tigp/ymu functions of the molecules and organelles in the cell ueng-cheng yang sept. 13, 2005
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TIGP/YMU
Functions of the molecules and organelles in the cell
Ueng-Cheng Yang
Sept. 13, 2005
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Cells: the basic unit of life
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Prokaryotic & eukaryotic cells
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Feeling of scales
Cell
Size
rangeMost Cells
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Why are cells small?
• Cells must exchange gases & other molecules with environment…
• Nutrients in, Wastes out
• As size increases, the rate of diffusion exchange slows down. For example, hypoxia is observed when the diameter of tumor is larger than 2 mm
• This is due to the ratio of surface area to volume
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Diffusion
• Concentration gradient
• It takes days to diffuse across a cell
• It can prevent colloidal particle from sedimenting (Tyndall effect).
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Organelles are functional units inside a cell
Cytoplasm cytosol organelles
Nucleus nucleolar nuclearplasm
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Sizes of cells and organelles
Bacteria 1 –5 m
Animal and Plant cells 10-50 m
Nucleus 5-6 m Mitochondria 2-3 m Chloroplasts 5-10 m
Nerve cells > 1 m
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Why is it necessary to have compartments?
• Increase efficiency, e.g. mitochondria
• Segregate molecules, e.g. lysosome
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Mitochondria
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Lysosome & peroxisome
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Compartments Are Formed by Lipids
• Membranes are phospholipids• Lipids are not soluble in water• Membranes can prevent molecules
from freely passing through the boundaries
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What Are Lipids?
• Triacyl glycerides
• Phospholipids
• Cholesterol
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Triacyl Glycerides
OR1 -C-O-CH2
OR2 -C-O-CH OR3 -C-O-CH2
fatty acid part glycerol part
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Ester and Phosphoester
R'-OH +
alcohol
OR-C OH
acid
OR-C O-R' H ester
R'-OH +
alcohol
OHO-P-OH OH
phosphoric acid
OHO-P-O-R' OH
phospho- ester
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Phospholipids Are Surfactants
O Lecithine CH3 -(CH2 )n - C-O-CH2 n ~ 16-20
O n' ~ 16-20 CH3 -(CH2 )n' -C-O-CH
O + CH3 Hydrophobic Tail CH2 -O-P-O-CH2 -CH2 -N-CH3
O- CH3
Hydrophilic Head
+
-+
-
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Surfactants Help to StabilizeThe Suspension
Soap removes oil Micelles
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Lipid Bilayer and Membrane
Hydrophobic Integral Peripheral tails protein protein Cholesterol
Hyrodphilic Polysaccharides head
HO
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How Can A Hydrophilic Molecule Pass through A Hydrophobic
Membrane?
Crossing the junction of two cells
Get into the cell from environment
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Endoplasmic reticulum (ER)
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Golgi apparatus
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Exocytosis And Endocytosis
exocytosis endocytosis
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Types of Endocytosis
• Phagocytosis ("cell eating solid particle")
• Pinocytosis ("cell drinking dissolved material")
• Receptor-mediated endocytosis ("cell taking up specific proteins")
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Receptor-Mediated Endocytosis And Capping
binding clustering capping
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Membrane Fluidity
Human + Mouse Fused
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How to Maintain the Dynamic Membranes?
• The final equilibrium of a suspension is phase separation.
• Mechanical mixing or something else is required for maintaining the micelles.
• Growing pains: How do you get new material all the time?
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Steady State
Input Output
Water levelappears constant
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What are the macroscopic differences of different
types of cells?
• Adipose tissue cells
• Capillary cells
• Muscle cells
• Nerve cells
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Cytoskeleton
microtubules: - tubulin - 25 nm (d)intermed. filaments: - vimentin or keratin - 10 nm (d)microfilament: - actin - 7 nm (d)
anti-actin anti-vimentin
anti-tubulin anti-keratin
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Orders in A Cell
• Compartments and localization
• Cytoskeleton and polarity
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The Importance of Polarity
It's easier to propagate asymmetry than to create asymmetry.
Cell division Budding yeast Frog oocyte
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The Origin of Polarity/ Asymmetry
WaterCHCl3
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The Second Law of Thermodynamics
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Orders Can Be Maintained by Energy Input
Water can flow upwards if ...
