduate OfficePacific Hall 1129

Add / DropPrereqsMajoretc.

Administrative ?http://www.biology.ucsd.edu/classes/bild1.SP10/

http://www.biology.ucsd.edu/classes/bild1.SP10/

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I. Introduction to Cells

The cell is life’s fundamental unit

The cell is the smallest form of life

EUKARYOTIC CELL

Membrane

Cytoplasm

Organelles

Nucleus(contains DNA)

1 µm

PROKARYOTIC CELL

DNA (no nucleus)

Membrane

25 µm

Cells only arise from pre-existing cells

Newt lung cell undergoing cell division

The cell is life’s fundamental unitAll life forms are made from one or more cells

Mitosis in cells of an onion root

The cell is life’s fundamental unit

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Scientific study of cells

Discovery Science:describe observations

Hypothesis-Based Science:propose and test explanations

- better understanding of nature

- biotechnology applications

Figure 1.4 Levels of Biological Organization

1 The biosphere

2 Ecosystems

3 Communities

4 Populations

5 Organisms

BILD3

8 Cells

6 Organs and organ systems

7 Tissues

10 Molecules

9 Organelles

50 µm

10 µm

1 µmCell

Atoms

BILD1

BILD2

Figure 1.4 Levels of Biological OrganizationII. Atoms and Bonds

ELEMENT: Cannot be broken down into other substances.

25 / 92 Natural elements are essential for life

Element % of Human Body Weight

? 65% ? 19% ? 10% ? 3%

} These 4 elementsmake up 96% ofliving matter

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II. Atoms and Bonds

ELEMENT: Cannot be broken down into other substances.

25 / 92 Natural elements are essential for life

Element % of Human Body Weight

O 65% C 19% H 10% N 3%

Elements combine to form chemical bonds and compounds

} These 4 elementsmake up 96% ofliving matter

Types of Bonds

1. Covalent

2. Ionic

3. Hydrogen

4. Van Der Waals interactions

stre

ngth

ATOM: Smallest unit of matter that retains the properties of an element.

Nucleus

(a) (b) In this even more simplifiedmodel, the electrons areshown as two small bluespheres on a circle around thenucleus.

Cloud of negativecharge (2 electrons)

Electrons

This model represents theelectrons as a cloud ofnegative charge, as if we hadtaken many snapshots of the 2electrons over time, with eachdot representing an electron‘sposition at one point in time.

helium (He)

Secondshell

Helium2He

Firstshell

Thirdshell

Hydrogen1H

2He

4.00Atomic mass

Atomic number

Element symbol

Electron-shelldiagram

Lithium3Li

Beryllium4Be

Boron3B

Carbon6C

Nitrogen7N

Oxygen8O

Fluorine9F

Neon10Ne

Sodium11Na

Magnesium12Mg

Aluminum13Al

Silicon14Si

Phosphorus15P

Sulfur16S

Chlorine17Cl

Argon18Ar

Figure 2.9 Electron-shell diagramsVALENCE: bonding capacity, determined by the

unpaired valence electrons in outermost shell

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Figure 2.11 Covalent Bonds

Hydrogen atoms (2 H)

Hydrogenmolecule (H2)

1 In each hydrogenatom, the single electronis held in its orbital byits attraction to theproton in the nucleus.

When two hydrogenatoms approach eachother, the electron ofeach atom is alsoattracted to the protonin the other nucleus.

2

The two electronsbecome shared in a covalent bond,forming an H2molecule.

3

+ +

+ +

+ +

COVALENT BOND: Sharing of electrons between elements

MOLECULE: elements held together by covalent bonds

Figure 2.12 Examples of Covalent bonds

Name(molecularformula)

Electron-shell

diagram

Structuralformula

(c)

H

Methane (CH4). Four hydrogen atoms can satisfy the valence ofone carbonatom, formingmethane.

Space-fillingmodel

Hydrogen (H2). Two hydrogen atoms can form a single bond.

(a)H H

O OOxygen (O2). Two oxygen atoms share two pairs of electrons to form a double bond.

(b)

Water (H2O). Two hydrogenatoms and one oxygen atom arejoined by covalent bonds to produce a molecule of water.

O H

H

H H

HO

H

O O

H

HH C H

H

H

HC

(d)

Single

Double

Polar

Nonpolar

Figure 2.13 Polar covalent bonds in a water molecule

This results in a partial negative charge on theoxygen and apartial positivecharge onthe hydrogens.

