bi 1 week 8 recitation presentation 7 - its.caltech.edubi1/bi1__micro-_to_macro... · bi 1 week 8...
TRANSCRIPT
Bi 1 Week 8
Symbiosis / Ecology
Symbiotic Relationships of Plants and their Microbiome
Recall Ann Hirsh’s lecture at the beginning of the term.
Today’s Topic
Nitrogen Fixation
Do you know how much of our atmosphere is made of nitrogen?
Nitrogen is a building block of life.
Nitrogen Fixation
The Atmosphere: 78 percent N2 But… Plants need NH3
Nitrogen Fixation
The Atmosphere: 78 percent N2 But… Plants need NH3
ΔG0 = -‐45.2 kJ / mol NH3
EA = 420 kJ / mol (without catalysis)
Luckily… Life uses proteins (enzymes) to catalyze reactions like this!
thermodynamics vs. kinetics
Nitrogenase N2 + 8 e– + 8 H+ + 16 ATP → 16 ADP + 16 Pi + 2 NH3 + H2
EA ~ 400 kJ / mol NH3
Nitrogenase N2 + 8 e– + 8 H+ + 16 ATP → 16 ADP + 16 Pi + 2 NH3 + H2
EA ~ 400 kJ / mol NH3
Stepwise Catalytic Conversion (steps have lower EA)
Nitrogenase Structure
Back to relating protein structure and function:
Amino acid sequence encoded by nif genes (Primary Structure)
Alpha Helices (Secondary Structure)
Β-‐Sheets (Secondary Structure)
Protein Molecule (Tertiary Structure)
Protein Complex (Quaternary Structure)
Nitrogenase Structure + Function
Back to relating protein structure and function:
The different metal centers enable essential ET throughout the protein in this process.
FeMo cofactor
Nitrogenase Structure + Function
Back to relating protein structure and function:
The different metal centers enable essential ET throughout the protein in this process.
FeMo cofactor
J. Peters (CCE) D. Rees (CCE)
Nitrogenase in Rhizobia
Rhizobia are soil bacteria that _ix nitrogen (actively express nitrogenases) after becoming established inside the root nodules of legumes.
Establishing the Partnership
Rhizobia
Legume
Rhizobia
Legume
Establishing the Partnership
Flavonoids are given off by legume roots when they need more nitrogen _ixing partners
Rhizobia
Legume
Establishing the Partnership
Rhizobia secrete Nod factors
Establishing the Partnership
Rhizobia
Legume Bacteria enter the plant through root hairs. A nodule then forms around the infection.
Plant Controls O2 Supply to Bacteria
LEGUME BACTERIA
O2 control
leghemoglobin
PDB 2DGM
Plant Provides Energy for Bacteria
LEGUME BACTERIA
O2 control
Energy
Bacteria provides Fixed Nitrogen for Plant
LEGUME BACTERIA
O2 control
Energy
Fixed Nitrogen
Symbiosis has Checks and Balances
LEGUME BACTERIA
O2 control
Energy
Fixed Nitrogen
Signaling Pathways (Think about Ann Hirsh’s lecture)
N2 Fixing Symbiosis in the Deep Ocean
Caltech Lab Link hBp://www.gps.caltech.edu/people/vorphan/research/Nitrogen_FixaOon
FISH Fluorescence in-‐situ Hybridization
Used to localize the presence and absence of speci_ic RNA or DNA sequences on chromosomes.
Dekas et al. used two different probes: Red: ANME-‐2 (target: Eel932) Green: Desulfobateraceae (target: DSS658)
NanoSIMS single-‐cell-‐resolution nanometer secondary ion mass spectrometry
Ion beam
Target Surface
Method: _luorescent probes that bind to certain RNA or DNA sequences
Used to localize the presence and absence of speci_ic RNA or DNA sequences on chromosomes.
Dekas et al. used two different probes: Red: ANME-‐2 (target: Eel932) Green: Desulfobateraceae (target: DSS658)
Method: _luorescent probes that bind to certain RNA or DNA sequences
FISH Fluorescence in-‐situ Hybridization
NanoSIMS single-‐cell-‐resolution nanometer secondary ion mass spectrometry
rRNA Trees
Trees not Ladders
Fish Mouse Human Gorilla
Fish
Mouse
Gorilla
Human
PhylogeneOc trees are like family trees
cousin you brother
mother
grandmother
uncle
Tree Terminology
A B C D
Root
Node
Leaf
MonophyleOc clade
Different ways to display trees
Unrooted
Rooted Rooted
A
A
B
B
C
C
D
A
B
C
D
Rooted A
B
C
D
D
Are these trees different?
A B C D A B C D
A B C D A B C D
How to make a tree
Alignment Tree DNA rRNA sequence PCR, Sequencing ClustalW PhyML
Seq 1 A G T G T Seq 2 A G T A T Seq 3 C G C T G Seq 4 C G T C A
3 4 1 2 1
2
3
4
Phylip!