Welcome to
BILD1: The Cell
BILD1: The Cell
Spring 2010
GOALS: 1.
Dr. Amy Kiger
Learn the structures and mechanisms of action for 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?)
Assistant Professor, Cell & Developmental Biology Natural Sciences Building 6109 akiger@ucsd.edu
2.
Learn Cell Biology is an Experimental Science How do we know what we know? What new questions are raised still to be tested?
All information is on website!! http://www.biology.ucsd.edu/classes/bild1.SP10/
3.
Prepare you for future biology courses and for a future in medicine or science
Course Meetings
http://www.biology.ucsd.edu/classes/bild1.SP10/
http://www.biology.ucsd.edu/classes/bild1.SP10/
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Lectures
Syllabus posted on website Monday / Wednesday, 5:00-6:20 PM, Solis 107 NOTE! No Office Hours or Sections this week
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Midterm Exams In class - Same time, Same place
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Final Exam place to be determined
#1 Wednesday, April 14 #2 Wednesday, May 5
Friday, June 11, 7:00-10:00 PM
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Course Meetings
Course TAs
http://www.biology.ucsd.edu/classes/bild1.SP10/
http://www.biology.ucsd.edu/classes/bild1.SP10/
Divya Ahuja •
Kristin Carr
Weekly Sections, starting Monday, April 5
Jonathon Chang
- 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
Thao Dang Arpi Hambarchyan Arek Hidirsah
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Exam Review Sessions
Aubri Kottek
TA-led Reviews and Q&A prior to all Exams.
Hong Law Patricia Villegas Debra Yeh
Course Etiquitte
Course Work
http://www.biology.ucsd.edu/classes/bild1.SP10/
http://www.biology.ucsd.edu/classes/bild1.SP10/
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• • • •
Arrive on Time Turn off phones Do not disturb others Participate! – Questions will be fielded and are also welcome
Reading of assigned text, as on syllabus
Biology, 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
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Exams
Academic Integrity
http://www.biology.ucsd.edu/classes/bild1.SP10/
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NO MAKE UPS! Check your exam schedules now! No rescheduled exams given
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Only pen and ID allowed, closed book and notes
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Regrade policies
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– – – – –
http://www.biology.ucsd.edu/classes/bild1.SP10/
• Absolutely no cheating tolerated • UCSD Policies enforced
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
All work must be done by the student to whom it is assigned, without any unauthorized aid of any kind http://blink.ucsd.edu/Blink/External/Topics/Policy/0,1162,19400,00.html
Course Grading
Resources
http://www.biology.ucsd.edu/classes/bild1.SP10/
• Grading by curve
http://www.biology.ucsd.edu/classes/bild1.SP10/
• Weekly Professor Office Hours – Tuesdays, 3:00-4:30 PM
Average at B-/C+ Curve used to rescale (lowers cut-offs, to your advantage) Your grade is independent of other student grades
Note: this and next week, Wednesday 3:30-5:00 PM instead
Natural Science Building Room 6109 - By appointment, when necessary
• Your Final Grade:
• 25% Midterm Exam 1 • 25% Midterm Exam 2 • 50% Final Exam (Comprehensive)
Borderline grades are influenced by participation in Sections
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Weekly TA Office Hours - 10 options each week, as posted on website - Extra office hours will be held during exam weeks
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Email Contact
Resources
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• Please join Google Groups - BILD1 message board – – – –
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
Free membership Set-up options to receive emails with new postings Read, post, reply Students, TAs, Instructors
•
http://groups.google.com/group/bild1sp10
Administrative ?
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.
http://www.biology.ucsd.edu/classes/bild1.SP10/
http://www.biology.ucsd.edu/classes/bild1.SP10/
Biology Student Affairs Undergraduate Office Pacific Hall 1129
Add / Drop Prereqs Major etc.
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The cell is life’s fundamental unit The cell is the smallest form of life EUKARYOTIC CELL
I. Introduction to Cells
PROKARYOTIC CELL
Membrane
DNA (no nucleus)
Cytoplasm
Membrane
Nucleus (contains DNA)
Organelles 1 µm
The cell is life’s fundamental unit
All life forms are made from one or more cells
Cells only arise from pre-existing cells
Newt lung cell undergoing cell division
The cell is life’s fundamental unit
25 µm
Mitosis in cells of an onion root
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Figure 1.4 Levels of Biological Organization
Scientific study of cells
BILD3
1 The biosphere
2 Ecosystems
Discovery Science: describe observations
Hypothesis-Based Science: propose and test explanations
3 Communities
- better understanding of nature - biotechnology applications 4 Populations
5 Organisms
Figure 1.4 Levels of Biological Organization 9 Organelles 1 µm
Cell
BILD1
II. Atoms and Bonds ELEMENT: Cannot be broken down into other substances.
8 Cells
25 / 92 Natural elements are essential for life BILD2
Atoms
Element 10 µm
7 Tissues 50 µm
10 Molecules
? ? ? ?
% of Human Body Weight 65% 19% 10% 3%
}
These 4 elements make up 96% of living matter
6 Organs and organ systems
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II. Atoms and Bonds
Types of Bonds
ELEMENT: Cannot be broken down into other substances.
1. Covalent
25 / 92 Natural elements are essential for life % of Human Body Weight
O C H N
65% 19% 10% 3%
}
These 4 elements make up 96% of living matter
2. Ionic
strength
Element
3. Hydrogen 4. Van Der Waals interactions
Elements combine to form chemical bonds and compounds
ATOM: Smallest unit of matter that retains the properties of an element.