H2O

δ–

O

H Hδ+ δ+

Because oxygen (O) is more electronegative than hydrogen (H), shared electrons are pulled more toward oxygen.

Figure 2.14 Electron transfer and ionic bonding

Cl–Chloride ion(an anion)

–

The lone valence electron of a sodiumatom is transferred to join the 7 valenceelectrons of a chlorine atom.

1 Each resulting ion has a completedvalence shell. An ionic bond can formbetween the oppositely charged ions.

2

Na NaCl Cl

+

NaSodium atom

(an unchargedatom)

ClChlorine atom(an uncharged

atom)

Na+

Sodium on(a cation)

Sodium chloride (NaCl)

IONIC BOND: Transfer of electrons between atoms

COMPOUND: ≥2 elements in a fixed ratio

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Figure 2.15 Ionic Compounds

Na+

Cl–

sodium chloride crystal

Figure 2.16 A hydrogen bond

Water(H2O)

Ammonia(NH3)

δ– δ+

OH

H

δ+

δ–

N

HH H

A hydrogenbond results from the attraction between thepartial positive charge on the hydrogen atom of water and the partial negative charge on the nitrogen atom of ammonia.δ+

δ+

δ+

HYDROGEN BOND: H shared between polar molecules

Figure p. 41, Van der Waals interactions

VAN DER WAALS: slight interactions betweennonpolar covalent molecules

III. Water

• H20 is a polar molecule attracted to itself. This is the critical factor for all of water’s most important properties.

• Most important molecule for life on Earth.

• Life began in water and evolved here for 3 Billion years before spreading to land.

• Our cells are 70-95% water; we can only survive for 1 week without water.

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Figure 3.2 Hydrogen bonds between water molecules

Hydrogenbonds

δ +

δ+

H

Hδ+

δ+

δ–

δ–

δ–

δ–

Properties of Water:

• ICE FLOATS: Solid H20 is ~10% less dense than liquid form. This unusual feature results in a crystal-like matrix of H20 molecules in ice. Insulates water underneath.

• COHESION: Water molecules stay close together due to hydrogen bonding.

• HIGH SPECIFIC HEAT: A great deal of energy is required to break H-bonds to release/vaporize individual molecules.

• EVAPORATIVE COOLING: H20 molecules with highest energy leave water reservoir as vapor, lowering the T of remaining liquid.

• EXCELLENT SOLVENT: Dissolves polar and nonpolar substances and salts.

Figure 3.7 Water is an excellent solvent (dissolving agent)

NegativeOxygen regions

of polar watermolecules are

attracted to sodiumcations (Na+).

+

+

+

+Cl –

–

–

–

–

Na+Positivehydrogen regions

of water moleculescling to chloride

anions (Cl–).

+

+

+

+

–

–

–

–

–

–Na+

Cl–

A crystal of table saltdissolving in water

Figure 3.8 A water-soluble protein

This oxygen isattracted to a slightpositive charge onthe lysozymemolecule.

This oxygen is attracted to a slightnegative charge on the lysozyme molecule.

(a) Lysozyme molecule in a nonaqueous environment

(b) Lysozyme molecule (purple) in an aqueous environment such as tears or saliva

(c) Ionic and polar regions on the protein’s Surface attract water molecules.

δ+

δ–

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IV. Acids & Bases

• Dissociation of water results in ions.

H2O H+ + OH-

Hydrogen ion Hydroxide ion

• Pure water has equal concentrations: [H+] = [OH-].

• Pure water is NEUTRAL, or pH 7.

(H3O+ )

pH ScaleH+Measures level of acidity

H+

pH = -log [H+]

• ACID: Increases [H+],or reduces pH

• BASE: Reduces [H+], or increases pH

V. Buffers

• Compound that prevents sudden change in pH.

• Critical for most cells to maintain pH 6-8.

Lectures

• Please check / fix email.

• Today: Read Chapters 1-3.

• Wednesday: Read Chapter 4.

Reminders• No TA Sections / Office Hrs this week.

• Problem Set # 1.Homework• Chapter Self-Quizzes.

• Use class website.

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http://www.biology.ucsd.edu/classes/bild1.SP10/

Tonight’s Soundtrack