Chapter 1

Introduction of the Study of Cell and Molecular Biology

8/27/15
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Cell Biology
based on the premise that studying the parts of the whole can explain the whole
Early Microscopes & the Discovery of Cells
The discovery of cells followed the invention of the microscope by Robert Hook, and was then
refined by Anton Leewenhoek
Cell theory began in the mid 1800s by Schleiden, Schwann, and Virchow
all organisms are composed of one or more cell
cell is the structural unit of life
cells arise from pre-existing cells by division (mitosis or meiosis)
Culturing (Human) Cells
Life is the most basic property of cells
Cells can grow and reproduce in culture for extended periods.
HeLa cells are the first human cells for extended cell culturing
Hela cells are cultured tumor cells isolated from a cancer patient (Henrietta Lacks) by George
Gey in 1951
cultured cells are an essential tool for cell biologists
9 Basic Properties of Cells
Complex and organized
Have a genetic program (DNA) and means to use it
Capable of replicating/reproducing
caution: on cellular level yes, but there are exceptions if you havent reproduced
Acquire and utilize energy (metabolism, mostly of glucose)
Carry out a variety of chemical reactions (biochem)
Engage in mechanical activities: do stuff
respond to stimuli
Capable of self-regulation (homeostasis)
Evolve
Cells are Highly Complex and Organized
cellular processes are highly regulated
cells from different species share similar structure, composition, and metabolic functions that
have been conserved throughout evolution
Cells Possess a Genetic PRogram and the Means to Use It
DNA
genes encode information to build each cell and the organism
genes encode information for cellular reproduction, activity, and structure
NEW: epigenetics
additional information to DNA that dont change the sequence
changes from prolonged starvation can be inheritable and changes flags in the DNA for which
genes to activate for up to 3-5 genes
NEW: Project ENCODE
all that junk DNA isnt junk

ii.

what the noncoding DNA does, a lot of it is control sequences that give us additional control
mechanisms
7. Cells are Capable of Producing More of Themselves
a. cells reproduce (mitosis) and each daughter cells receives a complete set of genetic instructions.
This process is used to replicate individual cells
i.
control and regulate when this occurs
b. This egg cell is generated via meiosis and is used for sexual reproduction of an organism
i.
polar body: egg that is supposed to die but instead has a polar body,
ii.
female has to give all cell materials for the cell to use to reproduce
8. Cells Acquire and Utilize Energy
a. photosynthesis provides fuel for all living organisms
b. Animal cells derive energy from the products of photosynthesis, mainly in the form of glucose
c. Cell can convert glucose into ATP--a substance with readily available energy
d. every living thing can burn glucose in glycolysis
9. Cells Carry Out a Variety of Chemical RXNs
a. Photosynthesis
b. Glycolysis
c. Krebs
d. Carb metabolism and glycation
i.
modify surfaces of proteins and cells
ii.
glycation: higher sugar intake the more sugar stays on surface of proteins and speeds up break
down of the body
e. Proteins, enzymes, and facial peels
f. Lipids (fats, cholesterol, Vitamin D)
i.
critical in diets
g. RNA
h. Cell-Cell communications
i. Immune responses and defense
j. Toxin production
k. and MORE
10. Cells Engage in Mechanical Activities
a. intracellular transport: cytoskeleton
b. Muscle contraction
c. Amoeboid movement
11. Cells are Able to Respond to Stimuli
a. cells migrate away from predators
i.
track light
b. many can follow nutrient concentration gradients
i.
follow path of glucose
c. most respond to light
i.
light shining on face reduces wrinkles and sunburn
ii.
UV causes inflammatory response then yellow light turns that response off
iii.
cells goes around obstacle to get to light source
d. receptors on cell surface to interact with environment
i.
whether they should replicate to fill wholes
e. simple cell contact (confluent)

i.
ii.

