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Essential Cell Biology

Chapter01. Introducing to cells: Cells are the fundamental units of life



A.Unity and diversity of Cells
1.Cells vary enormously in appearance ,function ,chemical requirements
i.e. Size: a bacterium(m); eggs(mm~cm)
[nerve cell is long to process signals/ paramecium uses cilia to move/ plant stem cell
(outside:pectin,orange/inside:cellulose,red)/ neutrophil engulfing dysfunctional red cells]
2. Living Cells all have a similar Basic Chemistry
What are living things? Reproduce, react, grow
Cells are composed of the same sorts of molecules that participate in the same types of chemical reactions
(Chapter 2).
i.e. gene and DNAs(made of ATCG 4 monomers, called nucleotides)(Chapter 4~8)
(duplicate)DNA(transcript)mRNA(translate/rRNA)amino acids(assemble)proteins
(the sequence (3-dimensional) of 20 types of amino acids determines the behavior of proteins)
Proteins dominate the cell!!
i.e.2. Viruses reproduce by parasitizing. They carry DNA or RNA (encased by protein).
3.All Cells evolved from the same ancestor
*Cells reproduce by duplicating its DNA and in two, and give one to its successor. Corrupted duplication is
called Mutation, which my impose either malicious, neutral, or benign effect on cells (Fewer changes in
the gene pool)
*With sexual reproduction, gene can be mixed and rearranged.(More changes in the gene pool)
Gene changes and selections in millions of generations(adapting environment)Evolution
Evolution explains why cells are so similar in their fundamentals which inherited their genetic instructions
from the same ancestor.
4. Genes provide instructions for a cell
*Compound of genes = genome
i.e. Stem cells(Genome)differentiated cell types
*Each cell is capable of doing all tasks, but depending on its environment and its history, using the
information encoded in its DNA to guide its activities.

B. Cells under the Microscope
1.The invention of the light Microscope led to the discovery of Cells
Cells are too small to be seen with the naked eye. They were not made visible until the seventeenth century,
when the lenses are refined to the point that the microscope was invented. Robert Hooke named cork cell
walls as cell. The emergence of cell biology is by Matthias Schleiden and Theodor Schwann who collected
and documented the cells and tissues.cell theory(present day cells) *Darwin(past cells)
2. Cells, organelles, and even Molecules Can Be seen with Microscope
Using the light microscope (maximum magnify to 200nm)is difficult to see the internal structure of
cells(small and colorless)
fixed samples: stain cells with dye and cut into slice(dead tissues)(and other alternatives: fluorescence
microscopes, confocal microscopes)
*Electron microscope can magnify further but the sample need to be fixeddead tissues
Electron microscopy enables biologists to see the structure up to molecules thick.

C. The prokaryotic cell(bacterium and archaea)
*simplest structure: no organelles, nucleus, cytoskeleton/m size/cell wall/ribosome/DNA or
RNA/spherical, rodlike, or corkscrew-shaped/Reproduces fastlarge numbers,evolve fast
1. In shape and structure, prokaryotes may seem limited, but in terms of chemistry, they live widely within
different chemical requirements.
*photosynthetic bacteriaChloroplasts/aerobic bacteriaMitochondria
2. Bacteria and archaea: archaea live in harsh environment similar to primitive Earth(unfound in daily life)


