Transcript CELL BIOLOGY 1 (BIOL 200) (2005S): COURSE OUTLINE

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CELL BIOLOGY 1 (BIOL 200)
(2006S): COURSE OUTLINE
• INSTRUCTOR
Dr. Santokh Singh
Department of Botany
Bioscience Bldg.# 2528 (Second Floor)
Telephone: 604-822-3330,
E-mail: [email protected]
OFFICE HOURS: during lecture breaks or by
appointment
TUTORIAL COORDINATOR AND TAs
• TUTORIAL COORDINATOR
Jamie Pighin, Dept. Botany,
E-mail: [email protected]
• TEACHING ASSISTANTS
Apurva Bhargava,
E-mail: [email protected]
Jacqueline Monaghan, E-mail:
[email protected]
PRE-REQUISITE COURSES
• All of BIOL 112 and one of CHEM 123 or
CHEM 113; or all of
• SCIE 1, or all of BIOL 121 and co-requisite
of all of CHEM 203
TEXTBOOK
Essential Cell Biology
Eds. B. Alberts et al.
Garland Publishing,
2nd Edition, 2004.
COURSE CONTENT
Nine Units:
1.
2.
3.
4.
5.
6.
7.
8.
9.
Introduction of Cell Structure & Function
Informational Macromolecules
Interphase nucleus
Biological Information Flow (Transcription &
Translation)
Structure & Function of Membranes
Mitochondria & Chloroplasts
Endomembranes
Cytoskeleton
Cell Cycle
TEACHING & LEARNING
• Lecture outlines; powerpoint slides;
textbook; tutorials
• Course website URL:
https://www.botany.ubc.ca/biol200/
COURSE EVALUATION
• Tutorials: 25%
• Mid-term examination: 25%
• Final Examination: 50%
EXAMINATION DATES
• Midterm Examination (in class):
June 29 (1 - 1:50 PM)
• Final Examination (in class):
July 7 (1 - 3:30 PM)
POLICIES
• A student must pass the lecture component to pass the course. The
maximum grade obtainable by students failing the lecture portion of the
course is 45%
• An individual student's marks for each of the three components, tutorial
grade, midterm exam and final exam will be counted (No grades will be
dropped)
• Both midterm and final exams may contain short answer, multiple choice,
fill-in the blanks, definitions, experimental, and essay questions
• Final exam will be cumulative: All lecture and tutorial material may be
covered
• If you miss the final exam you must contact the office of the Dean of
Science as soon as possible
Objectives for BIOL 200
• Have a functional grasp of the structure and
function of all major eukaryotic cell systems
• Understand how these systems interact in the
execution of complex processes, i.e. secretion or
cell division
• Know the basic experimental techniques
employed in cell biology research
• Facilitate the integration of concepts and data
from many subsequent courses e.g.
biochemistry, genetics and physiology
Course approach
• Presentation of material with emphasis on
basic points
• Provision of specific details on tricky points
• Discussion of key concepts and their
experimental basis
• Discussion of specific types of exam
questions
BIOL 200 (Section 921)
Lecture # 1; June 19, 2006
•
Reading: Essential Cell Biology (ECB) 2nd edition. Chap 1 and Chap 2,
Chap 5, pages 169-177
Background Study Material: Study Panels 2-1, 2-2, 2-3, 2-4, 2-5, 2-6, 2-7
(pages 66-79).
•
•
Good questions: 1-6, 1-7, 1-9, 1-10, 1-12, 1-18
Assignments: 1.Make a diagram relating the relative size of a typical
nucleus, mitochondrion, a bacterium and a ribosome.
2. Practice to identify the cell organelles in electron micrographs of a variety
of cell types using the Image Database website:
http://www.biomedia.cellbiology.ubc.ca/
•
1.
2.
3.
Learning Objectives
Be able to critically define cells and organelles
Know the major classes of eukaryotic cell organelles and their functions.
Develop a general feel for the flow of information and the flow of material in
cells.
4. Know the different types of microscopy and their functions
5. Know the mechanism and key reactions of synthesis of macromolecules
6. Know the different forces that stabilize the DNA structure
Concepts of organisms and cells
• Organisms are made of
cells.
e.g. a bacterium, a
butterfly, a rose, and a
dolphin
• Cells are the basic unit of
life with a fundamentally
similar chemistry. They
are small, membranebound and arise from
preexisting cells.
e.g. a nerve cell,
Paramecium (protozoan),
plant stem cells, a
bacterium, a human white
blood cell
Diversity of cells: amazingly different shapes
and functions
Unity of cells
•
•
•
Living cells have a similar basic
chemistry and information flow
Cells have evolved from same
ancestors
Cells from different species share
similar genes (e.g. defects in the
gene “Kit” result in white patches
on foreheads of both the human
baby and the mouse.
