Functions of the molecules and organelles in the cell : Functions of the molecules and organelles in the cell Ueng-Cheng Yang
Sept. 13, 2005
Slide2 : Cells: the basic unit of life
Slide3 : Prokaryotic & eukaryotic cells
Slide4 : Feeling of scales Cell
Size
range Most Cells
Slide5 : 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
Diffusion : Diffusion Concentration gradient
It takes days to diffuse across a cell
It can prevent colloidal particle from sedimenting (Tyndall effect).
Organelles are functional units inside a cell : Organelles are functional units inside a cell Cytoplasm
cytosol
organelles Nucleus
nucleolar
nuclearplasm
Slide8 : 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
Why is it necessary to have compartments? : Why is it necessary to have compartments? Increase efficiency, e.g. mitochondria
Segregate molecules, e.g. lysosome
Mitochondria : Mitochondria
Lysosome & peroxisome : Lysosome & peroxisome
Compartments Are Formed by Lipids : Compartments Are Formed by Lipids Membranes are phospholipids
Lipids are not soluble in water
Membranes can prevent molecules from freely passing through the boundaries
What Are Lipids? : What Are Lipids? Triacyl glycerides
Phospholipids
Cholesterol
Triacyl Glycerides : Triacyl Glycerides
Ester and Phosphoester : Ester and Phosphoester
Phospholipids Are Surfactants : Phospholipids Are Surfactants
Surfactants Help to Stabilize The Suspension : Surfactants Help to Stabilize The Suspension
Lipid Bilayer and Membrane : Lipid Bilayer and Membrane
How Can A Hydrophilic Molecule Pass through A Hydrophobic Membrane? : How Can A Hydrophilic Molecule Pass through A Hydrophobic Membrane? Crossing the junction of two cells
Get into the cell from environment
Endoplasmic reticulum (ER) : Endoplasmic reticulum (ER)
Golgi apparatus : Golgi apparatus
Exocytosis And Endocytosis : Exocytosis And Endocytosis
Types of Endocytosis : Types of Endocytosis Phagocytosis ("cell eating solid particle")
Pinocytosis ("cell drinking dissolved material")
Receptor-mediated endocytosis ("cell taking up specific proteins")
Receptor-Mediated Endocytosis And Capping : Receptor-Mediated Endocytosis And Capping binding clustering capping
Membrane Fluidity : Membrane Fluidity Human + Mouse Fused
How to Maintain the Dynamic Membranes? : 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?
Steady State : Steady State
What are the macroscopic differences of different types of cells? : What are the macroscopic differences of different types of cells? Adipose tissue cells
Capillary cells
Muscle cells
Nerve cells
Cytoskeleton : Cytoskeleton microtubules: - tubulin - 25 nm (d)
intermed. filaments:
- vimentin or keratin - 10 nm (d)
microfilament: - actin - 7 nm (d)
Orders in A Cell : Orders in A Cell Compartments and localization
Cytoskeleton and polarity
The Importance of Polarity : The Importance of Polarity It's easier to propagate asymmetry than to create asymmetry.
The Origin of Polarity/ Asymmetry : The Origin of Polarity/ Asymmetry
The Second Law of Thermodynamics : The Second Law of Thermodynamics
Orders Can Be Maintained by Energy Input : Orders Can Be Maintained by Energy Input Water can flow upwards if ...
How can a cell maintain all the structures? : How can a cell maintain all the structures? Energy can compensate the entropy loss G = H - T S
=> Metabolism is a life phenomenon
Discussion : Discussion Is phage or virus a life?
Slide37 : 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
Slide38 : YM-Bioinfo
What Is Life? : What Is Life? Growth and development
Metabolism
Homeostasis
Movement
Response to stimuli
Reproduction
Evolution and adaptation
Amino Acids Are the Structural Units of Proteins : Amino Acids Are the Structural Units of Proteins (http://www.ym.edu.tw/bio/bch/aa.htm)
Types of amino acids : 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.
Lysine (K) and arginine (R) : Lysine (K) and arginine (R) Basic amino acids
(positively charged at pH 7)
Histidine (H) : Histidine (H) Frequently used in general acid and base catalysis
Aspartate (D) and glutamate (E) : Aspartate (D) and glutamate (E) Derived from intermediate metabolites
OAA => Asp; a-KG => Glu : OAA => Asp; a-KG => Glu OAA citrate isocitrate a-ketoglutarate succinyl CoA succinate malate fumarate -2H
-CO2 -2H
-CO2 CoA -2H -2H CoA + GTP acetyl CoA release CO2 reforming the carrier H2O TCA cycle
What’s the difference among … : What’s the difference among … -ic acid: e.g. acetic acid
-tate: e.g. acetate
-yl: e.g. acetyl O
R-C-OH
O
R-C-O-
O
R-C- For acetic acid derivatives, R=CH3
Hydrophilic and uncharged : Hydrophilic and uncharged gly, cys, ser, thr, tyr, asn, gln
glycine : glycine The only amino acid that does not have stereochemistry
alanine : alanine Pyruvate => ala
This is a hydrophobic amino acid. It was discussed here for understanding the structure of Ser and Cys.
serine and cysteine : serine and cysteine Oxygen and sulfur are in the same column in periodic table
=> Should have similar properties
Periodic table : Periodic table * Picture made from screenshot of http://www.shef.ac.uk/~chem/web-elements/
threonine and tyrosine : threonine and tyrosine Ser, thr, and tyr have hydroxyl group, so they can be phosphorylated
Phosphorylation cascade and signal amplification : Phosphorylation cascade and signal amplification
glutamine and asparagine : glutamine and asparagine Gln helps to transport NH3 to kidney
Amine and Amide : Amine and Amide
Hydrophobic amino acids : Hydrophobic amino acids Ala + val, leu, ile, met, phe, trp, pro
Valine (V), leucine (L), and isoleucine (I) : Valine (V), leucine (L), and isoleucine (I) hydrophobic and branched
Methionine (M) : Methionine (M) S-adenosyl methionine is a methyl group donor in the cell
Phenylalanine (F) and tryptophan (W) : Phenylalanine (F) and tryptophan (W) A well known genetic disease: phenylketonuria
Proline (P) : Proline (P) The only imino acid in 20 amino acids. It distort the normal peptide geometry.
How to Use Mage? : How to Use Mage? Demonstration
Schiff’s base : Schiff’s base A way to form C-N bond
Types of amino acids : 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