D. The eukaryotic cell
*bigger and sophiscater than bacteria/ live as single-celled or multi-cellular organism/have a nucleus and
organelles
1. Nucleus: most prominent organelle which contains most of the DNA/enclosed by single-layer envelope
*Chromosomes is dispersed as invisible threads usually; becoming visible when the cell is about to divide.
2. Mitochondria: most conspicuous in cells, distinctive structure / two separate membranes/ contain its
own DNA and reproduce by dividing in two/ derive from bacteria
*generates chemical energy for the cell from oxidation and produce ATPs.
*ps. Because of Mitochondria, eukaryotic cells arent tend to be anaerobic.(compared to bacterium)
3. Chloroplasts: large green organelles/found only on plants and algae/ two membranes and internal
stacks/ contain its own DNA and reproduce by dividing in two/ derive from bacteria
* perform photosynthesis: green under light and greenness fades in dark
* Chloroplasts is a little bigger than Mitochondria
4. Intracellular Compartments: Surrounded by single membranes
*import raw materials and to export manufactured substances and waste products, using endocytosis and
exocytosis to pinch off small vesicles containing proteins and other materials
a. Endoplasmic reticulum (ER) :most cell components, exporting materials are made
Ribosome-coated(on cytosol side) ER (Rough ER) is specialized for protein secretion, and is continuous
with the membrane or nucleus envelopes.
b. Golgi apparatus: receives and modifies (routing) the molecules made in ERs/ inconspicuous under
microscopes
c.Lysosomes: small, irregularly shaped organelles using to break down unwanted molecules for recycling
or excretion
d.Peroxisomes: environment for reactions in which hydrogen peroxide is generated and degraded
*multiple functions in different cells
5. Cytosol: cytoplasm that is not including organelles, and is the largest single compartment in cell
*contains molecules that it behaves like gel/protein synthesis
6. Cytoskeleton: long filaments of protein which radiate out from a central site to the membrane
a. actin filaments: thinnest/exist in all cells but more inside muscle cells, which generates contractile forces
b. microtubules: thickest/hollow/when dividing cells they gain into array that pulls the chromosomes aside
c. intermediate filaments: strengthen the cell mechanically
7. The cell interior is in constant motion
8. History
The eukaryotic, bacterial, and Achaean lineages diverged from one another very early. Then eukaryotes
acquired mitochondria (before plants, animals, and fungi divided); later still, a subset of eukaryotes
acquired chloroplasts(plants only).
*Eukaryotic ancestor: protozoans: behave diversely/
i.e. Didinium: swims at high speed with cilia/ 10 times of size than human cells/devour other cells

E. Model organisms
*Certain organisms are easier to study in the laboratory: reproduce rapidly/convenient for genetic
manipulations/ multicellular but transparent..
1.E.coli: Molecular Biologists: grown easily/single, circular DNA
2.S.cerevisiae(yeast):Study on eukaryotes: small, immobile ,single-celled fungus/genetic analysis and
division cycle/ interchangeably in with human cells
3.Arabidopsis: Study on multicellular organisms and plants: easy to grow and reproduce/ close evolutionary
relationshipstudy on gene gain knowledge of evolution of plants
4.Animal Studies:
a. Drosophila melanogaster(fruit fly): foundations of classical genetics/high resemblance with human
genome/knowledge about animals growth
b. Caenorhabditis elegans: high resemblance with human genome/ regularity
c. zebrafish: transparent around its early birth
d. mice: mammalian genetics, development, immunology, and cell biology/ testament
e. human
5.Gene engineering: by comparing genome, we know the differencehomologous
* if two genes have similar sequencesboth genes descended from common ancestor
* most streamlined genome is a bacterium called Carsonella ruddii
* Most organisms possess significantly more than the functional genes
*Genome size=the DNA quantity in a genome, which differed among species.
Essential Cell Biology
Chapter02. Chemical Components of Cells: pastanimus(vital force); noworganic chemistry+ watery
requirement+ complex+ polymeric molecular

A.Chemical Bonds
1. Atoms: (Skip)
2. Outermost electrons: determines how atoms act (Skip)
* This exchange by sharing electrons between two atom generates the two types of chemical bonds
a.ionic bond: donated from one atom to another
b.covalent bond: share a pair of electrons(polar covalent bonds allow molecules to interact through
electrical forces as ionic bonds)
c.hydrogen bond: puts water and proteins together
* The distribution of elements: in earthO, Si, Al / in bodyC, H, O, N(over 99%)/IA,IIA,P,S(1%)
3. Acid/Base: hydrogen tend to give up its electronH+this proton can react with water molecule,
generating a hydronium ion (H3O+)(the reaction is easy to reverse)
*H3O
+
= 10
7
M(in pure water) *pH scale(Skip) *weak acid is not tend to dissociate
*buffer: weak acid/base tend to receive back their electron

