Download What is a cell?

Thermodynamics of life
Does life contradict the 2-nd law of thermodynamics? No!!
Energy conservation:
- when a rock falls potential energy becomes kinetic energy
E = K + V = const. > 0
- when it hits the ground, E = 0 !
- due to friction, E went to heat, Q -> E = Q
- friction transforms mechanical energy into heat = random
motion of atoms in the rock+ground
- 1-st law of thermodynamics:
ΔU = Q + W
(the change in the energy of the system is equal to the inflow of
heat plus the work done on it).
Can you use the heat from the rock+ground to make the rock jump
back up?
No!! Not because of energy conservation. But because Q is a lower
quality of energy. To convert it to mechanical energy, E, you will
always get less than Q, E < Q -> Mechanical energy = high quality
• Q is in the Brownian motion of atoms – larger if T grows. The
randomness is measured by S (entropy).
• How much useful energy is in the system, F (free energy)
F = U – TS
• An open system at fixed T will change only to lower its F. If F
minimal = system in equilibrium
• A process will take place if it lowers U (rocks tend to fall) or
increases S (disorder tends to increase)
• A closed system will change only to increase its entropy, S (2nd law of thermodynamics)
• A drop of ink in water will always mix up. Never will the ink
come back together to form back the drop.
• Then how can a mixture of H, C, O, N, P combine to make an E.
coli?
• Earth is not a closed system!!
• Light from the Sun (high quality energy) illuminates the Earth.
To keep T = const, the energy will have to be irradiated by the
Earth back to the cosmos (low quality energy)
• There is “flow of order” into the Earth.
• Plants take in high quality energy from the sun to build complex
molecules from simple ones. They also give out heat.
• Plants capture order
from the Sun.
• Animals do that
indirectly.
Cells
How do cells organize their many processes?
a) Bilayer membranes self-assemble -> separate
compartments
b) Active transport -> motors move on tracks to
deliver synthesized materials
c) Biochemical processes are specific -> enzymes
only act on the target molecule
What is in a cell?
The different length scales:
a) 5 E. coli, b) 2 yeast, c) red blood cell, d) white blood cell, e)
sperm, f) skin, g) muscle, h) neuron (light microscopy, 103x)
a) molecules, b) E. coli, c) HIV (virus), d) phage (electron
microscopy, 105x)
a) Carbon atom, b) Glucose (a sugar), c) ATP (nucleotide), d)
clorophyl, e) transfer RNA, f) antibody, g) ribosome, h) polio virus, i)
myosine (motor), j) DNA, k) actin (cell skeleton), l) 10 enzymes for
glycolysis: glucose -> ATP, m) a large enzyme
Cell anatomy
Nucleus – DNA, nuclear membrane
Cytoplasm – cell skeleton, organelles (mitochondria, ribosomes, …)
Envelope – membrane, cell wall
Yeast cells (electron
microscope)
Prokaryotes – simplest cells – no nucleus, only ribosomes, cell wall
- bacteria, archaea
E. coli - Cw – cell wall, N – nucleoid (DNA), R - ribosomes
Eukaryotes
- larger (> 10 µm), many organelles
- mitochondria – transform processed food into ATP
- endoplasmic reticulum – produces membranes and exports stuff
out of the cell
- Golgi apparatus – processes stuff coming from the endoplasmic
reticulum
DNA is packed in chromosomes
- 1 m human DNA in 46 chromosomes (23 pairs)
What are the molecules in the cell?
Small molecules
- basically only C, H, N, O, Ca, K, P and S. Other atoms in very
small amounts.
- water – 70%
- HPO42- - phosphate
- ring molecules – sugars (1 ring - glucose, ribose, 2 rings sucrose), DNA bases (1 ring – cytosine, thymine – pyrimidines; 2
rings – guanine, adenine – purines), RNA bases – like DNA but
thymine -> uracil)
DNA complementarity
Watson
Crick
- base+sugar (ribose or deoxyribose) + i*phosphate -> nucleotide,
e.g. adenosine monophosphate (AMP), ADP, ATP
- ATP -> ADP – burning fuel
- fatty acids – chain of carbons with COOH at the end, building
blocks of phospholipids (membranes)
- amino acids – 20, building blocks of proteins
a) R – side group, b) polypeptide (histidine, cysteine, valine)
Molecular composition of bacteria
Medium-size molecules
- phospholipids – 2 fatty acids (tails) + (glycerol +
phosphate+head group) (head)
- Head - hydrophilic, tail – hydrophobic -> in water form bilayer
(membrane)
phosphate
glycerol
DPPC (dipalmitoyl phosphtidycholine)
Bilayer (membrane)
- fats – 3 fatty acids + glycerol - triglycerides
Large molecules
- many are polymers
- polynucleotides – ribose + nucleotides -> ribonucleic acid
(RNA), deoxyribose -> deoxyribonucleic acid (DNA)
- 2 strands of DNA with complementary bases form a helix –
contains the genetic information
Double stranded DNA
Transfer RNA (tRNA)
It binds amino acid
phenylalanine, transports it to
the ribosome, then releases it