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Learning objectives

by the end of todays class, students should be able to


1) recall general course policies (or look them up on
Blackboard)
2) put important dates/times in calendar
3) explain the cell theory
4) compare and contrast eukaryotes and
prokaryotes
5) compare and contrast archea, bacteria, and
different types of animal cells
6) describe different types of microscopy and
their pros/cons
7) Be able to identify the type of microscopy used
8) Understand the difference between
magnification and resolution
9) describe the functions of different eukaryotic
cell components

Team Biol303
Spring15
Faculty:

Dr. Karen Whitworth &


Dr. Phyllis Robinson

Graduate Student Teaching Assistants:


Juan Valdez & Khoa Tran

Peer Discussion Leaders:


Alicia, Arissa, Austin, Aviva, Chiamaka, Clark, Erin, Gabriela,
Henry, Lavanya, Maniraj, Mashhood, Mekha Nisha, Ob inna,
Simin, Shahzeb, Syrena

Tutoring coordinated by Dr. Sue Gdovins and LRC

BIOL 303 Administrative


Issues

Please refer to the Biol303 Blackboard site for


official, current information
including course policies and the exam
schedule
Please review the rules of Academic Integrity
Discussion sections are mandatory (as
assigned)
Clickers are mandatory
Online assignments are mandatory (and due
Tuesdays)
your homework: write down your clicker ID and
register your clickers on the Bb website before 2/2/16
Syllabus quiz due ASAP

Snow Days vs Cell Biology

Lecture 3 materials have already been posted online under Course


Documents
Must pass Syllabus quiz to see Course Documents
Must complete these lecture videos prior to attending week 2
discussion section (Tuesday 2/2/16 through Monday 2/8/16)

EXAM schedule
Dates

Place/Time
Lectures

I: Tuesday, Feb. 16,


Eng 027/11:30a-12:45p
1-6
II: Thursday, Mar. 10,
Eng 027/11:30a-12:45p
7-12
III: Tuesday, Apr. 12,
Eng 027/11:30a-12:45p
13-18
IV: Tuesday, May 10,
Eng 027/11:30a-12:45p
19-25
Comprehensive Final Exam:
THURSDAY May 12, Eng 027: 10:30a-12:30p

etiquette and academic


conduct
please be on time, attentive, and respectful of
your classmates and instructors. cell phones
should be silenced, and computers should be
used for course-related work.

By enrolling in this course, each student assumes the


responsibilities of an active participant in UMBCs scholarly
community in which everyones academic work and
behavior are held to the highest standards of honesty.
Cheating, fabrication, plagiarism, and helping others to
commit these acts are all forms of academic dishonesty,
and they are wrong. For a full discussion of academic
integrity, please see your student handbook.

BIOL 303 Learning Goals


About cell biology: 1) to know the structure and
function of cellular components and organelles; 2) to
understand how molecular mechanisms enable cellular
functions; 3) to relate genetic inputs to cellular function
and genetic changes to potential pathologies; 4) to
understand the experimental evidence informing current
models in cell biology.

In preparation for future work (in upper level


courses and beyond): 5) to develop/sharpen skills in
question-asking; 6) to improve mathematical
competency and intuition in biology, as required for
addressing modern biological problems; 7) to augment
problem-solving and critical thinking skills through
problem sets, reading assignments, and discussion; 8)

Successful BIOL 303 students


1)
2)
3)
4)
5)
6)
7)
8)

read (in a timely manner),


pay attention and put away distractions ,
participate in class,
write/take notes/draw,
practice asking questions,
practice answering questions,
Define terms/vocabulary that are unknown
study regularly and effectively (in a way that
works for them),
9) pay the most attention to key ideas,
10)reconcile new ideas with old ones,
11)Practice teaching the material to others
12)have fun (maybe) and learn a lot (certainly)

Cell Bio Study Themes


Structure/Function
LOTS of proteins and their binding partners
There will be quite a bit of vocabulary to keep straight

How changes in conformation alter function


What causes these changes in conformation?
Why is this important?

Predict what the impact would be if this proteins function


were lost
How does a cell biologist test this?

Location within cell


Where does this process occur or this protein localize?
How do proteins get there?
How do they remain there?
How does a cell biologist test this?

a look into a cell


http://www.xvivo.net/animation/the-inner-life-of-the-cell/

by the end of 303, you should be able to explain what is going on in this movie!

What is considered a cell?