Scale of things: how big/small is a cell and
its parts
Light microscopy
• Light microscopy involves visible light and
glass lenses to form an image of the
specimen.
• Advantages: Live cells can be viewed.
Images show color if specimens are
stained with dyes.
Disadvantages: Limit of resolution is 0.2
um.
Specialized types of light microscopy
• Phase contrast and differential interference contrast microscopy –
enhance and amplify variations in refractive index within specimen.
• Fluorescence microscopy - uses fluorescent dyes and antibodies to
bind to and detect certain proteins or other molecules. These
fluorescent molecules absorb ultraviolet light and emit light of a
lower wavelength. Fluorescently labeled cells glow bright against a
dark background.
• Confocal scanning light microscopy (CCLM) -type of fluorescent
microscope: uses a laser beam to excite the fluorochrome in a thin
slice called a Z-section or optical section. The light emitted by the
fluorochrome is focussed on a site, i.e. "confocal", with a pinhole
aperture that removes out of focus fluorescence. Allows many slices
of a structure to be gathered as digital image files and then 3-D
reconstructions made on the computer.
Different types of light microscopy
Transmission electron microscopy
•
Transmission electron microscopy
(TEM) is highly analogous to light
microscope. Beam of electrons go
through thin layer of sample and
are either diffracted by interacting
with sample or go straight through
(transmitted).
Resolution of the electron
microscope about 0.2 nm
Pros: good resolution of size
range important to cells (200 nm
to 0.2 nm; size from organelles to
macromolecules).
Cons: samples must be able to
withstand electron bombardment
and vacuum, so elaborate sample
preparation is necessary (fixation,
resin embedding, sectioning into
slices 50-100 nm, heavy metal
stain). Hard to reconstruct 3-D
structure from 2-D slices.
Fig. 1-8: TEM of a thin section of a liver cell
Scanning electron microscopy
• Scanning electron
microscopy (SEM)-beam of
electrons is scanned across
a sample and as it hits the
sample, secondary
electrons are ejected. These
are collected by a
secondary electron detector
which electronically builds
an image based on the
electron intensity (from
white to black).
Pros: great for surfaces, 3-D
images
Cons: electrons require
vacuum so most samples
have to be fixed and dried.
From: Becker et al. World of the Cell
What is the structure and
function of this organelle?
What is the structure and
function of this organelle?
What is the structure and
function of this organelle?
What is the structure and
function of this organelle?
What is the structure and
function of this organelle?
What is the structure and
function of this organelle?
Chemical composition of a bacterial cell
Characteristics of macromolecules in cells
•
Macromolecules are polymers
consisting of (usually) bifunctional
monomers joined by a condensation
reaction.
•
Macromolecules typically have an
overall molecular polarity. They join by
a condensation reaction that joins the
'head' of one monomer to the 'tail' of
the next.
•
The sequence of monomers can be
determined by either informational or
non- informational systems. Both are
dependent on enzymes.
•
Nucleic acids and Proteins are an
example of informational
macromolecules
•
Polysaccharides and Fats/Lipids are
examples of non-informational
macromolecules
Macromolecules in cells
Macromolecules and their
monomeric subunits
Sugars are subunits of
Polysaccharides
Fatty acids as subunits of lipids
Triglycerol
Palmitic acid
Phospholipid in
Cell membrane
Amino acids are the subunits of
proteins
Nucleotides are the subunits of
DNA and RNA
The structural hierarchy in the molecular organization
of cells (Lehninger Principles of Biochemistry Fig. 3.26)
What is happening in this experiment
regarding DNA’s characteristics?
Fig. 5-3, p. 173
Fig. 5-4: DNA is genetic material.
Important
macromolecule
panel!
panel 2-6,
page 76
Fig. 5-6: Complementary base pairing
A=T
G C
Fig. 5-2: DNA structure
Base pairing holds together the two two strands of the DNA
double helix
Fig. 5-7, p. 175
DNA is synthesized
in a 5’ to 3’
direction
[Fig. 6-10 (p. 202)]
Watson +Crick (1962 Nobel prize)
DNA model features:
• DNA is composed of 2 chains forming a right-handed helix.
• The chains run antiparallel to one another (5' to 3' vs. 3' to
5')
• Sugar phosphate backbone (negatively charged) is
hydrophilic, facing solution
• Bases projecting towards the center stacked one on top of
the other, form a hydrophobic core
• Rules of base pairing: A pairs with T (or U in RNA); G pairs
with C (Fig 5-6 p. 175)
• Purine always hydrogen bonds with pyrimidine
(purines=A+G; pyrimidines=T(U)+C)
• Number of hydrogen bonds varies:
-The A::T bond has two hydrogen bonds
-The C:::G bond has three hydrogen bonds