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How can a cell maintain all the structures?
Energy can compensate the entropy loss G = H - T S
=> Metabolism is a life phenomenon
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Discussion
Is phage or virus a life?
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Genome Structure of the SARS virus(Marra et al., Rota et al., Ruan et al., 2003)
The RNA genome contains about 30k bps, having five major open reading frames (ORFs): ORF1a and ORF1b: replicase polyprotein (13149, 7887 bps) S: spike glycoprotein (3768 bps) E: small envelope protein (231 bps) M: membrane glycoproteins (666 bps) N: nucleocapsid protein (1269 bps)and 7 unknown ORF’s X’s (total 2595 bps)
YM-Bioinfo
TIGP/YMUYM-Bioinfo
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What Is Life?
• Growth and development
• Metabolism
• Homeostasis
• Movement
• Response to stimuli
• Reproduction
• Evolution and adaptation
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Amino Acids Are the Structural Units of Proteins
NH2
H-C-COOH RAmino Acid
NH2
H-C-COO-
R (-)
NH3+
H-C-COOH R (+)
NH3+
H-C-COO-
R no charge
OH- OH-
(http://www.ym.edu.tw/bio/bch/aa.htm)
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Types of amino acids
• Charged– Positively charged: 3– Negatively charged: 2
• Hydrophilic, uncharged: 7
• Hydrophobic: 8Try to memorize it, so their properties become a “reflex” for you.
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Lysine (K) and arginine (R)
Basic amino acids
(positively charged at pH 7)
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Histidine (H)
Frequently used in general acid and base catalysis
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Aspartate (D) and glutamate (E)
Derived from intermediate metabolites
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OAA => Asp; -KG => Glu
OAA citrate
isocitrate
-ketoglutarate
succinyl CoAsuccinate
malate
fumarate
-2H-CO2
-2H-CO2
CoA
-2H
-2H
CoA + GTP
acetyl CoA
release CO2
reforming the carrier
H2O
TCA cycle
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What’s the difference among …
-ic acid: e.g. acetic acid
-tate: e.g. acetate
-yl: e.g. acetyl
OR-C-OH
OR-C-O-
OR-C-
For acetic acid derivatives, R=CH3
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Hydrophilic and uncharged
gly, cys, ser, thr, tyr, asn, gln
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glycine
The only amino acid that does not have stereochemistry
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alanine
Pyruvate => alaThis is a hydrophobic amino acid. It was discussed here for understanding the structur
e of Ser and Cys.
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serine and cysteine
Oxygen and sulfur are in the same column in periodic table
=> Should have similar properties
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Periodic table
* Picture made from screenshot of http://www.shef.ac.uk/~chem/web-elements/
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threonine and tyrosine
Ser, thr, and tyr have hydroxyl group, so they can be phosphorylated
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Phosphorylation cascade and signal amplification
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glutamine and asparagine
Gln helps to transport NH3 to kidney
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Amine and Amide
HR-N Hprimary amine
R'R-N Hsecondary amine
R'R-N R"tertiary amine
HR-N + H
amine
OR-C OH
acid
OR-C N-R H amide
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Hydrophobic amino acids
Ala + val, leu, ile, met, phe, trp, pro
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Valine (V), leucine (L), and isoleucine (I)
hydrophobic and branched
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Methionine (M)
S-adenosyl methionine is a methyl group donor in the cell
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Phenylalanine (F) and tryptophan (W)
A well known genetic disease: phenylketonuria
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Proline (P)
The only imino acid in 20 amino acids. It distort the normal peptide geometry.
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How to Use Mage?
Demonstration
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Schiff’s base
A way to form C-N bond
O OHR-C-H + H2N-R’ R-C-N-R’ R-C=N-R’ + H2O H
= --
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Types of amino acids
• Charged– Positively charged: Lys, Arg, His– Negatively charged: Asp, Glu
• Hydrophilic: Gly, Ser, Cys, Thr, Tyr, Asn, Gln
• Hydrophobic: Ala, Val, Leu, Ile, Met, Pro, Phe, Trp
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