when they touch they will stop growing

confluent: all cells are packed together with no gaps
12. Cells are Capable of Self-Regulation
a. CANCER
b. Cells must maintain relatively constant internal environments despite a fluctuating outside world
i.
too much sodium can kill your cells
c. ion concentrations
d. membrane potential
e. must be able to sense when to divide (mitosis)
f. detecting DNA damage
i.
needs to fix it or induce apoptosis if too bad, cancer cells dont do this
g. embryonic development
i.
when good time to start making the parts of the body during pregnancy
13. Cells Evolve
a. From LUCA (last universal common ancestor) to all the types of cells we see today
b. Bacteria are NOT primitive! They are just as evolved as we are!
i.
see antibiotic come in they can send it back out, resistance strains
c. Eukaryotic cells have changed over time as well
i.
new organelles
d. Endosymbiosis led to more complex forms of cells with more internal organelles
e. lateral gene transfer may have been crucial for early prokaryotic evolution
9/1/15
14. Bacterium
a. Cells keep DNA in nucleus to keep it away from reactions happening in the cell that can break
down the DNA
b. in prokaryotes it is just kept to the side
c. cytoplasm= proteins made, break down glucose, build macromolecues
d. bacteria flagellum, pilus, ribosome, DNA of nucleoid, cell wall, plasma membrane, capsule,
cytoplasm
15. Plant Cell
a. membrane bound organelles (phospholipid bilayers)
b. main difference: cell wall, chloroplasts, central vacuole (storage, fluid filled, junk drawer)
16. Animal Cell
a. same as plants minus cell wall, chloroplasts, central vacuole!
b. plant cells can do anything that an animal cell
17. Eukaryotic cell structure: epithelial cell from the male rat reproductive tract
a. muscle cells= lots of mitochondria and maybe even multiple nucleus,
b. skin= fewer mitochondria and only 1 nucleus
c. things vary among tissues, different tissues = different functions
d. nucleolus = where ribosomes are made
e. finger like projections, get more surface area to volume because more packed
i.
help grab nutrients, more surface area more nutrients it can grab
18. Cytoplasm: A crowded compartment in a eukaryotic cell
a. actin filaments in red, darker blue = cell wall, cyan = ribosomes
19. Cellular reproduction: Eukaryotes and prokaryotes

a. cell division in eukaryotes: DNA and microtubes and two daughter cells
b. bacterial conjugation: sharing of DNA through the F pilus, exchange of DNA through sharing
i.
pilus = DNA unspools and snakes its way through the tube then curls back up and not it has new
genetics (this is lateral gene transfer)
20. Flagella: difference between prokaryotes and eukaryotes
a. prokaryotes (bacteria): multiple flagella attached for locomotion
b. eukaryotes: sperm spin around two structures, if mutated or broken, flagella wont work and
sperm wont be able to swim
21. Types of Prokaryotic Cells
a. domain
b. domain
c. includes smallest known cells - mycoplasma
d. includes cyanobacteria - some photosynthetic bacteria
i.
cyanobacteria gave rise to green plants and oxygen-rich atmosphere
ii.
some bacteria capable of nitrogen fixation
iii.
green polar bears!
22. Prokaryotic Diversity
a. prokaryotes are identified and classified on the basis of specific DNA sequences
b. recent evidence indicates that prokaryotes are more diverse and numerous than previous thought
c. there are more bacteria in and on your body than there are human cells...we are walking
colonies!!
d. most bacteria is not pathogenic, just take up space, and prevent dangerous bacteria from housing
space, large portion of our world is carbon in bacteria
23. Experimental Pathways: The origin of Eukaryotic Cells
a. Prokaryotic cells arose first and gave rise to eukaryotic cells
b. Endosymbiont Theory: organelles in eukaryotic cells (mitochondria and chloroplasts) evolved
from smaller prokaryotic cells
24. Why do we think this?
a. Chloroplasts and mitochondria have a double membrane layer suggesting that they invaded a
host cell
b. They have their own DNA that is distinct from that of the host
i.
chloroplast DNA is more closely related to cyanobacteria
ii.
mitochondrial DNA resembles proteobacteria
c. They replicate independently of the host
i.
good thing because your muscles get more mitochondria when you do aerobic workouts
ii.
training for marathon, mitochondria replicates when use aerobic respiration, dont hit muscle
fatigue as early, and will die off if you stop exercising, constantly recycled
25. Nucleotide Sequence Similarities
a. between representative member of the Three Primary Kingdoms
b. ribosome rRNA sequences in different groups, DNA in eukaryotes was 29-36% similar, but other
RNAs nothing came close to being similar to get the idea of 3 domains of life.
26. 3 Domains of Life
a. Based on nucleotide sequences of single genes, Woese proposed three major cell lineages
i.
bacteria: Gram positive/negative and cyanobacteria
ii.
Archaea: halophiles, thermophiles, methanogens, acidophiles

iii.