The Cell Theory
1) All organisms are composed of
one (or
more) cells
2) The cell is the structural unit of life
3) Cells can arise only by division
from preexisting cells

Properties of cells:
High Complex and Organized

Complexity requires order (organization) and simplicity

Properties of cells:
Capable of Producing
Possess Genetic Program More of Themselves
and Means to Use it

Capable of Self Regulation

Properties of cells:
Acquire and Utilize Energy

Carry Out a Variety of Chemical


Rxns

Properties of cells:
Engage in Mechanical Activities

Properties of cells:
Cells Evolve
All living organisms evolved from a
single, common ancestral cell (3 bill.
yrs ago)

if you were a cell, what


would your biggest
challenges
be?

group (3-5 students) discussion think


deeply about your answers

cells are diverse

mammalian
nerve cell

Paramecium
(protozoa)

Heliobacter
Chlamydomonas
pylori
(algae)
Saccharomyces
(bacteria)
cerevisiea
(fungi)

and specialized for certain lifestyles/jobs

two different classes of cells: prokaryotic vs eukaryotic

share:

ALL CELLS ARE COMPLEX AND WELL-ORDERED


molecular structure of plasma membranes,
DNA
molecular mechanisms for transcription,
translation, metabolic and energy pathways,
breaking down proteins

differ by (some examples):

membrane-bound organelles (like a nucleus)


size
reproduction strategies
copy # of genes per cell, DNA organization

an aside: viruses are not


cells
require CELLS to
replicate, assemble
made up of capsid
(of proteins)
surrounding nucleic
acids, may have a
membrane (stolen)
can cause cell
death or
misregulation
Image from Graham Colm

prokaryotes

image from Ladyofhats

bacteria and archaea


a one-celled organism
no nucleus or
organelles
do have
circular DNA
(nucleoid),
plasma membrane,
ribosomes,
cytoplasm
cell wall

can be different
shapes
reproduce by fission
some carry out
photosynthesis,
nitrogen
fixation
studies
in Esherichia
coli (E. coli) have
revealed much about cell biology

prokaryotes: bacteria and archaea


extremes of Archaea phylogenetic tree of life
grow in harsh
environments
(thermophiles above
90o C; halophiles
require very high salt )
structure similar to
bacteria, but by DNA
(16SrRNA) sequence
they are related to
eukaryotes.

eukaryotes
protists, fungi, plants, and
animals
can be one cell or many cells
bigger than prokaryotes
membrane-bound nucleus
with pores and linear
chromosomes
plasma membrane (plus cell
wall in plants)
many organelles
complex cytoskeleton
wide variety of shapes and
sizes
some sexual reproduction
plants carry out
photosynthesis

plant cell

animal cell

Ladyofhats imag

organism
molecules

multicellular
organ
tissue
cells
organisms

organelles

multicellular organisms are made up


of many different cell types

how are different cells made


different?
genetic programs.
start as fertilized egg, divide and differentiate
become particular cell types that express
different genes (and thereby different
macromolecules) at different times

Central Dogma:
Protein

DNA

RNA

(other important molecules are imported or build by proteins


(enzymes))

Model Organisms (Various Eukaryotes)


E. coli (prokaryote) Saccharomyces c. (fungi/yeast, euk) Arabidopsis t. (plant, euk)

C. elegans (nematode/worm, euk) Drosophila m. (fruitfly, euk)

M. muscullus (mouse, euk)

what we know about cells depends on how we study them

microscopy and its many


variants
biochemistry
genetics
cell culture
model organisms

scanning electron micrograph of human cel

Mycoplasma mycoides JCVIsyn1.0.


Compound microscopy (left)
and
scanning electron

t
r
a
n
s
m
i
s
s

Major Types of Microscopy


Light Microscopy
Bright Field Microscopy
Fluorescence Microscopy
Confocal Microscopy

Electron Microscopy
Scanning EM
Transmission EM

Major Types of Microscopy


Irradiati Max
on
Resoluti
Source
on
Bright
Field
Microscopy
Fluorescen
ce
Microscopy
Confocal
Microscopy
Scanning
Electron
Microscopy
Transmissi
on

Live vs
Fixed
cells?

Example Other
s of
Details
Techniqu
es

magnification versus
resolution

Resolution is a distance (with


units)
-If two objects in your
specimen are farther apart
than the resolution distance,
then they can be viewed as
two, distinct objects.
-If two objects in your
specimen are closer together
than the resolution distance,

what you see depends on how you look

one cell type three


ways

Light Microscopy
live or fixed cells
Stained or unstained
cells
white light or
transmitted light

ways to look at a cell:


1.1) Light microscopy
bright field

phase-contrast

differential
interference
contrast
(DIC/Nomarski)

Bright Field microscopy max resolution: 0.2 microns


(m)=200nm
This resolution depends upon the wavelengths of
visible light used in light microscopy: ~400-700nm

ways to look at a cell:


1.2) fluorescent light
microscopy
Can be used with live or fixed specimens
Same limit of resolution as white light
microscopy

HeLa

HeLa cells
Red-ER
marker
(genetic),
green-a live
mitochondrial
stain,
blue- DNA
dye (Image from
invitrogen.com)

for some cell bio fun:

http://www.invitrogen.com/site/us/en/home/support/Research-Tools/Cell-S
taining-Tool.html

ways to look at a cell:


1.2) fluorescent light
microscopy
Can observe fluorophores (even in
live cells!)
Fluorophores absorb light and release
energy as longer wavelengths in visible
spectrum = fluorescence
uses UV light and filters to separate
different wavelengths of light from
fluorescent molecules

ways to look at a cell:


1.2) fluorescent light
microscopy
uses UV light and
filters to separate
different
wavelengths of
light from
fluorescent
molecules

fluorescent proteins revolutionized cell biology


expressed genetically
and viewed live

Green Fluorescent Protein


(GFP) derived from a jellyfish gene and
optimized for expression in other
organisms

Non toxic (usually) so can see in living


cells
Small, so can link to proteins or domains of
interest and usually the FUSION protein
displays the correct sub-cellular
localization/trafficking
Now in a large variety of colors -->

Nobel Prize in Chemistry, 2008

ways to look at a cell:


1.3) Confocal Microscopy
uses lasers as illumination
can visualize only one focal
plane at at time= optical
sections
Ideal for specimens that are
larger/thicker
multiple focal planes that
give rise to
interference from
points above/
below focal
plane

ways to look at a cell:


1.3) Confocal Microscopy

2.1: scanning electron microscopy


(SEM) reveals specimen topography
specimens are dehydrated (critical point drying) then metal coated
a beam of electrons are scanned across the sample, which they
bounce off; they are collected differentially by a detector

Better resolution with


EM methods than
Light Microscopy
Max Resolution ~5nm
http://med.kuleuven.be/cme-mg/services/EM_Facility/ImageGallery_en.htm

2.2: transmission electron


microscopy (TEM)
yields very high resolution images
best case white-light image from BrightField

TEM image
uses electrons; max resolution in
practice; 0.1nm - 2nm
cells must be fixed (killed!) and
treated with electron dense
material.
one disadvantage potential for
artifacts

advantages/disadvantages
of EM

fantastic magnification
and resolution

lots of processing can alter samples

eukaryotic cells are organized by


organelles, which have different
essential functions

cells are organized and PACKED

outsidecarbohydrate chains
attached to plasma membrane
long strands of DNA
DNA binding proteins
pyruvate dehydrogenase
glycolytic enzymes
Mycoplasma mycoides
bacterial cell
Illustration by David S.
Goodsell,

ribosomes

(so.. be careful how you think about schematics)

nucleus the
cells HQ
1. Chromatin: Genetic
material plus associated
proteins (lectures 4,5)
2. Nucleolus: site of
ribosomal RNA synthesis and
subunit assembly
3. Nucleoplasm: nonnucleolar regions of nucleus
4. Nuclear matrix:
Supportive structure

membranes hold things together


(and keep things apart)
(more in lectures 7-10 & on)
Phospholipid bilayer, associated
proteins,
cholesterol
Selectively allows molecules
in/out of cells and organelles
by diffusion or channels
separates incompatible
reactions, facilitates others

endomembrane system (lectures 16-18)

Series of interconnected, closed,


membrane-bound
vesicles that traffic cellular contents
Nuclear Envelope (2 layer)
Rough Endoplasmic
Reticulum (RER) protein
manufacturing (ribosomes)
smooth ER (SER)
makes
phospholipids,
fatty acids

Endoplasmic reticulum (ER) and Golgi apparatus

Golgi apparatus - protein processor,


sorter
1. Vesicles from rER travel to
and fuse with cis Golgi
2. Proteins traffic through;
modified
3. At trans end, vesicle buds off

Signal sequences target vesicles/proteins to


different locales
(plasma membrane, lysosomes, etc.)

mitochondrion the power


house
Site of
intracellular
energy
generation via
ATP production
during aerobic
respiration
Has its own genome

Enzymes in matrix and on cristae convert glucose


to CO2 + H2O releasing ATP (energy)

chloroplasts convert light to usable


energy

cytosol not just a swimming


pool
20-30% of cellular proteins are in
cytosol
plus fat, carbohydrates -much
interaction!
Site of much cellular metabolism,
ribosomes
the Cytoskeleton (lectures
13-15) is made up of proteins
that give cells structure and
provide highways to move
components

David
David S.
S. Goodsell
Goodsell 1999.
1999.