C.Molecules in Cells
1. Cell is Formed from Carbon Compounds(organic chem)
2. Four major Families: Sugars, fatty acids, amino acids, and nucleotides
* Organic molecules are synthesized and broken down into same set of compounds.
3. Sugars are energy sources/ to compose cellulose, glycogen, chitin, glycolipids(decorating membranes)
and starch
* (CH
2
O)
n
: carbohydrates
*Glucose (formula C
6
H
12
O
6
)
a. isomer: d-form (mannose) and the l-form (galactose)
b.strcture: i.e. chair configuration

* Two monosaccharaides linked together make a disaccharide (condensation reactions/hydrolysis)
oligo-poly
4. Fatty acids & lipid: membrane/ food reserve(triacylglycerol)( in cytoplasm in form of droplets)
*hydrocarbon chain, hydrophobic, not reactive + carboxyl(COOH) group, which behaves as an
acid(dissociates), hydrophilic, and reactiveamphipathic
*Saturated fat: straight, no double bonds, i.e.(Stearic acid, Palmitic acid, animal, hard margarine)
Unsaturated fat: kink, i.e.(oleic acid, plants, soft margarine)
*phospholipid:
a. two fatty acid chains, the third site on the glycerol is linked to a hydrophilic phosphate group
amphipathicmembrane
5. amino acids(R+H+COOH+NH
2
): proteins
*ionized amino acid: COO
-
/NH
3
+

*link between two amino acids is called a peptide bond(amino+amino=2+H
2
O)
(condensation reaction): NH
2
=N-terminus; COOH= C-terminus
*Twenty types of amino acids are commonly found in proteins(selection)
*optical isomers(only L-form can be found in proteins)
*for 20 amino types, carry a charge/ polar/ hydrophobic/chemical versatilefunction of proteins
6. Nucleotides: Nucleoside (nitrogen ring(acid) + 5-carbon sugar) + Phosphate groups(base)
*ionized nucleotides: PO
-
/NH
3
+

*act as biological information(nucleotidesribonucleotidesRNA)
pyrimidine(six-membered ring): C/T/U ; guanine(five-membered ring + six-membered ring): A/G
(nucleotide is named after the base it contains)
*DNA(de(2-c)oxyribose): stablelong-term storage(A-T C-G)
/ RNA(ribose): transient carrier(base pairing)(A-U C-G)
*short-term energy carrier: ATP (phosphoanhydride bonds = energy): ATPADP+Pi(power)

D. Macromolecules: constructed by linking small organic molecules (called monomers, or subunits)
*in body: water 70% chemicals 30%(proteins (15%)/RNA (6%)/phospholipids (2%)/DNA
(1%)/polysaccharides (2%)/others)
*i.e. enzyme(proteins): ribulose bisphosphate carboxylase in chloroplasts, converts CO
2
to sugars/tubulin
self-assembles/Histone proteins/molecular motors
1.Sequence
*polymer grows in common: condensation reaction(with catalysis)
*sequence of subunits determines the macromolecules traits(except polysaccharides)math
2.Bonds
a. electrostatic attractions(weak in water): bond and guide enzymes
b. hydrogen bonds: unique properties of water/hold two strands of the DNA helix(unpack by enzyme
because very weak)
c. van der waals attractions & London disperse force: attraction between large molecules with
complementary shapes
d. hydrophobic interaction: i.e. membranes
3. Macromolecular Complex(function as enzymes)
*noncovalent bonds are individually very weak, they can add up to as strong as bonds
*forming intricate machines i.e. ribosome is composed of about 90 macromolecules
Essential Cell Biology
Chapter03. Energy, Catalysis and Biosynthesis
* living things: they create and maintain order(S<0)(consuming energy)cell chemical reaction
*metabolism: molecular A(enzyme/catalysis)molecular B
(catabolism=breaking down/anabolism=synthesis)