Eukarya: plants, animals, fungi, protists

27. Origin of the Nucleus
a. DNA suggests that nuclear DNA may be more related to Archaea, while organelle DNA may be
more Eubacterial. However, some bleed-through is noted: so how do genes get from organelle
to nucleus?
b. based on whole genomes, many organisms appear to be genetic mosaics
i.
lateral gene transfer (LGT) results in organism with both parental DNA and DNA from other
organism in the environment
ii.
bacteria and Eukarya show evidence of LGT in their genomes
c. DIAGRAM: gene for antibiotic resistance and put in chloroplast but gene has to be in the
nucleus, gene has to jump from chloroplast into nucleus, and this happened in 16/250,000. Not
sure how but cells were resistant. Happens with our mitochondrial genes as well
28. Primitive Cell Bits & Their Relationships
a. early studies on RNA, enzymes, ribosomes show that prokaryotic and eukaryotic cells are
related...BUT
b. informational genes (transcription and translation) seem to be more closely related to Archaea,
while
i.
mix of archaea and eubacteria cell
c. operational genes (enzymes, amino acid production, etc.) seem to be more closely related to
Eubacteria. What give?
i.
maybe it really is bot: maybe eukaryotes are a fusion of a prokaryotic and eukaryotic cell
lineage! Some work supports this and suggest that one type of prokaryotic cell got engulfed by
another--and this relationship became mutualistic over time. This is the endosymbiosis idea--and
it applies to our DNA as well as mitochondria & chloroplasts
29. Types of Eukaryotic Cells: Cell Specialization
a. Unicellular eukaryotes are complex single-celld organism.
b. Vorticells have a contractile
c. multicellular
i.
differentiation
1. red cells dont have a nucleus, bone cells living in little pockets, muscle cells have more
mitochondria, actin, myosin, compared to your fat cells.
ii.
numbers
iii.
despite
1. plasma membrane, cytoplasm, ribosomes, DNA
30. Basic Properties of Cells: Model Organism
a. E. Coli- generic bacteria, grows in almost anything, most strains arent pathogenic, have a certain
smell.
i.
has nucleoid region
b. Yeast: smells like beer or baking bread.
c. Mustard plant
d. nematode plants
e. fruit fly
f. mouse
g. full genetic information is available for these species
31. The Human Perspective: Cell Replacement Theory

a. Stem cells are undifferentiated cells capable of self-renewal and differentiation

i.
adult stem cells can be used to replace damaged or diseased adult tissue
ii.
hematopoietic stem cells can produce blood cells in bone marrow
iii.
neural stem cells may be sued to treat neurodegenerative disorders
b. Embryonic stem (ES) cells have even greater potential for differentiation (pluripotent) than adult
stem cells
i.
ES cells must be differentiated in vitro
ii.
The use of ES cells involved ethical considerations
32. Using Adult Somatic Cells to generate Embryonic Stem Cells
a. A procedure to obtaining differentiated cells for use in cell replacement theory
i.
acquire both somatic cell and egg
ii.
remove nucleus from egg
iii.
transfer nucleus from somatic cell to egg
iv. Grow ES cells into blastocyst (NOT easy; low rate of success without other techniques to
stimulate division
1. if development continues, clones develop!
33. Induced Pluripotent (iPS) cells has been demonstrated in culture
a. involves reprogramming a fully differentiated cell into a pluripotent stem cell
b. these cells have been used to correct certain disease conditions in experimental animals
c. Studies to reveal the mechanisms of iPS could have significant medical applications
34. The Sizes of Cells and their components
a. cells are commonly measured in units of micrometers (1 um=10^-6 meters) and nanometers
(1nm = 10^-9 meters)
b. cell size is limited by
i.
the volume of cytoplasm that can be supported by the genes in the nucleus
ii.
by the volume of cytoplasm that can be supported by exchange of nutrients
iii.
the distance over which substances can efficiently travel through the cytoplasm via diffusion
35. Synthetic Biology
a. is a field oriented to create a living cell in the laboratory
b. develop novel life forms, beginning with existing organisms
c. applications to medicine, industry, or environment
d. good prospect after replacing the genome of one bacterium with that of closely related species
e. BioBricks: small building blocks to build custom genes
36. First Synthetic Life Form: Synthia
a. Mycoplasma mycoides JCVI-syn
b. synthetic genome based heavily on bacterial that causes mastitis in goats (udder infection)
c. 1 billion bp code assemlbed by computer and synthesized in lab
d. DNA was microinjected into a cell without DNA and started growing and dividing successfully
37. Viruses are NOT CELLS
a. viruses are pathogens and intracellular obligate parasites
b. a virion is a virus particle outside the host cell
c. Viral structure
i.
genetic material and can be single stranded DNA or RNA
ii.
protein capsid surrounds the genetic material
iii.
a lipid envelope may surround the capsid in some viruses
d. Viroids are pathogens, consisting of small, naked RNA molecule

e. Viroids cause disease by interfering with gene expression in host cells

38. Viruses: Structural Diversity
a. virus and host
b. viruses have surface proteins that bind to the surface of the host cell (often cia come receptor on
the host cell surface)
c. Viral specificity for a vertain host is determined by the virus surface proteins (think lock and
key)
39. Viruses
a. Viral infection types:
i.
Lytic infection: the virus redirects the host into making more virus particles, the host cell lyses
and releases the viruses.
ii.
Integration: the virus integrates its DNA (called a provirus) into the host cells chromosomes.
1. Infected host may behave normally until external stimulus activates provirus, leading to lysis.
2. Host may give rise to viral progeny by budding.
3. Host may become malignant
40. So what are Viruses?
a. Escaped genes hypothesis: theyre selfish genetic elements that replicate within a host genome;
at some point, they assimilated enough proteins to allow independent existence outside hosts
b. Reduction hypothesis: originated in parasitic organisms; over time, genes were lost as parasite
became more dependent on host
c. Relics of RNA world hypothesis: may be remnants of the original RNA world and may represent
pre-cellular life (before LUCA)