Figure 2.9 Electron-shell diagrams VALENCE: bonding capacity, determined by the unpaired valence electrons in outermost shell
Electrons Cloud of negative charge (2 electrons)
Hydrogen 1H
Nucleus
Atomic mass
2 He 4.00
First shell
Atomic number
Helium 2He
Element symbol
Electron-shell diagram Lithium 3Li
Beryllium 4Be
Sodium 11Na
Magnesium 12Mg
Boron 3B
Carbon 6C
Nitrogen 7N
Silicon 14Si
Phosphorus 15P
Oxygen 8O
Fluorine 9F
Neon 10Ne
Sulfur 16S
Chlorine 17Cl
Argon 18Ar
Second shell
helium (He) (a) This model represents the electrons as a cloud of negative charge, as if we had taken many snapshots of the 2 electrons over time, with each dot representing an electron‘s position at one point in time.
(b) In this even more simplified
model, the electrons are shown as two small blue spheres on a circle around the nucleus.
Aluminum 13Al
Third shell
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Figure 2.11 Covalent Bonds
Figure 2.12 Examples of Covalent bonds
COVALENT BOND: Sharing of electrons between elements 1
In each hydrogen atom, the single electron is held in its orbital by its attraction to the proton in the nucleus.
2 When two hydrogen atoms approach each other, the electron of each atom is also attracted to the proton in the other nucleus.
Hydrogen atoms (2 H)
+
+
+
Name (molecular formula) (a) Hydrogen (H2 ). Two hydrogen atoms can form a single bond.
H
(b) Oxygen (O2 ). Two oxygen atoms share two pairs of electrons to form a double bond.
+
+
(d) Methane (CH4 ). Four hydrogen atoms can satisfy the valence of one carbon atom, forming methane.
+
Hydrogen molecule (H2)
H
O
(c) Water (H2 O). Two hydrogen atoms and one oxygen atom are joined by covalent bonds to produce a molecule of water.
3 The two electrons become shared in a covalent bond, forming an H2 molecule.
Structural formula
Electronshell diagram
O
O
H
H
H
H
Single
O
O
Double
O
H
Polar
H
H C
H
Spacefilling model
H H
H
H
C
Nonpolar
H
H
MOLECULE: elements held together by covalent bonds
Figure 2.13 Polar covalent bonds in a water molecule
IONIC BOND: Transfer of electrons between atoms
Because oxygen (O) is more electronegative than hydrogen (H), shared electrons are pulled more toward oxygen.
1 The lone valence electron of a sodium
atom is transferred to join the 7 valence electrons of a chlorine atom.
δ–
This results in a partial negative charge on the oxygen and a partial positive charge on the hydrogens.
O
H
H
δ+
Figure 2.14 Electron transfer and ionic bonding
δ+
Na
Cl
Na Sodium atom (an uncharged atom)
Cl Chlorine atom (an uncharged atom)
2 Each resulting ion has a completed valence shell. An ionic bond can form between the oppositely charged ions.
+
–
Na
Cl
Na+ Sodium on (a cation)
Cl– Chloride ion (an anion)
Sodium chloride (NaCl)
H2 O
COMPOUND: ≥2 elements in a fixed ratio
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Figure 2.16 A hydrogen bond
Figure 2.15 Ionic Compounds
HYDROGEN BOND: H shared between polar molecules δ–
sodium chloride crystal
δ+ H
Water (H2O)
O
H δ+ δ– Na+ Cl–
Ammonia (NH3 )
N H δ+
H H
δ+
A hydrogen bond results from the attraction between the partial positive charge on the hydrogen atom of water and the partial negative charge on the nitrogen atom of ammonia.
δ+
Figure p. 41, Van der Waals interactions
III. Water • 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.
VAN DER WAALS: slight interactions between nonpolar covalent molecules
• H20 is a polar molecule attracted to itself. This is the critical factor for all of water’s most important properties.
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Figure 3.2 Hydrogen bonds between water molecules
Properties of Water: • COHESION: Water molecules stay close together due to hydrogen bonding.
δ– δ+
Hydrogen bonds
H
δ+
δ–
• 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.
H
δ+
δ–
• 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.
δ–
δ+
• EXCELLENT SOLVENT: Dissolves polar and nonpolar substances and salts.
Figure 3.7 Water is an excellent solvent (dissolving agent) Negative Oxygen regions of polar water molecules are attracted to sodium cations (Na+). Positive hydrogen regions of water molecules cling to chloride anions (Cl– ).
Figure 3.8 A water-soluble protein
–
Na+ +
–
+ +
–
–
Na+ Cl –
+ +
δ–
+
+ Cl–
–
–
+
δ+
–
This oxygen is attracted to a slight negative charge on the lysozyme molecule.
–
–
–
This oxygen is attracted to a slight positive 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.
A crystal of table salt dissolving in water
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pH Scale
IV. Acids & Bases
Measures level of acidity • Dissociation of water results in ions. H2O
H+ Hydrogen ion
OH-
+
Hydroxide ion
(H3O+ ) • Pure water has equal concentrations: [H+] = [OH-]. • Pure water is NEUTRAL, or pH 7.
H+
pH = -log [H+] • ACID: Increases [H+], or reduces pH
• BASE: Reduces [H+], or increases pH
H+
V. Buffers
Lectures
• Today: Read Chapters 1-3. • Wednesday: Read Chapter 4.
• Compound that prevents sudden change in pH. • Critical for most cells to maintain pH 6-8.
Homework
• Problem Set # 1. • Chapter Self-Quizzes.
Reminders
• Please check / fix email. • No TA Sections / Office Hrs this week. • Use class website.
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http://www.biology.ucsd.edu/classes/bild1.SP10/
Tonight’s Soundtrack
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