Transcript 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
Most
Cells
Size
range
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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
Mitochondria
Chloroplasts
5-6 m
2-3 m
5-10 m
Nerve cells
>1m
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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
O
R1 -C-O-CH2
O
R2 -C-O-CH
O
R3 -C-O-CH2
fatty acid part glycerol part
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Ester and Phosphoester
O
R'-OH
+
R-C
R-C
OH
alcohol
R'-OH
alcohol
O
acid
O
+ HO-P-OH
OH
phosphoric
acid
O-R'
H
ester
O
HO-P-O-R'
OH
phosphoester
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Phospholipids Are Surfactants
O
CH3 -(CH2 )n - C-O-CH2
O
CH3 -(CH2 )n' -C-O-CH
Hydrophobic Tail
+
-
Lecithine
n ~ 16-20
n' ~ 16-20
O
+ CH3
CH2 -O-P-O-CH2 -CH2 -N-CH3
O
CH3
+
Hydrophilic Head
-
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Surfactants Help to Stabilize
The Suspension
Soap removes oil
Micelles
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Lipid Bilayer and Membrane
Hyrodphilic
head
Polysaccharides
Hydrophobic Integral Peripheral
tails
protein protein
HO
Cholesterol
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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 level
appears 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
anti-actin
microtubules:
- tubulin
- 25 nm (d)
intermed. filaments:
- vimentin or
keratin
anti-tubulin
- 10 nm (d)
microfilament:
- actin
- 7 nm (d)
anti-vimentin
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
Water
CHCl3
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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)
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YM-Bioinfo
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YM-Bioinfo
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
R
Amino Acid
(http://www.ym.edu.tw/bio/bch/aa.htm)
NH3+
NH2
NH3+
OH
- OH
H-C-COOH
H-C-COO
H-C-COO
R
R
R
(+)
(-)
no charge
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Types of amino acids
• Charged
– Positively charged: 3
– Negatively charged: 2
• Hydrophilic,
uncharged: 7
• Hydrophobic: 8
Try 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; a-KG => Glu
acetyl CoA
OAA
citrate
-2H
release CO2
isocitrate
TCA cycle
-2H
-CO2
H2O
reforming
a-ketoglutarate
fumarate the carrier
CoA
-2H
succinate succinyl CoA
-2H
-CO2
CoA + GTP
malate
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What’s the difference among …
O
R-C-OH
-ic acid: e.g. acetic acid
O
R-C-O-
-tate: e.g. acetate
O
R-C-
-yl: e.g. acetyl
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 => ala
This is a hydrophobic amino acid. It was
discussed here for understanding the
structure 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
H
R'
R'
R-N
R-N
R-N
H
primary
amine
H
secondary
amine
R"
tertiary
amine
H
R-N
O
+
H
amine
R-C
O
R-C
OH
acid
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
OH
R-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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