Lecture 2

4 September 2008

The origin of self (cells)

Shahid Naeem
(Chapters 4, 5, 9.1-9.5)
 Lecture 2
• Where we were in our last exciting
episode
• From atoms to macromolecules
• Self versus non self
• The cell: structure and function
The Chemical Hand We Were Dealt
Element Universe Earth Crust Life
H 92,700 120 2,900 60,600
He 7,200 <0.1 <0.1 0
O 50 48,900 60,400 26,700
Ne 20 <0.1 <0.1 0
N 15 0.3 7 2,400
C 8 99 55 10,700
Si 2.3 14,000 20,500 <1
Mg 2.1 12,500 1,800 11
Fe 1.4 18,900 1,900 <1

Units = atoms per 100,000

 Biogeochemistry

• 100 gigatons C/year photosynthetic

fixation
• 0.14 gigatons N/ biological fixation
• 0.02 gigatons S biogenic emission
/year
• 4 gigatons P cycled among biota/year
• 0.27 gigatons aerosol production/year
 James Lovelock
(Gaia hypothesis)

GAS PLANET
VENUS ABIOTIC MARS BIOTIC
EARTH EARTH
(PRESENT)
CO2 98% 98% 95% 0.03%
N2 1.9% 1.9% 2.7% 79%
O2 trace trace 0.13% 21%
temp. (oC) 477 290±50 -53 13
(surface)
atmospheric 90 60 0.064 1.0
pressure
 (Organic)
Biochemistry
•Functional groups – give organic
molecules their properties
•acidic
•basic
•charged
•soluble in water (hydrophylic)
•hydrophobic
•…
•The same is true for the R
groups in amino acids (fig. 3.20)
 Main Points of Biochemistry
• Subunits to macromolecules
• Monomers to polymers
• 4 classes of biological important
molecules (biomolecules)
1. Sugars - carbohydrates
2. Nucleotides – nucleic acids
3. Amino acids – proteins
4. Fatty acids – lipids
 Biological Molecules

Attach and detach monomers

Carbohydrates
 Carbohydrates

Monomers combine to make polymers by dehydration synthesis

Carbohydrates
 Nucleic Acids

Nucleotide
ATP → ADP + P + energy
 Nucleic Acids

(we’ll consider genes,

gene function, and gene
regulation, in the second
half)
Proteins
Proteins
Proteins
Lipids
Lipids
Fig. 5.1
Phospholipids

Plasma membrane!
Fig. 5.2
Page 63

Membrane + Membrane Proteins

Fig. 4.3

Prokaryotic cell
(bacteria and archaea)
Fig. 4.6

Eukaryotic cell
(plants, animals, fungi, protists)
Fig. 4.8.a
Fig. 4.10
Fig. 4.11
Fig. 4.12
Fig. 4.17
Fig. 4.7
Fig. 4.18
Fig. 4.20

Cytoskeleton
 Textbook has useful tables
(we’ll continue considering organelles next week)
Fig. 5.5

Material transport in cells:

Passive
 Material transport in cells: Passive
Fig. 5.16
Fig. 5.17

Bulk Transport: Endocytosis

Fig. 5.18.a

Bulk Transport: Exocytosis

Fig. 9.1

Cell signaling
Fig. 9.3

Cell signaling:
Kinases and Phosphatases
Fig. 9.4

Cell surface receptors

Chemically gated ion channel Enzymatic

Guanosine diphosphate G protein-coupled receptor

Fig. 9.5

Intracellular receptors
Fig. 9.7

Signal transduction
via receptor kinase

An external receptor domain

with an internal kinase
(“phosphorylator”) domain
Fig. 9.8

Mitogen activated protein (MAP) kinase

(generates mitosis)
Fig. 9.9