A.Use of energy: to maintain and actually generate order for living things
1. Biological order is made by the release of heat energy
* the second law of thermodynamics: universe tend to become disordered(S>0) / first law of
thermodynamics: energy can be converted but cannot be created or destroyed.
*entropy(skip)
*surrounding+cell system do not defy the 2
nd
law(environment entropy>cell entropy)
2. Energy source: Photosynthetic organisms use sunlight to synthesize organic molecules
*no matter if it is a consumer or producer, energy came from sun
*Sun(photosynthesis(anabolism) by plants, algae, and some bacteria)
chemicals+heat(catabolism)energy+heat
[photosynthesis] light energy + CO
2
+ H
2
O sugars + O
2
+ heat energy
1
st
stage: energy from sunlight is stored in chemical bond/O
2
derived by splitting of water by light
2
nd
stage: energy is released/ sugars manufactured from CO
2
and H
2
O
3. oxidation(respiration): Sugars + O
2
H
2
O + CO
2
+power
*complementary with photosynthesis
* Carbon utilization therefore forms a huge cycle in biosphere(nitrogen, phosphorus, and sulfur)

4. Oxidation and reduction involve electron Transfers
Oxidation: add O/ add e
-
/ remove H
Reduction: remove O/ remove e
-
/ add H

B. Free energy and catalysis
1.Enzymes lower the energy barriers that prevent chemical reactions from occurring
Enzymes/Catalyst + Substrates: allow larger proportion of the random scatters/ lower activation energy
*enzymes: making reactions happen when temp is low; do not change after reaction; corresponds to only
one particular reaction(active site substrates selection/ guide to certain path);do not affectG, therefore
equilibrium do not move
2. The free-energy Change: determine if reactions will occur or not
*Free energy(disorderliness)energy that can be harnessed to do work or drive chemical reactions
G<0: disorderliness gain / spontaneously occurs
G>0: orderliness gain / couple with anotherG<0 reaction(entireG<0)
3. The Concentration of reactants influences the free-energy Change and a reactions direction
*AB: when [B] is larger than [A], the reaction tends to forward A
4.Standard free-energy change(G): reactants are fixed to 1 M
*i.e. YX: G=G+RTln([X]/[Y])
4. Chemical equilibrium
Chemical reactions will proceed until they reach a state of equilibrium(G=0)
Many reactions are kept in disequilibrium because the products are consumed in subsequent reaction.
5. equilibrium constant K=[X]/[Y]
*when equilibrium(37C): G= 0.616ln(K)=-1.42log(K)product accumulates when energy-friendly
6.Complex reaction(A + B AB) K = [AB]/[A][B]
7.Equilibrium constant denotation: strength of molecular interactions(ex.A + B AB)
* A + B AB, k
1
(associate power); AB A + B, k
2
(dissociate power):
K=(k
1
/k
2
)=bond strength(K big and AB dissociates, bond weak)
8. Addability in Free energy
XYZ: G(X-Z)=G(X-Y)+G(Y-Z)
*therefore, conversion efficiency can be ameliorate(with calculation)
9. Rapid diffusion
* random walk model(diffusion)(1m/sec(the bigger the slower))/ faster with energy-consuming ways
The scattering of substrates in comparison to water(55 M) is very rare + enzyme cope with 50000 times
collision per secA random encounter of substrateenzymesubstrate complex(bond identifying)
10. V
max
and K
M
measure enzyme performance
* V
max
: maximum rate of substrate the enzyme can tantalize in a period
K
M
(Michaelis constant): substrate concentration when 0.5V
max